@article{callister_jimenez-madrigal_whetten_murillo_2024, title={Genomic predictions and candidate single nucleotide polymorphisms for growth, form, and wood properties of teak clones}, volume={73}, ISSN={["2509-8934"]}, url={https://doi.org/10.2478/sg-2024-0002}, DOI={10.2478/sg-2024-0002}, abstractNote={Abstract}, number={1}, journal={SILVAE GENETICA}, author={Callister, Andrew N. and Jimenez-Madrigal, Jose P. and Whetten, Ross W. and Murillo, Olman}, year={2024}, month={Jan}, pages={13–23} }
 @article{pais_ristaino_whetten_xiang_2024, title={Metagenomic study reveals hidden relationships among fungal diversity, variation of plant disease, and genetic distance in <i>Cornus florida</i> (Cornaceae)}, volume={14}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2023.1282188}, abstractNote={IntroductionUnderstanding patterns of plant-microbe interactions across plant species and populations is a critical yet poorly characterized aspect in the field of plant pathology. Microbial DNA sequences present as contaminants in omics data of plants obtained using next-generation sequencing methods provide a valuable source to explore the relationships among endophytic microbial diversity, disease and genetic differentiation of host plants, and environmental variation, but few such studies have been conducted.  The flowering dogwood tree (Cornus florida L.), an ecologically important species in North America, is threatened by powdery mildew and dogwood anthracnose diseases, and knowledge of the microbial diversity harbored within genetically and environmental distinct populations of this species remains largely unknown.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Pais, Andrew and Ristaino, Jean and Whetten, Ross and Xiang, Qiu-Yun}, year={2024}, month={Jan} }
 @article{walker_maynor_isik_heine_whetten_payn_quate_mckeand_2024, title={Stem Defect Rates and Ice Storm Damage for Families of Pinus taeda from Coastal and Piedmont Provenances Planted on a North Carolina Piedmont Site}, volume={4}, ISSN={["1938-3738"]}, url={https://doi.org/10.1093/forsci/fxae016}, DOI={10.1093/forsci/fxae016}, abstractNote={Abstract}, journal={FOREST SCIENCE}, author={Walker, Trevor D. and Maynor, Jessica A. and Isik, Fikret and Heine, Austin J. and Whetten, Ross W. and Payn, Kitt G. and Quate, T. Austin and McKeand, Steven E.}, year={2024}, month={Apr} }
 @article{festa_whetten_2023, title={Analysis of Gene Expression Differences Between Eastern and Western Loblolly Pine Seed Sources}, url={https://doi.org/10.1101/2023.04.24.538124}, DOI={10.1101/2023.04.24.538124}, abstractNote={Abstract}, author={Festa, Adam R and Whetten, Ross}, year={2023}, month={Apr} }
 @article{whetten_jayawickrama_cumbie_martins_2023, title={Genomic Tools in Applied Tree Breeding Programs: Factors to Consider}, volume={14}, ISSN={["1999-4907"]}, url={https://doi.org/10.3390/f14020169}, DOI={10.3390/f14020169}, abstractNote={The past three decades have seen considerable research into the molecular genetics and genomics of forest trees, and a variety of new tools and methods have emerged that could have practical applications in applied breeding programs. Applied breeders may lack specialized knowledge required to evaluate claims made about the advantages of new methods over existing practices and are faced with the challenge of deciding whether to invest in new approaches or continue with current practices. Researchers, on the other hand, often lack experience with constraints faced by applied breeding programs and may not be well-equipped to evaluate the suitability of the method they have developed to a particular program. Our goal here is to outline social, biological, and economic constraints relevant to applied breeding programs to inform researchers, and to summarize some new methods and how they may address those constraints to inform breeders. The constraints faced by programs breeding tropical species grown over large areas in relatively uniform climates with rotations shorter than 10 years differ greatly from those facing programs breeding boreal species deployed in many different environments, each with relatively small areas, with rotations of many decades, so different genomic tools are likely to be appropriate.}, number={2}, journal={FORESTS}, author={Whetten, Ross W. and Jayawickrama, Keith J. S. and Cumbie, W. Patrick and Martins, Gustavo S.}, year={2023}, month={Feb} }
 @article{ousmael_whetten_xu_nielsen_lamour_hansen_2023, title={Identification and high-throughput genotyping of single nucleotide polymorphism markers in a non-model conifer (<i>Abies nordmanniana</i> (Steven) Spach)}, volume={13}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-023-49462-x}, abstractNote={Abstract}, number={1}, journal={SCIENTIFIC REPORTS}, author={Ousmael, Kedra and Whetten, Ross W. and Xu, Jing and Nielsen, Ulrik B. and Lamour, Kurt and Hansen, Ole K.}, year={2023}, month={Dec} }
 @article{gatjens-boniche_jimenez-madrigal_whetten_valenzuela-diaz_aleman-gutierrez_hanson_pinto-tomas_2023, title={Microbiome and plant cell transformation trigger insect gall induction in cassava}, volume={14}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2023.1237966}, abstractNote={Several specialised insects can manipulate normal plant development to induce a highly organised structure known as a gall, which represents one of the most complex interactions between insects and plants. Thus far, the mechanism for insect-induced plant galls has remained elusive. To study the induction mechanism of insect galls, we selected the gall induced by Iatrophobia brasiliensis (Diptera: Cecidomyiidae) in cassava (Euphorbiaceae: Manihot esculenta Crantz) as our model. PCR-based molecular markers and deep metagenomic sequencing data were employed to analyse the gall microbiome and to test the hypothesis that gall cells are genetically transformed by insect vectored bacteria. A shotgun sequencing discrimination approach was implemented to selectively discriminate between foreign DNA and the reference host plant genome. Several known candidate insertion sequences were identified, the most significant being DNA sequences found in bacterial genes related to the transcription regulatory factor CadR, cadmium-transporting ATPase encoded by the cadA gene, nitrate transport permease protein (nrtB gene), and arsenical pump ATPase (arsA gene). In addition, a DNA fragment associated with ubiquitin-like gene E2 was identified as a potential accessory genetic element involved in gall induction mechanism. Furthermore, our results suggest that the increased quality and rapid development of gall tissue are mostly driven by microbiome enrichment and the acquisition of critical endophytes. An initial gall-like structure was experimentally obtained in M. esculenta cultured tissues through inoculation assays using a Rhodococcus bacterial strain that originated from the inducing insect, which we related to the gall induction process. We provide evidence that the modification of the endophytic microbiome and the genetic transformation of plant cells in M. esculenta are two essential requirements for insect-induced gall formation. Based on these findings and having observed the same potential DNA marker in galls from other plant species (ubiquitin-like gene E2), we speculate that bacterially mediated genetic transformation of plant cells may represent a more widespread gall induction mechanism found in nature.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Gatjens-Boniche, Omar and Jimenez-Madrigal, Jose Pablo and Whetten, Ross W. and Valenzuela-Diaz, Sandro and Aleman-Gutierrez, Alvaro and Hanson, Paul E. and Pinto-Tomas, Adrian A.}, year={2023}, month={Nov} }
 @article{festa_whetten_2023, title={Transcriptomic Prediction of Breeding Values in Loblolly Pine}, url={https://doi.org/10.1101/2023.03.21.533546}, DOI={10.1101/2023.03.21.533546}, abstractNote={Abstract}, author={Festa, Adam R and Whetten, Ross}, year={2023}, month={Mar} }
 @article{kloppe_whetten_kim_powell_lück_douchkov_whetten_hulse‐kemp_balint‐kurti_cowger_2023, title={Two pathogen loci determine <i>Blumeria graminis}, volume={238}, ISSN={0028-646X 1469-8137}, url={http://dx.doi.org/10.1111/nph.18809}, DOI={10.1111/nph.18809}, abstractNote={Summary}, number={4}, journal={New Phytologist}, publisher={Wiley}, author={Kloppe, Tim and Whetten, Rebecca B. and Kim, Saet‐Byul and Powell, Oliver R. and Lück, Stefanie and Douchkov, Dimitar and Whetten, Ross W. and Hulse‐Kemp, Amanda M. and Balint‐Kurti, Peter and Cowger, Christina}, year={2023}, month={Mar}, pages={1546–1561} }
 @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={Abstract}, 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} }
 @misc{matallana-ramirez_whetten_sanchez_payn_2021, title={Breeding for Climate Change Resilience: A Case Study of Loblolly Pine (Pinus taeda L.) in North America}, volume={12}, ISSN={["1664-462X"]}, url={https://doi.org/10.3389/fpls.2021.606908}, DOI={10.3389/fpls.2021.606908}, abstractNote={Earth’s atmosphere is warming and the effects of climate change are becoming evident. A key observation is that both the average levels and the variability of temperature and precipitation are changing. Information and data from new technologies are developing in parallel to provide multidisciplinary opportunities to address and overcome the consequences of these changes in forest ecosystems. Changes in temperature and water availability impose multidimensional environmental constraints that trigger changes from the molecular to the forest stand level. These can represent a threat for the normal development of the tree from early seedling recruitment to adulthood both through direct mortality, and by increasing susceptibility to pathogens, insect attack, and fire damage. This review summarizes the strengths and shortcomings of previous work in the areas of genetic variation related to cold and drought stress in forest species with particular emphasis on loblolly pine (Pinus taedaL.), the most-planted tree species in North America. We describe and discuss the implementation of management and breeding strategies to increase resilience and adaptation, and discuss how new technologies in the areas of engineering and genomics are shaping the future of phenotype-genotype studies. Lessons learned from the study of species important in intensively-managed forest ecosystems may also prove to be of value in helping less-intensively managed forest ecosystems adapt to climate change, thereby increasing the sustainability and resilience of forestlands for the future.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Matallana-Ramirez, Lilian P. and Whetten, Ross W. and Sanchez, Georgina M. and Payn, Kitt G.}, year={2021}, month={Apr} }
