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}
Pub Date : 2024-11-12DOI: 10.1016/j.plgene.2024.100476
Anindita Chakraborty , Stephen J. Wylie
The aim of this review is to summarize current advancements in the application of CRISPR to ameliorate allergenicity in plant-based foods. The literature on food allergens highlights the negative impacts on quality of life for many sufferers. Efforts to select low-allergenicity crop varieties through conventional means have had limited success. Here we review the literature describing gene editing to eliminate allergenicity genes and measure subsequent allergen expression. Gene editing is a means of inserting or deleting nucleotides at precise locations/genes in the genome, and the most widely used technology is CRISPR (clustered regularly interspaced short palindromic repeats) along with an endonuclease such as Cas9 (CRISPR/Cas9). An example are the α-amylase/trypsin inhibitors (ATIs) in wheat that are responsible for bakers' asthma. CRISPR was utilized to simultaneously knock down two ATI subunits, resulting in reduced expression of both subunits. Between 1.4 % and 4.5 % of children suffer from peanut allergy. Progress toward knock down of expression of genes encoding known allergens in peanuts is reviewed. Other allergenic plant species of interest in this review are soy and mustard. Gene editing has the potential to manipulate expression of allergen genes to reduce allergenicity, but as some allergens play important roles in physiological processes such as biotic and abiotic stress amelioration, simply targeting their genes with CRISPR to abolish expression is not always feasible.
{"title":"Gene editing for allergen amelioration in plants – A review","authors":"Anindita Chakraborty , Stephen J. Wylie","doi":"10.1016/j.plgene.2024.100476","DOIUrl":"10.1016/j.plgene.2024.100476","url":null,"abstract":"<div><div>The aim of this review is to summarize current advancements in the application of CRISPR to ameliorate allergenicity in plant-based foods. The literature on food allergens highlights the negative impacts on quality of life for many sufferers. Efforts to select low-allergenicity crop varieties through conventional means have had limited success. Here we review the literature describing gene editing to eliminate allergenicity genes and measure subsequent allergen expression. Gene editing is a means of inserting or deleting nucleotides at precise locations/genes in the genome, and the most widely used technology is CRISPR (clustered regularly interspaced short palindromic repeats) along with an endonuclease such as Cas9 (CRISPR/Cas9). An example are the α-amylase/trypsin inhibitors (ATIs) in wheat that are responsible for bakers' asthma. CRISPR was utilized to simultaneously knock down two ATI subunits, resulting in reduced expression of both subunits. Between 1.4 % and 4.5 % of children suffer from peanut allergy. Progress toward knock down of expression of genes encoding known allergens in peanuts is reviewed. Other allergenic plant species of interest in this review are soy and mustard. Gene editing has the potential to manipulate expression of allergen genes to reduce allergenicity, but as some allergens play important roles in physiological processes such as biotic and abiotic stress amelioration, simply targeting their genes with CRISPR to abolish expression is not always feasible.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"40 ","pages":"Article 100476"},"PeriodicalIF":2.2,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142704349","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 : 2024-11-02DOI: 10.1016/j.plgene.2024.100475
Alina A. Alimova , Maria V. Gureeva , Mariya I. Gladkikh , Ekaterina Yu Nesterova , Mikhail Yu Syromyatnikov , Artem P. Gureev
It is known that plant mitochondria and mitochondrial DNA (mtDNA) are more resistant to damage than animal mitochondria. We hypothesized that this phenomenon may be related to alternative respiratory pathways in plants mitochondria, in particular alternative oxidase (AOX). The results of a pot experiment demonstrated that the application of the fungicide difenoconazole at concentrations that were 3-, 5-, and 10-times higher than the recommended dosage resulted in a 106 %, 76 %, and 90 % increase in mitochondrial DNA damage in tomato shoots, respectively, in comparison to the shoots treated with difenoconazole at the dosage recommended by the manufacturer. Inhibition of shoot growth was observed in response to treatment with difenoconazole at a dose 10times higher than recommended. It is noteworthy that when tomatoes were treated with difenoconazole at this concentration, there was a tendency for the expression of inducible aox1a. In a field experiment, difenoconazole at a concentration of 5 times higher than recommended resulted in a 10 % increase in mtDNA damage in the fruits compared to the control. Similar results were obtained in an in vitro experiment. The addition of low doses of difenoconazole to intact tomato mitochondria did not cause mtDNA damage. The observed damages occured only when 200 μM difenoconazole was added. In contrast, incubation of 20 μM difenoconazole with SHAM, which inhibits AOX, resulted in a 115 % increase in mtDNA damage compared to the use of the same concentration without difenoconazole. This finding is consistent with the damaging effect induced by 200 μM difenoconazole. The increase in difenoconazole toxicity induced by SHAM and the elevation in aox1a gene expression resulting from the treatment with a 10 times higher than the recommended dose of difenoconazole may signify a pivotal function of AOX in the increased resistance of plant mtDNA to the pesticide exposure.
