Plants possess the remarkable ability to thrive in challenging environments by synthesizing a diverse array of specialized metabolites, which play crucial roles in defense against biotic and abiotic stresses. Despite their significance, the low natural yield of these bioactive compounds, coupled with genetic variability and environmental influences, poses significant challenges for their extraction and utilization. In recent years, plant tissue culture has emerged as a viable alternative for the controlled and consistent production of secondary metabolites. Among various strategies to boost metabolite synthesis in vitro, elicitation has proven to be the one of the most effective in triggering plant defense mechanisms and enhance secondary metabolite accumulation. This review comprehensively explores the role of elicitation in promoting secondary metabolite synthesis in plant cell cultures, with a particular focus on the mechanisms and regulatory functions of key elicitors like salicylic acid and methyl jasmonate. It delves into the classification of elicitors, their effects on various in vitro culture systems, and the potential of nanoparticles as novel elicitors. Additionally, the review discusses the co-culture technique as a promising strategy for biotechnological mining of secondary metabolites. The review also highlights the role of elicitation in improving stress tolerance in plants and emphasizes the need for continued research to overcome existing challenges and fully realize the potential of these strategies. This paper is a valuable resource for scholars and professionals in plant biotechnology, nanotechnology, and related fields, offering insights into the current state of knowledge, and future directions for enhancing secondary metabolite production in plants.
{"title":"Elicitation strategies for enhanced secondary metabolite synthesis in plant cell cultures and its role in plant defense mechanism","authors":"Nidhi Selwal , Khojin Supriadi , Farida Rahayu , Deden Sukmadjaja , Aniswatul Khamidah , Kurniawan Budiaarto , Sri Satya Antarlina , Mustika Tripatmasari , Atif Khurshid Wani","doi":"10.1016/j.plgene.2024.100485","DOIUrl":"10.1016/j.plgene.2024.100485","url":null,"abstract":"<div><div>Plants possess the remarkable ability to thrive in challenging environments by synthesizing a diverse array of specialized metabolites, which play crucial roles in defense against biotic and abiotic stresses. Despite their significance, the low natural yield of these bioactive compounds, coupled with genetic variability and environmental influences, poses significant challenges for their extraction and utilization. In recent years, plant tissue culture has emerged as a viable alternative for the controlled and consistent production of secondary metabolites. Among various strategies to boost metabolite synthesis <em>in vitro</em>, elicitation has proven to be the one of the most effective in triggering plant defense mechanisms and enhance secondary metabolite accumulation. This review comprehensively explores the role of elicitation in promoting secondary metabolite synthesis in plant cell cultures, with a particular focus on the mechanisms and regulatory functions of key elicitors like salicylic acid and methyl jasmonate. It delves into the classification of elicitors, their effects on various <em>in vitro</em> culture systems, and the potential of nanoparticles as novel elicitors. Additionally, the review discusses the co-culture technique as a promising strategy for biotechnological mining of secondary metabolites. The review also highlights the role of elicitation in improving stress tolerance in plants and emphasizes the need for continued research to overcome existing challenges and fully realize the potential of these strategies. This paper is a valuable resource for scholars and professionals in plant biotechnology, nanotechnology, and related fields, offering insights into the current state of knowledge, and future directions for enhancing secondary metabolite production in plants.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"41 ","pages":"Article 100485"},"PeriodicalIF":2.2,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143176481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-16DOI: 10.1016/j.plgene.2024.100487
Akram Ali Baloch , Kaleem U. Kakar , Sumera Rais , Zarqa Nawaz , Abdulwareth A. Almoneafy , Agha Muhammad Raza , Samiullah Khan , Raqeeb Ullah
Cyclic nucleotide-gated ion channels (CNGCs) are important in cellular signaling, enabling ion passage, mainly calcium, across cell membranes in animals and plants. In plants, CNGCs are involved in cation transport, influencing growth, pathogen defense, and stress resistance. The CNGC gene family in Brassica juncea (L.) Czern (BjCNGCs) has not been well studied previously. We conducted a wide-ranging genome-wide analysis of BjCNGCs using available genomic data, covering genomic characterization, evolution, synteny analysis, gene mapping, structure, conserved motifs, cis-acting elements, potential protein association networks, post-translational modifications, and regulation. RT-qPCR assays were performed to investigate the expression patterns of selected BjCNGC genes in response to growth and stress. Our study identified 39 BjCNGC genes predicted to be present on fourteen chromosomes. Almost 49 % of these genes are positioned in conserved syntenic blocks of LF, MF-I, and MF-II sub-genomes, with a gene deletion (Bra024083 and BniB002576) from the MF-I block during intraspecific hybridization. The remaining genes evolved through segmental duplications 0.22 to 0.67 million years ago under purifying selection. Phylogenetic analysis classified the BjCNGC family into four groups, with groups III and IV further subdivided into A and B. We recognized 17 miRNA target sites, six of which are involved in stress resistance, coupled with phosphorylation for regulatory control. In-silico methods revealed gene structures, conserved motifs, and protein interaction networks. The study identified several CNGCs in Brassica juncea (L.) Czern showed significant responses to various stresses. Remarkably, certain CNGCs showed increased responses to black rot and TuMV, while others were more reactive to salinity and drought conditions. These findings suggest that targeting specific CNGCs through future genomic selection and breeding efforts could enhance crop production by introducing desirable stress-resistant traits in Brassica.
