@article{alan_payn_mckeand_isik_2023, title={Genetic Parameter Estimates from a Polymix Breeding Population of Pinus taeda L.}, url={https://doi.org/10.1093/forsci/fxad006}, DOI={10.1093/forsci/fxad006}, abstractNote={Abstract Estimation of genetic parameters from progeny testing is essential for many important decisions in forest tree breeding. In this study, we estimated heritabilities, trait-trait genetic correlations, and genotype by environment (GxE) interactions using a large multi-environmental data set of Pinus taeda L. in the southern United States. In the study, 284 parents were pollinated with a pollen mix and were field tested in four different test series. A total of twenty tests (two to seven tests per series) were established using randomized complete block design with single tree plots. Half-sib family-mean heritability estimates within individual test series varied considerably for all the traits. Pooled estimates of half-sib family-mean heritability estimates across series were 0.81 for fusiform rust incidence; they were relatively lower for tree height (0.68), diameter at breast height (DBH; 0.66), and stem straightness (0.58). Genetic correlations between pairs of traits were low except for height and diameter, which had a high genetic correlation (0.79). Additive genetic correlations between pairs of sites within test series (as a measure of GxE) varied. The pooled estimates ranged between 0.65 (DBH) to 0.80 (fusiform rust). The results suggest that polymix mating is efficient for parental selection in Pinus taeda L. and for deployment in the seed orchards. Study Implications: This study focused on genetic variation in the Piedmont breeding population of Pinus taeda L. in the United States. The Piedmont population was developed for more inland and colder regions of the species. Fusiform rust disease incidence of pine species of southeastern United States is a major threat to pine plantations. Understanding the level of genetic control on disease outcome is vital to develop sound breeding strategies and recommend deployment practices to mitigate the economic loss of landowners. The results provide valuable information to breeders to select disease-resistant genotypes to breed and put into seed orchards to mass-produce stock for planting.}, journal={Forest Science}, author={Alan, Murat and Payn, Kitt and Mckeand, Steve and Isik, Fikret}, year={2023}, month={Mar} }
 @article{lin_shalizi_walker_lauer_carrasco_gujjula_suren_isik_2023, title={Low-density AgriSeq targeted genotyping-by-sequencing markers are efficient for pedigree quality control in Pinus taeda L. breeding}, volume={19}, ISSN={["1614-2950"]}, DOI={10.1007/s11295-023-01608-8}, number={4}, journal={TREE GENETICS & GENOMES}, author={Lin, Yu-Ming and Shalizi, Mohammad Nasir and Walker, Trevor D. D. and Lauer, Edwin and Carrasco, Claudio D. D. and Gujjula, Krishna Reddy and Suren, Haktan and Isik, Fikret}, year={2023}, month={Aug} }
 @article{shalizi_walker_heine_payn_isik_bullock_mckeand_2023, title={Performance Based on Measurements from Individual-Tree Progeny Tests Strongly Predicts Early Stand Yield in Loblolly Pine}, volume={2}, ISSN={["1938-3738"]}, url={https://doi.org/10.1093/forsci/fxad002}, DOI={10.1093/forsci/fxad002}, abstractNote={Abstract To facilitate the utility of genetic improvement in loblolly pine, individual-tree volume (productivity) scores estimated from single-tree plot or row-plot progeny test designs were compared with stand-level volume per unit area from block plots. A large number of families representing a wide range of progeny test scores for volume were established in growth and yield trials to generalize the results to families created by the breeding program. Individual-tree volume scores from progeny tests strongly corresponded with stand-level volume from block plots, especially after accounting for site quality and the risk of fusiform rust disease. A ten-point increase in the volume score from progeny test data was estimated to increase stand-level volume by 3.9 m3 ha-1 at age 6 years. A prediction model is presented that includes a new statistic, rust risk index, which is the expected rust incidence for a family at a new site when the hazard of rust for a checklot can be estimated from historical data. The study results through age 6 years corroborate the Performance Rating System as effective in guiding family deployment decisions. The models presented are based on pre-crown closure data at 6 years and will be updated with older measurements as the study matures. Study Implications: The Performance Rating System (PRS™) has been a successful tool for presenting genetic merit of improved loblolly pine families for landowners and forest managers in a more coherent and standardized manner. This system can be easily applied in other forest tree improvement programs, because it makes genetic improvement user-friendly for silviculturists and forest managers. Landowners can use this system to make decisions for selecting improved families suited to their specific forest management objectives. Seed orchard and nursery managers also depend on the PRS to choose the families to produce and as a third-party verification to market their genetic merit to customers. This study demonstrates that higher stand-level volume per unit area can be achieved when forest managers plant fast growing families with low fusiform rust disease risk on productive sites. The combined effect of genetic improvement for productivity and fusiform rust disease resistance is significant on stand-level volume per unit area.}, journal={FOREST SCIENCE}, author={Shalizi, Mohammad Nasir and Walker, Trevor D. and Heine, Austin J. and Payn, Kitt G. and Isik, Fikret and Bullock, Bronson P. and McKeand, Steven E.}, year={2023}, month={Feb} }
 @article{goda_isik_2022, title={AgMate: An Optimal Mating Software for Monoecious Species. A LongTerm Breeding Example for
            <i>Pinus taeda
            L.}, volume={2022}, ISSN={2791-1969}, url={http://dx.doi.org/10.31220/agrirxiv.2022.00145}, DOI={10.31220/agrirxiv.2022.00145}, abstractNote={Abstract Breeding objectives aim to optimize two crucial but contrasting goals of maximizing genetic gain while managing genetic diversity. In advanced generations, this becomes a challenge in monoecious conifer tree species breeding programs because they suffer from inbreeding. Developing an algorithm that maximizes genetic gain while maintaining genetic diversity for monoecious species is imperative. While methods and algorithms for animal breeding are well-established, an efficient algorithm suited to monoecious species remains elusive. Towards this goal, we have adopted an evolutionary genetic algorithm, the Differential Evolution algorithm, to optimize mate pair designing in Pinus taeda (loblolly pine), a widely planted pine species in the southern USA. AgMate, an optimal mating for monoecious species software, is a multi-functional, completely automated optimization software. It utilizes genetic relationships and breeding values as input to create an optimal mating list. AgMate maximizes the genetic gain and minimizes the increase in average coancestry and inbreeding in the proposed progeny. AgMate was more effective in optimizing mating lists than positive assortative mating and random mating in short-term and long-term settings. AgMate mating list resulted in an average 93% genetic gain each cycle for ten cycles while simultaneously minimizing the increase in coancestry to 0.086. The framework and methods adapted for Pinus taeda are also relevant to the breeding of other monoecious species.}, journal={agriRxiv}, publisher={CABI Publishing}, author={Goda, Khushi and Isik, Fikret}, year={2022}, month={Jan} }
 @article{borthakur_busov_cao_du_gailing_isik_ko_li_li_niu_et al._2022, title={Current status and trends in forest genomics}, volume={2}, ISSN={2767-3812}, url={http://dx.doi.org/10.48130/fr-2022-0011}, DOI={10.48130/fr-2022-0011}, abstractNote={Forests are not only the most predominant of the Earth's terrestrial ecosystems, but are also the core supply for essential products for human use. However, global climate change and ongoing population explosion severely threatens the health of the forest ecosystem and aggravtes the deforestation and forest degradation. Forest genomics has great potential of increasing forest productivity and adaptation to the changing climate. In the last two decades, the field of forest genomics has advanced quickly owing to the advent of multiple high-throughput sequencing technologies, single cell RNA-seq, clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genome editing, and spatial transcriptomes, as well as bioinformatics analysis technologies, which have led to the generation of multidimensional, multilayered, and spatiotemporal gene expression data. These technologies, together with basic technologies routinely used in plant biotechnology, enable us to tackle many important or unique issues in forest biology, and provide a panoramic view and an integrative elucidation of molecular regulatory mechanisms underlying phenotypic changes and variations. In this review, we recapitulated the advancement and current status of 12 research branches of forest genomics, and then provided future research directions and focuses for each area. Evidently, a shift from simple biotechnology-based research to advanced and integrative genomics research, and a setup for investigation and interpretation of many spatiotemporal development and differentiation issues in forest genomics have just begun to emerge.}, number={1}, journal={Forestry Research}, publisher={Maximum Academic Press}, author={Borthakur, Dulal and Busov, Victor and Cao, Xuan Hieu and Du, Qingzhang and Gailing, Oliver and Isik, Fikret and Ko, Jae-Heung and Li, Chenghao and Li, Quanzi and Niu, Shihui and et al.}, year={2022}, pages={0–0} }
 @article{shalizi_payn_isik_2022, title={Genetic linkage between the training and selection sets impacts the predictive ability of SNP markers in a cloned population of Pinus taeda L.}, volume={18}, ISSN={["1614-2950"]}, url={https://doi.org/10.1007/s11295-021-01532-9}, DOI={10.1007/s11295-021-01532-9}, number={1}, journal={TREE GENETICS & GENOMES}, publisher={Springer Science and Business Media LLC}, author={Shalizi, Mohammad Nasir and Payn, Kitt G. and Isik, Fikret}, year={2022}, month={Feb} }
 @inbook{isik_2022, title={Genomic Prediction of Complex Traits in Perennial Plants: A Case for Forest Trees}, ISBN={9781071622049 9781071622056}, ISSN={1064-3745 1940-6029}, url={http://dx.doi.org/10.1007/978-1-0716-2205-6_18}, DOI={10.1007/978-1-0716-2205-6_18}, abstractNote={This chapter provides an overview of the genomic selection progress in long-lived forest tree species. Factors affecting the prediction accuracy in genomic prediction are assessed with examples from empirical studies. Infrastructure and resources required for the implementation of genomic selection are evaluated. Some general guidelines are provided for the successful application of genomic selection in forest tree breeding programs.}, booktitle={Methods in Molecular Biology}, publisher={Springer US}, author={Isik, Fikret}, year={2022}, pages={493–520} }
 @article{shalizi_payn_walker_isik_heine_mckeand_2022, title={Long-term evaluation of intra- and inter-provenance hybrids of loblolly pine in the Piedmont region of the southeastern United States}, volume={522}, ISSN={["1872-7042"]}, url={http://dx.doi.org/10.1016/j.foreco.2022.120469}, DOI={10.1016/j.foreco.2022.120469}, abstractNote={Long-term response of two intra- and two inter-provenance populations of loblolly pine (Pinus taeda L.) were evaluated in the Piedmont region of the southeastern United States. In total, 82 polycross families of the Atlantic Coastal (C) and Piedmont (P) provenances (C×C, P×P) and their hybrids (C×P, P×C) were field tested for growth, sawtimber potential, and survival through age 19 years. The Coastal pure (C×C) families were the tallest, and the hybrid populations (C×P, P×C) were intermediate for height. The four populations did not differ for diameter at breast height. The hybrid C×P population, followed by the C×C population, showed significantly higher stand volumes per hectare. These two populations maintained higher survival and stand density compared to the Piedmont pure populations. Sawtimber potential was significantly higher in the Piedmont pure families at the coldest study sites, presumably due to defect in the C×C and C×P from cold damage. No significant genotype-by-environment interactions were detected for any traits. The genetic gain for height, stand volume, and survival was considerable in the C×C and C×P over the Piedmont source, suggesting potential for benefiting from the faster growth of the Coastal material in the Piedmont region. The performance of the Coastal intra- and inter-provenance populations was marginally affected by the minimum winter temperatures (MWT). These results indicate that the Coastal and the hybrid families can be planted in the Piedmont region with MWT’s of −13 °C or greater and where the difference in MWT between the origin of the Coastal parents and the test sites was not extreme (e.g., the difference did not exceed 2.8 °C). These MWT limits encompass the southern Piedmont of North Carolina (<35.615 °N) and the Piedmont of South Carolina, Georgia, and Alabama.}, journal={FOREST ECOLOGY AND MANAGEMENT}, publisher={Elsevier BV}, author={Shalizi, Mohammad Nasir and Payn, Kitt G. and Walker, Trevor D. and Isik, Fikret and Heine, Austin J. and McKeand, Steven E.}, year={2022}, month={Oct} }
 @article{goda_isik_2022, title={Optimal mating of Pinus taeda L. under different scenarios using differential evolution algorithm}, url={https://doi.org/10.1101/2022.07.18.500513}, DOI={10.1101/2022.07.18.500513}, abstractNote={Abstract A newly developed software, AgMate, was used to perform optimized mating for monoecious Pinus taeda L. breeding. Using a computational optimization procedure called differential evolution (DE), AgMate was applied under different breeding population sizes scenarios (50, 100, 150, 200, 250) and candidate contribution scenarios (max use of each candidate was set to 1 or 8), to assess its efficiency in maximizing the genetic gain while controlling inbreeding. Real pedigree data set from North Carolina State University Tree Improvement Co-op with 962 Pinus taeda were used to optimize objective functions accounting for coancestry of parents and expected genetic gain and inbreeding of the future progeny. AgMate results were compared with those from another widely used mating software called MateSel (Kinghorn, 1999). For the proposed mating list for 200 progenies, AgMate resulted in an 83.7% increase in genetic gain compared with the candidate population. There was evidence that AgMate performed similarly to MateSel in managing coancestry and expected genetic gain, but MateSel was superior in avoiding inbreeding in proposed mate pairs. The developed algorithm was computationally efficient in maximizing the objective functions and flexible for practical application in monoecious diploid conifer breeding. Study implications A dataset from a breeding population of loblolly pine ( Pinus taeda L.) was analyzed using an optimal mating software, AgMate (developed by the authors), to optimize the selection, contribution, and mating of candidates simultaneously. The software helps breeders make decisions on which tree to cross with which tree and how many times, such that the trees are not related to each other and would result in the best performing progenies. AgMate is effective in meeting the breeding objectives for monoecious species. The open-source, easy-to-use, and flexible AgMate software, also available as a website, is invaluable in helping breeders to create optimal matings for future generations, which balance the pursuit of maximizing genetic gain while maintaining genetic diversity.}, author={Goda, Khushi and Isik, Fikret}, year={2022}, month={Jul} }
 @article{heine_walker_jett_isik_mckeand_2022, title={Pollination Bag Type Affects Ovule Development and Seed Yields in Pinus taeda L.}, volume={12}, ISSN={["1938-3738"]}, url={https://doi.org/10.1093/forsci/fxac052}, DOI={10.1093/forsci/fxac052}, abstractNote={Abstract Loblolly pine (Pinus taeda L.) is the most widely planted forest tree species in the United States. Most of the seedlings used to establish these plantations come from seed collected in open-pollinated seed orchards, but an increasing number are coming from controlled crosses, about 15%–20% of the loblolly pine seedling crops in the last five years. To produce this seed, millions of pollination bags are installed each spring in orchards throughout the southeastern United States; over 2.6 million bags were installed in 2022. This study evaluated 13 pollination bag types available for use in the mass production of control-cross seed. Using cone analysis, significant differences were found among bag types for the proportion of ovules resulting in filled seed, empty seed, and first-year aborts. Due to differences in the efficacy of orchard management, study trees varied greatly in their proportion of ovules resulting in filled seed and first-year aborts. Under good orchard management, open-pollinated cones had 72% of their ovules as filled seed and 12% in first-year aborted ovules. The best pollination bag type had 62% of its ovules as filled seed with 22% in first-year aborted ovules. These differences are apparently due to the quality of pollen used in the controlled crosses. Study Implications: Compared with open-pollinated families, full-sibling crosses among elite parents of loblolly pine produce more market value to landowners due to greater productivity, increased disease resistance, and enhanced stem form. Specific crosses of loblolly pine have occupied about 15%–20% of the recent seedling market because the seed are costly and difficult to produce. This study tested pollination bag types to determine their effectiveness in producing control-cross seed. Some bag types were superior in increasing seed yield, but seed yields for open-pollinated cones tended to be higher, suggesting problems in the control-cross process. Cone analysis is a useful tool for seed orchard managers to diagnose problems in seed production. Understanding and correcting these problems will help managers increase their production of full-sibling seed and lead to the establishment of new plantations with increased forest productivity.}, journal={FOREST SCIENCE}, author={Heine, Austin J. and Walker, Trevor D. and Jett, Jackson B. and Isik, Fikret and McKeand, Steven E.}, year={2022}, month={Dec} }
 @article{lauer_holland_isik_2022, title={Prediction ability of genome-wide markers in Pinus taeda L. within and between population is affected by relatedness to the training population and trait genetic architecture}, volume={12}, ISSN={["2160-1836"]}, url={https://doi.org/10.1093/g3journal/jkab405}, DOI={10.1093/g3journal/jkab405}, abstractNote={Abstract Genomic prediction has the potential to significantly increase the rate of genetic gain in tree breeding programs. In this study, a clonally replicated population (n = 2063) was used to train a genomic prediction model. The model was validated both within the training population and in a separate population (n = 451). The prediction abilities from random (20% vs 80%) cross validation within the training population were 0.56 and 0.78 for height and stem form, respectively. Removal of all full-sib relatives within the training population resulted in ∼50% reduction in their genomic prediction ability for both traits. The average prediction ability for all 451 individual trees was 0.29 for height and 0.57 for stem form. The degree of genetic linkage (full-sib family, half sib family, unrelated) between the training and validation sets had a strong impact on prediction ability for stem form but not for height. A dominant dwarfing allele, the first to be reported in a conifer species, was discovered via genome-wide association studies on linkage Group 5 that conferred a 0.33-m mean height reduction. However, the QTL was family specific. The rapid decay of linkage disequilibrium, large genome size, and inconsistencies in marker-QTL linkage phase suggest that large, diverse training populations are needed for genomic selection in Pinus taeda L.}, number={2}, journal={G3-GENES GENOMES GENETICS}, publisher={Oxford University Press (OUP)}, author={Lauer, Edwin and Holland, James and Isik, Fikret}, editor={Lipka, AEditor}, year={2022}, month={Feb} }
 @article{walker_cumbie_isik_2022, title={Single-Step Genomic Analysis Increases the Accuracy of Within-Family Selection in a Clonally Replicated Population of Pinus taeda L.}, volume={68}, ISSN={["1938-3738"]}, url={https://doi.org/10.1093/forsci/fxab054}, DOI={10.1093/forsci/fxab054}, abstractNote={Abstract The use of genomic markers in forest tree breeding is expected to improve the response to selection, especially within family. To evaluate the potential improvements from genotyping, we analyzed a large Pinus taeda L. clonal population (1,831 cloned individuals) tested in multiple environments. Of the total, 723 clones from five full-sib families were genotyped using 10,337 single-nucleotide polymorphism markers. Single-step models with genomic and pedigree-based relationships produced similar heritability estimates. Breeding value predictions were greatly improved with inclusion of genomic relationships, even when clonal replication was abundant. The improvement was limited to genotyped individuals and attributable to accounting for the Mendelian sampling effect. Reducing clonal replication by omitting data indicated that genotyping improved breeding values similar to clonal replication. Genomic selection predictive ability (masking phenotypes) was greater for stem straightness (0.68) than for growth traits (0.41 to 0.44). Predictive ability for a new full-sibling family was poorer than when full-sibling relationships were present between model training and validation sets. Species that are difficult to propagate clonally can use genotyping to improve within-family selection. Clonal testing combined with genotyping can produce breeding value accuracies adequate to graft selections directly into deployment orchards without progeny testing.}, number={1}, journal={FOREST SCIENCE}, publisher={Oxford University Press (OUP)}, author={Walker, Trevor D. and Cumbie, W. Patrick and Isik, Fikret}, year={2022}, month={Feb}, pages={37–52} }
