Identification Of Arabidopsis genes associated with cold tolerance based on integrated bioinformatics analysis

Journal of plant interactions

article

Meili Guo¹  Xin Liu²  Yusu Jiang¹  Jinhuan Yu¹  Tao Meng¹ 

[1] a Department of Food and Biochemistry Engineering, Yantai Vocational College;b Central Laboratory, The Affiliated Yantai Yuhuangding Hospital of Qingdao University

关键词: Arabidopsis thaliana;    cold stress;    DEGs;    integrated bioinformatics analysis;    photoprotection;    cell wall homeostasis;   

DOI  :  10.1080/17429145.2021.1955164

学科分类：纳米科学和纳米技术

来源: Taylor & Francis

【 摘 要 】

Cold stress is a major environmental factor that limits plant growth and productivity. Plants have evolved various strategies to adapt to these environmental conditions. To better explain the mechanisms used to survive environmental challenges, we retrieved the cold-responsive genes of Arabidopsis thaliana from the Gene Expression Omnibus (GEO) database. The GEO raw data were normalized by the quantile method, and then the differentially expressed genes (DEGs) under cold stress were screened using the robust rank aggregation (RRA) algorithm, including 261 upregulated and 177 downregulated genes out of more than 20,000 genes. Further, the integrated bioinformatics analyses of PUBMED, PANTHER, DAVID, and STRING indicated that the upregulated DEGs were involved in cellular response to red light, negative regulation of circadian rhythm, photoprotection, monosaccharide transport, cold acclimation, and phosphate ion homeostasis, while the downregulated DEGs were associated with the indole glucosinolate biosynthetic process, regulation of RNA splicing, water transport, cell wall modification, cell wall loosening, cellular water homeostasis, and cell wall homeostasis. Furthermore, the up-regulated DEGs had about four times protein-protein-interactions (PPIs) than the down-regulated DEGs, and the cold-responsive genes were identified using Cytoscape software. Furthermore, qRT-PCR of low-temperatureresponsive protein 78 (LTI78), transducin family protein (SWA1), and arginine methyltransferase 11 (PRMT11) were performed to validate the outcome of integrated bioinformatics analysis. Our work will improve our knowledge of cold-responsive mechanisms and these DEGs might be targets for plant cold stress-resistance research.

【 授权许可】

CC BY|CC BY-NC