{"title":"Genome-wide analysis of CNGC gene family in Brassica juncea (L.) Czern reveals key targets for stress resistance and crop improvement","authors":"Akram Ali Baloch , Kaleem U. Kakar , Sumera Rais , Zarqa Nawaz , Abdulwareth A. Almoneafy , Agha Muhammad Raza , Samiullah Khan , Raqeeb Ullah","doi":"10.1016/j.plgene.2024.100487","DOIUrl":"10.1016/j.plgene.2024.100487","url":null,"abstract":"<div><div>Cyclic nucleotide-gated ion channels (CNGCs) are important in cellular signaling, enabling ion passage, mainly calcium, across cell membranes in animals and plants. In plants, CNGCs are involved in cation transport, influencing growth, pathogen defense, and stress resistance. The <em>CNGC</em> gene family in <em>Brassica juncea</em> (L.) Czern (<em>BjCNGCs</em>) has not been well studied previously. We conducted a wide-ranging genome-wide analysis of <em>BjCNGCs</em> using available genomic data, covering genomic characterization, evolution, synteny analysis, gene mapping, structure, conserved motifs, cis-acting elements, potential protein association networks, post-translational modifications, and regulation. RT-qPCR assays were performed to investigate the expression patterns of selected <em>BjCNGC</em> genes in response to growth and stress. Our study identified 39 <em>BjCNGC</em> genes predicted to be present on fourteen chromosomes. Almost 49 % of these genes are positioned in conserved syntenic blocks of LF, MF-I, and MF-II sub-genomes, with a gene deletion (<em>Bra024083</em> and <em>BniB002576</em>) from the MF-I block during intraspecific hybridization. The remaining genes evolved through segmental duplications 0.22 to 0.67 million years ago under purifying selection. Phylogenetic analysis classified the BjCNGC family into four groups, with groups III and IV further subdivided into A and B. We recognized 17 miRNA target sites, six of which are involved in stress resistance, coupled with phosphorylation for regulatory control. <em>In-silico</em> methods revealed gene structures, conserved motifs, and protein interaction networks. The study identified several <em>CNGCs</em> in <em>Brassica juncea</em> (L.) Czern showed significant responses to various stresses. Remarkably, certain <em>CNGCs</em> showed increased responses to black rot and TuMV, while others were more reactive to salinity and drought conditions. These findings suggest that targeting specific <em>CNGCs</em> through future genomic selection and breeding efforts could enhance crop production by introducing desirable stress-resistant traits in <em>Brassica</em>.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"41 ","pages":"Article 100487"},"PeriodicalIF":2.2,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143176495","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-13DOI: 10.1016/j.plgene.2024.100483
Heba Ebeed , Ahmed El-helely
Threonine aldolase is important in amino acid metabolism. This study characterized the threonine aldolase genes in wheat by identifying THA genes and examining their expression profiles during grain-filling under drought stress. Querying the wheat genome database with the Arabidopsis THA protein retrieved 15 non-redundant wheat homologs, of which five putative homologs harbored a threonine aldolase domain. The identified TaTHA genes are located on chromosome 2 and show a complex distribution pattern among wheat subgenomes, with possible duplication events in the A and B genomes. Structural analysis revealed a rather conserved exon-intron organization, together with physicochemical properties, while motif analysis revealed two novel wheat-specific motifs. Tissue and development expression profiling revealed that TaTHA1 and TaTHA2 were expressed at high levels, indicating their importance for the core metabolic processes, while the other three genes, TaTHA3, TaTHA4, and TaTHA5, were expressed in a tissue-specific manner. Subsequently, upregulation of the expression of THA genes in specific grain-filling stages during drought stress was found, indicating a role in the regulation of threonine metabolism, although no differences in threonine content were found. These results shed lights on the functional roles of THA genes in wheat and their potential involvement in stress responses, providing important information that can be used for crop improvement and breeding strategies.
