Stage-preferential transcriptome profiling reveals senescence associated transcriptional programs linked to nutrient remobilization in rice flag leaves during grain filling.

Leaf senescence during grain filling in cereals redistributes carbon, nitrogen, and mineral nutrients from source leaves to developing grains, thereby strongly affecting yield formation. Here, we profiled rice flag leaf transcriptomes at five reproductive stages (1 week before heading, heading, and 1, 3, and 5 weeks after heading) and identified stage-preferential genes using an intersection-based criterion in which genes upregulated at one stage were compared with those at all other stages. Transcriptional reprogramming was most pronounced at heading, with 419 preferentially expressed genes, and at five weeks after heading, with 1317 genes. Genes preferentially expressed at heading were enriched in jasmonate-related and defense-associated processes, whereas genes preferentially expressed at five weeks after heading were associated with senescence, nutrient transport, alternative respiration, and plastid regulation. A STRING-guided protein-protein interaction network integrating genes preferentially expressed at five weeks after heading with reference genes from the Leaf Senescence Database identified hub candidates associated with chloroplast and chlorophyll turnover and nitrogen remobilization. Quantitative RT-PCR analysis in the pale-green leaf mutant (pgl) revealed broadly reduced expression of representative hub genes, suggesting attenuation of late-stage senescence network activity. Together, these findings provide a stringent stage-resolved framework for prioritizing regulators of late senescence in rice flag leaves during grain filling.