Background
Calcium-dependent protein kinases (CDPKs), play multiple roles in plant development, growth and response to bio- or abiotic stresses. Calmodulin-like domains typically contain four EF-hand motifs for Ca²⁺ binding. The CDPK gene family can be divided into four subgroups in
Arabidopsis
, and it has been identified in many plants, such as rice, tomato, but has not been investigated in alfalfa (
Medicago sativa
subsp.
sativa
) yet.
Results
In our study, 38 non-redundant
MsCDPK
genes were identified from the “XinJiangDaYe” alfalfa genome. They can be divided into four subgroups which is the same as in
Arabidopsis
and
Medicago truncatula
, and there were 15, 12,10 and 1 in CDPK I, II, III and IV, respectively. RNA-seq analysis revealed tissue-specificity of 38
MsCDPK
genes. After researching the transcriptome data, we found these 38 MsCDPK members responsive to drought, salt, and cold stress treatments. Further analysis showed that the expression of almost all the
MsCDPKs
is regulated by abiotic stresses. In addition, we chose
MsCDPK03
,
MsCDPK26
,
MsCDPK31
and
MsCDPK36
for RT-qPCR validation which was from CDPK I-IV subgroups respectively. The result showed that the expression of these four genes was significantly induced by drought, salt and cold treatments. The subcellular location experiment showed that these four proteins were all located in nucleus.
Conclusion
In our study, we identified 38 distinct
MsCDPK
genes within the alfalfa genome, which were classified into four groups. We conducted a comprehensive analysis of various gene features, including physicochemical properties, phylogenetic relationships, exon-intron structures, conserved motifs, chromosomal locations, gene duplication events,
cis
-regulatory elements, 3D structures, and tissue-specific expression patterns, as well as responses to drought, salt, and cold stresses. These results also provide a solid foundation for further investigations into the functions of MsCDPKs aimed at improving drought tolerance in autotetraploid cultivated alfalfa through genetic engineering.
Supplementary Information
The online version contains supplementary material available at 10.1186/s12870-024-05993-7.