Transcriptome sequencing analysis of overexpressed SikCDPK1 in tobacco reveals mechanisms of cold stress response

• Published in: BMC genomics Vol. 25; no. 1; pp. 971 - 13
• Main Authors: Shi, Guangzhen, Zhu, Xinxia
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 16-10-2024; BioMed Central; BMC
• Subjects: Adaptation; Analysis; Annotations; Anopheles; Biological activity; Biological effects; Calcium; Calcium signalling; Care and treatment; Cold; Cold tolerance; Cold treatment; Cold-Shock Response - genetics; Diseases and pests; DNA binding proteins; Electric properties; Enrichment; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Plant; Gene sequencing; Genes; Genetic aspects; Genetic engineering; Genetic transcription; Genomes; Growth; Hardiness; Kinases; Leaves; MAP kinase; Metabolic pathways; Moisture content; Nicotiana - genetics; Nicotiana - metabolism; Phenotypes; Physiology; Plant layout; Plant Proteins - genetics; Plant Proteins - metabolism; Plant resistance; Plants; Plants, Genetically Modified; Protein kinases; Protein Kinases - genetics; Protein Kinases - metabolism; RNA; RNA-seq; Sequence analysis; Signal transduction; SikCDPK1; Software; Substance abuse; Technology assessment; Tobacco; Tobacco (Plant); Transcription factors; Transcriptome; Transcriptome sequencing; Transcriptomes; Transgenic plants; Water content; China; Beijing China; Transcriptome sequencing; Cold; RNA-seq; SikCDPK1
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-024-10801-5

Cold is a significant limiting factor in productivity, particularly in northwestern and eastern China. Calcium-Dependent Protein Kinases (CDPKs), a primary calcium signaling sensor in plants, play an important role in their response to cold. Snow lotus (Sasussured involucrata Kar L) is a plant that thrives in harsh climates and grows in northwest China. However, there were no reports on the transcriptome of OE-SikCDPK1 transgenic tobacco in response to cold.
When exposed to cold stress, OE-SikCDPK1 plants displayed a cold-tolerant phenotype compared to non-transgenic tobacco. Under cold conditions, relative water content reduced, relative conductivity increased, malondialdehyde levels rose, and cold-responsive gene expression increased. The OE-SikCDPK1 gene and non-transgenic tobacco were employed for research purposes. The transcriptome of leaves was sequenced using the HISAT2 sequencing platform, and the data were used to examine gene function annotation and differentially expressed genes (DEGs). 53,022 DEGs in tobacco leaves under cold treatment were obtained. The GO enrichment results revealed that it was enriched for biological-process, defense response and other processes under cold stress. The KEGG pathway enrichment analysis revealed that the metabolic pathways of significant enrichment of DEGs under cold stress mainly involved MAPK signaling pathway transduction. The transcription factor identification results showed that the transcription factors with the largest number of differential expressions under cold treatment were mainly from WRKY, AP2, MYB, bHLH, NAC and other transcription factor families.
The cold tolerance mechanism of snow lotus SikCDPK1 was comprehensively analyzed at the transcriptional level for the first time using RNA-seq technology. This study demonstrates that SikCDPK1 can respond to cold by participating in the MAPK signaling pathway and regulating the expression levels of transcription factors, including WRKY, AP2, MYB, bHLH, and NAC. These results offer valuable insights for further exploration of the cold tolerance mechanism associated with SikCDPK1.