@article{martins_yuliarto_yong_melia_maretha_sharma_lakey_ordway_acosta_hodge_2024, title={Estimation of Additive and Dominance Effects in an Acacia crassicarpa Multi-Environment Progeny Trial Using Genomic Pedigree Reconstruction}, volume={2}, ISSN={["1938-3738"]}, DOI={10.1093/forsci/fxae004}, abstractNote={Abstract}, journal={FOREST SCIENCE}, author={Martins, Gustavo S. and Yuliarto, Muhammad and Yong, Wong Ching and Melia, Tisha and Maretha, Maggie V and Sharma, Mukesh and Lakey, Nathan and Ordway, Jared and Acosta, Juan Jose and Hodge, Gary}, year={2024}, month={Feb} }
 @article{castillo_acosta_hodge_vann_lewis_2023, title={Analysis of alkaloids and reducing sugars in processed and unprocessed tobacco leaves using a handheld near infrared spectrometer}, volume={1}, ISSN={["1751-6552"]}, DOI={10.1177/09670335221148594}, abstractNote={ Near infrared (NIR) spectroscopy calibration models were developed to predict chemical properties of flue-cured tobacco ( Nicotiana tabacum L.) leaf samples using a microPHAZIRTM handheld NIR spectrometer. The sample data set consisted of 348 leaf-bundled samples of upper-stalk flue-cured tobacco leaves collected from an array of cultivars evaluated in multiple locations. Unprocessed leaf samples were intact whole unground leaves collected from curing barns. Processed leaf samples were further dried and ground before scanning. The NIR prediction models for percent reducing sugars, percent total alkaloids, and percent nicotine were very good for processed leaves [r2 (SEP in %) values = 0.98 (0.82), 0.92 (0.17), and 0.92 (0.14), respectively]. The models for the same three variables for unprocessed leaves were also very good, with only slightly lower fit statistics [r2 (SEP) = 0.93 (1.58), 0.87 (0.22), and 0.88 (0.18), respectively). Fit statistics for anabasine NIR models were intermediate with r2 (SEP in %) values ranging from 0.73 (0.003) to 0.76 (0.003), while the lowest fit statistics were observed for anatabine and norticotine with r2 (SEP in %) ranging from 0.49 (0.005) to 0.55 (0.017), respectively, for both unprocessed and processed leaves. Hence, use of a handheld NIR spectrometer would be of more limited value for these variables. The chemical composition of flue-cured tobacco leaf samples for some chemical traits can be directly assessed at the point when the leaves exit the curing barns, thus minimizing the need to dry and grind samples for colorimetric and chromatographic analyses. }, journal={JOURNAL OF NEAR INFRARED SPECTROSCOPY}, author={Castillo, Miguel S. and Acosta, Juan J. and Hodge, Gary R. and Vann, Matthew C. and Lewis, Ramsey S.}, year={2023}, month={Jan} }
 @article{ibarra_hodge_acosta_2023, title={Quantitative Genetics of a Hybrid Population of Eucalyptus nitens x Eucalyptus globulus: Estimation of Genetic Parameters and Implications for Breeding Strategies}, volume={14}, ISSN={["1999-4907"]}, url={https://doi.org/10.3390/f14020381}, DOI={10.3390/f14020381}, abstractNote={In Chile, interspecific hybrids between Eucalyptus nitens × Eucalyptus globulus (GloNi) were developed by Arauco Forestry to capture specific traits from each parental species: growth rate and cold resistance from E. nitens (NIT) and wood properties from E. globulus (GLO). Field tests of E. nitens × E. globulus were distributed in two geographic zones: Arauco (12 tests) and Valdivia (15 tests), where growth and wood properties measurements were recorded at different ages. The hybrid population is composed of clones from 28 full-sib families, being the result of crossing 12 E. nitens females and 8 E. globulus males. Progeny from each of these families were vegetatively propagated and tested on each growth zone, with a total of 1214 clones developed. The quantitative genetic parameter estimates reveal high genetic variation in hybrid volume gain and wood properties, which make possible large genetic gain in all traits analyzed. Additionally, E. nitens has a considerable impact on the volume gain of the hybrid, making it important to test more parents in future interspecific crosses in both hybrid zones. In contrast, E. globulus demonstrated zero impact in volume. In wood traits, E. globulus in Arauco zone demonstrates a large effect on the genetic variability of these traits; meanwhile, in the Valdivia zone, E. nitens and E. globulus parents contributed roughly similar amounts of genetic variation. The high General Hybridizing Ability (GHA) and General Combining Ability (GCA) relationship between hybrid progeny and pure species progeny performance indicates that parents could be selected for interspecific crosses based on pure species test results for volume and wood properties.}, number={2}, journal={FORESTS}, author={Ibarra, Luis and Hodge, Gary and Acosta, Juan Jose}, year={2023}, month={Feb} }
