Transcriptome Analyses Reveal Distinct Grain Filling Mechanisms Between Low Light–Tolerant and Low Light–Sensitive Rice (Oryza sativa L.) Varieties Under Low Light Conditions

Low light conditions, caused by prolonged cloudy and rainy weather during the grain-filling stage, lead to significant reductions in rice quality and yield. However, the molecular mechanisms underlying grain filling under low light remain poorly understood. In this study, two Japonica rice varieties, Xinfeng 6 (Xin 6; low light–tolerant) and Nipponbare (NP; low light–sensitive), were employed to investigate these mechanisms. Under low light conditions, Xin 6 exhibited less pronounced changes in 1000-grain weight, chalkiness, starch and storage protein content, and endosperm starch granule structure compared to NP. Transcriptome analyses revealed that the number of genes regulated by low light in NP grains was approximately threefold higher than that in Xin 6 grains. Notably, a significant number of genes associated with sucrose-starch synthesis, glycolysis, and abscisic acid, calcium, and mitogen-activated protein kinase signalling pathways were downregulated in NP but remained unaffected in Xin 6. Gene network analyses suggest that Tre6P signalling integrates respiration, starch synthesis, low-temperature response and trehalose synthesis in grains under low light. These findings provide novel insights into the molecular mechanisms of low light tolerance in rice.