Genetic screening of Australian barley varieties using microsatellite markers

The most widely used molecular marker system is based on the use of RFLPs. These are highly reliable and informative but they are technically demanding to assay and expensive. Marker assays based on the Polymerase Chain Reaction (PCR) offer a far more user-friendly marker system. PCR based techniques such as RAPDs are unreliable and generally not transferable between crosses. However, microsatellites (di- or tri-nucleotide repeat sequences) also known as Simple Sequence Repeats (SSR) offer highly reliable, co-dominant markers. Microsatellites are becoming more widely used for marker assisted breeding and variety identification due to their high level of polymorphism and ease of use. Forty-three barley microsatellite markers were used to genotype 180 barley varieties. Primer pairs were synthesized and screened on a panel of four genetically diverse genotypes. Seventeen of them giving unambiguous and polymorphic DNA banding patterns were selected for allele typing study. Allele typing was carried out by using primers labeled with fluorescent dyes and the PCR products were separated and analyzed on the ABI Prism 310 automated capillary electrophoresis system. Among 17 labelled primer pairs examined four gave inconsistent PCR product results and were excluded from the study. The remaining 13 primer pairs detected a total of 115 alleles. Microsatellites with (GA)n repeats revealed the highest number of different alleles. Genetic mapping of a range of other barley microsatellites is currently underway.