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

Abstract

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.

Comprehensive In Silico Characterization and Expression Profiling of TCP Gene Family in Rapeseed

“…Rapeseed is an allotetraploid crop that practices broad genome replication and combination activities ( Song et al, 2020 ). Nevertheless, rapeseed yield is pretentious by numerous environmental factors such as cold, heat, drought, salinity, and heavy metals toxicity ( Raza et al, 2021a ; Raza et al, 2021b ; He et al, 2021 ; Raza, 2021 ; Su et al, 2021 ). The TCP TFs are antique plant-specific proteins ( Cubas et al, 1999 ).…”

“…Gene duplication events of TCP genes were also spotted in several plant species ( Ma et al, 2014 ; Lin et al, 2016 ; Yin et al, 2018 ; Wen et al, 2020 ). Apart from duplication events, exon-intron associations and numbers can also explain the evolutionary story of the gene family ( Xu et al, 2012 ; Raza et al, 2021a ; Su et al, 2021 ). The BnTCPs gene structure compared with the same group presented that TCP genes contribute to analogous exon/intron allocation in terms of exon and intron numbers; in the meantime, BnTCPs with the same class exhibited comparable motif patterns.…”

“…As described in our recent studies ( Raza et al, 2021a ; Su et al, 2021 ), two methods were used to recognize TCP genes in the B. napus genome, i.e., BLASTP and the Hidden Markov Model (HMM). The genome of B. napus (ZhongShuang 11; ZS11 variety) was downloaded from the BnPIR database ( http://cbi.hzau.edu.cn/bnapus/index.php ).…”

“…Rapeseed ( Brassica napus L.) is the second most crucial oilseed crop and possesses a complex genome. However, its growth and productivity are significantly affected at physiological, biochemical, and molecular levels in response to various plant hormones and abiotic stress conditions ( Raza et al, 2021a ; He et al, 2021 ; Raza, 2021 ; Su et al, 2021 ). To date, the TCP gene family and key TCP genes responding to abiotic stress have not been fully characterized in rapeseed.…”

Genome-Wide Characterization of Glutathione Peroxidase (GPX) Gene Family in Rapeseed (Brassica napus L.) Revealed Their Role in Multiple Abiotic Stress Response and Hormone Signaling

“…As defined in recent reports [28,29], two methods were employed to classify GPX genes in the Brassica napus genome, including BLASTP and the Hidden Markov Model (HMM) [28]. The sequence of Brassica napus genome was downloaded from the BnPIR database (http://cbi.hzau.edu.cn/bnapus/index.php, accessed on 1 July 2021) [30].…”