 @article{jackson_christie_reynolds_marais_tii‐kuzu_caballero_kampman_visser_naidoo_kain_et al._2021, title={A genome‐wide SNP genotyping resource for tropical pine tree species}, volume={22}, ISSN={1755-098X 1755-0998}, url={http://dx.doi.org/10.1111/1755-0998.13484}, DOI={10.1111/1755-0998.13484}, abstractNote={We performed gene and genome targeted SNP discovery towards the development of a genome-wide, multispecies genotyping array for tropical pines. Pooled RNA-seq data from shoots of seedlings from five tropical pine species was used to identify transcript-based SNPs resulting in 1.3 million candidate Affymetrix SNP probe sets. In addition, we used a custom 40 K probe set to perform capture-seq in pooled DNA from 81 provenances representing the natural ranges of six tropical pine species in Mexico and Central America resulting in 563 K candidate SNP probe sets. Altogether, 300 K RNA-seq (72%) and 120 K capture-seq (28%) derived SNP probe sets were tiled on a 420 K screening array that was used to genotype 576 trees representing the 81 provenances and commercial breeding material. Based on the screening array results, 50 K SNPs were selected for commercial SNP array production including 20 K polymorphic SNPs for P. patula, P. tecunumanii, P. oocarpa and P. caribaea, 15 K for P. greggii and P. maximinoi, 13 K for P. elliottii and 8K for P. pseudostrobus. We included 9.7 K ancestry informative SNPs that will be valuable for species and hybrid discrimination. Of the 50 K SNP markers, 25% are polymorphic in only one species, while 75% are shared by two or more species. The Pitro50K SNP chip will be useful for population genomics and molecular breeding in this group of pine species that, together with their hybrids, represent the majority of fast-growing tropical and subtropical pine plantations globally.}, number={2}, journal={Molecular Ecology Resources}, publisher={Wiley}, author={Jackson, Colin and Christie, Nanette and Reynolds, Sharon Melissa and Marais, Gerhard C. and Tii‐kuzu, Yokateme and Caballero, Madison and Kampman, Tamanique and Visser, Erik A. and Naidoo, Sanushka and Kain, Dominic and et al.}, year={2021}, month={Aug}, pages={695–710} }
 @article{lauer_isik_2021, title={Correction: Major QTL confer race-nonspecific resistance in the co-evolved Cronartium quercuum f. sp. fusiforme-Pinus taeda pathosystem}, volume={7}, url={https://doi.org/10.1038/s41437-021-00458-1}, DOI={10.1038/s41437-021-00458-1}, abstractNote={Fusiform rust disease, caused by the endemic fungus Cronartium quercuum f. sp. fusiforme, is the most damaging disease affecting economically important pine species in the southeast United States. Unlike the major epidemics of agricultural crops, the co-evolved pine-rust pathosystem is characterized by steady-state dynamics and high levels of genetic diversity within environments. This poses a unique challenge and opportunity for the deployment of large-effect resistance genes. We used trait dissection to study the genetic architecture of disease resistance in two P. taeda parents that showed high resistance across multiple environments. Two mapping populations (full-sib families), each with ~1000 progeny, were challenged with a complex inoculum consisting of 150 pathogen isolates. High-density linkage mapping revealed three major-effect QTL distributed on two linkage groups. All three QTL were validated using a population of 2057 cloned pine genotypes in a 6-year-old multi-environmental field trial. As a complement to the QTL mapping approach, bulked segregant RNAseq analysis revealed a small number of candidate nucleotide binding leucine-rich repeat genes harboring SNP associated with disease resistance. The results of this study show that in P. taeda, a small number of major QTL can provide effective resistance against genetically diverse mixtures of an endemic pathogen. These QTL vary in their impact on disease liability and exhibit additivity in combination.}, journal={Heredity}, publisher={Springer Science and Business Media LLC}, author={Lauer, Edwin and Isik, Fikret}, year={2021}, month={Sep} }
 @article{lauer_sims_mckeand_isik_2021, title={Genetic Parameters and Genotype-by-Environment Interactions in Regional Progeny Tests of Pinus taeda L. in the Southern USA}, volume={67}, ISSN={["1938-3738"]}, url={https://doi.org/10.1093/forsci/fxaa035}, DOI={10.1093/forsci/fxaa035}, abstractNote={Abstract Genetic parameters were estimated using a five-series multienvironment trial of Pinus taeda L. in the southern USA. There were 324 half-sib families planted in five test series across 37 locations. A set of six variance/covariance matrices for the genotype-by-environment (G × E) effect for tree height and diameter were compared on the basis of model fit. In single-series analysis, extended factor analytical models provided generally superior model fit to simpler models for both traits; however, in the combined-series analysis, diameter was optimally modeled using simpler variance/covariance structures. A three-way compound term for modeling G × E interactions among and within series yielded substantial improvements in terms of model fit and standard errors of predictions. Heritability of family means ranged between 0.63 and 0.90 for both height and diameter. Average additive genetic correlations among sites were 0.70 and 0.61 for height and diameter, respectively, suggesting the presence of some G × E interaction. Pairs of sites with the lowest additive genetic correlations were located at opposite ends of the latitude range. Latent factor regression revealed a small number of parents with large factor scores that changed ranks significantly between southern and northern environments.}, number={1}, journal={FOREST SCIENCE}, publisher={Oxford University Press (OUP)}, author={Lauer, Edwin and Sims, Andrew and McKeand, Steven and Isik, Fikret}, year={2021}, month={Feb}, pages={60–71} }
 @article{grans_isik_purnell_peszlen_mckeand_2021, title={Genetic Variation and the Effect of Herbicide and Fertilization Treatments on Wood Quality Traits in Loblolly Pine}, volume={67}, ISSN={["1938-3738"]}, url={https://doi.org/10.1093/forsci/fxab026}, DOI={10.1093/forsci/fxab026}, abstractNote={Abstract The effect of silvicultural treatments (herbicide, fertilization, herbicide + fertilization) and the interactions with genetic effects were investigated for wood quality traits in a 16-year-old loblolly pine (Pinus taeda L.) genetic test established in southwest Georgia, USA. Fertilizer and herbicide treatment combinations were applied multiple times to main plots containing 25 open-pollinated families as sub plots. Significant differences among treatments were found for all traits. Squared acoustic velocity, used as a surrogate for wood stiffness, was higher in herbicide-only plots compared with other treatments. Wood density was considerably lower in fertilization plots. A large proportion of variance observed for wood quality traits was explained by additive genetic effects, with individual-tree heritabilities ranging from 0.78 (ring 7–16 section wood density) to 0.28 (ring 2–6 section wood density). Corresponding family-mean heritability values were well over 0.86. Genotype-by-treatment interactions were nonsignificant for all traits, indicating no need to match families to silvicultural treatments. Wood quality traits had weak genetic correlations with growth and stem quality traits (stem slenderness, sweep, and branch angle) with a range of −0.33 to 0.43, suggesting that recurrent selection on growth or stem quality traits would not adversely affect wood quality in loblolly pine.}, number={5}, journal={FOREST SCIENCE}, publisher={Oxford University Press (OUP)}, author={Grans, Daniel and Isik, Fikret and Purnell, Robert C. and Peszlen, Ilona M. and McKeand, Steven E.}, year={2021}, month={Oct}, pages={564–573} }
 @article{chan_isik_2021, title={Genetic Variation in Frost Tolerance, Uromycladium acaciae Rust Resistance, and Growth in an Acacia mearnsii Population}, volume={67}, ISSN={["1938-3738"]}, url={https://doi.org/10.1093/forsci/fxab032}, DOI={10.1093/forsci/fxab032}, abstractNote={Abstract Genetic variation in frost tolerance, resistance to the rust fungus Uromycladium acaciae, growth, stem form, and gummosis were evaluated in 110 open-pollinated families of black wattle (Acacia mearnsii De Wild). Families were tested at six frost-prone sites in northern KwaZulu-Natal and southeastern Mpumalanga, South Africa. Frost-hardy provenances were susceptible to rust disease and had poor growth. Locally grown F1 seed sources that originated from cold-hardy Australian seed sources had better growth and were tolerant to rust, but at a cost of lower frost tolerance. Considerable genetic variation was observed between families within seed sources for frost damage (hfm2 = 0.77), rust incidence (hfm2 = 0.89), and height (hfm2 = 0.80). The corresponding narrow-sense heritabilities (hi2) were 0.30, 0.80, and 0.32. Genotype-by-environment interaction levels were low for most traits. Except for a strong genetic correlation between tree height and diameter (0.90), all the pairs of traits had weak to moderate genetic correlations. Recurrent selection will be successful in improving frost tolerance and rust incidence. However, the current population comprises limited germplasm that is both tolerant to frost and resistant to rust. Thus, we recommend infusing germplasm from known cold-hardy Australian provenances into the current population to increase genetic variation for frost tolerance, rust, and growth.}, number={5}, journal={FOREST SCIENCE}, publisher={Oxford University Press (OUP)}, author={Chan, Julian Moreno and Isik, Fikret}, year={2021}, month={Oct}, pages={574–586} }
 @article{alan_isik_2021, title={Genetic relationships between terminal shoot length, number of flushes and height in a 4-year-old progeny test of Pinus brutia Ten}, volume={78}, ISSN={["1297-966X"]}, url={https://doi.org/10.1007/s13595-021-01040-9}, DOI={10.1007/s13595-021-01040-9}, abstractNote={In this study, genetic variation in polycyclic growth was investigated in a young Pinus brutia Ten. study in Turkey. The number of flushes was partially under additive genetic control and was moderately correlated with the tree height at age 4. Pinus brutia is the most economically important tree species in Turkey. Previous limited studies suggested that its cyclic shoot elongation pattern can be useful for selecting seed sources for breeding and conservation of genetic resources. Understand the degree of genetic control of terminal shoot growth, number of flushes, and total tree height at early ages and assess the genetic relationships between the traits to guide decisions for breeding and gene conservation. Open-pollinated progenies of 188 trees from eight different seed sources were tested in three locations in the Aegean region of Turkey. Variance components, heritability and additive genetic correlations were estimated for tree height, terminal shoot length, and number of flushes. Traits were moderately under genetic control at the family. Terminal shoot length explained 76% of the variation in tree height. A strong genetic correlation (0.96) was found between tree height and terminal shoot length, while the number of flushes had a moderate genetic correlation with height (0.59). Northern seed sources tended to display less height growth, partially due to fewer flushes and lower shoot length. Shoot elongation in the species is partially under additive genetic control and could be useful to select for early height in breeding programs.}, number={2}, journal={ANNALS OF FOREST SCIENCE}, publisher={Springer Science and Business Media LLC}, author={Alan, Murat and Isik, Fikret}, year={2021}, month={Jun} }
 @article{xu_nielsen_isik_jensen_hansen_2021, title={Genetic variation and inheritance of susceptibility to Neonectria neomacrospora and Christmas tree traits in a progeny test of Nordmann fir}, volume={78}, ISSN={["1297-966X"]}, url={https://doi.org/10.1007/s13595-021-01039-2}, DOI={10.1007/s13595-021-01039-2}, abstractNote={Pronounced additive genetic variation and high narrow-sense heritability for lesion length caused by Neonectria neomacrospora were found in a Nordmann fir progeny test. Significant inbreeding depression was detected in traits important for Christmas tree production. Recurrent selection for multiple traits would be successful for Christmas tree quality traits. The fungal pathogen N. neomacrospora causes severe damage in Nordmann fir Christmas trees in Denmark. Family variation in disease susceptibility in the species has not been investigated before. This is the first combined genetic analysis of susceptibility to N. neomacrospora and Christmas tree traits in Nordmann fir. Evaluate the genetic variation of susceptibility to N. neomacrospora and five Christmas tree traits in Nordmann fir. Five Christmas tree traits were measured on 2413 trees in a progeny test. Artificial inoculation was conducted on detached twigs of full-sib progenies with a N. neomacrospora isolate to assess the resistance/susceptibility. Observed variation was partitioned into genetic and environmental causes to understand the heritable control of the traits. Pronounced additive genetic variation was observed in susceptibility to N. neomacrospora and Christmas tree traits. Narrow-sense heritability for susceptibility to N. neomacrospora was 0.63. Significant differences between selfings and outcrossed trees were detected for all traits. Significant improvement for Christmas tree quality could be observed in the breeding process. Resistance to N. neomacrospora disease and other Christmas tree characteristics can be improved through recurrent selection.}, number={1}, journal={ANNALS OF FOREST SCIENCE}, publisher={Springer Science and Business Media LLC}, author={Xu, Jing and Nielsen, Ulrik Brauner and Isik, Fikret and Jensen, Martin and Hansen, Ole Kim}, year={2021}, month={Mar} }
 @article{mphahlele_isik_hodge_myburg_2021, title={Genomic Breeding for Diameter Growth and Tolerance to Leptocybe Gall Wasp and Botryosphaeria/Teratosphaeria Fungal Disease Complex in Eucalyptus grandis}, volume={12}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2021.638969}, abstractNote={Eucalyptus grandis is one of the most important species for hardwood plantation forestry around the world. At present, its commercial deployment is in decline because of pests and pathogens such as Leptocybe invasa gall wasp ( Lepto ), and often co-occurring fungal stem diseases such as Botryosphaeria dothidea and Teratosphaeria zuluensis ( BotryoTera ). This study analyzed Lepto , BotryoTera , and stem diameter growth in an E. grandis multi-environmental, genetic trial. The study was established in three subtropical environments. Diameter growth and BotryoTera incidence scores were assessed on 3,334 trees, and Lepto incidence was assessed on 4,463 trees from 95 half-sib families. Using the Eucalyptus EUChip60K SNP chip, a subset of 964 trees from 93 half-sib families were genotyped with 14,347 informative SNP markers. We employed single-step genomic BLUP (ssGBLUP) to estimate genetic parameters in the genetic trial. Diameter and Lepto tolerance showed a positive genetic correlation (0.78), while BotryoTera tolerance had a negative genetic correlation with diameter growth (−0.38). The expected genetic gains for diameter growth and Lepto and BotryoTera tolerance were 12.4, 10, and −3.4%, respectively. We propose a genomic selection breeding strategy for E. grandis that addresses some of the present population structure problems.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Mphahlele, Makobatjatji M. and Isik, Fikret and Hodge, Gary R. and Myburg, Alexander A.}, year={2021}, month={Feb} }
 @article{shalizi_cumbie_isik_2021, title={Genomic prediction for fusiform rust disease incidence in a large cloned population of Pinus taeda}, volume={11}, ISSN={["2160-1836"]}, url={https://doi.org/10.1093/g3journal/jkab235}, DOI={10.1093/g3journal/jkab235}, abstractNote={In this study, 723 Pinus taeda L. (loblolly pine) clonal varieties genotyped with 16920 SNP markers were used to evaluate genomic selection for fusiform rust disease caused by the fungus Cronartium quercuum f. sp. fusiforme. The 723 clonal varieties were from five full-sib families. They were a subset of a larger population (1831 clonal varieties), field-tested across 26 locations in the southeast US. Ridge regression, Bayes B, and Bayes Cπ models were implemented to study marker-trait associations and estimate predictive ability for selection. A cross-validation scenario based on a random sampling of 80% of the clonal varieties for the model building had higher (0.71-0.76) prediction accuracies of genomic estimated breeding values compared with family and within-family cross-validation scenarios. Random sampling within families for model training to predict genomic estimated breeding values of the remaining progenies within each family produced accuracies between 0.38 and 0.66. Using four families out of five for model training was not successful. The results showed the importance of genetic relatedness between the training and validation sets. Bayesian whole-genome regression models detected three QTL with large effects on the disease outcome, explaining 54% of the genetic variation in the trait. The significance of QTL was validated with GWAS while accounting for the population structure and polygenic effect. The odds of disease incidence for heterozygous AB genotypes were 10.7 and 12.1 times greater than the homozygous AA genotypes for SNP11965 and SNP6347 loci, respectively. Genomic selection for fusiform rust disease incidence could be effective in P. taeda breeding. Markers with large effects could be fit as fixed covariates to increase the prediction accuracies, provided that their effects are validated further.}, number={9}, journal={G3-GENES GENOMES GENETICS}, publisher={Oxford University Press (OUP)}, author={Shalizi, Mohammad Nasir and Cumbie, W. Patrick and Isik, Fikret}, year={2021}, month={Sep} }
 @article{lauer_isik_2021, title={Major QTL confer race-nonspecific resistance in the co-evolved Cronartium quercuum f. sp. fusiforme-Pinus taeda pathosystem}, volume={6}, ISSN={["1365-2540"]}, url={https://doi.org/10.1038/s41437-021-00451-8}, DOI={10.1038/s41437-021-00451-8}, abstractNote={Fusiform rust disease, caused by the endemic fungus Cronartium quercuum f. sp. fusiforme, is the most damaging disease affecting economically important pine species in the southeast United States. Unlike the major epidemics of agricultural crops, the co-evolved pine-rust pathosystem is characterized by steady-state dynamics and high levels of genetic diversity within environments. This poses a unique challenge and opportunity for the deployment of large-effect resistance genes. We used trait dissection to study the genetic architecture of disease resistance in two P. taeda parents that showed high resistance across multiple environments. Two mapping populations (full-sib families), each with ~1000 progeny, were challenged with a complex inoculum consisting of 150 pathogen isolates. High-density linkage mapping revealed three major-effect QTL distributed on two linkage groups. All three QTL were validated using a population of 2057 cloned pine genotypes in a 6-year-old multi-environmental field trial. As a complement to the QTL mapping approach, bulked segregant RNAseq analysis revealed a small number of candidate nucleotide binding leucine-rich repeat genes harboring SNP associated with disease resistance. The results of this study show that in P. taeda, a small number of major QTL can provide effective resistance against genetically diverse mixtures of an endemic pathogen. These QTL vary in their impact on disease liability and exhibit additivity in combination.}, journal={HEREDITY}, publisher={Springer Science and Business Media LLC}, author={Lauer, Edwin and Isik, Fikret}, year={2021}, month={Jun} }
 @article{maynor_isik_walker_whetten_heine_payn_mckeand_2021, title={Provenance and Family Variation in Biomass Potential of Loblolly Pine in the Piedmont of North Carolina}, volume={67}, ISSN={["1938-3738"]}, url={https://doi.org/10.1093/forsci/fxaa056}, DOI={10.1093/forsci/fxaa056}, abstractNote={Abstract Considerable genetic differences in loblolly pine (Pinus taeda L.) exist for growth, stem form, and wood quality traits that influence biomass/biofuel production. By planting genetically superior trees with desirable biomass/biofuel traits, it is possible to substantially increase the amount of biomass and potential sawtimber trees produced from plantations. Ten of the fastest growing loblolly pine families from two provenances, Atlantic Coastal Plain and Piedmont, were tested for their biomass potential in North Carolina on a Piedmont site. At this northern Piedmont site at age six years, there were no provenance differences for biomass production or for trees with sawtimber potential. Variation in volume and sawtimber potential was significant at the family level. For biomass plantations, risks can be mitigated because of shorter rotation length, allowing for a higher-risk seed lot to capture greater gains in terms of volume. For a longer-rotation sawtimber stand, a more conservative family deployment strategy should be considered to maintain stem quality at the end of the rotation. Understanding the different seed source families and harvest regimes is essential to ensure profitable returns from pine plantations.}, number={3}, journal={FOREST SCIENCE}, publisher={Oxford University Press (OUP)}, author={Maynor, Jessica A. and Isik, Fikret and Walker, Trevor D. and Whetten, Ross W. and Heine, Austin J. and Payn, Kitt G. and McKeand, Steven E.}, year={2021}, month={Jun}, pages={312–320} }
