@article{spitzer_isik_whetten_farjat_mckeand_2017, title={Correspondence of Loblolly Pine Response for Fusiform Rust Disease from Local and Wide-Ranging Tests in the Southern United States}, volume={63}, ISSN={["1938-3738"]}, DOI={10.5849/fs-2016-093r1}, abstractNote={Fusiform rust is the most economically important disease of loblolly pine (Pinus taeda L.) in the southern United States. Estimates of family resistance to rust are critical for deployment decisions because 95% of loblolly pine plantations are established with individual families. If families show significant interactions with different pathogen inocula, then the performance of some families in different regions may not be predictable. This study compared rust breeding values of 56 loblolly families estimated from two independent sets of trials. We regressed the rust incidence breeding values of the families estimated from broadly based field tests on breeding values of the same families estimated from narrowly based tests. The model F test was highly significant (P < 0.0001), and breeding values based on local testing explained 75% of the variation in breeding values based on wide-range geographic testing, indicating that local rust breeding values are relatively reliable predictors of families' performance across a broad range of sites. Family rankings were highly consistent across test sites within broadly and narrowly based testing schemes as shown by type B genetic correlations (0.90 and 0.91). We conclude that field testing provides a reliable prediction of the operational value of loblolly families for deployment in regions with a high hazard for fusiform rust. Management and Policy Implications When choosing loblolly pine families to be planted on sites where resistance to fusiform rust is necessary, foresters and landowners can have confidence in the performance data coming from a range of field trials. Results show that local testing for rust resistance in relatively narrow geographic regions provides reasonably reliable rust disease resistance/susceptibility predictions and adequate predictive power for deployment decisions across a broad range of planting sites in the Gulf and Atlantic Coastal Plain regions of the southeastern United States.}, number={5}, journal={FOREST SCIENCE}, publisher={Oxford University Press (OUP)}, author={Spitzer, Jesse and Isik, Fikret and Whetten, Ross W. and Farjat, Alfredo E. and McKeand, Steven E.}, year={2017}, month={Oct}, pages={496–503} }
 @article{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, Alfredo and Reich, Brian J. and Guinness, Joseph and Whetten, Ross and McKeand, Steven and Isik, Fikret}, year={2017}, month={Feb}, pages={909–920} }
 @article{farjat_chamblee_isik_whetten_mckeand_2017, title={Variation among Loblolly Pine Seed Sources across Diverse Environments in the Southeastern United States}, volume={63}, ISSN={0015-749X}, url={http://dx.doi.org/10.5849/forsci.15-107}, DOI={10.5849/forsci.15-107}, abstractNote={Seven seed sources of first-generation plantation selections of loblolly pine (Pinus taeda L.) were evaluated for six traits in test sites across most of its native range east of the Mississippi River in the southeastern United States. The traits evaluated were survival, height, volume, straightness, stem forking, and incidence of fusiform rust disease (caused by Cronartium quercuum [Berk.] Miyabe ex Shirai f. sp. fusiforme). At age 8 years, survival was high, with most seed sources having survival greater than 75% at all but two test sites. South Carolina Coastal and Georgia-Florida Coastal seed sources exhibited the fastest growth and most resistance to fusiform rust, whereas the Virginia seed source exhibited the slowest growth but had the best stem form. Test sites and seed source were significantly different for all traits. Seed source × site interactions (genotype × environment [G × E]) were also significant for all traits except stem forking. Low type B genetic correlation values (rB <0.67) for height, volume, and straightness suggest the presence of G × E interactions. The South Carolina Coastal and Virginia seed sources contributed disproportionally the most to G × E interactions for growth traits, but environmental contributions to G × E interactions were distributed relatively uniformly across most test sites. The results indicate that when seed sources are moved outside of their adaptive range, important G × E interactions should be expected and the difference among seed sources originating from a wide range of climates are expected to be more pronounced in older ages.}, number={1}, journal={Forest Science}, publisher={Oxford University Press (OUP)}, author={Farjat, Alfredo E. and Chamblee, Aaron K. and Isik, Fikret and Whetten, Ross W. and McKeand, Steven E.}, year={2017}, month={Feb}, pages={39–48} }
 @article{isik_bartholome_farjat_chancerel_raffin_sanchez_plomion_bouffier_2016, title={Genomic selection in maritime pine}, volume={242}, ISSN={["0168-9452"]}, DOI={10.1016/j.plantsci.2015.08.006}, abstractNote={A two-generation maritime pine (Pinus pinaster Ait.) breeding population (n=661) was genotyped using 2500 SNP markers. The extent of linkage disequilibrium and utility of genomic selection for growth and stem straightness improvement were investigated. The overall intra-chromosomal linkage disequilibrium was r(2)=0.01. Linkage disequilibrium corrected for genomic relationships derived from markers was smaller (rV(2)=0.006). Genomic BLUP, Bayesian ridge regression and Bayesian LASSO regression statistical models were used to obtain genomic estimated breeding values. Two validation methods (random sampling 50% of the population and 10% of the progeny generation as validation sets) were used with 100 replications. The average predictive ability across statistical models and validation methods was about 0.49 for stem sweep, and 0.47 and 0.43 for total height and tree diameter, respectively. The sensitivity analysis suggested that prior densities (variance explained by markers) had little or no discernible effect on posterior means (residual variance) in Bayesian prediction models. Sampling from the progeny generation for model validation increased the predictive ability of markers for tree diameter and stem sweep but not for total height. The results are promising despite low linkage disequilibrium and low marker coverage of the genome (∼1.39 markers/cM).}, journal={PLANT SCIENCE}, publisher={Elsevier BV}, author={Isik, Fikret and Bartholome, Jerome and Farjat, Alfredo and Chancerel, Emilie and Raffin, Annie and Sanchez, Leopoldo and Plomion, Christophe and Bouffier, Laurent}, year={2016}, month={Jan}, pages={108–119} }
 @article{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} }