Natural Variation and Expression of OsCFF1 Affect the Formation of Rice Chalkiness

Chalkiness, as a major undesired-index for rice quality evaluation, is the opaque/white structure in rice endosperm, and determines the rice grade and price to a large extent. Reducing chalkiness remains one of the most important goals for breeders and producers. In this study, we identified a rice chalkiness formation-related gene (OsCFF1) that encodes a glycosyltransferase (GT). Through screening of OsCFF1 alleles in 60 rice cultivars, four genotypes were identified, including WT and three natural variations. Cultivars with natural variations that cause the function loss of OsCFF1 usually produce fewer chalky grains. Higher OsCFF1 expression during the grain-filling period is usually associated with a higher degree of chalkiness. Notably, the chalkiness in gene-edited rice kernels was decreased by more than 90% after knocking out OsCFF1 through CRISPR/Cas9, indicating a quality reversal from inferior rice with high chalkiness to superior rice with very little chalkiness. We also found that OsCFF1 might catalyze the glycosylation of GA_4, and the corresponding mechanism requires in-depth exploration. In summary, OsCFF1 is a key factor controlling the formation of rice chalkiness and demonstrates enormous potential for application in high-quality rice breeding.