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United States Department of Agriculture

Agricultural Research Service

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Research Project: Development of SNP Resources for High-Throughput Genotyping to Advance Genomic, Genetic and Breeding Research in Wheat

Location: Wheat Genetics, Quality Physiology and Disease Research

2012 Annual Report


1a.Objectives (from AD-416):
To identify new molecular markers.


1b.Approach (from AD-416):
Sequence cDNA libraries from diverse U.S. germplasm to identify new SNP alleles. Using bioinformatics identify useful SNP alleles. Using the allumnia SNP platform over 4000 SNPs will be mapped in multiple CAP mapping populations.


3.Progress Report:

The objective of the SNP grant was to sequence relevant wheat cultivars, utilize the sequence information to identify new single nucleotide polymorphisms and develop SNP based molecular markers. Progress on this objective has exceeded expectations. Efforts coordinated by the western regional genotyping lab resulting in 1,824 wheat lines including 6 mapping populations being tested against 9,000 SNP. Results from the assay included 7504 polymorphic markers of which 7160 were mapped to chromosomes. The resulting 9.5 million datapoints are being evaluated for their relevance in each breeding program and SNP markers are currently available for multiple stripe rust genes, agronomic traits and are be implemented in genome selection efforts for marker assisted selection. The manuscript reporting the initial phase of the SNP grant is currently in review. A continuation of the SNP grant project is also underway and this fall 2,300 PNW germplasm will be genotyped with 90,000 SNP. This project supports parent project 5348-21000-023-00D, Objective 2, Sub-objective A.


Last Modified: 8/21/2014
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