 @article{caballero_lauer_bennett_zaman_mcevoy_acosta_jackson_townsend_eckert_whetten_et al._2021, title={Toward genomic selection in Pinus taeda: Integrating resources to support array design in a complex conifer genome}, volume={9}, ISSN={["2168-0450"]}, url={https://doi.org/10.1002/aps3.11439}, DOI={10.1002/aps3.11439}, abstractNote={An informatics approach was used for the construction of an Axiom genotyping array from heterogeneous, high-throughput sequence data to assess the complex genome of loblolly pine (Pinus taeda).High-throughput sequence data, sourced from exome capture and whole genome reduced-representation approaches from 2698 trees across five sequence populations, were analyzed with the improved genome assembly and annotation for the loblolly pine. A variant detection, filtering, and probe design pipeline was developed to detect true variants across and within populations. From 8.27 million variants, a total of 642,275 were evaluated and 423,695 of those were screened across a range-wide population.The final informatics and screening approach delivered an Axiom array representing 46,439 high-confidence variants to the forest tree breeding and genetics community. Based on the annotated reference genome, 34% were located in or directly upstream or downstream of genic regions.The Pita50K array represents a genome-wide resource developed from sequence data for an economically important conifer, loblolly pine. It uniquely integrates independent projects that assessed trees sampled across the native range. The challenges associated with the large and repetitive genome are addressed in the development of this resource.}, number={6}, journal={APPLICATIONS IN PLANT SCIENCES}, publisher={Wiley}, author={Caballero, Madison and Lauer, Edwin and Bennett, Jeremy and Zaman, Sumaira and McEvoy, Susan and Acosta, Juan and Jackson, Colin and Townsend, Laura and Eckert, Andrew and Whetten, Ross W. and et al.}, year={2021}, month={Jun} }
 @article{shalizi_gezan_mckeand_sherrill_cumbie_whetten_isik_2020, title={Correspondence between Breeding Values of the Same Pinus taeda L. Genotypes from Clonal Trials and Half-Sib Seedling Progeny Trials}, volume={66}, ISSN={0015-749X 1938-3738}, url={http://dx.doi.org/10.1093/forsci/fxaa016}, DOI={10.1093/forsci/fxaa016}, abstractNote={Abstract The correspondence between breeding values of 65 loblolly pine (Pinus taeda L.) genotypes from clonal genetic tests and half-sib seedling progeny tests was studied in the southern United States. The two experiments were established separately, 10 years apart. Additive genetic variance estimates from clonal tests were larger compared with the estimates from the half-sib progeny tests, regardless of the covariance structure used in the statistical models and the traits. However, clone-mean and half-sib family-mean heritability estimates were comparable for all traits, ranging between 0.88 and 0.99. Based on the independent analysis, the correlation between the breeding values of the same genotypes from two propagule types was moderate (0.59) for tree height and stem volume. The combined analysis resulted in a strong genetic correlation (>0.93) between the breeding values of two propagule types. Herein the large discrepancy is mainly the outcome of different data analytical approaches. Conclusively, selecting genotypes for deployment based on clonal testing may not be optimal, but forest tree breeders can use the results from clonal tests to make some informed decisions.}, number={5}, journal={Forest Science}, publisher={Oxford University Press (OUP)}, author={Shalizi, Mohammad Nasir and Gezan, Salvador Alejandro and McKeand, Steven E and Sherrill, Joshua R and Cumbie, W Patrick and Whetten, Ross W and Isik, Fikret}, year={2020}, month={Sep}, pages={600–611} }
 @article{calleja-rodriguez_pan_funda_chen_baison_isik_abrahamsson_wu_2020, title={Evaluation of the efficiency of genomic versus pedigree predictions for growth and wood quality traits in Scots pine}, volume={21}, ISSN={["1471-2164"]}, DOI={10.1186/s12864-020-07188-4}, abstractNote={Genomic selection (GS) or genomic prediction is a promising approach for tree breeding to obtain higher genetic gains by shortening time of progeny testing in breeding programs. As proof-of-concept for Scots pine (Pinus sylvestris L.), a genomic prediction study was conducted with 694 individuals representing 183 full-sib families that were genotyped with genotyping-by-sequencing (GBS) and phenotyped for growth and wood quality traits. 8719 SNPs were used to compare different genomic with pedigree prediction models. Additionally, four prediction efficiency methods were used to evaluate the impact of genomic breeding value estimations by assigning diverse ratios of training and validation sets, as well as several subsets of SNP markers.Genomic Best Linear Unbiased Prediction (GBLUP) and Bayesian Ridge Regression (BRR) combined with expectation maximization (EM) imputation algorithm showed slightly higher prediction efficiencies than Pedigree Best Linear Unbiased Prediction (PBLUP) and Bayesian LASSO, with some exceptions. A subset of approximately 6000 SNP markers, was enough to provide similar prediction efficiencies as the full set of 8719 markers. Additionally, prediction efficiencies of genomic models were enough to achieve a higher selection response, that varied between 50-143% higher than the traditional pedigree-based selection.Although prediction efficiencies were similar for genomic and pedigree models, the relative selection response was doubled for genomic models by assuming that earlier selections can be done at the seedling stage, reducing the progeny testing time, thus shortening the breeding cycle length roughly by 50%.}, number={1}, journal={BMC GENOMICS}, author={Calleja-Rodriguez, Ainhoa and Pan, Jin and Funda, Tomas and Chen, Zhiqiang and Baison, John and Isik, Fikret and Abrahamsson, Sara and Wu, Harry X.}, year={2020}, month={Nov} }
 @article{mphahlele_isik_mostert-o'neill_reynolds_hodge_myburg_2020, title={Expected benefits of genomic selection for growth and wood quality traits inEucalyptus grandis}, volume={16}, ISSN={["1614-2950"]}, DOI={10.1007/s11295-020-01443-1}, number={4}, journal={TREE GENETICS & GENOMES}, author={Mphahlele, Makobatjatji M. and Isik, Fikret and Mostert-O'Neill, Marja M. and Reynolds, S. Melissa and Hodge, Gary R. and Myburg, Alexander A.}, year={2020}, month={Jun} }
 @article{heine_walker_mckeand_jett_isik_2020, title={Pollination Bag Type Has a Significant Impact on Cone Survival in Mass Production of Controlled Pollinated Seeds in Loblolly Pine}, volume={66}, ISSN={0015-749X 1938-3738}, url={http://dx.doi.org/10.1093/forsci/fxaa013}, DOI={10.1093/forsci/fxaa013}, abstractNote={Abstract Since 2009, deployment of full-sib families of loblolly pine (Pinus taeda L.) has gained prominence in the southeastern United States. To produce full-sib seed, a pollination bag is used to isolate female strobili from outside pollen contamination, and a known pollen is applied at the time of maximum female strobilus receptivity. The goal of this study was to compare prototype pollination bags made by PBS International to the industry standard kraft paper pollination bag with and without a support wire for female strobili survival and to assess their efficiency for mass production of controlled cross loblolly pine seed. A multiyear study compared 13 pollination bag types at more than nine seed orchard sites across the southeastern United States. There were significant differences among bag types for conelet survival at the time of bag removal that persisted until cone harvest 18 months later. Female strobili bagged in prototype PBS-I2 were over three times more likely to survive to cone harvest than strobili inside the traditional kraft pollination bag. Two of the PBS bag types had the highest estimated filled seed per bag. One PBS bag was faster to install and remove than the kraft paper bag with a support wire.}, number={5}, journal={Forest Science}, publisher={Oxford University Press (OUP)}, author={Heine, Austin J and Walker, Trevor D and McKeand, Steven E and Jett, Jackson B and Isik, Fikret}, year={2020}, month={Jun}, pages={589–599} }
 @article{frey_durmus_sills_isik_comer_2020, title={Potential Alternative Tree Species as Substrates for Forest Farming of Log-grown Shiitake Mushrooms in the Southeastern United States}, volume={30}, ISSN={["1943-7714"]}, DOI={10.21273/HORTTECH04721-20}, abstractNote={Shiitake ( Lentinula edodes ) is an edible mushroom-producing fungus. “Natural log-grown” shiitake mushrooms are favored by consumers and are often produced by small farmers and hobbyists in the United States. The tree species most often recommended as a substrate for shiitake is white oak ( Quercus alba ), which has many other economic uses. We tested two strains of shiitake in log substrates of three common, low-value tree species in the southeastern United States to identify potential alternatives to white oak. We found that sweetgum ( Liquidambar styraciflua ) was a good substitute for white oak, both in terms of mushroom production and financial returns. Red maple ( Acer rubrum ) had less potential, with lower production and marginal financial returns, and ailanthus ( Ailanthus altissima ) was not a suitable alternative substrate. Of the two shiitake strains tested, a commercially available strain performed better than a naturalized strain that was isolated from an uninoculated log. Further research is needed to identify other potential alternative substrates and production techniques in the southeastern United States and other regions.}, number={6}, journal={HORTTECHNOLOGY}, author={Frey, Gregory E. and Durmus, Tank and Sills, Erin O. and Isik, Fikret and Comer, Marcus M.}, year={2020}, month={Dec}, pages={741-+} }
 @article{isik_mckeand_2019, title={Fourth cycle breeding and testing strategy for Pinus taeda in the NC State University Cooperative Tree Improvement Program}, volume={15}, ISSN={["1614-2950"]}, url={https://doi.org/10.1007/s11295-019-1377-y}, DOI={10.1007/s11295-019-1377-y}, number={5}, journal={TREE GENETICS & GENOMES}, publisher={Springer Science and Business Media LLC}, author={Isik, Fikret and McKeand, Steven E.}, year={2019}, month={Oct} }
 @article{walker_isik_mckeand_2019, title={Genetic Variation in Acoustic Time of Flight and Drill Resistance of Juvenile Wood in a Large Loblolly Pine Breeding Population}, volume={65}, ISSN={0015-749X 1938-3738}, url={http://dx.doi.org/10.1093/forsci/fxz002}, DOI={10.1093/forsci/fxz002}, abstractNote={Abstract Acoustic time of flight and drill resistance (surrogates for wood stiffness and density, respectively) were measured on 11,097 standing trees from 269 pollen-mix families of loblolly pine (Pinus taeda L.) in 6- to 9-year-old progeny tests at eight sites across the southeastern United States. Specific gravity was measured on two test sites. The phenotypic correlation between specific gravity and drill resistance was moderate (r = 0.68), whereas the genetic correlation was very strong (rg = 0.96). Narrow-sense heritabilities for acoustic time of flight and drill resistance were around 0.35 for individual trees and very strong (0.90) for family means. High genetic correlations (>0.80) between pairs of sites suggested a low genotype-by-environment interaction for both traits. Genetic correlations between wood quality traits and other economic traits (growth and stem straightness) were low except for a moderate correlation between acoustic time of flight and tree slenderness (rg = –0.64). The checklot ranked near the middle for both wood quality traits, implying no inadvertent selection occurred in this population that has been selected intensively for volume productivity. This study is the first to apply these tools in a large breeding program, and results suggest they are effective for selecting genotypes for wood quality.}, number={4}, journal={Forest Science}, publisher={Oxford University Press (OUP)}, author={Walker, Trevor D and Isik, Fikret and McKeand, Steven E}, year={2019}, month={Mar}, pages={469–482} }
 @article{shalizi_isik_2019, title={Genetic parameter estimates and GxE interaction in a large cloned population of Pinus taeda L.}, volume={15}, ISSN={["1614-2950"]}, url={https://doi.org/10.1007/s11295-019-1352-7}, DOI={10.1007/s11295-019-1352-7}, number={3}, journal={TREE GENETICS & GENOMES}, publisher={Springer Science and Business Media LLC}, author={Shalizi, Mohammad Nasir and Isik, Fikret}, year={2019}, month={Jun} }
 @article{chan_isik_2019, title={Genetic variation in resistance to Uromycladium acaciae fungus, growth, gummosis, and stem form in Acacia mearnsii populations}, volume={15}, ISSN={["1614-2950"]}, DOI={10.1007/s11295-019-1341-x}, number={3}, journal={TREE GENETICS & GENOMES}, author={Chan, Julian Moreno and Isik, Fikret}, year={2019}, month={Jun} }
 @misc{calleja-rodriguez_pan_funda_chen_baison_isik_abrahamsson_wu_2019, title={Genomic prediction accuracies and abilities for growth and wood quality traits of Scots pine, using genotyping-by-sequencing (GBS) data}, url={http://dx.doi.org/10.1101/607648}, DOI={10.1101/607648}, abstractNote={ABSTRACT Higher genetic gains can be achieved through genomic selection (GS) by shortening time of progeny testing in tree breeding programs. Genotyping-by-sequencing (GBS), combined with two imputation methods, allowed us to perform the current genomic prediction study in Scots pine ( Pinus sylvestris L.). 694 individuals representing 183 full-sib families were genotyped and phenotyped for growth and wood quality traits. 8719 SNPs were used to compare different genomic prediction models. In addition, the impact on the predictive ability (PA) and prediction accuracy to estimate genomic breeding values was evaluated by assigning different ratios of training and validation sets, as well as different subsets of SNP markers. Genomic Best Linear Unbiased Prediction (GBLUP) and Bayesian Ridge Regression (BRR) combined with expectation maximization (EM) imputation algorithm showed higher PAs and prediction accuracies than Bayesian LASSO (BL). A subset of approximately 4000 markers was sufficient to provide the same PAs and accuracies as the full set of 8719 markers. Furthermore, PAs were similar for both pedigree- and genomic-based estimations, whereas accuracies and heritabilities were slightly higher for pedigree-based estimations. However, prediction accuracies of genomic models were sufficient to achieve a higher selection efficiency per year, varying between 50-87% compared to the traditional pedigree-based selection.}, publisher={Cold Spring Harbor Laboratory}, author={Calleja-Rodriguez, Ainhoa and Pan, Jin and Funda, Tomas and Chen, Zhi-Qiang and Baison, John and Isik, Fikret and Abrahamsson, Sara and Wu, Harry X.}, year={2019}, month={Apr} }
 @article{wang_matthews_williams_shi_yang_tunlaya-anukit_chen_li_liu_lin_et al._2018, title={Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis}, volume={9}, ISSN={2041-1723}, url={http://dx.doi.org/10.1038/s41467-018-03863-z}, DOI={10.1038/s41467-018-03863-z}, abstractNote={Abstract A multi-omics quantitative integrative analysis of lignin biosynthesis can advance the strategic engineering of wood for timber, pulp, and biofuels. Lignin is polymerized from three monomers (monolignols) produced by a grid-like pathway. The pathway in wood formation of Populus trichocarpa has at least 21 genes, encoding enzymes that mediate 37 reactions on 24 metabolites, leading to lignin and affecting wood properties. We perturb these 21 pathway genes and integrate transcriptomic, proteomic, fluxomic and phenomic data from 221 lines selected from ~2000 transgenics (6-month-old). The integrative analysis estimates how changing expression of pathway gene or gene combination affects protein abundance, metabolic-flux, metabolite concentrations, and 25 wood traits, including lignin, tree-growth, density, strength, and saccharification. The analysis then predicts improvements in any of these 25 traits individually or in combinations, through engineering expression of specific monolignol genes. The analysis may lead to greater understanding of other pathways for improved growth and adaptation.}, number={1}, journal={Nature Communications}, publisher={Springer Science and Business Media LLC}, author={Wang, Jack P. and Matthews, Megan L. and Williams, Cranos M. and Shi, Rui and Yang, Chenmin and Tunlaya-Anukit, Sermsawat and Chen, Hsi-Chuan and Li, Quanzi and Liu, Jie and Lin, Chien-Yuan and et al.}, year={2018}, month={Apr}, pages={1579} }
 @misc{grattapaglia_silva-junior_resende_cappa_muller_tan_isik_ratcliffe_el-kassaby_2018, title={Quantitative Genetics and Genomics Converge to Accelerate Forest Tree Breeding}, volume={9}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2018.01693}, abstractNote={Forest tree breeding has been successful at delivering genetically improved material for multiple traits based on recurrent cycles of selection, mating, and testing. However, long breeding cycles, late flowering, variable juvenile-mature correlations, emerging pests and diseases, climate, and market changes, all pose formidable challenges. Genetic dissection approaches such as quantitative trait mapping and association genetics have been fruitless to effectively drive operational marker-assisted selection (MAS) in forest trees, largely because of the complex multifactorial inheritance of most, if not all traits of interest. The convergence of high-throughput genomics and quantitative genetics has established two new paradigms that are changing contemporary tree breeding dogmas. Genomic selection (GS) uses large number of genome-wide markers to predict complex phenotypes. It has the potential to accelerate breeding cycles, increase selection intensity and improve the accuracy of breeding values. Realized genomic relationships matrices, on the other hand, provide innovations in genetic parameters' estimation and breeding approaches by tracking the variation arising from random Mendelian segregation in pedigrees. In light of a recent flow of promising experimental results, here we briefly review the main concepts, analytical tools and remaining challenges that currently underlie the application of genomics data to tree breeding. With easy and cost-effective genotyping, we are now at the brink of extensive adoption of GS in tree breeding. Areas for future GS research include optimizing strategies for updating prediction models, adding validated functional genomics data to improve prediction accuracy, and integrating genomic and multi-environment data for forecasting the performance of genetic material in untested sites or under changing climate scenarios. The buildup of phenotypic and genome-wide data across large-scale breeding populations and advances in computational prediction of discrete genomic features should also provide opportunities to enhance the application of genomics to tree breeding.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Grattapaglia, Dario and Silva-Junior, Orzenil B. and Resende, Rafael T. and Cappa, Eduardo P. and Muller, Barbara S. F. and Tan, Biyue and Isik, Fikret and Ratcliffe, Blaise and El-Kassaby, Yousry A.}, year={2018}, month={Nov} }
 @article{spitzer_isik_whetten_farjat_mckeand_2017, title={Correspondence of Loblolly Pine Response for Fusiform Rust Disease from Local and Wide-Ranging Tests in the Southern United States}, volume={63}, ISSN={["1938-3738"]}, DOI={10.5849/fs-2016-093r1}, abstractNote={Fusiform rust is the most economically important disease of loblolly pine (Pinus taeda L.) in the southern United States. Estimates of family resistance to rust are critical for deployment decisions because 95% of loblolly pine plantations are established with individual families. If families show significant interactions with different pathogen inocula, then the performance of some families in different regions may not be predictable. This study compared rust breeding values of 56 loblolly families estimated from two independent sets of trials. We regressed the rust incidence breeding values of the families estimated from broadly based field tests on breeding values of the same families estimated from narrowly based tests. The model F test was highly significant (P < 0.0001), and breeding values based on local testing explained 75% of the variation in breeding values based on wide-range geographic testing, indicating that local rust breeding values are relatively reliable predictors of families' performance across a broad range of sites. Family rankings were highly consistent across test sites within broadly and narrowly based testing schemes as shown by type B genetic correlations (0.90 and 0.91). We conclude that field testing provides a reliable prediction of the operational value of loblolly families for deployment in regions with a high hazard for fusiform rust. Management and Policy Implications When choosing loblolly pine families to be planted on sites where resistance to fusiform rust is necessary, foresters and landowners can have confidence in the performance data coming from a range of field trials. Results show that local testing for rust resistance in relatively narrow geographic regions provides reasonably reliable rust disease resistance/susceptibility predictions and adequate predictive power for deployment decisions across a broad range of planting sites in the Gulf and Atlantic Coastal Plain regions of the southeastern United States.}, number={5}, journal={FOREST SCIENCE}, publisher={Oxford University Press (OUP)}, author={Spitzer, Jesse and Isik, Fikret and Whetten, Ross W. and Farjat, Alfredo E. and McKeand, Steven E.}, year={2017}, month={Oct}, pages={496–503} }
