Molecular characterization and comparative analysis of two waxy alleles in barley

Two alleles of the barley waxy locus were characterized from non-waxy cultivar Bowman and waxy cultivar CDC Candle, respectively. Their nucleotide and protein sequences were compared with other known waxy genes. The comparison results indicated that there were 100 polymorphic sites, among which 69 were in the non-coding region and 31 were in the coding region. Out of 100 polymorphic sites, 45 were trans-version, 35 were transition and 20 were indels. A 397 bp deletion and a 193 bp insertion in the promoter region and a 15 bp insertion in the coding region were found in CDC Candle, but not in Bowman. A deletion (11 bp) was detected in Bowman, which exhibited no effects on normal waxy expression. In summary, the 397 bp deletion was supposed to account for the reduction of GBSS I, resulting in the low amylose in CDC Candle; whereas other polymorphic sites might be not correlated with amylose synthesis.