{"title":"Alternative oxidase of plants mitochondria is related with increased resistance of tomato mtDNA to the difenoconazole exposure","authors":"Alina A. Alimova , Maria V. Gureeva , Mariya I. Gladkikh , Ekaterina Yu Nesterova , Mikhail Yu Syromyatnikov , Artem P. Gureev","doi":"10.1016/j.plgene.2024.100475","DOIUrl":"10.1016/j.plgene.2024.100475","url":null,"abstract":"<div><div>It is known that plant mitochondria and mitochondrial DNA (mtDNA) are more resistant to damage than animal mitochondria. We hypothesized that this phenomenon may be related to alternative respiratory pathways in plants mitochondria, in particular alternative oxidase (AOX). The results of a pot experiment demonstrated that the application of the fungicide difenoconazole at concentrations that were 3-, 5-, and 10-times higher than the recommended dosage resulted in a 106 %, 76 %, and 90 % increase in mitochondrial DNA damage in tomato shoots, respectively, in comparison to the shoots treated with difenoconazole at the dosage recommended by the manufacturer. Inhibition of shoot growth was observed in response to treatment with difenoconazole at a dose 10times higher than recommended. It is noteworthy that when tomatoes were treated with difenoconazole at this concentration, there was a tendency for the expression of inducible <em>aox1a</em>. In a field experiment, difenoconazole at a concentration of 5 times higher than recommended resulted in a 10 % increase in mtDNA damage in the fruits compared to the control. Similar results were obtained in an in vitro experiment. The addition of low doses of difenoconazole to intact tomato mitochondria did not cause mtDNA damage. The observed damages occured only when 200 μM difenoconazole was added. In contrast, incubation of 20 μM difenoconazole with SHAM, which inhibits AOX, resulted in a 115 % increase in mtDNA damage compared to the use of the same concentration without difenoconazole. This finding is consistent with the damaging effect induced by 200 μM difenoconazole. The increase in difenoconazole toxicity induced by SHAM and the elevation in aox1a gene expression resulting from the treatment with a 10 times higher than the recommended dose of difenoconazole may signify a pivotal function of AOX in the increased resistance of plant mtDNA to the pesticide exposure.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"40 ","pages":"Article 100475"},"PeriodicalIF":2.2,"publicationDate":"2024-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142663665","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}
Formins are highly conserved proteins with multiple domains that play an important role in the interaction with microfilaments and microtubules and thus regulate actin organisation and cytoskeletal dynamics. Despite their importance in plant development and response to stress, the study of FORMIN (FH) genes in cotton, an important fibre crop, remains limited. The genetic diversity of these genes is critical for improving the adaptability of cotton to environmental stress, which is a major challenge for cotton breeding programmes aimed at improving abiotic stress tolerance.
Results
Through comprehensive bioinformatics approaches, we identified 46, 50 and 27 putative FH genes in Gossypium hirsutum, G. barbadense and their diploid ancestors G. arboreum and G. raimondii, respectively. A phylogenetic analysis classified these genes into five subfamilies and revealed evolutionary relationships to Arabidopsis thaliana. Syntenic and collinear analyses showed that genomic duplications in cotton have driven the expansion of the FH gene family. Structural analysis showed significant variations in sequence length and conserved motifs. Promoter analysis revealed several cis-acting elements associated with growth, stress response and hormonal signalling. Protein-protein interaction predictions suggest involvement in hormone signalling, cytoskeletal regulation and cell wall dynamics. Differential expression of G. hirsutum FH (GhFH) genes in different cotton tissues under drought and osmotic stress was confirmed by qRT-PCR.
Conclusion
This study provides new insights into the functional diversity and evolutionary dynamics of FH genes in cotton and emphasises their potential role in improving abiotic stress tolerance. By identifying key regulatory genes involved in stress adaptation, this research contributes to the development of more resilient cotton varieties through targeted breeding strategies. The results underline the importance of genetic diversity in enabling cotton breeding programmes to overcome the challenges posed by abiotic stress.
