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Diallo S, Badiane FA, Kabkia BNA, Diédhiou I, Diouf M, Diouf D. Genetic diversity and population structure of cowpea mutant collection using SSR and ISSR molecular markers. Sci Rep 2024; 14:31833. [PMID: 39738245 DOI: 10.1038/s41598-024-83087-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Accepted: 12/11/2024] [Indexed: 01/01/2025] Open
Abstract
Cowpea is a seed legume, important for food and nutritional security in Africa's arid and semi-arid zones. Despite its importance, cowpea is experiencing a loss of genetic diversity due to climate change. Therefore, this study aimed to evaluate the genetic variability of 33 cowpea mutant collections using 20 SSR and 13 ISSR markers. This analysis shows an average number of alleles of 5.15 for SSR and 6.7 for ISSR. The highest average genetic distance based on Nei's index among subgroups was 0.740 and the value of polymorphism information content varied from 0.02 to 0.23 for SSR and from 0.05 to 0.36 for ISSR. Our results revealed high genetic diversity based on the GD (0.126), Fst (0.513), and Shannon information index (0.246). The population structure analysis showed 3 and 4 clusters for ISSR and SSR markers, respectively. Genetic variation, as assessed by analysis of molecular variance, mostly indicates higher genetic diversity within the population than among populations. The hierarchical clustering of combined SSR and ISSR markers grouped the accessions into four groups, supporting the STRUCTURE analysis results. Additionally, the combination of SSR and ISSR provided better information on the level of genetic diversity, and population structure, and was more effective in determining the relationship between cowpea collection. This study enhances our understanding of the genetic organization of our mutant collection which can be used in breeding programs in the era of climate change.
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Kohli M, Bansal H, Aski M, Mishra GP, Shashidhar BR, Roy A, Gupta S, Sinha SK, Mishra BK, Kumari N, Kumar A, Kumar RR, Nair RM, Dikshit HK. Genome-wide association mapping of biochemical traits and its correlation with MYMIV resistance in mungbean (Vigna radiata L. Wilczek). Sci Rep 2024; 14:31805. [PMID: 39738266 DOI: 10.1038/s41598-024-82836-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2024] [Accepted: 12/09/2024] [Indexed: 01/01/2025] Open
Abstract
The mungbean yellow mosaic India virus (MYMIV, Begomovirus vignaradiataindiaense) causes Yellow Mosaic Disease (YMD) in mungbean (Vigna radiata L.). The biochemical assays including total phenol content (TPC), total flavonoid content (TFC), ascorbic acid (AA), DPPH (2,2-diphenyl-1-picrylhydrazyl), and FRAP (Ferric Reducing Antioxidant Power) were used to study the mungbean plants defense response to MYMIV infection. A wide range was recorded for the Area Under Disease Progress Curve (AUDPC; 1.75-1266.98) and coefficient of infection (CI; 0.33-45.53). In YMD susceptible genotypes, significant variations were observed for TPC [2001.27-2834.13 mgGAE/100 g dry weight (DW)], TFC (252.65-341.30 mg/100 g DW), AA (40.33-64.69 mg/100 g DW), DPPH (32.11-53.47% scavenging effect DW), and FRAP (48.99-101.22 µmol Fe2+/g DW). Similarly, in resistant genotypes also wide range was recorded for TPC (1788.50-2286.38 mgGAE/100 g DW), TFC (206.12-337.32 mg/100 gDAS samples varied from 384.6.46-47.64% scavenging effect DW), and FRAP (53.68-114.24 µmol Fe2+/g DW). Except for FRAP, other studied parameters were in the lower range in the resistant genotypes than the susceptible genotypes. Genome-wide association studies (GWAS) of 132 genotypes have identified 31,953 single nucleotide polymorphism (SNPs). MLM (Mixed Linear Model) and BLINK (Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway) models have identified 119 shared SNPs for various biochemical traits and MYMIV resistance. The key candidate genes include VRADI09G06940 (YMD resistance, TIR-NBS-LRR class, chr. 9), VRADI01G05030 [flavonoid biosynthesis; MYB65 transcription factor (TF); chr. 1], VRADI03G07600 (phenol biosynthesis; GATA TF 16; chr. 3), VRADI04G08470 (ascorbic acid; heat shock protein 70 kDa protein; chr. 4), VRADI04G07510 (FRAP; subtilisin-like protease SBT1.9; chr. 4), and VRADI05G02870 (DPPH; vacuolar protein sorting-associated protein 2; chr. 5). The identified genomic resources will enhance mungbean genomics and facilitate the advancement of genomic-assisted breeding in mungbean.
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Parween A, Sahoo JP, Mahapatra M, Das BP, Pattnaik S, Sunani SK. Morpho-biochemical and molecular profiling for Charcoal Rot (CR) disease resistance in Mung Bean [Vigna radiata (L.) Wilczek] landraces. Mol Biol Rep 2024; 52:76. [PMID: 39718653 DOI: 10.1007/s11033-024-10187-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2024] [Accepted: 12/17/2024] [Indexed: 12/25/2024]
Abstract
BACKGROUND Charcoal Rot (CR) poses a significant threat to mung bean crops by reducing yield, making the development of resistant varieties crucial for stable production and food security. This study evaluated 19 newly identified mung bean landraces using biochemical traits and SSR markers, revealing genetic variability, CR disease reactions, and traits influencing yield and resistance, which provide valuable insights for breeding CR-resistant, high-yielding varieties. METHODS AND RESULTS Mung bean landraces were evaluated for their response to CR using 4 biochemical parameters, and 10 SSR markers to assess genetic variability and disease resistance. The results revealed substantial variability in morpho-quantitative traits, and showed a significant variation in CR disease reaction (21% resistance, and 16% moderately resistance). Biochemical characterization suggested that, phenolic content (PHE), Peroxidase (POX) and polyphenol oxidase (PPO) activities exhibited narrow ranges, suggesting more uniformity in these biochemical traits under CR stress. Yield (YLD) showed a positive correlation with the number of pods per plant (NPDP) (0.459), PPO (0.912), PHE (0.867), and total chlorophyll (TCL) (0.864), but showed a negative correlation with POX (-0.64), indicating their positive influence on productivity. Conversely, CR resistance was strongly negatively correlated with YLD (-0.86). Moreover, as per the principal component analysis (PCA), 80.5% of the total variance was explained by the first three principal components. However, molecular characterization suggested the PIC values ranged from 0.281 to 0.871, with an average 0.58 indicating moderate to high polymorphism. Principal coordinate analysis (PCoA) grouped landraces based on their genetic makeup under CR stress, and the first three axes explained most of the variation (82.03%). Phylogenetic tree analysis confirmed the PCoA groupings with similarity coefficient varied from 0.57 to 0.98, suggesting the landraces within a cluster had lower genetic distances, and resistant and moderately CR resistant landraces fell into separate clusters. CONCLUSION The findings can be effectively utilized to develop CR-resistant mung bean varieties with enhanced productivity, contributing to stable mung bean production and food security.
