Genome-wide identification of the SOD gene family and expression analysis under drought and salt stress in barley

Zhang, Xian; Zhang, Lantian; Chen, Yuyu; SiYi, Wang; Fang, Yunxia; Zhang, Xiaoqin; Wu, Yuhuan; Xue, Dawei

doi:10.1007/s10725-021-00695-8

Cited by 45 publications

(28 citation statements)

References 48 publications

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“…These include 8 Br Cu-ZnSODs and 9 Br Fe-MnSODs genes based on domain organization. Variable number of SOD genes have also been reported earlier in different crops like 7 SOD ’s in case of A. thaliana ( Kliebenstein et al, 1998 ), 8 in sorghum ( Filiz and Tombuloğlu, 2015 ), 18 in G. hirsutum ( Wang et al, 2017 ), 10 in tea plant ( Zhou et al, 2019 ) 7 in Barley ( Zhang et al, 2021 ) whereas 23 SOD ’s were identified and reported in T. aestivum in an another investigation ( Tyagi et al, 2017 ). Similarly in Barley, seven SOD genes were identified which included four Cu/Zn-SODs, two Fe-SODs and one Mn-SOD and all the SODs genes were distributed in 2, 4 and 7 chromosomes, respectively.…”

Section: Discussionsupporting

confidence: 53%

“…Similarly in Barley, seven SOD genes were identified which included four Cu/Zn-SODs, two Fe-SODs and one Mn-SOD and all the SODs genes were distributed in 2, 4 and 7 chromosomes, respectively. ( Zhang et al, 2021 ). The molecular evolutionary genetic analysis grouped SOD s of olive pollen independently into three clades of Cu/Zn- SODs , Fe- SODs and Mn- SOD s ( Zafra et al, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

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Insilco identification and characterization of superoxide dismutase gene family in Brassica rapa

Qureshi

Sofi

Dar

et al. 2021

Saudi Journal of Biological Sciences

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Superoxide Dismutase SODs are defense associated proteins that detoxify ROS and primarily serve as scavengers. They have been described in numerous plant species, but their in-depth characterization in Brassica rapa has not been reported. Therefore, the present investigation on genome wide study of SOD gene family was conducted to identify Br SOD genes, their domain-based organization, gene structure analysis, phylogenetic analysis, intron-exon structure of genes and expression analysis. The sequence characterization of Super oxide dismutase gene family in Brassica rapa , their syntenic associateship of conserved motifs and phylogenetic correlationship, prediction of cis -elements and determing the expression analysis in distinct tissues namely plant callus, root, stem, leaf, flower, and silique under abiotic conditions have been analysed using different software’s. The study on SOD gene family identified 17 Br SOD genes which were grouped into eight Br Cu-ZnSODs and nine Br Fe-MnSODs domain-based organization. Furthermore, the conserved character of Br SODs were confirmed by intron-exon organisation, motif arrangements and domain architectural investigations. Expression analysis using RNA Sequence data of different developmental stages proclaimed that genes were manifested in all six tissues with an exception of Br Cu-ZnSOD3, which was not manifested in roots; however, whose transcript was detected in all other tested tissues. The study has genome wide insight into the occurrence and functional specifications of Br SOD gene family in Brassica rapa that can be potentially utilized in breeding program for resilience to climate change and abiotic stresses tolerance Brassica variety.

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Section: Discussionsupporting

confidence: 53%

Section: Discussionmentioning

confidence: 99%

Insilco identification and characterization of superoxide dismutase gene family in Brassica rapa

Qureshi

Sofi

Dar

et al. 2021

Saudi Journal of Biological Sciences

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“…ROS production under typical and stress environments is measured and scavenged through SODs, which act as the primary markers of an enzyme complicated in ROS scavenging, and play a crucial role in plants’ physiological and biochemical procedures to survive with environmental cues [ 3 ]. Over the last few years, SOD family genes have been documented in different plant species, such as five SOD genes in Zostera marina [ 60 ], seven genes in Medicago truncatula [ 12 ] and barley [ 61 ], eight genes in sorghum [ 62 ], nine genes in tomato [ 63 ], ten genes in grapevine [ 64 ], 18 genes in cotton [ 28 ], 25 genes in banana [ 65 ], 26 genes in wheat [ 66 ], and 29 genes in B. juncea [ 67 ]. Thus far, there is no wide-ranging investigation of the SOD family genes in rapeseed.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Analysis and Expression Profile of Superoxide Dismutase (SOD) Gene Family in Rapeseed (Brassica napus L.) under Different Hormones and Abiotic Stress Conditions

