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Genome-wide analysis of the maize superoxide dismutase (SOD) gene family reveals important roles in drought and salt responses

Abstract

Superoxide dismutase proteins (SODs) are antioxidant enzymes with important roles in abiotic stress responses. The SOD gene family has been systematically analyzed in many plants; however, it is still poorly understood in maize. Here, a bioinformatics analysis of maize SOD gene family was conducted by describing gene structure, conserved motifs, phylogenetic relationships, gene duplications, promoter cis-elements and GO annotations. In total, 13 SOD genes were identified in maize and five members were involved in segmental duplication. Phylogenetic analysis indicated that SODs from maize and other plants comprised two groups, which could be further classified into different subgroups, with most members in the same subgroup having the same subcellular localization. The ZmSOD promoters contained 2-10 stress-responsive cis-elements with different distributions. Heatmap analysis indicated that ZmSODs were expressed in most of the detected tissues and organs. The expression patterns of ZmSODs were investigated under drought and salt treatments by qRT-PCR, and most members were responsive to drought or salt stress, especially some ZmSODs with significant expression changes were identified, such as ZmCSD2 and ZmMSD2, suggesting the important roles of ZmSODs in abiotic stress responses. Our results provide an important basis for further functional study of ZmSODs in future study.

Keywords:
Maize; SOD ; phylogenetic analysis; expression patterns; abiotic stress

Introduction

Reactive oxygen species (ROS) are inevitable products in the process of cellular metabolism that act as signal molecules to regulate many physiological processes in plants (Gechev et al., 2006Gechev TS, Breusegem FV, Stone JM, Denev I and Laloi C (2006) Reactive oxygen species as signals that modulate plant stress responses and programmed cell death. Bioessays 28:1091-1101.). However, abiotic stresses, such as drought, salt and extreme temperature, often induce the production and accumulation of ROS in plant cells (Karuppanapandian et al., 2011Karuppanapandian T, Moon J-C, Kim C, Manoharan K and Kim W (2011) Reactive oxygen species in plants: Their generation, signal transduction, and scavenging mechanisms. Aust J Crop Sci 5:709-725.), and the presence of excess ROS negatively affects cell growth and even leads to cell death (Mittler, 2002Mittler R (2002) Oxidative stress, antioxidants and stress tolerance. Trends Plant Sci 7:405-410.; Lee et al., 2007Lee S-H, Ahsan N, Lee K-W, Kim D-H, Lee D-G, Kwak S-S, Kwon S-Y, Kim T-H and Lee B-H (2007) Simultaneous overexpression of both CuZn superoxide dismutase and ascorbate peroxidase in transgenic tall fescue plants confers increased tolerance to a wide range of abiotic stresses. J Plant Physiol 164:1626-1638.). Efficient mechanisms have been established to cope with ROS toxicity during the long-term evolution of plants. For example, many studies have shown that some enzymes that remove ROS, such as superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and glutathione peroxidase (GPX), can protect plants from various abiotic stresses (Mittler et al., 2004Mittler R, Vanderauwera S, Gollery M and Van Breusegem F (2004) Reactive oxygen gene network of plants. Trends Plant Sci 9:490-498.; Sugimoto et al., 2014Sugimoto M, Oono Y, Gusev O, Matsumoto T, Yazawa T, Levinskikh MA, Sychev VN, Bingham GE, Wheeler R and Hummerick M (2014) Genome-wide expression analysis of reactive oxygen species gene network in Mizuna plants grown in long-term spaceflight. BMC Plant Biol 14:4.).

SODs are the first defense of the plant antioxidant system, and play important roles in protecting plants against oxidative stress (Nath et al., 2014Nath K, Kumar S, Poudyal RS, Yang YN, Timilsina R, Park YS, Nath J, Chauhan PS, Pant B and Lee C-H (2014) Developmental stage-dependent differential gene expression of superoxide dismutase isoenzymes and their localization and physical interaction network in rice (Oryza sativa L.). Genes Genom 36:45-55.; Wang et al., 2017Wang W, Zhang X, Deng F, Yuan R and Shen F (2017) Genome-wide characterization and expression analyses of superoxide dismutase (SOD) genes in Gossypium hirsutum. BMC Genomics 18:376.). They mitigate ROS hazards by catalyzing the conversion of superoxide (O2-) into hydrogen peroxide (H2O2) and molecular oxygen (O2) under oxidative stress (Gopavajhula et al., 2013Gopavajhula VR, Chaitanya KV, Khan PAA, Shaik JP, Reddy PN and Alanazi M (2013) Modeling and analysis of soybean (Glycine max. L) Cu/Zn, Mn and Fe superoxide dismutases. Genet Mol Biol 36:225-236.), and play significantly roles in protecting the stability of cell membrane and slowing oxidative damage (Karuppanapandian et al., 2011Karuppanapandian T, Moon J-C, Kim C, Manoharan K and Kim W (2011) Reactive oxygen species in plants: Their generation, signal transduction, and scavenging mechanisms. Aust J Crop Sci 5:709-725.). SODs are very widespread in living organisms. In plants, genome-wide analysis of SOD family genes has been performed in many species, including Arabidopsis (Kliebenstein et al., 1998Kliebenstein DJ, Monde RA and Last RL (1998) Superoxide dismutase in Arabidopsis: An eclectic enzyme family with disparate regulation and protein localization. Plant Physiol 118:637-650.), rice (Nath et al., 2014Nath K, Kumar S, Poudyal RS, Yang YN, Timilsina R, Park YS, Nath J, Chauhan PS, Pant B and Lee C-H (2014) Developmental stage-dependent differential gene expression of superoxide dismutase isoenzymes and their localization and physical interaction network in rice (Oryza sativa L.). Genes Genom 36:45-55.), wheat (Jiang et al., 2019Jiang W, Yang L, He Y, Zhang H, Li W, Chen H, Ma D and Yin J (2019) Genome-wide identification and transcriptional expression analysis of superoxide dismutase (SOD) family in wheat (Triticum aestivum). PeerJ 7:e8062.), sorghum (Filiz and Tombuloglu, 2015Filiz E and Tombuloglu H (2015) Genome-wide distribution of superoxide dismutase (SOD) gene families in Sorghum bicolor. Turk J Biol 39:49-59.), upland cotton (Wang et al., 2017Wang W, Zhang X, Deng F, Yuan R and Shen F (2017) Genome-wide characterization and expression analyses of superoxide dismutase (SOD) genes in Gossypium hirsutum. BMC Genomics 18:376.), and Medicago (Song et al., 2018Song J, Zeng L, Chen R, Wang Y and Zhou Y (2018) In silico identification and expression analysis of superoxide dismutase (SOD) gene family in Medicago truncatula. 3 Biotech 8:348.). These studies have indicated that SODs are encoded by a small gene family; for example, seven SOD genes were found in Medicago, and eight members were reported in both of the Arabidopsis and rice genomes. SODs are metalloenzymes, whose proteins require metal cofactors to have catalytic activity (Forman and Fridovich, 1973Forman HJ and Fridovich I (1973) On the stability of bovine superoxide dismutase. The effects of metals. J Biol Chem 248:2645-2649.). Based on the type of metal cofactor, plant SODs can be divided into three groups, iron SODs (FeSODs), manganese SODs (MnSODs), and copper/zinc SODs (Cu/ZnSODs) (Alscher et al., 2002Alscher RG, Erturk N and Heath LS (2002) Role of superoxide dismutases (SODs) in controlling oxidative stress in plants. J Exp Bot 53:1331-1341.; Fink and Scandalis, 2002Fink RC and Scandalis JG (2002) Molecular evolution and structure-function relationships of the superoxide dismutase gene families in angiosperms and their relationship to other eukaryotic and prokaryotic superoxide dismutases. Arch Biochem Biophys 399:19-36.).

