Integrated transcriptome and co-expression network analysis revealed the molecular mechanism of cold tolerance in japonica rice at booting stage (PRJCA042262)

Low-temperature is a critical factor limiting rice yield and quality, particularly during the booting stage, where chilling injury disrupts pollen development and significantly reduces the seed-setting rate. In this study, we systematically investigated the molecular mechanisms underlying cold tolerance in japonica rice by analyzing phenotypic and transcriptome data from 14 japonica rice varieties under cold stress at the booting stage, combined with weighted gene co-expression network analysis (WGCNA). The results demonstrated that cold stress significantly reduced yield-related traits in all tested varieties, with the most pronounced decline observed in the seed-setting rate, which served as a reliable indicator for evaluating cold tolerance. Transcriptome analysis identified 6,240 and 7,996 differentially expressed genes (DEGs) in cold-tolerant and cold-sensitive varieties, respectively, from which a core set of 1,875 cold-tolerance-related genes was screened. KEGG enrichment analysis revealed that these genes were significantly enriched in pathways closely associated with cold tolerance, including plant hormone signal transduction and the MAPK signaling pathway. Furthermore, WGCNA analysis identified a seed-setting rate-associated blue module, which contained 10 highly connected candidate genes and 20 core transcription factors potentially involved in cold tolerance. This study provides novel insights into the molecular mechanisms of cold tolerance in rice and offers valuable targets for molecular breeding of cold-resistant cultivars.