{"title":"Genomic insights into threonine aldolase genes in wheat: Characterization and expression analysis during grain filling under drought stress","authors":"Heba Ebeed , Ahmed El-helely","doi":"10.1016/j.plgene.2024.100483","DOIUrl":"10.1016/j.plgene.2024.100483","url":null,"abstract":"<div><div>Threonine aldolase is important in amino acid metabolism. This study characterized the threonine aldolase genes in wheat by identifying <em>THA</em> genes and examining their expression profiles during grain-filling under drought stress. Querying the wheat genome database with the Arabidopsis THA protein retrieved 15 non-redundant wheat homologs, of which five putative homologs harbored a threonine aldolase domain. The identified <em>TaTHA</em> genes are located on chromosome 2 and show a complex distribution pattern among wheat subgenomes, with possible duplication events in the A and B genomes. Structural analysis revealed a rather conserved exon-intron organization, together with physicochemical properties, while motif analysis revealed two novel wheat-specific motifs. Tissue and development expression profiling revealed that <em>TaTHA1</em> and <em>TaTHA2</em> were expressed at high levels, indicating their importance for the core metabolic processes, while the other three genes, <em>TaTHA3</em>, <em>TaTHA4</em>, and <em>TaTHA5</em>, were expressed in a tissue-specific manner. Subsequently, upregulation of the expression of <em>THA</em> genes in specific grain-filling stages during drought stress was found, indicating a role in the regulation of threonine metabolism, although no differences in threonine content were found. These results shed lights on the functional roles of <em>THA</em> genes in wheat and their potential involvement in stress responses, providing important information that can be used for crop improvement and breeding strategies.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"41 ","pages":"Article 100483"},"PeriodicalIF":2.2,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143176496","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-11DOI: 10.1016/j.plgene.2024.100482
Md Rihan Kabir Shuvo, Asifur Rob Bhuya, Abdullah Al Nahid, Ajit Ghosh
Catalase (CAT) controls plant growth and development primarily by scavenging H2O2 from reactive oxygen species (ROS). As an antioxidant enzyme, catalase reduces ROS by converting H2O2 into H2O to shield cells from oxidative stress-induced apoptosis. The CAT gene family has been identified in many plants except Sorghum bicolor. In this study, five SbCAT proteins encoded by three genes were identified in the genome of S. bicolor. Three conserved amino acids, one active catalytic site, one heme-ligand signature, and three peroxisomal targeting signal 1 (PTS1) sequences were shared by all SbCAT proteins. The presence of different cis-regulatory elements indicated that SbCAT genes might be involved in the developmental and stress adaptation pathways. SbCAT genes showed variable expression in various tissues and responses to hormonal, abiotic, and biotic stresses. The findings from this study may aid in future research on the functions of SbCAT genes in stress modulation and crop improvement.