Increasing numbers of studies have indicated that SOD genes have important roles in response to abiotic stresses (Wang et al., 2004Wang B, Lüttge U and Ratajczak R (2004) Specific regulation of SOD isoforms by NaCl and osmotic stress in leaves of the C3 halophyte Suaeda salsa L. J Plant Physiol 161:285-293.; Pilon et al., 2011Pilon M, Ravet K and Tapken W (2011) The biogenesis and physiological function of chloroplast superoxide dismutases. Biochim Biophys Acta 1807:989-998.; Asensio et al., 2012Asensio AC, Gil-Monreal M, Pires L, Gogorcena Y, Aparicio-Tejo PM and Moran JF (2012) Two Fe-superoxide dismutase families respond differently to stress and senescence in legumes. J Plant Physiol 169:1253-1260.; Verma et al., 2019Verma D, Lakhanpal N and Singh K (2019) Genome-wide identification and characterization of abiotic-stress responsive SOD (superoxide dismutase) gene family in Brassica juncea and B. rapa. BMC Genomics 20:227.). With the development of high-throughput sequencing technology, the expression patterns of SOD family genes in stress responses have been extensively studied. For example, nine SOD genes were identified in tomato, and most members showed altered expression under salt and drought stresses according to microarray data analysis (Feng et al., 2016Feng K, Yu JH, Cheng Y, Ruan MY, Wang R, Ye Q, Zhou G, Li Z, Yao Z, Yang Y et al. (2016) The SOD gene family in tomato: Identification, phylogenetic relationships, and expression patterns. Front Plant Sci 7:1279. ). In Medicago, differential expression was detected for most of the seven MtSOD genes under various stress treatments based on microarray analysis and high-throughput sequencing (Song et al., 2018Song J, Zeng L, Chen R, Wang Y and Zhou Y (2018) In silico identification and expression analysis of superoxide dismutase (SOD) gene family in Medicago truncatula. 3 Biotech 8:348.). In foxtail millet, the expression patterns of SOD genes were detected under drought, salt, and cold treatments by quantitative real-time PCR (qRT-PCR), and each SOD was found to respond to at least one abiotic stress (Wang et al., 2018bWang T, Song H, Zhang B, Lu Q, Liu Z, Zhang S, Guo R, Wang C, Zhao Z, Liu J et al. (2018b) Genome-wide identification, characterization, and expression analysis of superoxide dismutase (SOD) genes in foxtail millet (Setaria italica L.). 3 Biotech 8:486.). Importantly, the biological functions of some SOD genes involved in stress responses have been demonstrated in transgenic plants. For example, Zhang et al. (2014Zhang D-Y, Yang H, Li X-S, Li H-Y and Wang Y-C (2014) Overexpression of Tamarix albiflonum TaMnSOD increases drought tolerance in transgenic cotton. Mol Breeding 34:1-11.) showed that overexpression of a Tamarix albiflonum SOD gene, TaMnSOD, can improve cotton’s tolerance to drought stress by enhancing root development and the regulation of superoxide scavenging (Zhang et al., 2014Zhang D-Y, Yang H, Li X-S, Li H-Y and Wang Y-C (2014) Overexpression of Tamarix albiflonum TaMnSOD increases drought tolerance in transgenic cotton. Mol Breeding 34:1-11.). In wheat, overexpression of the TaSOD2 gene increased salt resistance in transgenic wheat and Arabidopsis plants (Wang et al., 2016Wang M, Zhao X, Xiao Z, Yin X, Xing T and Xia G (2016) A wheat superoxide dismutase gene TaSOD2 enhances salt resistance through modulating redox homeostasis by promoting NADPH oxidase activity. Plant Mol Biol 91:115-130.).

As an important cereal crop around the world, maize (Zea mays L.) has been widely used in genetics and evolution research. However, the growth and yield of maize were seriously affected by various abiotic stresses, and identifying stress-responsive genes and applying them in molecular breeding is one of the effective ways to cope with abiotic stress. Although several SOD genes have been identified in maize, systematic analysis of this family has not been reported at whole genome level with the latest genome data, especially for their functional roles in abiotic stress responses (Cannon et al., 1987Cannon RE, White JA and Scandalios JG (1987) Cloning of cDNA for maize superoxide dismutase 2 (SOD2). Proc Natl Acad Sci U S A 84:179-183.; Zhu and Scandalios, 1994Zhu D and Scandalios JG (1994) Differential accumulation of manganese-superoxide dismutase transcripts in maize in response to abscisic acid and high osmoticum. Plant Physiol 106:173-178.; Sytykiewicz, 2014Sytykiewicz H (2014) Differential expression of superoxide dismutase genes in aphid-stressed maize (Zea mays L.) seedlings. PLoS One 9:e94847.). In this study, 13 maize SOD genes (ZmSODs) were identified in the current genome, and systematic analysis was performed using bioinformatics method. The expression patterns of the 13 genes were also investigated in maize seedlings under drought and salt treatments. The results lay an important foundation for further evolutionary research of plant SOD gene family and provide useful information for identification of key ZmSODs in response to abiotic stress.

Material and Methods

Identification of ZmSOD genes in maize

To identify SOD-encoding proteins in the maize genome, Hidden Markov Model (HMM) profiles of the Cu/ZnSOD domain (PF00080) and Fe/MnSOD domains (N-terminal domain, PF00081; C-terminal domain, PF02777) were initially obtained from the Pfam database (http://pfam.xfam.org/) (Finn et al., 2006Finn RD, Mistry J, Schuster-Böckler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R et al. (2006) Pfam: Clans, web tools and services. Nucleic Acids Res 34:D247-D251.). Subsequently, we used the HMM profile of each type of SOD proteins as a query to execute a local BLASTP search against the maize genome (v4) (p-value = 0.001). All candidate sequences that met the standards were analyzed in the Pfam database to confirm that each sequence contained the related domains. Redundant sequences were removed based on alignments using the ClustalW software (Thompson et al., 1994Thompson JD, Higgins DG and Gibson TJ (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680.), and the non-redundant members were used for further analysis. The ExPASy (https://web.expasy.org/protparam/) and WoLF PSORT online tools (https://www.genscript.com/wolf-psort.html) (Horton et al., 2007Horton P, Park K-J, Obayashi T, Fujita N, Harada H, Adams-Collier CJ and Nakai K (2007) WoLF PSORT: Protein localization predictor. Nucleic Acids Res 35:W585-W587.) were used to predict physico-chemical characteristics and subcellular localizations, respectively. Based on their positions in the genome annotations, the chromosomal distributions of the maize SOD genes were displayed from top to bottom on the chromosomes using the MapInspect software. Gene duplication analysis of ZmSODs was performed according to previous study (Si et al., 2019Si WN, Hang T, Guo M, Chen Z, Liang Q, Gu L and Ding T (2019) Whole-genome and transposed duplication contributes to the expansion and diversification of TLC genes in maize. Int J Mol Sci 20:5484.).

