Systems Genetics Identifies a Novel Regulatory Domain of Amylose Synthesis

TLDR

A deeper understanding of the regulation of starch biosynthesis in rice endosperm is crucial for tailoring digestibility without sacrificing grain quality. The study aimed to identify significant association peaks on chromosomes 6 and 7 linked to starch structure via a genome‑wide association study of debranched starch from 320 indica rice samples. The authors employed a GWAS combined with systems genetics and a gene‑regulatory network to link starch structure to amylose/amylopectin ratios and to digestibility kinetics. They identified promoter SNPs in Granule Bound Starch Synthase I and a nonsynonymous SNP in a bHLH transcription factor that define haplotypes affecting amylose and amylopectin levels, linked these haplotypes to digestibility kinetics, and proposed them as markers for breeding rice with tailored starch digestibility.

Abstract

A deeper understanding of the regulation of starch biosynthesis in rice (Oryza sativa) endosperm is crucial in tailoring digestibility without sacrificing grain quality. In this study, significant association peaks on chromosomes 6 and 7 were identified through a genomewide association study (GWAS) of debranched starch structure from grains of a 320 indica rice diversity panel using genotyping data from the high-density rice array. A systems genetics approach that interrelates starch structure data from GWAS to functional pathways from a gene regulatory network identified known genes with high correlation to the proportion of amylose and amylopectin. An SNP in the promoter region of Granule Bound Starch Synthase I was identified along with seven other SNPs to form haplotypes that discriminate samples into different phenotypic ranges of amylose. A GWAS peak on chromosome 7 between LOC_Os07g11020 and LOC_Os07g11520 indexed by a nonsynonymous SNP mutation on exon 5 of a bHLH transcription factor was found to elevate the proportion of amylose at the expense of reduced short-chain amylopectin. Linking starch structure with starch digestibility by determining the kinetics of cooked grain amylolysis of selected haplotypes revealed strong association of starch structure with estimated digestibility kinetics. Combining all results from grain quality genomics, systems genetics, and digestibility phenotyping, we propose target haplotypes for fine-tuning starch structure in rice through marker-assisted breeding that can be used to alter the digestibility of rice grain, thus offering rice consumers a new diet-based intervention to mitigate the impact of nutrition-related noncommunicable diseases.