Genome-wide identification and characterization of the soybean SOD family during alkaline stress

Wenxiu Lu; Huizi Duanmu; Yanhua Qiao; Xiaoxia Jin; Yang Yu; Lijie Yu; Chao Chen

doi:10.7717/peerj.8457

Genome-wide identification and characterization of the soybean SOD family during alkaline stress

PeerJ. 2020 Feb 5:8:e8457. doi: 10.7717/peerj.8457. eCollection 2020.

Authors

Wenxiu Lu^#¹, Huizi Duanmu^#², Yanhua Qiao¹, Xiaoxia Jin¹, Yang Yu³, Lijie Yu¹, Chao Chen¹

Affiliations

¹ School of Life Science and Technology, Harbin Normal University, Harbin, China.
² Key Laboratory of Molecular Biology, College of Heilongjiang Province, College of Life Sciences, Heilongjiang University, Harbin, China.
³ Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China.

^# Contributed equally.

Abstract

Background: Superoxide dismutase (SOD) proteins, as one kind of the antioxidant enzymes, play critical roles in plant response to various environment stresses. Even though its functions in the oxidative stress were very well characterized, the roles of SOD family genes in regulating alkaline stress response are not fully reported.

Methods: We identified the potential family members by using Hidden Markov model and soybean genome database. The neighbor-joining phylogenetic tree and exon-intron structures were generated by using software MEGA 5.0 and GSDS online server, respectively. Furthermore, the conserved motifs were analyzed by MEME online server. The syntenic analysis was conducted using Circos-0.69. Additionally, the expression levels of soybean SOD genes under alkaline stress were identified by qRT-PCR.

Results: In this study, we identified 13 potential SOD genes in soybean genome. Phylogenetic analysis suggested that SOD genes could be classified into three subfamilies, including MnSODs (GmMSD1-2), FeSODs (GmFSD1-5) and Cu/ZnSODs (GmCSD1-6). We further investigated the gene structure, chromosomal locations and gene-duplication, conserved domains and promoter cis-elements of the soybean SOD genes. We also explored the expression profiles of soybean SOD genes in different tissues and alkaline, salt and cold stresses, based on the transcriptome data. In addition, we detected their expression patterns in roots and leaves by qRT-PCR under alkaline stress, and found that different SOD subfamily genes may play different roles in response to alkaline stress. These results also confirmed the hypothesis that the great evolutionary divergence may contribute to the potential functional diversity in soybean SOD genes. Taken together, we established a foundation for further functional characterization of soybean SOD genes in response to alkaline stress in the future.

Keywords: Alkaline; Evolution; Expression patterns; Phylogenetic analysis; Soybean.

Grants and funding

This work was supported by the Heilongjiang Natural Science Foundation (C2017039), the Project of Heilongjiang Education Department (12531178), Fundamental Research Funds for the Heilongjiang Provincial Universities (KJCXZD201717) and the PhD Research Fund (XKB201914). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.