Genome-wide association study (GWAS) and transcription analysis of candidate genes for rice grain eating and cooking quality (ECQ) traits

Rice eating and cooking quality (ECQ) is a key determinant of consumer preference and market value, governed by complex genetic and biochemical mechanisms. This study aimed to dissect the genetic architecture underlying three major ECQ-related traits including amylose content (AC), gelatinization temperature (GT), and gel consistency (GC), using a panel of 243 diverse rice accessions through a genome-wide association study (GWAS), epistatic interaction analysis, haplotype analysis, and gene expression profiling. Phenotypic evaluation revealed extensive variability for all three traits, accompanied by high narrow-sense heritability estimates, indicating strong genetic control. Based on the FarmCPU model, 29 significant SNPs corresponding to 23 quantitative trait loci (QTLs)-11 for GT, 6 for GC, and 6 for AC-were identified across 10 chromosomes. Among them, qAC6-1, overlapping with the Waxy (WX1/GBSS1) gene, was determined as the major locus for AC; qGC2-1 on chromosome 2 emerged as the principal region governing GC; and three major GT-related QTLs (qGT6-1, qGT6-2, qGT6-3) were located near the SSIIa gene on chromosome 6. Epistatic analysis revealed 18 significant interactions (4 for AC, 6 for GC, and 8 for GT), underscoring the polygenic and interactive nature of rice quality traits. Haplotype analysis within qGC2-1 identified three haplogroups, among which H001-defined by the SNP combination "G/T/G/A"-was associated with superior gel consistency. Functional annotation and RNA-Seq expression profiling identified 12 candidate genes potentially involved in ECQ regulation, including WX1, Amy2A, IRX9, OsNAC1, PMEI25, and OsFbox132. Quantitative RT-PCR validated the expression of key genes (WX1, Amy2A, and IRX9) at different seed developmental stages in high- and low-quality rice genotypes. Overall, the integration of genomic, haplotypic, and transcriptional analyses provides new insights into the molecular control of rice grain quality. The identified QTLs, candidate genes, and favorable haplotypes serve as valuable genomic resources for marker-assisted selection and molecular breeding strategies aimed at developing rice varieties with superior eating and cooking qualities.