Genome-wide association study (GWAS) for digestibility in rice straw.

Abstract

Genome-wide association study (GWAS) based on linkage disequilibrium (LD) of single nucleotide polymorphism (SNP) provides a promising tool for the detection and fine mapping of quantitative trait loci (QTL) in plants. In this study, the authors showed GWAS for saccharification (digestibility) trait of rice straw-based on genotyping by sequencing (GBS) and the ability of sugar released from the straw of 170 rice accessions of Indica rice subspecies that were collected in Vietnam. In the GBS result, the authors obtained a total of 328,656 SNPs stored in Hapmap on the 12 chromosomes. The average density of SNP markers in our panel was 1SNP/1 kb in the rice genome. The saccharification (sugar released) from the straw of 170 rice accessions ranged from 27.92-132.56 nmol/mg/hour (for straw harvested in Spring 2017) and from 31.98-148.63 nmol/mg/hour (for straw harvested in Summer season 2017). The results of GWAS for saccharification, at Log10(P-value) ≥3 with significant p<0.001 the authors identified 7 peak SNPs on chromosome 6 with the frequency of minor allen from 23 to 35%. Base on the LD to search within ±200 kb of peak SNP, and base on whether the function of the gens had been characterized before in rice, the authors identified 24 candidate genes on chromosome 6 for saccharification. Among them, 4 genes are LOC_Os06g39070 (GT1), LOC_Os06g39080 (GT1), LOC_Os06g39390 (AT10) and LOC_Os06g39470 (AT8) have functions related to cell wall synthesis and lignocellulose degradation in rice. These candidate genes are further researched to develop molecular markers used in rice breeding with the trait of high saccharification of straw and to detect genes for high saccharification rice straw.