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Li J, Li Z, Wu Z, Sun Y, Niu S, Guo M, Zhang L. Molecular Characteristics of Bean Common Mosaic Virus Occurring in Inner Mongolia, China. Genes (Basel) 2024; 15:133. [PMID: 38275614 PMCID: PMC10815410 DOI: 10.3390/genes15010133] [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: 11/17/2023] [Revised: 01/12/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
Bean common mosaic virus (BCMV) was detected on common bean (Phaseolus vulgaris) plants showing wrinkled and/or narrow leaves, curling, shrinking and chlorosis of leaves, dwarfing of plants, and mottled pods in Inner Mongolia and named BCMV-22Huhe. Its genome has a size of 10,062 bp and was deposited in GenBank under the accession number OR778613. It is closely related to BCMV-Az (GenBank accession no. KP903372, in China) in the lineage of AzBMV. A recombination event was detected for BCMV-22Huhe among the 99 BCMV isolates published in the NCBI GenBank database, showing that BCMV-CJ25 (MK069986, found in Mexico) was a potential major parent, and the minor parent is unknown. This work is the first description of the occurrence of BCMV in Inner Mongolia, China.
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Affiliation(s)
- Jingru Li
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot 010018, China (Z.L.)
| | - Zhengnan Li
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot 010018, China (Z.L.)
| | - Zhanmin Wu
- Ordos Center of Agriculture and Animal Husbandry Ecology and Resource Protection, Ordos 017000, China
| | - Yu Sun
- Ordos Center of Agriculture and Animal Husbandry Ecology and Resource Protection, Ordos 017000, China
| | - Suqing Niu
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010010, China
| | - Mengze Guo
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot 010018, China (Z.L.)
| | - Lei Zhang
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot 010018, China (Z.L.)
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Kareem KT, Oduwaye OF, Adediji AO, Akinyosoye ST, Adetumbi AJ. Effect of bean common mosaic virus on seed germination and yield of cowpea ( Vigna unguiculata [L.] Walp.) breeding lines and characterisation of virus strains. Virusdisease 2023; 34:204-212. [PMID: 37408549 PMCID: PMC10317912 DOI: 10.1007/s13337-023-00812-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 02/13/2023] [Indexed: 07/07/2023] Open
Abstract
The study was conducted to characterise bean common mosaic virus strain Blackeye (BCMV-BICM) and determine the likelihood of seed transmission in cowpea breeding lines. F6 cowpea lines obtained from crosses between 'Ife-Brown' and 'IT-95 K-193-12' were planted at five locations in Southwest Nigeria for multilocational evaluation. Virus symptoms were observed on leaves of the breeding lines planted in Ibadan at eight weeks after planting. Enzyme-linked immunosorbent assay (ELISA) was used to determine the presence of six viruses: BCMV-BICM, cowpea aphid-borne mosaic virus, cucumber mosaic virus, cowpea mottle virus, southern bean mosaic virus and cowpea mild mottle virus. Seed transmission tests were carried out to determine virus transmission by seeds while growth and yield components of the cowpea lines were obtained. Reverse transcription polymerase chain reaction, sequencing and phylogenetic analyses were also used to characterise the BCMV-BICM isolates. The observed symptoms, leaf curling and mosaics, were typical of BCMV-BICM infection and ELISA results confirmed the presence of only BCMV-BICM. Line 'L-22-B' had the highest yield of 1653.9 kgha-1 followed by 'L-43-A' (1072 kgha-1). A non-significant relationship existed between the virus and germination parameters and similarly, the relationship between virus titres and yield parameters was not significant. Sequence analysis of the virus coat protein (CP) gene revealed the presence of three isolates with 96.87-97.47% nucleotide and 98.2-98.65% amino acid similarities and a 99.10-99.55% match with BCMV-BICM CP genes in GenBank. The deduced CP gene sequences showed unique changes at specific sites, while phylogenetic inferences revealed at least two separate origins for the isolates. Seed transmission is evident in all the cowpea breeding lines and 'L-22-B' and 'L-43-A' showed significant tolerance to BCMV-BICM. Thus, it is recommended that seeds from infected fields should not be used for further planting to prevent the introduction of viruses into new areas where their effect could be devastating in susceptible lines. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-023-00812-3.
