Genome-Wide Association Study of Cooked Rice Textural Properties and Starch Physicochemical Properties in indica Rice

Rice cooking and eating qualities (CEQ) are mainly determined by cooked rice textural parameters and starch physicochemical properties. However, the genetic bases of grain texture and starch properties in rice have not been fully understood. We conducted a genome-wide association study for apparent amylose content (AAC), starch pasting viscosities, and cooked rice textural parameters using 279 indica rice accessions from the 3000 Rice Genome Project. We identified 26 QTLs in the whole population and detected SNPs with the lowest p-value at the Waxy locus for all traits except pasting temperature. Additionally, we detected significant SNPs at the SUBSTANDARD STARCH GRAIN6 (SSG6) locus for AAC, setback (SB), hardness, adhesiveness, chewiness (CHEW), gumminess (GUM), and resilience. We subsequently divided the population using a SNP adjacent to the Waxy locus, and identified 23 QTLs and 12 QTLs in two sub-panels. In these sub-panels, SSG6 was also identified to be associated with pasting parameters including peak viscosity, hot paste viscosity, cold paste viscosity, and consistency viscosity. Furthermore, a candidate gene encoding monosaccharide transporter 5 (OsMST5) was identified to be associated with AAC, breakdown, SB, CHEW, and GUM. In total, 45 QTLs were co-localized with known genes or previously reported QTLs. These identified genes and QTLs provide valuable information for genetic manipulation to improve rice CEQ.