{"title":"Identification, characterization, and expression profiling of catalase gene family in Sorghum bicolor L.","authors":"Md Rihan Kabir Shuvo, Asifur Rob Bhuya, Abdullah Al Nahid, Ajit Ghosh","doi":"10.1016/j.plgene.2024.100482","DOIUrl":"10.1016/j.plgene.2024.100482","url":null,"abstract":"<div><div>Catalase (CAT) controls plant growth and development primarily by scavenging H<sub>2</sub>O<sub>2</sub> from reactive oxygen species (ROS). As an antioxidant enzyme, catalase reduces ROS by converting H<sub>2</sub>O<sub>2</sub> into H<sub>2</sub>O to shield cells from oxidative stress-induced apoptosis. The <em>CAT</em> gene family has been identified in many plants except <em>Sorghum bicolor</em>. In this study, five SbCAT proteins encoded by three genes were identified in the genome of <em>S. bicolor</em>. Three conserved amino acids, one active catalytic site, one heme-ligand signature, and three peroxisomal targeting signal 1 (PTS1) sequences were shared by all SbCAT proteins. The presence of different cis-regulatory elements indicated that <em>SbCAT</em> genes might be involved in the developmental and stress adaptation pathways. <em>SbCAT</em> genes showed variable expression in various tissues and responses to hormonal, abiotic, and biotic stresses. The findings from this study may aid in future research on the functions of <em>SbCAT</em> genes in stress modulation and crop improvement.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"41 ","pages":"Article 100482"},"PeriodicalIF":2.2,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143177789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-10DOI: 10.1016/j.plgene.2024.100484
Ying Duan , Zenglin Li
Anthocyanins are essential for imparting color to plants and offer protective bioactive benefits against a range of environmental stressors. The synthesis of anthocyanins is controlled by a complex regulatory network. Emerging research emphasizes the pivotal role of ubiquitination in modulating anthocyanin levels, particularly through the targeting of key proteins for degradation within the jasmonic acid and gibberellic acid signaling pathways. Here, we will summarize these new findings and highlight the most recent research outcomes. Finally, some potential research hotspots related to this field will be proposed.
{"title":"The colorful clash: JA and GA signaling in apple anthocyanin biosynthesis through ubiquitination-dependent degradation","authors":"Ying Duan , Zenglin Li","doi":"10.1016/j.plgene.2024.100484","DOIUrl":"10.1016/j.plgene.2024.100484","url":null,"abstract":"<div><div>Anthocyanins are essential for imparting color to plants and offer protective bioactive benefits against a range of environmental stressors. The synthesis of anthocyanins is controlled by a complex regulatory network. Emerging research emphasizes the pivotal role of ubiquitination in modulating anthocyanin levels, particularly through the targeting of key proteins for degradation within the jasmonic acid and gibberellic acid signaling pathways. Here, we will summarize these new findings and highlight the most recent research outcomes. Finally, some potential research hotspots related to this field will be proposed.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"41 ","pages":"Article 100484"},"PeriodicalIF":2.2,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143176494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Faba bean (Vicia faba L.) is a popular legume due to its nutritional, medicinal and environmental benefits. But vicine and convicine (VC) remain as the main threats for “favism” in individuals with genetic deficiency of Glucose-6-phosphate dehydrogenase (G6PDH) enzyme. Re-sequencing-based allele mining involving allele-specific Tetra-ARMS PCR has revealed a 92 bp InDel (Insertion-Deletion), designated as “InDel1.4” in the intron-4 of VC1 gene and a coding-SNP (T/C) at position +1588 in the exon-5. Consequently, three distinct haplotypes (Hap-1, Hap-2 and Hap-3) were identified based on the size of the intron-4 and the allelic status of the SNP in exon-5. LC-MS/MS analysis confirms that the vicine concentration varied between 3.489 and 10.025 g/kg in the entire collection of germplasm. A strong correlation (r = 0.84**) was observed between haplotypes and variation in vicine concentration. Translation of the sequenced fragments revealed that, the coding-SNP doesn't not change the amino acid composition of the VC1 protein. Therefore, the coding-SNP was found to be a synonymous SNP. As the InDel1.4 was located within few hundred base pairs away from the previously reported “AT insertional-mutation”, which was responsible for very low or near-zero VC faba bean, and also shows correlation with vicine content, the InDel could be utilized for a simple, reliable and cost-effective molecular marker assisted selection and crop improvement for developing faba beans with reduced VC. The Hap-1 and Hap-2 have tremendous potential to be utilized in haplotype-based breeding for faba bean improvement to combat favism.
