Location: Cereal Crops Research2012 Annual Report
1a. Objectives (from AD-416):
1) Develop extensive phenotyping capabilities to evaluate breeding lines and core germplasm collections for biotic stresses, nitrogen use efficiency and drought stress; 2) identify beneficial alleles for these traits in core germplasm collections and in elite breeding populations and use them for breeding applications; 3) develop and implement large- and small-scale SNP genotyping platforms for barley and wheat breeding programs, and test novel sequence-based genotyping platforms; 4) integrate genotypic and phenotypic information in the public databases; 5) develop, test and use collaborative approaches to train plant breeders in modern field and lab techniques.
1b. Approach (from AD-416):
U.S. barley and wheat breeders will provide standardized field-based evaluations of biotic and abiotic stress tolerance, nitrogen use efficiency and yield from genotyped breeding lines and segregation populations. Physiologists will develop high throughput phenotyping methods for drought, heat and nitrogen use efficiency. A highly parallel SNP genotyping platforms developed by Illumina will be used to genotype over 8,000 wheat and barley core collections to evaluate genetic diversity. Based on genotype and phenotype data, a subset of germplasm will be selected to cross with elite lines to generate mapping populations to identify SNP markers associated with biotic and abiotic stresses. Large-scale SNP genotyping platforms will be developed to integrate genomic selection (GS) approach in the practical breeding scheme in wheat. The smaller-scale SNP genotyping platforms containing markers linked to known genes and previously identified marker-trait associations will be developed for breeding applications using marker-assisted selection and GS approaches in wheat and barley. A project database will be developed to integrate genotype, phenotype and pedigree data. Theoretical framework and web-based tools will also be developed to help breeders implement MAS and GS in barley and wheat breeding programs.
3. Progress Report:
In 2011, the Fargo lab genotyped 4416 wheat and 2420 barley accessions deposited at National Small Grains Collections in Aberdeen, ID using 9000-SNP platform developed for both wheat and barley. The large amount of SNP genotype data were delivered and uploaded to the project database in October, 2011. These data will allow the breeders to select lines for developing mapping populations and to explore genetic diversity to be incorporated in the breeding programs. In 2012, the Fargo lab will continue using the high-density SNP genotyping arrays to evaluate populations segregating for traits associated with biotic and abiotic stresses developed for wheat and barley using the association mapping approach. In wheat, the project is taking advantage of a concurrent development of a new SNP array containing 92,000 SNPs by the project members. Because of the much lower per data point cost and higher data throughput, the 92K wheat SNP array will be used to genotype the wheat samples submitted in 2012. The Fargo lab is coordinating with wheat and barley breeders on preparing sample submission for DNA preparation. ADODR monitoring activities to evaluate research progress included regular discussions, including conference calls and email among PI’s of the project, and a formal meeting in association with the annual Plant and Animal Genome Conference in San Diego, CA.