 @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}, 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{festa_whetten_2021, title={Simulation of Pedigree vs. fully-informative marker based relationships matrices in a Loblolly Pine breeding population}, url={https://doi.org/10.1101/2021.11.30.468863}, DOI={10.1101/2021.11.30.468863}, abstractNote={Abstract}, author={Festa, Adam R and Whetten, Ross}, year={2021}, month={Dec} }
 @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={PremiseAn 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).}, 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{kurt_matallana-ramirez_kohlway_whetten_frampton_2020, title={A fast, flexible and inexpensive protocol for DNA and RNA extraction for forest trees}, volume={29}, ISSN={["2171-9845"]}, DOI={10.5424/fs/2020292-16730}, abstractNote={Aim of the study: DNA and RNA extraction are still one of the most important and challenging steps of many molecular genetics applications such as Next-Generation Sequencing technologies. In this study, traditional laboratory preparation protocols and commercially available nucleic acids extraction kits’ features were combined into a procedure suitable for extraction of either DNA or RNA in 96-well plate format at high throughput.Area of study: The study covers forest tree species from the United States of America.Materials and methods: The DNA and RNA protocol were tested on 27 species, including especially recalcitrant forest tree species, from five angiosperm and three gymnosperm families. DNA was also extracted from stored (from 2 to 6 years) silica-dried samples of 11 species of Pinaceae.Main results: The spectrophotometric analysis of DNA and RNA showed that gymnosperms yielded lower quantity, but higher quality nucleic acids than angiosperms which have variable results among species. The quantity and quality of DNA from stored samples were generally lower than fresh silica-dried samples. The RNA results showed high-enough yield (6.6 to 8.8 RIN) for downstream analyses.Research highlights: It was demonstrated that high quality and high molecular weight nucleic acids for Next-Generation Sequencing applications can be isolated from hundreds of samples from a wide range of taxonomic groups. The new protocol has features similar to both traditional laboratory and commercial extraction kits; is easy to set up in any molecular research laboratory, can be applied to a large number of samples (hundreds) in a working day, uses inexpensive reagents and supplies, and is compatible with automation.Key words: Angiosperms; gymnosperms; isolation protocol; nucleic acids.}, number={2}, journal={FOREST SYSTEMS}, author={Kurt, Yusuf and Matallana-Ramirez, Lilian and Kohlway, William and Whetten, Ross and Frampton, John}, year={2020} }
 @article{hansen_lamour_whetten_xu_cuenca_islam_nielsen_2020, title={Ad hoc breeding of a genetically depauperate landrace of noble fir (Abies procera Rehder) using SNP genotyping via high-throughput targeted sequencing}, volume={16}, url={https://doi.org/10.1007/s11295-020-01460-0}, DOI={10.1007/s11295-020-01460-0}, number={5}, journal={Tree Genetics & Genomes}, publisher={Springer Science and Business Media LLC}, author={Hansen, Ole K. and Lamour, Kurt and Whetten, Ross and Xu, Jing and Cuenca, Argelia and Islam, Md. Shofiqul and Nielsen, Ulrik Braüner}, year={2020}, month={Oct} }
 @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}, 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{pais_whetten_xiang_2020, title={Population structure, landscape genomics, and genetic signatures of adaptation to exotic disease pressure in Cornus florida L.—Insights from GWAS and GBS data}, url={https://doi.org/10.1111/jse.12592}, DOI={10.1111/jse.12592}, abstractNote={Abstract}, journal={Journal of Systematics and Evolution}, author={Pais, Andrew L. and Whetten, Ross W. and Xiang, Qiu‐Yun}, year={2020}, month={Sep} }
 @article{čepl_stejskal_lhotáková_holá_korecký_lstibůrek_tomášková_kočová_rothová_palovská_et al._2018, title={Heritable variation in needle spectral reflectance of Scots pine (Pinus sylvestris L.) peaks in red edge}, volume={219}, ISSN={0034-4257}, url={http://dx.doi.org/10.1016/j.rse.2018.10.001}, DOI={10.1016/j.rse.2018.10.001}, abstractNote={Foliar reflectance is readily used in evaluating physiological status of agricultural crops and forest stands. However, in the case of forest trees, underlying genetics of foliar spectral reflectance and pigment content have rarely been investigated. We studied a structured population of Scots pine, replicated on two sites, with the selected trees´ pedigree reconstructed via DNA markers. This allowed us to decompose phenotypic variance of pigment and reflectance traits into its causal genetic components, and to estimate narrow-sense heritability (h2). We found statistically significant h2 ranging from 0.07 to 0.22 for most of the established reflectance indices. Additionally, we investigated the profile of heritable variation along the reflectance curve in 1 nm wavelength (WL) bands. We show that the maximum h2 value (0.39; SE 0.13) across the 400 to 2500 nm spectral range corresponds to the red edge inflection point, in this case to 722 nm WL band. Resultant h2 distribution indicates that additive gene effects fluctuate along the reflectance curve. Furthermore, h2 of the most widely used formats of reflectance indices, i.e. the simple ratio and the normalized difference, was estimated for all WL bands combined along the observed reflectance spectrum. The highest h2 estimates for both formats were obtained by combining WL bands of the red edge spectrum. These new genetically driven pigment- and spectral reflectance- based markers (proxies of adaptive traits) may facilitate selection of stress resistant plant genotypes. Recent development of high-resolution spectral sensors carried by airborne and spaceborn devices make foliage spectral traits a viable technology for mass phenotyping in forest trees.}, journal={Remote Sensing of Environment}, publisher={Elsevier BV}, author={Čepl, Jaroslav and Stejskal, Jan and Lhotáková, Zuzana and Holá, Dana and Korecký, Jiří and Lstibůrek, Milan and Tomášková, Ivana and Kočová, Marie and Rothová, Olga and Palovská, Markéta and et al.}, year={2018}, month={Dec}, pages={89–98} }
 @article{holliday_aitken_cooke_fady_gonzalez-martinez_heuertz_jaramillo-correa_lexer_staton_whetten_et al._2017, title={Advances in ecological genomics in forest trees and applications to genetic resources conservation and breeding}, volume={26}, ISSN={["1365-294X"]}, DOI={10.1111/mec.13963}, abstractNote={Forest trees are an unparalleled group of organisms in their combined ecological, economic and societal importance. With widespread distributions, predominantly random mating systems and large population sizes, most tree species harbour extensive genetic variation both within and among populations. At the same time, demographic processes associated with Pleistocene climate oscillations and land‐use change have affected contemporary range‐wide diversity and may impinge on the potential for future adaptation. Understanding how these adaptive and neutral processes have shaped the genomes of trees species is therefore central to their management and conservation. As for many other taxa, the advent of high‐throughput sequencing methods is expected to yield an understanding of the interplay between the genome and environment at a level of detail and depth not possible only a few years ago. An international conference entitled ‘Genomics and Forest Tree Genetics’ was held in May 2016, in Arcachon (France), and brought together forest geneticists with a wide range of research interests to disseminate recent efforts that leverage contemporary genomic tools to probe the population, quantitative and evolutionary genomics of trees. An important goal of the conference was to discuss how such data can be applied to both genome‐enabled breeding and the conservation of forest genetic resources under land use and climate change. Here, we report discoveries presented at the meeting and discuss how the ecological genomic toolkit can be used to address both basic and applied questions in tree biology.}, number={3}, journal={MOLECULAR ECOLOGY}, author={Holliday, Jason A. and Aitken, Sally N. and Cooke, Janice E. K. and Fady, Bruno and Gonzalez-Martinez, Santiago C. and Heuertz, Myriam and Jaramillo-Correa, Juan-Pablo and Lexer, Christian and Staton, Margaret and Whetten, Ross W. and et al.}, year={2017}, month={Feb}, pages={706–717} }
 @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 Ͻ 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.}, 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{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={ABSTRACT 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, A. and Reich, B. J. and Guinness, J. and Whetten, Ross and McKeand, S. and Isik, Fikret}, year={2017}, pages={909–920} }
 @article{kohlway_whetten_benson_frampton_2017, title={Response of Turkish and Trojan fir to Phytophthora cinnamomi and P. cryptogea}, volume={32}, ISSN={0282-7581 1651-1891}, url={http://dx.doi.org/10.1080/02827581.2017.1280076}, DOI={10.1080/02827581.2017.1280076}, abstractNote={ABSTRACT Phytophthora root rot, primarily caused by the oomycete Phytophthora cinnamomi, is a large problem for the Christmas tree industry in North Carolina. Fraser fir (Abies fraseri) has no known innate resistance to this pathogen while some exotic fir species, such as Trojan (Abies equi-trojani) and Turkish (Abies bornmuelleriana) fir display varying amounts of resistance. A Phytophthora-resistance screening trial was completed with 1600 seedlings from 12 Turkish and Trojan fir families and Fraser and momi fir (A. firma). Seedlings from each family or species were inoculated with each of eight Phytophthora isolates, six P. cinnamomi and two Phytophthora cryptogea, in an effort to describe variability in isolate aggressiveness. Mortality was assessed as percent shoot necrosis bi-weekly for 16 weeks. Overall, rankings of resistance in fir species confirmed previous single-isolate-based results; momi fir was the most resistant, followed by Turkish, Trojan, and Fraser fir. P. cinnamomi isolates were generally more aggressive than P. cryptogea isolates. The two P. cryptogea isolates resulted in 5.6% and 0.8% mortality on Turkish fir, and 10.9% and 6.7% mortality on Trojan fir, the first reported resistance screen of these host-pathogen combinations. Pearson’s correlation testing identified a high degree of correlation between most isolates and overall mean mortality. Turkish and Trojan fir families appear to possess resistance to Phytophthora species common in North Carolina.}, number={5}, journal={Scandinavian Journal of Forest Research}, publisher={Informa UK Limited}, author={Kohlway, W. H. and Whetten, R. W. and Benson, D. M. and Frampton, J.}, year={2017}, month={Feb}, pages={406–411} }
 @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} }