背景Formins是具有多个结构域的高度保守蛋白，在与微丝和微管的相互作用中发挥重要作用，从而调节肌动蛋白的组织和细胞骨架的动态。尽管FORMIN（FH）基因在植物发育和应激反应中具有重要作用，但对棉花这种重要纤维作物中FORMIN（FH）基因的研究仍然有限。结果通过综合生物信息学方法，我们在 Gossypium hirsutum、G. barbadense 及其二倍体祖先 G. arboreum 和 G. raimondii 中分别鉴定出 46、50 和 27 个推测的 FH 基因。系统进化分析将这些基因分为五个亚家族，并揭示了它们与拟南芥的进化关系。同源分析和共线分析表明，棉花基因组的重复推动了 FH 基因家族的扩展。结构分析表明，序列长度和保守基序存在显著差异。启动子分析揭示了几个与生长、应激反应和激素信号有关的顺式作用元件。蛋白质-蛋白质相互作用预测表明，该基因参与激素信号、细胞骨架调节和细胞壁动力学。通过 qRT-PCR 验证了在干旱和渗透胁迫下不同棉花组织中 G. hirsutum FH（GhFH）基因的差异表达。通过确定参与胁迫适应的关键调控基因，这项研究有助于通过有针对性的育种策略培育更具抗逆性的棉花品种。研究结果强调了遗传多样性对于棉花育种计划克服非生物胁迫挑战的重要性。
{"title":"Genome-wide identification and characterization of FORMIN genes in cotton: Implications for abiotic stress tolerance","authors":"Rasmieh Hamid , Feba Jacob , Zahra Ghorbanzadeh , Mohsen Mardi , Shohreh Ariaeenejad , Mehrshad Zeinalabedini , Mohammad Reza Ghaffari","doi":"10.1016/j.plgene.2024.100474","DOIUrl":"10.1016/j.plgene.2024.100474","url":null,"abstract":"<div><h3>Background</h3><div>Formins are highly conserved proteins with multiple domains that play an important role in the interaction with microfilaments and microtubules and thus regulate actin organisation and cytoskeletal dynamics. Despite their importance in plant development and response to stress, the study of FORMIN (FH) genes in cotton, an important fibre crop, remains limited. The genetic diversity of these genes is critical for improving the adaptability of cotton to environmental stress, which is a major challenge for cotton breeding programmes aimed at improving abiotic stress tolerance.</div></div><div><h3>Results</h3><div>Through comprehensive bioinformatics approaches, we identified 46, 50 and 27 putative <em>FH</em> genes in <em>Gossypium hirsutum</em>, <em>G. barbadense</em> and their diploid ancestors <em>G. arboreum</em> and G. <em>raimondii</em>, respectively. A phylogenetic analysis classified these genes into five subfamilies and revealed evolutionary relationships to <em>Arabidopsis thaliana</em>. Syntenic and collinear analyses showed that genomic duplications in cotton have driven the expansion of the FH gene family. Structural analysis showed significant variations in sequence length and conserved motifs. Promoter analysis revealed several cis-acting elements associated with growth, stress response and hormonal signalling. Protein-protein interaction predictions suggest involvement in hormone signalling, cytoskeletal regulation and cell wall dynamics. Differential expression of <em>G. hirsutum</em> FH (GhFH) genes in different cotton tissues under drought and osmotic stress was confirmed by qRT-PCR.</div></div><div><h3>Conclusion</h3><div>This study provides new insights into the functional diversity and evolutionary dynamics of FH genes in cotton and emphasises their potential role in improving abiotic stress tolerance. By identifying key regulatory genes involved in stress adaptation, this research contributes to the development of more resilient cotton varieties through targeted breeding strategies. The results underline the importance of genetic diversity in enabling cotton breeding programmes to overcome the challenges posed by abiotic stress.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"40 ","pages":"Article 100474"},"PeriodicalIF":2.2,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142554879","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 : 2024-10-28DOI: 10.1016/j.plgene.2024.100473
Masaki Odahara , Maai Mori , Keiji Numata
Angiosperm mitochondrial genomes have highly complex and diverse structures that are partly due to frequent insertions of nuclear and chloroplast DNA (cpDNA) into mitochondrial DNA (mtDNA). This suggests the existence of mechanisms for gene transfer from chloroplasts to mitochondria, but these have yet to be discovered. In this study, we aimed to capture chloroplast-to-mitochondrion gene transfer by analyzing the translocation of a marker gene, sul, encoding a bacterial dihydropteroate synthase that confers sulfonamide resistance in tobacco (Nicotiana tabacum), to mtDNA. First, we created tobacco chloroplast transformants in which sul, surrounded on both sides by ∼1 kb of mitochondrial homologous sequences that enable targeted integration into mtDNA, was introduced into the chloroplast genome. Heat shock enhanced sul expression in the transformants, suggesting that chloroplast degradation can stimulate gene transfer from chloroplasts to mitochondria. Shoot regeneration using the heat-shocked chloroplast transformants under sulfadiazine selection resulted in several transformants with moderate resistance to sulfadiazine. Deep sequencing analysis of the target mitochondrial locus detected sul in the sulfadiazine-resistant (SR) plants, but an integration efficiency was 0.0011–0.0051 %. We validated the results by ruling out sul integration into nuclear mitochondrial DNA (NuMT). From these results, we propose the established system is capable of capturing gene transfer from chloroplasts to mitochondria in tobacco, but the transfer efficiency is substantially lower than those from organelles to nucleus.
