Exploring the glycaemic impact and culinary qualities of rice through Genome-Wide Association studies on starch composition and viscosity profiles

Abstract

Starch is the major component in rice grain that determines not just the cooking and eating quality of rice but also the nutritive value of a particular rice variety. It also plays a key role in determining the consumer acceptance of a variety, its trade and market value. Thus, it is essential to assess the available genetic variation for starch composition in the rice germplasm and its effective utilization in varietal improvement programmes. In assessing the nutritional value of rice, resistant starch has received a lot of attention lately. It plays vital roles in reducing glycaemic index and post prandial glucose. The study evaluated a set of 192 rice genotypes of diverse origins for starch composition and viscosity parameters and observed significant variation for these traits. Genome-wide association studies (GWAS) using the multi-locus models BLINK and FarmCPU in GAPIT software resulted in the identification of 45 significant Marker Trait Associations (MTAs) distributed in 11 of the 12 chromosomes except chromosome 8. A total of 15 annotated genes in the 250 kb LD region flanking the significant SNP were identified as putative candidates through insilico analysis. Some of the important genes underlying the MTAs found were GBSSI, OsACS, SSG6, RSR1 and OsPUL which are known to be associated with starch synthesis in rice. The significant MTAs could be deployed in manipulating the starch composition and developing tailored rice varieties for various consumer needs.