Comprehensive GWAS and Transcriptome Analysis Discovered Candidate Gene Associated with Starch Pasting Properties of Temperate japonica rice (Oryza sativa L.).

Abstract

The growing market demand for high eating quality (EQ) rice, driven by improved living standards, highlights the need to better understand its complex genetic architecture. Starch pasting properties are critical determinants of rice EQ, yet their genetic basis remains incompletely understood. This study aimed to unravel the genetic factors underlying starch pasting properties in temperate japonica rice panel of 284 accessions comprising landraces and improved varieties. Genome-wide association studies conducted for two years identified 59 significant lead SNPs. Among them, consistent lead SNPs on chromosomes 2 and 8, in addition to the well-characterized Wx gene on chromosome 6 were detected from multiple traits and years. LD block analysis and transcriptome analysis of accessions with extreme phenotypes identified OsGLUTN (Os02g0224300/LOC_Os02g13130), a gene encoding a high molecular weight glutenin subunit-like protein, as a strong candidate. Clustering patterns of differential gene expressions showed higher expression of OsGLUTN in low-viscosity cultivars and lower expression in high-viscosity cultivars. Haplotype analysis revealed significant variations in viscosity traits associated to OsGLUTN alleles, and functional validation using enhancer active tagging line showed significantly reduced starch viscosity, confirming its role in EQ regulation. While the Wx accounted for most viscosity traits, the identification of novel loci on chromosomes 2 and 8 highlights additional genetic factors to EQ variation. These findings deepen our understanding of how storage protein metabolism impacts rice grain quality. The identification of OsGLUTN provides a foundation for breeding programs focused on developing rice varieties with improved cooking and eating qualities, addressing growing consumer demand for premium rice.