 @article{pais_whetten_xiang_2016, title={Ecological genomics of local adaptation in Cornus florida L. by genotyping by sequencing}, volume={7}, ISSN={2045-7758}, url={http://dx.doi.org/10.1002/ece3.2623}, DOI={10.1002/ece3.2623}, abstractNote={Abstract}, number={1}, journal={Ecology and Evolution}, publisher={Wiley}, author={Pais, Andrew L. and Whetten, Ross W. and Xiang, Qiu-Yun Jenny}, year={2016}, month={Dec}, pages={441–465} }
 @article{čepl_holá_stejskal_korecký_kočová_lhotáková_tomášková_palovská_rothová_whetten_et al._2016, title={Genetic variability and heritability of chlorophyll a fluorescence parameters in Scots pine (Pinus sylvestris L.)}, volume={36}, ISSN={0829-318X 1758-4469}, url={http://dx.doi.org/10.1093/treephys/tpw028}, DOI={10.1093/treephys/tpw028}, abstractNote={Current knowledge of the genetic mechanisms underlying the inheritance of photosynthetic activity in forest trees is generally limited, yet it is essential both for various practical forestry purposes and for better understanding of broader evolutionary mechanisms. In this study, we investigated genetic variation underlying selected chlorophyll a fluorescence (ChlF) parameters in structured populations of Scots pine (Pinus sylvestris L.) grown on two sites under non-stress conditions. These parameters were derived from the OJIP part of the ChlF kinetics curve and characterize individual parts of primary photosynthetic processes associated, for example, with the exciton trapping by light-harvesting antennae, energy utilization in photosystem II (PSII) reaction centers (RCs) and its transfer further down the photosynthetic electron-transport chain. An additive relationship matrix was estimated based on pedigree reconstruction, utilizing a set of highly polymorphic single sequence repeat markers. Variance decomposition was conducted using the animal genetic evaluation mixed-linear model. The majority of ChlF parameters in the analyzed pine populations showed significant additive genetic variation. Statistically significant heritability estimates were obtained for most ChlF indices, with the exception of DI0/RC, φD0 and φP0 (Fv/Fm) parameters. Estimated heritabilities varied around the value of 0.15 with the maximal value of 0.23 in the ET0/RC parameter, which indicates electron-transport flux from QA to QB per PSII RC. No significant correlation was found between these indices and selected growth traits. Moreover, no genotype × environment interaction (G × E) was detected, i.e., no differences in genotypes' performance between sites. The absence of significant G × E in our study is interesting, given the relatively low heritability found for the majority of parameters analyzed. Therefore, we infer that polygenic variability of these indices is selectively neutral.}, number={7}, journal={Tree Physiology}, publisher={Oxford University Press (OUP)}, author={Čepl, Jaroslav and Holá, Dana and Stejskal, Jan and Korecký, Jiří and Kočová, Marie and Lhotáková, Zuzana and Tomášková, Ivana and Palovská, Markéta and Rothová, Olga and Whetten, Ross W. and et al.}, editor={Schnitzler, Jörg-PeterEditor}, year={2016}, month={Apr}, pages={883–895} }
 @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{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{qi_yu_liu_pais_ranney_whetten_xiang_2015, title={Phylogenomics of polyploid Fothergilla (Hamamelidaceae) by RAD-tag based GBS-insights into species origin and effects of software pipelines}, volume={53}, ISSN={1674-4918}, url={http://dx.doi.org/10.1111/jse.12176}, DOI={10.1111/jse.12176}, abstractNote={Abstract}, number={5}, journal={Journal of Systematics and Evolution}, publisher={Wiley}, author={Qi, Zhe-Chen and Yu, Yi and Liu, Xiang and Pais, Andrew and Ranney, Thomas and Whetten, Ross and Xiang, Qiu-Yun Jenny}, year={2015}, month={Sep}, pages={432–447} }
 @article{neale_wegrzyn_stevens_zimin_puiu_crepeau_cardeno_koriabine_holtz-morris_liechty_et al._2014, title={Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies}, volume={15}, ISSN={["1474-760X"]}, DOI={10.1186/gb-2014-15-3-r59}, abstractNote={The size and complexity of conifer genomes has, until now, prevented full genome sequencing and assembly. The large research community and economic importance of loblolly pine, Pinus taeda L., made it an early candidate for reference sequence determination.We develop a novel strategy to sequence the genome of loblolly pine that combines unique aspects of pine reproductive biology and genome assembly methodology. We use a whole genome shotgun approach relying primarily on next generation sequence generated from a single haploid seed megagametophyte from a loblolly pine tree, 20-1010, that has been used in industrial forest tree breeding. The resulting sequence and assembly was used to generate a draft genome spanning 23.2 Gbp and containing 20.1 Gbp with an N50 scaffold size of 66.9 kbp, making it a significant improvement over available conifer genomes. The long scaffold lengths allow the annotation of 50,172 gene models with intron lengths averaging over 2.7 kbp and sometimes exceeding 100 kbp in length. Analysis of orthologous gene sets identifies gene families that may be unique to conifers. We further characterize and expand the existing repeat library based on the de novo analysis of the repetitive content, estimated to encompass 82% of the genome.In addition to its value as a resource for researchers and breeders, the loblolly pine genome sequence and assembly reported here demonstrates a novel approach to sequencing the large and complex genomes of this important group of plants that can now be widely applied.}, number={3}, journal={GENOME BIOLOGY}, author={Neale, David B. and Wegrzyn, Jill L. and Stevens, Kristian A. and Zimin, Aleksey V. and Puiu, Daniela and Crepeau, Marc W. and Cardeno, Charis and Koriabine, Maxim and Holtz-Morris, Ann E. and Liechty, John D. and et al.}, year={2014} }
 @article{moraga-suazo_orellana_quiroga_balocchi_sanfuentes_whetten_hasbún_valenzuela_2014, title={Development of a genetic linkage map for Pinus radiata and detection of pitch canker disease resistance associated QTLs}, volume={28}, ISSN={0931-1890 1432-2285}, url={http://dx.doi.org/10.1007/s00468-014-1090-2}, DOI={10.1007/s00468-014-1090-2}, number={6}, journal={Trees}, publisher={Springer Science and Business Media LLC}, author={Moraga-Suazo, P. and Orellana, L. and Quiroga, P. and Balocchi, C. and Sanfuentes, E. and Whetten, R. W. and Hasbún, R. and Valenzuela, S.}, year={2014}, month={Sep}, pages={1823–1835} }
 @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{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}, 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{alberto_aitken_alía_gonzález-martínez_hänninen_kremer_lefèvre_lenormand_yeaman_whetten_et al._2013, title={Potential for evolutionary responses to climate change - evidence from tree populations}, volume={19}, ISSN={1354-1013}, url={http://dx.doi.org/10.1111/gcb.12181}, DOI={10.1111/gcb.12181}, abstractNote={Abstract}, number={6}, journal={Global Change Biology}, publisher={Wiley}, author={Alberto, Florian J. and Aitken, Sally N. and Alía, Ricardo and González-Martínez, Santiago C. and Hänninen, Heikki and Kremer, Antoine and Lefèvre, François and Lenormand, Thomas and Yeaman, Sam and Whetten, Ross and et al.}, year={2013}, month={Apr}, pages={1645–1661} }
 @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_eckert_wegrzyn_whetten_neale_goldfarb_2011, title={Association genetics of carbon isotope discrimination, height and foliar nitrogen in a natural population of Pinus taeda L}, volume={107}, ISSN={0018-067X 1365-2540}, url={http://dx.doi.org/10.1038/hdy.2010.168}, DOI={10.1038/hdy.2010.168}, abstractNote={Loblolly pine, Pinus taeda L., is one of the most widely planted, commercially and ecologically important tree species in North America. We took an association genetics approach, using an unimproved population of 380 clonally replicated unrelated trees, to test 3,938 single nucleotide polymorphisms (SNPs) in as many genes for association with phenotypic variation in carbon isotope discrimination, foliar nitrogen concentration and total tree height after two growing seasons. Best linear unbiased prediction (BLUP) was used with a spatial adjustment to remove environmental variation from phenotypic data derived from a common garden experiment. After correction for multiple testing, a total of 14 SNPs were associated with the traits of carbon isotope discrimination (n = 7), height (n = 1) and foliar nitrogen concentration (n = 6) using 380 clones. Tails of the population phenotypic distribution were compared for allele frequency differences, revealing 10 SNPs with allele frequency in at least one tail significantly different from the overall population. Eight associated SNPs were in sequences similar to known genes, such as an AP2 transcription factor related to carbon isotope discrimination and glutamate decarboxylase associated with foliar nitrogen concentration, and others were from unknown genes without homologs in Arabidopsis.}, number={2}, journal={Heredity}, publisher={Springer Science and Business Media LLC}, author={Cumbie, W P and Eckert, A and Wegrzyn, J and Whetten, R and Neale, D and Goldfarb, B}, year={2011}, month={Jan}, pages={105–114} }
 @article{sato_yajima_tokunaga_whetten_2011, title={Comparison between tracheary element lignin formation and extracellular lignin-like substance formation during the culture of isolated Zinnia elegans mesophyll cells}, volume={66}, ISSN={["0006-3088"]}, DOI={10.2478/s11756-010-0130-7}, abstractNote={Lignin is synthesized not only during morphogenesis of vascular plants but also in response to various stresses. Isolated Zinnia elegans mesophyll cells can differentiate into tracheary elements (TEs), and deposit lignin into cell walls in TE-inductive medium (D medium). Meanwhile isolated mesophyll cells cultured in hormone-free medium (Co medium) accumulate stress lignin-like substance during culture. Therefore this culture system is suitable for study of lignin and lignin-like substance formation.In D medium lignin was deposited in TEs, but in Co medium, extracellular lignin-like substance accumulated. Analysis of the culture media indicated the presence of dilignols in D culture, but not in Co culture. To investigate the fate of lignin precursors, we added coniferyl alcohol (CA) in each culture. In Co medium, CA was polymerized into dilignols rapidly but they were present only temporarily, and in D medium CA was polymerized into dilignols relatively slowly but their content increased continually.Meanwhile, in Co culture, peroxidase activity in the medium was much higher than the peroxidase activity bound ionically to the cell walls. In D culture, ionically bound peroxidase activity was higher than that in the medium. These results may suggest that lignin deposition in TEs is related to ionically bound peroxidases in D culture, and lignin-like substance deposition in the medium is related to peroxidases in the medium in Co culture.}, number={1}, journal={BIOLOGIA}, author={Sato, Yasushi and Yajima, Youko and Tokunaga, Naohito and Whetten, Ross}, year={2011}, month={Feb}, pages={88–95} }