 @article{mostert-o'neill_tate_reynolds_mphahlele_berg_verryn_acosta_borevitz_myburg_2022, title={Genomic consequences of artificial selection during early domestication of a wood fibre crop}, volume={7}, ISSN={["1469-8137"]}, url={https://doi.org/10.1111/nph.18297}, DOI={10.1111/nph.18297}, abstractNote={Summary}, journal={NEW PHYTOLOGIST}, author={Mostert-O'Neill, Marja M. and Tate, Hannah and Reynolds, S. Melissa and Mphahlele, Makobatjatji M. and Berg, Gert and Verryn, Steve D. and Acosta, Juan J. and Borevitz, Justin O. and Myburg, Alexander A.}, year={2022}, month={Jul} }
 @article{perek_hodge_tambarussi_biernaski_acosta_2022, title={Predicted genetic gains for growth traits and wood resistance in Pinus maximinoi and Pinus tecunumanii}, volume={22}, ISSN={["1984-7033"]}, url={https://doi.org/10.1590/1984-70332022v22n2a23}, DOI={10.1590/1984-70332022v22n2a23}, abstractNote={Tree breeders use traits of economic interest as productivity, stem form and wood quality, to select individuals for advanced generations. We determined the genetic control of growth volume, tree height and diameter, stem form and wood resistance, and calculated a selection index for Pinus maximinoi and P. tecunumanii, selected individuals were used to establish a seedling seed orchard (SSO). The largest genetic gain obtained in SSO for P. maximinoi was 21.48% for volume, while for P. tecunumanii it was 21.87% for stem form. There is enough genetic variability for genetic gain in future generations in tests of P. maximinoi and P. tecunumanii progenies. The selection index provided satisfactory total genetic gains for several traits, being more recommended than the BLUP method in order to support the selection and ranking of superior genetic materials in the progeny tests with greater probability of retaining favorable alleles over generations.}, number={2}, journal={CROP BREEDING AND APPLIED BIOTECHNOLOGY}, author={Perek, Matheus and Hodge, Gary and Tambarussi, Evandro Vagner and Biernaski, Fabricio Antonio and Acosta, Juan}, year={2022} }
 @article{rocha_benatti_siqueira_souza_bianchin_souza_miranda fernandes_oda_stape_yassue_et al._2022, title={Quantitative trait loci related to growth and wood quality traits in Eucalyptus grandis W. Hill identified through single- and multi-trait genome-wide association studies}, volume={18}, ISSN={["1614-2950"]}, DOI={10.1007/s11295-022-01570-x}, number={6}, journal={TREE GENETICS & GENOMES}, author={Rocha, Lucas Fernandes and Benatti, Thiago Romanos and Siqueira, Leandro and Souza, Izabel Christina and Bianchin, Isadora and Souza, Aguinaldo Jose and Miranda Fernandes, Aline Cristina and Oda, Shinitiro and Stape, Jose Luiz and Yassue, Rafael Massahiro and et al.}, year={2022}, month={Dec} }
 @article{kropat_laleicke_acosta_2022, title={Towards Inline Prediction of Color Development for Wood Stained with Chemical Stains Using Near-Infrared Spectroscopy}, volume={72}, ISSN={["0015-7473"]}, DOI={10.13073/FPJ-D-22-00021}, abstractNote={Abstract}, number={2}, journal={FOREST PRODUCTS JOURNAL}, author={Kropat, Marcel and Laleicke, Paul Frederik and Acosta, Juan Jose}, year={2022}, pages={130–139} }
 @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} }
 @article{mostert-o'neill_reynolds_acosta_lee_borevitz_myburg_2021, title={Genomic evidence of introgression and adaptation in a model subtropical tree species,Eucalyptus grandis}, volume={30}, ISSN={["1365-294X"]}, url={http://dx.doi.org/10.1111/mec.15615}, DOI={10.1111/mec.15615}, abstractNote={Abstract}, number={3}, journal={MOLECULAR ECOLOGY}, publisher={Wiley}, author={Mostert-O'Neill, Marja Mirjam and Reynolds, Sharon Melissa and Acosta, Juan Jose and Lee, David John and Borevitz, Justin O. and Myburg, Alexander Andrew}, year={2021}, month={Feb}, pages={625–638} }
 @article{lu_payn_pandey_acosta_heine_walker_young_2021, title={HYPERSPECTRAL IMAGING WITH COST-SENSITIVE LEARNING FOR HIGH-THROUGHPUT SCREENING OF LOBLOLLY PINE (PINUS TAEDA L.) SEEDLINGS FOR FREEZE TOLERANCE}, volume={64}, ISSN={["2151-0040"]}, url={http://dx.doi.org/10.13031/trans.14708}, DOI={10.13031/trans.14708}, abstractNote={Highlights}, number={6}, journal={TRANSACTIONS OF THE ASABE}, publisher={American Society of Agricultural and Biological Engineers (ASABE)}, author={Lu, Yuzhen and Payn, Kitt G. and Pandey, Piyush and Acosta, Juan J. and Heine, Austin J. and Walker, Trevor D. and Young, Sierra}, year={2021}, pages={2045–2059} }