{"title":"Discovery of potential haplotypes associated with varying levels of vicine content due to the InDel1.4 and a coding-SNP in the VC1 gene in faba bean (Vicia faba L.)","authors":"Sadhan Debnath , Wricha Tyagi , Mayank Rai , Kuldeep Singh , Sujan Majumder , Naveen Duhan , Ng Tombisana Meetei","doi":"10.1016/j.plgene.2024.100481","DOIUrl":"10.1016/j.plgene.2024.100481","url":null,"abstract":"<div><div>Faba bean (<em>Vicia faba</em> L.) is a popular legume due to its nutritional, medicinal and environmental benefits. But vicine and convicine (VC) remain as the main threats for “favism” in individuals with genetic deficiency of Glucose-6-phosphate dehydrogenase (G6PDH) enzyme. <em>Re</em>-sequencing-based allele mining involving allele-specific Tetra-ARMS PCR has revealed a 92 bp InDel (Insertion-Deletion), designated as “InDel1.4” in the intron-4 of <em>VC1</em> gene and a coding-SNP (T/C) at position +1588 in the exon-5. Consequently, three distinct haplotypes (Hap-1, Hap-2 and Hap-3) were identified based on the size of the intron-4 and the allelic status of the SNP in exon-5. LC-MS/MS analysis confirms that the vicine concentration varied between 3.489 and 10.025 g/kg in the entire collection of germplasm. A strong correlation (<em>r</em> = 0.84**) was observed between haplotypes and variation in vicine concentration. Translation of the sequenced fragments revealed that, the coding-SNP doesn't not change the amino acid composition of the VC1 protein. Therefore, the coding-SNP was found to be a synonymous SNP. As the InDel1.4 was located within few hundred base pairs away from the previously reported “AT insertional-mutation”, which was responsible for very low or near-zero VC faba bean, and also shows correlation with vicine content, the InDel could be utilized for a simple, reliable and cost-effective molecular marker assisted selection and crop improvement for developing faba beans with reduced VC. The Hap-1 and Hap-2 have tremendous potential to be utilized in haplotype-based breeding for faba bean improvement to combat favism.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"41 ","pages":"Article 100481"},"PeriodicalIF":2.2,"publicationDate":"2024-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143176498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mycoplasma like organisms (MLO) is responsible for sesame phyllody which affects the seed yield and oil production. Mutant lines scanned with triggered innate immune system and proteomic insights aid to develop phyllody-resistant sesame genotypes. However, little information is known about the subtle changes in the sub-domains of R- gene in the mutant population. In this study, sesame genotype TMV7 was subjected to gamma radiation at different dosages, and the mutant population was selected based on their response to phyllody disease. The mutants were screened for key phenotypic traits such as seed and oil yield and percent disease incidence. Consequently, nine outstanding mutants were forwarded for subsequent generations (M2) with a population size of 400 plants per mutant line. Mutants showing less disease incidence and higher seed/oil yield were used for molecular docking and abundance of R-gene transcripts. Out of nine mutant populations developed, Mut1 and Mut3 showed least disease incidence and higher oil yield. Molecular docking of nucleotide binding ARC domain of R-protein revealed a significant increase in the interaction of H bonding with ADP in Mut1 which is mediated by Gly- residue of the P-loop. The substituted Pro140 forms hydrophobic alkyl bonding which is responsible for the folding of protein. Post infection studies showed that the expression of R-gene has increased by 29.5 folds in the mutant lines as compared with the TMV7 (non-irradiated). The study showed that the innate immunity developed in the phyllody resistant lines is accompanied with the amino-acid substitution in the NB-ARC domain of R-protein. The lines identified with higher resistance and oil yield can be used to develop sesame phyllody resistant genotypes with improved yield.
{"title":"Effect of gamma-ray induced mutagenesis on the NBS-LRR domain of mycoplasma resistance proteins in sesame (Sesamum indicum L.)”","authors":"Asish K. Binodh , Sugitha Thankappan , R.M. Saravana Kumar , Naveenkumar Ramasamy , Ramchander Selvaraj , Raghupathy Karthikeyan","doi":"10.1016/j.plgene.2024.100480","DOIUrl":"10.1016/j.plgene.2024.100480","url":null,"abstract":"<div><div>Mycoplasma like organisms (MLO) is responsible for sesame phyllody which affects the seed yield and oil production. Mutant lines scanned with triggered innate immune system and proteomic insights aid to develop phyllody-resistant sesame genotypes. However, little information is known about the subtle changes in the sub-domains of <em>R-</em> gene in the mutant population. In this study, sesame genotype TMV7 was subjected to gamma radiation at different dosages, and the mutant population was selected based on their response to phyllody disease. The mutants were screened for key phenotypic traits such as seed and oil yield and percent disease incidence. Consequently, nine outstanding mutants were forwarded for subsequent generations (M<sub>2</sub>) with a population size of 400 plants per mutant line. Mutants showing less disease incidence and higher seed/oil yield were used for molecular docking and abundance of <em>R</em>-gene transcripts. Out of nine mutant populations developed, Mut1 and Mut3 showed least disease incidence and higher oil yield. Molecular docking of nucleotide binding ARC domain of R-protein revealed a significant increase in the interaction of H bonding with ADP in Mut1 which is mediated by Gly- residue of the <em>P</em>-loop. The substituted Pro140 forms hydrophobic alkyl bonding which is responsible for the folding of protein. Post infection studies showed that the expression of <em>R-</em>gene has increased by 29.5 folds in the mutant lines as compared with the TMV7 (non-irradiated). The study showed that the innate immunity developed in the phyllody resistant lines is accompanied with the amino-acid substitution in the NB-ARC domain of R-protein. The lines identified with higher resistance and oil yield can be used to develop sesame phyllody resistant genotypes with improved yield.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"41 ","pages":"Article 100480"},"PeriodicalIF":2.2,"publicationDate":"2024-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143177790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-26DOI: 10.1016/j.plgene.2024.100479
Wang Chen , Taswar Ahsan , Di Han , Wen-Rui Wang , Si-Tong Du , Chao-Qun Zang , Yu-Qian Huang , Ejaz Hussain Siddiqi
This study aimed to investigate the transcriptional response of peanut plants against the biocontrol agent Bacillus amyloliquefaciens TA-1. Gene expression analysis showed the highest number of Differentially expressed genes (DEGs) in downregulation in samples Bam_Am_1_vs_Bam_CK_1 compared to other samples (Bam_Am_2_vs_Bam_CK_2, and Bam_Am_3_vs_Bam_CK_3) After de novo annotation of the transcriptome, we analyzed the GO (Gene Ontology) enrichment of the DEGs to elucidate the main functional pathways impacted by TA-1. TA-1 induced qualitatively transcriptional modifications in all replicates, with a substantial impact on following GO terms, i.e., response to external stimulus, membrane parts, cell periphery, and catalytic activity. Further, (we analyzed the KEGG enrichment of DEGs to elucidate the main functional pathways that TA-1 impacts). The most enriched pathways were plant-pathogen interaction, mitogen-activated protein kinase (MAPK) signaling pathways, and phenylpropanoid biosynthesis. We also analyzed the KOG enrichment of DEGs. Most of the annotation was associated with functional groups in all treatments, which primarily pertained to signal transduction mechanisms, secondary metabolite biosynthesis, post-translational modification, protein turnover, and chaperones. These results highlight the qualitative transcriptional changes in peanut plants due to the application of the biocontrol agent, underscoring its potential impact on crop protection and enhancement.
{"title":"Transcriptome profiling in peanut (Arachis hypogaea) in response to biotic stress produce by Bacillus amyloliquefaciens TA-1","authors":"Wang Chen , Taswar Ahsan , Di Han , Wen-Rui Wang , Si-Tong Du , Chao-Qun Zang , Yu-Qian Huang , Ejaz Hussain Siddiqi","doi":"10.1016/j.plgene.2024.100479","DOIUrl":"10.1016/j.plgene.2024.100479","url":null,"abstract":"<div><div>This study aimed to investigate the transcriptional response of peanut plants against the biocontrol agent <em>Bacillus amyloliquefaciens</em> TA-1. Gene expression analysis showed the highest number of Differentially expressed genes (DEGs) in downregulation in samples Bam_Am_1_vs_Bam_CK_1 compared to other samples (Bam_Am_2_vs_Bam_CK_2, and Bam_Am_3_vs_Bam_CK_3) After de novo annotation of the transcriptome, we analyzed the GO (Gene Ontology) enrichment of the DEGs to elucidate the main functional pathways impacted by TA-1. TA-1 induced qualitatively transcriptional modifications in all replicates, with a substantial impact on following GO terms, i.e., response to external stimulus, membrane parts, cell periphery, and catalytic activity. Further, (we analyzed the KEGG enrichment of DEGs to elucidate the main functional pathways that TA-1 impacts). The most enriched pathways were plant-pathogen interaction, mitogen-activated protein kinase (MAPK) signaling pathways, and phenylpropanoid biosynthesis. We also analyzed the KOG enrichment of DEGs. Most of the annotation was associated with functional groups in all treatments, which primarily pertained to signal transduction mechanisms, secondary metabolite biosynthesis, post-translational modification, protein turnover, and chaperones. These results highlight the qualitative transcriptional changes in peanut plants due to the application of the biocontrol agent, underscoring its potential impact on crop protection and enhancement.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"41 ","pages":"Article 100479"},"PeriodicalIF":2.2,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142720351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-21DOI: 10.1016/j.plgene.2024.100478