Phylogenetic analysis of SOD proteins

To analyze the phylogenetic relationships of SOD proteins among different plants, the full-length amino acid sequences of 37 SOD proteins from maize, Arabidopsis, foxtail millet and rice were used to construct a phylogenetic tree with the MEGA 5.05 (Molecular Evolutionary Genetics Analysis) software. Arabidopsis, foxtail millet and rice SOD sequences were obtained from Joint Genome Institute (http://www.phytozome.net) according to previous studies (Kliebenstein et al., 1998Kliebenstein DJ, Monde RA and Last RL (1998) Superoxide dismutase in Arabidopsis: An eclectic enzyme family with disparate regulation and protein localization. Plant Physiol 118:637-650.; Nath et al., 2014Nath K, Kumar S, Poudyal RS, Yang YN, Timilsina R, Park YS, Nath J, Chauhan PS, Pant B and Lee C-H (2014) Developmental stage-dependent differential gene expression of superoxide dismutase isoenzymes and their localization and physical interaction network in rice (Oryza sativa L.). Genes Genom 36:45-55.; Wang et al., 2018bWang T, Song H, Zhang B, Lu Q, Liu Z, Zhang S, Guo R, Wang C, Zhao Z, Liu J et al. (2018b) Genome-wide identification, characterization, and expression analysis of superoxide dismutase (SOD) genes in foxtail millet (Setaria italica L.). 3 Biotech 8:486.). The phylogenetic tree was built using the neighbor-joining method with 1,000 bootstrap replicates, and the same method was used to construct an unrooted phylogenetic tree of the ZmSOD proteins.

Conserved motif, gene structure and promoter analysis of ZmSODs

Multiple Em for Motif Elicitation (MEME) (http://meme-suite.org/tools/meme) was used to discover conserved motifs among the 13 maize SOD proteins (Bailey et al., 2009Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren JY, Li WW and Noble WS (2009) MEME SUITE: Tools for motif discovery and searching. Nucleic Acids Res 37:W202-W208.). The motif number was set to 10 and the width of motifs was 6 to 50. The detected motifs were annotated using the Pfam database. Gene Structure Display Server (http://gsds.cbi.pku.edu.cn/index.php) was used to analyze the gene structure by comparing the coding sequence (CDS) with the genomic sequence of each predicted ZmSOD (Hu et al., 2015Hu B, Jin J, Guo A-Y, Zhang H, Luo J and Gao G (2015) GSDS2.0: An upgraded gene feature visualization server. Bioinformatics 31:1296-1297.). To predict putative stress-responsive cis-elements in the promoter regions of ZmSODs, the 2,000 bp flanking sequences upstream from the transcription start site (ATG) of each ZmSOD was obtained from the maize genomic sequence, and these promoter sequences were analyzed using PlantCARE (Lescot et al., 2002Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouze P and Rombauts S (2002) PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res 30:325-327.).

Expression patterns of ZmSODs in different tissues and organs

To determine the expression patterns of the SOD genes in maize tissues and organs, the publicly available transcriptome data published by Walley et al. (2016Walley JW, Sartor RC, Shen ZX, Schmitz RJ, Wu KJ, Urich MA, Nery JR, Smith LG, Schnable JC, Ecker JR et al. (2016) Integration of omic networks in a developmental atlas of maize. Science 353:814-818.) for 23 different developmental stages, were downloaded from MaizeGDB (http://www.maizegdb.org/). The fragments per kilobase of transcript per million mapped (FPKM) values were transformed and used to draw a heat map of ZmSODs as described in our previous study (Zhao et al., 2019Zhao Y, Hu F, Zhang X, Wei Q, Dong J, Bo C, Cheng B and Ma Q (2019) Comparative transcriptome analysis reveals important roles of nonadditive genes in maize hybrid An'nong 591 under heat stress. BMC Plant Biol 19:273.).

Plant material and stress treatments

The expression levels of the ZmSODs were investigated in maize seedlings under abiotic stress conditions. Seeds of the maize inbred line B73 were washed with sterile water three times, and placed in vermiculite for germination until the coleoptile grew to about 2 cm in length. Then, seeds with consistent germination were selected, washed with water, and placed on plastic tanks containing Hoagland’s nutrient solution in a plant growth chamber at 28 °C/23 °C (day/night) with a 16-h light/8-h dark photoperiod. At the three-leaf stage, the seedlings were used for drought and salt treatments to explore the possible functional roles of the ZmSODs in response to abiotic stress. Hoagland’s nutrient solution containing 20% (m/v) PEG-6000 or 200 mM NaCl was used for drought and salt treatment, respectively. At 0, 3, 6, 12, and 24 h after treatment, the third leaf of each seedling was harvested, and immediately frozen in liquid nitrogen, and stored at -80°C for RNA extraction.

RNA isolation and quantitative real-time PCR (qRT-PCR) analysis

Total RNA was extracted from the seedling samples using AG RNAex Pro Reagent (Accurate Biology, China). RNA quality and concentration were assessed by 1% agarose gel electrophoresis and P200+ Series Micro Volume Spectrophotometers (Pultton, USA), respectively. First-strand cDNA was generated from 1 μg of total RNA using HiScript® III RT SuperMix for qPCR (+ gDNA wiper) (Vazyme, China) according to the manufacturer’s instructions. Gene-specific primers were designed using the Primer3Plus online tool, and the NCBI database was used to verify the specificity of the primers (Table S1 Table S1 - Gene-specific primers used for qRT-PCR in this study. ). qRT-PCR reactions were carried out as described in our previous study (Zhao et al., 2019Zhao Y, Hu F, Zhang X, Wei Q, Dong J, Bo C, Cheng B and Ma Q (2019) Comparative transcriptome analysis reveals important roles of nonadditive genes in maize hybrid An'nong 591 under heat stress. BMC Plant Biol 19:273.). The maize GAPDH gene (accession number: NM_001111943.1) was utilized as an internal control for normalizing expression levels. Three biological and three technical repeats were performed for each gene.

