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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 6427 differentially expressed genes (DEGs) in XZX45 and SQSL, respectively. Among these DEGs, 4672 (G2) were shared by both cultivars, while 3472 DEGs (G1) were specific to XZX45, and 1755 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 \u201cresponse to cold\u201d 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 \u201cPyruvate metabolism\u201d, \u201cGlycolysis\/Gluconeogenesis\u201d, and \u201cStarch and sucrose metabolism\u201d, 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.<\/jats:p>","DOI":"10.3390\/plants12142675","type":"journal-article","created":{"date-parts":[[2023,7,18]],"date-time":"2023-07-18T01:35:16Z","timestamp":1689644116000},"page":"2675","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["Transcriptomic Profiling of Cold Stress-Induced Differentially Expressed Genes in Seedling Stage of Indica Rice"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-9116-8719","authenticated-orcid":false,"given":"Tao","family":"Yan","sequence":"first","affiliation":[{"name":"College of Agronomy, Hunan Agricultural University, Changsha 410128, China"},{"name":"Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meng","family":"Sun","sequence":"additional","affiliation":[{"name":"College of Agronomy, Hunan Agricultural University, Changsha 410128, China"},{"name":"Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rui","family":"Su","sequence":"additional","affiliation":[{"name":"College of Agronomy, Hunan Agricultural University, Changsha 410128, China"},{"name":"Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaozhong","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Agronomy, Hunan Agricultural University, Changsha 410128, China"},{"name":"Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7046-9101","authenticated-orcid":false,"given":"Xuedan","family":"Lu","sequence":"additional","affiliation":[{"name":"College of Agronomy, Hunan Agricultural University, Changsha 410128, China"},{"name":"Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0488-0781","authenticated-orcid":false,"given":"Yunhua","family":"Xiao","sequence":"additional","affiliation":[{"name":"College of Agronomy, Hunan Agricultural University, Changsha 410128, China"},{"name":"Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huabing","family":"Deng","sequence":"additional","affiliation":[{"name":"College of Agronomy, Hunan Agricultural University, Changsha 410128, China"},{"name":"Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiong","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Agronomy, Hunan Agricultural University, Changsha 410128, China"},{"name":"Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenbang","family":"Tang","sequence":"additional","affiliation":[{"name":"College of Agronomy, Hunan Agricultural University, Changsha 410128, China"},{"name":"Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China"},{"name":"Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410128, China"},{"name":"State Key Laboratory of Hybrid Rice, Changsha 410128, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guilian","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Agronomy, Hunan Agricultural University, Changsha 410128, China"},{"name":"Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,7,17]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1016\/S1369-5266(99)00047-3","article-title":"International Rice Genome Sequencing Project: The Effort to Completely Sequence the Rice Genome","volume":"3","author":"Sasaki","year":"2000","journal-title":"Curr. 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