 @article{spitzer_isik_whetten_farjat_mckeand_2017, title={Correspondence of Loblolly Pine Response for Fusiform Rust Disease from Local and Wide-Ranging Tests in the Southern United States}, DOI={10.5849/fs-2016-093}, journal={Forest Science}, publisher={Oxford University Press (OUP)}, author={Spitzer, Jesse and Isik, Fikret and Whetten, Ross and Farjat, Alfredo and McKeand, Steve}, year={2017} }
 @book{isik_holland_maltecca_2017, title={Genetic Data Analysis for Plant and Animal Breeding}, ISBN={9783319551753 9783319551777}, url={http://dx.doi.org/10.1007/978-3-319-55177-7}, DOI={10.1007/978-3-319-55177-7}, publisher={Springer International Publishing}, author={Isik, Fikret and Holland, James and Maltecca, Christian}, year={2017} }
 @article{duran_isik_zapata-valenzuela_balocchi_valenzuela_2017, title={Genomic predictions of breeding values in a cloned Eucalyptus globulus population in Chile}, volume={13}, ISSN={["1614-2950"]}, DOI={10.1007/s11295-017-1158-4}, number={4}, journal={TREE GENETICS & GENOMES}, author={Duran, Ricardo and Isik, Fikret and Zapata-Valenzuela, Jaime and Balocchi, Claudio and Valenzuela, Sofia}, year={2017}, month={Aug} }
 @article{farjat_reich_guinness_whetten_mckeand_isik_2017, title={Optimal Seed Deployment Under Climate Change Using Spatial Models: Application to Loblolly Pine in the Southeastern US}, volume={112}, DOI={10.1080/01621459.2017.1292179}, abstractNote={Provenance tests are a common tool in forestry designed to identify superior genotypes for planting at specific locations. The trials are replicated experiments established with seed from parent trees collected from different regions and grown at several locations. In this work, a Bayesian spatial approach is developed for modeling the expected relative performance of seed sources using climate variables as predictors associated with the origin of seed source and the planting site. The proposed modeling technique accounts for the spatial dependence in the data and introduces a separable Matérn covariance structure that provides a flexible means to estimate effects associated with the origin and planting site locations. The statistical model was used to develop a quantitative tool for seed deployment aimed to identify the location of superior performing seed sources that could be suitable for a specific planting site under a given climate scenario. Cross-validation results indicate that the proposed spatial models provide superior predictive ability compared to multiple linear regression methods in unobserved locations. The general trend of performance predictions based on future climate scenarios suggests an optimal assisted migration of loblolly pine seed sources from southern and warmer regions to northern and colder areas in the southern USA. Supplementary materials for this article are available online.}, number={519}, journal={Journal of the American Statistical Association}, publisher={Informa UK Limited}, author={Farjat, Alfredo and Reich, Brian J. and Guinness, Joseph and Whetten, Ross and McKeand, Steven and Isik, Fikret}, year={2017}, month={Feb}, pages={909–920} }
 @article{farjat_chamblee_isik_whetten_mckeand_2017, title={Variation among Loblolly Pine Seed Sources across Diverse Environments in the Southeastern United States}, volume={63}, ISSN={0015-749X}, url={http://dx.doi.org/10.5849/forsci.15-107}, DOI={10.5849/forsci.15-107}, abstractNote={Seven seed sources of first-generation plantation selections of loblolly pine (Pinus taeda L.) were evaluated for six traits in test sites across most of its native range east of the Mississippi River in the southeastern United States. The traits evaluated were survival, height, volume, straightness, stem forking, and incidence of fusiform rust disease (caused by Cronartium quercuum [Berk.] Miyabe ex Shirai f. sp. fusiforme). At age 8 years, survival was high, with most seed sources having survival greater than 75% at all but two test sites. South Carolina Coastal and Georgia-Florida Coastal seed sources exhibited the fastest growth and most resistance to fusiform rust, whereas the Virginia seed source exhibited the slowest growth but had the best stem form. Test sites and seed source were significantly different for all traits. Seed source × site interactions (genotype × environment [G × E]) were also significant for all traits except stem forking. Low type B genetic correlation values (rB <0.67) for height, volume, and straightness suggest the presence of G × E interactions. The South Carolina Coastal and Virginia seed sources contributed disproportionally the most to G × E interactions for growth traits, but environmental contributions to G × E interactions were distributed relatively uniformly across most test sites. The results indicate that when seed sources are moved outside of their adaptive range, important G × E interactions should be expected and the difference among seed sources originating from a wide range of climates are expected to be more pronounced in older ages.}, number={1}, journal={Forest Science}, publisher={Oxford University Press (OUP)}, author={Farjat, Alfredo E. and Chamblee, Aaron K. and Isik, Fikret and Whetten, Ross W. and McKeand, Steven E.}, year={2017}, month={Feb}, pages={39–48} }
 @inbook{wang_tunlaya-anukit_shi_yeh_chuang_isik_yang_liu_li_loziuk_et al._2016, title={A Proteomic-Based Quantitative Analysis of the Relationship Between Monolignol Biosynthetic Protein Abundance and Lignin Content Using Transgenic<i>Populus trichocarpa}, volume={5}, ISBN={9781118883303 9781118883266}, url={http://dx.doi.org/10.1002/9781118883303.ch4}, DOI={10.1002/9781118883303.ch4}, abstractNote={As part of a long-term project to develop a predictive model of lignin biosynthesis in the stem differentiating xylem of Populus trichocarpa, we explored the quantitative relationships of gene-specific monolignol pathway proteins and the amount of the lignin polymer. We determined the absolute abundance of monolignol pathway proteins in wild-type (Nisqually-1) and 80 transgenic trees, downregulated for the expression of genes in the monolignol pathway. Total lignin content for wild-type and transgenics ranged from 9.4 to 24.2%. Comparison of protein variation with lignin content showed that the proteins are produced in several-fold excess, suggesting that the monolignol pathway is highly homeostatic. Strong downregulation of xylem-specific PtrPAL2, 4, and 5 showed the most direct relationship with lignin content. These results are consistent with the Predictive Kinetic Metabolic Flux (PKMF) model of Wang et al., based on differential equations of mass action kinetics. Functional redundancy of multiple genes also moderates gene-specific effects. In addition, targeted production of specific proteins may affect the concentration of nontarget monolignol proteins, suggesting a yet-to-be-described level of coordinated control.}, booktitle={Recent Advances in Polyphenol Research}, publisher={John Wiley & Sons, Ltd}, author={Wang, Jack P. and Tunlaya-Anukit, Sermsawat and Shi, Rui and Yeh, Ting-Feng and Chuang, Ling and Isik, Fikret and Yang, Chenmin and Liu, Jie and Li, Quanzi and Loziuk, Philip L. and et al.}, editor={Kumi Yoshida, Veronique Cheynier and Quideau, StephaneEditors}, year={2016}, month={Dec}, pages={89–107} }
 @inbook{whetten_isik_mckeand_2016, place={Auburn, AL}, title={Factors Influencing Productivity of Pine Biomass in the Southeastern United States}, booktitle={On biofuels in the Southeast}, publisher={Auburn University}, author={Whetten, Ross and Isik, Fikret and McKeand, Steve}, year={2016} }
 @article{grans_isik_purnell_mckeand_2016, title={Genetic Variation in Response to Herbicide and Fertilization Treatments for Growth and Form Traits in Loblolly Pine}, volume={62}, ISSN={["1938-3738"]}, DOI={10.5849/forsci.16-029}, abstractNote={The effects of imposed silvicultural treatments and genetics on growth and form traits were investigated in a 15-year-old loblolly pine (Pinus taeda L.) trial in southwestern Georgia, USA. The trial consisted of four treatment combinations and 25 open-pollinated first- and second-generation families. Average individual-tree stem volume ranged from 185.2 dm3 in the combined fertilization and herbicide plots to 91.2 dm3 in the control plots. Variation among treatment combinations was significant for height, volume, sweep, and forking defect but was not significant for branch angle and fusiform rust disease incidence (caused by the fungus Cronartium quercuum [Berk.] Miyabe ex Shirai f. sp. fusiforme). Family effects were significant for all traits across treatments. Individual-tree heritability values ranged from 0.10 (stem sweep) to 0.39 (branch angle). Corresponding family-mean heritability values had a range of 0.60 (stem sweep) to 0.90 (branch angle). Genetic correlations between growth (height and volume) and other traits (rust, branch angle, stem forking, and stem sweep) were low and not significant. The lack of important culture × genetics interactions in the study indicates a low risk of losing value due to suboptimal matching between genetic material and silvicultural prescriptions.}, number={6}, journal={FOREST SCIENCE}, author={Grans, Daniel and Isik, Fikret and Purnell, Robert C. and McKeand, Steven E.}, year={2016}, month={Dec}, pages={633–640} }
 @article{isik_bartholome_farjat_chancerel_raffin_sanchez_plomion_bouffier_2016, title={Genomic selection in maritime pine}, volume={242}, ISSN={["0168-9452"]}, DOI={10.1016/j.plantsci.2015.08.006}, abstractNote={A two-generation maritime pine (Pinus pinaster Ait.) breeding population (n=661) was genotyped using 2500 SNP markers. The extent of linkage disequilibrium and utility of genomic selection for growth and stem straightness improvement were investigated. The overall intra-chromosomal linkage disequilibrium was r(2)=0.01. Linkage disequilibrium corrected for genomic relationships derived from markers was smaller (rV(2)=0.006). Genomic BLUP, Bayesian ridge regression and Bayesian LASSO regression statistical models were used to obtain genomic estimated breeding values. Two validation methods (random sampling 50% of the population and 10% of the progeny generation as validation sets) were used with 100 replications. The average predictive ability across statistical models and validation methods was about 0.49 for stem sweep, and 0.47 and 0.43 for total height and tree diameter, respectively. The sensitivity analysis suggested that prior densities (variance explained by markers) had little or no discernible effect on posterior means (residual variance) in Bayesian prediction models. Sampling from the progeny generation for model validation increased the predictive ability of markers for tree diameter and stem sweep but not for total height. The results are promising despite low linkage disequilibrium and low marker coverage of the genome (∼1.39 markers/cM).}, journal={PLANT SCIENCE}, publisher={Elsevier BV}, author={Isik, Fikret and Bartholome, Jerome and Farjat, Alfredo and Chancerel, Emilie and Raffin, Annie and Sanchez, Leopoldo and Plomion, Christophe and Bouffier, Laurent}, year={2016}, month={Jan}, pages={108–119} }
 @article{plomion_bartholome_lesur_boury_rodriguez-quilon_lagraulet_ehrenmann_bouffier_gion_grivet_et al._2016, title={High-density SNP assay development for genetic analysis in maritime pine (Pinus pinaster)}, volume={16}, ISSN={["1755-0998"]}, DOI={10.1111/1755-0998.12464}, abstractNote={Abstract Maritime pine provides essential ecosystem services in the south‐western M editerranean basin, where it covers around 4 million ha. Its scattered distribution over a range of environmental conditions makes it an ideal forest tree species for studies of local adaptation and evolutionary responses to climatic change. Highly multiplexed single nucleotide polymorphism ( SNP ) genotyping arrays are increasingly used to study genetic variation in living organisms and for practical applications in plant and animal breeding and genetic resource conservation. We developed a 9k Illumina Infinium SNP array and genotyped maritime pine trees from (i) a three‐generation inbred ( F 2) pedigree, (ii) the F rench breeding population and (iii) natural populations from P ortugal and the F rench A tlantic coast. A large proportion of the exploitable SNP s (2052/8410, i.e. 24.4%) segregated in the mapping population and could be mapped, providing the densest ever gene‐based linkage map for this species. Based on 5016 SNP s, natural and breeding populations from the F rench gene pool exhibited similar level of genetic diversity. Population genetics and structure analyses based on 3981 SNP markers common to the P ortuguese and F rench gene pools revealed high levels of differentiation, leading to the identification of a set of highly differentiated SNP s that could be used for seed provenance certification. Finally, we discuss how the validated SNP s could facilitate the identification of ecologically and economically relevant genes in this species, improving our understanding of the demography and selective forces shaping its natural genetic diversity, and providing support for new breeding strategies.}, number={2}, journal={MOLECULAR ECOLOGY RESOURCES}, author={Plomion, C. and Bartholome, J. and Lesur, I. and Boury, C. and Rodriguez-Quilon, I. and Lagraulet, H. and Ehrenmann, F. and Bouffier, L. and Gion, J. M. and Grivet, D. and et al.}, year={2016}, month={Mar}, pages={574–587} }
 @article{bartholome_bink_heerwaarden_chancerel_boury_lesur_isik_bouffier_plomion_2016, title={Linkage and Association Mapping for Two Major Traits Used in the Maritime Pine Breeding Program: Height Growth and Stem Straightness}, volume={11}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0165323}, abstractNote={Increasing our understanding of the genetic architecture of complex traits, through analyses of genotype-phenotype associations and of the genes/polymorphisms accounting for trait variation, is crucial, to improve the integration of molecular markers into forest tree breeding. In this study, two full-sib families and one breeding population of maritime pine were used to identify quantitative trait loci (QTLs) for height growth and stem straightness, through linkage analysis (LA) and linkage disequilibrium (LD) mapping approaches.The populations used for LA consisted of two unrelated three-generation full-sib families (n = 197 and n = 477). These populations were assessed for height growth or stem straightness and genotyped for 248 and 217 markers, respectively. The population used for LD mapping consisted of 661 founders of the first and second generations of the breeding program. This population was phenotyped for the same traits and genotyped for 2,498 single-nucleotide polymorphism (SNP) markers corresponding to 1,652 gene loci. The gene-based reference genetic map of maritime pine was used to localize and compare the QTLs detected by the two approaches, for both traits. LA identified three QTLs for stem straightness and two QTLs for height growth. The LD study yielded seven significant associations (P ≤ 0.001): four for stem straightness and three for height growth. No colocalisation was found between QTLs identified by LA and SNPs detected by LD mapping for the same trait.This study provides the first comparison of LA and LD mapping approaches in maritime pine, highlighting the complementary nature of these two approaches for deciphering the genetic architecture of two mandatory traits of the breeding program.}, number={11}, journal={PLOS ONE}, author={Bartholome, Jerome and Bink, Marco C. A. M. and Heerwaarden, Joost and Chancerel, Emilie and Boury, Christophe and Lesur, Isabelle and Isik, Fikret and Bouffier, Laurent and Plomion, Christophe}, year={2016}, month={Nov} }
 @article{bartholome_van heerwaarden_isik_boury_vidal_plomion_bouffier_2016, title={Performance of genomic prediction within and across generations in maritime pine}, volume={17}, ISSN={["1471-2164"]}, DOI={10.1186/s12864-016-2879-8}, abstractNote={Genomic selection (GS) is a promising approach for decreasing breeding cycle length in forest trees. Assessment of progeny performance and of the prediction accuracy of GS models over generations is therefore a key issue. A reference population of maritime pine (Pinus pinaster) with an estimated effective inbreeding population size (status number) of 25 was first selected with simulated data. This reference population (n = 818) covered three generations (G0, G1 and G2) and was genotyped with 4436 single-nucleotide polymorphism (SNP) markers. We evaluated the effects on prediction accuracy of both the relatedness between the calibration and validation sets and validation on the basis of progeny performance. Pedigree-based (best linear unbiased prediction, ABLUP) and marker-based (genomic BLUP and Bayesian LASSO) models were used to predict breeding values for three different traits: circumference, height and stem straightness. On average, the ABLUP model outperformed genomic prediction models, with a maximum difference in prediction accuracies of 0.12, depending on the trait and the validation method. A mean difference in prediction accuracy of 0.17 was found between validation methods differing in terms of relatedness. Including the progenitors in the calibration set reduced this difference in prediction accuracy to 0.03. When only genotypes from the G0 and G1 generations were used in the calibration set and genotypes from G2 were used in the validation set (progeny validation), prediction accuracies ranged from 0.70 to 0.85. This study suggests that the training of prediction models on parental populations can predict the genetic merit of the progeny with high accuracy: an encouraging result for the implementation of GS in the maritime pine breeding program.}, number={1}, journal={BMC GENOMICS}, publisher={Springer Nature}, author={Bartholome, Jerome and Van Heerwaarden, Joost and Isik, Fikret and Boury, Christophe and Vidal, Marjorie and Plomion, Christophe and Bouffier, Laurent}, year={2016}, month={Aug} }
 @article{xiong_mckeand_isik_wegrzyn_neale_zeng_da costa e silva_whetten_2016, title={Quantitative trait loci influencing forking defects in an outbred pedigree of loblolly pine}, volume={17}, ISSN={1471-2156}, url={http://dx.doi.org/10.1186/s12863-016-0446-6}, DOI={10.1186/s12863-016-0446-6}, abstractNote={The use of wood as an industrial raw material has led to development of plantation forestry, in which trees are planted, managed, and harvested as crops. The productivity of such plantations often exceeds that of less-intensively-managed forests, and land managers have the option of choosing specific planting stock to produce specific types of wood for industrial use. Stem forking, or division of the stem into two or more stems of roughly equal size, is a character trait important in determining the quality of the stem for production of solid wood products. This trait typically has very low individual-tree heritability, but can be more accurately assessed in clonally-replicated plantings where each genotype is represented by several individual trees. We report results from a quantitative trait mapping experiment in a clonally-replicated full-sibling family of loblolly pine (Pinus taeda L.). Quantitative trait loci influencing forking defects were identified in an outbred full-sibling family of loblolly pine, using single-nucleotide polymorphism markers. Genetic markers in this family segregated either in 1:2:1 (F2 intercross-like segregation) or 1:1 ratio (backcross-like segregation). An integrated linkage map combining markers with different segregation ratios was assembled for this full-sib family, and a total of 409 SNP markers were mapped on 12 linkage groups, covering 1622 cM. Two and three trait loci were identified for forking and ramicorn branch traits, respectively, using the interval mapping method. Three trait loci were detected for both traits using multiple-trait analysis. The detection of three loci for forking and ramicorn branching in a multiple-trait analysis could mean that there are genes with pleiotropic effects on both traits, or that separate genes affecting different traits are clustered together. The detection of genetic loci associated with variation in stem quality traits in this study supports the hypothesis that marker-assisted selection can be used to decrease the rate of stem defects in breeding populations of loblolly pine.}, number={1}, journal={BMC Genetics}, publisher={Springer Science and Business Media LLC}, author={Xiong, Jin S. and McKeand, Steven E. and Isik, Fikret and Wegrzyn, Jill and Neale, David B. and Zeng, Zhao-Bang and da Costa e Silva, Luciano and Whetten, Ross W.}, year={2016}, month={Oct} }
