The Barley Coordinated Agricultural Project: Enhancing the Efficiency of Breeding through Genomics.

The barley coordinated agricultural project (CAP) project leverages scientific strength in genomics, statistics, computer science, pathology, malt and food quality, and breeding to enhance the efficiency of barley breeding.  The overall plan is to genotype and phenotype advanced breeding lines from 10 U.S. barley breeding programs and to utilize these data to conduct association mapping to identify quantitative trait loci (QTL).  Along with our international collaborators, we mapped 2,943 single nucleotide polymorphisms (SNP).  From these SNPs, an international genotyping platform of 3,072 SNPs was developed.  To date, we have interrogated 2,880 breeding lines with 3,072 SNP markers and phenotyped these lines for over 40 traits including agronomic, disease resistance, and food and malting quality.  The barley CAP has used the SNP genotyping platform to estimate linkage disequilibrium (LD) in U.S. barley breeding germplasm, and the genetic relationships between breeding programs.  LD has been estimated to range from 20-30 cM.  Seven subpopulations explain the population structure of the 10 U.S. barley breeding programs.  A centralized database called The Hordeum Toolbox has been developed that houses all genotype and phenotype data.  QTL for a variety of traits including malting quality, winterhardiness, dormancy, preharvest sprouting, drought tolerance and resistance to Fusarium head blight (FHB), spot blotch, net blotch, African stem rust (Ug99), and common root rot have been detected.  Case studies of mapping QTL for resistance to FHB and spot blotch will be described. The utility of mapping resistance to FHB for enhancing parental selection will be described.