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Kumar S, Mukherjee SK, Sahoo L. A Method for Developing RNAi-Derived Resistance in Cowpea Against Geminiviruses. Methods Mol Biol 2022; 2408:191-210. [PMID: 35325424 DOI: 10.1007/978-1-0716-1875-2_13] [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] [Indexed: 06/14/2023]
Abstract
In plants, RNA interference (RNAi) is triggered by double-stranded RNA (dsRNA). Accordingly, various RNA silencing technologies involving hpRNA, artificial microRNA (miRNA), and virus-induced gene silencing (VIGS) are used for controlling the expression of genes. Such manipulations help understanding gene functions and crop improvement biotechnology. A typical hpRNA construct is comprised of an intron splicable perfect inverted repeat of the target gene sequences under the control of a strong promoter. Geminiviruses, especially Mungbean Yellow Mosaic India Virus (MYMIV) cause devastating diseases in legume plants including cowpea, incurring severe crop loss. RNAi, involving hpRNA construct as transgene, is used to control these diseases at the early stages of geminivirus infection in the host, preventing symptom development and viral DNA accumulation. In this chapter, we describe a detailed protocol for the identification of geminivirus isolates from the filed grown cowpea plants, characterization of virus isolates under the laboratory conditions, design and construct RNAi vectors for effective suppression of viral target genes, and consequent development of transgenic cowpea using Agrobacterium-mediated transformation protocol. These transgenics are subsequently evaluated for resistance to MYMIV.
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Affiliation(s)
- Sanjeev Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Sunil Kumar Mukherjee
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Lingaraj Sahoo
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India.
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Xu N, Yang Q, Yang X, Wang M, Guo M. Reconstruction and analysis of a genome-scale metabolic model for Agrobacterium tumefaciens. MOLECULAR PLANT PATHOLOGY 2021; 22:348-360. [PMID: 33433944 PMCID: PMC7865084 DOI: 10.1111/mpp.13032] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 11/22/2020] [Accepted: 12/07/2020] [Indexed: 05/20/2023]
Abstract
The plant pathogen Agrobacterium tumefaciens causes crown gall disease and is a widely used tool for generating transgenic plants owing to its virulence. The pathogenic process involves a shift from an independent to a living form within a host plant. However, comprehensive analyses of metabolites, genes, and reactions contributing to this complex process are lacking. To gain new insights about the pathogenicity from the viewpoints of physiology and cellular metabolism, a genome-scale metabolic model (GSMM) was reconstructed for A. tumefaciens. The model, referred to as iNX1344, contained 1,344 genes, 1,441 reactions, and 1,106 metabolites. It was validated by analyses of in silico cell growth on 39 unique carbon or nitrogen sources and the flux distribution of carbon metabolism. A. tumefaciens metabolic characteristics under three ecological niches were modelled. A high capacity to access and metabolize nutrients is more important for rhizosphere colonization than in the soil, and substantial metabolic changes were detected during the shift from the rhizosphere to tumour environments. Furthermore, by integrating transcriptome data for tumour conditions, significant alterations in central metabolic pathways and secondary metabolite metabolism were identified. Overall, the GSMM and constraint-based analysis could decode the physiological and metabolic features of A. tumefaciens as well as interspecific interactions with hosts, thereby improving our understanding of host adaptation and infection mechanisms.
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Affiliation(s)
- Nan Xu
- College of Bioscience and BiotechnologyYangzhou UniversityYangzhouChina
| | - Qiyuan Yang
- College of Bioscience and BiotechnologyYangzhou UniversityYangzhouChina
| | - Xiaojing Yang
- College of Bioscience and BiotechnologyYangzhou UniversityYangzhouChina
| | - Mingqi Wang
- College of Bioscience and BiotechnologyYangzhou UniversityYangzhouChina
| | - Minliang Guo
- College of Bioscience and BiotechnologyYangzhou UniversityYangzhouChina
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Bett B, Gollasch S, Moore A, Harding R, Higgins TJV. An Improved Transformation System for Cowpea ( Vigna unguiculata L. Walp) via Sonication and a Kanamycin-Geneticin Selection Regime. FRONTIERS IN PLANT SCIENCE 2019; 10:219. [PMID: 30873198 PMCID: PMC6401653 DOI: 10.3389/fpls.2019.00219] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 02/08/2019] [Indexed: 05/30/2023]
Abstract
An improved cowpea transformation method utilizing Agrobacterium-mediated gene delivery to explants derived from the cotyledonary nodes of imbibed cowpea seed is described. The explants were regenerated following a sonication procedure and a stringent selection comprising alternating regimes of kanamycin and geneticin. The method was reproducible and led to the recovery of independent fertile transgenic plants in the greenhouse at a level of about one per cent of starting explants. A transgene encoding an insecticidal protein from Bacillus thuringiensis was used to demonstrate the efficacy of the system.