 @article{pandey_payn_lu_heine_walker_acosta_young_2021, title={Hyperspectral Imaging Combined with Machine Learning for the Detection of Fusiform Rust Disease Incidence in Loblolly Pine Seedlings}, volume={13}, ISSN={["2072-4292"]}, url={https://doi.org/10.3390/rs13183595}, DOI={10.3390/rs13183595}, abstractNote={Loblolly pine is an economically important timber species in the United States, with almost 1 billion seedlings produced annually. The most significant disease affecting this species is fusiform rust, caused by Cronartium quercuum f. sp. fusiforme. Testing for disease resistance in the greenhouse involves artificial inoculation of seedlings followed by visual inspection for disease incidence. An automated, high-throughput phenotyping method could improve both the efficiency and accuracy of the disease screening process. This study investigates the use of hyperspectral imaging for the detection of diseased seedlings. A nursery trial comprising families with known in-field rust resistance data was conducted, and the seedlings were artificially inoculated with fungal spores. Hyperspectral images in the visible and near-infrared region (400–1000 nm) were collected six months after inoculation. The disease incidence was scored with traditional methods based on the presence or absence of visible stem galls. The seedlings were segmented from the background by thresholding normalized difference vegetation index (NDVI) images, and the delineation of individual seedlings was achieved through object detection using the Faster RCNN model. Plant parts were subsequently segmented using the DeepLabv3+ model. The trained DeepLabv3+ model for semantic segmentation achieved a pixel accuracy of 0.76 and a mean Intersection over Union (mIoU) of 0.62. Crown pixels were segmented using geometric features. Support vector machine discrimination models were built for classifying the plants into diseased and non-diseased classes based on spectral data, and balanced accuracy values were calculated for the comparison of model performance. Averaged spectra from the whole plant (balanced accuracy = 61%), the crown (61%), the top half of the stem (77%), and the bottom half of the stem (62%) were used. A classification model built using the spectral data from the top half of the stem was found to be the most accurate, and resulted in an area under the receiver operating characteristic curve (AUC) of 0.83.}, number={18}, journal={REMOTE SENSING}, publisher={MDPI AG}, author={Pandey, Piyush and Payn, Kitt G. and Lu, Yuzhen and Heine, Austin J. and Walker, Trevor D. and Acosta, Juan J. and Young, Sierra}, year={2021}, month={Sep} }
 @article{nel_acosta_hodge_2021, title={Initial growth results comparing first generation F1 and advanced-generation F2 Pinus patula x Pinus tecunumanii interspecific hybrid families}, volume={9}, ISSN={["2070-2639"]}, url={https://doi.org/10.2989/20702620.2021.1926370}, DOI={10.2989/20702620.2021.1926370}, abstractNote={The hybrid between Pinus patula and P. tecunumanii low elevation (PPTL) and high elevation (PPTH) sources was developed in the 1990s in South Africa and commercialised during the 2000s in response to high post-establishment mortality of P. patula caused by Fusarium circinatum. The growth and wood properties for these hybrids are also superior to the parental species. This study describes an experiment where F1 hybrid families and F2 advanced hybrid families of the Pinus patula × P. tecunumanii low elevation hybrid were compared in a progeny field experiment. Seed yield and early growth at three years is reported. The early results from this study indicate that there were no significant differences in growth between the F1 and F2 PPTL hybrid and both the F1 and F2 hybrid outperformed the pure P. patula control. These early results should be monitored further to determine if this trend continues. The F2 hybrid offers the opportunity to obtain tolerance of F. circinatum and better growth than P. patula at a much lower cost than that of deployment of the F1 PPTL hybrid.}, journal={SOUTHERN FORESTS-A JOURNAL OF FOREST SCIENCE}, publisher={National Inquiry Services Center (NISC)}, author={Nel, Andre and Acosta, Juan J. and Hodge, Gary R.}, year={2021}, month={Sep} }
