Wx alleles in rice: relationship with apparent amylose content of starch and a possible role in rice domestication

Abstract

The Waxy locus of rice is a highly polymorphic region embedded with microsatellite repeats in the 5'UTR leader intron 1 region, 23-bp duplication (wx motif) in exon 2, SNPs in exons 4, 6 and 10, p-Sine-r2 element in intron 1 and TnR-1 element in inton 13. Of the 80 polymorphic sites detected on the Wx gene, 24 are located in p-Sine-r2 and TnR-1 elements, revealing a higher substitution rate of bases in these two regions. All the cultivars with chalky endosperm had the 5'-AGTTATA-3' haplotype in intron 1 and 'A' to 'G' substitution at ?497 in exon 4. The AAC of starch from grains of all the accessions showed strong correlation (r=0.967) with GBSS-I activity in the grains. Based on the polymorphic sites of the Waxy locus and the GBSS-I activities, six allelic variants were defined which included wx, Wxop, Wxb, Wxin, Wxa2 and Wxa1, respectively, corresponded to glutinous, very low, low, intermediate, highII and highI amylose classes. Phylogenetic tree developed from alignment matrix of nucleotide sequences of the Waxy locus identified wx, Wxb and Wxin alleles with japonica lineage of Oryza sativa and the Wxop, Wxa2 and Wxa1 with indica lineage.