被子植物线粒体基因组的结构非常复杂多样，部分原因是核DNA和叶绿体DNA（cpDNA）频繁插入线粒体DNA（mtDNA）。这表明存在基因从叶绿体转移到线粒体的机制，但这些机制尚未被发现。在本研究中，我们旨在通过分析编码细菌二氢蝶酸合成酶的标记基因 sul 向 mtDNA 的转移，捕捉叶绿体向线粒体的基因转移。首先，我们创建了烟草叶绿体转化体，将两侧被线粒体同源序列（可定向整合到 mtDNA 中）包围的 sul 导入叶绿体基因组。热休克增强了转化体中 sul 的表达，表明叶绿体降解可刺激基因从叶绿体转移到线粒体。在磺胺嘧啶选择条件下，使用热休克叶绿体转化体进行嫩枝再生，产生了几种对磺胺嘧啶具有中等抗性的转化体。对目标线粒体基因座的深度测序分析在抗磺胺嘧啶（SR）植株中检测到了 sul，但整合效率为 0.0011-0.0051%。我们排除了 sul 与核线粒体 DNA（NuMT）整合的可能性，从而验证了这一结果。根据这些结果，我们认为已建立的系统能够捕获烟草中从叶绿体到线粒体的基因转移，但转移效率大大低于从细胞器到细胞核的转移效率。
{"title":"Analysis of marker gene transfer from chloroplasts to mitochondria in heat-shocked and selection-pressured tobacco","authors":"Masaki Odahara , Maai Mori , Keiji Numata","doi":"10.1016/j.plgene.2024.100473","DOIUrl":"10.1016/j.plgene.2024.100473","url":null,"abstract":"<div><div>Angiosperm mitochondrial genomes have highly complex and diverse structures that are partly due to frequent insertions of nuclear and chloroplast DNA (cpDNA) into mitochondrial DNA (mtDNA). This suggests the existence of mechanisms for gene transfer from chloroplasts to mitochondria, but these have yet to be discovered. In this study, we aimed to capture chloroplast-to-mitochondrion gene transfer by analyzing the translocation of a marker gene, <em>sul</em>, encoding a bacterial dihydropteroate synthase that confers sulfonamide resistance in tobacco (<em>Nicotiana tabacum</em>), to mtDNA. First, we created tobacco chloroplast transformants in which <em>sul</em>, surrounded on both sides by ∼1 kb of mitochondrial homologous sequences that enable targeted integration into mtDNA, was introduced into the chloroplast genome. Heat shock enhanced <em>sul</em> expression in the transformants, suggesting that chloroplast degradation can stimulate gene transfer from chloroplasts to mitochondria. Shoot regeneration using the heat-shocked chloroplast transformants under sulfadiazine selection resulted in several transformants with moderate resistance to sulfadiazine. Deep sequencing analysis of the target mitochondrial locus detected <em>sul</em> in the sulfadiazine-resistant (SR) plants, but an integration efficiency was 0.0011–0.0051 %. We validated the results by ruling out <em>sul</em> integration into nuclear mitochondrial DNA (NuMT). From these results, we propose the established system is capable of capturing gene transfer from chloroplasts to mitochondria in tobacco, but the transfer efficiency is substantially lower than those from organelles to nucleus.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"40 ","pages":"Article 100473"},"PeriodicalIF":2.2,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142572965","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 : 2024-10-22DOI: 10.1016/j.plgene.2024.100472
Kossi Lorimpo Adjah , Maxwell Darko Asante , Aboubacar Toure , Mawuli Aziadekey , Shailesh Yadav , Felix Frimpong , Francis Osei Amoako-Andoh , Daniel Dzorkpe Gamenyah
Climate change, an effective driver of unprecedented seasonal droughts, is greatly affecting rice production in Africa by threatening food security and safety. Rice, one of the major staple crops on the continent, can save the situation through the development of drought-tolerant cultivars, presenting a major challenge for future rice improvement programs as drought is regarded as a critical limitation in rain-fed ecosystems. This study sought to understand the genetic basis and inheritance behind the expression of tolerance of rice breeding lines to drought-stress through generation mean analysis. To achieve these objectives, two drought-sensitive genotypes (Jasmine 85 and CRI-Agrarice) were crossed with a drought-tolerant genotype (APO) to develop six populations (F1, F2, BC1, BC2, P1 and P2) under screenhouse drought-stress and non-stress evaluation. Data were collected on grain yield and yield-related traits among which the generation mean analysis was conducted. At least one transgressive phenotype was produced in the F2 population for each trait whether there is a significant difference or not among the parental lines under drought-stress. Under non-stress conditions, there was a significance for all six types of gene action for days to flowering in both crosses. Among both crosses and water-regimes, additive x additive gene interaction was significant for most of the traits even though the scaling tests were not significant indicating the effectiveness of selection in early generations. Therefore, either forward breeding or backcross breeding can be adopted as breeding strategies for rapid improvement for these lines to drought tolerance.