 @article{kurt_frampton_isik_landgren_chastagner_2016, title={Variation in needle and cone characteristics and seed germination ability of Abies bornmuelleriana and Abies equi-trojani populations from Turkey}, volume={40}, DOI={10.3906/tar-1502-101}, abstractNote={Turkish fir (Abies bornmuelleriana Mattf.) and Trojan fir (Abies equi-trojani (Aschers. Et Sint. Ex Boiss) Mattf.) are economically and ecologically important endemic species to Turkey. These species are also becoming increasingly popular in Europe and North America due to their suitable characteristics for use as Christmas trees coupled with their pest resistance. Provenance features, as well as needle and cone characteristics and seed germination ability, of three Turkish fir and two Trojan fir populations were studied. Provenance features (vigor score, crown score, and color) and mother tree characteristics (height class, diameter at breast height, and height) were very similar between species and among populations within species. Needles of Turkish fir were significantly (P < 0.05) longer and wider than those of Trojan fir. Turkish fir also had wider cones and a higher cone width/length ratio than Trojan fir. There were moderate, positive, and significant correlations between needle-cone characteristics and location variables (elevation, latitude, and longitude). Needle size tended to increase northwards, eastwards, and upwards along an altitudinal gradient. Cone width and the cone width/length ratio showed a weak trend of increasing northwards, while the cone width also showed a weak trend of increasing eastwards. Bract and cone length were not significantly correlated with any of the location variables. The overall mean cumulative germination percentage of Turkish fir seed (57%) was significantly higher (P < 0.05) than that of Trojan fir (36%). The natural genetic resources of both species should be conserved and managed sustainably to preserve the variation in their endemic locations because of their valuable benefits to Turkey and other countries.}, number={2}, journal={Turkish Journal of Agriculture and Forestry}, author={Kurt, Y. and Frampton, J. and Isik, Fikret and Landgren, C. and Chastagner, G.}, year={2016}, pages={169–176} }
 @inbook{isik_kumar_martínez-garcía_iwata_yamamoto_2015, title={Acceleration of Forest and Fruit Tree Domestication by Genomic Selection}, volume={74}, ISBN={["978-0-12-398548-4"]}, ISSN={0065-2296}, url={http://dx.doi.org/10.1016/bs.abr.2015.05.002}, DOI={10.1016/bs.abr.2015.05.002}, abstractNote={Abstract Trees are important sources of food, fibre, fodder, fuel, and timber. Fruit and forest trees provide habitat for wildlife, sequester carbon, and protect soil and water resources. Despite a very long history of domestication of some fruit tree species, such as apple, domestication and breeding of many tree species is still in their early stages. The domestication of trees can be accelerated by modern tree breeding practices. Advances in genomic technologies are providing valuable tools to tree breeders. Breeders can be more efficient in improving the traits of interest to increase productivity, and develop genetic resources that can adapt to changing environment and have resistance to disease and pests. In this chapter, we first briefly examined the current status of major forest (conifers, eucalypts) and fruit trees (apple, peach, pear) breeding across the world. We then described the breeding strategies employed to improve the populations. A summary of genomic resources available for major tree species is also covered. The challenges and opportunities of genomic selection applications are finally summarized.}, booktitle={Advances in Botanical Research}, publisher={Elsevier}, author={Isik, Fikret and Kumar, Satish and Martínez-García, Pedro J. and Iwata, Hiroyoshi and Yamamoto, Toshiya}, year={2015}, pages={93–124} }
 @article{ford_mckeand_jett_isik_2015, title={Effects of Inbreeding on Growth and Quality Traits in Loblolly Pine}, volume={61}, ISSN={0015-749X}, url={http://dx.doi.org/10.5849/forsci.13-185}, DOI={10.5849/forsci.13-185}, abstractNote={The effect of inbreeding in two provenances of loblolly pine (Pinus taeda L.) was investigated. Ten parent trees from each of the Coastal Plain and Piedmont provenances in the southern United States were mated to produce outcrossed (F = 0), half-sib mated (F = 0.125), full-sib mated (F = 0.25), and selfed (F = 0.5) progeny. Growth and quality traits were measured in the progeny of the four inbreeding levels at age 9. Inbreeding decreased height growth up to 21% and stem volume up to 33% but did not affect stem straightness or fusiform rust disease incidence. As expected from quantitative genetics theory, inbreeding depression was more pronounced in crosses between more closely related individuals. Responses to inbreeding varied within parental groups at each inbreeding level, especially depending on the pollen source. Most of the parent groups showed consistent decreases in vigor with increased inbreeding. However, one specific parent group actually had a positive growth response, demonstrating that such genotypes may be selected for advanced-generation breeding, especially when breeding strategies make use of crosses among related individuals. Variation among inbreeding levels and among parents within inbreeding levels presents opportunities as well as challenges for developing breeding strategies in forest trees.}, number={3}, journal={Forest Science}, publisher={Oxford University Press (OUP)}, author={Ford, Graham A. and McKeand, Steven E. and Jett, Jackson B. and Isik, Fikret}, year={2015}, month={Jun}, pages={579–585} }
 @article{egbäck_bullock_isik_mckeand_2015, title={Height-Diameter Relationships for Different Genetic Planting Stock of Loblolly Pine at Age 6}, volume={61}, ISSN={0015-749X}, url={http://dx.doi.org/10.5849/forsci.14-015}, DOI={10.5849/forsci.14-015}, number={3}, journal={Forest Science}, publisher={Oxford University Press (OUP)}, author={Egbäck, Samuel and Bullock, Bronson P. and Isik, Fikret and McKeand, Steven E.}, year={2015}, month={Jun}, pages={424–428} }
 @article{farjat_isik_reich_whetten_mckeand_2015, title={Modeling Climate Change Effects on the Height Growth of Loblolly Pine}, volume={61}, ISSN={0015-749X}, url={http://dx.doi.org/10.5849/forsci.14-075}, DOI={10.5849/forsci.14-075}, abstractNote={We present a statistical model to predict the effects of climate change on the height growth of loblolly pine (Pinus taeda L.) families in the southeastern United States. Provenance-progeny trials were used for assessing the response of loblolly pine seed sources to environmental change. Ordinary least squares, ridge regression, and LASSO regression were used to develop height growth prediction models. The approach integrates both genetic and environmental effects and is meant to overcome the critical limitations of population response function and transfer function methods by making full use of data from provenance trials. Prediction models were tested using a hypothetical future climate scenario with 5% decrease in precipitation and 0.5° C increase in maximum and minimum temperatures, relative to historical average values. Under this scenario, local families from the coastal plains of Georgia, Florida, and South Carolina showed the highest performance relative to the current climate in their native environments. As these seed sources were moved to colder northern and inland regions from their origin, we observed declines in their height growth. Similarly, the climatic change scenario suggested that performance of northern seed sources declined significantly when they were moved to more southern warmer regions. The statistical model can be used as a quantitative tool to model the effect of climatic variables on the performance of loblolly pine seed sources and may help to develop sound breeding deployment strategies.}, number={4}, journal={Forest Science}, publisher={Oxford University Press (OUP)}, author={Farjat, Alfredo E. and Isik, Fikret and Reich, Brian J. and Whetten, Ross W. and McKeand, Steven E.}, year={2015}, month={Aug}, pages={703–715} }
 @article{zapata-valenzuela_ogut_kegley_cumbie_isik_li_mckeand_2015, title={Seedling Evaluation of Atlantic Coastal and Piedmont Sources of <i>Pinus taeda</i> L. and Their Hybrids for Cold Hardiness}, volume={61}, ISSN={0015-749X}, url={http://dx.doi.org/10.5849/forsci.12-610}, DOI={10.5849/forsci.12-610}, abstractNote={Seedlings of 59 loblolly pine (Pinus taeda L.) polycross families representing four populations (Atlantic Coastal, Piedmont, Coastal × Piedmont, and Piedmont × Coastal) were evaluated for cold hardiness. Seedlings were preconditioned in phytotron environments and then subjected to a freezing treatment. Freezing injury, mortality, and size of seedlings were assessed. Significant differences in cold injury were found among populations and families within each population. The Piedmont families and hybrid seedlings with a Piedmont maternal parent had less injury and higher survival relative to those of the other populations. Most families with high cold injury had a Coastal maternal parent, whereas most families with the least cold injury had a Piedmont maternal parent. The large observed among- and within-population variations in cold injury suggested that family or individual-within-family selection could improve cold hardiness in loblolly pine. Based on the results of seedling growth and cold injury, there may be an advantage to deploying Piedmont × Coastal hybrids or Piedmont families on more adverse sites, e.g., cold sites. On the milder sites, deployment of Coastal × Piedmont hybrids or hardy Coastal families seems appropriate.}, number={1}, journal={Forest Science}, publisher={Oxford University Press (OUP)}, author={Zapata-Valenzuela, Jaime A. and Ogut, Funda and Kegley, Angela and Cumbie, Patrick and Isik, Fikret and Li, Bailian and McKeand, Steven E.}, year={2015}, month={Feb}, pages={169–175} }
 @article{wood_bullock_isik_mckeand_2015, title={Variation in Stem Taper and Growth Traits in a Clonal Trial of Loblolly Pine}, volume={61}, ISSN={["1938-3738"]}, DOI={10.5849/forsci.12-068}, abstractNote={As volume is the primary measure of value in loblolly pine (Pinus taeda L.) stands, knowledge about the stem taper of commonly deployed clones may better describe genetic gains made by each clonal variety and could provide more accurate volume estimates. Clonal varieties with combined low taper and fast growth can potentially offer great gains in uniformity, quality, and volume when deployed operationally. Clones propagated via somatic embryogenesis from 13 full-sib families and two open-pollinated families were measured in the eighth growing season across three sites in coastal Georgia and South Carolina. Three form quotients were used to analyze stem taper differences among clones and to assess taper impacts on total stem volume. Significant clonal variation was found for form quotients, indicating that genetic differences exist in stem taper among different clones. Clone mean heritability estimates for form quotients and growth traits were moderate to high (0.64–0.94), indicating that the use of form quotients could improve selection by accounting for taper in clones. However, taper impacts on total volume were minimal after accounting for dbh and total height, and differences among clones in total volume were sufficiently captured using a single combined-variable D2H equation. While selecting clones by total height and dbh may not necessarily capture clones with the least taper, this method was sufficient for selecting varieties with the largest volumes.}, number={1}, journal={FOREST SCIENCE}, publisher={Oxford University Press (OUP)}, author={Wood, Elizabeth R. and Bullock, Bronson P. and Isik, Fikret and McKeand, Steven E.}, year={2015}, month={Feb}, pages={76–82} }
 @article{ogut_maltecca_whetten_mckeand_isik_2014, title={Genetic Analysis of Diallel Progeny Test Data Using Factor Analytic Linear Mixed Models}, volume={60}, ISSN={["1938-3738"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84893424508&partnerID=MN8TOARS}, DOI={10.5849/forsci.12-108}, abstractNote={Multienvironmental trials are commonly used in plant breeding programs to select superior genotypes for specific sites or across multiple sites for breeding and deployment decisions. We compared the efficiency of factor analytic (FA) and other covariance structures for genetic analysis of height growth in Pinus taeda L. diallel progeny trials to account for heterogeneity in variances and covariances among different environments. Among the models fitted, FA models produced the smallest Akaike information criterion (AIC) model fit statistic. An unstructured (US) variance-covariance matrix produced a log likelihood value similar to that for the FA model but had a large number of parameters. As a result, some models with US covariance failed to converge. FA models captured both variance and covariance at the genetic level better than simpler models and provided more accurate predictions of breeding values. Narrow-sense heritability estimates for height from 10 different sites were about 0.20 when more complex variance structures were used, compared with 0.13 when simpler variance structures such as identity and block-diagonal variance structures were used. FA models are robust for modeling genotype × environment interaction, and they reduce the computational requirements of mixed-model analysis. On average, all 10 environments had additive genetic correlation of 0.83 and dominance genetic correlation of 0.91, suggesting that genotype × environment interaction should not be a concern for this specific population in the environments in which the genotypes were tested.}, number={1}, journal={FOREST SCIENCE}, publisher={Oxford University Press (OUP)}, author={Ogut, Funda and Maltecca, Christian and Whetten, Ross and McKeand, Steven and Isik, Fikret}, year={2014}, month={Feb}, pages={119–127} }
 @article{xiong_mckeand_whetten_isik_2014, title={Genetics of Stem Forking and Ramicorn Branches in a Cloned Loblolly Pine Family}, volume={60}, ISSN={0015-749X}, url={http://dx.doi.org/10.5849/forsci.12-018}, DOI={10.5849/forsci.12-018}, abstractNote={Forking defects and ramicorn branching were assessed in a cloned full-sib family of loblolly pine (Pinus taeda L.). The proportion of forking ranged from 13 to 21% across four test sites with a mean of 17%. Ramicorn branching incidence averaged 24% and varied from 18 to 31% over all sites. There were significant differences among clones within this family for all traits studied. The estimated clone mean repeatabilities were moderately high for forking defects (0.67–0.86). Through single trait selection with a selection differential of 4%, the proportion of trees with forks and ramicorn branches could be reduced 10 and 13%, respectively. Low to moderate unfavorable genetic correlations were found between growth traits and forking defects (0.12–0.45), suggesting that selection for either trait alone will negatively affect the genetic response for the other. No significant environmental correlations were found between forking and growth. A moderate significant positive genetic correlation between stem forking and ramicorn branching indicates that both traits may be partially controlled by the same genes and could be improved simultaneously. Strategies are discussed for within-family selection to capture more gain for increased growth and reduced stem forking for the breeding of loblolly pine.}, number={2}, journal={Forest Science}, publisher={Oxford University Press (OUP)}, author={Xiong, Jin S. and McKeand, Steven E. and Whetten, Ross W. and Isik, Fikret T.}, year={2014}, month={Apr}, pages={360–366} }
 @article{plomion_chancerel_endelman_lamy_mandrou_lesur_ehrenmann_isik_bink_heerwaarden_et al._2014, title={Genome-wide distribution of genetic diversity and linkage disequilibrium in a mass-selected population of maritime pine}, volume={15}, ISSN={["1471-2164"]}, DOI={10.1186/1471-2164-15-171}, abstractNote={The accessibility of high-throughput genotyping technologies has contributed greatly to the development of genomic resources in non-model organisms. High-density genotyping arrays have only recently been developed for some economically important species such as conifers. The potential for using genomic technologies in association mapping and breeding depends largely on the genome wide patterns of diversity and linkage disequilibrium in current breeding populations. This study aims to deepen our knowledge regarding these issues in maritime pine, the first species used for reforestation in south western Europe. Using a new map merging algorithm, we first established a 1,712 cM composite linkage map (comprising 1,838 SNP markers in 12 linkage groups) by bringing together three already available genetic maps. Using rigorous statistical testing based on kernel density estimation and resampling we identified cold and hot spots of recombination. In parallel, 186 unrelated trees of a mass-selected population were genotyped using a 12k-SNP array. A total of 2,600 informative SNPs allowed to describe historical recombination, genetic diversity and genetic structure of this recently domesticated breeding pool that forms the basis of much of the current and future breeding of this species. We observe very low levels of population genetic structure and find no evidence that artificial selection has caused a reduction in genetic diversity. By combining these two pieces of information, we provided the map position of 1,671 SNPs corresponding to 1,192 different loci. This made it possible to analyze the spatial pattern of genetic diversity (H e ) and long distance linkage disequilibrium (LD) along the chromosomes. We found no particular pattern in the empirical variogram of H e across the 12 linkage groups and, as expected for an outcrossing species with large effective population size, we observed an almost complete lack of long distance LD. These results are a stepping stone for the development of strategies for studies in population genomics, association mapping and genomic prediction in this economical and ecologically important forest tree species.}, number={1}, journal={BMC GENOMICS}, publisher={Springer Nature}, author={Plomion, Christophe and Chancerel, Emilie and Endelman, Jeffrey and Lamy, Jean-Baptiste and Mandrou, Eric and Lesur, Isabelle and Ehrenmann, Francois and Isik, Fikret and Bink, Marco C. A. M. and Heerwaarden, Joost and et al.}, year={2014}, month={Mar} }
 @article{isik_2014, title={Genomic selection in forest tree breeding: the concept and an outlook to the future}, volume={45}, ISSN={["1573-5095"]}, DOI={10.1007/s11056-014-9422-z}, abstractNote={Using large numbers of DNA markers to predict genetic merit [genomic selection (GS)] is a new frontier in plant and animal breeding programs. GS is now routinely used to select superior bulls in dairy cattle breeding. In forest trees, a few empirical proof of-concept studies suggest that GS could be successful. However, application of GS in forest tree breeding is still in its infancy. The major hurdle is lack of high throughput genotyping platforms for trees, and the high genotyping costs, though, the cost of genotyping will likely decrease in the future. There has been a growing interest in GS among tree breeders, forest geneticists, and tree improvement managers. A broad overview of pedigree reconstruction and GS is presented. Underlying reasons for failures of marker-assisted selection were summarized and compared with GS. Challenges of GS in forest tree breeding and the outlook for the future are discussed, and a GS plan for a cloned loblolly pine breeding population is presented. This review is intended for tree breeders, forest managers, scientist and students who are not necessarily familiar with genomic or quantitative genetics jargon.}, number={3}, journal={NEW FORESTS}, publisher={Springer Nature}, author={Isik, Fikret}, year={2014}, month={May}, pages={379–401} }
 @article{smith_bullock_isik_mckeand_2014, title={Modeling genetic effects on growth of diverse provenances and families of loblolly pine across optimum and deficient nutrient regimes}, volume={44}, ISSN={["1208-6037"]}, url={http://dx.doi.org/10.1139/cjfr-2013-0379}, DOI={10.1139/cjfr-2013-0379}, abstractNote={Optimal deployment of improved loblolly pine (Pinus taeda L.) planting stock in the southeastern United States requires knowing how diverse seed sources and families perform over time across the wide range of sites used for plantations. This study tests if the relative growth performance of provenances and families is the same at the individual-tree and stand levels for family block plantings and determines what type of adjustment may be required to account for genetic differences when modeling growth and yield. Ten open-pollinated families from two very different provenances, Atlantic Coastal Plain and “Lost Pines” Texas, were grown in single-family block plots to test for growth differences between provenances and among families under severely deficient and optimal nutrition regimes on a nutrient-deficient, dry site. The three-parameter Chapman–Richards function was fit to plot means over time by provenance, family, and nutrition treatments. Models with provenance- or family-specific parameters of the Chapman–Richards function were tested for significant improvement over global parameters. At age 14 years, family, provenance, and nutrition treatments all significantly affected individual-tree growth traits of height, diameter, and volume. Significant nutrition by provenance interactions were found for stand-level traits of basal area per hectare and volume per hectare. Family differences were also significant for these traits. Provenance- or family-specific asymptotic parameters accounted for differences in growth over time. Several traits required the use of local asymptotic and rate parameters in the fertilized treatment only. For modeling growth, a multiplier would be sufficient to account for genetic effects on the majority of traits.}, number={11}, journal={CANADIAN JOURNAL OF FOREST RESEARCH}, publisher={Canadian Science Publishing}, author={Smith, Ben C. and Bullock, Bronson P. and Isik, Fikret and McKeand, Steven E.}, year={2014}, month={Nov}, pages={1453–1461} }
