Natural variation of an E3 ubiquitin ligase encoding gene Chalk9 regulates grain chalkiness in rice.

Grain chalkiness is an undesirable trait affecting rice quality, concerning both consumers and breeders. However, the genetic mechanisms underlying rice chalkiness remain largely elusive. Here, we identify Chalk9 as a major gene associated with grain chalkiness in a natural population. Chalk9 encodes an E3 ubiquitin ligase that targets OsEBP89 for its ubiquitination and degradation. Low expression of Chalk9 results in excessive accumulation of OsEBP89, disrupting the homeostasis of storage components and leading to the chalkiness phenotype. A 64-bp insertion/deletion in the Chalk9 promoter contributes to its differential transcriptional levels, thus causing chalkiness variation among rice varieties. Moreover, the elite allele Chalk9-L reduces grain chalkiness, without compromising yield. Chalk9-L is strongly selected in japonica but exhibits a complex evolutionary trajectory in indica. Our findings reveal the molecular and genetic mechanisms underlying chalkiness and provide a potential strategy for breeding rice varieties with improved quality.