Transcriptomic analysis of field-grown rice (Oryza sativa L.) reveals responses to shade stress in reproductive stage

The number of spikelets per panicle is a key factor affecting rice (Oryza sativa L.) yield, and is regulated by many different environmental cues, such as light intensity. In this study, we found that shade led to a reduction in the number of secondary branches and fewer spikelets per panicle. Rice grown in the shade had an increased spikelet degradation rate. We studied the genes that respond to shade in rice using transcriptome sequencing, which revealed that rice floral genes OsFKF1 and OsDof12 expression levels were suppressed by shading. However, Heading date 1 (Hd1), Heading date 3a (Hd3a), and Early heading date 1 (Ehd1) were induced and RICE FLOWERING LOCUS T 1 (RFT1) was suppressed without any obvious change in heading time. Furthermore, the expression level of spikelet differentiation-related genes OsFOR1, FON1, OsPBP1 and OsSPL16 were influenced by shade stress, may led to changes in spike structural. Shade affected the expression of growth-related genes that are involved in metabolism, DNA synthesis/chromatin structure, and the environmental adaptation pathway. Genes involved in chloroplast development were downregulated in leaves under shade. In addition, genes that regulate energy expenditure were suppressed by shade in both young panicles and leaves, indicating that damage to the leaf photosynthetic apparatus reduces the energetic costs of the plant. Organic synthesis-related genes were suppressed in young panicles of plants under shade, suggesting that shade slows panicle development. The identification of novel differentially expressed genes provides new insights into the effects of light deficiency on young panicle development in rice.