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Wu Y, Zhang K, Zhang B, Li Y, Liu G, Liang Z, Zhang J. Characterization of the complete mitochondrial genome of the rice bean (Vigna umbellata). BMC PLANT BIOLOGY 2024; 24:1239. [PMID: 39716065 DOI: 10.1186/s12870-024-05963-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 12/11/2024] [Indexed: 12/25/2024]
Abstract
BACKGROUND Rice bean (Vigna umbellata), an underrated legume crop, demonstrates strong adaptability to poor soil fertility and has significant potential to enhance global food security. It is valuable both as a vegetable and fodder crop due to its high protein content, essential fatty acids, and micronutrients. Despite the sequencing of a high-quality genome of rice bean, its mitochondrial genome (mitogenome) sequence has not yet been reported. RESULTS For the first time, the rice bean mitogenome was assembled and annotated using PacBio HiFi sequencing and Geseq software. The mitogenome is a circular molecule with a length of 404,493 bp, containing 32 protein-coding genes, 17 tRNAs, and 3 rRNAs. Codon usage and sequence repeats were also determined. Six gene migration events from the chloroplast to the mitogenome were detected in rice bean. A phylogenetic analysis, including the rice bean mitogenome and 25 other taxa (23 of which are Fabales species), clarified the evolutionary and taxonomic status of rice bean. Additionally, a collinearity analysis of seven Fabales mitogenomes revealed high structural variability. In total, 473 RNA editing sites in protein-coding genes were identified. CONCLUSIONS This study presents the first sequencing, assembly, annotation, and analysis of the rice bean mitogenome, providing valuable background information for understanding the evolution of this species. These findings lay the groundwork for future genetic studies and molecular breeding efforts aimed at improving rice bean.
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Khanbo S, Phadphon P, Naktang C, Sangsrakru D, Waiyamitra P, Narong N, Yundaeng C, Tangphatsornruang S, Laosatit K, Somta P, Pootakham W. A chromosome-scale genome assembly of mungbean ( Vigna radiata). PeerJ 2024; 12:e18771. [PMID: 39726742 PMCID: PMC11670757 DOI: 10.7717/peerj.18771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Accepted: 12/05/2024] [Indexed: 12/28/2024] Open
Abstract
Background Mungbean (Vigna radiata) is one of the most socio-economically important leguminous food crops of Asia and a rich source of dietary protein and micronutrients. Understanding its genetic makeup is crucial for genetic improvement and cultivar development. Methods In this study, we combined single-tube long-fragment reads (stLFR) sequencing technology with high-throughput chromosome conformation capture (Hi-C) technique to obtain a chromosome-level assembly of V. radiata cultivar 'KUML4'. Results The final assembly of the V. radiata genome was 468.08 Mb in size, with a scaffold N50 of 40.75 Mb. This assembly comprised 11 pseudomolecules, covering 96.94% of the estimated genome size. The genome contained 253.85 Mb (54.76%) of repetitive sequences and 27,667 protein-coding genes. Our gene prediction recovered 98.3% of the highly conserved orthologs based on Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis. Comparative analyses using sequence data from single-copy orthologous genes indicated that V. radiata diverged from V. mungo approximately 4.17 million years ago. Moreover, gene family analysis revealed that major gene families associated with defense responses were significantly expanded in V. radiata. Conclusion Our chromosome-scale genome assembly of V. radiata cultivar KUML4 will provide a valuable genomic resource, supporting genetic improvement and molecular breeding. This data will also be valuable for future comparative genomics studies among legume species.
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Markou P, Garagounis C, Fasoula DA, Ioannides IM, Omirou M, Papadopoulou KK. Identification, functional characterization and expression profiling of three triterpene synthases from the legume plant Vigna unguiculata. Biochem Biophys Res Commun 2024; 738:150935. [PMID: 39515095 DOI: 10.1016/j.bbrc.2024.150935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 10/27/2024] [Accepted: 10/30/2024] [Indexed: 11/16/2024]
Abstract
Oxidosqualene cyclases (OSCs) are important regulatory enzymes involved in cyclization reactions of 2, 3-oxidosqualene to form triterpenes and sterols. This study presents the identification and characterization of three OSC genes, a β - amyrin synthase (VuβAS), a lupeol synthase (VuLUS) and a cycloartenol synthase (VuCAS) in Vigna unguiculata, an edible leguminous plant with high nutritional and nutraceutical value. Phylogenetic analysis showed that the VuβAS, VuLUS and VuCAS were clustered within the clades of previously characterized β - amyrin synthases, lupeol synthases and cycloartenol synthases. Heterologous expression in Saccharomyces cerevisiae and Gas Chromatography - Mass Spectrometry (GC - MS) analysis in different plant stages confirmed their specific functions. VuβAS showed higher expression in roots from early germinating seedlings to older plants (4-day to 28-day), while VuLUS expression levels were higher in the roots of older plants only (14-day to 28-day). VuCAS expression was increased in all the tissues of 4-day seedlings, with a peak in stem and leaves and a lower accumulation in radicles. These findings revealed the presence and function of OSC genes in V. unguiculata, and future research could lead to the discovery of promising biologically active compounds.