{"title":"Transgressive segregation and generation mean analysis reveal the gene action underlying the inheritance of drought tolerance in rice","authors":"Kossi Lorimpo Adjah , Maxwell Darko Asante , Aboubacar Toure , Mawuli Aziadekey , Shailesh Yadav , Felix Frimpong , Francis Osei Amoako-Andoh , Daniel Dzorkpe Gamenyah","doi":"10.1016/j.plgene.2024.100472","DOIUrl":"10.1016/j.plgene.2024.100472","url":null,"abstract":"<div><div>Climate change, an effective driver of unprecedented seasonal droughts, is greatly affecting rice production in Africa by threatening food security and safety. Rice, one of the major staple crops on the continent, can save the situation through the development of drought-tolerant cultivars, presenting a major challenge for future rice improvement programs as drought is regarded as a critical limitation in rain-fed ecosystems. This study sought to understand the genetic basis and inheritance behind the expression of tolerance of rice breeding lines to drought-stress through generation mean analysis. To achieve these objectives, two drought-sensitive genotypes (Jasmine 85 and CRI-Agrarice) were crossed with a drought-tolerant genotype (APO) to develop six populations (F<sub>1</sub>, F<sub>2</sub>, BC<sub>1</sub>, BC<sub>2</sub>, P<sub>1</sub> and P<sub>2</sub>) under screenhouse drought-stress and non-stress evaluation. Data were collected on grain yield and yield-related traits among which the generation mean analysis was conducted. At least one transgressive phenotype was produced in the F<sub>2</sub> population for each trait whether there is a significant difference or not among the parental lines under drought-stress. Under non-stress conditions, there was a significance for all six types of gene action for days to flowering in both crosses. Among both crosses and water-regimes, additive x additive gene interaction was significant for most of the traits even though the scaling tests were not significant indicating the effectiveness of selection in early generations. Therefore, either forward breeding or backcross breeding can be adopted as breeding strategies for rapid improvement for these lines to drought tolerance.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"40 ","pages":"Article 100472"},"PeriodicalIF":2.2,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142530805","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}
Plants are constantly exposed to a plethora of pathogens including bacteria, fungi, and viruses posing significant challenges to global food security. The susceptibility of plants to these pathogens is often determined by specific genes within their genome. Understanding the role of susceptibility genes in plant-pathogen interactions is crucial for devising effective strategies to combat crop diseases. This review elucidates the importance of susceptibility genes in plants concerning their interactions with fungal, bacterial and viral pathogens. Susceptibility genes often encode proteins involved in crucial cellular processes such as signal transduction, defense response and pathogen recognition. Pathogens exploit vulnerabilities in these genes to establish infection and multiply within the host plant. In addition, advances in genome editing technologies offer promising avenues to enhance plant resistance against pathogens by targeting susceptibility genes. Techniques such as genome editing tools and epigenomic modification allow precise changes to be made in plant genomes, including the elimination or modification of susceptibility genes to confer resistance. However, ethical considerations and regulatory frameworks need to be addressed to ensure the potential use of gene editing in agriculture.
