Genome-Wide Analysis of Soybean Polyamine Oxidase Genes Reveals Their Roles in Flower Development and Response to Abiotic Stress

Abstract

Polyamine oxidase (PAO) is an important enzyme that functions in the catabolism of polyamines. While plant PAOs have been studied in several species, there is a lack of research on this gene family in soybean (Glycine max L.), one of the major food crops worldwide. Here, a genome-wide analysis identified 16 GmPAOs from the soybean genome, which were unevenly distributed in nine soybean chromosomes and were then phylogenetically classified into three groups. Collinearity analysis identified 17 duplicated gene pairs from the GmPAO family, and their Ka/Ks values were all less than one, indicating that the GmPAO family has undergone purifying selection during evolution. Analyses of the conserved motif and gene structure revealed the sequence differences among the GmPAOs of the three groups, suggestive of their functional differentiation. Additionally, the prediction of the secondary and tertiary structure of the GmPAOs provided a further basis for revealing their biological functions. A number of cis-acting elements relevant to development, phytohormone, and stress response were discovered in the promoter regions of the GmPAOs, which might be responsible for their functional diversities. Expression pattern analysis indicated that more than half of the GmPAOs showed preference in flower, two showed specificity in stem and shoot apical meristem, whereas four were barely expressed in all samples. Expression profiling of the GmPAOs also revealed that they were involved in the response to abiotic stresses, including cold, drought, and especially submergence stress. All these results lay an important foundation for further characterizing the functional roles of GmPAOs in soybean development and response to abiotic stresses.

Keywords: Glycine max L.; PAO; bioinformatic analysis; stress response; tissue-specific expression.

Figure 1

Phylogenetic relationship of polyamine oxidases from Arabidopsis, rice, and soybean. The evolutionary tree was constructed by MEGA-X software through the maximum likelihood (ML) method and Le_Gascuel_2008 model. Bootstrap analysis (1000 replicates) was conducted to estimate the reliability of the tree. The four groups are distinguished by different color areas. PAO proteins of Arabidopsis, rice, and soybean are marked with an empty circle, an empty triangle, and a solid square, respectively.

Figure 2

Collinear analysis of GmPAOs. The 20 soybean chromosomes are situated in a circle, and GmPAOs are mapped to them. Collinear gene pairs are linked using gray curves.

Figure 3

Phylogenetic relationship, conserved motif, and gene structure of GmPAOs. (a) Phylogenetic tree constructed with the amino acid sequences of GmPAOs by the ML method and bootstrap analysis (1000 replicates). The three GmPAO groups (I–III) were indicated with different color areas. (b) Conserved motif analysis. The 6 motifs are denoted with different colored rectangles. (c) Exon–intron structure of GmPAO genes. Green rectangles indicate UTRs, yellow rectangles indicate exons, and black lines indicate introns.

Figure 4

Promoter analysis of GmPAOs. Cis-acting elements related to development (green), plant hormone response (orange), and stress response (blue) were identified in the promoters of GmPAOs. The numbers of each kind of element are shown in separate color blocks.

Figure 5

Expression analysis of GmPAOs in different soybean organs/tissues. (a) Expression level of GmPAOs in nine soybean organs/tissues; numbers in the color blocks indicate FPKM values. The color scale represents log2 format-converted FPKM values, with red indicating high expression levels and blue indicating low expression levels. (b) Expression correlation of GmPAOs; green represents negative correlation, and red represents positive correlation.

Figure 6

Expression pattern of GmPAOs in anther, sepal, ovary, and stigma. Numbers in the color blocks indicate FPKM values. The color scale represents log2 format-converted FPKM values, with yellow indicating high expression levels and blue indicating low expression levels.

Figure 7

Expression profile of GmPAOs in soybean leaves under cold stress. Gene expression level is represented as DESeq-normalized transcript counts. Error bars indicate standard deviations of three replicates. Asterisks stand for significant differences (Student’s t-test), * p < 0.05, ** p < 0.01.

Figure 8

Expression profile of GmPAOs in soybean root (a) and leaves (b) under drought stress. Gene expression level is represented as FPKM values. Error bars indicate standard deviations of three replicates. Asterisks stand for significant differences (Student’s t-test), * p < 0.05, ** p < 0.01.

Figure 9

Expression profile of GmPAOs in soybean root and leaves under submergence stress. Numbers in the color blocks indicate mean FPKM values of three replicates. The color scale represents log2 format-converted FPKM values, with red indicating high expression levels and blue indicating low expression levels.