 @article{chen_song_wang_lin_ducoste_shuford_liu_li_shi_nepomuceno_et al._2014, title={Systems Biology of Lignin Biosynthesis in <i>Populus trichocarpa</i>: Heteromeric 4-Coumaric Acid:Coenzyme A Ligase Protein Complex Formation, Regulation, and Numerical Modeling}, volume={26}, ISSN={1040-4651 1532-298X}, url={http://dx.doi.org/10.1105/tpc.113.119685}, DOI={10.1105/tpc.113.119685}, abstractNote={As a step toward predictive modeling of flux through the pathway of monolignol biosynthesis in stem differentiating xylem of Populus trichocarpa, we discovered that the two 4-coumaric acid:CoA ligase (4CL) isoforms, 4CL3 and 4CL5, interact in vivo and in vitro to form a heterotetrameric protein complex. This conclusion is based on laser microdissection, coimmunoprecipitation, chemical cross-linking, bimolecular fluorescence complementation, and mass spectrometry. The tetramer is composed of three subunits of 4CL3 and one of 4CL5. 4CL5 appears to have a regulatory role. This protein-protein interaction affects the direction and rate of metabolic flux for monolignol biosynthesis in P. trichocarpa. A mathematical model was developed for the behavior of 4CL3 and 4CL5 individually and in mixtures that form the enzyme complex. The model incorporates effects of mixtures of multiple hydroxycinnamic acid substrates, competitive inhibition, uncompetitive inhibition, and self-inhibition, along with characteristic of the substrates, the enzyme isoforms, and the tetrameric complex. Kinetic analysis of different ratios of the enzyme isoforms shows both inhibition and activation components, which are explained by the mathematical model and provide insight into the regulation of metabolic flux for monolignol biosynthesis by protein complex formation.}, number={3}, journal={The Plant Cell}, publisher={Oxford University Press (OUP)}, author={Chen, Hsi-Chuan and Song, Jina and Wang, Jack P. and Lin, Ying-Chung and Ducoste, Joel and Shuford, Christopher M. and Liu, Jie and Li, Quanzi and Shi, Rui and Nepomuceno, Angelito and et al.}, year={2014}, month={Mar}, pages={876–893} }
 @article{frampton_isik_benson_2013, title={Genetic variation in resistance to Phytophthora cinnamomi in seedlings of two Turkish Abies species}, volume={9}, ISSN={["1614-2942"]}, DOI={10.1007/s11295-012-0529-0}, number={1}, journal={TREE GENETICS & GENOMES}, publisher={Springer Nature}, author={Frampton, John and Isik, Fikret and Benson, D. Michael}, year={2013}, month={Feb}, pages={53–63} }
 @article{zapata-valenzuela_whetten_neale_mckeand_isik_2013, title={Genomic Estimated Breeding Values Using Genomic Relationship Matrices in a Cloned Population of Loblolly Pine}, volume={3}, ISSN={2160-1836}, url={http://dx.doi.org/10.1534/g3.113.005975}, DOI={10.1534/g3.113.005975}, abstractNote={Abstract Replacement of the average numerator relationship matrix derived from the pedigree with the realized genomic relationship matrix based on DNA markers might be an attractive strategy in forest tree breeding for predictions of genetic merit. We used genotypes from 3461 single-nucleotide polymorphism loci to estimate genomic relationships for a population of 165 loblolly pine (Pinus taeda L.) individuals. Phenotypes of the 165 individuals were obtained from clonally replicated field trials and were used to estimate breeding values for growth (stem volume). Two alternative methods, based on allele frequencies or regression, were used to generate the genomic relationship matrices. The accuracies of genomic estimated breeding values based on the genomic relationship matrices and breeding values estimated based on the average numerator relationship matrix were compared. On average, the accuracy of predictions based on genomic relationships ranged between 0.37 and 0.74 depending on the validation method. We did not detect differences in the accuracy of predictions based on genomic relationship matrices estimated by two different methods. Using genomic relationship matrices allowed modeling of Mendelian segregation within full-sib families, an important advantage over a traditional genetic evaluation system based on pedigree. We conclude that estimation of genomic relationships could be a powerful tool in forest tree breeding because it accurately accounts both for genetic relationships among individuals and for nuisance effects such as location and replicate effects, and makes more accurate selection possible within full-sib crosses.}, number={5}, journal={G3&#58; Genes|Genomes|Genetics}, publisher={Genetics Society of America}, author={Zapata-Valenzuela, Jaime and Whetten, Ross W. and Neale, David and McKeand, Steve and Isik, Fikret}, year={2013}, month={Apr}, pages={909–916} }
 @article{el-kassaby_isik_whetten_2013, title={Modern Advances in Tree Breeding}, DOI={10.1007/978-94-007-7076-8_18}, abstractNote={Traditional tree improvement programs are long-term endeavours requiring extensive resources. They require establishing mating designs, installing progeny tests on multiple sites to evaluate parents and their offspring over large geographic areas, monitoring those tests over extended periods of time, and eventual analysis of measurements to assess economic traits. Most tree breeding programs follow the classical recurrent selection scheme, resulting in the generation of multiple breeding and production populations. This process, while successful in attaining appreciable gains, remained static for a long time. The availability of plentiful, reliable, and most of all increasingly affordable genetic markers brought about drastic changes to present-day breeding methods. In this chapter, we focus on four significant genetic marker-dependent approaches with significant potential to directly or indirectly change contemporary tree breeding methods. These include pedigree reconstruction, pedigree-free models, association genetics, and genomic selection.}, journal={Challenges and Opportunities for the World's Forests in the 21st Century}, publisher={Springer Netherlands}, author={El-Kassaby, Yousry A. and Isik, Fikret and Whetten, Ross W.}, year={2013}, month={Oct}, pages={441–459} }
 @article{cumbie_isik_mckeand_2012, title={Genetic Improvement of Sawtimber Potential in Loblolly Pine}, volume={58}, ISSN={["1938-3738"]}, DOI={10.5849/forsci.09-060}, abstractNote={Progeny from 48 elite parents of loblolly pine (Pinus taeda L.) were bred in a disconnected diallel mating design and were planted at four sites across the lower coastal plain of the southeastern United States. Height, dbh, volume, fusiform rust incidence (caused by the fungus Cronartium quercuum [Berk.] Miyabe ex Shirai f. sp. fusiforme), stem forking, stem sweep, branch angle, branch diameter, branch frequency, and a sawtimber potential score were measured after six growing seasons. There were significant differences among families for all traits measured. Individual-tree narrow-sense heritability estimates ranged from 0.06 to 0.22 and half-sib family-mean heritability estimates ranged from 0.73 to 0.98. Height and volume were the traits most highly correlated with the sawtimber potential score of individual trees. From multiple regression, 79% of the variation in sawtimber potential breeding values can be attributed to variation in volume, rust incidence, stem sweep, and forking breeding values. The potential dollar value of loblolly pine was increased as much as 162% over local checks when both volume and sawtimber potential were used to select the 10 best parents from the population. Implementation of a selection index on currently measured traits is a promising opportunity to make gains in the proportion of sawtimber produced from improved germplasm of loblolly pine in the southeastern United States.}, number={2}, journal={FOREST SCIENCE}, publisher={Oxford University Press (OUP)}, author={Cumbie, W. Patrick and Isik, Fikret and McKeand, Steven E.}, year={2012}, month={Apr}, pages={168–177} }
 @article{zapata-valenzuela_isik_maltecca_wegrzyn_neale_mckeand_whetten_2012, title={SNP markers trace familial linkages in a cloned population of Pinus taeda-prospects for genomic selection}, volume={8}, ISSN={["1614-2950"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84869878413&partnerID=MN8TOARS}, DOI={10.1007/s11295-012-0516-5}, abstractNote={Advances in DNA sequencing technology have made possible the genotyping of thousands of single-nucleotide polymorphism (SNP) markers, and new methods of statistical analysis are emerging to apply these advances in plant breeding programs. We report the utility of markers for prediction of breeding values in a forest tree species using empirical genotype data (3,406 polymorphic SNP loci). A total of 526 Pinus taeda L. clones tested widely in field trials were phenotyped at age 5 years. Only 149 clones from 13 full-sib crosses were genotyped. Markers were fit simultaneously to predict marker additive and dominance effects. Subsets of the 149 genotyped clones were used to train a model using all markers. Cross-validation strategies were followed for the remaining subset of genotyped individuals. The accuracy of genomic estimated breeding values ranged from 0.61 to 0.83 for wood lignin and cellulose content, and from 0.30 to 0.68 for height and volume traits. The accuracies of predictions based on markers were comparable with the accuracies based on pedigree. Because of the small number of SNP markers used and the relatively small population size, we suggest that observed accuracies in this study trace familial linkage rather than historical linkage disequilibrium with trait loci. Prediction accuracies of models that use only a subset of markers were generally comparable with the accuracies of the models using all markers, regardless of whether markers are associated with the phenotype. The results suggest that using SNP loci for selection instead of phenotype is efficient under different relative lengths of the breeding cycle, which would allow cost-effective applications in tree breeding programs. Prospects for applications of genomic selection to P. taeda breeding are discussed.}, number={6}, journal={TREE GENETICS & GENOMES}, publisher={Springer Nature}, author={Zapata-Valenzuela, Jaime and Isik, Fikret and Maltecca, Christian and Wegrzyn, Jill and Neale, David and McKeand, Steve and Whetten, Ross}, year={2012}, month={Dec}, pages={1307–1318} }
 @article{cumbie_isik_li_goldfarb_2011, title={Effects of propagule type on genetic parameters of wood density and growth in a loblolly pine progeny test at ages 10 and 11 years}, volume={7}, ISSN={1614-2942 1614-2950}, url={http://dx.doi.org/10.1007/s11295-011-0402-6}, DOI={10.1007/s11295-011-0402-6}, number={6}, journal={Tree Genetics & Genomes}, publisher={Springer Science and Business Media LLC}, author={Cumbie, W. Patrick and Isik, Fikret and Li, Bailian and Goldfarb, Barry}, year={2011}, month={Jul}, pages={1147–1158} }
 @article{aspinwall_king_domec_mckeand_isik_2011, title={Genetic effects on transpiration, canopy conductance, stomatal sensitivity to vapour pressure deficit, and cavitation resistance in loblolly pine}, volume={4}, ISSN={1936-0584}, url={http://dx.doi.org/10.1002/eco.197}, DOI={10.1002/eco.197}, abstractNote={Physiological uniformity and genetic effects on canopy-level gas-exchange and hydraulic function could impact loblolly pine (Pinus taeda L.) plantation sustainability and ecosystem dynamics under projected changes in climate. Over a 1-year period, we examined genetic effects on mean and maximum mid-day canopy conductance (Gs, Gsmax) and transpiration (E, max-E) within a juvenile loblolly pine plantation composed of ‘genotypes’ (e.g. different genetic entries) from each of the three different genetic groups (clones, full-sibs, open-pollinated). We also compared reference canopy conductance (Gs−ref or Gs at a vapour pressure deficit (D) = 1 kPa), maximum E (Emax) in response to D, stomatal sensitivity to D, specific hydraulic conductivity (ks), and cavitation resistance among genotypes. Based on genetic and physiological principles, we hypothesized that (1) within genotypes, physiological uniformity will increase as inherent genetic diversity decreases and (2) genotypes with greater ks and higher canopy-level gas-exchange rates will be more sensitive to increases in D, and more susceptible to loss of ks. In our results, high- and low-genetic diversity genotypes showed no differences in E and Gs uniformity over time. However, E and max-E were significantly different among genotypes, and genotypes showed significant seasonal variability in Gs and Gsmax. Additionally, there were significant differences in Emax, Gs−ref, Gs sensitivity to D, and the pressure at which 50% loss of ks occurs (P50) among individual genotypes. We found no relationship between mean hydraulic conductivity parameters and overall Gs−ref or Gs sensitivity. However, the genotype full embolism point (P88) and loss of ks rate (LCrate) both showed a significant positive relationship with genotype Gs−ref during the spring, indicating that genotypes with higher Gs were less resistant to cavitation. Overall, genetic effects on canopy-level gas-exchange and cavitation resistance were significant, implying that physiological differences among genotypes might affect stand water use, carbon gain, drought tolerance, and hydrologic processes. Contrary to our expectations, uniformity in physiological process rates did not increase as inherent genetic diversity decreased, suggesting that clonal genotypes exhibit high physiological plasticity under plantation conditions. Lastly, our results imply that genotypes with higher spring-time gas-exchange rates may be more susceptible to catastrophic loss of ks. With changes in climate expected to continue, physiological differences among genotypes may affect loblolly pine plantation carbon and water cycling. Copyright © 2011 John Wiley & Sons, Ltd.}, number={2}, journal={Ecohydrology}, publisher={Wiley}, author={Aspinwall, Michael J. and King, John S. and Domec, Jean-Christophe and McKeand, Steven E. and Isik, Fikret}, year={2011}, month={Jan}, pages={168–182} }
 @article{isik_mora_schimleck_2011, title={Genetic variation in Pinus taeda wood properties predicted using non-destructive techniques}, volume={68}, ISSN={1286-4560 1297-966X}, url={http://dx.doi.org/10.1007/s13595-011-0035-9}, DOI={10.1007/s13595-011-0035-9}, abstractNote={Tree breeders have been reluctant to include wood traits in tree improvement programs owing to logistic difficulties and the cost associated with the assessing the traits. We aimed to evaluate the efficiency of two non-destructive techniques for genetic parameters estimation in three diallel test series of loblolly pine (Pinus taeda L.). The traits were measured by acoustics (velocity, stiffness) and predicted by calibration models based on near infrared (NIR) spectra (air-dry density, microfibril angle, modulus of elasticity, coarseness, wall thickness). Acoustic and NIR-predicted traits were not correlated with diameter based on 30 full-sib family means of each diallel series. Correlations between traits were in accordance with previous published results. Additive genetic variation was considerable for all traits. Specific combining ability variances were not significant. The traits predicted by acoustic and NIR methods had high narrow-sense individual tree and family mean heritability values. Individual tree narrow sense heritability ranged from 0.14 (tracheid coarseness) to 0.92 (air-dry density). As expected, family mean heritability values of most traits exceeded 0.80. The high heritabilities suggest that acoustic and NIR-based methods can efficiently be used for screening loblolly pine progeny tests for surrogate wood traits. Such methods can save considerable resources in tree breeding programs that aim to improve wood quality.}, number={2}, journal={Annals of Forest Science}, publisher={Springer Science and Business Media LLC}, author={Isik, Fikret and Mora, Christian R. and Schimleck, Laurence R.}, year={2011}, month={Feb}, pages={283–293} }
 @article{isik_whetten_zapata-valenzuela_ogut_mckeand_2011, title={Genomic selection in loblolly pine - from lab to field}, volume={5}, DOI={10.1186/1753-6561-5-s7-i8}, abstractNote={Background Tree breeding is logistically complex and expensive, and breeders have long sought to use molecular markers to accelerate breeding. A candidate gene approach based on testing for association between the presence of DNA sequence variation in or near candidate genes, and phenotypic variation in a population has long been explored [1,2]. However, using candidate gene approach (QTLs) has not been successful in breeding [3,4]. QTL-trait associations detected in one genetic background are often not observed in other families, because of recombination of genes during the segregation and low levels of linkage disequilibrium in the population. A new technology called genomic selection (GS) is revolutionizing dairy cattle breeding. In GS, marker effects are first estimated in a large training population (>500) with both phenotypic and genotypic data. Subsequently, estimated marker effects are used to predict breeding values in validation populations for which marker genotypes but not phenotypes are available [4]. Several dairy cattle breeding companies now routinely use GS to select and market bulls. The success of GS in cattle breeding is largely based on bovine genome sequencing and discovery of thousands of SNP markers. GS application, if successful, will have a great impact on forest tree breeding because of their complex and logistically difficult breeding programs. Although, there have been several simulation studies examining the effective population size, linkage disequilibrium, and heritability on the predicted accuracy of GS in tree breeding [5], GS has not yet been demonstrated for forest trees using empirical markers data, mainly due to lack of sufficient dense markers. Methods Biallelic SNP markers provided by the CTGN project (http://dendrome.ucdavis.edu/ctgn/) were used for genotyping. A population of 149 cloned full-sib offspring of loblolly pine (Pinus taeda L.) was phenotyped. Fitting 3406 informative SNP markers simultaneously, we estimated genome-wide breeding values and compared them with breeding values based on pedigree model. Variances explained by the marker additive and dominant effects were obtained.}, number={S7}, journal={BMC Proceedings}, publisher={Springer Nature}, author={Isik, Fikret and Whetten, Ross and Zapata-Valenzuela, Jaime and Ogut, Funda and McKeand, Steven}, year={2011}, month={Sep} }
 @article{el-kassaby_mansfield_isik_stoehr_2011, title={In situ wood quality assessment in Douglas-fir}, volume={7}, ISSN={["1614-2950"]}, DOI={10.1007/s11295-010-0355-1}, number={3}, journal={TREE GENETICS & GENOMES}, publisher={Springer Nature}, author={El-Kassaby, Yoursy A. and Mansfield, Shawn and Isik, Fikret and Stoehr, Michael}, year={2011}, month={Jun}, pages={553–561} }
 @article{isik_amerson_whetten_garcia_mckeand_2011, title={Interactions of Fr genes and mixed-pathogen inocula in the loblolly pine-fusiform rust pathosystem}, volume={8}, ISSN={1614-2942 1614-2950}, url={http://dx.doi.org/10.1007/s11295-011-0416-0}, DOI={10.1007/s11295-011-0416-0}, number={1}, journal={Tree Genetics & Genomes}, publisher={Springer Science and Business Media LLC}, author={Isik, Fikret and Amerson, Henry V. and Whetten, Ross W. and Garcia, Saul A. and McKeand, Steven E.}, year={2011}, month={Aug}, pages={15–25} }
 @article{xiong_isik_mckeand_whetten_2010, title={Genetic variation of stem forking in loblolly pine}, volume={56}, number={5}, journal={Forest Science}, author={Xiong, J. S. and Isik, F. and McKeand, S. E. and Whetten, R. W.}, year={2010}, pages={429–436} }
 @article{aspinwall_li_mckeand_isik_gumpertz_2010, title={Prediction of whole-stem alpha-cellulose yield, lignin content, and wood density in juvenile and mature loblolly pine}, volume={34}, number={2}, journal={Southern Journal of Applied Forestry}, author={Aspinwall, M. J. and Li, B. L. and McKeand, S. E. and Isik, F. and Gumpertz, M. L.}, year={2010}, pages={84–90} }
 @article{eckard_isik_bullock_li_gumpertz_2010, title={Selection efficiency for solid wood traits in pinus taeda using time-of-flight acoustic and micro-drill resistance methods}, volume={56}, number={3}, journal={Forest Science}, author={Eckard, J. T. and Isik, F. and Bullock, B. and Li, B. L. and Gumpertz, M.}, year={2010}, pages={233–241} }
 @article{bains_isik_strong_jaquish_mclean_el-kassaby_2009, title={Genetic resistance of spruce to gall-forming adelgids (Hemiptera: Adelgidae)}, volume={39}, ISSN={["1208-6037"]}, DOI={10.1139/x09-164}, abstractNote={Adelgids (Hemiptera: Adelgidae) gall vegetative and reproductive shoots of interior spruce (Picea spp.), causing growth impairment, seed loss, and aesthetic decline. We tested the theory that susceptibility to galling is under genetic control in spruce. We assessed natural galling incidence in a spruce progeny test located in southern British Columbia. The experiment was composed of a replicated 13-parent incomplete, partial diallel with 42 full-sib families. Moderate evidence of genetic control of susceptibility–resistance was observed with individual narrow-sense heritability of 0.17. We observed considerable genetic variation among parents for resistance to gall formation as shown by high heritability (0.87) of family means. Breeding values for parental susceptibility to adelgid attack ranged between 0.25 and 0.76, indicating that selection for reduced susceptibility would be successful. The benefits of screening for resistance to adelgid attack are discussed in relation to adelgid pest management, insect’s life-cycle, and tree health.}, number={12}, journal={CANADIAN JOURNAL OF FOREST RESEARCH}, author={Bains, B. and Isik, F. and Strong, W. B. and Jaquish, B. and McLean, J. A. and El-Kassaby, Y. A.}, year={2009}, month={Dec}, pages={2536–2541} }
