Polymorphism analysis of the asi gene from barley

Studies of genetic variability in crop plants are often based on polymorphism of DNA markers from anonymous genomic sites using highly polymorphic markers eg. SSRs. However variability at the level of the functional gene has been less studied even though it is a portion of this variability that is likely to create most of the genetically based phenotypic variability utilised by breeders in improvement programs. To determine the distribution, extent and type of variability between barley varieties at this level the asi gene of barley was analysed by sequencing a 2.3kb region comprising the promoter, coding and downstream regions from fourteen barley varieties. The asi gene is an intronless gene whose product functions as an inhibitor of a-amylase and subtilisin. The barley varieties studied were mostly cultivated varieties bred in Australia but included a wild barley (Hordeum spontaneum) and a North African landrace. As expected the wild barley variety had the largest number of SNPs and indels compared to the consensus sequence. However ten of the cultivated barley varieties had identical sequences over the 2.3kb of sequence except for the number of repeats in a microsatellite sequence in the promoter region. To compare the level of polymorphism displayed by the microsatellite with that based on SNP and indel haplotypes a further 36 barley varieties were genotyped for microsatellite length and selected sequence polymorphisms in the promoter and coding region.