Sequence polymorphism in the Waxy locus and its relationship with apparent amylose content of endosperm starch in cultivars of rice (Oryza sativa L.) from Northeast India

Abstract

The Northeast India, being at the confluence of Indo-Malayan and Indo-Chinese biogeographic realms, represents one of the world “biodiversity hotspots”. With a rich diversity of cultivars, the rice gene pool of the region shows marked variations in various quality traits including aroma and starch quality. Since starch quality is primarily determined by its apparent amylose content and that the Waxy locus controls much of the variation in apparent amylose content, the linkage between sequence polymorphism in the Waxy locus and the apparent amylose content assumes significance. Our investigations on the relationship between SNPs in Waxy locus and variations in AAC of starch varieties of rice from North East India clearly reveal that in accessions having the sequence AGTTAT in 5′ leader intron splice site, “Ex6C” allele was associated with starches having 0–2% AAC and “Ex6A” allele was associated with starches having between 2 and 12% AAC. Based on combination of “G/T” polymorphism in 5′ leader intron splice site, length polymorphism in exon 2 and “A/C” polymorphism in exon 6, the Waxy locus of rice can have four allelic forms viz. “Int1T-Ex2(23 bp)2-Ex6C”, “Int1T-Ex2(23 bp)1-Ex6A”, “Int1G-Ex2(23 bp)1-Ex6C” and “Int1G-Ex2(23 bp)1-Ex6A” which correlate specifically with “waxy”, “very low”, “low/intermediate” and “high amylo-” cultivars, respectively. Phylogenetic tree on alignment matrix of nucleotide sequences of the p-SINEI element of the Waxy locus clustered the upland and japonica cultivars separately from the lowland and indica cultivars, thereby establishing the role of transposons in the Waxy locus in differentiation of upland/japonica and lowland/indica cultivars.