 @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} }
 @misc{whetten_kellison_2010, title={Research gap analysis for application of biotechnology to sustaining US forests}, volume={108}, number={4}, journal={Journal of Forestry}, author={Whetten, R. W. and Kellison, R.}, year={2010}, pages={193–201} }
 @article{whetten_valenzuela_frampton_2009, title={Polymerase chain reaction of template for massively-parallel pyrosequencing}, volume={20}, number={2}, journal={Journal of Biomolecular Techniques}, author={Whetten, R. W. and Valenzuela, S. and Frampton, I.}, year={2009}, pages={128–134} }
 @article{morse_whetten_dubos_campbell_2009, title={Post-translational modification of an R2R3-MYB transcription factor by a MAP Kinase during xylem development}, volume={183}, ISSN={["1469-8137"]}, DOI={10.1111/j.1469-8137.2009.02900.x}, abstractNote={Despite the pivotal role played by R2R3-MYB family members in the regulation of plant gene expression, little is known about post-translational regulation of these proteins. In animals, the MYB family member, c-MYB, is post-translationally modified by a mitogen-activated protein kinase (MAPK), p42(mapk). In order to test the hypothesis that R2R3-MYB proteins may be regulated by MAPK activity, interplay between a R2R3-MYB family member expressed in differentiating pine xylem (Pinus taeda MYB4, PtMYB4) and MAPK proteins expressed in the same tissue was examined. One of the MAPK proteins expressed in pine xylem, PtMAPK6, phosphorylated PtMYB4. Recombinant PtMAPK6 phosphorylated PtMYB4 on serine-236, located in the C-terminal activation domain of this transcription factor in a context that is found in other plant MYB proteins. Modification of the PtMAPK6 target serine in PtMYB4 did not appear to alter DNA binding in vitro but did alter the ability of PtMYB4 to promote transcriptional activation in yeast. PtMAPK6 activity was detected in developing xylem cells that had ceased cell division and formed secondary walls. Together, the data support a role for PtMAPK6 during early xylem development and suggest a function for this kinase in regulating gene expression through phosphorylation of PtMYB4.}, number={4}, journal={NEW PHYTOLOGIST}, author={Morse, Alison M. and Whetten, Ross W. and Dubos, Christian and Campbell, Malcolm M.}, year={2009}, pages={1001–1013} }
 @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} }
 @article{sato_whetten_2006, title={Characterization of two laccases of loblolly pine (Pinus taeda) expressed in tobacco BY-2 cells}, volume={119}, ISSN={["0918-9440"]}, DOI={10.1007/s10265-006-0020-9}, abstractNote={We previously showed that eight laccase genes (Lac 1-Lac 8) are preferentially expressed in differentiating xylem and are associated with lignification in loblolly pine (Pinus taeda) [Sato et al. (2001) J Plant Res 114:147-155]. In this study we generated transgenic tobacco suspension cell cultures that express the pine Lac 1 and Lac 2 proteins, and characterized the abilities of these proteins to oxidize monolignols. Lac 1 and Lac 2 enzymatic activities were detected only in the cell walls of transgenic tobacco cells, and could be extracted with high salt. The optimum pH for laccase activity with coniferyl alcohol as substrate was 5.0 for Lac 1 and between 5.0 and 6.0 for Lac 2. The activities of Lac 1 and Lac 2 increased as the concentration of CuSO(4) in the reaction mixtures increased in the range from 1 to 100 microM. Both enzymes were able to oxidize coniferyl alcohol and to produce dimers of coniferyl alcohol. These results are consistent with the hypothesis that Lac 1 and Lac 2 are involved in lignification in differentiating xylem of loblolly pine.}, number={6}, journal={JOURNAL OF PLANT RESEARCH}, author={Sato, Yasushi and Whetten, Ross W.}, year={2006}, month={Nov}, pages={581–588} }
 @article{busov_johannes_whetten_sederoff_spiker_lanz-garcia_goldfarb_2004, title={An auxin-inducible gene from loblolly pine ( Pinus taeda L.) is differentially expressed in mature and juvenile-phase shoots and encodes a putative transmembrane protein}, volume={218}, ISSN={0032-0935 1432-2048}, url={http://dx.doi.org/10.1007/s00425-003-1175-4}, DOI={10.1007/s00425-003-1175-4}, abstractNote={We have isolated a gene from loblolly pine, 5NG4, that is highly and specifically induced by auxin in juvenile loblolly pine shoots prior to adventitious root formation, but substantially down-regulated in physiologically mature shoots that are adventitious rooting incompetent. 5NG4 was highly auxin-induced in roots, stems and hypocotyls, organs that can form either lateral or adventitious roots following an auxin treatment, but was not induced to the same level in needles and cotyledons, organs that do not form roots. The deduced amino acid sequence shows homology to the MtN21 nodulin gene from Medicago truncatula. The expression pattern of 5NG4 and its homology to a protein from Medicago involved in a root-related process suggest a possible role for this gene in adventitious root formation. Homology searches also identified similar proteins in Arabidopsis thaliana and Oryza sativa. High conservation across these evolutionarily distant species suggests essential functions in plant growth and development. A 38-member family of genes homologous to 5NG4 was identified in the A. thaliana genome. The physiological significance of this redundancy is most likely associated with functional divergence and/or expression specificity of the different family members. The exact biochemical function of the gene is still unknown, but sequence and structure predictions and 5NG4::GFP fusion protein localizations indicate it is a transmembrane protein with a possible transport function.}, number={6}, journal={Planta}, publisher={Springer Science and Business Media LLC}, author={Busov, Victor B. and Johannes, Eva and Whetten, Ross W. and Sederoff, Ronald R. and Spiker, Steven L. and Lanz-Garcia, Carmen and Goldfarb, Barry}, year={2004}, month={Apr}, pages={916–927} }
 @article{egertsdotter_zyl_mackay_peter_kirst_clark_whetten_sederoff_2004, title={Gene Expression during Formation of Earlywood and Latewood in Loblolly Pine: Expression Profiles of 350 Genes}, volume={6}, ISSN={1435-8603 1438-8677}, url={http://dx.doi.org/10.1055/s-2004-830383}, DOI={10.1055/s-2004-830383}, abstractNote={Abstract:  The natural variability of wood formation in trees affords opportunities to correlate transcript profiles with the resulting wood properties. We have used cDNA microarrays to study transcript abundance in developing secondary xylem of loblolly pine (Pinus taeda) over a growing season. The cDNAs were selected from a collection of 75 000 ESTs that have been sequenced and annotated (http:web.ahc.umn.edubiodatansfpine). Cell wall thickness and climatic data were related to earlywood and latewood formation at different time points during the growing season. Seventy‐one ESTs showed preferential expression in earlywood or latewood, including 23 genes with no significant similarity to genes in GenBank. Seven genes involved in lignin synthesis were preferentially expressed in latewood. The studies have provided initial insights into the variation of expression patterns of some of the genes related to the wood formation process.}, number={6}, journal={Plant Biology}, publisher={Wiley}, author={Egertsdotter, U. and Zyl, L. M. and MacKay, J. and Peter, G. and Kirst, M. and Clark, C. and Whetten, R. and Sederoff, R.}, year={2004}, month={Nov}, pages={654–663} }
 @article{myburg_vogl_griffin_sederoff_whetten_2004, title={Genetics of Postzygotic Isolation in Eucalyptus: Whole-Genome Analysis of Barriers to Introgression in a Wide Interspecific Cross of Eucalyptus grandis and E. globulus}, volume={166}, ISSN={0016-6731 1943-2631}, url={http://dx.doi.org/10.1534/genetics.166.3.1405}, DOI={10.1534/genetics.166.3.1405}, abstractNote={Abstract}, number={3}, journal={Genetics}, publisher={Genetics Society of America}, author={Myburg, Alexander A. and Vogl, Claus and Griffin, A. Rod and Sederoff, Ronald R. and Whetten, Ross W.}, year={2004}, month={Mar}, pages={1405–1418} }
 @article{zhang_brown_whetten_loopstra_neale_kieliszewski_sederoff_2003, title={An arabinogalactan protein associated with secondary cell wall formation in differentiating xylem of loblolly pine}, volume={52}, ISSN={["0167-4412"]}, url={http://dx.doi.org/10.1023/a:1023978210001}, DOI={10.1023/a:1023978210001}, abstractNote={Arabinogalactan proteins (AGPs) are abundant plant proteoglycans implicated in plant growth and development. Here, we report the genetic characterization, partial purification and immunolocalization of a classical AGP (PtaAGP6, accession number AF101785) in loblolly pine (Pinus taeda L.). A PtaAGP6 full-length cDNA clone was expressed in bacteria. PtaAGP6 resembles tomato LeAGP-1 and Arabidopsis AtAGP17-19 in that they all possess a subdomain composed of basic amino acids. The accessibility of this domain in the glycoprotein makes it possible to label the PtaAGP6 epitopes on the cell surface or in the cell wall with polyclonal antibodies raised against this subdomain. The antibodies recognize the peptide of the basic subdomain and bind to the intact protein molecule. A soluble protein-containing fraction was purified from the differentiating xylem of pine trees by using beta-glucosyl Yariv reagent (beta-glcY) and was recognized by antibodies against the basic subdomain. Immunolocalization studies showed that the PtaAGP6 epitopes are restricted to a file of cells that just precede secondary cell wall thickening, suggesting roles in xylem differentiation and wood formation. The location of apparent labeling of the PtaAGP6 epitopes is separated from the location of lignin deposition. Multiple single nucleotide polymorphisms (SNPs) were detected in EST variants. Denaturing HPLC analysis of PCR products suggests that PtaAGP6 is encoded by a single gene. Mobility variation in denaturing gel electrophoresis was used to map PtaAGP6 SNPs to a site on linkage group 5.}, number={1}, journal={Plant Molecular Biology}, author={Zhang, Y. and Brown, G. and Whetten, R. and Loopstra, C.A. and Neale, D. and Kieliszewski, M.J. and Sederoff, R.R.}, year={2003}, pages={91–102} }
 @article{kirst_johnson_baucom_ulrich_hubbard_staggs_paule_retzel_whetten_sederoff_2003, title={Apparent homology of expressed genes from wood-forming tissues of loblolly pine (Pinus taeda L.) with Arabidopsis thaliana}, volume={100}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.1132171100}, DOI={10.1073/pnas.1132171100}, abstractNote={
            Pinus taeda
            L. (loblolly pine) and
            Arabidopsis thaliana
            differ greatly in form, ecological niche, evolutionary history, and genome  size.
