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United States Department of Agriculture

Agricultural Research Service

Research Project: SMALL GRAINS GENETICS AND GERMPLASM ENHANCEMENT

Location: Small Grains and Potato Germplasm Research

Title: The art of attrition: development of robust oat microsatellites

Authors
item Dumlupinar, Z. -
item Campbell, Robert
item Jellen, E.N. -
item Anderson, J. -
item Bonman, John
item Carson, Martin
item Chao, Shiaoman
item Obert, D. -
item Jackson, E. -

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 27, 2012
Publication Date: N/A

Interpretive Summary: Microsatellite or simple sequence repeat (SSR) are a type of molecular marker that can be used to improve the efficiency of plant breeding. We developed 160 new SSR markers for oat. These markers will be made publically available to oat breeders and other scientists and should help improve efforts to develop new oat varieties for growers in the US.

Technical Abstract: Microsatellite or simple sequence repeat (SSR) markers are important tools for genetic analyses, especially those targeting diversity, based on the fact that multiple alleles can occur at a given locus. Currently, only 160 genomic-based SSR markers are publicly available for oat, most of which have low polymorphism and ambiguous banding patterns. The primary objective of this study was to apply the art of attrition to develop robust oat-based microsatellite markers from newly enriched genomic libraries. Microsatellite motifs characterized by (CA/GT), (AAT/TTA), (ATG/TAC) and (CATC/GTAG) repeats were targeted for enrichment. Preliminary screening of each library showed that 90% of clones from the (CA/GT) and 79% of the clones from the (ATG/TAC) libraries contained repeats, while < 11% of the clones from (AAT/TTA) and (CATC/GTAG) libraries contained repeats. Subsequent sequencing of 1,536 clones from both the (CA/GT) and (ATG/TAC) libraries resulted in 539 and 578 motifs for which primers could be designed, respectively. Of the 1,177 total sequences containing microsatellites, 98 were redundant. Primers designed to 520 of the non-redundant motifs amplified fragments using standard PCR conditions and 246 produced polymorphic alleles across 11 oat lines. One hundred and twenty-five of the polymorphic markers produced highly reproducible assays that interrogated 369 alleles at 193 loci. Of these, 79 robust assays interrogated 146 co-dominant alleles. These makers will be useful for a wide-range of genetic analyses in oat including assessment of diversity and marker-assisted breeding.

Last Modified: 9/2/2014
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