 @article{lu_walker_acosta_young_pandey_heine_payn_2021, title={Prediction of Freeze Damage and Minimum Winter Temperature of the Seed Source of Loblolly Pine Seedlings Using Hyperspectral Imaging}, volume={67}, ISSN={["1938-3738"]}, url={https://doi.org/10.1093/forsci/fxab003}, DOI={10.1093/forsci/fxab003}, abstractNote={Abstract}, number={3}, journal={FOREST SCIENCE}, publisher={Oxford University Press (OUP)}, author={Lu, Yuzhen and Walker, Trevor D. and Acosta, Juan J. and Young, Sierra and Pandey, Piyush and Heine, Austin J. and Payn, Kitt G.}, year={2021}, month={Jun}, pages={321–334} }
 @article{whittier_hodge_lopez_saravitz_acosta_2021, title={The use of near infrared spectroscopy to predict foliar nutrient levels of hydroponically grown teak seedlings}, volume={7}, ISSN={["1751-6552"]}, DOI={10.1177/09670335211025649}, abstractNote={ Due to a combination of durability, strength, and aesthetically pleasing color, teak ( Tectona grandis L.f.) is globally regarded as a premier timber species. High value, in combination with comprehensive harvesting restrictions from natural populations, has resulted in extensive teak plantation establishment throughout the tropics and subtropics. Plantations directly depend on the production of healthy seedlings. In order to assist growers in efficiently diagnosing teak seedling nutrient issues, a hydroponic nutrient study was conducted at North Carolina State University. The ability to accurately diagnose nutrient disorders prior to the onset of visual symptoms through the use of near infrared (NIR) technology will allow growers to potentially remedy seedling issues before irreversible damage is done. This research utilized two different near infrared (NIR) spectrometers to develop predictive foliar nutrient models for 13 nutrients and then compared the accuracy of the models between the devices. Destructive leaf sampling and laboratory grade NIR spectroscopy scanning was compared to nondestructive sampling coupled with a handheld NIR device used in a greenhouse. Using traditional wet lab foliar analysis results for calibration, nutrient prediction models for nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), sulfur (S), copper (Cu), molybdenum (Mo), magnesium (Mg), boron (B), calcium (Ca), manganese (Mn), iron (Fe), sodium (Na), and zinc (Z) were developed using both NIR devices. Models developed using both techniques were good for N, P, and K (R2 > 0.80), while the B model was adequate only with the destructive sampling procedure. Models for the remaining nutrients were not suitable. Although destructive sampling and desktop scanning procedure generally produced models with higher correlations they required work and time for sample preparation that might reduce the value of this NIR approach. The results suggest that both destructive and nondestructive sampling NIR calibrations can be useful to monitor macro nutrient status of teak plants grown in a nursery environment. }, journal={JOURNAL OF NEAR INFRARED SPECTROSCOPY}, author={Whittier, William Andrew and Hodge, Gary R. and Lopez, Juan and Saravitz, Carole and Acosta, Juan Jose}, year={2021}, month={Jul} }
 @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{hodge_acosta_2020, title={An Algorithm for Genetic Analysis of Full-Sib Datasets with Mixed-Model Software Lacking a Numerator Relationship Matrix Function, and a Comparison with Results from a Dedicated Genetic Software Package}, volume={11}, url={https://doi.org/10.3390/f11111169}, DOI={10.3390/f11111169}, abstractNote={Research Highlights: An algorithm is presented that allows for the analysis of full-sib genetic datasets using generalized mixed-model software programs. The algorithm produces variance component estimates, genetic parameter estimates, and Best Linear Unbiased Prediction (BLUP) solutions for genetic values that are, for all practical purposes, identical to those produced by dedicated genetic software packages. Background and Objectives: The objective of this manuscript is to demonstrate an approach with a simulated full-sib dataset representing a typical forest tree breeding population (40 parents, 80 full-sib crosses, 4 tests, and 6000 trees) using two widely available mixed-model packages. Materials and Methods: The algorithm involves artificially doubling the dataset, so that each observation is in the dataset twice, once with the original female and