Genome-wide identification, characterization, and expression analysis of superoxide dismutase (SOD) genes in foxtail millet (Setaria italica L.).

Shulin Zhang,Renhai Peng,Ruilin Guo,Tao Wang,Zilin Zhao,Cong Wang,Quanwei Lu,Hui Song,Baohong Zhang,Jinrong Liu,Zhen Liu

doi:10.1007/s13205-018-1502-x

Abstract

Superoxide dismutases (SODs) play important roles in plant growth, development, and response to abiotic stresses. Despite SOD gene families have been identified in various plant species, little is known in foxtail millet (Setaria italica L.). In this study, a systematic analysis of SOD gene family was performed in foxtail millet and the expression pattern of SOD genes in response to abiotic stressors was analyzed at the whole-genomic level. Eight SOD genes were identified in foxtail millet, including 4 Cu/ZnSODs, 3 FeSODs, and 1 MnSOD. These SiSODs are unevenly distributed across 5 of the 9 chromosomes. Phylogenetic analysis showed that SOD proteins could be divided into two major categories (Cu/ZnSODs and Fe-MnSODs), containing seven subgroups, from foxtail millet and other plant species. SOD genes have conserved motif and exon/intron composition in the same subgroup among Setaria italica, Setaria viridis, and Oryza sativa. Additionally, many cis-elements that respond to different stressors were distributed at different densities in the promoters of 8 SiSODs. The expression patterns of SiSODs in different tissues and different abiotic stressors indicated that the SiSODs may play important roles in reactive oxygen species scavenging, caused by various stressors in foxtail millet. This study provides a foundation for the further cloning and functional verification of the SOD gene family response to environmental stimuli in foxtail millet.

Highlights

Reactive oxygen species (ROS), such as hydroxyl radical (.OH), superoxide (.O2−) and hydrogen peroxide ( H2O2), are a series of byproducts that are produced by the metabolism of cells
A total of eight Superoxide dismutase (SOD) genes were identified in foxtail millet, including 4 Cu/ZnSODs (SiCSD1, 2, 3 and 4) with a copper-zinc domain, 3 FeSODs (SiFSD1, 2 and 3) and 1 MnSOD (SiMSD) with an iron/manganese SOD alphahairpin domain and an iron/manganese SOD C-terminal domain, respectively (Table 1)
Some important characteristics of SOD genes and proteins in foxtail millet are shown in Table 1 through physicochemical analysis, including the length of amino acid sequences, isoelectric point, molecular weight (MW), genomic location, instability index and subcellular localizations

Summary

Introduction

Reactive oxygen species (ROS), such as hydroxyl radical (.OH), superoxide (.O2−) and hydrogen peroxide ( H2O2), are a series of byproducts that are produced by the metabolism of cells. The present study was performed to identify the SOD gene family members in the foxtail millet genome and to characterize them using in silico tools, and to analyze their expression patterns during stress treatments; our results should help to comprehensively understand the putative roles of SiSODs in response to abiotic stresses in this important crop. The coding and genomic sequences of SOD genes of Setaria italica, Setaria viridis, and Oryza sativa were downloaded from JGI database (https://phytozome.jgi.doe.gov/pz/portal.html), and gene structure was analyzed through Gene Structure Display Server (GSDS) (http://gsds.cbi.pku.edu.cn/). To obtain the phylogenetic relationship of SOD proteins among different plant species, a total of 51 SOD protein sequences were identified from Setaria italica, Setaria viridis, Arabidopsis thaliana, Oryza sativa, Sorghum bicolor, and Glycine max. The primers for qRT-PCR are listed in supplementary Table S1

Results

Discussion

Conclusions