Genome-wide identification, phylogeny, and expression profiling analysis of shattering genes in rapeseed and mustard plants

Afridi, Mahideen; Ahmad, Khurshid; Malik, Shahana Seher; Rehman, Nazia; Yasin, Muhammad; Khan, Shujaul Mulk; Hussain, Adil; Khan, Muhammad Ramzan

doi:10.1186/s43141-022-00408-2

Cited by 3 publications

(1 citation statement)

References 36 publications

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“…Genome-wide studies of various gene families in Brassicaceae have consistently indicated their expansion compared with Arabidopsis. Notable examples are not limited to but include APX, NPR, DOF, shattering genes, SOD, and PEBP [68][69][70][71][72][73]. Regarding amphidiploids, the presence of twelve genes suggests these species inherited six genes from each of their parental species, corresponding to the GTR genes found in Arabidopsis [42].…”

Section: Discussionmentioning

confidence: 99%

Studying Salt-Induced Shifts in Gene Expression Patterns of Glucosinolate Transporters and Glucosinolate Accumulation in Two Contrasting Brassica Species

Fatima,

Khan,

Iqbal

et al. 2024

Metabolites

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Brassica crops are well known for the accumulation of glucosinolates—secondary metabolites crucial for plants’ adaptation to various stresses. Glucosinolates also functioning as defence compounds pose challenges to food quality due to their goitrogenic properties. Their disruption leaves plants susceptible to insect pests and diseases. Hence, a targeted reduction in seed glucosinolate content is of paramount importance to increase food acceptance. GLUCOSINOLATE TRANSPORTERS (GTRs) present a promising avenue for selectively reducing glucosinolate concentrations in seeds while preserving biosynthesis elsewhere. In this study, 54 putative GTR protein sequences found in Brassica were retrieved, employing Arabidopsis GTR1 and GTR2 templates. Comprehensive bioinformatics analyses, encompassing gene structure organization, domain analysis, motif assessments, promoter analysis, and cis-regulatory elements, affirmed the existence of transporter domains and stress-related regulatory elements. Phylogenetic analysis revealed patterns of conservation and divergence across species. Glucosinolates have been shown to increase under stress conditions, indicating a potential role in stress response. To elucidate the role of GTRs in glucosinolate transportation under NaCl stress in two distinct Brassica species, B. juncea and B. napus, plants were subjected to 0, 100, or 200 mM NaCl. Based on the literature, key GTR genes were chosen and their expression across various plant parts was assessed. Both species displayed divergent trends in their biochemical profiles as well as glucosinolate contents under elevated salt stress conditions. Statistical modelling identified significant contributors to glucosinolate variations, guiding the development of targeted breeding strategies for low-glucosinolate varieties. Notably, GTR2A2 exhibited pronounced expressions in stems, contributing approximately 52% to glucosinolate content variance, while GTR2B1/C2 displayed significant expression in flowers. Additionally, GTR2A1 and GTR1A2/B1 demonstrated noteworthy expression in roots. This study enhances our understanding of glucosinolate regulation under stress conditions, offering avenues to improve Brassica crop quality and resilience.

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Section: Discussionmentioning

confidence: 99%

Studying Salt-Induced Shifts in Gene Expression Patterns of Glucosinolate Transporters and Glucosinolate Accumulation in Two Contrasting Brassica Species

Fatima,

Khan,

Iqbal

et al. 2024

Metabolites

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Correction: Genome-wide identification, phylogeny, and expression profiling analysis of shattering genes in rapeseed and mustard plants

Afridi

Ahmad

Malik

et al. 2022

Journal of Genetic Engineering and Biotechnology

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In Silico Analysis: Molecular Characterization and Evolutionary Study of CLCN Gene Family in Buffalo

Fu,

Khan,

Wang

et al. 2024

Genes

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Chloride channels (ClCs) have received global interest due to their significant role in the regulation of ion homeostasis, fluid transport, and electrical excitability of tissues and organs in different mammals and contributing to various functions, such as neuronal signaling, muscle contraction, and regulating the electrolytes’ balance in kidneys and other organs. In order to define the chloride voltage-gated channel (CLCN) gene family in buffalo, this study used in silico analyses to examine physicochemical properties, evolutionary patterns, and genome-wide identification. We identified eight CLCN genes in buffalo. The ProtParam tool analysis identified a number of important physicochemical properties of these proteins, including hydrophilicity, thermostability, in vitro instability, and basic nature. Based on their evolutionary relationships, a phylogenetic analysis divided the eight discovered genes into three subfamilies. Furthermore, a gene structure analysis, motif patterns, and conserved domains using TBtool demonstrated the significant conservation of this gene family among selected species over the course of evolution. A comparative amino acid analysis using ClustalW revealed similarities and differences between buffalo and cattle CLCN proteins. Three duplicated gene pairs were identified, all of which were segmental duplications except for CLCN4-CLCN5, which was a tandem duplication in buffalo. For each gene pair, the Ka/Ks test ratio findings showed that none of the ratios was more than one, indicating that these proteins were likely subject to positive selection. A synteny analysis confirmed a conserved pattern of genomic blocks between buffalo and cattle. Transcriptional control in cells relies on the binding of transcription factors to specific sites in the genome. The number of transcription factor binding sites (TFBSs) was higher in cattle compared to buffalo. Five main recombination breakpoints were identified at various places in the recombination analysis. The outcomes of our study provide new knowledge about the CLCN gene family in buffalo and open the door for further research on candidate genes in vertebrates through genome-wide studies.

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Genome-wide identification, phylogeny, and expression profiling analysis of shattering genes in rapeseed and mustard plants

Cited by 3 publications

References 36 publications

Studying Salt-Induced Shifts in Gene Expression Patterns of Glucosinolate Transporters and Glucosinolate Accumulation in Two Contrasting Brassica Species

Studying Salt-Induced Shifts in Gene Expression Patterns of Glucosinolate Transporters and Glucosinolate Accumulation in Two Contrasting Brassica Species

Correction: Genome-wide identification, phylogeny, and expression profiling analysis of shattering genes in rapeseed and mustard plants

In Silico Analysis: Molecular Characterization and Evolutionary Study of CLCN Gene Family in Buffalo

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