Transcriptomic analyses provide molecular insight into the cold stress response of cold-tolerant alfalfa

• Published in: BMC plant biology 2024-08, Vol.24 (1), p.741-16, Article 741
• Main Authors: Pu, Xiaojian, Fu, Yunjie, Xu, Chengti, Li, Xiuzhang, Wang, Wei, De, Kejia, Wei, Xijie, Yao, Xixi
• Format: Article
• Language: English
• Subjects: Abscisic acid; Acclimation; Acclimatization; Acclimatization - genetics; Alfalfa; Assembly; Botanical research; Cellular stress response; Cold acclimation; Cold acclimatization; Cold resistance; Cold stress; Cold Temperature; Cold tolerance; Cold weather; Cold-Shock Response - genetics; Cultivars; Data analysis; Environmental aspects; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Plant; Genes; Genetic aspects; High altitude; Kinases; Low temperature resistance; Medicago sativa; Medicago sativa - genetics; Medicago sativa - physiology; Metabolic pathways; Metabolism; Network analysis; Nitrogen; Nitrogen metabolism; Photosynthesis; Physiological aspects; Phytohormones; Plant genetics; Plant hormones; Plant Proteins - genetics; Plant Proteins - metabolism; Protein turnover; Proteins; Quality control; Ribosomal proteins; Seeds; Signal transduction; Software; Stress (Physiology); Temperature; Transcription activation; Transcription factor; Transcription factors; Transcriptome; Transcriptomes; Transcriptomics; Tricarboxylic acid cycle; Ubiquitination; Variance analysis
• ISSN: 1471-2229; 1471-2229
• DOI: 10.1186/s12870-024-05136-y

Daye No.3 is a novel cultivar of alfalfa (Medicago sativa L.) that is well suited for cultivation in high-altitude regions such as the Qinghai‒Tibet Plateau owing to its high yield and notable cold resistance. However, the limited availability of transcriptomic information has hindered our investigation into the potential mechanisms of cold tolerance in this cultivar. Consequently, we conducted de novo transcriptome assembly to overcome this limitation. Subsequently, we compared the patterns of gene expression in Daye No. 3 during cold acclimatization and exposure to cold stress at various time points. A total of 15 alfalfa samples were included in the transcriptome assembly, resulting in 141.97 Gb of clean bases. A total of 441 DEGs were induced by cold acclimation, while 4525, 5016, and 8056 DEGs were identified at 12 h, 24 h, and 36 h after prolonged cold stress at 4 °C, respectively. The consistency between the RT‒qPCR and transcriptome data confirmed the accuracy and reliability of the transcriptomic data. KEGG enrichment analysis revealed that many genes related to photosynthesis were enriched under cold stress. STEM analysis demonstrated that genes involved in nitrogen metabolism and the TCA cycle were consistently upregulated under cold stress, while genes associated with photosynthesis, particularly antenna protein genes, were downregulated. PPI network analysis revealed that ubiquitination-related ribosomal proteins act as hub genes in response to cold stress. Additionally, the plant hormone signaling pathway was activated under cold stress, suggesting its vital role in the cold stress response of alfalfa. Ubiquitination-related ribosomal proteins induced by cold acclimation play a crucial role in early cold signal transduction. As hub genes, these ubiquitination-related ribosomal proteins regulate a multitude of downstream genes in response to cold stress. The upregulation of genes related to nitrogen metabolism and the TCA cycle and the activation of the plant hormone signaling pathway contribute to the enhanced cold tolerance of alfalfa.