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Affiliation(s)
- Bosibori Bett
- CSIRO Agriculture and Food, Canberra, ACT, Australia
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
- Biotechnology Centre, Kenya Agricultural & Livestock Research Organisation, Nairobi, Kenya
| | | | - Andy Moore
- CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Robert Harding
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Thomas J. V. Higgins
- CSIRO Agriculture and Food, Canberra, ACT, Australia
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
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Kumar S, Tanti B, Patil BL, Mukherjee SK, Sahoo L. RNAi-derived transgenic resistance to Mungbean yellow mosaic India virus in cowpea. PLoS One 2017; 12:e0186786. [PMID: 29077738 PMCID: PMC5659608 DOI: 10.1371/journal.pone.0186786] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/06/2017] [Indexed: 11/21/2022] Open
Abstract
Cowpea is an important grain legume crop of Africa, Latin America, and Southeast Asia. Leaf curl and golden mosaic diseases caused by Mungbean yellow mosaic India virus (MYMIV) have emerged as most devastating viral diseases of cowpea in Southeast Asia. In this study, we employed RNA interference (RNAi) strategy to control cowpea-infecting MYMIV. For this, we generated transgenic cowpea plants harbouring three different intron hairpin RNAi constructs, containing the AC2, AC4 and fusion of AC2 and AC4 (AC2+AC4) of seven cowpea-infecting begomoviruses. The T0 and T1 transgenic cowpea lines of all the three constructs accumulated transgene-specific siRNAs. Transgenic plants were further assayed up to T1 generations, for resistance to MYMIV using agro-infectious clones. Nearly 100% resistance against MYMIV infection was observed in transgenic lines, expressing AC2-hp and AC2+AC4-hp RNA, when compared with untransformed controls and plants transformed with empty vectors, which developed severe viral disease symptoms within 3 weeks. The AC4-hp RNA expressing lines displayed appearance of milder symptoms after 5 weeks of MYMIV-inoculation. Northern blots revealed a positive correlation between the level of transgene-specific siRNAs accumulation and virus resistance. The MYMIV-resistant transgenic lines accumulated nearly zero or very low titres of viral DNA. The transgenic cowpea plants had normal phenotype with no yield penalty in greenhouse conditions. This is the first demonstration of RNAi-derived resistance to MYMIV in cowpea.
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Affiliation(s)
- Sanjeev Kumar
- Department of Bioscience and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
- Department of Botany, Gauhati University, Guwahati, Assam, India
| | - Bhaben Tanti
- Department of Botany, Gauhati University, Guwahati, Assam, India
| | - Basavaprabhu L. Patil
- ICAR-National Research Centre on Plant Biotechnology, LBS Centre, IARI, Pusa Campus, New Delhi, India
| | - Sunil Kumar Mukherjee
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Lingaraj Sahoo
- Department of Bioscience and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
- * E-mail:
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Xiong H, Shi A, Mou B, Qin J, Motes D, Lu W, Ma J, Weng Y, Yang W, Wu D. Genetic Diversity and Population Structure of Cowpea (Vigna unguiculata L. Walp). PLoS One 2016; 11:e0160941. [PMID: 27509049 PMCID: PMC4980000 DOI: 10.1371/journal.pone.0160941] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/27/2016] [Indexed: 11/19/2022] Open
Abstract
The genetic diversity of cowpea was analyzed, and the population structure was estimated in a diverse set of 768 cultivated cowpea genotypes from the USDA GRIN cowpea collection, originally collected from 56 countries. Genotyping by sequencing was used to discover single nucleotide polymorphism (SNP) in cowpea and the identified SNP alleles were used to estimate the level of genetic diversity, population structure, and phylogenetic relationships. The aim of this study was to detect the gene pool structure of cowpea and to determine its relationship between different regions and countries. Based on the model-based ancestry analysis, the phylogenetic tree, and the principal component analysis, three well-differentiated genetic populations were postulated from 768 worldwide cowpea genotypes. According to the phylogenetic analyses between each individual, region, and country, we may trace the accession from off-original, back to the two candidate original areas (West and East of Africa) to predict the migration and domestication history during the cowpea dispersal and development. To our knowledge, this is the first report of the analysis of the genetic variation and relationship between globally cultivated cowpea genotypes. The results will help curators, researchers, and breeders to understand, utilize, conserve, and manage the collection for more efficient contribution to international cowpea research.
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Affiliation(s)
- Haizheng Xiong
- Department of Horticulture, University of Arkansas, Fayetteville, Arkansas, United States of America
- State Key Lab of Rice Biology, IAEA Collaborating Center, Zhejiang University, Hangzhou, China
| | - Ainong Shi
- Department of Horticulture, University of Arkansas, Fayetteville, Arkansas, United States of America
- * E-mail: (AS); (BM)
| | - Beiquan Mou
- US Department of Agriculture, Agricultural Research Service (USDA-ARS), Salinas, California, United States of America
- * E-mail: (AS); (BM)
| | - Jun Qin
- Department of Horticulture, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Dennis Motes
- Vegetable Research Center, University of Arkansas, Alma, Arkansas, United States of America
| | - Weiguo Lu
- Department of Horticulture, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Jianbing Ma
- Department of Horticulture, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Yuejin Weng
- Department of Horticulture, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Wei Yang
- Department of Horticulture, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Dianxing Wu
- State Key Lab of Rice Biology, IAEA Collaborating Center, Zhejiang University, Hangzhou, China
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