Rice is the foremost crop catering to the major calorific requirement of the human population but has the disadvantage ofhaving high glycaemic index (GI). The fine quality rice varieties, BPT and RNR have been recently identified as having low GI in natureand are grown mostly in southern parts of India. Starch (80%) is the major component of rice endosperm attributing to GI. The study aimedto unravel the molecular basis of low GI through targeted pooled amplicon sequencing of major starch biosynthetic genes. A total of 13candidate genes involved in starch synthesis were amplified and pooled in equimolar proportion for sequencing. Single-nucleotidepolymorphisms (SNP$_{s}$) and insertions/deletions (Indels) were detected in both coding and noncoding regions. Among the genes that areunder study, the highest number of variations were identified in starch synthase I (SSI) followed by starch synthase IIIA (SSIIIA) genes.Nonsynonymous SNP$_{s}$ with high probability of effecting gene function were validated by Sanger sequencing and molecular docking.Identified causative SNP$_{s}$ were mapped on 3000 rice genome database and their allele frequencies were obtained. The outcome of this studyhas a potential to be applied in breeding programmes to obtain low GI rice varieties with added beneficial traits.