 @article{grans_hannrup_isik_lundqvist_mckeand_2009, title={Genetic variation and relationships to growth traits for microfibril angle, wood density and modulus of elasticity in a Picea abies clonal trial in southern Sweden}, volume={24}, ISSN={["1651-1891"]}, DOI={10.1080/02827580903280061}, abstractNote={Abstract Genetic variation in wood density, microfibril angle (MFA), wood stiffness (MOE), height, diameter and volume was investigated in a 26-year-old Norway spruce [(Picea abies (L.) Karst.] clonal trial in southern Sweden. Wood quality measurements were performed on 10 mm increment cores using SilviScan. For MFA, mean values of annual rings showed the highest value (30°) at ring 2 counting from the pith, followed by a steep decrease and a gradual stabilization around ring 12 at approximately 14°. MOE showed a monotonic increase from 5 GPa to 14 GPa when moving from pith to bark. High broad-sense heritability values were found for wood density (0.48), MFA (0.41) and MOE (0.50). All growth traits displayed heritability values of similar magnitudes as reported in earlier studies. The generally high age–age correlations between different sections of the wood cores suggested that early selection for wood quality traits would be successful. Owing to unfavorable genetic correlations between volume and MOE, the correlated response indicated that selection for volume only at age 10 would result in a 0.27% decrease in weighted MOE at age 26 for every 1% increase in volume. Keywords: Juvenile woodsolid wood productsX-ray diffraction Acknowledgements This study was supported by funds from the Swedish Tree Breeding Association, the Nordic Forest Research Co-operation committee (SNS), the Swedish Research Council Formas, and the Gunnar and Lilian Nicholson Fellowship at NC State University. Also, thanks to Skogforsk, STFI-Packforsk, the North Carolina State University Department of Forestry and Environmental Resources, the NCSU Cooperative Tree Improvement Program, and the Swedish University of Agricultural Sciences (SLU), School for Forest Engineers. In addition, the following persons made contributions to the study: Gudmund Ahlberg (Skogforsk), Robert Evans (CSIRO Forestry and Forest Products), Åke Hansson (STFI-Packforsk), Bo Karlsson (Skogforsk), Lars Olsson (STFI-Packforsk), Gunnar Jansson (Skogforsk) and Arne Steffenrem (Norwegian Forest and Landscape Institute).}, number={6}, journal={SCANDINAVIAN JOURNAL OF FOREST RESEARCH}, publisher={Informa UK Limited}, author={Grans, Daniel and Hannrup, Bjorn and Isik, Fikret and Lundqvist, Sven-Olof and McKeand, Steve}, year={2009}, pages={494–503} }
 @article{mora_schimleck_isik_mahon_clark_daniels_2009, title={Relationships between acoustic variables and different measures of stiffness in standing Pinus taeda trees}, volume={39}, ISSN={["0045-5067"]}, DOI={10.1139/X09-062}, abstractNote={Acoustic tools are increasingly used to estimate standing-tree (dynamic) stiffness; however, such techniques overestimate static stiffness, the standard measurement for determining modulus of elasticity (MOE) of wood. This study aimed to identify correction methods for standing-tree estimates making dynamic and static stiffness comparable. Sixty Pinus taeda L. trees, ranging from 14 to 19 years old, obtained from genetic tests established in the southeastern United States, were analyzed. Standing-tree acoustic velocities were measured using the TreeSonic tool. Acoustic velocities were also recorded in butt logs cut from the same trees using the Director HM200. A strong but biased relationship between tree and log velocities was observed, with tree velocities 32% higher (on average) than the corresponding log velocities. Two correction methods, one for calibrating tree velocities and one for accounting for differences in wood moisture content, were used to determine an adjusted MOE. After correction, adjusted MOE estimates were in good agreement with static longitudinal MOE values measured on clearwood specimens obtained from the trees, and no systematic bias was observed. The results of this study show that acoustic estimates of MOE on standing trees largely depend on how the data are processed and the reference method used.}, number={8}, journal={CANADIAN JOURNAL OF FOREST RESEARCH-REVUE CANADIENNE DE RECHERCHE FORESTIERE}, publisher={Canadian Science Publishing}, author={Mora, Christian R. and Schimleck, Laurence R. and Isik, Fikret and Mahon, Jerry M., Jr. and Clark, Alexander, III and Daniels, Richard F.}, year={2009}, month={Aug}, pages={1421–1429} }
 @article{sherrill_mullin_bullock_mckeand_purnell_gumpertz_isik_2008, title={An evaluation of selection for volume growth in loblolly pine}, volume={57}, ISSN={["2509-8934"]}, DOI={10.1515/sg-2008-0004}, abstractNote={Abstract Total inside-bark volume is the most important selection criterion for productivity in tree breeding programs in the Southeastern U.S. Tree breeders typically estimate total inside-bark volume based on outside-bark diameter at breast height and total height without accounting for stem taper or bark thickness. To make a direct determination of total inside- and outside-bark volume, a loblolly pine (Pinus taeda L.) open-pollinated family trial replicated with cultural treatments of weed control and fertilization was measured. This direct measurement was compared to typical volume estimates. In this trial, approximately 40 individuals from each of 25 open-pollinated first- and second-generation families were destructively sampled in the 13 th growing season. Selection for volume using a combined-variable (diameter 2 * height) equation was found to be highly effective for making volume gain. There was a high correlation between estimated and directly-measured total inside-bark volumes (0.99). Bark thickness and stem taper had low importance for stem volume selection. There was a positive genetic correlation between bark thickness and diameter at breast height (0.66). This indicates that selection for larger diameters may produce individuals with thicker bark, which may eventually affect total inside-bark volume estimates.}, number={1}, journal={SILVAE GENETICA}, author={Sherrill, J. R. and Mullin, T. J. and Bullock, B. P. and McKeand, S. E. and Purnell, R. C. and Gumpertz, M. L. and Isik, F.}, year={2008}, pages={22–28} }
 @article{isik_gumpertz_li_goldfarb_sun_2008, title={Analysis of cellulose microfibril angle using a linear mixed model in Pinus taeda clones}, volume={38}, ISSN={["1208-6037"]}, DOI={10.1139/X08-010}, abstractNote={Variation in microfibril angle (MFA) (degrees) among loblolly pine ( Pinus taeda L.) full-sib families and clones was investigated using 43 clones from nine full-sib crosses tested at two locations. When the experiments were 12 years old, a total of 316 trees were drilled and 12 mm thick wood increment cores were collected. MFA for each growth ring in the wood core was measured using the SilviScan-2 tool. A quadratic mixed model was fitted to evaluate the MFA variation over different rings. Among the error covariance structures tested in the model, autoregressive order 1 was the best model for producing MFA estimates with the smallest errors. Estimated MFA was about 33° in the pith (ring 1) of the trees and decreased to 18° in the outer wood (ring 11). Full-sib crosses and clones within crosses explained about 12.5% of the total phenotypic variation. Repeatability of full-sib family means (H 2 f = 0.46) was moderate but repeatability of clone means was high (H 2 c = 0.79). Although it is possible to improve (decrease) MFA with recurrent selection in tree improvement programs to improve lumber quality, cost efficient and rapid methods for measuring MFA are needed.}, number={6}, journal={CANADIAN JOURNAL OF FOREST RESEARCH}, publisher={Canadian Science Publishing}, author={Isik, Fikret and Gumpertz, Marcia and Li, Bailian and Goldfarb, Barry and Sun, Xuan}, year={2008}, month={Jun}, pages={1676–1689} }
 @article{isik_bullock_2008, title={Forestry and natural resource management in Turkey}, volume={21}, journal={Sylvanet}, author={Isik, F. and Bullock, B.}, year={2008}, pages={9–10} }
 @article{mckeand_li_grissom_isik_jayawickrama_2008, title={Genetic parameter estimates for growth traits from diallel tests of loblolly pine throughout the southeastern United States}, volume={57}, ISSN={["2509-8934"]}, DOI={10.1515/sg-2008-0016}, abstractNote={Abstract Variation in heritability and in genetic correlation estimates were evaluated for juvenile tree height and volume for six testing areas of loblolly pine (Pinus taeda L.) in the southeastern United States. Variance components and their functions (heritability and type B genetic correlations) were estimated from 265 six-parent disconnected diallel series, tested in almost 1000 trials (4 tests per diallel series). Original data were collected at age 6 years from about one million trees (265 diallel series x 30 crosses x 36 trees per cross/site x 4 sites) planted in field tests. Genetic tests were from the second cycle of breeding in the North Carolina State University - Industry Cooperative Tree Improvement Program. The overall unbiased individual-tree narrow-sense heritability for height was 0.19 and for volume was 0.16. The broad-sense heritabilities for height (0.24) and for volume (0.22) were higher than narrow-sense heritabilities due to the presence of non-additive genetic variance. There were moderate regional differences in these estimates, with tests in the Lower Gulf Coastal Plain tending to have the highest heritabilities for growth traits. There was very little association between site index and heritability, but heritabilities were higher on sites with the highest survival and highest test precision. Genotype x environment interactions were generally low both for half-sib and full-sib families, indicating that families can be operationally deployed to different sites with little concern about unpredictable performance.}, number={3}, journal={SILVAE GENETICA}, author={McKeand, S. E. and Li, B. and Grissom, J. E. and Isik, F. and Jayawickrama, K. J. S.}, year={2008}, pages={101–110} }
 @article{mora_schimleck_isik_2008, title={Near infrared calibration models for the estimation of wood density in Pinus taeda using repeated sample measurements}, volume={16}, ISSN={["0967-0335"]}, DOI={10.1255/jnirs.816}, abstractNote={Near infrared (NIR) diffuse reflectance was used for the estimation of air-dry density and basic density in wood radial strip samples obtained at breast height (1.4 m) from 60 Pinus taeda trees established in three progeny tests in the south-eastern United States. NIR calibration models were fitted using raw spectra and pre-processed spectra with second derivative, multiplicative scatter correction and orthogonal signal correction. Successful calibrations were obtained for both wood properties using data collected in consecutive 10 mm sections from the samples. Data pre-processing did not result in model improvements compared to the models fitted using raw data. The effects of using repeated measures were evaluated by incorporating serial correlation into the partial least squares regression algorithm. The empirical autocorrelation of the normalised residuals showed that serial dependence among residuals was successfully removed by using an autoregressive correlation structure of second order. However, because the initial dependence among observations was not strong, the predictions were similar using the modified algorithm to those obtained with the traditional approach. These results indicate that the use of repeated measurements does not represent a serious problem for the development of NIR calibration models for the prediction of wood properties using radial samples measured in 10 mm sections and that the specification of the correlation structure may not be required when the models are used only for predictive purposes.}, number={6}, journal={JOURNAL OF NEAR INFRARED SPECTROSCOPY}, publisher={SAGE Publications}, author={Mora, Christian R. and Schimleck, Laurence R. and Isik, Fikret}, year={2008}, pages={517–528} }
 @article{isik_li_goldfarb_mckeand_2008, title={Prediction of wood density breeding values of Pinus taeda elite parents from unbalanced data: A method for adjustment of site and age effects using common checklots}, volume={65}, ISSN={["1286-4560"]}, DOI={10.1051/forest:2008018}, abstractNote={• Wood density of elite parents of loblolly pine (Pinus taeda L.) was investigated in 6 to 18 year-old progeny trials. The sampling was carried out separately in seven testing regions in the southeastern US. A checklot was the only connection between elite parents planted at different trials in a testing region.


• We used a data normalization method suggested for unbalanced designs in cDNA microarray experiments to remove confounding site and age effects using the checklot as a reference sample. Wood density breeding values of parents were predicted by fitting a linear mixed model to the normalized data.


• Using the reference samples to remove site and age effects appears to be an effective method for analysis of unbalanced progeny tests data. In general, wood density (kg/m3) decreased from coastal to inland plantings and from the southern to the northern planting. Considerable genetic variation for wood density was detected among these fast-growing elite parents in six of seven testing regions, with half-sib family mean heritabilities ranging from 0.71 to 0.97 within a testing region. With the exception of two regions, checklots were stable across trials in a region, based on regressing the checklot means on trial means.}, number={4}, journal={ANNALS OF FOREST SCIENCE}, publisher={Springer Nature}, author={Isik, Fikret and Li, Bailian and Goldfarb, Barry and McKeand, Steve}, year={2008}, month={Jun} }
 @article{isik_amerson_whetten_garcia_li_mckeand_2008, title={Resistance of <i>Pinus taeda</i> families under artificial inoculations with diverse fusiform rust pathogen populations and comparison with field trials}, volume={38}, ISSN={0045-5067 1208-6037}, url={http://dx.doi.org/10.1139/x08-111}, DOI={10.1139/X08-111}, abstractNote={Controlled inoculations with 10 bulk inocula of Cronartium quercuum (Berk) Miyabe ex Shirai f.sp. fusiforme were carried out on open-pollinated progeny of 25 fast-growing Pinus taeda L. parents. The parents had a range of breeding values for resistance to fusiform rust in progeny field trials. There were highly significant differences among the half-sib families in response to inoculations, and these differences were very reproducible; the half-sib family-mean heritability of resistance to controlled inoculation was 0.97. All of the families that were susceptible in the field were susceptible in controlled inoculations, and most (12 of 17) of the field-resistant families were resistant in response to controlled inoculations. Significant pathogenic variability was observed among the different bulk inocula, although this accounted for only 1.9% of the total variation. Genetic differences among families within field-resistant or field-susceptible groups accounted for 13.7% of the total variation. The family by inocula interaction was highly significant, but a single field-resistant family contributed 44% of the total family by inocula interaction variance, and two other field-resistant families also showed significant interactions.}, number={10}, journal={Canadian Journal of Forest Research}, publisher={Canadian Science Publishing}, author={Isik, Fikret and Amerson, Henry V. and Whetten, Ross W. and Garcia, Saul A. and Li, Bailian and McKeand, Steven E.}, year={2008}, month={Oct}, pages={2687–2696} }
 @article{isik_amerson_whetten_garcia_li_mckeand_2008, title={Resistance of Pinus taeda families under artificial inoculations with diverse fusiform rust pathogen populations and comparison with field trials (vol 38, pg 2687, 2008)}, volume={38}, ISSN={["0045-5067"]}, DOI={10.1139/x08-910}, number={12}, journal={CANADIAN JOURNAL OF FOREST RESEARCH-REVUE CANADIENNE DE RECHERCHE FORESTIERE}, author={Isik, Fikret and Amerson, Henry V. and Whetten, Ross W. and Garcia, Saul A. and Li, Bailian and McKeand, Steven E.}, year={2008}, month={Dec}, pages={3151–3151} }
 @inproceedings{frampton_isik_braham_2007, title={Genetic Variation in the Economic Value of Fraser Fir (Abies fraseri) Christmas Trees in North Carolina, USA}, booktitle={Eighth International Christmas Tree Research & Extension Conference IUFRO}, author={Frampton, J. and Isik, F. and Braham, A.}, year={2007} }
 @inproceedings{cumbie_mckeand_espinoza_isik_grissom_2007, title={Improvements in stem form and growth of elite genotypes in loblolly pine}, booktitle={Proceedings of the 29th Southern Forest Tree Improvement Conference}, author={Cumbie, W. P. and McKeand, S. E. and Espinoza, J. and Isik, F. and Grissom, J. E.}, year={2007}, pages={108–111} }
 @article{lise_kaya_isik_sabuncu_kandemir_onde_2007, title={The impact of over-exploitation on the genetic structure of Turkish red pine (Pinus brutia Ten.) populations determined by RAPD markers}, volume={41}, ISSN={["2242-4075"]}, DOI={10.14214/sf.291}, abstractNote={<ja:p>To determine the possible impact of over-exploitation on the genetic structure of Turkish red pine (Pinus brutia Ten.) populations, three natural and three over-exploited (human degraded) populations of the species in the Mediterranean region of Turkey were investigated with Randomly Amplified Polymorphic DNA (RAPD). With the 80 RAPD primers tested, 12 of them yielded 137 polymorphic RAPD fragments. Four of the studied populations maintained unique fragments. The mean proportion of polymorphic fragments for all populations ranged from 89.8 to 98.9% and there were no significant differences between natural (94.8%) vs. over-exploited populations (92.7%). The estimated heterozygosity values suggested that Turkish red pine maintains high levels of genetic diversity (range 0.24–0.28) though studied populations and grouped ones as natural (H = 0.28) vs. over-exploited (0.27) did not differ significantly. The mean F value indicated that the large portion of the total genetic diversity was within populations (93%), but this value was lower in the natural populations (92%) than in the over-exploited ones (94%). In over-exploited populations, excess of homozygosity was observed (about 6% higher) as compared to natural populations, indicating impacts of inbreeding in P. brutia.<ja:sub>e</ja:sub><ja:sub>ST</ja:sub></ja:p>}, number={2}, journal={SILVA FENNICA}, publisher={Finnish Society of Forest Science}, author={Lise, Yildiray and Kaya, Zeki and Isik, Fikret and Sabuncu, Rumi and Kandemir, Irfan and Onde, Sertac}, year={2007}, pages={211–220} }
 @inproceedings{isik_whetten_garcia_cumbie_mckeand_grissom_batista_2007, title={Using markers in breeding, testing and selection
in loblolly pine ? current and future research.}, booktitle={Conference Proceedings}, author={Isik, F. and Whetten, R. and Garcia, S. and Cumbie, P. and McKeand, S. and Grissom, J. and Batista, T.}, year={2007} }
 @article{isik_whetten_garcia_cumbie_mckeand_grissom_batista_2007, title={Using markers in breeding, testing and selection in loblolly pine: Current and future research}, journal={GENECAR Meeting: Application of DNA based tools for genetic research, molecular breeding, management and monitoring of genetic resources}, author={Isik, F. and Whetten, R. and Garcia, S. and Cumbie, P. and McKeand, S. and Grissom, J. and Batista, T.}, year={2007} }
 @article{sykes_li_isik_kadla_chang_2006, title={Genetic variation and genotype by environment interactions of juvenile wood chemical properties in Pinus taeda L.}, volume={63}, ISSN={["1286-4560"]}, DOI={10.1051/forest:2006073}, abstractNote={Genetic variation and genotype by environment interaction (G×E) were studied in several juvenile wood traits of 11 year-old loblolly pine trees (Pinus taeda L.). Wafer thin (200 µm) samples from juvenile (ring 3) and transition (ring 8) wood of 12 mm increment cores were analyzed. Transition wood had higher α-cellulose content (46.1%), longer fiber (1.98 mm), and higher coarseness (0.34), but lower lignin (29.7%) than juvenile wood (cellulose 40.9%, fiber length 1.4 mm, coarseness 0.28 and lignin 30.3%). General combining ability variance for the traits explained 2% to 10% of the total variance, whereas the specific combining ability variance was negligible, except for α-cellulose content in transition wood (2%). Specific combining ability by site interaction variance explained from 5% (fiber length) to 37% (lignin) of the total variance. Weak individual-tree heritabilities were found for all the traits, except coarseness, which was moderately high in both juvenile (0.39) and transition wood (0.30). Full-sib and half-sib family heritabilities of traits ranged 0.29 to 0.72. Genetic correlations of wood quality traits with volume and stem straightness were weak, while favorable genetic correlations of lignin with cellulose, coarseness and fiber length were observed. Implications on forest tree improvement programs were discussed. heritability / genetic correlation / α-cellulose / coarseness / lignin}, number={8}, journal={ANNALS OF FOREST SCIENCE}, publisher={EDP Sciences}, author={Sykes, Robert and Li, Bailian and Isik, Fikret and Kadla, John and Chang, H. -M.}, year={2006}, month={Dec}, pages={897–904} }
 @inproceedings{frampton_isik_2006, title={Low input improvement of Christmas trees}, booktitle={Proceedings, IUFRO Division 2 Joint Conference : low input breeding and genetic conservation of forest tree species : 9-13 October 2006 Antalya Turkey}, author={Frampton, J. and Isik, F.}, year={2006}, pages={60} }
 @inproceedings{isik_mckeand_li_amerson_2006, title={Marker aided selection of loblolly pine clones}, booktitle={Consortium for Plant Biotechnology Symposium}, author={Isik, F. and McKeand, S. and Li, B. and Amerson, H.}, year={2006} }
 @article{frampton_isik_2006, title={Perspectives on Turkey}, volume={33}, number={2}, journal={Limbs & Needles}, author={Frampton, J. and Isik, F.}, year={2006}, pages={17–19} }
 @article{isik_frampton_2006, title={Perspectives on forestry in Turkey}, volume={19}, number={1}, journal={Sylvanet}, author={Isik, F. and Frampton, J.}, year={2006}, pages={13–15} }
 @inproceedings{aspinwall_li_mckeand_isik_gumpertz_2006, title={Predicting whole-stem wood properties in loblolly pine}, volume={40}, booktitle={Information Exchange Group 40 Conference, Incorporating Genetic Advances into Forest Productivity Systems: Value for All Landowners.