male parent identification, and once with the female and male parent identities switched. Five linear models were examined: two models using a dedicated genetic software program (ASREML) with the capacity to specify A or other pedigree-related functions, and three models with the doubled dataset and a parent (or sire) linear model (ASREML, SAS Proc Mixed, and R lme4). Results: The variance components, genetic parameters, and BLUPs of the parental breeding values, progeny breeding values, and full-sib family-specific combining abilities were compared. Genetic parameter estimates were essentially the same across all the analyses (e.g., the heritability ranged from h2 = 0.220 to 0.223, and the proportion of dominance variance ranged from d2 = 0.057 to 0.058). The correlations between the BLUPs from the baseline analysis (ASREML with an individual tree model) and the doubled-dataset/parent models using SAS Proc Mixed or R lme4 were never lower than R = 0.99997. Conclusions: The algorithm can be useful for analysts who need to analyze full-sib genetic datasets and who are familiar with general-purpose statistical packages, but less familiar with or lacking access to other software.}, number={11}, journal={Forests}, publisher={MDPI AG}, author={Hodge, Gary R. and Acosta, Juan Jose}, year={2020}, month={Nov}, pages={1169} }
 @article{acosta_castillo_hodge_2020, title={Comparison of benchtop and handheld near-infrared spectroscopy devices to determine forage nutritive value}, volume={60}, ISSN={["1435-0653"]}, url={http://dx.doi.org/10.1002/csc2.20264}, DOI={10.1002/csc2.20264}, abstractNote={Abstract}, number={6}, journal={CROP SCIENCE}, publisher={Wiley}, author={Acosta, J. J. and Castillo, M. S. and Hodge, G. R.}, year={2020}, pages={3410–3422} }
 @article{bekewe_castillo_acosta_rivera_2020, title={Defoliation management effects on nutritive value of ‘performer’ switchgrass}, volume={60}, ISSN={0011-183X 1435-0653}, url={http://dx.doi.org/10.1002/csc2.20036}, DOI={10.1002/csc2.20036}, abstractNote={Abstract}, number={3}, journal={Crop Science}, publisher={Wiley}, author={Bekewe, Perejitei E. and Castillo, Miguel S. and Acosta, Juan J. and Rivera, R.}, year={2020}, month={Mar}, pages={1682–1689} }
 @article{tyrmi_vuosku_acosta_li_sterck_cervera_savolainen_pyhäjärvi_2020, title={Genomics of Clinal Local Adaptation in Pinus sylvestris Under Continuous Environmental and Spatial Genetic Setting}, volume={10}, url={https://doi.org/10.1534/g3.120.401285}, DOI={10.1534/g3.120.401285}, abstractNote={Abstract}, number={8}, journal={G3: Genes|Genomes|Genetics}, publisher={Genetics Society of America}, author={Tyrmi, Jaakko S. and Vuosku, Jaana and Acosta, Juan J. and Li, Zhen and Sterck, Lieven and Cervera, Maria T. and Savolainen, Outi and Pyhäjärvi, Tanja}, year={2020}, month={Aug}, pages={2683–2696} }
 @article{martins_yuliarto_antes_sabki_prasetyo_unda_mansfield_hodge_acosta_2020, title={Wood and Pulping Properties Variation of Acacia crassicarpa A.Cunn. ex Benth. and Sampling Strategies for Accurate Phenotyping}, volume={11}, url={https://doi.org/10.3390/f11101043}, DOI={10.3390/f11101043}, abstractNote={Research Highlights: This study provides a comprehensive set of wood and pulping properties of Acacia crassicarpa A.Cunn. ex Benth. to assess variation and efficient sampling strategies for whole-tree level phenotyping. Background and Objectives: A. crassicarpa is an important tree species in Southeast Asia, with limited knowledge about its wood properties. The objective of this study was to characterize important wood properties and pulping performance of improved germplasm of the species. Furthermore, we investigated within-tree patterns of variation and evaluated the efficiency of phenotyping strategies. Materials and Methods: Second-generation progeny trials were studied, where forty 50-month-old trees were selected for destructive sampling and assessed for wood density, kraft pulp yield, α-cellulose, carbohydrate composition, and lignin content and composition (S/G ratio). We estimated the phenotypic correlations among traits determined within-tree longitudinal variation and its importance for whole-tree level phenotyping. Results: The mean whole-tree disc basic density was 481 kg/m3, and the screened kraft pulp yield was 53.8%. The reliabilities of each sampling position to predict whole-tree properties varied with different traits. For basic density, pulp yield, and glucose content, the ground-level sampling could reliably predict the whole-tree property. With near infrared reflectance spectroscopy predictions as an indirect measurement method for disc basic density, we verified reduced reliability values for breast height sampling but sufficiently correlated to allow accurate ranking and efficient selection of genotypes in a breeding program context. Conclusions: We demonstrated the quality of A. crassicarpa as a wood source for the pulping industry. The wood and pulping traits have high levels of phenotypic variation, and standing tree sampling strategies can be performed for both ranking and high-accuracy phenotyping purposes.