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Deshahalli Divakara D, Gore PG, Tripathi K, Katral A, Roy Choudhury D, Abhishek GJ, Ragi S, Thippeswamy D, Muthusamy V, Sharma DK, Singh R, Bhatt KC. Exploring genetic diversity of potential legume, Vigna angularis (Willd.) Ohwi and Ohashi through agro-morphological traits and SSR markers analysis. PLoS One 2024; 19:e0312845. [PMID: 39642148 PMCID: PMC11623801 DOI: 10.1371/journal.pone.0312845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 10/15/2024] [Indexed: 12/08/2024] Open
Abstract
Adzuki bean, an underutilized grain legume, has a significant potential for enhancing food and nutritional security. The main obstacles to developing new cultivars and promoting the adzuki bean as a mainstream pulse crop are a lack of awareness about its potential and insufficient information on crop its genetic diversity. Here, we aimed to explore the untapped potential of adzuki bean germplasm by evaluating its agro-morphological traits and diversity at the molecular level and also to identify trait-specific germplasm by utilizing 100 adzuki bean accessions conserved in the Indian National Genebank. Significant variations was recorded for the morphological traits and identified promising accessions exhibiting desirable traits, such as early flowering (IC341945, EC340257 and EC340283), number of primary branches (IC341945 and IC469175), number of clusters per plant (EC000264, IC167611 and IC341939), number of pods per plant (IC469175, EC34264, EC000264), early maturity (EC340283; EC120460; IC341941) and number of seeds per pod (EC340240, IC455396 and IC341955). Molecular characterization of diverse accessions using 22 polymorphic SSR markers identified a total of 50 alleles, with a mean of 2.27 alleles per loci. The polymorphic information content (PIC) ranged from 0.03 to 0.46, indicating informativeness of markers in distinguishing diverse accessions. Further, the gene diversity among the accessions ranged from 0.03 to 0.57 with a mean of 0.19. Population structure analysis grouped the accessions into three genetic groups, supported by Principal Coordinate Analysis (PCoA) and a phylogenetic tree. Additionally, Analysis of Molecular Variance (AMOVA) confirmed a substantial genetic diversity among the adzuki bean accessions. Thus, the combined assessment of agro-morphological traits and molecular markers effectively distinguished adzuki bean accessions and provided valuable insights in understanding untapped variation at both morphological and molecular levels. The promising accessions identified in the study hold potential for integration into legume improvement programs through introgression breeding, contributing to the development of adzuki bean varieties with target trait.
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Zhao Q, Yang Z, Zhou Z, Yang Y, Wang W. Toxicity mechanism of organosilicon adjuvant in combination with S-metolachlor on Vigna angularis. JOURNAL OF HAZARDOUS MATERIALS 2024; 480:135978. [PMID: 39342851 DOI: 10.1016/j.jhazmat.2024.135978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 09/07/2024] [Accepted: 09/25/2024] [Indexed: 10/01/2024]
Abstract
The widespread use of S-metolachlor (ME) in agriculture to suppress weeds and boost crop yields, particularly in cultivating Vigna angularis, is well established. However, the application of organosilicon adjuvants with herbicides has potential threats to non-target crops. This study investigates the toxicity symptoms and mechanisms when V. angularis is exposed to ME in conjunction with a common organosilicon adjuvant. Results indicate that ME inhibits the growth of V. angularis seedlings, and adding adjuvants could aggravate the negative effects of ME. According to the growth index of seedlings, the adjuvant increased the toxicity of ME by 84-96 %. Additionally, the chlorophyll content, root permeability, and antioxidant indicators in the seedlings were also adversely affected. Integrated metabolomics and transcriptomics analyses reveal that differentially abundant metabolites (DAMs) and differentially expressed genes (DEGs) are mainly enriched in four ways: "lysine degradation," "ABC transporters," "phenylalanine metabolism," and "monoterpenoid biosynthesis." The metabolic pathways and gene regulatory network involving 11 DAMs and 22 DEGs are associated with the physiological processes affected by ME and the adjuvant. This study provides guidance for the application of herbicides and their adjuvants in agricultural production to minimize adverse effects on non-target crops.
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Srichan M, Laosatit K, Lin Y, Yuan X, Chen X, Somta P. QTL-seq and QTL mapping identify a new locus for Cercospora leaf spot (Cercospora canescens) resistance in mungbean (Vigna radiata) and a cluster of Receptor-like protein 12 (RLP12) genes as candidate genes for the resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:278. [PMID: 39601832 DOI: 10.1007/s00122-024-04782-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 11/10/2024] [Indexed: 11/29/2024]
Abstract
KEY MESSAGE QTL-seq, linkage mapping, and whole-genome resequencing revealed a new locus (qCLS5.1) controlling Cercospora canescens resistance in mungbean and Receptor-like protein 12 (RLP12) genes as candidate genes for the resistance. Cercospora leaf spot (CLS) disease, caused by Cercospora canescens, is a common disease of mungbean (Vigna radiata). In this study, the genetics of CLS resistance was investigated in a new source of resistance (accession V2817) and the resistance was finely mapped to identify candidate genes. F2 and F2:3 populations of the cross V1197 (susceptible) × V2718 and a BC1F1 population of the cross V1197 × (V1197 × V2817) were used in this study. Segregation analysis suggested that the resistance is controlled by a single dominant gene. QTL-seq using F2 individuals revealed that a single QTL (designated qCLS5.1) on chromosome 5 controlled the resistance. The qCLS5.1 was confirmed in the F2:3 and BC1F1 populations by QTL analysis. Fine mapping using 978 F2 individuals localized qCLS5.1 to a 48.94 Kb region containing three tandemly duplicated Receptor-like protein 12 (RLP12) genes. Whole-genome resequencing and alignment of V1197 and V2817 revealed polymorphisms causing amino acid changes and premature stop codons in the three RLP12 genes. Collectively, these results show that qCLS5.1 is a new locus for CLS resistance in mungbean, and a cluster of RLP12 genes are candidate genes for the resistance. The new locus qCLS5.1 will be useful for molecular breeding of durable CLS-resistant mungbean cultivars.