Elias Shewabez , Laura Mugnai , Wuletaw Tadesse , Admas Alemu
Stripe rust, also known as yellow rust, caused by Puccinia striiformis f. sp. tritici (Pst), is among the most destructive fungal diseases affecting global wheat productivity. Identifying genetic loci associated with Pst resistance is crucial for developing durable Pst-resistant wheat varieties. This study aimed to discover genetic markers linked to Pst-resistance in wheat using a 15 K single-nucleotide polymorphism (SNP) array. Field screenings were conducted over two years (2018 and 2019) on a panel of 245 wheat breeding lines developed by the International Center for Agricultural Research in the Dry Areas (ICARDA) at the Kulumsa Agricultural Research Center in Ethiopia. Importantly, 36 breeding lines exhibited consistent immunity or resistance across both growing seasons. Genome-wide association studies (GWAS) identified 34 marker-trait associations (MTAs) across 10 loci that surpassed the significance threshold. Half of these SNP markers were located on chromosome 7B, while the remaining were distributed across chromosomes 1B, 2B, 4B, 5 A, and 6B. Many identified quantitative trait loci (QTLs) were in close proximity to known Pst resistance genes/QTLs, suggesting they correspond to the same genetic regions. Additionally, three QTLs—EWYY5A.2, EWYY6B.1, and EWYY7B.3—were notably distant from any of previously identified Pst resistance genes, emerging as potential novel loci from this study. These QTLs represent promising candidates for marker-assisted selection, facilitating the development of wheat cultivars with enhanced resistance to Pst. Additionally, this study recommends incorporating the 36 consistently resistant lines into national and international wheat breeding programs to enhance Pst disease management efforts.
{"title":"Unraveling the genetic architecture of stripe rust resistance in ICARDA spring wheat","authors":"Elias Shewabez , Laura Mugnai , Wuletaw Tadesse , Admas Alemu","doi":"10.1016/j.plgene.2024.100478","DOIUrl":"10.1016/j.plgene.2024.100478","url":null,"abstract":"<div><div>Stripe rust, also known as yellow rust, caused by <em>Puccinia striiformis</em> f. sp. <em>tritici</em> (<em>Pst</em>), is among the most destructive fungal diseases affecting global wheat productivity. Identifying genetic loci associated with <em>Pst</em> resistance is crucial for developing durable <em>Pst-</em>resistant wheat varieties. This study aimed to discover genetic markers linked to <em>Ps</em>t-resistance in wheat using a 15 K single-nucleotide polymorphism (SNP) array. Field screenings were conducted over two years (2018 and 2019) on a panel of 245 wheat breeding lines developed by the International Center for Agricultural Research in the Dry Areas (ICARDA) at the Kulumsa Agricultural Research Center in Ethiopia. Importantly, 36 breeding lines exhibited consistent immunity or resistance across both growing seasons. Genome-wide association studies (GWAS) identified 34 marker-trait associations (MTAs) across 10 loci that surpassed the significance threshold. Half of these SNP markers were located on chromosome 7B, while the remaining were distributed across chromosomes 1B, 2B, 4B, 5 A, and 6B. Many identified quantitative trait loci (QTLs) were in close proximity to known <em>Pst</em> resistance genes/QTLs, suggesting they correspond to the same genetic regions. Additionally, three QTLs—<em>EWYY5A.2, EWYY6B.1, and EWYY7B.3</em>—were notably distant from any of previously identified <em>Pst</em> resistance genes, emerging as potential novel loci from this study. These QTLs represent promising candidates for marker-assisted selection, facilitating the development of wheat cultivars with enhanced resistance to <em>Pst.</em> Additionally, this study recommends incorporating the 36 consistently resistant lines into national and international wheat breeding programs to enhance <em>Pst</em> disease management efforts.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"41 ","pages":"Article 100478"},"PeriodicalIF":2.2,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142758823","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-16DOI: 10.1016/j.plgene.2024.100477
