Genome-Wide Identification and Characterization of CDPK Family Reveal Their Involvements in Growth and Development and Abiotic Stress in Sweet Potato and Its Two Diploid Relatives

Abstract

Calcium-dependent protein kinase (CDPKs) is one of the calcium-sensing proteins in plants. They are likely to play important roles in growth and development and abiotic stress responses. However, these functions have not been explored in sweet potato. In this study, we identified 39 CDPKs in cultivated hexaploid sweet potato (Ipomoea batatas, 2n = 6x = 90), 35 CDPKs in diploid relative Ipomoea trifida (2n = 2x = 30), and 35 CDPKs in Ipomoea triloba (2n = 2x = 30) via genome structure analysis and phylogenetic characterization, respectively. The protein physiological property, chromosome localization, phylogenetic relationship, gene structure, promoter cis-acting regulatory elements, and protein interaction network were systematically investigated to explore the possible roles of homologous CDPKs in the growth and development and abiotic stress responses of sweet potato. The expression profiles of the identified CDPKs in different tissues and treatments revealed tissue specificity and various expression patterns in sweet potato and its two diploid relatives, supporting the difference in the evolutionary trajectories of hexaploid sweet potato. These results are a critical first step in understanding the functions of sweet potato CDPK genes and provide more candidate genes for improving yield and abiotic stress tolerance in cultivated sweet potato.

Keywords: CDPK; Ipomoea batatas; Ipomoea trifida; Ipomoea triloba; abiotic stress; hormone treatment; tissue specificity.

Figure 1

Chromosomal localization and distribution of CDPK genes in I. batatas (A), I. trifida (B), and I. triloba (C). The bars on the left margin represent chromosomes. The chromosome numbers are displayed on the left side of the chromosomes, and the gene names are displayed on the right side. Detail chromosomal location information is listed in Table S1.

Figure 2

Phylogenetic analysis of the CDPK family in I. batatas, I. trifida, I. triloba, and Arabidopsis. A total of 143 CDPKs were divided into five subgroups (group I to V) according to the evolutionary distance. The pink pentagrams, blue cycles, yellow triangles, and green squares represent IbCDPKs in I. batatas, ItfCDPKs in I. trifida, ItbCDPKs in I. triloba, and AtCPKs in Arabidopsis, respectively.

Figure 3

Conserved motifs and exon–intro structure analysis of IbCDPKs, ItfCDPKs, and ItbCDPKs family. (A) Ten conserved motifs of CDPKs are shown in different colors. (B) Exon–intron structures of IbCDPKs, ItfCDPKs, and ItbCDPKs. The purple boxes, black boxes, and black lines represent the CDS, UTRs, and introns, respectively.

Figure 4

Cis-elements analysis of IbCDPKs. The cis-elements were divided into five groups. The degree of red colors represents the number of cis-elements upstream of the IbCDPKs.

Figure 5

Protein interaction network of IbCDPKs in I. batatas according to orthologues in Arabidopsis. Network nodes represent proteins, green nodes represent AtCPKs and other colored nodes represent interacting proteins. Lines represent protein–protein interaction which was experimentally determined.

Figure 6

Gene expression patterns of CDPKs in leaf, petiole, stem, pigmented root, and tuberous root of I. batatas. The values were determined by RT-qPCR from three biological replicates consisting of pools of three plants, and the results were analyzed using the comparative C_T method. The fold change is shown in the boxes. Different lowercase letters indicate significant differences (p < 0.05; Student’s t-test).

Figure 7

Gene expression patterns of ItfCDPKs (A) and ItbCDPKs (B) in root 1, root 2, stem, leaf, flower and flower bud of I. trifida as determined by RNA-seq. Log₂ (FPKM + 1) is shown in the boxes.

Figure 8

Gene expression patterns of IbCDPKs in response to different phytohormones, i.e., (A) ABA, (B) GA, (C) IAA, and (D) MeJA of I. batatas. The values were determined by RT-qPCR from three biological replicates consisting of pools of three plants, and the results were analyzed using the comparative C_T method. The expression of 0 h in each treatment was considered “1”. The fold change is shown in the boxes. Different lowercase letters indicate significant differences (p < 0.05; Student’s t-test).

Figure 9

Gene expression patterns of ItfCDPKs (A) and ItbCDPKs (B) in response to different phytohormone (ABA, IAA, GA3, and BAP) in I. trifida and I. triloba as determined by RNA-seq. Log₂ (FPKM + 1) is shown in the boxes.

Figure 10

Gene expression patterns of IbCDPKs in response to abiotic stresses, i.e., (A) NaCl, (B) PEG, (C) H₂O₂, and (D) cold, of I. batatas. The values were determined by RT-qPCR from three biological replicates consisting of pools of three plants, and the results were analyzed using the comparative C_T method. The expression of 0 h in each treatment was considered “1”. The fold change is shown in the boxes. Different lowercase letters indicate significant differences (p < 0.05; Student’s t-test).

Figure 11

Gene expression patterns of ItfCDPKs (A) and ItbCDPKs (B) under abiotic stress (cold, heat, salt, and drought) in I. trifida and I. triloba as determined by RNA-seq. Log₂ (FPKM+1) is shown in the boxes.