{"title":"Targeted editing of susceptibility genes for plant disease resistance: Current state and future hopes","authors":"Lingareddy Usha Rani , Manisha Shelke , Maddi Sandhya , Govindasamy Senthilraja","doi":"10.1016/j.plgene.2024.100471","DOIUrl":"10.1016/j.plgene.2024.100471","url":null,"abstract":"<div><div>Plants are constantly exposed to a plethora of pathogens including bacteria, fungi, and viruses posing significant challenges to global food security. The susceptibility of plants to these pathogens is often determined by specific genes within their genome. Understanding the role of susceptibility genes in plant-pathogen interactions is crucial for devising effective strategies to combat crop diseases. This review elucidates the importance of susceptibility genes in plants concerning their interactions with fungal, bacterial and viral pathogens. Susceptibility genes often encode proteins involved in crucial cellular processes such as signal transduction, defense response and pathogen recognition. Pathogens exploit vulnerabilities in these genes to establish infection and multiply within the host plant. In addition, advances in genome editing technologies offer promising avenues to enhance plant resistance against pathogens by targeting susceptibility genes. Techniques such as genome editing tools and epigenomic modification allow precise changes to be made in plant genomes, including the elimination or modification of susceptibility genes to confer resistance. However, ethical considerations and regulatory frameworks need to be addressed to ensure the potential use of gene editing in agriculture.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"40 ","pages":"Article 100471"},"PeriodicalIF":2.2,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142530806","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}
Late embryogenesis abundant (LEA) proteins play defensive roles during seed maturation and seed germination processes. However, there is no such investigation was carried out in chickpea. In present study, genome wide identification and characterization of LEA encoding genes has been investigated, and identified 65 and 74 LEA encoding genes in desi and kabuli cultivar of chickpea, respectively. All these genes have been classified into eight subfamilies on the bases of their phylogenetic analysis and conserved domain. Maximum members of LEA encoding genes were found to be a part of the LEA_2 gene family. The analysis of physicochemical properties of LEAs was also conducted. LEA encoding genes have been found to be located in all chromosomes (8 chr) of chickpea and identified as involved in response to stimulus, biological processes, molecular functions and cellular components based upon gene ontology analysis. Gene expression analysis of randomly selected 8 LEA encoding genes has been carried out during different seed developmental stages which revealed the higher expression of LEA encoding genes during later stage of seed development in chickpea and proved their potential role in desiccation process during seed maturation. During seed germination, expression analysis of LEA encoding genes was found to be higher during the initial stages of seed germination. In conclusion, this work highlights the genome wide identification and characterization of LEA encoding genes in chickpea and proposed potential roles during seed developmental processes. This information could also be useful as a reference investigation for molecular breeding of chickpea for recalcitrant behaviour of seed.
{"title":"Genome-wide identification and expression analysis of genes encoding late embryogenesis proteins in Cicer arietinum","authors":"Reetu Singh , Varnika Rana , Sudesh Kumar Yadav , Vinay Kumar","doi":"10.1016/j.plgene.2024.100469","DOIUrl":"10.1016/j.plgene.2024.100469","url":null,"abstract":"<div><div>Late embryogenesis abundant (LEA) proteins play defensive roles during seed maturation and seed germination processes. However, there is no such investigation was carried out in chickpea. In present study, genome wide identification and characterization of LEA encoding genes has been investigated, and identified 65 and 74 LEA encoding genes in desi and kabuli cultivar of chickpea, respectively. All these genes have been classified into eight subfamilies on the bases of their phylogenetic analysis and conserved domain. Maximum members of LEA encoding genes were found to be a part of the LEA_2 gene family. The analysis of physicochemical properties of LEAs was also conducted. LEA encoding genes have been found to be located in all chromosomes (8 chr) of chickpea and identified as involved in response to stimulus, biological processes, molecular functions and cellular components based upon gene ontology analysis. Gene expression analysis of randomly selected 8 LEA encoding genes has been carried out during different seed developmental stages which revealed the higher expression of LEA encoding genes during later stage of seed development in chickpea and proved their potential role in desiccation process during seed maturation. During seed germination, expression analysis of LEA encoding genes was found to be higher during the initial stages of seed germination. In conclusion, this work highlights the genome wide identification and characterization of LEA encoding genes in chickpea and proposed potential roles during seed developmental processes. This information could also be useful as a reference investigation for molecular breeding of chickpea for recalcitrant behaviour of seed.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"40 ","pages":"Article 100469"},"PeriodicalIF":2.2,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142423509","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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