            Arabidopsis
            is a small, herbaceous, annual dicotyledon, whereas  pines are large, long-lived, coniferous forest trees. Such diverse plants  might be expected to differ in a large number of functional genes. We have  obtained and analyzed 59,797 expressed sequence tags (ESTs) from wood-forming  tissues of loblolly pine and compared them to the gene sequences inferred from  the complete sequence of the
            Arabidopsis
            genome. Approximately 50% of  pine ESTs have no apparent homologs in
            Arabidopsis
            or any other  angiosperm in public databases. When evaluated by using contigs containing  long, high-quality sequences, we find a higher level of apparent homology  between the inferred genes of these two species. For those contigs 1,100 bp or  longer, ≈90% have an apparent
            Arabidopsis
            homolog (
            E
            value < 10
            -
            10
            ). Pines and
            Arabidopsis
            last  shared a common ancestor ≈300 million years ago. Few genes would be  expected to retain high sequence similarity for this time if they did not have  essential functions. These observations suggest substantial conservation of  gene sequence in seed plants.
          }, number={12}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Kirst, M. and Johnson, A. F. and Baucom, C. and Ulrich, E. and Hubbard, K. and Staggs, R. and Paule, C. and Retzel, E. and Whetten, R. and Sederoff, R.}, year={2003}, month={May}, pages={7383–7388} }
 @article{goldfarb_lanz-garcia_lian_whetten_2003, title={Aux/IAA gene family is conserved in the gymnosperm, loblolly pine (Pinus taeda)}, volume={23}, ISSN={0829-318X 1758-4469}, url={http://dx.doi.org/10.1093/treephys/23.17.1181}, DOI={10.1093/treephys/23.17.1181}, abstractNote={We isolated five members of the Aux/IAA gene family in loblolly pine (Pinus taeda L.). Degenerate primers complementary to conserved regions of angiosperm Aux/IAA genes were used to amplify fragments that were, in turn, used as probes to screen a cDNA library constructed from auxin-treated hypocotyls. The five unique clones, named PTIAA1-5, contain the four highly conserved domains that are characteristic of the Aux/IAA proteins. All clones contain the bipartite nuclear localization signal (NLS) between Domains I and II that is predicted in most angiosperm Aux/IAA genes, but only one, PTIAA2, contains the conserved NLS in Domain IV. The five invariant residues in Domain II that have been found to constitute part of a protein destabilization element in Arabidopsis thaliana (L.) Heynh. are conserved in all the PTIAAs. A postulated phosphorylation site located between Domains I and II and proximal to the conserved bipartite NLS was conserved in 20 out of 36 genes in this analysis, including the pine genes. Transcripts of all five PTIAAs accumulated specifically in the hypocotyls in response to exogenous auxin treatment and were induced by all auxins tested. Transcript abundance above basal levels in response to 1-naphthaleneacetic acid treatment was first detected after 10 min (PTIAA3) to 3 h (PTIAA2) in the different genes and remained above basal levels throughout 7 days. Induction of PTIAA2 was inhibited by the protein synthesis inhibitor cycloheximide, indicating that PTIAA2 is a secondary response gene. Phylogenetic analysis showed that all five pine genes clustered within a single class (Class I) of the dendrogram. Clone PTIAA2 has a sequence that is relatively distinct from the other four and is the most closely related to the angiosperm genes of Class I. Class I contains both primary and secondary auxin response genes, suggesting that it is the original lineage and that other gene classes have evolved subsequent to the angiosperm/gymnosperm divergence.}, number={17}, journal={Tree Physiology}, publisher={Oxford University Press (OUP)}, author={Goldfarb, B. and Lanz-Garcia, C. and Lian, Z. and Whetten, R.}, year={2003}, month={Dec}, pages={1181–1192} }
 @article{clore_turner_morse_whetten_2003, title={Changes in mitogen-activated protein kinase activity occur in the maize pulvinus in response to gravistimulation and are important for the bending response}, volume={26}, ISSN={["0140-7791"]}, DOI={10.1046/j.1365-3040.2003.00990.x}, abstractNote={ABSTRACT}, number={7}, journal={PLANT CELL AND ENVIRONMENT}, author={Clore, AM and Turner, WS and Morse, AM and Whetten, RW}, year={2003}, month={Jul}, pages={991–1001} }
 @article{patzlaff_newman_dubos_whetten_smith_mcinnis_bevan_sederoff_campbell_2003, title={Characterisation of PtMYB1, an R2R3-MYB from pine xylem}, volume={53}, ISSN={0167-4412}, url={http://dx.doi.org/10.1023/b:plan.0000019066.07933.d6}, DOI={10.1023/b:plan.0000019066.07933.d6}, abstractNote={A cDNA encoding a member of the R2R3-MYB family of transcription factors was cloned from a library constructed from differentiating Pinus taeda (loblolly pine) xylem RNA. This MYB family member, Pinus taeda MYB1 (PtMYB1), was most abundantly expressed in differentiating xylem, as assessed by both ribonuclease protection assays, and by northern blot analysis with poly(A)-enriched RNA. Similar to other plant R2R3-MYB family members, recombinant Pt MYB1 protein was able to bind to AC elements in electrophoretic mobility shift assays (EMSAs). AC elements are DNA motifs rich in adenosine and cytosine that have been implicated in the xylem-localised regulation of genes encoding lignin biosynthetic enzymes. Pt MYB1 not only bound to AC elements, but was also able to induce AC-element-dependent shifts in the electrophoretic mobility of a plant promoter that contains three AC elements, the minimal PHENYLALANINE AMMONIA-LYASE 2 (PAL2) promoter from Phaseolus vulgaris. Transcriptional activation assays conducted using yeast showed that Pt MYB1 also activated transcription, and that it did so in an AC-element-dependent fashion. Pt MYB1 also activated transcription from the minimal PAL2 promoter in plant cells in an AC-element-dependent fashion, as revealed by transient transcriptional activation assays with microprojectile-bombarded tobacco NT-1 cells. Taken together, these finding are consistent with the hypothesis that Pt MYB1 may regulate transcription from cis -acting AC elements in pine xylem.}, number={4}, journal={Plant Molecular Biology}, publisher={Springer Nature}, author={Patzlaff, Astrid and Newman, Lisa J. and Dubos, Christian and Whetten, Ross W. and Smith, Caroline and McInnis, Stephanie and Bevan, Michael W. and Sederoff, Ronald R. and Campbell, Malcolm M.}, year={2003}, month={Nov}, pages={597–608} }
 @article{patzlaff_mcinnis_courtenay_surman_newman_smith_bevan_mansfield_whetten_sederoff_et al._2003, title={Characterisation of a pine MYB that regulates lignification}, volume={36}, ISSN={0960-7412 1365-313X}, url={http://dx.doi.org/10.1046/j.1365-313x.2003.01916.x}, DOI={10.1046/j.1365-313x.2003.01916.x}, abstractNote={Summary}, number={6}, journal={The Plant Journal}, publisher={Wiley}, author={Patzlaff, Astrid and McInnis, Stephanie and Courtenay, Adrian and Surman, Christine and Newman, Lisa J. and Smith, Caroline and Bevan, Michael W. and Mansfield, Shawn and Whetten, Ross W. and Sederoff, Ronald R. and et al.}, year={2003}, month={Dec}, pages={743–754} }
 @article{myburg_griffin_sederoff_whetten_2003, title={Comparative genetic linkage maps of Eucalyptus grandis, Eucalyptus globulus and their F1 hybrid based on a double pseudo-backcross mapping approach}, volume={107}, ISSN={0040-5752 1432-2242}, url={http://dx.doi.org/10.1007/s00122-003-1347-4}, DOI={10.1007/s00122-003-1347-4}, abstractNote={Comparative genetic mapping in interspecific pedigrees presents a powerful approach to study genetic differentiation, genome evolution and reproductive isolation in diverging species. We used this approach for genetic analysis of an F(1) hybrid of two Eucalyptus tree species, Eucalyptus grandis (W. Hill ex Maiden.) and Eucalyptus globulus (Labill.). This wide interspecific cross is characterized by hybrid inviability and hybrid abnormality. Approximately 20% of loci in the genome of the F(1) hybrid are expected to be hemizygous due to a difference in genome size between E. grandis (640 Mbp) and E. globulus (530 Mbp). We investigated the extent of colinearity between the two genomes and the distribution of hemizygous loci in the F(1) hybrid using high-throughput, semi-automated AFLP marker analysis. Two pseudo-backcross families (backcrosses of an F(1) individual to non-parental individuals of the parental species) were each genotyped with more than 800 AFLP markers. This allowed construction of de novo comparative genetic linkage maps of the F(1) hybrid and the two backcross parents. All shared AFLP marker loci in the three single-tree parental maps were found to be colinear and little evidence was found for gross chromosomal rearrangements. Our results suggest that hemizygous AFLP loci are dispersed throughout the E. grandis chromosomes of the F(1) hybrid.}, number={6}, journal={Theoretical and Applied Genetics}, publisher={Springer Science and Business Media LLC}, author={Myburg, A. A. and Griffin, A. R. and Sederoff, R. R. and Whetten, R. W.}, year={2003}, month={Jul}, pages={1028–1042} }
 @article{heath_ramakrishnan_sederoff_whetten_chevone_struble_jouenne_chen_van zyl_grene_et al._2002, title={Studying the functional genomics of stress responses in loblolly pine with the Expresso microarray experiment management system}, volume={3}, ISSN={["1532-6268"]}, DOI={10.1002/cfg.169}, abstractNote={Conception, design, and implementation of cDNA microarray experiments present a variety of bioinformatics challenges for biologists and computational scientists. The multiple stages of data acquisition and analysis have motivated the design of Expresso, a system for microarray experiment management. Salient aspects of Expresso include support for clone replication and randomized placement; automatic gridding, extraction of expression data from each spot, and quality monitoring; flexible methods of combining data from individual spots into information about clones and functional categories; and the use of inductive logic programming for higher-level data analysis and mining. The development of Expresso is occurring in parallel with several generations of microarray experiments aimed at elucidating genomic responses to drought stress in loblolly pine seedlings. The current experimental design incorporates 384 pine cDNAs replicated and randomly placed in two specific microarray layouts. We describe the design of Expresso as well as results of analysis with Expresso that suggest the importance of molecular chaperones and membrane transport proteins in mechanisms conferring successful adaptation to long-term drought stress.}, number={3}, journal={COMPARATIVE AND FUNCTIONAL GENOMICS}, author={Heath, L. S. and Ramakrishnan, N. and Sederoff, R. R. and Whetten, R. W. and Chevone, B. I. and Struble, C. A. and Jouenne, V. Y. and Chen, D. W. and Van Zyl, L. and Grene, R. and et al.}, year={2002}, month={Jun}, pages={226–243} }
 @inbook{whetten_sun_zhang_sederoff_2001, title={Functional genomics and cell wall biosynthesis in loblolly pine}, ISBN={9789401038614 9789401006682}, url={http://dx.doi.org/10.1007/978-94-010-0668-2_16}, DOI={10.1007/978-94-010-0668-2_16}, booktitle={Plant Cell Walls}, publisher={Springer Netherlands}, author={Whetten, Ross and Sun, Ying-Hsuan and Zhang, Yi and Sederoff, Ron}, year={2001}, pages={275–291} }
