Identifications of genes involved in ABA and MAPK signaling pathways positively regulating cold tolerance in rice

Cold stress (CS) significantly impacts rice growth during seedling and heading stages. This study based on two-year field observations identified two rice lines, L9 (cold stress-sensitive) and LD18 (cold stress-tolerant) showing contrasting CS response. L9 exhibited 38% reduction in photosynthetic efficiency, whereas LD18 remained unchanged, correlating with seed rates. Transcriptome analysis identified differentially expressed genes (DEGs) with LD18 showing enriched pathways (carbon fixation, starch/sucrose metabolism, glutathione metabolism). LD18 displayed dramatically enhanced expression of MAPK-related genes ( LOC4327351 , LOC4352460 , LOC4337850 ) and increased ABA signaling genes ( LOC4333690 , LOC4345611 , LOC4335640 ) compared to L9 exposed to CS. Results from qPCR confirmed the enhanced expression of the three MAPK-related genes in LD18 while dramatic reduction in L9 under CS relative to that under CK. We also observed up to 66% reduction in expression levels of the three genes related to ABA signaling pathway in L9 relative to LD18 under CS. In consistent with results of photosynthetic efficiency, metabolic analysis suggests pyruvate metabolism, TCA cycle and carbon metabolism enrichment in LD18 under CS. The study reveals reprogramming of the carbon assimilation metabolic pathways, emphasizing the critical roles of the key DEGs involved in ABA and MAPK signaling pathways in positive regulation of LD18 response to CS, offering the foundation towards cold tolerance breeding through targeted gene editing.