Results

Identification of SOD proteins in maize

Using the local BLASTP program, a total of 13 non-redundant SOD proteins were obtained with predicted Cu/ZnSOD or Fe/MnSOD domains after confirmation with the Pfam database. The number of SOD proteins in the maize genome was significantly higher than in Arabidopsis and rice. Based on their phylogenetic relationships, chromosomal distributions and metal cofactors, the 13 SOD genes were named ZmCSD1-ZmCSD6, ZmFSD1-ZmFSD5, ZmMSD1 and ZmMSD2. According to the physico-chemical characteristics predicted by the Expasy tool, we found that the protein lengths, molecular weights (MWs), and isoelectric points (pI) of the ZmSOD members had large ranges. The protein lengths of the ZmSODs ranged from 152 to 386 aa, and the molecular weights of the ZmSODs varied from 15.07 to 42.87 kDa. The isoelectric points of the ZmSODs ranged from 5.33 to 8.84. According to the subcellular localization predictions, the highest number of members was localized in mitochondria, including ZmFSD1, ZmFSD2, ZmFSD3, ZmFSD5, ZmMSD1 and ZmMSD2, while only three proteins (ZmCSD3, ZmCSD4 and ZmFSD4) were localized in chloroplasts. In addition, four proteins, including ZmCSD1, ZmCSD2, ZmCSD5, and ZmCSD6, were localized in cytoplasm (Table 1).

Table 1 -
Sequence characteristics of the 13 SOD genes identified in maize.

Phylogenetic relationships and gene structure

The full-length ZmSOD sequences were aligned and used to construct an unrooted phylogenetic tree to analyze their phylogenetic relationships. The result indicated that the 13 ZmSODs could be divided into two groups (I-II) with high bootstrap value support, indicating their conserved phylogenetic relationships (Figure 1A). To further support the phylogenetic relationships of the ZmSODs, gene structure analysis was performed for the 13 ZmSODs using GSDS online tool (Figure 1B). We found that intron numbers in the genomic sequences of the ZmSODs ranged from 4 to 7. Three ZmSODs (ZmCSD3, ZmCSD5 and ZmFSD4), contained seven introns, while ZmFSD1 and ZmMSD1 contained four introns. According to the phylogenetic tree and gene structure analysis, we found that the gene pair ZmCSD2-ZmCSD6 exhibited a highly similar exon-intron organization pattern, suggesting their close relationship.

Figure 1 -
Phylogenetic relationships and gene structures of maize SOD proteins. A. Unrooted tree of the 13 ZmSODs. The tree was constructed with 1,000 bootstrap replicates by the neighbor-joining method using the MEGA5.05 software. B. Exon-intron structures of the ZmSODs.

To further investigate the phylogenetic relationships of SOD proteins in dicot and monocot plants, a phylogenetic tree was constructed based on an alignments of 37 full-length protein sequences, including 13 sequences from maize, 8 from foxtail millet (SiCSD1, SiCSD2, SiCSD3, SiCSD4, SiFSD1, SiFSD2, SiFSD3 and SiMSD), 8 from rice (cCuZn-SOD1, cCuZn-SOD2, CuZn-SOD-L, pCuZn-SOD, CuZn-SOD-CCh, Fe-SOD3, Fe-SOD2 and Mn-SOD1), and 8 from Arabidopsis (AtCSD1, AtCSD2, AtCSD3, AtFSD1, AtFSD2, AtFSD3, AtMSD1 and AtMSD2). According to the phylogenetic tree, the 37 SOD proteins could be divided into two groups: group I (Fe/MnSODs) and group II (Cu/ZnSODs), which was consistent with the types of domains they contained (Figure 2). Group I contained 19 SOD proteins, which could be further divided into three subgroups (a-c). In group II, 18 SOD proteins were divided into four subgroups (d-g). We found that most SOD proteins clustered in the same subgroups shared the same predicted subcellular localization (Table 1). For example, ZmFSD1, ZmFSD2, ZmFSD3, ZmFSD5 and other plants’ mitochondrial FeSODs formed subgroup a. ZmCSD2, ZmCSD5 and ZmCSD6 were contained in subgroup g, and these ZmSODs and other plant SOD proteins were predicted to be localized in the cytoplasm. In each subgroup, we found that the ZmSODs exhibited closer relationships with foxtail millet or rice members than those of Arabidopsis. We also constructed a maximum likelihood (ML) tree with the same SOD protein sequences using MEGA 5.05 software, and the results were largely consistent with the phylogenetic relationships in the NJ tree (Figure S1 Figure S1 - Maximum likelihood phylogenetic tree of 37 SOD proteins from different plant species. The Maximum Likelihood (ML) tree was constructed. ), which further supported the reconstruction of the NJ tree.

Figure 2 -
Phylogenetic relationships of 37 SOD proteins from different plant species.

Conserved motifs, chromosomal distributions and gene duplications

MEME was used to investigate the conserved motifs among ZmSODs, and 10 motifs were identified (Table S2 Table S2 - Conserved motif sequences of maize SOD proteins. ). For the Cu/ZnSOD proteins, motifs 2 and 3 encoding the Cu/ZnSOD domain (PF00080) were detected in each of the six ZmCSDs except ZmCSD4 (Figure 3). Motif 1 encoding a Fe/MnSOD domain (N-terminal domain, PF00081) was found in each of the Fe/MnSOD proteins, while Motif 5 encodes a Fe/MnSOD domain (C-terminal domain, PF02777), was detected in ZmFSD1, ZmFSD2 and ZmFSD5. Notably, ZmSODs in the same phylogenetic group tended to have similar motif distribution patterns, which further supported the phylogenetic classification. The chromosomal locations of the ZmSODs were obtained from the maize genome database. As shown in Figure 4A, eight of the 10 chromosomes harbored ZmSODs; no ZmSOD genes were found on chromosomes 3 or 4. Most of the genes were distributed on chromosomes 1, 6 and 9, while chromosomes 2, 5, 7, 8 and 10 each contained only one SOD gene. Gene duplications, including tandem and segmental duplications, were investigated to explore the potential expansion mechanism of ZmSOD family. According to the syntenic analysis, five genes (ZmCSD2, ZmCSD5, ZmCSD6, ZmFSD2 and ZmFSD3) were involved in the segmental duplication, and no tandem duplications were detected in ZmSOD gene family (Figure 4B).

Figure 3 -
Conserved motif analysis of ZmSOD proteins.

Figure 4 -
Chromosomal locations and syntenic analysis of the ZmSOD genes. A. Chromosomal locations of the 13 ZmSODs. B. Synteny and gene duplication analysis among ZmSODs in the maize genome.

Promoter analysis of ZmSODs

Increasing evidence indicates that SOD genes play important roles in responses to abiotic stresses. To explore the possible regulatory mechanisms of ZmSODs involved in stress responses, the putative stress-responsive cis-elements were investigated in the promoter sequences of the ZmSODs. Four cis-elements, including the abscisic acid responsiveness element (ABRE), dehydration-responsive element (DRE), MYB binding site involved in drought-inducibility (MBS) and low temperature-responsive element (LTR), were detected in this study. The number of detected cis-elements in the 13 promoter regions ranged from 2 to 10 (Figure 5). Each of the ZmFSD5 and ZmCSD5 promoters had 10 cis-elements, respectively, while ZmCSD4 had the least number (2). The distributions of cis-elements in the ZmSOD promoters showed significant differences, which might suggest the different roles or regulatory mechanisms of ZmSODs in responses to abiotic stresses.

