Genome-wide analysis of the CDPK gene family and their important roles response to cold stress in white clover

ABSTRACT

Calcium-dependent protein kinases (CDPKs) are an important class of calcium-sensitive response proteins that play an important regulatory role in response to abiotic stresses. To date, little is known about the CDPK genes in white clover. White clover is a high-quality forage grass with high protein content, but it is susceptible to cold stress. Therefore, we performed a genome-wide analysis of the CDPK gene family in white clover and identified 50 members of the CDPK genes. Phylogenetic analysis using CDPKs from the model plant Arabidopsis divided the TrCDPK genes into four groups based on their sequence similarities. Motif analysis showed that TrCDPKs within the same group had similar motif compositions. Gene duplication analysis revealed the evolution and expansion of TrCDPK genes in white clover. Meanwhile, a genetic regulatory network (GRN) containing TrCDPK genes was reconstructed, and gene ontology (GO) annotation analysis of these functional genes showed that they contribute to signal transduction, cellular response to stimuli, and biological regulation, all of which are important processes in response to abiotic stresses. To determine the function of TrCDPK genes, we analyzed the RNA-seq dataset and found that most TrCDPK genes were highly up-regulated under cold stress, particularly in the early stages of cold stress. These results were validated by qRT-PCR experiments, implying that TrCDPK genes are involved in various gene regulatory pathways in response to cold stress. Our study may help to further investigate the function of TrCDPK genes and their role in response to cold stress, which is important for understanding the molecular mechanisms of cold tolerance in white clover and improving its cold tolerance.

KEYWORDS:

• White clover
• CDPK
• Genetic regulation network
• Cold stress
• RNA-seq

Acknowledgments

This research was funded by the National Key Research and Development Program (2022YFF1302404), Natural Science Foundation of Heilongjiang Province (grant number LH2022C050), and Natural and Science Foundation of China (grant number U21A20182). The data analysis work was supported by high-performance computing center of Harbin Normal University.

Disclosure statement

No potential conflict of interest was reported by the authors.

Authors contributions

YS, CG, and WY conceived and the study, ML, XC, WH, and QL conducted the experiments, YS, ML, WY, and XC analyzed the data, YS, ML, and CG wrote the manuscript, all authors read and approved the final manuscript.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/15592324.2023.2213924

Additional information

Funding

The work was supported by the National Key Research and Development Program of China [2022YFF1302404]; Natural Science Foundation of Heilongjiang Province [LH2022C050]; Natural and Science Foundation of China [U21A20182]