 @article{whetten_sun_zhang_sederoff_2001, title={Functional genomics and cell wall biosynthesis in loblolly pine}, volume={47}, ISSN={0167-4412}, url={http://dx.doi.org/10.1023/a:1010652003395}, DOI={10.1023/a:1010652003395}, number={1/2}, journal={Plant Molecular Biology}, publisher={Springer Science and Business Media LLC}, author={Whetten, Ross and Sun, Ying-Hsuan and Zhang, Yi and Sederoff, Ron}, year={2001}, month={Sep}, pages={275–291} }
 @article{tang_whetten_sederoff_2001, title={Genotypic control of high-frequency adventitious shoot regeneration via somatic organogenesis in loblolly pine}, volume={161}, ISSN={0168-9452}, url={http://dx.doi.org/10.1016/s0168-9452(01)00394-6}, DOI={10.1016/s0168-9452(01)00394-6}, abstractNote={Mature zygotic embryos of 24 genotypes of loblolly pine (Pinus taeda L.) were used as explants to establish an adventitious shoot regeneration system through somatic organogenesis. Callus formation frequencies of 18.2 (genotype 11-1103) -77.7% (genotype 7-100) have been induced from mature zygotic embryos of all genotypes tested on callus induction medium (basal salts) containing 2,4-dichlorophenoxyacetic acid (2,4-D) or alpha-naphthaleneacetic acid (NAA), 6-benzyladenine (BA), and kinetin. Adventitious shoot regeneration via organogenesis with the frequency of 5.4 (genotype 11-1103 and 7-2) -77.2% (genotype 8-1082) was obtained from callus and tissue cultures derived from mature zygotic embryos of 24 genotypes of loblolly pine. The highest mean number of 18 adventitious buds per piece of callus 0.5x0.5 cm(2) in size was obtained from genotype 8-1082. Elongation of adventitious buds was achieved on TE medium supplemented with 0.5 mg/l indole-3-butyric acid (IBA) and 1 mg/l BA. After rooting, regenerated plantlets were established in soil. These results suggested that adventitious shoot regeneration via somatic organogenesis was influenced by the genotypes. The in vitro regeneration procedure established in this investigation could be used for clonal micropropagation of some genotypes of loblolly pine, as well as for establishing a transformation system in coniferous species.}, number={2}, journal={Plant Science}, publisher={Elsevier BV}, author={Tang, Wei and Whetten, Ross and Sederoff, Ron}, year={2001}, month={Jul}, pages={267–272} }
 @article{myburg_remington_dm o'malley_sederoff_whetten_2001, title={High-throughput AFLP analysis using infrared dye-labeled primers and an automated DNA sequencer}, volume={30}, ISSN={["0736-6205"]}, DOI={10.2144/01302tt04}, abstractNote={ Amplified fragment length polymorphism (AFLP) analysis is currently the most powerful and efficient technique for the generation of large numbers of anonymous DNA markers in plant and animal genomes. We have developed a protocol for high-throughput AFLP analysis that allows up to 70 000 polymorphic marker genotype determinations per week on a single automated DNA sequencer. This throughput is based on multiplexed PCR amplification of AFLP fragments using two different infrared dyelabeled primer combinations. The multiplexed AFLPs are resolved on a two-dye, model 4200 LI-COR® automated DNA sequencer, and the digital images are scored using semi-automated scoring software specifically designed for complex AFLP banding patterns (AFLP-Quantar™). Throughput is enhanced by using high-quality genomic DNA templates obtained by a 96-well DNA isolation procedure. }, number={2}, journal={BIOTECHNIQUES}, author={Myburg, AA and Remington, DL and DM O'Malley and Sederoff, RR and Whetten, RW}, year={2001}, month={Feb}, pages={348-+} }
 @article{sato_wuli_sederoff_whetten_2001, title={Molecular Cloning and Expression of Eight Laccase cDNAs in Loblolly Pine (Pinus taeda)*}, volume={114}, ISSN={0918-9440}, url={http://dx.doi.org/10.1007/pl00013978}, DOI={10.1007/pl00013978}, number={2}, journal={Journal of Plant Research}, publisher={Springer Science and Business Media LLC}, author={Sato, Yasushi and Wuli, Bao and Sederoff, Ronald and Whetten, Ross}, year={2001}, month={Jun}, pages={147–155} }
 @article{tang_sederoff_whetten_2001, title={Regeneration of transgenic loblolly pine (Pinus taeda L.) from zygotic embryos transformed with Agrobacterium tumefaciens}, volume={213}, ISSN={["1432-2048"]}, DOI={10.1007/s004250100566}, abstractNote={Embryos of 24 open-pollinated families of loblolly pine (Pinus teade L.) were used as explants to conduct in vitro regeneration. Then, Agrobacterium tumefaciens strain GV3101 harboring the plasmid pPCV6NFHygGUSINT was used to transform mature zygotic embryos of seven families of loblolly pine. The frequency of transformation varied among families infected with A. tumefaciens. The highest frequency (100%) of transient beta-glucuronidase (GUS)-expressing embryos was obtained from family 11-1029 with over 300 blue spots per embryo. Expression of the GUS reporter gene was observed in cotyledons, hypocotyls, and radicles of co-cultivated mature zygotic embryos, as well as in callus and shoots derived from co-cultivated mature zygotic embryos. Ninety transgenic plants were regenerated from hygromycin-resistant callus derived from families W03. 8-1082 and 11-1029. and 19 transgenic plantlets were established in soil. The presence of the GUS gene in the plant genome was confirmed by polymerase chain reaction. Southern blot, and plant DNA/T-DNA junction analysis. These results suggest that an efficient A. tumefaciens-mediated transformation protocol for stable integration of foreign genes into loblolly pine has been developed and that this transformation system could be useful for future studies on transferring economically important genes to loblolly pine.}, number={6}, journal={PLANTA}, author={Tang, W and Sederoff, R and Whetten, R}, year={2001}, month={Oct}, pages={981–989} }
 @article{remington_whetten_liu_dm o'malley_1999, title={Construction of an AFLP genetic map with nearly complete genome coverage in Pinus taeda}, volume={98}, ISSN={["0040-5752"]}, DOI={10.1007/s001220051194}, abstractNote={De novo construction of complete genetic linkage maps requires large mapping populations, large numbers of genetic markers, and efficient algorithms for ordering markers and evaluating order confidence. We constructed a complete genetic map of an individual loblolly pine (Pinus taeda L.) using amplified fragment length polymorphism (AFLP) markers segregating in haploid megagametophytes and PGRI mapping software. We generated 521 polymorphic fragments from 21 AFLP primer pairs. A total of 508 fragments mapped to 12 linkage groups, which is equal to the Pinus haploid chromosome number. Bootstrap locus order matrices and recombination matrices generated by PGRI were used to select 184 framework markers that could be ordered confidently. Order support was also evaluated using log likelihood criteria in MAPMAKER. Optimal marker orders from PGRI and MAPMAKER were identical, but the implied reliability of orders differed greatly. The framework map provides nearly complete coverage of the genome, estimated at approximately 1700 cM in length using a modified estimator. This map should provide a useful framework for merging existing loblolly pine maps and adding multiallelic markers as they become available. Map coverage with dominant markers in both linkage phases will make the map useful for subsequent quantitative trait locus mapping in families derived by self-pollination.}, number={8}, journal={THEORETICAL AND APPLIED GENETICS}, author={Remington, DL and Whetten, RW and Liu, BH and DM O'Malley}, year={1999}, month={Jun}, pages={1279–1292} }
 @article{wenck_quinn_whetten_pullman_sederoff_1999, title={High-efficiency Agrobacterium-mediated transformation of Norway spruce (Picea abies) and loblolly pine (Pinus taeda)}, volume={39}, DOI={10.1023/a:1006126609534}, abstractNote={Agrobacterium-mediated gene transfer is the method of choice for many plant biotechnology laboratories; however, large-scale use of this organism in conifer transformation has been limited by difficult propagation of explant material, selection efficiencies and low transformation frequency. We have analyzed co-cultivation conditions and different disarmed strains of Agrobacterium to improve transformation. Additional copies of virulence genes were added to three common disarmed strains. These extra virulence genes included either a constitutively active virG or extra copies of virG and virB, both from pTiBo542. In experiments with Norway spruce, we increased transformation efficiencies 1000-fold from initial experiments where little or no transient expression was detected. Over 100 transformed lines expressing the marker gene beta-glucuronidase (GUS) were generated from rapidly dividing embryogenic suspension-cultured cells co-cultivated with Agrobacterium. GUS activity was used to monitor transient expression and to further test lines selected on kanamycin-containing medium. In loblolly pine, transient expression increased 10-fold utilizing modified Agrobacterium strains. Agrobacterium-mediated gene transfer is a useful technique for large-scale generation of transgenic Norway spruce and may prove useful for other conifer species.}, number={3}, journal={Plant Molecular Biology}, author={Wenck, A. R. and Quinn, M. and Whetten, Ross and Pullman, G. and Sederoff, R.}, year={1999}, pages={407–416} }
 @article{marques_araujo_ferreira_whetten_dm o'malley_liu_sederoff_1998, title={AFLP genetic maps of Eucalyptus globulus and E-tereticornis}, volume={96}, ISSN={["1432-2242"]}, DOI={10.1007/s001220050795}, number={6-7}, journal={THEORETICAL AND APPLIED GENETICS}, author={Marques, CM and Araujo, JA and Ferreira, JG and Whetten, R and DM O'Malley and Liu, BH and Sederoff, R}, year={1998}, month={May}, pages={727–737} }
 @article{allona_quinn_shoop_swope_st cyr_carlis_riedl_retzel_campbell_sederoff_et al._1998, title={Analysis of xylem formation in pine by cDNA sequencing}, volume={95}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.95.16.9693}, abstractNote={
            Secondary xylem (wood) formation is likely to involve some genes expressed rarely or not at all in herbaceous plants. Moreover, environmental and developmental stimuli influence secondary xylem differentiation, producing morphological and chemical changes in wood. To increase our understanding of xylem formation, and to provide material for comparative analysis of gymnosperm and angiosperm sequences, ESTs were obtained from immature xylem of loblolly pine (
            Pinus taeda
            L.). A total of 1,097 single-pass sequences were obtained from 5′ ends of cDNAs made from gravistimulated tissue from bent trees. Cluster analysis detected 107 groups of similar sequences, ranging in size from 2 to 20 sequences. A total of 361 sequences fell into these groups, whereas 736 sequences were unique. About 55% of the pine EST sequences show similarity to previously described sequences in public databases. About 10% of the recognized genes encode factors involved in cell wall formation. Sequences similar to cell wall proteins, most known lignin biosynthetic enzymes, and several enzymes of carbohydrate metabolism were found. A number of putative regulatory proteins also are represented. Expression patterns of several of these genes were studied in various tissues and organs of pine. Sequencing novel genes expressed during xylem formation will provide a powerful means of identifying mechanisms controlling this important differentiation pathway.
