Genetic diversity analysis of specialty glutinous and low-amylose rice (Oryza sativa L.) landraces of Assam based on Wx locus and microsatellite diversity

Abstract

The sticky rice of Assam is traditionally classified as bora (glutinous) and chokuwa (semi-glutinous) based on their stickiness after cooking. The Waxy (Wx) gene encodes for granule-bound starch synthase (GBSS) that controls the synthesis of amylose, which is a key determinant of rice end-use quality attributes. In this report, we analysed the level of variation in grain quality traits in a collection of bora and chokuwa cultivars, and examined the nucleotide diversity at the Wx locus of selected rice accessions to identify the possible cause of low-amylose in these rice cultivar groups. The Wx gene sequencing from 24 bora and chokuwa cultivars revealed several nucleotide variations that can explain the variation in the amylose phenotypes. The nucleotide polymorphisms in the downstream intron regions were similar to those reported in Bangladeshi Beruin cultivars. Among the Wx polymorphisms, the CTn microsatellite in exon 1 and G/T SNP in intron 1 (G/T-Int1) should be considered for marker assisted breeding involving bora cultivars. The Wx gene tree, classified the bora accessions possessing the G/T-Int1 SNP as japonicas. However, cluster analysis using microsatellite markers classified the bora and chokuwa cultivars as indica, and intermediate of indica-aus. The findings of this study supplemented our understanding on the evolution of the Wx gene under human selection. The results will assist plant breeders to effectively improve the bora and chokuwa landraces.