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Leng Y, Niu ZB, Liu SH, Qiao FJ, Liu GF, Cheng B, Li SW. Characterisation of cytochrome c oxidase-coding genes from mung bean and their response to cadmium stress based on genome-wide identification and transcriptome analysis. Mol Biol Rep 2024; 52:17. [PMID: 39589562 DOI: 10.1007/s11033-024-10102-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 11/11/2024] [Indexed: 11/27/2024]
Abstract
BACKGROUND Cytochrome c oxidase (COX) is a crucial mitochondrial enzyme in the electron transport chain of plants, implicated in energy production and stress responses. Despite its importance, the function of COX in leguminous plants, especially under heavy metal stress like cadmium (Cd), remains understudied. METHODS AND RESULTS In this study, COX genes (COX s) were identified based on the genome annotation file in mung bean (Vigna radiata (Linn.) R. Wilczek), and the gene structure, physicochemical properties and systematic relationships of the relevant amino acid sequences were analyzed by using bioinformatics method. The effects of Cd on the transcription levels and activities of COX in mung bean roots, stems, and leaves were detected to understand the mechanism of COX in mung bean in response to cadmium (Cd) stress. Transcriptome sequencing revealed tissue-specific expression with roots showed the highest levels. Cd stress significantly altered the expression and activity of VrCOXs, particularly in roots and stems, with varied responses among different genes. CONCLUSIONS The differential response of VrCOX s to Cd stress indicates a role in the plant stress tolerance mechanism. The study provides insights into the function of COXs in legumes and a foundation for further research into Cd tolerance mechanisms, which could be vital for enhancing legume production and ensuring food safety in contaminated environments.
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Sivaramakrishnan NK, Kothandaraman SV, Perumal R, Ganesan MV, Nallusamy S, K T. Deciphering Temporal Metabolome Dynamics in Response to MYMV: Contrasting Patterns in Resistant and Susceptible Blackgram ( Vigna mungo L. Hepper) Cultivars. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:25620-25637. [PMID: 39527729 DOI: 10.1021/acs.jafc.4c06400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2024]
Abstract
Blackgram (Vigna mungo L. Hepper) production is hindered by mungbean yellow mosaic virus (MYMV) with disease incidence up to 85% in hot spot locations of Tamil Nadu, India. Field screening of 50 genotypes identified Mash 114 as resistant and CO 5 as susceptible cultivars. To understand the resistance mechanism, temporal metabolome variations of resistant (RC) and susceptible (SC) cultivars were assessed at 3, 6, and 12 days post-inoculation with MYMV via whitefly transmission using GC-MS. The study included aviruliferous whitefly and healthy controls. Data analysis identified 98 differential compounds across various metabolic groups. Principal component analysis (PCA) and hierarchical cluster analysis (HCA) revealed distinct metabolic profiles, with RC accumulating antiviral terpenoids such as ursolic acid, betulin, and umbelliprenin, while SC upregulated lipids and fatty acids favoring virus replication. These findings provide insights for breeders to identify resistant sources and pave the way for improved MYMV management strategies using antiviral products.
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Zhang R, Wang K, Liu J, Yang G, Peng Y, Zhang Z, Gao X. Overlapping Transcriptome Alterations Reveal the Mechanism of Interaction between Selenium and Zinc and Their Common Effect on Essential Nutrient Metabolism in Mung Bean ( Vigna radiata L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:25423-25435. [PMID: 39496279 DOI: 10.1021/acs.jafc.4c07945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2024]
Abstract
Selenium (Se) and zinc (Zn) deficiencies have become serious global food security and public health problems. Biofortification through foliar fertilizer is a nonspecific, low-tech, and cost-effective strategy. Se and Zn have overlapping physiological roles and interacting relationships in plants. Mung bean is superior for Se enrichment and an excellent Zn carrier. However, the molecular mechanism underlying the interaction between Se and Zn in the mung bean remains unclear. Herein, Se and Zn accumulation, antioxidant activities, physiological determination, and transcriptomic analysis were performed under both Se and Zn treatments. Common essential roles of Se and Zn in mung bean were reflected by the comprehensively altered ten physiological indexes under both Se2 (24 g·ha-1) and Zn1 (1.2 kg·ha-1) treatments. Overlapping transcriptome changes and common DEGs in two compared groups revealed that the upregulated expression of sulfate transporters (SULTRs), phosphate transporters (PHTs), and Zinc-regulated/Iron-regulated-like protein (ZIP) family genes under Se and Zn treatments directly promoted both Se and Zn intakes. Furthermore, the altered Se/Sulfur, nitrogen, and carbohydrate metabolisms are closely interlinked with the uptake and assimilation of Se and Zn via the 20 key genes that we filtered through the protein-protein interaction (PPI) network analysis. Further analysis indicated that l-methionine γ-lyase (E 4.4.1.11) genes may play an important role in the transamination of selenomethionine and its derivatives; glutamine synthetase (GS), nitrate reductase (NR), and starch synthase (SS) genes may regulate the nitrogen assimilation and carbohydrate metabolism, which provide more carriers for Se and Zn; glutathione peroxidase (GPx), glutamate-cysteine ligase catalytic subunit (GCLC), and serine acetyltransferase (SAT) genes may accelerate the GSH-GSSH cycle and promote Se and Zn storages. This study provides new molecular insights into the comprehensive improvement of the nutritional quality of mung beans in Se and Zn biofortification productions.
