Abstract:
Starch quality is one of the most important agronomic traits in rice (Oryza sativa L). In this study, we identified single
nucleotide polymorphisms (SNPs) in the Waxy and Alk genes of eight rice varieties and their associations with starch
physicochemical properties.vi.e.vamylose content (AC) and gelatinization temperature (GT). Seven Sri Lankan rice varieties,
Pachchaperumal, Herathbanda, At 354, Bg 352, Balasuriya, H 6 and Bw 295-5 were detected as high amylose varieties while
Nipponbare exhibited low amylose content. In silico analysis of the Waxy gene revealed that all tested Sri Lankan varieties
possessed ‘G’ (Wxa allele) instead of ‘T’ in the first intron which could explain varieties with high and intermediate amylose
content. All Sri Lankan varieties had ‘A’ instead of ‘C’ in exon 6 of the Waxy gene and this fact was tally with the varieties
showing high amylose content. Therefore, possessing the Wxa allele in the first intron and ‘A’ in exon 6 could be used as a
molecular marker for the selection of high amylose varieties as validated using several Sri Lankan varieties. All Sri Lankan
varieties except, Bw 295-5 exhibited the intermediate type of GT which could not be explained using the so far reported allelic
differences in the Alk gene. However, Bw 295-5 which is a low GT variety had two nucleotide polymorphisms in the last exon of
the Alk gene, i.e. ‘G’ and ‘TT’ that represent low GT class. Therefore, it can be concluded that sequence variations of Waxy and
Alk genes reported in this study are useful in breeding local rice varieties with preferential amylose content and GT class.
