Natural variation of a transcriptional repressor encoding gene GPC6 confers grain protein content in rice

ABSTRACT Grain protein content (GPC) is well‐known to negatively influence the eating and cooking quality in rice. However, the genetic mechanism underlying the natural variation of GPC is very limited. Here, we identify GPC6 as a key determinant through genome–wide association analysis. GPC6 encodes a protein with a MYB–like domain, functioning as a transcriptional repressor to modulate the expression of storage protein synthesis genes ( Alb1 , Pro13b.5 , RM1 , OsGluB1b , OsGluB7 ) and two regulators ( RISBZ1 and PDIL1 – 1 ). Further, one functional SNP (−1,471 T/C) in the GPC6 promoter was identified, which defines two haplotypes: high–expression GPC6 T (Low protein) and low–expression GPC6 C (High protein). Notably, the GPC6 T allele has been subject to artificial selection in modern East Asian japonica rice varieties. Collectively, these findings provide a crucial foundation for understanding the genetic mechanisms underlying the rice GPC variation and an important target gene for quality improvement practice.