Raza

Gao

et al. 2021

Antioxidants

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Superoxide dismutase (SOD) is an important enzyme that acts as the first line of protection in the plant antioxidant defense system, involved in eliminating reactive oxygen species (ROS) under harsh environmental conditions. Nevertheless, the SOD gene family was yet to be reported in rapeseed (Brassica napus L.). Thus, a genome-wide investigation was carried out to identify the rapeseed SOD genes. The present study recognized 31 BnSOD genes in the rapeseed genome, including 14 BnCSDs, 11 BnFSDs, and six BnMSDs. Phylogenetic analysis revealed that SOD genes from rapeseed and other closely related plant species were clustered into three groups based on the binding domain with high bootstrap values. The systemic analysis exposed that BnSODs experienced segmental duplications. Gene structure and motif analysis specified that most of the BnSOD genes displayed a relatively well-maintained exon–intron and motif configuration within the same group. Moreover, we identified five hormones and four stress- and several light-responsive cis-elements in the promoters of BnSODs. Thirty putative bna-miRNAs from seven families were also predicted, targeting 13 BnSODs. Gene ontology annotation outcomes confirm the BnSODs role under different stress stimuli, cellular oxidant detoxification processes, metal ion binding activities, SOD activity, and different cellular components. Twelve BnSOD genes exhibited higher expression profiles in numerous developmental tissues, i.e., root, leaf, stem, and silique. The qRT-PCR based expression profiling showed that eight genes (BnCSD1, BnCSD3, BnCSD14, BnFSD4, BnFSD5, BnFSD6, BnMSD2, and BnMSD10) were significantly up-regulated under different hormones (ABA, GA, IAA, and KT) and abiotic stress (salinity, cold, waterlogging, and drought) treatments. The predicted 3D structures discovered comparable conserved BnSOD protein structures. In short, our findings deliver a foundation for additional functional investigations on the BnSOD genes in rapeseed breeding programs.

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“…Recent barley genome sequencing accomplishments have facilitated further studies on barley genomics. Studies on the SBP-box [ 19 ], WRKY [ 20 ], ABC [ 21 ], F-box [ 22 ], and SOD [ 23 ] gene family in barley have been successfully completed. Although the functions of several HMA proteins in barley have been reported [ 24 , 25 ], genome-wide analysis of the HvHMA family is lacking.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification of the HMA Gene Family and Expression Analysis under Cd Stress in Barley

Zhang

Yang

Zhang

et al. 2021

Plants

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In recent years, cadmium (Cd) pollution in soil has increased with increasing industrial activities, which has restricted crop growth and agricultural development. The heavy metal ATPase (HMA) gene family contributes to heavy metal stress resistance in plants. In this study, 21 HMA genes (HvHMAs) were identified in barley (Hordeumvulgare L., Hv) using bioinformatics methods. Based on phylogenetic analysis and domain distribution, barley HMA genes were divided into five groups (A–E), and complete analyses were performed in terms of physicochemical properties, structural characteristics, conserved domains, and chromosome localization. The expression pattern analysis showed that most HvHMA genes were expressed in barley and exhibited tissue specificity. According to the fragments per kilobase of exon per million fragments values in shoots from seedlings at the 10 cm shoot stage (LEA) and phylogenetic analysis, five HvHMA genes were selected for expression analysis under Cd stress. Among the five HvHMA genes, three (HvHMA1, HvHMA3, and HvHMA4) were upregulated and two (HvHMA2 and HvHMA6) were downregulated following Cd treatments. This study serves as a foundation for clarifying the functions of HvHMA proteins in the heavy metal stress resistance of barley.

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Genome-wide identification of the SOD gene family and expression analysis under drought and salt stress in barley

Cited by 45 publications

References 48 publications

Insilco identification and characterization of superoxide dismutase gene family in Brassica rapa

Insilco identification and characterization of superoxide dismutase gene family in Brassica rapa

Genome-Wide Analysis and Expression Profile of Superoxide Dismutase (SOD) Gene Family in Rapeseed (Brassica napus L.) under Different Hormones and Abiotic Stress Conditions

Genome-Wide Identification of the HMA Gene Family and Expression Analysis under Cd Stress in Barley

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