2012 Annual Report 1a.Objectives (from AD-416): Extensively phenotype and genotype diverse and designed germplasm pools to mine and deploy alleles that improve barley and wheat adaptation and performance under biotic and abiotic stress, and couple these activities with the training of a new generation of plant breeders 1b.Approach (from AD-416): Develop and implement large- and small-scale SNP genotyping platforms for barley and wheat breeding programs, and test novel sequence-based genotyping platforms. Provide replicated rust resistance phenotypic data on multiple sets of hard winter wheat lines grown in the field and greenhouse. Integrate the genotypic and phenotypic information into GRIN, GrainGenes, and Gramene databases and develop web-based tools to help breeders use this information. 3.Progress Report: A core collection of approximately 1400 diverse winter wheat lines from the National Small Grains Collection in Aberdeen, ID was assessed for adult plant resistance to leaf rust in the greenhouse, and in the field at Castroville, TX, and Hutchinson, KS. An association mapping panel of hard winter wheat with a total of approximately 300 lines was also assessed at the same locations. All of the wheat lines have been genotyped on a high density marker platform. These two sets will be tested for an additional year at several locations. Subsequently, they will be subjected to association analysis and leaf rust resistance genes will be identified. We are particularly interested in identifying new genes that are effective at the adult stage. Four mapping populations for minor gene resistance to leaf rust, stripe rust, or stem rust were developed from crosses of CIMMYT spring wheats with hard white winter wheat. Populations were advanced to the BC1F4 generation. Testing for resistance will begin in the greenhouse and the field in the 2012/2013 cycle. These populations will be tested for two years and then the resistance genes will be mapped. The purpose is to identify new useful resistance genes and molecular markers that can be used for marker-assisted selection of resistance to all three rust species. Genomic selection (GS) is a new statistical approach that allows plant breeders to select the best breeding lines based on genome-wide DNA (molecular) markers. One important component for applying GS in breeding programs is the availability of low-cost molecular markers. In this work, we showed how next-generation sequencing can be applied to a wheat breeding program to produce robust, yet inexpensive, DNA markers in an approach called “genotyping-by-sequencing” (GBS). Relative to other species, the wheat genome is very large and complex, making it difficult to generate molecular markers for breeding and genetics studies. GBS is an excellent tool for breeding purposes and DNA markers can be discovered simultaneously with assaying the whole population of interest. Further, we showed that GBS markers can be used to predict the performance of breeding lines for grain yield, heading date, and thousand kernel weight. The low per sample cost of GBS will enable widespread application of GS in breeding programs. This can lead to increasing the rate of genetic gain and rapid development of new cultivars.