Identification of Marker-Trait Associations In the Virginia Tech Winter Barley Program Using Genome-Wide Mapping.

Currently only a limited number of molecular markers are being utilized by the Virginia Tech winter barley (Hordeum vulgare) breeding program. Genetic markers associated with important agronomic traits would be of great value for further implementing marker assisted breeding within the program. A set of 361 advanced lines from the Virginia Tech winter barley breeding program were screened using two Barley oligonucleotide pool assays (OPAs), consisting of 3,072 single nucleotide polymorphisms (SNPs) as a part of the US Barley CAP.  Four years of phenotypic data collected at two locations for important traits including grain yield, test weight, heading date, plant height, stem length, lodging resistance, and resistance to leaf rust (Puccinia hordei), net blotch (Pyrenophora teres), and powdery mildew (Blumeria graminis f. sp. hordei) were analyzed in this study. Quality data including Beta-glucan, grain protein, grain hardness (SKCS), grain width, grain weight, hull proportion, amylase content, phenolic compound content, and polyphenol oxidase content were also analyzed. All lines included in the study were hulled or hulless 6-row winter barley. Population structure was accounted for using Principle component analysis (P), while kinship (K) was calculated based on random SNPs throughout the genome. Analysis of the P+K file was performed using the mixed linear model (MLM) function in TASSEL version 3.0. Initial analysis identified significant SNPs associated with yield, test weight, heading date, plant height, polyphenol oxidase content, and resistance to leaf rust and powdery mildew. Significant associations corresponding to previously described genes for resistance and agronomic traits were identified.