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GENOMICS, MOLECULAR GENETICS & BIOTECHNOLOGY

Expansion of PCR-based Marker Resources in Oat by Surveying Genome-Derived SSR Markers from Barley and Wheat

USDA-ARS, Small Grains and Potato Germplasm Research Unit, 1691 South 2700 West, Aberdeen, ID 83210

^* Corresponding author (gongsheh{at}uidaho.edu).

Identifying polymerase chain reaction (PCR)-based markers in crop genomes and amplifying them with specific primer pairs has provided convenient molecular markers for mapping projects. Oat (Avena sativa L.) lags behind other crops in the utilization of PCR-based markers due to limited development of genomic and genetic resources in Avena species. We surveyed 356 genome-derived simple sequence repeat (SSR) markers from wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.), chosen on the basis of even dispersal across different chromosomes, to search for an alternate method of expanding the PCR-based marker pool in oat. Primer pairs for these SSR markers were tested for amplification and polymorphism between parental lines from Ogle1040/TAM-O-301 (OT) and Kanota/Ogle157 (KO) mapping populations. Eighty-nine of 210 wheat primer pairs (42%) and 56 of 146 barley primer pairs (38%) successfully amplified sequences in oat. Forty-five percent of the amplified markers, representing 19% of the total markers, showed polymorphism between parental lines of at least one mapping population. The polymorphism was primarily the presence or absence of a product band. Fifteen PCR products from 10 primer pairs were tested for reproducibility by amplifying each marker in the OT population. When assayed with the same PCR conditions used in the survey, the segregation ratio of 14 markers did not differ from the 1:1 ratio expected for a single locus. This study indicates that genomic SSR primer pairs from wheat and barley may be a good way to efficiently generate PCR-based DNA markers for oat genetics research.

Abbreviations: CTAB, cetyl trimethyl ammonium bromide • EST, expressed sequence tag • KO, Kanota x Ogle157 • OT, Ogle1040 x TAM-O-301 • PCR, polymerase chain reaction • RIL, recombinant inbred line • SSR, simple sequence repeat