}, number={10}, journal={Forests}, publisher={MDPI AG}, author={Martins, Gustavo Salgado and Yuliarto, Muhammad and Antes, Rudine and Sabki and Prasetyo, Agung and Unda, Faride and Mansfield, Shawn D. and Hodge, Gary R. and Acosta, Juan Jose}, year={2020}, month={Sep}, pages={1043} }
 @article{acosta_fahrenkrog_neves_resende_dervinis_davis_holliday_kirst_2019, title={Exome Resequencing Reveals Evolutionary History, Genomic Diversity, and Targets of Selection in the Conifers Pinus taeda and Pinus elliottii}, volume={11}, ISSN={1759-6653}, url={http://dx.doi.org/10.1093/gbe/evz016}, DOI={10.1093/gbe/evz016}, abstractNote={Abstract Loblolly pine (Pinus taeda) and slash pine (Pinus elliottii) are ecologically and economically important pine species that dominate many forest ecosystems in the southern United States, but like all conifers, the study of their genetic diversity and demographic history has been hampered by their large genome size. A small number of studies mainly based on candidate-gene sequencing have been reported for P. taeda to date, whereas none are available for P. elliottii. Targeted exome resequencing has recently enabled population genomics studies for conifers, approach used here to assess genomic diversity, signatures of selection, population structure, and demographic history of P. elliottii and P. taeda. Extensive similarities were revealed between these species: both species feature rapid linkage disequilibrium decay and high levels of genetic diversity. Moreover, genome-wide positive correlations for measures of genetic diversity between the species were also observed, likely due to shared structural genomic constraints. Also, positive selection appears to be targeting a common set of genes in both pines. Demographic history differs between both species, with only P. taeda being affected by a dramatic bottleneck during the last glacial period. The ability of P. taeda to recover from a dramatic reduction in population size while still retaining high levels of genetic diversity shows promise for other pines facing environmental stressors associated with climate change, indicating that these too may be able to adapt successfully to new future conditions even after a drastic population size contraction.}, number={2}, journal={Genome Biology and Evolution}, publisher={Oxford University Press (OUP)}, author={Acosta, Juan J and Fahrenkrog, Annette M and Neves, Leandro G and Resende, Márcio F R and Dervinis, Christopher and Davis, John M and Holliday, Jason A and Kirst, Matias}, editor={Pritham, EllenEditor}, year={2019}, month={Jan}, pages={508–520} }
 @article{de moraes_dos santos_de lima_aguiar_missiaggia_da costa dias_rezende_gonçalves_acosta_kirst_et al._2018, title={Genomic selection prediction models comparing sequence capture and SNP array genotyping methods}, volume={38}, ISSN={1380-3743 1572-9788}, url={http://dx.doi.org/10.1007/s11032-018-0865-3}, DOI={10.1007/s11032-018-0865-3}, number={9}, journal={Molecular Breeding}, publisher={Springer Science and Business Media LLC}, author={de Moraes, Bráulio Fabiano Xavier and dos Santos, Rodrigo Furtado and de Lima, Bruno Marco and Aguiar, Aurélio Mendes and Missiaggia, Alexandre Alves and da Costa Dias, Donizete and Rezende, Gabriel Dehon Peçanha Sampaio and Gonçalves, Flávia Maria Avelar and Acosta, Juan J. and Kirst, Matias and et al.}, year={2018}, month={Sep} }
