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ARS Home » Pacific West Area » Aberdeen, Idaho » Small Grains and Potato Germplasm Research » Research » Publications at this Location » Publication #198969
Title: ENLARGEMENT OF PCR-BASED MARKER RESOURCES IN OAT BY SURVEYING GENOMIC-DERIVED SSRS FROM BARLEY AND WHEAT

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

Submitted to: American Oat Workers Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 5/20/2006
Publication Date: 7/22/2006
Citation: Hu, G., Jackson, E.W., Bonman, J.M. 2006. Enlargement of pcr-based marker resources in oat by surveying genomic-derived ssrs from barley and wheat. American Oat Workers Conference Proceedings. 52

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.

Technical Abstract: Simple sequence repeats (SSRs), a relatively new generation of DNA markers, are developing rapidly in most crop species. SSR’s are advantageous as markers because they are present in large numbers, are evenly dispersed, and are highly polymorphic. Oat lags behind other crops in use of the SSR markers due to limited investment in developing genomic and genetic resources in Avena. To search for an alternative means to enlarge the SSRs pool in oat, we surveyed 356 genomic derived SSR markers from wheat and barley chosen based on even dispersal across different chromosomes. These were tested for amplification and polymorphism in parental lines of the main mapping populations of oat; TAM O-301, Ogle1040, Kanota156, and Ogle157. Eighty-nine of 210 wheat SSRs (42%) and fifty six of 146 barley SSRs (38%) successfully amplified in oat. At least 66 markers (45% of the amplified markers and 19% of total markers) showed polymorphism between the parental lines of at least one mapping population. The percentage of polymorphic SSRs among the amplified primers is comparable to that for oat-derived SSRs in published data. Work is underway to determine if the polymorphic SSRs from the Ogle X TAM O-301 population can be mapped. The survey results indicate that genomic SSRs from wheat and barley may be good sources of SSR markers for oat genetics research. The genomic relationships regarding DNA marker amplification provides clues for adapting other types of DNA markers, such as SNPs, from barley and wheat to oat in the future.