Superoxide dismutases in bread wheat ( Triticum aestivum L.): Comprehensive characterization and expression analysis during development and, biotic and abiotic stresses
“…Extended SOD gene number in B. juncea could be owed to the tetraploid nature (AABB, 2n = 36) of the genome. Previously 7 SODs have been reported in A. thaliana [17] , 8 in Sorghum bicolor [44], 18 in G. hirsutum [16] and 23 in T. aestivum [18]. Also the high gene number in B. juncea was similar to the findings in polyploid plants like G. hirsutum.…”
Section: Discussionsupporting
confidence: 53%
“…SOD family and its response to stress has been well studied and reported previously in plants like Zea mays, Arabidopsis thaliana, Medicago sativa, Musa acuminata, Triticum aestivum, Gossypium hirsutum and various other known plants, wherein the gene number varies from 7 to a maximum of 23 with A. thaliana and Z. mays containing 7 [ 17 ], G. hirsutum with 18 [ 16 ] and T. aestivum having 23 genes [ 18 ]. SOD has been described to be involved in various abiotic stress related responses such as heat, drought, salt, low temperature conditions [ 16 , 18 , 19 ]. In B. napus high SOD activity has been observed in salt-tolerant varieties compared to salt-sensitive one.…”
BackgroundAbiotic stresses like drought, heat, cold and salinity cause major productivity loss in the rapeseed-mustard crops (Brassica). Major efforts have been made in the past to identify genes that provide resistance against such stresses. Superoxide dismutase (SOD) proteins, member of the metallo-enzyme family play vital role in protecting plants against abiotic stresses. In the present study, genome-wide analysis of abiotic stress responsive SOD gene family has been done in B. juncea and B. rapa.ResultsA total of 29 and 18 SOD genes were identified in B. juncea and B. rapa respectively and chromosome location mapping indicated their wide distribution across genome. On the basis of domain composition, the SODs were phylogenetically classified into sub-groups which was also substantiated by the gene structure and sub-cellular locations of SOD proteins. Functional annotation of SODs was also done by Gene Ontology (GO) mapping and the result was corroborated by the identified cis-regulatory elements in the promoter region of SOD genes. Based on FPKM analysis of SRA data available for drought, heat and salt stress, we identified 14 and 10 abiotic stress responsive SOD genes in B. rapa and B. juncea respectively. The differential expression analysis under drought and heat stress of identified abiotic-stress responsive SOD genes was done through quantitative Real Time PCR.ConclusionWe identified abiotic-stress responsive genes that could help in improving the plant tolerance against abiotic stresses. This was the first study to describe the genome-wide analysis of SOD gene family in B. rapa and B. juncea, and the results will help in laying basic ground for future work of cloning and functional validation of SOD genes during abiotic stresses leading to Brassica crop improvement.Electronic supplementary materialThe online version of this article (10.1186/s12864-019-5593-5) contains supplementary material, which is available to authorized users.
“…Extended SOD gene number in B. juncea could be owed to the tetraploid nature (AABB, 2n = 36) of the genome. Previously 7 SODs have been reported in A. thaliana [17] , 8 in Sorghum bicolor [44], 18 in G. hirsutum [16] and 23 in T. aestivum [18]. Also the high gene number in B. juncea was similar to the findings in polyploid plants like G. hirsutum.…”
Section: Discussionsupporting
confidence: 53%
“…SOD family and its response to stress has been well studied and reported previously in plants like Zea mays, Arabidopsis thaliana, Medicago sativa, Musa acuminata, Triticum aestivum, Gossypium hirsutum and various other known plants, wherein the gene number varies from 7 to a maximum of 23 with A. thaliana and Z. mays containing 7 [ 17 ], G. hirsutum with 18 [ 16 ] and T. aestivum having 23 genes [ 18 ]. SOD has been described to be involved in various abiotic stress related responses such as heat, drought, salt, low temperature conditions [ 16 , 18 , 19 ]. In B. napus high SOD activity has been observed in salt-tolerant varieties compared to salt-sensitive one.…”
BackgroundAbiotic stresses like drought, heat, cold and salinity cause major productivity loss in the rapeseed-mustard crops (Brassica). Major efforts have been made in the past to identify genes that provide resistance against such stresses. Superoxide dismutase (SOD) proteins, member of the metallo-enzyme family play vital role in protecting plants against abiotic stresses. In the present study, genome-wide analysis of abiotic stress responsive SOD gene family has been done in B. juncea and B. rapa.ResultsA total of 29 and 18 SOD genes were identified in B. juncea and B. rapa respectively and chromosome location mapping indicated their wide distribution across genome. On the basis of domain composition, the SODs were phylogenetically classified into sub-groups which was also substantiated by the gene structure and sub-cellular locations of SOD proteins. Functional annotation of SODs was also done by Gene Ontology (GO) mapping and the result was corroborated by the identified cis-regulatory elements in the promoter region of SOD genes. Based on FPKM analysis of SRA data available for drought, heat and salt stress, we identified 14 and 10 abiotic stress responsive SOD genes in B. rapa and B. juncea respectively. The differential expression analysis under drought and heat stress of identified abiotic-stress responsive SOD genes was done through quantitative Real Time PCR.ConclusionWe identified abiotic-stress responsive genes that could help in improving the plant tolerance against abiotic stresses. This was the first study to describe the genome-wide analysis of SOD gene family in B. rapa and B. juncea, and the results will help in laying basic ground for future work of cloning and functional validation of SOD genes during abiotic stresses leading to Brassica crop improvement.Electronic supplementary materialThe online version of this article (10.1186/s12864-019-5593-5) contains supplementary material, which is available to authorized users.
