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.
In 2011, the Fargo lab established the capability of carrying out high density SNP marker genotyping using the Infinium assay method developed by Illumina. A set of 2420 cultivated barley lines and 4416 cultivated wheat lines, including 546 tetraploid and 3870 hexaploid germplasm, were selected from the National Small Grains Collections maintained by USDA-ARS, Aberdeen, ID. The DNA plates of these accessions were sent to Fargo and are being genotyped with 9000 SNP array platforms previously developed by the collaborators for both wheat and barley. The genotype data will be released to the project database for access by the project collaborators.