          }, number={16}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Allona, I and Quinn, M and Shoop, E and Swope, K and St Cyr, S and Carlis, J and Riedl, J and Retzel, E and Campbell, MM and Sederoff, R and et al.}, year={1998}, month={Aug}, pages={9693–9698} }
 @misc{mackay_o'malley_whetten_sederoff_1998, title={Method of altering lignin in trees}, volume={5,824,842}, number={1998 Oct. 20}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={MacKay, J. and O'Malley, D. and Whetten, R. and Sederoff, R.}, year={1998} }
 @misc{whetten_mackay_sederoff_1998, title={Recent advances in understanding lignin biosynthesis}, volume={49}, ISSN={["1040-2519"]}, DOI={10.1146/annurev.arplant.49.1.585}, abstractNote={▪ Abstract  After a long period of little change, the basic concepts of lignin biosynthesis have been challenged by new results from genetic modification of lignin content and composition. New techniques for making directed genetic changes in plants, as well as improvements in the analytical techniques used to determine lignin content and composition in plant cell walls, have been used in experimental tests of the accepted lignin biosynthetic pathway. The lignins obtained from genetically modified plants have shown unexpected properties, and these findings have extended the known range of variation in lignin content and composition. These results argue that the accepted lignin biosynthetic pathway is either incomplete or incorrect, or both; and also suggest that plants may have a high level of metabolic plasticity in the formation of lignins. If this is so, the properties of novel lignins could be of significant scientific and practical interest.}, number={1998}, journal={ANNUAL REVIEW OF PLANT PHYSIOLOGY AND PLANT MOLECULAR BIOLOGY}, author={Whetten, RW and MacKay, JJ and Sederoff, RR}, year={1998}, pages={585–609} }
 @article{ralph_mackay_hatfield_omalley_whetten_sederoff_1997, title={Abnormal lignin in a loblolly pine mutant}, volume={277}, ISSN={["1095-9203"]}, DOI={10.1126/science.277.5323.235}, abstractNote={
            Novel lignin is formed in a mutant loblolly pine (
            Pinus taeda
            L.) severely depleted in cinnamyl alcohol dehydrogenase (E.C. 1.1.1.195), which converts coniferaldehyde to coniferyl alcohol, the primary lignin precursor in pines. Dihydroconiferyl alcohol, a monomer not normally associated with the lignin biosynthetic pathway, is the major component of the mutant's lignin, accounting for ∼30 percent (versus ∼3 percent in normal pine) of the units. The level of aldehydes, including new 2-methoxybenzaldehydes, is also increased. The mutant pines grew normally indicating that, even within a species, extensive variations in lignin composition need not disrupt the essential functions of lignin.
          }, number={5323}, journal={SCIENCE}, author={Ralph, J and MacKay, JJ and Hatfield, RD and OMalley, DM and Whetten, RW and Sederoff, RR}, year={1997}, month={Jul}, pages={235–239} }
 @article{mackay_omalley_presnell_booker_campbell_whetten_sederoff_1997, title={Inheritance, gene expression, and lignin characterization in a mutant pine deficient in cinnamyl alcohol dehydrogenase}, volume={94}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.94.15.8255}, abstractNote={
            We have discovered a mutant loblolly pine (
            Pinus taeda
            L.) in which expression of the gene encoding cinnamyl alcohol dehydrogenase (CAD; EC
            1.1.1.195
            ) is severely reduced. The products of CAD, cinnamyl alcohols, are the precursors of lignin, a major cell wall polymer of plant vascular tissues. Lignin composition in this mutant shows dramatic modifications, including increased incorporation of the substrate of CAD (coniferaldehyde), indicating that CAD may modulate lignin composition in pine. The recessive
            cad-n1
            allele, which causes this phenotype, was discovered in a tree heterozygous for this mutant allele. It is inherited as a simple Mendelian locus that maps to the same genomic region as the
            cad
            locus. In mutant plants, CAD activity and abundance of
            cad
            RNA transcript are low, and free CAD substrate accumulates to a high level. The wood of the mutant is brown, whereas the wood in wild types is nearly white. The wood phenotype resembles that of brown midrib (
            bm
            ) mutants and some transgenic plants in which xylem is red-brown due to a reduction in CAD activity. However, unlike transgenics with reduced CAD, the pine mutant has decreased lignin content. Wood in which the composition of lignin varies beyond previous expectations still provides vascular function and mechanical support.
          }, number={15}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={MacKay, JJ and OMalley, DM and Presnell, T and Booker, FL and Campbell, MM and Whetten, RW and Sederoff, RR}, year={1997}, month={Jul}, pages={8255–8260} }
 @inbook{o'malley_whetten_1997, title={Molecular markers and forest trees}, booktitle={DNA markers: Protocols, applications, and overviews}, publisher={New York: Wiley-VCH}, author={O'Malley, D. M. and Whetten, R.}, editor={G. Caetano-Anolles, P. M. GresshoffEditor}, year={1997}, pages={237–257} }
 @article{voo_whetten_o'malley_sederoff_1995, title={4-Coumarate: Coenzyme A Ligase from Loblolly Pine Xylem: Isolation, Characterization, and Complementary DNA Cloning}, volume={108}, ISSN={["1532-2548"]}, url={http://dx.doi.org/10.1104/pp.108.1.85}, DOI={10.1104/pp.108.1.85}, abstractNote={4-Coumarate:CoA ligase (4CL, EC 6.2.1.12) was purified from differentiating xylem of loblolly pine (Pinus taeda L.). The pine enzyme had an apparent molecular mass of 64 kD and was similar in size and kinetic properties to 4CL isolated from Norway spruce. The pine enzyme used 4-coumaric acid, caffeic acid, ferulic acid, and cinnamic acid as substrates but had no detectable activity using sinapic acid. 4CL was inhibited by naringenin and coniferin, products of phenylpropanoid metabolism. Although the lignin composition in compression wood is higher in p-hydroxyphenyl units than lignin from normal wood, there was no evidence for a different form of 4CL enzyme in differentiating xylem that was forming compression wood. cDNA clones for 4CL were obtained from a xylem expression library. The cDNA sequences matched pine xylem 4CL protein sequences and showed 60 to 66% DNA sequence identity with 4CL sequences from herbaceous angiosperms. There were two classes of cDNA obtained from pine xylem, and the genetic analysis showed that they were products of a single gene.}, number={1}, journal={Plant Physiology}, publisher={American Society of Plant Biologists}, author={Voo, K.S. and Whetten, R.W. and O'Malley, D.M. and Sederoff, R.R.}, year={1995}, pages={85–97} }
 @article{chaparro_werner_whetten_o'malley_1995, title={Characterization of an Unstable Anthocyanin Phenotype and Estimation of Somatic Mutation Rates in Peach}, volume={86}, ISSN={1465-7333 0022-1503}, url={http://dx.doi.org/10.1093/oxfordjournals.jhered.a111560}, DOI={10.1093/oxfordjournals.jhered.a111560}, abstractNote={The peach [Prunus persica (L.) Batsch] cultivar Pillar shows variegation in anthocyanin production in both vegetative and reproductive tissues. This phenotype is heritable, although the degree of variegation differs with genetic background in progency of outcrosses. Genetic evidence supports the hypothesis that the unstable phenotype is caused by an active transposable element. Reversion to wild-type anthocyanin production in Pillar gave rise to mericlinal and periclinal chimeras of pigmented and nonpigmented tissues. Reversion events in LI and Lll histogenic cell layers of Pillar produced different phenotypes that could be easily distinguished. The reversion rate in the LI and LII layers was determined using the rate at which periclinal mutant buds and shoots were formed. The reversion rates to wild type in the LI and Lll histogenic layers ranged from 0 to 10−2, and from 0 to 3.6 × 10−2 mutations per branching event, respectively. In families where reversion rates in the LI and LII histogenic layers could both be measured, the reversion rate in the LI layer was about fourfold greater than in the Lll.}, number={3}, journal={Journal of Heredity}, publisher={Oxford University Press (OUP)}, author={Chaparro, J. X. and Werner, D. J. and Whetten, R. W. and O'Malley, D. M.}, year={1995}, month={May}, pages={186–193} }
 @article{mackay_liu_whetten_sederoff_o'malley_1995, title={Genetic analysis of cinnamyl alcohol dehydrogenase in loblolly pine: single gene inheritance, molecular characterization and evolution}, volume={247}, ISSN={0026-8925 1617-4623}, url={http://dx.doi.org/10.1007/bf00290344}, DOI={10.1007/bf00290344}, abstractNote={The gene encoding the monolignol biosynthetic enzyme cinnamyl alcohol dehydrogenase (CAD, E.C. 1.1.1.195) can be expressed in response to different developmental and environmental cues. Control of Cad gene expression could involve either differential regulation of more than one Cad gene or, alternatively combinatorial regulation of a single Cad gene. In loblolly pine (Pinus taeda L.), we found several electrophoretic variants (allozymes) of CAD and a high level of heterozygosity (he = 0.46). Analysis of inheritance patterns of pine CAD allozymes gave segregation ratios that were consistent with Mendelian expectations for a single functional gene. The identity of the full-length Cad cDNA sequence was confirmed by alignment with peptide sequences obtained from purified active enzyme and by extensive similarity to Cad sequences from other species. Southern blot analysis of genomic DNA using the Cad cDNA as a hybridization probe gave simple patterns, consistent with our interpretation that pine Cad is a single-copy gene. Phylogenetic analysis and evolution rate estimates showed that Cad sequences are diverging less rapidly in the gymnosperms than in the angiosperms. The Cad mRNA was present in both lignifying tissues and a non lignifying tissue (the megagametophyte) of pine. The presence of a single gene suggests that different regulatory mechanisms for a single Cad gene, rather than differential regulation of several genes, can account for its expression in response to different cues.}, number={5}, journal={MGG Molecular & General Genetics}, publisher={Springer Nature}, author={MacKay, John J. and Liu, Weiwei and Whetten, Ross and Sederoff, Ronald R. and O'Malley, David M.}, year={1995}, pages={537–545} }