 @article{hodge_acosta_unda_woodbridge_mansfield_2018, title={Global near infrared spectroscopy models to predict wood chemical properties of Eucalyptus}, volume={26}, ISSN={0967-0335 1751-6552}, url={http://dx.doi.org/10.1177/0967033518770211}, DOI={10.1177/0967033518770211}, abstractNote={ Global near infrared spectroscopy models (multiple-species, multiple-sites) were developed to predict chemical properties of Eucalyptus wood. The sample data set included 186 samples from four data sets (five species) originating from six countries: Eucalyptus urophylla from Argentina, Colombia, Venezuela, and South Africa; Eucalyptus dunnii from Uruguay; Eucalyptus globulus and Eucalyptus nitens from Chile; and Eucalyptus grandis from Colombia. The 186 samples were all preselected from larger collections of 400 to nearly 1800 samples to represent the range of chemical and spectral variation in each data set. The chemical traits modeled were total lignin, insoluble lignin, soluble lignin, syringyl–guaiacyl ratio (S/G), glucose, xylose, galactose, arabinose, and mannose. Single-species models and global multiple-species models were developed for each chemical constituent. For the global model, the R2cv for total lignin, insoluble lignin and syringyl–guaiacyl ratio were 0.95, 0.96, and 0.86, respectively. An alternate expression of the syringyl–guaiacyl relationship (S/(S+G)) resulted in better near infrared calibrations (e.g., for the global model, R2cv = 0.95). The global models for sugar content were also very good, but were slightly inferior to those for the lignin related traits, with R2cv = 0.74 for glucose, 0.89 for xylose, and from 0.72 to 0.91 for the minor sugars. To investigate the utility of the global models to predict chemical traits for species not included in the calibration, three-species calibrations were used to predict each trait in a fourth species data set. The prediction fit statistics ranged from excellent to poor depending on the species and trait, but in general the predictions would be at least moderately useful for most species-trait combinations. For some species-trait combinations with poor initial predictions from the global model, the inclusion of 10 samples from the “new” species into the calibration global model improved the fit statistics substantially. The global calibrations will be useful in tree breeding programs to rank species, families, and clones for important wood chemical traits. }, number={2}, journal={Journal of Near Infrared Spectroscopy}, publisher={SAGE Publications}, author={Hodge, Gary R and Acosta, Juan Jose and Unda, Faride and Woodbridge, William C and Mansfield, Shawn D}, year={2018}, month={Apr}, pages={117–132} }
 @article{naidoo_christie_acosta_mphahlele_payn_myburg_külheim_2018, title={Terpenes associated with resistance against the gall wasp, Leptocybe invasa, in Eucalyptus grandis}, volume={41}, ISSN={0140-7791}, url={http://dx.doi.org/10.1111/pce.13323}, DOI={10.1111/pce.13323}, abstractNote={Abstract}, number={8}, journal={Plant, Cell & Environment}, publisher={Wiley}, author={Naidoo, Sanushka and Christie, Nanette and Acosta, Juan J. and Mphahlele, Makobatjatji M. and Payn, Kitt G. and Myburg, Alexander A. and Külheim, Carsten}, year={2018}, month={Jun}, pages={1840–1851} }
 @article{albert_barbazuk_depamphilis_der_leebens-mack_ma_palmer_rounsley_sankoff_schuster_et al._2013, title={The Amborella Genome and the Evolution of Flowering Plants}, volume={342}, ISSN={["1095-9203"]}, url={http://science.sciencemag.org/content/342/6165/1241089.long}, DOI={10.1126/science.1241089}, abstractNote={Shaping Plant Evolution}, number={6165}, journal={Science}, author={Albert, Victor A. and Barbazuk, W. Bradley and dePamphilis, Claude W. and Der, Joshua P. and Leebens-Mack, James and Ma, Hong and Palmer, Jeffrey D. and Rounsley, Steve and Sankoff, David and Schuster, Stephan C. and et al.}, year={2013}, month={Dec}, pages={1456–1457} }
 @article{resende_muñoz_acosta_peter_davis_grattapaglia_resende_kirst_2011, title={Accelerating the domestication of trees using genomic selection: accuracy of prediction models across ages and environments}, volume={193}, ISSN={0028-646X}, url={http://dx.doi.org/10.1111/j.1469-8137.2011.03895.x}, DOI={10.1111/j.1469-8137.2011.03895.x}, abstractNote={• Genomic selection is increasingly considered vital to accelerate genetic improvement. However, it is unknown how accurate genomic selection prediction models remain when used across environments and ages. This knowledge is critical for breeders to apply this strategy in genetic improvement. • Here, we evaluated the utility of genomic selection in a Pinus taeda population of c. 800 individuals clonally replicated and grown on four sites, and genotyped for 4825 single-nucleotide polymorphism (SNP) markers. Prediction models were estimated for diameter and height at multiple ages using genomic random regression best linear