Genome-Wide Identification and Characterization of the Soybean Snf2 Gene Family and Expression Response to Rhizobia

Abstract

Sucrose nonfermenting 2 (Snf2) family proteins are the core component of chromatin remodeling complexes that can alter chromatin structure and nucleosome position by utilizing the energy of ATP, playing a vital role in transcription regulation, DNA replication, and DNA damage repair. Snf2 family proteins have been characterized in various species including plants, and they have been found to regulate development and stress responses in Arabidopsis. Soybean (Glycine max) is an important food and economic crop worldwide, unlike other non-leguminous crops, soybeans can form a symbiotic relationship with rhizobia for biological nitrogen fixation. However, little is known about Snf2 family proteins in soybean. In this study, we identified 66 Snf2 family genes in soybean that could be classified into six groups like Arabidopsis, unevenly distributed on 20 soybean chromosomes. Phylogenetic analysis with Arabidopsis revealed that these 66 Snf2 family genes could be divided into 18 subfamilies. Collinear analysis showed that segmental duplication was the main mechanism for expansion of Snf2 genes rather than tandem repeats. Further evolutionary analysis indicated that the duplicated gene pairs had undergone purifying selection. All Snf2 proteins contained seven domains, and each Snf2 protein had at least one SNF2_N domain and one Helicase_C domain. Promoter analysis revealed that most Snf2 genes had cis-elements associated with jasmonic acid, abscisic acid, and nodule specificity in their promoter regions. Microarray data and real-time quantitative PCR (qPCR) analysis revealed that the expression profiles of most Snf2 family genes were detected in both root and nodule tissues, and some of them were found to be significantly downregulated after rhizobial infection. In this study, we conducted a comprehensive analysis of the soybean Snf2 family genes and demonstrated their responsiveness to Rhizobia infection. This provides insight into the potential roles of Snf2 family genes in soybean symbiotic nodulation.

Keywords: ATP-dependent chromatin remodeling; Glycine max; Snf2 gene family; nodulation; rhizobia.

Figure 1

Phylogenetic tree of Snf2 family proteins from soybean and Arabidopsis. The maximum likelihood tree was constructed using MEGAX software with 1000 bootstrap replications. Blue circles and red pentagrams represent Snf2 family proteins from soybean and Arabidopsis, respectively. Different groups of proteins are distinguished using different background colors.

Figure 2

The distribution of soybean Snf2 family genes across chromosomes.

Figure 3

Black curves connect segmentally duplicated gene pairs.

Figure 4

Protein domain analysis of the Snf2 family proteins, as well as the gene structure analysis of the Snf2 family genes. (A) Seven conserved motifs of Snf2 family proteins were identified by CDD, shown with different colors representing distinct motifs. At the bottom, the scale bars denote the lengths of the protein sequences. (B) The gene structures of Snf2 family genes are illustrated, with yellow boxes representing the coding sequences (CDS), black lines indicating introns, and green boxes depicting untranslated regions (UTR). The scale bars at the bottom indicate the lengths of the genomic sequences.

Figure 5

Prediction of cis-elements in the promoter regions of Snf2 family genes. Different colored boxes represent different types of cis-element. The scale bars at the bottom of the figure indicate the length of the promoter sequence.

Figure 6

A heat map was generated based on the Reads Per Kilobase of exon model per Million mapped reads (RPKM) values of soybean Snf2 genes to depict the expression patterns of the Snf2 family genes in the root and nodule, as well as its response to rhizobium. (A) Heat map illustrating the expression patterns of Snf2 family genes in roots and nodules of soybean. (B) Heat map illustrating the expression patterns of Snf2 family genes in root hair at 12/24 h after inoculation (HAI). The expression data of the Snf2 genes were row scale normalized respectively.

Figure 7

Snf2 gene expression patterns in roots and nodules and their reaction to rhizobium. (A) The expression patterns of specific Snf2 genes in roots and nodules were analyzed using qRT-PCR (B) Expression patterns of Snf2 genes in root hair were analyzed using qRT-PCR at 12/24 h after rhizobium inoculation (HAI). The color scale ranges from white to red, indicating low or high levels of gene expression. The term ‘mock’ refers to samples without rhizobia inoculation. Data was the most representation of three biological replicates, and the GmActin11 gene was chosen as the internal reference. A Student’s t-test was applied to assess the significances of the difference between the two groups. * p < 0.05. ** p < 0.01. “ns” indicates that there is no significant difference.