Figure 5 -
Cis-elements in the promoter regions of the ZmSOD genes. Four types of putative stress-responsive cis-elements, including ABRE, DRE, LTR and MBS, were shown with different colors.

Gene Ontology (GO) enrichment analysis of ZmSODs

To explore the possible functional roles of the ZmSODs, GO terms for these genes were annotated using the clusterProfiler R package (Yu et al., 2012Yu G, Wang L-G, Han Y and He Q-Y (2012) ClusterProfiler: An R package for comparing biological themes among gene clusters. OMICS 16:284-287.), and divided into three categories, including cellular component, molecular function, and biological process (Figure 6). The results indicated that the ZmSODs were significantly (adjusted p-value < 0.05) enriched in 17 GO terms. Six GO terms, including extracellular space (GO:0005615), chloroplast nucleoid (GO:0042644), extracellular region (GO:0005576), mitochondrial matrix (GO:0005759), thylakoid (GO:0009579) and peroxisome (GO:0005777), were enriched in the cellular component category. Three GO terms, including superoxide dismutase activity (GO:0004784), copper ion binding (GO:0005507), and manganese ion binding (GO:0030145), were enriched in the molecular function category. Eight GO terms, including response to reactive oxygen species (GO:0000302), response to hydrogen peroxide (GO:0042542), response to iron ion (GO:0010039), response to osmotic stress (GO:0006970), protein homotetramerization (GO:0051289), response to herbicide (GO:0009635), metal ion transport (GO:0030001) and response to abscisic acid (GO:0009737), were enriched in the biological process category. We noted that the highest number of ZmSODs (12) was enriched in the “superoxide dismutase activity” molecular function term, three genes were enriched in the “response to reactive oxygen species” biological process term, and one gene was enriched in the “response to osmotic stress” biological process terms. These results suggested that ZmSODs have significant roles in the responses to abiotic stress.

Figure 6 -
Gene Ontology (GO) enrichment analysis of the ZmSOD genes.

Expression patterns of ZmSODs at different developmental stages

To explore the possible functions of the ZmSODs, the expression patterns of the 13 ZmSODs were analyzed in 23 different tissues and organs using publicly available transcript data (Walley et al., 2016Walley JW, Sartor RC, Shen ZX, Schmitz RJ, Wu KJ, Urich MA, Nery JR, Smith LG, Schnable JC, Ecker JR et al. (2016) Integration of omic networks in a developmental atlas of maize. Science 353:814-818.). All the 13 ZmSODs showed detectable expression levels in most of the 23 tissues and developmental stages (Figure 7) with different expression patterns. According to their expression levels, the 13 ZmSODs could be divided into two groups. The first group included 7 members (ZmFSD3, ZmCSD1, ZmCSD4, ZmFSD2, ZmFSD4, ZmFSD1 and ZmFSD5) with low expression, while the second group exhibited relatively higher expression, including ZmCSD3, ZmMSD2, ZmCSD5, ZmMSD1, ZmCSD2 and ZmCSD6. We noted that ZmMSD genes had high expression levels in all stages except B73 mature pollen while ZmFSD genes had low expression levels in most stages. In addition, some SOD genes showed similar expression patterns that reflected their close relationships, especially for two pairs of genes (ZmCSD2 and ZmCSD6, and ZmFSD1 and ZmFSD5), which might suggest their similar functions in plant growth and development.

Figure 7 -
Expression pattern analysis of the ZmSOD genes in different tissues and organs using transcript data. Expression patterns of the 13 ZmSODs were investigated in 23 different tissues and organs using publicly transcriptome data. FPKM showed “NA” (not available) was replaced by FPKM = 0, and all FPKM values were transformed into log2 (FPKM+1) to create the heatmap.

Expression analysis of ZmSODs under drought and salt treatments

The expression levels of the ZmSODs were investigated under drought and NaCl treatments using qRT-PCR to understand their possible roles in responses to abiotic stresses. Under drought stress, expression levels of ZmCSD2, ZmCSD5 and ZmMSD2 were significantly up-regulated with large fold changes at the 6, 12 and 24 h, respectively, while ZmFSD2 was significantly down-regulated at three of the four time points (Figure 8A). Notably, some ZmSODs exhibited significant differences across the four time points. For example, ZmCSD3 expression was significantly up-regulated at 3 h, but significantly down-regulated expression was observed at 6, 12 and 24 h. ZmFSD4 expression was significantly up-regulated at 12 h, but significantly down-regulated was shown at 24 h after drought treatment. In addition, some ZmSODs exhibited significant up- or down-regulated expression only at particular time points, such as ZmCSD1 and ZmFSD5. Under salt stress, we found that expression levels of ZmCSD1, ZmCSD2, ZmCSD4, ZmCSD5, ZmMSD1 and ZmMSD2 were significantly up-regulated at all of the four time points (Figure 8B). As observed under drought stress, significant expression differences were observed for some ZmSODs across the four time points, for example, ZmFSD3 exhibited significantly up-regulated expression at 12 and 24 h, and significantly down-regulated expression was observed at 3 h. In addition, significantly up-regulated expression was only observed at particular time points for ZmCSD3 and ZmFSD2. Under salt treatment, we found that the expression levels of most ZmSODs exhibited larger fold changes than that observed under drought stress. These findings suggested the important roles of ZmSODs in responses to drought or salt stress, but may have different regulatory mechanisms.

Figure 8 -
Expression pattern analysis of ZmSOD genes under drought (A) and salt (B) treatments by qRT-PCR. The X-axis is the time course of treatment, and seedlings were sampled at 0 (CK), 3, 6, 12 and 24 h after drought or salt treatment, respectively. The Y-axis shows the relative expression levels.

Discussion

Environmental stresses, such as drought, heat and salinity, have serious effects on plant growth and development. Studies have indicated that ROS accumulation can causes oxidative stress because the equilibrium of oxidative reactions is disrupted by abiotic stresses (Apel and Hirt, 2004Apel K and Hirt H (2004) Reactive oxygen species: Metabolism, oxidative stress, and signal transduction. Annu Rev Plant Biol 55:373-399.; Quan et al., 2008Quan L-J, Zhang B, Shi W-W and Li H-Y (2008) Hydrogen peroxide in plants: A versatile molecule of the reactive oxygen species network. J Integr Plant Biol 50:2-18.). Toxic ROS can greatly harm the survival of plants, such as through inactivation of enzymes and membrane lipids (Apel and Hirt, 2004Apel K and Hirt H (2004) Reactive oxygen species: Metabolism, oxidative stress, and signal transduction. Annu Rev Plant Biol 55:373-399.). SOD is one of the antioxidant enzymes that have been demonstrated to have important roles in protecting plant cells from oxidative damage (Fink and Scandalis, 2002Fink RC and Scandalis JG (2002) Molecular evolution and structure-function relationships of the superoxide dismutase gene families in angiosperms and their relationship to other eukaryotic and prokaryotic superoxide dismutases. Arch Biochem Biophys 399:19-36.). SOD family genes have been studied in several plant species, and identification of the maize SOD genes and determination of their functional roles in responses to drought and salt stresses will provide excellent gene resources for resistance breeding to various abiotic stresses.