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Xue R, Liu Y, Feng M, Huang Y, Zhao Y, Chen J, Li T, Zhong C, Ge W. Genome-wide characterization of PEBP genes in Mung bean (Vigna radiata L.) with functional analysis of VrFT1 in relation to photoperiod. Sci Rep 2024; 14:26413. [PMID: 39488543 PMCID: PMC11531570 DOI: 10.1038/s41598-024-73936-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 09/23/2024] [Indexed: 11/04/2024] Open
Abstract
Mung bean (Vigna radiata L.), a widely cultivated legume, belongs to the Fabaceae family's Papilionoideae subfamily. Although Phosphatidylethanolamine-binding protein (PEBP) genes have been identified in several plant species, their presence and function in mung bean remain largely unexplored. In this study, we identified seven VrPEBP genes from mung bean and classified them into four clades: FT, MFT, TFL and FT-like. Cis-regulatory element analysis revealed that VrPEBP genes may play a role in light, hormone, and stress responses. Quantitative real-time PCR (qRT-PCR) analysis indicated that VrPEBPs were constitutively expressed in various tissues. However, tissue-specific expression patterns were observed among VrPEBP genes. Under short-day (SD) conditions, VrFT1 and VrMFT1 exhibited significantly higher expression levels than under long-day (LD) conditions at 8 and 4 h, respectively. Conversely, VrTFL2 and VrTFL3 showed significantly higher expression levels under LD conditions compared to SD conditions at 8 and 12 h, respectively. The varied expression patterns of these genes under different photoperiod suggest their potential involvement in the photoperiodic regulation of flowering in mung bean. Additionally, phenotypic analysis of transgenic Arabidopsis plants overexpressing VrFT1 revealed higher expression levels under SD conditions and predicted its role in promoting flowering. These results provide valuable insights into the evolution and function of PEBP genes in mung bean and lay the foundation for further research on their regulatory mechanisms and potential applications in mung bean improvement.
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Zhang Y, Hou R, Yao X, Wang X, Li W, Fang X, Ma X, Li S. VrNIN1 interacts with VrNNC1 to regulate root nodulation in mungbean. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 216:109131. [PMID: 39305558 DOI: 10.1016/j.plaphy.2024.109131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 08/30/2024] [Accepted: 09/15/2024] [Indexed: 11/08/2024]
Abstract
Node Inception (NIN) plays a crucial role in legume symbiosis by participating in both infection and nodule formation processes. However, its specific function in mungbean (Vigna radiata) remains poorly understood. This study aimed to functionally characterize the VrNIN1 gene in mungbean through an enhanced hairy root transformation approach. Examination of proVrNIN1: GUS hairy roots via GUS staining indicated the expression of VrNIN1 in later root promodia, nodule primordia, and nodules. Phenotypic evaluation revealed that overexpression or silencing of VrNIN1 led to a significant reduction in nodule numbers in hairy roots compared to controls. Additionally, interaction between VrNIN1 and VrNNC1 was confirmed through yeast two-hybrid, luciferase complementation and Co-immunoprecipitation assays. VrNNC1 expression was observed in the vascular bundle and cortex of roots and root nodules, where it notably suppressed nodule formation in transgenic hairy roots. Furthermore, gene expression analysis demonstrated the involvement of VrNIN1 and VrNNC1 in regulating root nodulation by modulating the expression of VrRIC1 and VrEDOD40. This study not only optimized the genetic transformation system for hairy roots in mungbean, but also provided mechanistic insights into the regulatory role of VrNIN1 in root nodule symbiosis in mungbean.
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Zhang S, Guo Y, Zhang P, Ai J, Wang Y, Wang F. Functional characterization of VrNAC15 for drought resistance in mung beans. Gene 2024; 926:148621. [PMID: 38821326 DOI: 10.1016/j.gene.2024.148621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 05/16/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
Drought stress has become an important limiting factor in mung bean production, and NAC(NAM/ATAF/CUC) transcription factors are crucial for plant growth under stress conditions, so it is important to study the regulatory role of NAC transcription factors in mung bean under drought stress. In this investigation, VrNAC15, along with its promoter, was cloned, and its structure was meticulously analyzed. Using qPCR, we examined the tissue-specific expression patterns of VrNAC15, particularly under drought stress and ABA exposure. Additionally, We performed ectopic expression of VrNAC15 in Arabidopsis to assess its function.. Gene sequence analysis revealed that VrNAC15 has a total length of 1014 bp, encoding 337 amino acids. It contains a NAM domain, localizes within the nucleus, and exhibits transcriptional activation. Promoter analysis of VrNAC15 identified essential core promoter elements and cis-acting elements related to abscisic acid, methyl jasmonate, gibberellin, adversity stress, light, and metabolism. Expression analysis demonstrated the concentration of VrNAC15 in leaves, with significant alterations following ABA and drought treatments in mung beans. Cluster analysis revealed that VrNAC15 may enhanced drought tolerance in transgenic plants through its expression. Transgenic experiments supported these findings, showing that heterologous expression of VrNAC15 led to enhanced antioxidant and osmotic adjustment capabilities in Arabidopsis plants. This resulted in the maintenance of cell membrane structural integrity during drought stress and normal physiological and biochemical metabolic reactions within cells. This research provides valuable insights into the structural and functional characteristics of the VrNAC15, setting the stage for future endeavors in molecular breeding for improved drought resistance in mung beans.
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Wicaksono A, Buaboocha T. Genome-wide identification of CAMTA genes and their expression dependence on light and calcium signaling during seedling growth and development in mung bean. BMC Genomics 2024; 25:992. [PMID: 39443876 PMCID: PMC11515718 DOI: 10.1186/s12864-024-10893-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 10/11/2024] [Indexed: 10/25/2024] Open
Abstract
BACKGROUND Calmodulin-binding transcription activator (CAMTA) is comprised of a group of transcription factors and plays an important role in the Ca2+ signaling pathway, mediating various molecular responses via interactions with other transcription factors and binding to the promoter region of specific genes. Mung beans (Vigna radiata) are one of the most commonly consumed commodities in Asia. To date, CAMTA proteins have not been characterized in this important crop plant. RESULTS Eight paralogous VrCAMTA genes were identified and found to be distributed on five of the 11 chromosomes. The proteins possessed CG-1 DNA-binding domains with bipartite NLS signals, ankyrin domains, CaM-binding IQ motifs, and CaM-binding domain (CaMBD). The 2 kb upstream regions of VrCAMTA genes contained sequence motifs of abscisic acid-responsive elements (ABRE) and ethylene-responsive elements (ERE), and binding sites for transcription factors of the bZIP and bHLH domains. Analysis of RNA-seq data from a public repository revealed ubiquitous expression of the VrCAMTA genes, as VrCAMTA1 was expressed at the highest level in seedling leaves, whereas VrCAMTA8 was expressed at the lowest level, which agreed with the RT-qPCR analysis performed on the first true leaves. On day four after leaf emergence, all VrCAMTA genes were upregulated, with VrCAMTA1 exhibiting the highest degree of upregulation. In darkness on day 4, upregulation was not observed in most VrCAMTA genes, except VrCAMTA7, for which a low degree of upregulation was found, whereas no difference was found in VrCAMTA8 expression between light and dark conditions. Treatment with calcium ionophores enhanced VrCAMTA expression under light and/or dark conditions at different times after leaf emergence, suggesting that calcium signaling is involved in the light-induced upregulation of VrCAMTA gene expression. CONCLUSIONS The expression dependence of nearly all VrCAMTA genes on light and calcium signaling suggests their possible differential but likely complementary roles during the early stages of mung bean growth and development.
