Genome-wide characterization of the aldehyde dehydrogenase gene superfamily in soybean and its potential role in drought stress response

Abstract

Background: Aldehyde dehydrogenases (ALDHs) represent a group of enzymes that detoxify aldehydes by facilitating their oxidation to carboxylic acids, and have been shown to play roles in plant response to abiotic stresses. However, the comprehensive analysis of ALDH superfamily in soybean (Glycine max) has been limited.

Results: In present study, a total of 53 GmALDHs were identified in soybean, and grouped into 10 ALDH families according to the ALDH Gene Nomenclature Committee and phylogenetic analysis. These groupings were supported by their gene structures and conserved motifs. Soybean ALDH superfamily expanded mainly by whole genome duplication/segmental duplications. Gene network analysis identified 1146 putative co-functional genes of 51 GmALDHs. Gene Ontology (GO) enrichment analysis suggested the co-functional genes of these 51 GmALDHs were enriched (FDR < 1e-3) in the process of lipid metabolism, photosynthesis, proline catabolism, and small molecule catabolism. In addition, 22 co-functional genes of GmALDHs are related to plant response to water deprivation/water transport. GmALDHs exhibited various expression patterns in different soybean tissues. The expression levels of 13 GmALDHs were significantly up-regulated and 14 down-regulated in response to water deficit. The occurrence frequencies of three drought-responsive cis-elements (ABRE, CRT/DRE, and GTGCnTGC/G) were compared in GmALDH genes that were up-, down-, or non-regulated by water deficit. Higher frequency of these three cis-elements was observed for the group of up-regulated GmALDH genes as compared to the group of down- or non- regulated GmALDHs by drought stress, implying their potential roles in the regulation of soybean response to drought stress.

Conclusions: A total of 53 ALDH genes were identified in soybean genome and their phylogenetic relationships and duplication patterns were analyzed. The potential functions of GmALDHs were predicted by analyses of their co-functional gene networks, gene expression profiles, and cis-regulatory elements. Three GmALDH genes, including GmALDH3H2, GmALDH12A2 and GmALDH18B3, were highly induced by drought stress in soybean leaves. Our study provides a foundation for future investigations of GmALDH gene function in soybean.

Keywords: ALDH; Drought stress; Gene network; Phylogenetic analysis; Soybean; cis-element.

Fig. 1

Phylogenetic tree of ALDH proteins from G. max (Gm), A. thaliana (At), O. sativa (Os), P. vulgaris (Pv), and M. truncatula (Mt). Alignment of 145 ALDH protein sequences from five plant species was conducted with ClustalW2, and the phylogenetic tree was constructed using MEGA 5.2 based on the Neighbor-joining (NJ) method. Bootstrap values in percentage (1000 replicates) are labeled on the nodes

Fig. 2

Gene structures and protein motifs of the soybean ALDH superfamily. a. The exon/intron structures of soybean ALDH genes. The relative position is proportionally displayed based on the kilobase scale at the bottom of the figure. Yellow boxes, gray lines, and blue boxes represent exons, introns, and upstream/downstream regions, respectively. b. The conserved motifs in soybean ALDHs. Different motifs and their relative positions are represented by the colored boxes

Fig. 3

WGD/segmental duplications of soybean ALDH genes. Twenty soybean chromosomes are displayed in different colors. WGD/segmentally duplicated GmALDH gene pairs are linked by different colored lines. The illustration was generated using CIRCOS software

Fig. 4

Heat map of the expression profiles of GmALDHs in eight different soybean tissues. The color scale represents the relative transcript abundance of the GmALDH genes in eight soybean tissues. The heat map with hierarchical clustering of GmALDH genes was constructed based on log10 (FPKM + 1) values using MeV 4.9 software by average linage with Euclidean distance. The FPKM values were obtained from the RNA-seq data at Phytozome v11.0

Fig. 5

Relative expression levels of six GmALDHs in different soybean tissues by qRT-PCR. For each gene, the relative expression level in stem was set as one, and the soybean 60S gene was used as the internal control. The data represent the mean ± SD of three replicates

Fig. 6

Heap map of the expression profiles of GmALDHs in soybean plants subjected to drought stress for 0, 6, 12 and 24 h. The color scale is based on the log10 (FPKM + 1) values. FPKM values of 53 GmALDHs were obtained from the RNA-seq data using leaf samples of the drought-tolerant soybean cultivar, PI416937. The heat map with hierarchical clustering of GmALDH genes was constructed using MeV 4.9 software by average linage with Euclidean distance

Fig. 7

Relative expression levels of six soybean ALDHs in response to a simulated drought stress. The drought tolerant soybean cultivar, KF-1, was grown hydroponically for two weeks and then exposed to 20% PEG treatment. The relative expression levels of six ALDH genes at 3, 6, 12, 24, 48, and 72 h were determined by qRT-PCR in comparison with 0 h. The soybean 60S gene was used as the internal control. The data represent the mean ± SD of three replicates

Fig. 8

Analysis of the cis-elements in the promoter regions of soybean ALDH genes. a. Predicted cis-elements in the 1500 bp upstream regions of six GmALDH genes. The names of the cis-elements are indicated at the bottom of the figure. The scale indicates the relative position of each cis-element relative to the translation start codon, ATG. b. Frequency of three drought-responsive cis-elements present in the promoter regions of different groups of soybean ALDHs. The frequencies of ABRE, CRT/DRE, and GTGCnTGC/G cis-elements in up-regulated, down-regulated and non-responsive GmALDH genes under drought stress are shown in different colored bars. Changes in expression were determined by the criteria of P value < 0.05 and │log₂ fold change│ ≥ 2 comparing drought-stressed soybean plants with control