Variability in amylose content of Bangladeshi rice cultivars due to unique SNPs in Waxy allele

• Sequence polymorphism in Wx locus of 22 Bangladeshi rice landraces was analyzed.
• Most of the Bangladeshi landraces showed SNP patterns reported in South & Southeast Asian varieties.
• Three Beruin cultivars lacked the known glutinous alleles but had waxy or low amylose.
• Novel Wx promoter/intronic mutations in these 3 Beruin cultivars may explain their glutinous phenotype.

Waxy gene (Granule Bound Starch Synthase I) is responsible for amylose synthesis in the rice endosperm. Several mutations in this gene have been shown to be responsible for variable amylose content (AC) phenotypes. The G/T mutation in 5′ splice site of Waxy intron 1 has been traced as the origin of the glutinous rice phenotype and differentiates low AC from non-glutinous intermediate/high AC rice. Sequencing of Waxy promoter and 5′ noncoding regions from 22 rice cultivars showed that the evolutionary pattern of all Bangladeshi non-glutinous and most glutinous rice accessions are in line with the general patterns of South and Southeast Asia. However, three cultivars Khara Beruin, Modhu Beruin White and Kathali Beruin Red with low to very low amylose lacked the G/T splice site mutation. These were more closely related to non-glutinous cultivars based on their SNP patterns in promoter and noncoding regions. Further sequencing revealed a unique C deletion at a pyrimidine tract of intron 5 of these three cultivars that may cause slippage of intron splicing. Additional SNPs at intron 9 and 10 were also identified among these cultivars. These Bangladeshi-genotype-specific mutations could be the cause of waxy or low amylose phenotypes in these glutinous accessions.