@article{rutkoski_benson_jia_brown-guedira_jannink_sorrells_2012, title={Evaluation of Genomic Prediction Methods for Fusarium Head Blight Resistance in Wheat}, volume={5}, ISSN={["1940-3372"]}, DOI={10.3835/plantgenome2012.02.0001}, abstractNote={Fusarium head blight (FHB) resistance is quantitative and difficult to evaluate. Genomic selection (GS) could accelerate FHB resistance breeding. We used U.S. cooperative FHB wheat nursery data to evaluate GS models for several FHB resistance traits including deoxynivalenol (DON) levels. For all traits we compared the models: ridge regression (RR), Bayesian LASSO (BL), reproducing kernel Hilbert spaces (RKHS) regression, random forest (RF) regression, and multiple linear regression (MLR) (fixed effects). For DON, we evaluated additional prediction methods including bivariate RR models, phenotypes for correlated traits, and RF regression models combining markers and correlated phenotypes as predictors. Additionally, for all traits, we compared different marker sets including genomewide markers, FHB quantitative trait loci (QTL) targeted markers, and both sets combined. Genomic selection accuracies were always higher than MLR accuracies, RF and RKHS regression were often the most accurate methods, and for DON, marker plus trait RF regression was more accurate than all other methods. For all traits except DON, using QTL targeted markers alone led to lower accuracies than using genomewide markers. This study indicates that cooperative FHB nursery data can be useful for GS, and prior information about correlated traits and QTL could be used to improve accuracies in some cases.}, number={2}, journal={PLANT GENOME}, author={Rutkoski, Jessica and Benson, Jared and Jia, Yi and Brown-Guedira, Gina and Jannink, Jean-Luc and Sorrells, Mark}, year={2012}, month={Jul}, pages={51–61} }
 @article{benson_brown-guedira_murphy_sneller_2012, title={Population Structure, Linkage Disequilibrium, and Genetic Diversity in Soft Winter Wheat Enriched for Fusarium Head Blight Resistance}, volume={5}, ISSN={["1940-3372"]}, DOI={10.3835/plantgenome2011.11.0027}, abstractNote={The occurrence of epidemics of Fusarium head blight (FHB), caused by Fusarium graminearum Schwabe, in U.S. winter wheat (Triticum aestivum L.) during the past two decades led to significant emphasis on development of resistant cultivars. Understanding the genetic diversity, population structure (PS), and linkage disequilibrium (LD) in winter wheat in the eastern United States is important for marker‐assisted breeding and association analysis in this germplasm. Lines selected from collaborative FHB screening nurseries were genotyped with simple sequence repeat (SSR), sequence tagged site (STS), and Diversity Array Technology (DArT) markers to assess LD, genetic diversity, and PS. The genomewide average of LD decay to r2 < 0.2 was 9.9 cM and moderate levels of LD (r2 > 0.2) were generally constrained to markers less than 5 cM apart. Although the lines evaluated were targeted to distinct production zones of the eastern winter wheat region, cluster and principal component analyses did not detect separation of lines into subpopulations. The short, intense breeding history for scab resistance may have localized effects on LD. Lack of subgroups within our population could be due to intercrossing among common resistant parents and indicate frequent admixture and germplasm exchange among U.S. winter wheat programs focused on development of FHB resistant cultivars.}, number={2}, journal={PLANT GENOME}, author={Benson, Jared and Brown-Guedira, Gina and Murphy, J. Paul and Sneller, Clay}, year={2012}, month={Jul}, pages={71–80} }