Allele mining for Granule bound starch synthase1 (GBSS1) gene governing amylose content in aromatic rice (Oryza sativa L.) germplasm Dixit Deepshikha1, Siddiqui N.1, Bollinedi Haritha, Krishnan Gopala S., Malik Ankit, Bhowmick P. K., Ellur R. K., Nagarajan M.2, Vinod K. K., Singh A. K.* Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110 012, India 1Amity Institute of Biotechnology, Amity University, Noida, 201 313, Uttar Pradesh, India 2Rice Breeding and Genetics Research Centre, ICAR-IARI, Aduthurai, 612 101, Tamil Nadu, India *Corresponding Author: A. K. Singh, Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110 012, India, E-Mail: aks_gene@yahoo.com
Online Published on 14 August, 2024. Abstract The current research investigated sequence polymorphism and allelic variation in the GBSS1 gene responsible for determining the apparent amylose content (AAC) in an aromatic rice germplasm panel. Analysis of 271 germplasm accessions from India revealed a wide range of variation in AAC, from 4.81% (Manipur Black Rice) to 35.88% (IGSR -3-1-5). Re-sequencing and sequence analysis of a representative subset of 28 accessions unveiled a nucleotide diversity (π) of 0.00374, identifying 72 sequence variants. Two novel non-synonymous SNPs were identified: a G/A transition in exon 2, resulting in the substitution of glutamic acid at the 91st position with lysine, and a C/T transition in exon 11, substituting alanine at the 468thposition with valine. Additionally, two previously reported SNPs were validated: A/C in exon 6 (Tyr224Ser) and C/T in exon 10 (Pro415Ser). Furthermore, a 23 bp exon 2 duplication was found in Manipur Black Rice (4.81%), Bhogali Bora (6.20%), and NJ-72 (7.36%), indicating the prevalence of this allele in the very low AAC category (3-9%) in addition to the glutinous or waxy rice category with 0-2% AAC. These findings are significant for manipulating starch content in aromatic rice germplasm. Top Keywords Amylose, Granule-bound starch synthase I, Rice, SNP, Waxy allele. Top |