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United States Department of Agriculture

Agricultural Research Service

Research Project: INTEGRATION OF NUTRITIONAL, GENETIC AND PHYSIOLOGICAL APPROACHES TO IMPROVE PRODUCTION EFFICIENCY OF RAINBOW TROUT Title: Expansion of Pcr-Based Marker Resources in Oat by Surveying Genomic-Derived Ssrs from Barley and Wheat

Authors
item Hu, Gongshe
item Jackson, Eric
item Bonman, John

Submitted to: Agronomy Society of America, Crop Science Society of America, Soil Science Society of America Meeting
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 29, 2006
Publication Date: September 1, 2007
Repository URL: http://riley.nal.usda.gov/nal_web/digi/submission.html
Citation: Hu, G., Jackson, E.W., Bonman, J.M. 2007. Expansion of pcr-based marker resources in oat by surveying genomic-derived ssrs from barley and wheat. Agronomy Society of America, Crop Science Society of America, Soil Science Society of America Meeting. Crop Sci. 47:2004-2012 (2007).

Interpretive Summary: SSR (Simple Sequence Repeat) is new generation of DMA markers. It can be used for genetic study and assistant selection for desired traits in early stage of germplasm development and breeding. Large number of SSRs is available in most crop plants except oat. Development of oat SSR markers is very important for oat genetics and breeding. This study is to use an alternative approach to develop SSR markers in oat. We investigated the possibility of transfer SSRs from related species. Our results from systemic survey of SSRs from barley and wheat species showed that they are good resources for rapid development of SSRs in oat. SSR markers we identified in this research will be assigned to the corresponding locations in oat chromosomes that will greatly improve the genetic map of oat genome and provide more useful information in utilization of DNA markers in oat.

Technical Abstract: Identifying simple sequence repeat (SSR) regions in crop genomes and amplifying them with specific primer sets have provided a relatively new generation of molecular markers for mapping projects. SSRs are advantageous to most of other markers because they are present in large numbers, are evenly dispersed across the genome, and are highly polymorphic. Oat lags behind other crops in the utilization of SSR markers due to limited investment in developing genomic and genetic resources in Avena species. We surveyed 356 genomic derived SSR markers from wheat and barley, chosen on the basis of even dispersal across different chromosomes, to search for an alternate method to expand the SSR marker pool in oat. These markers were tested for amplification and polymorphism in parental lines from the major mapping populations of oat: TAM0-301, Ogle1040, Kanota156, and Ogle157. Eighty-nine of 210 wheat SSRs (42%) and fifty-six of 146 barley SSRs (38%) successfully amplified in oat. Forty-five percent of the amplified markers, or 19% of the total markers, showed polymorphism between parental lines of at least one mapping population. The percentage of polymorphic SSRs amplified was comparable to that for oat-derived SSRs in previously published data. The survey results indicate that genomic SSRs from wheat and barley may be good sources of DNA markers for oat genetics research.

Last Modified: 10/24/2014
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