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Kumari N, Aski MS, Mishra GP, Roy A, Dikshit HK, Saxena S, Kohli M, Mandal B, Sinha SK, Mishra DC, Mondal MF, Kumar RR, Kumar A, Nair RM. Development of infectious clones of mungbean yellow mosaic India virus (MYMIV, Begomovirus vignaradiataindiaense) infecting mungbean [Vigna radiata (L.) R. Wilczek] and evaluation of a RIL population for MYMIV resistance. PLoS One 2024; 19:e0310003. [PMID: 39436879 PMCID: PMC11495560 DOI: 10.1371/journal.pone.0310003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 08/23/2024] [Indexed: 10/25/2024] Open
Abstract
Yellow mosaic disease (YMD) is a major constraint for the low productivity of mungbean, mainly in South Asia. Addressing this issue requires a comprehensive approach, integrating field and challenge inoculation evaluations to identify effective solutions. In this study, an infectious clone of Begomovirus vignaradiataindiaense (MYMIV) was developed to obtain a pure culture of the virus and to confirm resistance in mungbean plants exhibiting resistance under natural field conditions. The infectivity and efficiency of three Agrobacterium tumefaciens strains (EHA105, LBA4404, and GV3101) were evaluated using the susceptible mungbean genotype PS16. Additionally, a recombinant inbred line (RIL) population comprising 175 lines derived from Pusa Baisakhi (MYMIV susceptible) and PMR-1 (MYMIV resistant) cross was developed and assessed for YMD response. Among the tested Agrobacterium tumefaciens strains, EHA105 exhibited the highest infectivity (84.7%), followed by LBA4404 (54.7%) and GV3101 (9.80%). Field resistance was evaluated using the coefficient of infection (CI) and area under disease progress curve (AUDPC), identifying seven RILs with consistent resistant reactions (CI≤9) and low AUDPC (≤190). Upon challenge inoculation, six RILs exhibited resistance, while RIL92 displayed a resistance response, with infection occurring in less than 10% of plants after 24 to 29 days post inoculation (dpi). Despite some plants remaining asymptomatic, MYMIV presence was confirmed through specific PCR amplification of the MYMIV coat protein (AV1) gene. Quantitative PCR revealed a very low relative viral load (0.1-5.1% relative fold change) in asymptomatic RILs and the MYMIV resistant parent (PMR1) compared to the susceptible parent (Pusa Baisakhi). These findings highlight the potential utility of the developed infectious clone and the identified MYMIV-resistant RILs in future mungbean breeding programs aimed at cultivating MYMIV-resistant varieties.
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Piromyou P, Pruksametanan N, Nguyen HP, Songwattana P, Wongdee J, Nareephot P, Greetatorn T, Teamtisong K, Tittabutr P, Boonkerd N, Sato S, Boonchuen P, Okazaki S, Teaumroong N. NopP2 effector of Bradyrhizobium elkanii USDA61 is a determinant of nodulation in Vigna radiata cultivars. Sci Rep 2024; 14:24541. [PMID: 39424841 PMCID: PMC11489812 DOI: 10.1038/s41598-024-75294-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Accepted: 10/03/2024] [Indexed: 10/21/2024] Open
Abstract
The symbiotic relationship between legumes and rhizobia is known to be influenced by specific rhizobial type III effectors (T3Es) in certain cases. In this study, we present evidence that the symbiosis between Vigna radiata and Bradyrhizobium elkanii USDA61 is controlled by a T3E called NopP2, and this interaction is highly dependent on the genetic makeup of the host plant. NopP2 plays a crucial role in promoting nodulation in various V. radiata varieties. Additionally, NopP2 is essential for early infection and the formation of nodules in compatible plants. Through evolutionary analysis, we discovered that bradyrhizobial NopPs can be categorized into two distinct clusters: NopP1 and NopP2. Furthermore, both types of bradyrhizobial NopPs were conserved within their respective groups. Our findings suggest that NopP2 serves as a mechanism for optimizing the symbiotic relationship between V. radiata and B. elkanii USDA61 by interacting with the pathogenesis related-10 (PR10) protein and reducing effector-triggered immunity (ETI) responses.