Seyed Mohammad Mahdi Mortazavian , Mahdieh Arshadi-Bidgoli , Dariush Sadeghi , Mohammad Reza Bakhtiarizadeh
Cumin (Cuminum cyminum L.), a member of the Apiaceae family, exhibits a wide range of native ecotypes from the Eastern Mediterranean to India. Despite its significant culinary and medicinal applications, the availability of transcriptomic and genomic data for cumin remains limited, hindering advances in molecular genetics and breeding research. This study presents the first sequencing of the cumin transcriptome using RNA sequencing technology, generating 34,711,979, 48,649,265, 127,370,622, and 52,990,923 reads from the flowers of cumin plants. In total, 51,777 transcripts were de novo assembled, with an average length of 717.09 bp and an N50 value of 1110 bp. Approximately 70 % (36,166) of these transcripts were annotated in at least one public database (UniprotKB, Nr, Pfam, GO, and KEGG). Furthermore, 1556 simple sequence repeats (SSRs) were identified, distributed across 1465 transcripts. The most prevalent SSR motifs were di-nucleotide (70.05 %) and tri-nucleotide (26.16 %) repeats, followed by tetra-nucleotide (2.18 %), penta-nucleotide (0.90 %), and hexanucleotide repeats (0.71 %). The most frequent di-nucleotide and tri-nucleotide repeats were GA/TC (33.58 %) and CAG/CTG (10.32 %), respectively. Functional enrichment analysis indicated that transcripts containing SSRs play significant roles in metabolic processes, DNA/nucleotide binding, protein modification processes, and biosynthetic/developmental processes. For marker validation, 10 EST-SSR primer pairs were tested across 31 cumin genotypes, identifying 34 alleles with polymorphism information content (PIC) values ranging from 0.32 to 0.46. The mean genetic diversity index (MI) and effective multiplex ratio (EMR) were 1.22 and 2.98, respectively. Additionally, two clusters were identified through UPGMA analysis. The SSR markers identified in this study hold potential for applications in genetic mapping, population genetic analysis, genetic diversity studies, and marker-assisted breeding in cumin and related species.
{"title":"Identified and validation of EST-SSR in the transcriptome sequences by RNA-Seq in cumin (Cuminum Cyminum L.)","authors":"Seyed Mohammad Mahdi Mortazavian , Mahdieh Arshadi-Bidgoli , Dariush Sadeghi , Mohammad Reza Bakhtiarizadeh","doi":"10.1016/j.plgene.2024.100477","DOIUrl":"10.1016/j.plgene.2024.100477","url":null,"abstract":"<div><div>Cumin (<em>Cuminum cyminum</em> L.), a member of the Apiaceae family, exhibits a wide range of native ecotypes from the Eastern Mediterranean to India. Despite its significant culinary and medicinal applications, the availability of transcriptomic and genomic data for cumin remains limited, hindering advances in molecular genetics and breeding research. This study presents the first sequencing of the cumin transcriptome using RNA sequencing technology, generating 34,711,979, 48,649,265, 127,370,622, and 52,990,923 reads from the flowers of cumin plants. In total, 51,777 transcripts were de novo assembled, with an average length of 717.09 bp and an N50 value of 1110 bp. Approximately 70 % (36,166) of these transcripts were annotated in at least one public database (UniprotKB, Nr, Pfam, GO, and KEGG). Furthermore, 1556 simple sequence repeats (SSRs) were identified, distributed across 1465 transcripts. The most prevalent SSR motifs were di-nucleotide (70.05 %) and tri-nucleotide (26.16 %) repeats, followed by tetra-nucleotide (2.18 %), penta-nucleotide (0.90 %), and hexanucleotide repeats (0.71 %). The most frequent di-nucleotide and tri-nucleotide repeats were GA/TC (33.58 %) and CAG/CTG (10.32 %), respectively. Functional enrichment analysis indicated that transcripts containing SSRs play significant roles in metabolic processes, DNA/nucleotide binding, protein modification processes, and biosynthetic/developmental processes. For marker validation, 10 EST-SSR primer pairs were tested across 31 cumin genotypes, identifying 34 alleles with polymorphism information content (PIC) values ranging from 0.32 to 0.46. The mean genetic diversity index (MI) and effective multiplex ratio (EMR) were 1.22 and 2.98, respectively. Additionally, two clusters were identified through UPGMA analysis. The SSR markers identified in this study hold potential for applications in genetic mapping, population genetic analysis, genetic diversity studies, and marker-assisted breeding in cumin and related species.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"40 ","pages":"Article 100477"},"PeriodicalIF":2.2,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142704970","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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