Molecular Mechanisms of Grain Chalkiness Variation in Rice Panicles

Grain chalkiness adversely affects rice quality, and the positional variation of grain chalkiness within a rice panicle presents a substantial obstacle to quality improvement in China. However, the molecular mechanism underlying this variation is unclear. This study conducted a genetic and physiological analysis of grains situated at distinct positions (upper, middle, and bottom primary branches of the rice panicle, denoted as Y1, Y2, and Y3) within a rice panicle using the Yangdao 6 variety. The results indicated that the percentage of chalky grains (PCG) in Y1 was the highest, i.e., 17.12% and 52.18% higher than that of Y2 and Y3, respectively. Y2 exhibited the highest degree of grain chalkiness (DGC), attributable to its greater area of endosperm chalkiness (AEC) than the others. Y3 demonstrated the lowest PCG and DGC. Additionally, Y1 and Y2 were characterized by lower amylose and protein contents, as well as looser starch granule morphology, in comparison to Y3. Compared with Y3, both the average and maximum filling rates of Y1 and Y2 increased markedly; however, the active filling duration was notably reduced by 7.10 d and 5.56 d, respectively. The analysis of genomic expression levels indicated an enrichment of starch and sucrose metabolism in Y1-vs.-Y2, Y2-vs.-Y3, and Y1-vs.-Y3, with 7 genes (5 up-regulated and 2 down-regulated), 53 genes (12 up-regulated and 41 down-regulated), and 12 genes (2 up-regulated and 10 down-regulated) in the Y1-vs.-Y2, Y2-vs.-Y3, and Y1-vs.-Y3. The majority of these genes were down-regulated, linking metabolic activity to grain filling and contributing to the occurrence of grain chalkiness in rice panicles. In conclusion, the metabolic processes associated with sucrose and starch play a crucial role in regulating grain filling and the formation of chalkiness in rice.