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United States Department of Agriculture

Agricultural Research Service

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Location: Cereal Crops Research

2013 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:
A high-density wheat SNP array containing 92,000 SNPs was developed and made available in the spring of 2012. This array was used to genotype 2,500 wheat samples submitted from six different locations in the US. These samples included spring wheat, soft and hard winter wheat association mapping panels, two sets of disease association mapping panels, and several bi-parental mapping populations. Additionally, 240 barley samples submitted from two locations were genotyped with a barley 9K SNP array. We coordinated seed/leaf tissue submissions for DNA preparation. The barley SNP data files were released to collaborators in October 2012. To ensure consistency of genotype scoring for the new 92K wheat array among labs, our lab collaborated with wheat scientists in the US and elsewhere on training the 92K array based on a set of 3,000 diverse samples of worldwide origin. During the training process, genotype scoring for each SNP was manually evaluated and annotated. The final SNP annotation information was widely distributed and shared among ARS genotyping centers. The wheat SNP genotype data files were released to collaborators and the project database curator in April 2013.

4. Accomplishments

Last Modified: 06/27/2017
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