unbiased predictor (BLUP). • Accuracies of prediction models ranged from 0.65 to 0.75 for diameter, and 0.63 to 0.74 for height. The selection efficiency per unit time was estimated as 53-112% higher using genomic selection compared with phenotypic selection, assuming a reduction of 50% in the breeding cycle. Accuracies remained high across environments as long as they were used within the same breeding zone. However, models generated at early ages did not perform well to predict phenotypes at age 6 yr. • These results demonstrate the feasibility and remarkable gain that can be achieved by incorporating genomic selection in breeding programs, as long as models are used at the relevant selection age and within the breeding zone in which they were estimated.}, number={3}, journal={New Phytologist}, publisher={Wiley}, author={Resende, M. F. R., Jr and Muñoz, P. and Acosta, J. J. and Peter, G. F. and Davis, J. M. and Grattapaglia, D. and Resende, M. D. V. and Kirst, M.}, year={2011}, month={Oct}, pages={617–624} }
 @article{stability of genomic selection prediction models across ages and environments_2011, url={http://dx.doi.org/10.1186/1753-6561-5-s7-o14}, DOI={10.1186/1753-6561-5-s7-o14}, abstractNote={Background A tree breeding program is characterized by long generation intervals which, over time, result in a much smaller number of breeding cycles when compared to annual crops. Moreover, most economically important traits in a tree-breeding program are quantitatively inherited, display low heritability and are expressed late in the life cycle. Genomic Selection (GS) is expected to be particularly valuable for tree species, leading to shorter generation intervals and improved genetic gain over time. The main factors that affect the accuracy of GS prediction models are the level of linkage disequilibrium (LD) in the training population, the training population size, the heritability of the trait and the number of QTL regulating its variation. However, it is yet largely unknown how stable prediction models are across environments and different ages. This knowledge is critical for tree breeders that wish to use genomic selection in their genetic improvement program. Here, we report the first assessment of the utility of genomic selection in a conifer species. We developed prediction models for growth traits measured at multiple sites, to evaluate the impact of genotype by environment interactions in their accuracy. Training populations were also measured over multiple ages and models were developed to assess their value in predicting breeding values later in the lifecycle.}, journal={BMC Proceedings}, year={2011}, month={Dec} }
 @article{echavarría_correa_patiño_acosta_rueda_2006, title={Evaluación de métodos estadísticos utilizados en trabajos de grado y tesis en los programas de la facultad de ciencias agropecuarias, en un período de tres años}, volume={59}, url={https://www.redalyc.org/articulo.oa?id=179914075012}, number={2}, journal={Revista Facultad Nacional de Agronomía}, author={Echavarría, H. and Correa, G. and Patiño, J.F. and Acosta, J.J. and Rueda, J.A.}, year={2006}, pages={3565–3580} }
 @article{echavarría sánchez_correa londoño_patiño díez_acosta jaramillo_rueda restrepo_2006, title={Evaluación de métodos estadísticos utilizados en trabajos de grado y tesis en los programas de la facultad de ciencias agropecuarias, en un período de tres años.}, volume={59}, url={https://revistas.unal.edu.co/index.php/refame/article/view/24349}, number={2}, journal={Revista Facultad Nacional de Agronomía, Medellín.}, author={Echavarría Sánchez, H. and Correa Londoño, G. and Patiño Díez, J. and Acosta Jaramillo, J. and Rueda Restrepo, J.}, year={2006}, month={Aug}, pages={3465–3580} }
 @article{ruiz suescún_2005, title={Escorrentía superficial en bosques montanos naturales y plantados de Antioquia, Colombia}, volume={S.l.], v. 58, n. 1}, url={https://revistas.unal.edu.co/index.php/refame/article/view/21509/22498}, journal={Revista Facultad Nacional de Agronomía, Medellín.}, author={Ruiz Suescún, Oscar Andrés}, year={2005}, month={Apr}, pages={2635–2649,} }
 @article{ruiz_acosta_león_2005, title={Escorrentía superficial en bosques montanos naturales y plantados de Antioquia, Colombia}, volume={58}, url={http://www.bdigital.unal.edu.co/24359/1/21509-73485-1-PB.pdf}, number={1}, journal={Revista Facultad Nacional de Agronomía}, author={Ruiz, O.A. and Acosta, J.J. and León, J.D.}, year={2005}, pages={2635–2649} }