Exchange Group 40 Conference, Incorporating Genetic Advances into Forest
Productivity Systems: Value for All Landowners.}, author={Aspinwall, M. and Li, B. and McKeand, S. and Isik, F. and Gumpertz, M.}, year={2006} }
 @inproceedings{eckard_isik_bullock_2006, title={Prediction of whole-stem solid wood properties of superior loblolly pine clones for deployment}, volume={40}, booktitle={Information Exchange Group 40 Conference, Incorporating Genetic Advances into Forest Productivity Systems: Value for All Landowners}, author={Eckard, J. T. and Isik, F. and Bullock, B. P.}, year={2006}, pages={25} }
 @article{isik_2005, title={Genetic Improvement of Virginia Pine (Pinus virginiana Mill.) for Christmas Tree Production.}, volume={11}, journal={Forest Genetics}, author={Isik, F.}, year={2005}, pages={137–147} }
 @article{frampton_isik_2005, title={Genetic improvement of Virginia pine (Pinus virginiana Mill.) for Christmas tree production}, volume={11}, journal={Forest Genetics}, author={Frampton, J. and Isik, F.}, year={2005}, pages={137–147} }
 @inproceedings{isik_li_goldfarb_2005, title={Genetic variation in MFA, MOE and wood density among clones of Pinus taeda L.}, volume={28}, booktitle={28th Southern Forest Tree Improvement Conference}, author={Isik, F. and Li, B. and Goldfarb, B.}, year={2005} }
 @article{isik_isik_kurt_semiz_2005, title={Genotypic selectivity of test environments on different ecological zones}, volume={10}, journal={10th European Ecological Congress}, author={Isik, K. and Isik, F. and Kurt, Y. and Semiz, G.}, year={2005} }
 @article{isik_goldfarb_lebude_li_mckeand_2005, title={Predicted genetic gains and testing efficiency from two loblolly pine clonal trials}, volume={35}, ISSN={["1208-6037"]}, DOI={10.1139/X05-064}, abstractNote={Clonal field trials were established at two sites using rooted cuttings from 450 clones of eight full-sib families of loblolly pine (Pinus taeda L.). Height, survival, fusiform rust infection (caused by Cronartium quercuum (Berk) Miyabe ex Shirai f.sp. fusiforme), bole straightness, and diameter were measured after four growing seasons. There were significant differences among full-sib families and among clones within families for all traits studied. Moderately high within-family repeatabilities of clone means (0.50 to 0.75) for growth traits and a very high within-family repeatability of clone means (0.94) for fusiform rust infection were estimated. When the best eight clones were selected regardless of family structure, the volume yield was 52% greater than that of the unimproved seedlings at two sites. Selection of the best two clones from each of four families produced only slightly lower estimated genetic gains than the above scenario. The probability of fusiform rust infection ranged from 0.08 to 0.93 among clones at the South Carolina site. Predicted genetic gain for rust resistance was relatively insensitive to selection intensity, as there were numerous clones with high apparent resistance. The number of ramets per clone necessary to reliably characterize performance on one site was estimated to be between four and six. These results contribute to estimates of the gains available from clonal forestry and will help guide clonal testing and selection programs. Implementation of clonal forestry and cost issues are discussed.}, number={7}, journal={CANADIAN JOURNAL OF FOREST RESEARCH}, author={Isik, F and Goldfarb, B and LeBude, A and Li, BL and McKeand, S}, year={2005}, month={Jul}, pages={1754–1766} }
 @article{isik_boos_li_2005, title={The distribution of genetic parameter estimates and confidence intervals from small disconnected diallels}, volume={110}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-005-1957-0}, number={7}, journal={THEORETICAL AND APPLIED GENETICS}, publisher={Springer Nature}, author={Isik, F and Boos, DD and Li, BL}, year={2005}, month={May}, pages={1236–1243} }
 @inproceedings{morris_goldfarb_isik_li_chang_sederoff_kadla_2005, title={Variation of a-cellulose content and related metabolites during wood formation in loblolly pine}, volume={13}, booktitle={13th ISWFPC Proceedings}, author={Morris, C. R. and Goldfarb, B. and Isik, F. and Li, C. S. and Chang, H.-M. and Sederoff, R. and Kadla, J. F.}, year={2005} }
 @inproceedings{goldfarb_lebude_isik_mckeand_li_2004, title={Advance and Challenges in Clonal Forestry with Rooted Cuttings of Loblolly Pine}, booktitle={Forest Genetics and Tree Breeding in the Age of Genomics: Progress and Future,  IUFRO Joint Conference of Division 2, Conference Proceedings}, author={Goldfarb, B. and LeBude, A. and Isik, F. and McKeand, S. and Li, B.}, editor={Li, B. and McKeand, S.Editors}, year={2004}, pages={41} }
 @inproceedings{li_jansson_isik_godlfarb_2004, title={Breeding and selection strategies for full-sib families and clones in Loblolly pine}, booktitle={IEG-40 Meeting}, author={Li, B. and Jansson, G. and Isik, F. and Godlfarb, B.}, year={2004} }
 @inproceedings{isik_li_goldfarb_frampton_mckeand_2004, title={Cloned genotypes are more efficient than seedlings for indirect selection}, booktitle={Forest Genetics and Tree Breeding in the Age of Genomics: Progress and Future,  IUFRO Joint Conference of Division 2, Conference Proceedings}, author={Isik, F. and Li, B. and Goldfarb, B. and Frampton, J. and McKeand, S.}, editor={Li, B. and McKeand, S.Editors}, year={2004}, pages={465} }
 @article{isik_li_goldfarb_2004, title={Cloned progeny testing for within-family selection in forest tree improvement programs}, volume={2}, journal={IUFRO Joint Conference of Division 2: Forest Genetics and Tree Breeding in the Age of Genomics: Progress and Future}, author={Isik, F. and Li, B. and Goldfarb, B.}, year={2004} }
 @inproceedings{goldfarb_mckeand_lebude_cumbie_isik_li_2004, title={Deployment issues: what kinds of research, development
and demonstration activities are needed to address critical topics, such as public concerns, performance monitoring, and technologies for merchandising harvested clones?}, booktitle={Conference Proceedings}, author={Goldfarb, B. and McKeand, S. E. and LeBude, A. V. and Cumbie, W. P. and Isik, F. and Li, B.}, year={2004} }
 @article{goldfarb_mckeand_lebude_cumbie_isik_li_2004, title={Deployment issues: what kinds of research, development and demonstration activities are needed to address critical topics, such as public concerns, performance monitoring, and technologies for merchandising harvested clones?}, journal={Agenda 2020 Technology Summit II: Meeting the Challenge of Deployment}, author={Goldfarb, B. and McKeand, S. E. and LeBude, A. V. and Cumbie, W. P. and Isik, F. and Li, B.}, year={2004} }
 @article{isik_li_goldfarb_frampton_mckeand_2004, title={Efficiency of clones versus seedlings for correlated response of wood density}, journal={IEG-40 Meeting}, author={Isik, F. and Li, B. and Goldfarb, B. and Frampton, J. and McKeand, S.}, year={2004} }
 @article{isik_li_frampton_goldfarb_2004, title={Efficiency of seedlings and rooted cuttings for testing and selection in Pinus taeda}, volume={50}, number={1}, journal={Forest Science}, author={Isik, F. and Li, B. L. and Frampton, J. and Goldfarb, B.}, year={2004}, pages={44–53} }
 @inproceedings{isik_isik_kaya_semiz_2004, title={Environmental factors that determine within-species variation}, booktitle={Turkish Red Pine National Ecology and Environment Congress}, author={Isik, K. and Isik, F. and Kaya, N. and Semiz, G. V.}, year={2004} }
 @article{frampton_isik_2004, title={Genetic improvement of Pinus virginiana Mill. for Christmas tree production}, volume={11}, ISBN={1335-048x}, number={2}, journal={Forest Genetics}, author={Frampton, J. and Isik, F.}, year={2004}, pages={139} }
 @article{sykes_isik_li_kadla_chang_2004, title={Genetic variation in physiochemical wood properties in loblolly pine (Pinus taeda L.)}, volume={2}, number={12}, journal={TAPPI Journal}, author={Sykes, R. and Isik, F. and Li, B. and Kadla, J. and Chang, H.-M.}, year={2004}, pages={3–8} }
 @article{isik_h._f._siklar_2004, title={Genetics of Mediterranean conifers: a brief report on three conifer species in Turkey}, volume={2}, journal={IUFRO Joint Conference of Division 2: Forest Genetics and Tree Breeding in the Age of Genomics: Progress and Future}, author={Isik, K. Ozturk and H., Isik and F. and Siklar, S.}, year={2004} }
 @article{li_belonger_isik_2004, title={Hybrid heterosis of Larix decidua and L. leptolepis in US and implications on breeding strategies}, volume={2}, journal={Proceedings of International Symposium Larix}, author={Li, B. and Belonger, P. and Isik, F.}, year={2004} }
 @article{goldfarb_lebude_gocke_li_isik_mckeand_2004, title={Producing rooted cutting reforestation stock of Loblolly pine: progress and challenges}, journal={IEG-40 Meeting}, author={Goldfarb, B. and LeBude, A. and Gocke, M. and Li, B. and Isik, F. and McKeand, S.}, year={2004} }
 @article{xiang_li_isik_2004, title={Time trend of genetic parameters in growth traits of Pinus taeda L.}, volume={52}, number={3}, journal={Silvae Genetica}, author={Xiang, B. and Li, B. and Isik, F.}, year={2004}, pages={114–121} }
 @article{isik_toplu_2004, title={Variation in juvenile traits of natural black poplar (Populus nigra L.) clones in Turkey}, volume={27}, ISSN={["0169-4286"]}, DOI={10.1023/A:1025071515826}, number={2}, journal={NEW FORESTS}, author={Isik, F and Toplu, F}, year={2004}, month={Mar}, pages={175–187} }
 @article{isik_li_frampton_2003, title={Estimates of additive, dominance and epistatic genetic variances from a clonally replicated test of loblolly pine}, volume={49}, number={1}, journal={Forest Science}, author={Isik, F. and Li, B. L. and Frampton, J.}, year={2003}, pages={77–88} }
 @article{goldfarb_isik_lebude_mckeand_li_2003, title={Four-year results from a clonal test of loblolly pine}, volume={27}, journal={Proc. 27th Biennial Southern Forest Tree Improvement Conference}, author={Goldfarb, B. and Isik, F. and LeBude, A. and McKeand, S. and Li, B.}, year={2003}, pages={42} }
 @article{frampton_isik_rosier_2003, title={Genetic improvement of virginia pine for christmas tree production}, volume={27}, journal={Proc. 27th Biennial Southern Forest Tree Improvement Conference}, author={Frampton, J. and Isik, F. and Rosier, C.}, year={2003}, pages={31} }
 @article{sykes_isik_li_kadla_chang_2003, title={Genetic variation of juvenile wood properties in a loblolly pine progeny test}, volume={2}, number={12}, journal={TAPPI Journal}, author={Sykes, R. and Isik, F. and Li, B. L. and Kadla, J. and Chang, H. M.}, year={2003}, pages={08-} }
 @article{sykes_isik_li_kadla_chang_2003, title={Genetic variation of juvenile wood properties in loblolly pine diallel test}, volume={27}, journal={Proc. 27th Biennial Southern Forest Tree Improvement Conference}, author={Sykes, R. and Isik, F. and Li, B. and Kadla, J. and Chang, H-M.}, year={2003}, pages={27} }
 @article{isik_li_2003, title={Rapid assessment of wood density of live trees using the Resistograph for selection in tree improvement programs}, volume={33}, ISSN={["0045-5067"]}, DOI={10.1139/X03-176}, abstractNote={Wood density is traditionally determined by a volumetric method that is accurate but expensive for large-scale sampling. A new device called the Resistograph was investigated for rapid assessment of relative wood density of live trees in progeny trials. Fourteen full-sib families of loblolly pine (Pinus taeda L.) produced by a six-parent half-diallel mating design were tested at four sites. For each family, wood density was measured with the traditional volumetric method and then compared with the Resistograph readings (amplitude). Amplitude had weak (0.29) to moderate (0.65) phenotypic correlations with wood density on an individual-tree basis over the four sites. The family mean correlation between the two measurements, however, was much stronger (0.92). The additive genetic correlation between the two measures was also high (0.95). Individual-tree breeding values of amplitude yielded more accurate rankings than phenotypic values. The rankings of the parental, general-combining abilities were identical for the two measures. Both wood density and amplitude were under strong genetic control at the family level (full-sib family heritability (h 2 fs ) = 0.95 for wood density and h 2 fs = 0.85 for amplitude). The efficiency of using the Resistograph as a means of indirect selection for improvement of wood density was 87% at the family level. Results from this study suggest that the Resistograph could be used reliably and efficiently to assess relative wood density of live trees for selection in tree improvement programs. The method is rapid, nondestructive, and much cheaper than the traditional volumetric method.}, number={12}, journal={CANADIAN JOURNAL OF FOREST RESEARCH-REVUE CANADIENNE DE RECHERCHE FORESTIERE}, publisher={Canadian Science Publishing}, author={Isik, F and Li, BL}, year={2003}, month={Dec}, pages={2426–2435} }
 @article{isik_li_2003, title={Time trend of genetic parameter estimates in growth traits of Pinus Taeda L}, volume={52}, journal={Silvae Genetica}, author={Isik, F. and Li, B.-L.}, year={2003}, pages={114–121} }
 @article{isik_li_2003, title={Variation in estimation of genetic parameters from small disconnected diallel mating}, volume={27}, journal={Proc. 27th Biennial Southern Forest Tree Improvement Conference}, author={Isik, F. and Li, B.}, year={2003}, pages={20} }
 @article{mccall_isik_2003, title={Volume gains of loblolly pine rooted clones at age 10 on two sites in Florida and Alabama}, volume={27}, journal={Proc. 27th Biennial Southern Forest Tree Improvement Conference}, author={McCall, E. and Isik, F.}, year={2003}, pages={43} }
 @article{isik_isik_yildirim_li_2002, title={Annual shoot growth components related to growth of Pinus brutia}, volume={22}, ISSN={["0829-318X"]}, DOI={10.1093/treephys/22.1.51}, abstractNote={Shoot elongation patterns of Pinus brutia Ten. were studied in six natural populations and 10 open-pollinated families within each population. The data were collected from a provenance-progeny trial that was thinned at Ages 13 and 17 years. Annual height increment was partitioned into first flush (spring shoot) and subsequent flushes (summer shoots) and the contribution of each to annual height increment was measured from Ages 7 to 17. Spring shoot elongation patterns were similar in all populations and families for 9 out of 10 years. In contrast, at all ages, populations differed significantly in total summer shoot growth and number of summer flushes. Families within populations differed in number of summer flushes in 7 out of 10 years. Summer shoot growth was the major cause of the differences in annual height growth among the six populations. Significant and high correlations were observed between summer shoot growth at Ages 7 to 12 and height at Age 13. A population from near the middle of the species' altitudinal range had more summer flushes than populations from higher or lower elevations, indicating an opportunistic growth pattern. Compared with mid-elevation populations, low- and high-elevation populations had more conservative growth patterns that depended mainly on growth of spring shoots. We conclude that summer shoot growth can serve as an explanatory variable to predict height growth of populations. Differences in shoot elongation patterns among Pinus brutia populations may be useful for selecting seed sources and for gene conservation programs.}, number={1}, journal={TREE PHYSIOLOGY}, author={Isik, F and Isik, K and Yildirim, T and Li, BL}, year={2002}, month={Jan}, pages={51–58} }
 @article{isik_s._f._cengiz_2002, title={Clonal variation of flower production in a Pinus brutia seed orchard}, journal={Proc. of International Conference on Conversation, Regeneration and Restoration of Mediterranean Pines and Their Ecosystems. MEDPINE 2}, author={Isik, K. Keskin and S., Isik and F. and Cengiz, Y.}, year={2002}, pages={30} }
 @article{frampton_isik_goldfarb_2002, title={Effects of nursery characteristics on field survival and growth of loblolly pine rooted cuttings}, volume={26}, number={4}, journal={Southern Journal of Applied Forestry}, author={Frampton, J. and Isik, F. and Goldfarb, B.}, year={2002}, pages={207–213} }
 @article{isik_li_frampton_goldfarb_2002, title={Seedling vs clonal testing options for loblolly pine}, journal={Proc. of Silviculture and Genetic Impact on productivity of southern pine forests. IEG-40 Meeting}, author={Isik, F. and Li, B. and Frampton, J. and Goldfarb, G.}, year={2002} }
 @article{isik_li_2002, title={Using Resistograph to estimate genetic parameters from progeny trials and comparison with actual wood density}, volume={17}, journal={Proc. of Rocky Mountain Ecosystems: Diversity, complexity and interactions. Joint Meeting of 17th North American Forest Biology Workshop and Western Forest Genetics Association}, author={Isik, F. and Li, B.}, year={2002}, pages={59} }
 @inproceedings{isik_li_frampton_2001, title={Comparison of genetic variances estimated from seedlings and rooted cuttings of the same families of Loblolly pine}, volume={26}, booktitle={Proceedings of the 26th Biennial Southern Forest Tree Improvement Conference}, publisher={Athens, GA : Georgia Center for Continuing Education, the University of Georgia}, author={Isik, F. and Li, B. and Frampton, J.}, year={2001}, pages={143–146} }
 @inproceedings{isik_keskin_sabuncu_sahin_bas_kaya_2001, title={Effects of water stress on the adaptive traits of Pinus brutia natural populations and families in a nursery trial}, booktitle={Proc. Global physiological and molecular responses to climatic stress of three Mediterranean conifers. Consequences for optimal use, conservation and sustainable improvement of their genetic resources}, author={Isik, F. and Keskin, S. and Sabuncu, R. and Sahin, M. and Bas, N. and Kaya, Z.}, year={2001} }
 @article{isik_li_2001, title={Genetic variation in wood density and its measurement using the Resistograph}, volume={26}, journal={Proc. 26th Biennial Southern Forest Tree Improvement Conference}, author={Isik, F. and Li, B.}, year={2001}, pages={120} }
 @inproceedings{isik_li_2001, title={Genetic variation in wood density and its measurement using the Resistograph}, volume={26}, booktitle={Proc. 26th Biennial Southern Forest Tree Improvement Conference}, author={Isik, F. and Li, B.}, year={2001} }
 @article{isik_keskin_mckeand_2000, title={Provenance variation and provenance-site interaction in Pinus brutia TEN.: Consequences on the defining of breeding zones}, volume={49}, number={4-5}, journal={Silvae Genetica}, author={Isik, F. and Keskin, S. and McKeand, S.}, year={2000}, pages={213–223} }
 @article{isik_isik_yildirim_li_2000, title={Shoot growth patterns related to growth and adaptation of Pinus brutia}, volume={11}, journal={Bildiri, IUFRO XXI World Forestry Congress}, author={Isik, F. and Isik, K. and Yildirim, T. and Li, B.}, year={2000} }
 @book{cengiz_isik_keskin_1999, place={Antalya, Turkey}, title={Fifth year results of Pinus brutia provenance trials}, number={11}, institution={Western Mediterranean Forest Research Institute}, author={Cengiz, Y. and Isik, F. and Keskin, S.}, year={1999} }
 @article{isik_isik_lee_1999, title={Genetic variation in Pinus brutia in Turkey: I. Growth, biomass and stem quality traits}, volume={6}, journal={Forest Genetics}, author={Isik, F. and Isik, K. and Lee, S. J.}, year={1999}, pages={89–99} }
 @inproceedings{isik_isik_lee_1999, title={Genetic variation in growth, biomass and stem quality traits in Pinus brutia in southern Turkey}, volume={25}, booktitle={25th Biennial Southern Forest Tree Improvement Conference}, author={Isik, F. and Isik, K. and Lee, S. J.}, year={1999}, pages={88–92} }
 @inproceedings{isik_1998, title={Differentiation of Pinus brutia populations revealed by principal component analysis}, booktitle={The Proceedings of International Symposium on in-situ Conservation of Plant Genetic Diversity}, author={Isik, F.}, year={1998}, pages={257–264} }
 @inproceedings{isik_1998, title={Efforts on conservation of forest genetic resources in Turkey}, booktitle={IUFRO All Division 2 Conference on Forest Genetics and Tree Improvement}, author={Isik, F.}, year={1998} }
 @article{isik_isik_1998, title={Genetic variation in Pinus brutia in Turkey: II. Branching and crown traits}, volume={48}, journal={Silvae Genetica}, author={Isik, K. and Isik, F.}, year={1998}, pages={293–302} }
 @book{isik_1998, place={Antalya, Turkey}, title={Genetic variation, heritability and genetic gains from Pinus brutia Ten. Provenance-progeny trials}, number={7}, institution={Western Mediterranean Forest Research Institute}, author={Isik, F.}, year={1998} }
 @inproceedings{isik_isik_1998, title={Results from an eighteen year old Pinus brutia provenance-progeny trials}, volume={75}, booktitle={Forestry Symposium in 75th Anniversary of Turkish Republic}, author={Isik, F. and Isik, K.}, year={1998} }
 @article{boydak_isik_dogan_1998, title={The effect of prescribed fire on the regeneration of Lebanon Cedar (Cedrus libani A. Rich) in Kas, Antalya locality}, volume={22}, journal={Turkish Journal of Agriculture and Forestry}, author={Boydak, M. and Isik, F. and Dogan, B.}, year={1998}, pages={399–404} }
 @article{kaya_isik_1997, title={The pattern of genetic variation in shoot growth of Pinus brutia populations sampled from the Taurus Mountains}, volume={46}, journal={Silvae Genetica}, author={Kaya, Z. and Isik, F.}, year={1997}, pages={73–81} }
 @inproceedings{isik_1996, title={Differentiation of Pinus brutia populations revealed by principal component analysis}, booktitle={The International Symposium on In-Situ Conservation of Plant Genetic Resources}, author={Isik, F.}, year={1996} }
 @inproceedings{isik_kaya_1993, title={Genetic variation in Pinus brutia TEN. populations along the a transect from the sea level to high elevations: Seedling traits.}, booktitle={International Pinus brutia Symposium}, author={Isik, F. and Kaya, Z.}, year={1993}, pages={243–253} }