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United States Department of Agriculture

Agricultural Research Service

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Research Project: Improving Barley and Wheat Germplasm for Changing Environments

Location: Plant Science Research

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 single nucleotide polymorphism (SNP) genotyping platforms for barley and wheat breeding programs, and test novel sequence-based genotyping platforms. Integrate the genotypic and phenotypic information into GRIN, GrainGenes, and Gramene databases and develop web-based tools to help breeders use this information.

We will develop 48 and 384 SNP platforms dedicated to known genes or previously identified marker-trait associations for barley and wheat. These SNP platforms will be available at the Small Grains Genotyping Centers for breeders to characterize breeding lines in advanced yield trials. Simultaneously, we will test new genotyping technologies based on high-throughput sequencing platforms (e.g. gene capture and sequence-based genotyping) in barley and wheat and implement them as they become economically feasible.


3.Progress Report:

This project is related to Objective 2 of the parent project to develop improved methods of marker-assisted selection and apply markers in development of improved cultivars of small grains.

Genotyping with 384 single nucleotide polymorphism (SNP) was performed on winter barely lines included in the first cycle of a population undergoing genomic selection for improvement of low temperature tolerance. Genotyping with a panel of SNP markers was also done on backcross populations of between wild and cultivated barley to identify and delineate chromosome regions introgressed from the wild species. A barley recombinant inbred line population was genotyped and genetic linkage map constructed for quantitative trait loci (QTL) mapping.

Using the KASP technology, new assays were developed that are diagnostic for alleles at the Rht1 loci, the Vrn1 gene, the R-loci for seed coat color, and several disease resistance genes, including Sr2, Lr9, Lr21, Lr34/Yr18, and Sr36/Pm6. These assays were evaluated on a panel of diverse wheat lines and are being used to genotype samples from breeding programs.

Seed of winter wheat lines to be genotyped with the new iSelect SNP assay having 90,000 wheat SNP were sent to Raleigh from wheat breeders in the eastern growing region. Genomic DNA was isolated from individual plants that are being grown in the greenhouse. DNA was sent to Fargo, ND for genotyping.


Last Modified: 7/27/2014
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