Genome-wide identification and expression analysis of the SPL transcription factor family and its response to abiotic stress in Pisum sativum L

Abstract

Squamous promoter binding protein-like (SPL) genes encode plant-specific transcription factors (TFs) that play essential roles in modulating plant growth, development, and stress response. Pea (Pisum sativum L.) is a coarse grain crop of great importance in food production, biodiversity conservation and molecular genetic research, providing genetic information and nutritional resources for improving agricultural production and promoting human health. However, only limited researches on the structure and functions of SPL genes exist in pea (PsSPLs). In this study, we identified 22 PsSPLs and conducted a genome-wide analysis of their physical characteristics, chromosome distribution, gene structure, phylogenetic evolution and gene expression patterns. As a result, the PsSPLs were unevenly distributed on the seven chromosomes of pea and harbored the SBP domain, which is composed of approximately 76 amino acid residues. The phylogenetic analysis revealed that the PsSPLs clustered into eight subfamilies and showed high homology with SPL genes in soybean. Further analysis showed the presence of segmental duplications in the PsSPLs. The expression patterns of 22 PsSPLs at different tissues, developmental stages and under various stimulus conditions were evaluated by qRT-PCR method. It was found that the expression patterns of PsSPLs from the same subfamily were similar in different tissues, the transcripts of most PsSPLs reached the maximum peak value at 14 days after anthesis in the pod. Abiotic stresses can cause significantly up-regulated PsSPL19 expression with spatiotemporal specificity, in addition, four plant hormones can cause the up-regulated expression of most PsSPLs including PsSPL19 in a time-dependent manner. Therefore, PsSPL19 could be a key candidate gene for signal transduction during pea growth and development, pod formation, abiotic stress and plant hormone response. Our findings should provide insights for the elucidating of development regulation mechanism and breeding for resistance to abiotic stress pea.

Keywords: Pisum sativum. L; PsSPL19; SPL genes; Abiotic stress; Genome-wide analysis; Growth and development; Plant hormone response.

Fig. 1

Phylogenetic analysis of SPL proteins in pea and Arabidopsis thaliana. 22 PsSPLs were divided into eight clades (I–IX) and indicated with different colors. The red pentacle represents Pea, the black circle represents Arabidopsis thaliana

Fig. 2

Phylogenetic relationships, gene structure, and motif distributions of PsSPL genes. Phylogenetic tree was constructed for each node with 1000 replicates using the NJ method (A). Exons and introns are indicated by yellow rectangles and grey lines, respectively (B). These numbers indicate the annotation file of the different phases of gene CDS, which are defined as “0”, “1”, and “2”. C Amino acid motifs in the SPL proteins (1–10) were represented by colored boxes, the black lines indicate relative protein lengths

Fig. 3

Schematic representation of the chromosomal distribution of PsSPLs. Vertical bars represent the chromosomes of Pea. The chromosome number is indicated to the left of each chromosome. The scale on the left represents chromosome length

Fig. 4

Schematic representation of the chromosomal distribution and interchromosomal relationships of PsSPLs. Colored lines denote all synteny blocks in the Pea genome, and the red lines denote duplicated SPL pairs. The chromosome number is denoted at the bottom of each chromosome

Fig. 5

Phylogenetic relationships and motif compositions of the PsSPLs with six different plant species (Arabidopsis thaliana, Solanum lycopersicum, Vitis vinifera, Sorghum bicolor Moench, Oryza sativa and Zea mays). Outer panel: an unrooted phylogenetic tree constructed using Geneious R11 with the neighbor-joining method. Inner panel: distribution of conserved motifs in SPL proteins. The differently colored boxes represent different motifs and their positions in each SPL protein sequence. The sequence information for each motif is provided in Additional file 2 (Table S2)

Fig. 6

Synteny analyses of the SPL genes between Pisum sativum and six representative plant species (Arabidopsis thaliana, Glycine max, Chenopodium quinoa, Oryza sativa, Triticum aestivum and Setaria italica). Gray lines on the background indicate the collinear blocks in Pisum sativum and other plant genomes; red lines highlight the syntenic of SPL gene pairs in Pisum sativum

Fig. 7

Tissue-specific gene expression of 22 PsSPLs and gene expression during fruit development. Expression patterns of 22 PsSPLs and in fruit of different stage and flower, leaf, root, stem were detected by qPCR. Error bars are obtained from three measurements. Lowercase letters indicate significant differences between treatments (α = 0.05, LSD) (A, C, E). Coexpression analysis of 22 PsSPLs (B, D, F)

Fig. 8

Expression of PsSPLs in plants subjected to abiotic stresses (PEG, NaCl, heat, and cool treatments) at the seedling stage in three organs (root, stem, and leaf). (A) Changes in expression of representative genes analyzed by qRT-PCR. Error bars were obtained from three measurements. The lowercase letter above the bar indicates a significant difference (α = 0.05, LSD) among the treatments. (B) Coexpression analysis of 22 PsSPLs in several plant organs. Positive numbers: positive correlations; negative numbers: negative correlations. Red numbers indicate a significant correlation at the 0.05 level

Fig. 9

Expression analysis of 22 PsSPLs in fruits in response to different hormones (JA, ABA, IAA, SA and GA). (A) qRT-PCR was utilized to detect the expression patterns of 22 PsSPLs. Error bars (n = 3) represent the standard error. Lowercase letters above the bars indicate significant differences (α = 0.05, LSD) among treatments. (B) Coexpression analysis of 22 PsSPLs. Positive numbers = positive correlation; negative numbers = negative correlation. Red numbers indicate a significant correlation at the 0.05 level