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Plants, Vol. 12, Pages 2675: Transcriptomic Profiling of Cold Stress-Induced Differentially Expressed Genes in Seedling Stage of Indica Rice
Plants doi: 10.3390/plants12142675
Authors: Tao Yan Meng Sun Rui Su Xiaozhong Wang Xuedan Lu Yunhua Xiao Huabing Deng Xiong Liu Wenbang Tang Guilian Zhang
Cold stress significantly constrains the growth, development, productivity, and distribution of rice, particularly the indica cultivar, known for its susceptibility to cold, limiting its cultivation to specific regions. This study investigated the genes associated with cold responsiveness in the roots of two indica cultivars, SQSL (cold-tolerant) and XZX45 (cold-susceptible), through transcriptome dynamics analysis during the seedling stage. The analysis identified 8144 and 6,427 differentially expressed genes (DEGs) in XZX45 and SQSL, respectively. Among these DEGs, 4,672 (G2) were shared by both cultivars, while 3,472 DEGs (G1) were specific to XZX45, and 1,755 DEGs (G3) were specific to SQSL. Additionally, 572 differentially expressed transcription factors (TFs) from 48 TF families, including WRKY, NAC, bHLH, ERF, bZIP, MYB, C2H2, and GRAS, were identified. Gene Ontology (GO) enrichment analysis revealed significant enrichment of DEGs in the G3 group, particularly in the “response to cold” category, highlighting the crucial role of these specific genes in response to cold stress in SQSL. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated pronounced enrichment of DEGs in the G3 group in metabolic pathways such as “Pyruvate metabolism,” “Glycolysis/Gluconeogenesis,” and “Starch and sucrose metabolism,” contributing to cold tolerance mechanisms in SQSL. Overall, this study provides comprehensive insights into the molecular mechanisms underlying cold responses in the indica cultivar, informing future genetic improvement strategies to enhance cold tolerance in susceptible indica rice cultivars.