Studies indicated that the number of SOD family genes has a large difference among different plant species. For example, 8 SOD genes were identified in both of rice and foxtail millet, while 26 members were identified from the whole genome of wheat. A total of 13 SOD genes were identified in the current maize genome, and further divided into two major types. Although there are large differences in the genome sizes of different plant species, the number of SOD family genes is not proportional to the genome size. It is believed that gene duplications, including tandem and segmental duplications, have important roles in the expansion of plant gene families (Cannon et al., 2004Cannon SB, Mitra A, Baumgarten A, Young ND and May G (2004) The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol 4:10.). The different numbers of SOD family genes should be mainly attributable to the ratio of gene duplications. Our study indicated that five ZmSODs were involved in the segmental duplication, which suggests that segmental duplication plays an important role in the expansion of maize SOD gene family.

Phylogenetic analysis indicated that the 37 SOD proteins from four species were divided into two groups, termed group I (Fe/MnSODs) and group II (Cu/ZnSODs). As observed in other studies, FeSODs and MnSODs from different plants were clustered together in group I with high bootstrap value support, suggesting that these genes may share common ancestral genes (Wang et al., 2017Wang W, Zhang X, Deng F, Yuan R and Shen F (2017) Genome-wide characterization and expression analyses of superoxide dismutase (SOD) genes in Gossypium hirsutum. BMC Genomics 18:376.; Song et al., 2018Song J, Zeng L, Chen R, Wang Y and Zhou Y (2018) In silico identification and expression analysis of superoxide dismutase (SOD) gene family in Medicago truncatula. 3 Biotech 8:348.). SODs from monocots (maize, foxtail millet, and rice) and dicots (Arabidopsis) tended to cluster separately, which was consistent with the evolutionary relationships of these species. The findings also suggested the independent evolution of plant SOD genes after the divergence of monocots and dicots. Interestingly, some maize SODs exhibited close phylogenetic relationships with their orthologs from other species than their paralog proteins, suggesting that the ortholog pairs may have originated from a common ancestor and diverged after the divergence of the grass genome. Our study was consistent with previous studies that SOD genes clustered in one phylogenetic branch tended to have the same subcellular localization (Song et al., 2018Song J, Zeng L, Chen R, Wang Y and Zhou Y (2018) In silico identification and expression analysis of superoxide dismutase (SOD) gene family in Medicago truncatula. 3 Biotech 8:348.; Wang et al., 2018bWang T, Song H, Zhang B, Lu Q, Liu Z, Zhang S, Guo R, Wang C, Zhao Z, Liu J et al. (2018b) Genome-wide identification, characterization, and expression analysis of superoxide dismutase (SOD) genes in foxtail millet (Setaria italica L.). 3 Biotech 8:486.), further supporting the phylogenetic reconstruction and the conserved evolution of plant SOD genes.

Cis-elements in gene promoters are important for transcriptional regulation (Hernandez-Garcia and Finer, 2014Hernandez-Garcia CM and Finer JJ (2014) Identification and validation of promoters and cis-acting regulatory elements. Plant Sci 217-218:109-119.). Therefore, stress-responsive cis-elements, including ABRE, DRE, MBS and LTR, were investigated in the promoters of the 13 ZmSODs. Previous studies indicated these stress-responsive cis-elements have important roles in regulating abiotic stress responses. For example, expression of RD29A was induced by drought, salt, ABA and low-temperature, both of DRE and ABRE elements were found in its promoter (Shinozaki and Yamaguchi-Shinozaki, 2000Shinozaki K and Yamaguchi-Shinozaki K (2000) Molecular responses to dehydration and low temperature: Differences and cross-talk between two stress signaling pathways. Curr Opin Plant Biol 3:217-223.; Narusaka et al., 2003Narusaka Y, Nakashima K, Shinwari ZK, Sakuma Y, Furihata T, Abe H, Narusaka M, Shinozaki K and Yamaguchi-Shinozaki K (2003) Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses. Plant J 34:137-148.). In maize, mutant analysis indicated that MBS element in ZmSO promoter was important for ABA- and drought-induced expression (Xu et al., 2019Xu Z, Wang M, Guo Z, Zhu X and Xia Z (2019) Identification of a 119-bp promoter of the maize sulfite oxidase gene (ZmSO) that confers high-level gene expression and ABA or drought inducibility in transgenic plants. Int J Mol Sci 20:3326.). In addition, LTR was shown to be involved in regulation of cold responsive, and it was also found in some drought or salt responsive gene promoters (Wang et al., 2018aWang C-T, Ru J-N, Liu Y-W, Li M, Zhao D, Yang J-F, Fu J-D and Xu Z-S (2018a) Maize WRKY transcription factor ZmWRKY106 confers drought and heat tolerance in transgenic plants. Int J Mol Sci 19:3046.; Xie et al., 2019Xie Z, Nolan TM, Jiang H and Yin Y (2019) AP2/ERF transcription factor regulatory networks in hormone and abiotic stress responses in Arabidopsis. Front Plant Sci 10:228.). We found that at least one type of the four stress-responsive cis-elements was detected in each of the ZmSODs, suggesting the important roles of the ZmSODs in abiotic stress responses. However, different distribution patterns were found among the 13 ZmSODs, even for the gene pair ZmCSD2-ZmCSD6. These findings may indicate different regulatory mechanisms of the ZmSODs in response to abiotic stress.

