Fine mapping of the grain chalkiness quantitative trait locus qCGP6 reveals the involvement of Wx in grain chalkiness formation.

This article focuses on the genetic and environmental factors influencing grain chalkiness in rice, a key determinant of rice appearance and quality. Using a recombinant inbred line (RIL) population derived from two indica rice varieties, Shuhui498 (R498) and Yihui3551 (R3551), the study identified 42 quantitative trait loci (QTLs) related to chalkiness, with two stable major QTLs, qCGP6 and qCGP8, detected across multiple environments. Fine mapping of qCGP6 pinpointed the Wx gene, which encodes granule-bound starch synthase I (GBSSI), as a key regulator of chalkiness; alleles Wxa and Wxin were associated with higher chalkiness and amylose content compared to Wxb. The study also demonstrated that the effect of Wx alleles on chalkiness is environment-dependent, particularly sensitive to light intensity, and that CRISPR/Cas9-mediated editing of the Wx promoter can reduce chalkiness by down-regulating Wx expression, offering a promising strategy for breeding rice varieties with improved eating and appearance qualities.