Advances in Barley Genomics: Association Analysis, Breeding Values, and Consensus Mapping
Endelman, Jeffrey B.
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As part of the USDA Barley Coordinated Agricultural Project, 899 two-row spring barley lines were genotyped at 3072 SNP markers and phenotyped for four food quality traits: kernel hardness, polyphenol oxidase (PPO) activity, total phenolics, and amylose content. Analysis of the existing consensus map for this marker set revealed significant distortion in the fine structure of the Hardness locus on chromosome 5H. To create a revised barley consensus map with improved fine structure, new algorithms for the simplification and linearization of consensus graphs were developed and implemented in the R package DAGGER. DAGGER uses quadratic programming to generate a consensus map with minimum error relative to the linkage maps while remaining ordinally consistent with them. The root-mean-squared error between the barley linkage maps and the DAGGER map was 0.82 cM per marker interval compared to 2.28 cM for the existing consensus map. Association mapping of the barley food quality traits identified significant features corresponding to the PPO locus on chromosome 2H and the Wax locus on 7H, but the majority of the genetic variation was unaccounted for. While the polygenic nature of the food quality traits makes traditional marker-assisted selection difficult, genomic selection is well suited for this complexity because all markers are included in the prediction model. A key method for the genomic prediction of breeding values is ridge regression (RR), which is equivalent to BLUP when the genetic covariance between lines is proportional to their similarity in genotype space. This additive model can be broadened to include epistatic effects by using other kernels, such as the Gaussian, which represent inner products in a complex feature space. To facilitate the use of RR and non-additive kernels in plant breeding, a new software package for R called rrBLUP was developed. When applied to the barley food quality traits, the cross-validation accuracy between phenotype and predicted breeding value ranged from 0.31 for total phenolics to 0.56 for kernel hardness. Although further research is needed, these results suggest genomic selection of barley food quality may be viable in the near future.