 @article{chaparro_werner_whetten_o'malley_1995, title={Inheritance, Genetic Interaction, and Biochemical Characterization of Anthocyanin Phenotypes in Peach}, volume={86}, ISSN={1465-7333 0022-1503}, url={http://dx.doi.org/10.1093/oxfordjournals.jhered.a111522}, DOI={10.1093/oxfordjournals.jhered.a111522}, abstractNote={Journal Article Inheritance, Genetic Interaction, and Biochemical Characterization of Anthocyanin Phenotypes in Peach Get access J. X. Chaparro, J. X. Chaparro Department of Horticultural Science, North Carolina State UniversityBox 7609, Raleigh, NC 27695-7609 Search for other works by this author on: Oxford Academic PubMed Google Scholar D. J. Werner, D. J. Werner Department of Horticultural Science, North Carolina State UniversityBox 7609, Raleigh, NC 27695-7609 Search for other works by this author on: Oxford Academic PubMed Google Scholar R. W. Whetten, R. W. Whetten Department of Forestry, North Carolina State UniversityRaleigh Search for other works by this author on: Oxford Academic PubMed Google Scholar D. M. O'Malley D. M. O'Malley Department of Forestry, North Carolina State UniversityRaleigh Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Heredity, Volume 86, Issue 1, January 1995, Pages 32–38, https://doi.org/10.1093/oxfordjournals.jhered.a111522 Published: 01 January 1995 Article history Received: 04 January 1994 Accepted: 13 June 1994 Published: 01 January 1995}, number={1}, journal={Journal of Heredity}, publisher={Oxford University Press (OUP)}, author={Chaparro, J. X. and Werner, D. J. and Whetten, R. W. and O'Malley, D. M.}, year={1995}, month={Jan}, pages={32–38} }
 @misc{whetten_sederoff_1995, title={LIGNIN BIOSYNTHESIS}, volume={7}, ISSN={["1532-298X"]}, DOI={10.2307/3870053}, number={7}, journal={PLANT CELL}, author={WHETTEN, R and SEDEROFF, R}, year={1995}, month={Jul}, pages={1001–1013} }
 @article{bao_o'malley_whetten_sederoff_1993, title={A Laccase Associated with Lignification in Loblolly Pine Xylem}, volume={260}, ISSN={0036-8075 1095-9203}, url={http://dx.doi.org/10.1126/science.260.5108.672}, DOI={10.1126/science.260.5108.672}, abstractNote={Peroxidase has been thought to be the only enzyme that oxidizes monolignol precursors to initiate lignin formation in plants. A laccase was purified from cell walls of differentiating xylem of loblolly pine and shown to coincide in time and place with lignin formation and to oxidize monolignols to dehydrogenation products in vitro. These results suggest that laccase participates in lignin biosynthesis and therefore could be an important target for genetic engineering to modify wood properties or to improve the digestibility of forage crops.}, number={5108}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Bao, W. and O'Malley, D. M. and Whetten, R. and Sederoff, R. R.}, year={1993}, month={Apr}, pages={672–674} }
 @article{o'malley_whetten_bao_chen_sederoff_1993, title={The role of laccase in lignification}, volume={4}, ISSN={0960-7412 1365-313X}, url={http://dx.doi.org/10.1046/j.1365-313x.1993.04050751.x}, DOI={10.1046/j.1365-313x.1993.04050751.x}, abstractNote={The enzymatic mechanism of monolignol polymerization in lignin biosynthesis is not known, although it has been the subject of significant interest for more than 60 years. Peroxidase had been considered to be the exclusive plant enzyme involved in the oxidative polymerization of lignin precursors. Recently, laccase and laccase‐like oxidase activities have been associated with lignification. Laccase is bound to lignifying plant cell walls and can polymerize lignin precursors in vitro. Strong circumstantial evidence from different species implicates this enzyme in the polymerization of lignin precursors. Lignin has a complex structure and it has been difficult to analyze the heterogeneity of lignin by chemical and physical techniques. If lignin precursors are polymerized by enzymes that differ in their catalytic properties, then lignin heterogeneity could be produced by differential expression of multiple enzymes during plant development. When laccase genes are correctly identified, these ideas can be tested in genetic experiments where gain or loss of function can be predicted by the presence or absence of the functional gene.}, number={5}, journal={The Plant Journal}, publisher={Wiley}, author={O'Malley, David M. and Whetten, Ross and Bao, Wuli and Chen, Chen-Loung and Sederoff, Ronald R.}, year={1993}, month={Nov}, pages={751–757} }
 @article{whetten_sederoff_1992, title={PHENYLALANINE AMMONIA-LYASE FROM LOBLOLLY-PINE - PURIFICATION OF THE ENZYME AND ISOLATION OF COMPLEMENTARY-DNA CLONES}, volume={98}, ISSN={["0032-0889"]}, DOI={10.1104/pp.98.1.380}, abstractNote={Phenylalanine ammonia-lyase (EC 4.3.1.5) has been purified from differentiating secondary xylem of loblolly pine (Pinus taeda L.). Native molecular weight of the enzyme was estimated to be 280,000, with a subunit molecular weight of 74,000; isoelectric point, 5.8; and Michaelis constant for i-phenylalanine, 27 micromolar. No evidence was obtained for the existence of isoforms of the enzyme, nor for negative cooperativity of substrate binding. Polyclonal antibodies were raised against the phenylalanine ammonia-lyase subunit and used to identify a pal clone in an expression library of xylem complementary DNA (cDNA). Polymerase chain reaction, using oligonucleotide primers made from N-terminal amino acid sequence and from the 5' end of the clone isolated from the expression library, was also used to isolate cDNA clones. These methods yielded cDNA clones covering the protein coding region of the pal messenger RNA. Comparisons of nucleotide sequence of pal cDNAs from pine, bean, sweet potato, and rice showed 60 to 62% identity between the pine clone and the angiosperm clones.}, number={1}, journal={PLANT PHYSIOLOGY}, author={WHETTEN, RW and SEDEROFF, RR}, year={1992}, month={Jan}, pages={380–386} }
 @article{whetten_sederoff_1991, title={Genetic engineering of wood}, volume={43}, ISSN={0378-1127}, url={http://dx.doi.org/10.1016/0378-1127(91)90133-g}, DOI={10.1016/0378-1127(91)90133-g}, abstractNote={The technology of genetic engineering provides an opportunity to accelerate tree improvement and to make directed modifications in the physical and chemical properties of wood. Modifications that lead to more efficient pulping of wood for paper may be among the earliest applications because of the information available on the pathway for lignin bisosynthesis. Other potential areas of application include fiber morphology, wood density, extractive content, biomass-utilization efficiency and dimensional stability. Widespread application of this technology awaits two developments: better methods of gene transfer, and a fundamental understanding of the development process of wood formation. If it can be successfully applied, genetic engineering will help to meet the projected demand for wood and paper products in the next century.}, number={3-4}, journal={Forest Ecology and Management}, publisher={Elsevier BV}, author={Whetten, Ross and Sederoff, Ronald}, year={1991}, month={Oct}, pages={301–316} }
 @article{whetten_organ_krasney_cox-foster_cavener_1988, title={Molecular structure and transformation of the glucose dehydrogenase gene in Drosophila melanogaster}, volume={120}, number={2}, journal={Genetics}, author={Whetten, R. and Organ, E. and Krasney, P. and Cox-Foster, D. and Cavener, D.}, year={1988}, pages={475–484} }
 @article{cavener_corbett_cox_whetten_1986, title={Isolation of the eclosion gene cluster and the developmental expression of the Gld gene in Drosophila melanogaster.}, volume={5}, ISSN={0261-4189}, url={http://dx.doi.org/10.1002/j.1460-2075.1986.tb04590.x}, DOI={10.1002/j.1460-2075.1986.tb04590.x}, abstractNote={During the development of Drosophila melanogaster the expression of glucose dehydrogenase (GLD) changes from non sex‐limited to male limited. We have isolated the Gld gene and three other functionally related genes in the eclosion gene cluster by the method of chromosome walking. The Gld gene has been identified by two deletions and a translocation which genetically define the gene. A 2.8‐kb RNA has been identified as the putative GLD mRNA. The temporal and spatial expression of this RNA is correlated with the expression of the GLD enzyme and levels of the steroid hormone ecdysterone. Using single‐strand antisense probes we have detected three RNA species. However these three transcripts are not derived from the Gld locus. One of these RNAs is weakly detected by the multiple cloning site of the pSP65 vector. The level of detection of this latter RNA is greatly increased by the insertion of a specific Gld gene fragment in the pSP65 vector.}, number={11}, journal={The EMBO Journal}, publisher={Wiley}, author={Cavener, D. and Corbett, G. and Cox, D. and Whetten, R.}, year={1986}, month={Nov}, pages={2939–2948} }