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Isah A, Ndana RW, Malann YD, Nwankwo OF, Ibrahim AB, Gidado RS. Biodiversity assessment and environmental risk analysis of the single line transgenic pod borer resistant cowpea. PeerJ 2024; 12:e18094. [PMID: 39434787 PMCID: PMC11493023 DOI: 10.7717/peerj.18094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 08/23/2024] [Indexed: 10/23/2024] Open
Abstract
Background The discussion surrounding biological diversity has reached a critical point with the introduction of Nigeria's first transgenic food crop, the pod borer-resistant (PBR) cowpea. Questions have been raised about the potential risks of the transgenic Maruca vitrata-resistant cowpea to human health and beneficial insects. Public apprehension, coupled with social activists' calling for the removal of this crop from the nation's food market, persists. However, there is a lack of data to counter the assertion that cultivating PBR cowpea may have adverse effects on biodiversity and the overall ecological system. This research, with its multifaceted objective of examining the environmental safety of PBR cowpea and assessing its impact on biodiversity compared to its non-transgenic counterpart, IT97KN, is of utmost importance in providing the necessary data to address these concerns. Methods Seeds for both the transgenic PBR cowpea and its isoline were obtained from the Institute for Agricultural Research (IAR) Zaria before planting at various farm sites (Addae et al., 2020). Throughout the experiment, local cultural practices were strictly followed to cultivate both transgenic and non-transgenic cowpeas. Elaborate taxonomic keys were used to identify arthropods and other non-targeted organisms. Principal component analysis (PCA) was used to evaluate potential modifications in all ecological niches of the crops. The lmer function of the R package lme4 was used to analyze diversity indices, including Shannon, Pielou, and Simpson. The Bray-Curtis index was used to analyzed potential modifications in the dissimilarities of non-targeted organisms' communities. Results Examination of ecological species abundance per counting week (CW) revealed no disruption in the biological properties of non-targeted species due to the cultivation of transgenic PBR cowpea. Analysis of species evenness and diversity indices indicated no significant difference between the fields of transgenic PBR cowpea and its isoline. Principal component analysis results demonstrated that planting PBR cowpea did not create an imbalance in the distribution of ecological species. All species and families observed during this study were more abundant in transgenic PBR cowpea fields than in non-transgenic cowpea fields, suggesting that the transformation of cowpea does not negatively impact non-targeted organisms and their communities. Evolution dynamics of the species community between transgenic and non-transgenic cowpea fields showed a similar trend throughout the study period, with no significant divergence induced in the community structure because of PBR cowpea planting. This study concludes that planting transgenic PBR cowpea positively influences biodiversity and the environment.
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Krylova EA, Burlyaeva MO, Tvorogova VE, Khlestkina EK. Contrast Relative Humidity Response of Diverse Cowpea ( Vigna unguiculata (L.) Walp.) Genotypes: Deep Study Using RNAseq Approach. Int J Mol Sci 2024; 25:11056. [PMID: 39456837 PMCID: PMC11507454 DOI: 10.3390/ijms252011056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Revised: 10/07/2024] [Accepted: 10/13/2024] [Indexed: 10/28/2024] Open
Abstract
Cowpea (Vigna unguiculata (L.) Walp.) is appreciated for its suitability for cultivation and obtaining good yields in relatively extreme farming conditions. It is resistant to high temperatures and drought. Moreover, food products prepared from Vigna are rich in many nutrients such as proteins, amino acids, carbohydrates, minerals, fiber, vitamins, and other bioactive compounds. However, in East and Southeast Asia, where the products of this crop are in demand, the climate is characterized by excessive humidity. Under these conditions, the vast majority of cowpea varieties tend to have indeterminate growth (elongated shoot length) and are unsuitable for mechanized harvesting. The molecular mechanisms for tolerance to high relative humidity remain the least studied in comparison with those for other abiotic stress factors (drought, heat, cold, flooding, etc.). The purpose of the work was to reveal and investigate differentially expressed genes in cowpea accessions having contrasting growth habits (determinate and indeterminate) under humid and drought conditions. We performed RNA-seq analysis using selected cowpea accessions from the VIR collection. Among the genotypes used, some have significant changes in their plant architecture in response to high relative humidity, while others were tolerant to these conditions. In total, we detected 1697 upregulated and 1933 downregulated genes. The results showed that phytohormone-related genes are involved in cowpea response to high relative humidity. DEGs associated with jasmonic acid signaling are proposed to be key contributors in the maintenance of compact architecture under humid conditions.
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Chowra UK, Regon P, Kobayashi Y, Koyama H, Panda SK. Characterization of Al 3+-toxicity responses and molecular mechanisms underlying organic acid efflux in Vigna mungo (L.) Hepper. PLANTA 2024; 260:116. [PMID: 39400747 DOI: 10.1007/s00425-024-04547-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2024] [Accepted: 10/04/2024] [Indexed: 10/15/2024]
Abstract
Aluminium (Al3+) toxicity in acidic soils poses a significant challenge for crop cultivation and reduces crop productivity. The primary defense mechanism against Al3+ toxicity involves the activation of organic acid secretion. In this study, responses of 9 Vigna mungo cultivars to Al3+ toxicity were investigated, with a particular emphasis on the root system and crucial genes involved in Al3+ tolerance using molecular cloning and expression analysis. Sensitive blackgram-KM2 cultivars exposed to 100-µM Al3+ toxicity for 72 h exhibited a root-growth inhibition of approximately 66.17%. Significant loss of membrane integrity and structural deformative roots were found to be the primary symptoms of Al3+ toxicity in blackgram. MATE (Multidrug and Toxic Compound Extrusion) and ALS3 (Aluminium Sensitive 3) genes were successfully cloned from a sensitive blackgram cv KM2 with phylogenetic analysis revealing their evolutionary relationship to Vigna radiata and Glycine max. The MATE gene is mainly localized in the plasma membrane, and highly expressed under Al3+, thus suggesting its role in transports of citrate-Al3+ complexes, and detoxifying Al3+ within plant cells. In addition, ALS3 was also induced under Al3+ toxicity, which codes the UDP-glucose transporter and is required for the maintenance of ions homeostasis. In summary, this study highlights the understanding of Al3+ toxicity and underlying molecular mechanisms linked to the efflux of organic acid in blackgram, ultimately aiding the framework for the development of strategies to enhance the resilience of blackgram and other pulse crops in Al-rich soils.