Plant growth and development is frequently threatened by various environmental stresses (Zhu, 2002Zhu J-K (2002) Salt and drought stress signal transduction in plants. Annu Rev Plant Biol 53:247-273.; Gong et al., 2020Gong Z, Xiong L, Shi H, Yang S, Herrera-Estrella LR, Xu G, Chao D-Y, Li J, Wang P-Y, Qin F et al. (2020) Plant abiotic stress response and nutrient use efficiency. Sci China Life Sci 63:635-674.; Lozano-Juste et al., 2020Lozano-Juste J, Alrefaei AF and Rodriguez PL (2020) Plant osmotic stress signaling: MAPKKKs meet SnRK2s. Trends Plant Sci 25:1179-1182.). At present, the expression patterns of SOD genes in response to abiotic stress have been investigated in many species, and the functional studies of some genes involved in stress response have also been demonstrated by biological experiments (Zhang et al., 2014Zhang D-Y, Yang H, Li X-S, Li H-Y and Wang Y-C (2014) Overexpression of Tamarix albiflonum TaMnSOD increases drought tolerance in transgenic cotton. Mol Breeding 34:1-11.; Wang et al., 2016Wang M, Zhao X, Xiao Z, Yin X, Xing T and Xia G (2016) A wheat superoxide dismutase gene TaSOD2 enhances salt resistance through modulating redox homeostasis by promoting NADPH oxidase activity. Plant Mol Biol 91:115-130.). According to the expression levels of ZmSODs under stress treatments, we found that most of the ZmSODs showed significant response to drought or salt stress treatment. Meanwhile, the significant expression differences among the 13 ZmSODs were also found. Some members exhibited similar expression patterns under different stresses. For example, significantly up-regulated expression of ZmCSD2 and ZmMSD2 was detected under both of drought and salt treatments, suggesting their conserved functional roles of these genes in response to abiotic stresses. However, different expression patterns between drought and salt treatments were also found. For example, ZmCSD4 exhibited significantly down-regulated expression at 6 and 12 h under drought stress, but significantly up-regulated expression was detected across the four time points under salt stress. In foxtail millet, the expression of SiMSD was significantly induced by drought and salt stresses, respectively (Wang et al.,2018bWang T, Song H, Zhang B, Lu Q, Liu Z, Zhang S, Guo R, Wang C, Zhao Z, Liu J et al. (2018b) Genome-wide identification, characterization, and expression analysis of superoxide dismutase (SOD) genes in foxtail millet (Setaria italica L.). 3 Biotech 8:486.). ZmMSD2 had a close phylogenetic relationship with SiMSD, and also exhibited significantly up-regulated expression under drought and salt stresses, which may indicate their conserved functions in stress responses. Importantly, we should note that some ZmSODs were up-regulated with a large fold changes under drought or salt treatment, such as ZmCSD2, ZmCSD5 and ZmMSD2. Our study provided an important foundation for the selection of important functional genes and application in stress resistance breeding in maize.

Conclusions

In this study, 13 maize SOD genes were identified using the BLASTP program and systematic bioinformatics analysis was performed for these members. The 13 ZmSODs were distributed on 8 of the 10 maize chromosomes, and five members were involved in segmental duplication, suggesting that segmental duplication plays an important role in the expansion of maize SOD gene family. SOD proteins from maize and three other plants members were divided into two groups (Fe/MnSODs and Cu/ZnSODs) according to phylogenetic analysis, which can be further classified into different subgroups. At least one of the four detect stress-responsive cis-elements was identified in each of the ZmSODs. Transcriptome data analysis showed that ZmSODs were expressed in most of the detected tissues and organs. Furthermore, qRT-PCR analysis indicated that most of the ZmSODs were responsive to drought or salt stress treatments, especially some genes with significant expression changes were identified. Our results lay an important foundation for further identifying important members and investigating the molecular functions of ZmSODs involved in abiotic stress responses.

Acknowledgements

This research was supported by Science and Technology Major Project of Anhui Province (18030701180) and Anhui Province University Natural Science Research Project (KJ2018A0143). We thank Guomin Han and Weina Si for their technical support in the study.