BackgroundPlant P-type II Ca2+ATPases are formed by two distinct groups of proteins (ACAs and ECAs) that perform pumping of Ca2+ outside the cytoplasm during homeostasis, and play vital functions during development and stress management. In the present study, we have performed identification and characterisation of P-type II Ca2+ATPase gene family in an important crop plant Triticum aestivum.ResultsHerein, a total of 33 TaACA and 9 TaECA proteins were identified from the various chromosomes and sub-genomes of Triticum aestivum. Phylogenetic analysis revealed clustering of the homoeologous TaACA and TaECA proteins into 11 and 3 distinct groups that exhibited high sequence homology and comparable structural organization as well. Both TaACA and TaECA group proteins consisted of eight to ten transmembrane regions, and their respective domains and motifs. Prediction of sub-cellular localization was found variable for most of the proteins; moreover, it was consistent with the evolutionarily related proteins from rice and Arabidopsis in certain cases. The occurrence of assorted sets of cis-regulatory elements indicated their diverse functions. The differential expression of various TaACA and TaECA genes during developmental stages suggested their roles in growth and development. The modulated expression during heat, drought, salt and biotic stresses along with the occurrence of various stress specific cis-regulatory elements suggested their association with stress response. Interaction of these genes with numerous development and stress related genes indicated their decisive role in various biological processes and signaling.ConclusionT. aestivum genome consisted of a maximum of 42 P-type II Ca2+ATPase genes, derived from each A, B and D sub-genome. These genes may play diverse functions during plant growth and development. They may also be involved in signalling during abiotic and biotic stresses. The present study provides a comprehensive insight into the role of P-type II Ca2+ATPase genes in T. aestivum. However, the specific function of each gene needs to be established, which could be utilized in future crop improvement programs.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4792-9) contains supplementary material, which is available to authorized users.
“…For instance, four pairs of conserved Cu/Zn binding sites, and four Fe and Mn binding sites were outside the β-barrel. The Cu/ZnSODs, Fe-and MnSODs bind to Cu/Zn, Fe, and Mn metal cofactors depending on the cellular localization and the availability of metal ions, respectively (Tyagi et al, 2017). In addition, under conditions of Mn or Cu restriction, the activity of MnSOD or Cu/ZnSOD are significantly inhibited, which suggested that the content of each metal ion in the subgroup of SOD proteins may determine the equilibrium between these isozymes (del Río et al, 1991) Gene expression analyses of SOD family genes have demonstrated that SODs have diverse expression patterns in different tissues of plants (Lin & Lai, 2013;Feng et al, 2016;Pan et al, 2019).…”
Superoxide dismutases (SODs) serve as the first line of defense in the plant antioxidant enzyme system, and play a primary role in the removal of reactive oxygen species (ROS). However, our understanding of the functions of the SOD family in Zostera marina is limited. In this study, a systematic analysis was conducted on the characteristics of the SOD genes in Z. marina at the whole-genome level. Five SOD genes were identified, consisting of two Cu/ZnSODs, two FeSODs, and one MnSOD. Phylogenetic analysis showed that ZmSOD proteins could be divided into two major categories (Cu/ZnSODs and Fe-MnSODs). Sequence motifs, gene structure, and the 3D-modeled protein structures further supported the phylogenetic analysis, with each subgroup having similar motifs, exon-intron structures, and protein structures. Additionally, several cis-elements were identified that may respond to biotic and abiotic stresses. Transcriptome analysis revealed expression diversity of ZmSODs in various tissues. Moreover, qRT-PCR analysis showed that the expression level of most ZmSOD genes trended to decreased expression with the increase of temperature, indicating that heat stress inhibits expression of ZmSODs and may result in reduced ability of ZmSODs to scavenge ROS. Our results provide a basis for further functional research on the SOD gene family in Z. marina, which will help to determine the molecular mechanism of ZmSOD genes in response to environmental stress.
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