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Habde SV, Punniyamoorthy D, Jegadeesan S. Mutation profiling through whole genome sequencing of electron beam-induced black gram ( Vigna mungo L. Hepper) mutant. Int J Radiat Biol 2024; 100:1665-1682. [PMID: 39374376 DOI: 10.1080/09553002.2024.2409666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 08/31/2024] [Accepted: 09/24/2024] [Indexed: 10/09/2024]
Abstract
PURPOSE Black gram (Vigna mungo [L.] Hepper) is an important annual legume with great economic, nutritional and ecological significance. Novel variations through induced mutagenesis can accelerate narrow genetic base-impeded black gram improvement. This is a first study on characterization of genome-wide mutation spectrum induced by electron beam (EB). MATERIALS AND METHODS Black gram genotype 'Pant U-31' was irradiated with 400 Gy EB generated in a 10 MeV LINAC. A stable mutant PM-32 (M6) was re-sequenced by combining Illumina (BIOO Scientific, Inc., Austin, TX) and Nanopore Technologies (Oxford, UK). Variants were predicted in reference to the available whole genome scaffold level draft assembly of parent 'Pant U-31'. RESULTS Genome analysis predicted a total of 76,893 genes of which 58,517 were annotated. The identified variants totaling 728,161, largely comprised (91.56%) of single base substitutions (SBSs) with a transition (Ti) to transversion (Tv) ratio of 1.95. Of the indels constituting 8.44% of total induced variants, insertions accounted for 4.29%, with preponderance of multiple bases (53.63%) and 2-5 bp insertions as the major class (33.71%). Multiple-base deletions (2-5 bases) formed the bulk (31.14%) of the total deletions. The genic variants (2438) with estimated high and moderate effects were located within 1271 predicted genes. A higher number of mutations were observed on chromosomes Vm1 (588) and Vm3 (428) with the highest frequency on chromosome Vm3 (every 0.07 Mb). CONCLUSIONS Our study reiterated the mutagenic utility of EB for inducing SBSs and small indels genome-wide. The knowledge gained from SNP-level profiling of EB-induced mutations can expedite comparative mutation breeding studies in legumes.
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Li W, He F, Wang X, Liu Q, Zhang X, Yang Z, Fang C, Xiang H. Chromosome genome assembly and annotation of Adzuki Bean (Vigna angularis). Sci Data 2024; 11:1074. [PMID: 39358398 PMCID: PMC11446921 DOI: 10.1038/s41597-024-03911-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/23/2024] [Indexed: 10/04/2024] Open
Abstract
Adzuki bean (Vigna angularis) is a significant dietary legume crop that is prevalent in East Asia. It also holds traditional medicinal importance in China. In this study, we report a high-quality, chromosome-level genome assembly of adzuki bean obtained by employing Illumina short-read sequencing, PacBio long-read sequencing, and Hi-C technology. The assembly spans 447.8 Mb, encompassing 96.32% of the estimated genome, with contig and scaffold N50 values of 16.5 and 41.0 Mb, respectively. More than 98.2% of the 1,614 BUSCO genes were fully identified, and 25,939 genes were annotated, with 98.23% of them being functionally identifiable. Vigna angularis was estimated to diverge successively from Vigna unguiculata and Vigna radiata about 15.3 and 8.7 million years ago (Ma), respectively. This chromosome-level reference genome of Vigna angularis provides a robust foundation for exploring the functional genomics and genome evolution of adzuki bean, thereby facilitating advancements in molecular breeding of adzuki bean.
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Yu L, Sussman H, Khmelnitsky O, Rahmati Ishka M, Srinivasan A, Nelson ADL, Julkowska MM. Development of a mobile, high-throughput, and low-cost image-based plant growth phenotyping system. PLANT PHYSIOLOGY 2024; 196:810-829. [PMID: 38696768 DOI: 10.1093/plphys/kiae237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/26/2024] [Accepted: 04/10/2024] [Indexed: 05/04/2024]
Abstract
Nondestructive plant phenotyping forms a key technique for unraveling molecular processes underlying plant development and response to the environment. While the emergence of high-throughput phenotyping facilities can further our understanding of plant development and stress responses, their high costs greatly hinder scientific progress. To democratize high-throughput plant phenotyping, we developed sets of low-cost image- and weight-based devices to monitor plant shoot growth and evapotranspiration. We paired these devices to a suite of computational pipelines for integrated and straightforward data analysis. The developed tools were validated for their suitability for large genetic screens by evaluating a cowpea (Vigna unguiculata) diversity panel for responses to drought stress. The observed natural variation was used as an input for a genome-wide association study, from which we identified nine genetic loci that might contribute to cowpea drought resilience during early vegetative development. The homologs of the candidate genes were identified in Arabidopsis (Arabidopsis thaliana) and subsequently evaluated for their involvement in drought stress by using available T-DNA insertion mutant lines. These results demonstrate the varied applicability of this low-cost phenotyping system. In the future, we foresee these setups facilitating the identification of genetic components of growth, plant architecture, and stress tolerance across a wide variety of plant species.
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Ongom PO, Ajibade YA, Mohammed SB, Dieng I, Fatokun C, Boukar O. HybridQC: A SNP-Based Quality Control Application for Rapid Hybridity Verification in Diploid Plants. Genes (Basel) 2024; 15:1252. [PMID: 39457376 PMCID: PMC11507623 DOI: 10.3390/genes15101252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Revised: 09/19/2024] [Accepted: 09/23/2024] [Indexed: 10/28/2024] Open
Abstract
Background/Objectives: Hybridity authentication is an important component of quality assurance and control (QA/QC) in breeding programs. Here, we introduce HybridQC v1.0, a QA/QC software program specially designed for parental purity and hybridity determination. HybridQC rapidly detects molecular marker polymorphism between parents of a cross and utilizes only the informative markers for hybridity authentication. Methods: HybridQC is written in Python and designed with a graphical user interface (GUI) compatible with Windows operating systems. We demonstrated the QA/QC analysis workflow and functionality of HybridQC using Kompetitive allele-specific PCR (KASP) SNP genotype data for cowpea (Vigna unguiculata). Its performance was validated in other crop data, including sorghum (Sorghum bicolor) and maize (Zea mays). Results: The application efficiently analyzed low-density SNP data from multiple cowpea bi-parental crosses embedded in a single Microsoft Excel file. HybridQC is optimized for the auto-generation of key summary statistics and visualization patterns for marker polymorphism, parental heterozygosity, non-parental alleles, missing data, and F1 hybridity. An added graphical interface correctly depicted marker efficiency and the proportions of true F1 versus self-fertilized progenies in the data sets used. The output of HybridQC was consistent with the results of manual hybridity discernment in sorghum and maize data sets. Conclusions: This application uses QA/QC SNP markers to rapidly verify true F1 progeny. It eliminates the extensive time often required to manually curate and process QA/QC data. This tool will enhance the optimization efforts in breeding programs, contributing to increased genetic gain.
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