Abstract
Objectives
Calcium-dependent protein kinases (CDPKs) function directly in plant development and stress responses. We used whole genome sequences and mRNA expression data to analyze the phylogenetic relationships, gene structure, collinearity, and differential expression of CDPKs in two differentially drought-tolerant potato varieties.
Results
In total, we identified 25 CDPK proteins belonging to four subfamilies. There was a significant collinear relationship among 13 CDPK genes belonging to four segmentally duplicated pairs. Subcellular prediction implied that all StCDPKs were localized at the plasma membrane. Analysis of promoter regions revealed that StCDPKs were photosensitive and responsive to biotic stress, abiotic stress, and hormone stimuli. RNA-seq analysis showed differential expression of StCDPKs among various potato tissues, and qPCR analysis revealed that 20 StCDPKs exhibited differential expression patterns under drought stress between drought-tolerant (QS9) and drought sensitive (Atl) potato varieties. Among these, the most strongly drought-induced genes were respectively StCDPK3 and StCDPK23, highlighting these as attractive candidate genes for further functional analyses of drought-stress responses in potato.
Conclusions
Our results demonstrating the tissue specific and drought stress-responsive StCDPK genes of potato both provide a reference for further research about the functions of CDPK family proteins and should support ongoing efforts for the further genetic improvement of potato.
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Supplemental materials
Supplementary Fig. 1 Physical locations of CDPK genes in S. tuberosum. In total, 25 StCDPK genes were mapped onto the 11 chromosomes of S. tuberosum. Green bars represent chromosomes in S. tuberosum, and the scale shows chromosome length.
Supplementary Fig. 2 Ten motifs identified in the promoter regions of StCDPK genes.
Supplementary Fig. 3 Distribution of cis-elements recognized by TF families of AT-Hook, AP2/ERF, Dof, bHLH, Dehydrin, bZIP and GATA.
Supplementary Fig. 4 Distribution of cis-elements recognized by TF families of NF-YB, TCP, WRKY, HSF, ZF-HD, Trehelix and MYB.
Supplementary Table 1 All protein sequences used for phylogenetic analysis in this study.
Supplementary Table 2 The FPKM value for StCDPKs expressed in different tissues (data was extracted from Spud DB, https://solanaceae.plantbiology.msu.edu/pgsc_download.shtml).
Supplementary Table 3 Sequences of primers for qPCR used in this study.
Supplementary Table 4 List of 25 CDPK genes in S. tuberosum and their basic characterizations.
Supplementary Table 5 The cis-element categories detected using PlantCARE for the promoters of 25 CDPK genes in S. tuberosum.
Supplementary Table 6 The ten predicted motif categories detected using MEME for the promoters of 25 CDPK genes in S. tuberosum.
Supplementary Table 7 Distribution of cis-element categories detected using PlantPAN for the promoters of 25 CDPK genes in S. tuberosum.
Supplementary Table 8 The statistics of cis-element categories detected using PlantPAN.
Supplementary Table 9 References or URLs for the software used in this study.
Funding
This work was supported by the National Natural Science Foundation of China (Grant Nos. 31960442, 31660432), the Special Fund for Discipline Construction of Gansu Agricultural University (GAU-XKJS-2018-084, GAU-XKJS-2018-085), and the Research Program Sponsored by Gansu Provincial Key Laboratory of Arid land Crop Science, Gansu Agricultural University (No. GSCS-2017-8).
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10529_2020_3037_MOESM1_ESM.png
Physical locations of CDPK genes in S. tuberosum. In total, 25 StCDPK genes were mapped onto the 11 chromosomes of S. tuberosum. Green bars represent chromosomes in S. tuberosum, and the scale shows chromosome length. (PNG 878 kb)
10529_2020_3037_MOESM3_ESM.png
Distribution of cis-elements recognized by TF families of AT-Hook, AP2/ERF, Dof, bHLH, Dehydrin, bZIP and GATA. (PNG 4797 kb)
10529_2020_3037_MOESM6_ESM.xlsx
The FPKM value for StCDPKs expressed in different tissues (data was extracted from Spud DB, https://solanaceae.plantbiology.msu.edu/pgsc_download.shtml). (XLSX 20 kb)
10529_2020_3037_MOESM11_ESM.xlsx
Distribution of cis-element categories detected using PlantPAN for the promoters of 25 CDPK genes in S. tuberosum. (XLSX 2732 kb)
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Bi, Z., Wang, Y., Li, P. et al. Evolution and expression analysis of CDPK genes under drought stress in two varieties of potato. Biotechnol Lett 43, 511–521 (2021). https://doi.org/10.1007/s10529-020-03037-2
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DOI: https://doi.org/10.1007/s10529-020-03037-2