References

  • Alscher RG, Erturk N and Heath LS (2002) Role of superoxide dismutases (SODs) in controlling oxidative stress in plants. J Exp Bot 53:1331-1341.
  • Apel K and Hirt H (2004) Reactive oxygen species: Metabolism, oxidative stress, and signal transduction. Annu Rev Plant Biol 55:373-399.
  • Asensio AC, Gil-Monreal M, Pires L, Gogorcena Y, Aparicio-Tejo PM and Moran JF (2012) Two Fe-superoxide dismutase families respond differently to stress and senescence in legumes. J Plant Physiol 169:1253-1260.
  • Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren JY, Li WW and Noble WS (2009) MEME SUITE: Tools for motif discovery and searching. Nucleic Acids Res 37:W202-W208.
  • Cannon RE, White JA and Scandalios JG (1987) Cloning of cDNA for maize superoxide dismutase 2 (SOD2). Proc Natl Acad Sci U S A 84:179-183.
  • Cannon SB, Mitra A, Baumgarten A, Young ND and May G (2004) The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana BMC Plant Biol 4:10.
  • Feng K, Yu JH, Cheng Y, Ruan MY, Wang R, Ye Q, Zhou G, Li Z, Yao Z, Yang Y et al (2016) The SOD gene family in tomato: Identification, phylogenetic relationships, and expression patterns. Front Plant Sci 7:1279.
  • Filiz E and Tombuloglu H (2015) Genome-wide distribution of superoxide dismutase (SOD) gene families in Sorghum bicolor Turk J Biol 39:49-59.
  • Fink RC and Scandalis JG (2002) Molecular evolution and structure-function relationships of the superoxide dismutase gene families in angiosperms and their relationship to other eukaryotic and prokaryotic superoxide dismutases. Arch Biochem Biophys 399:19-36.
  • Finn RD, Mistry J, Schuster-Böckler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R et al (2006) Pfam: Clans, web tools and services. Nucleic Acids Res 34:D247-D251.
  • Forman HJ and Fridovich I (1973) On the stability of bovine superoxide dismutase. The effects of metals. J Biol Chem 248:2645-2649.
  • Gechev TS, Breusegem FV, Stone JM, Denev I and Laloi C (2006) Reactive oxygen species as signals that modulate plant stress responses and programmed cell death. Bioessays 28:1091-1101.
  • Gong Z, Xiong L, Shi H, Yang S, Herrera-Estrella LR, Xu G, Chao D-Y, Li J, Wang P-Y, Qin F et al (2020) Plant abiotic stress response and nutrient use efficiency. Sci China Life Sci 63:635-674.
  • Gopavajhula VR, Chaitanya KV, Khan PAA, Shaik JP, Reddy PN and Alanazi M (2013) Modeling and analysis of soybean (Glycine max L) Cu/Zn, Mn and Fe superoxide dismutases. Genet Mol Biol 36:225-236.
  • Hernandez-Garcia CM and Finer JJ (2014) Identification and validation of promoters and cis-acting regulatory elements. Plant Sci 217-218:109-119.
  • Horton P, Park K-J, Obayashi T, Fujita N, Harada H, Adams-Collier CJ and Nakai K (2007) WoLF PSORT: Protein localization predictor. Nucleic Acids Res 35:W585-W587.
  • Hu B, Jin J, Guo A-Y, Zhang H, Luo J and Gao G (2015) GSDS2.0: An upgraded gene feature visualization server. Bioinformatics 31:1296-1297.
  • Jiang W, Yang L, He Y, Zhang H, Li W, Chen H, Ma D and Yin J (2019) Genome-wide identification and transcriptional expression analysis of superoxide dismutase (SOD) family in wheat (Triticum aestivum). PeerJ 7:e8062.
  • Karuppanapandian T, Moon J-C, Kim C, Manoharan K and Kim W (2011) Reactive oxygen species in plants: Their generation, signal transduction, and scavenging mechanisms. Aust J Crop Sci 5:709-725.
  • Kliebenstein DJ, Monde RA and Last RL (1998) Superoxide dismutase in Arabidopsis: An eclectic enzyme family with disparate regulation and protein localization. Plant Physiol 118:637-650.
  • Lee S-H, Ahsan N, Lee K-W, Kim D-H, Lee D-G, Kwak S-S, Kwon S-Y, Kim T-H and Lee B-H (2007) Simultaneous overexpression of both CuZn superoxide dismutase and ascorbate peroxidase in transgenic tall fescue plants confers increased tolerance to a wide range of abiotic stresses. J Plant Physiol 164:1626-1638.
  • Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouze P and Rombauts S (2002) PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res 30:325-327.
  • Lozano-Juste J, Alrefaei AF and Rodriguez PL (2020) Plant osmotic stress signaling: MAPKKKs meet SnRK2s. Trends Plant Sci 25:1179-1182.
  • Mittler R (2002) Oxidative stress, antioxidants and stress tolerance. Trends Plant Sci 7:405-410.
  • Mittler R, Vanderauwera S, Gollery M and Van Breusegem F (2004) Reactive oxygen gene network of plants. Trends Plant Sci 9:490-498.
  • Narusaka Y, Nakashima K, Shinwari ZK, Sakuma Y, Furihata T, Abe H, Narusaka M, Shinozaki K and Yamaguchi-Shinozaki K (2003) Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses. Plant J 34:137-148.
  • Nath K, Kumar S, Poudyal RS, Yang YN, Timilsina R, Park YS, Nath J, Chauhan PS, Pant B and Lee C-H (2014) Developmental stage-dependent differential gene expression of superoxide dismutase isoenzymes and their localization and physical interaction network in rice (Oryza sativa L.). Genes Genom 36:45-55.
  • Pilon M, Ravet K and Tapken W (2011) The biogenesis and physiological function of chloroplast superoxide dismutases. Biochim Biophys Acta 1807:989-998.
  • Quan L-J, Zhang B, Shi W-W and Li H-Y (2008) Hydrogen peroxide in plants: A versatile molecule of the reactive oxygen species network. J Integr Plant Biol 50:2-18.
  • Shinozaki K and Yamaguchi-Shinozaki K (2000) Molecular responses to dehydration and low temperature: Differences and cross-talk between two stress signaling pathways. Curr Opin Plant Biol 3:217-223.
  • Si WN, Hang T, Guo M, Chen Z, Liang Q, Gu L and Ding T (2019) Whole-genome and transposed duplication contributes to the expansion and diversification of TLC genes in maize. Int J Mol Sci 20:5484.
  • Song J, Zeng L, Chen R, Wang Y and Zhou Y (2018) In silico identification and expression analysis of superoxide dismutase (SOD) gene family in Medicago truncatula 3 Biotech 8:348.
  • Sugimoto M, Oono Y, Gusev O, Matsumoto T, Yazawa T, Levinskikh MA, Sychev VN, Bingham GE, Wheeler R and Hummerick M (2014) Genome-wide expression analysis of reactive oxygen species gene network in Mizuna plants grown in long-term spaceflight. BMC Plant Biol 14:4.
  • Sytykiewicz H (2014) Differential expression of superoxide dismutase genes in aphid-stressed maize (Zea mays L.) seedlings. PLoS One 9:e94847.
  • Thompson JD, Higgins DG and Gibson TJ (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680.
  • Verma D, Lakhanpal N and Singh K (2019) Genome-wide identification and characterization of abiotic-stress responsive SOD (superoxide dismutase) gene family in Brassica juncea and B. rapa BMC Genomics 20:227.
  • Walley JW, Sartor RC, Shen ZX, Schmitz RJ, Wu KJ, Urich MA, Nery JR, Smith LG, Schnable JC, Ecker JR et al (2016) Integration of omic networks in a developmental atlas of maize. Science 353:814-818.
  • Wang B, Lüttge U and Ratajczak R (2004) Specific regulation of SOD isoforms by NaCl and osmotic stress in leaves of the C3 halophyte Suaeda salsa L. J Plant Physiol 161:285-293.
  • Wang C-T, Ru J-N, Liu Y-W, Li M, Zhao D, Yang J-F, Fu J-D and Xu Z-S (2018a) Maize WRKY transcription factor ZmWRKY106 confers drought and heat tolerance in transgenic plants. Int J Mol Sci 19:3046.
  • Wang M, Zhao X, Xiao Z, Yin X, Xing T and Xia G (2016) A wheat superoxide dismutase gene TaSOD2 enhances salt resistance through modulating redox homeostasis by promoting NADPH oxidase activity. Plant Mol Biol 91:115-130.
  • Wang T, Song H, Zhang B, Lu Q, Liu Z, Zhang S, Guo R, Wang C, Zhao Z, Liu J et al (2018b) Genome-wide identification, characterization, and expression analysis of superoxide dismutase (SOD) genes in foxtail millet (Setaria italica L.). 3 Biotech 8:486.
  • Wang W, Zhang X, Deng F, Yuan R and Shen F (2017) Genome-wide characterization and expression analyses of superoxide dismutase (SOD) genes in Gossypium hirsutum BMC Genomics 18:376.
  • Xie Z, Nolan TM, Jiang H and Yin Y (2019) AP2/ERF transcription factor regulatory networks in hormone and abiotic stress responses in Arabidopsis. Front Plant Sci 10:228.
  • Xu Z, Wang M, Guo Z, Zhu X and Xia Z (2019) Identification of a 119-bp promoter of the maize sulfite oxidase gene (ZmSO) that confers high-level gene expression and ABA or drought inducibility in transgenic plants. Int J Mol Sci 20:3326.
  • Yu G, Wang L-G, Han Y and He Q-Y (2012) ClusterProfiler: An R package for comparing biological themes among gene clusters. OMICS 16:284-287.
  • Zhang D-Y, Yang H, Li X-S, Li H-Y and Wang Y-C (2014) Overexpression of Tamarix albiflonum TaMnSOD increases drought tolerance in transgenic cotton. Mol Breeding 34:1-11.
  • Zhao Y, Hu F, Zhang X, Wei Q, Dong J, Bo C, Cheng B and Ma Q (2019) Comparative transcriptome analysis reveals important roles of nonadditive genes in maize hybrid An'nong 591 under heat stress. BMC Plant Biol 19:273.
  • Zhu D and Scandalios JG (1994) Differential accumulation of manganese-superoxide dismutase transcripts in maize in response to abscisic acid and high osmoticum. Plant Physiol 106:173-178.
  • Zhu J-K (2002) Salt and drought stress signal transduction in plants. Annu Rev Plant Biol 53:247-273.

Edited by

Associate Editor: Marcio C. Silva-Filho

Publication Dates

  • Publication in this collection
    01 Oct 2021
  • Date of issue
    2021

History

  • Received
    28 Jan 2021
  • Accepted
    02 July 2021
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