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Affiliation(s)
- Kehinde Titilope Kareem
- Institute of Agricultural Research and Training, Obafemi Awolowo University, P.M.B. 5029, Moor Plantation, Ibadan, Oyo State Nigeria
| | - Olubusola Fehintola Oduwaye
- Institute of Agricultural Research and Training, Obafemi Awolowo University, P.M.B. 5029, Moor Plantation, Ibadan, Oyo State Nigeria
| | - Adedapo Olutola Adediji
- Pan African University Life and Earth Sciences Institute (PAULESI), FW73+7JJ, University Of Ibadan-Ajibode Road, Ibadan, Oyo State Nigeria
| | - Solomon Tayo Akinyosoye
- Institute of Agricultural Research and Training, Obafemi Awolowo University, P.M.B. 5029, Moor Plantation, Ibadan, Oyo State Nigeria
| | - Adedayo Johnson Adetumbi
- Institute of Agricultural Research and Training, Obafemi Awolowo University, P.M.B. 5029, Moor Plantation, Ibadan, Oyo State Nigeria
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Li Y, Ma E, Yang K, Zhao B, Li Y, Wan P. Genome-wide analysis of key gene families in RNA silencing and their responses to biotic and drought stresses in adzuki bean. BMC Genomics 2023; 24:195. [PMID: 37046231 PMCID: PMC10091639 DOI: 10.1186/s12864-023-09274-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 03/25/2023] [Indexed: 04/14/2023] Open
Abstract
BACKGROUND In plants, RNA silencing is an important conserved mechanism to regulate gene expression and combat against abiotic and biotic stresses. Dicer-like (DCL) and Argonaute (AGO) proteins and RNA-dependent RNA polymerase (RDR) are the core elements involved in gene silencing and their gene families have been explored in many plants. However, these genes and their responses to stresses have not yet been well characterized in adzuki bean. RESULTS A total of 11 AGO, 7 DCL and 6 RDR proteins were identified, and phylogenetic analyses of these proteins showed that they clustered into six, four and four clades respectively. The expression patterns of these genes in susceptible or resistant adzuki bean cultivars challenged with drought, bean common mosaic virus and Podosphaera xanthii infections were further validated by quantitative RT-PCR. The different responses of these proteins under abiotic and biotic stresses indicated their specialized regulatory mechanisms. CONCLUSIONS In this study, 24 genes of the DCL, AGO and RDR gene families in adzuki bean were identified, and the sequence characterization, structure of the encoded proteins, evolutionary relationship with orthologues in other legumes and gene expression patterns under drought and biotic stresses were primarily explored, which enriched our understanding of these genes in adzuki bean. Our findings provide a foundation for the comparative genomic analyses of RNA silencing elements in legume plants and further new insights into the functional complexity of RNA silencing in the response to various stresses in adzuki bean.
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Affiliation(s)
- Yongqiang Li
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture Rural Affairs, College of Biological Science and Resources Environment, Beijing University of Agriculture, HuilongguanBeinonglu 7, Changping District, Beijing, 102206, China.
| | - Enze Ma
- Beijing Key Laboratory of New Technology in Agricultural Application, College of Plant Science and Technology, Beijing University of Agriculture, HuilongguanBeinonglu 7, Changping District, Beijing, 102206, China
| | - Kai Yang
- Beijing Key Laboratory of New Technology in Agricultural Application, College of Plant Science and Technology, Beijing University of Agriculture, HuilongguanBeinonglu 7, Changping District, Beijing, 102206, China
| | - Bo Zhao
- Beijing Key Laboratory of New Technology in Agricultural Application, College of Plant Science and Technology, Beijing University of Agriculture, HuilongguanBeinonglu 7, Changping District, Beijing, 102206, China
| | - Yisong Li
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture Rural Affairs, College of Biological Science and Resources Environment, Beijing University of Agriculture, HuilongguanBeinonglu 7, Changping District, Beijing, 102206, China
| | - Ping Wan
- Beijing Key Laboratory of New Technology in Agricultural Application, College of Plant Science and Technology, Beijing University of Agriculture, HuilongguanBeinonglu 7, Changping District, Beijing, 102206, China.
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Çelik A, Emiralioğlu O, Yeken MZ, Çiftçi V, Özer G, Kim Y, Baloch FS, Chung YS. A novel study on bean common mosaic virus accumulation shows disease resistance at the initial stage of infection in Phaseolus vulgaris. Front Genet 2023; 14:1136794. [PMID: 37021006 PMCID: PMC10067576 DOI: 10.3389/fgene.2023.1136794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/06/2023] [Indexed: 04/07/2023] Open
Abstract
Accurate and early diagnosis of bean common mosaic virus (BCMV) in Phaseolus vulgaris tissues is critical since the pathogen can spread easily and have long-term detrimental effects on bean production. The use of resistant varieties is a key factor in the management activities of BCMV. The study reported here describes the development and application of a novel SYBR Green-based quantitative real-time PCR (qRT-PCR) assay targeting the coat protein gene to determine the host sensitivity to the specific NL-4 strain of BCMV. The technique showed high specificity, validated by melting curve analysis, without cross-reaction. Further, the symptoms development of twenty advanced common bean genotypes after mechanical BCMV-NL-4 infection was evaluated and compared. The results showed that common bean genotypes exhibit varying levels of host susceptibility to this BCMV strain. The YLV-14 and BRS-22 genotypes were determined as the most resistant and susceptible genotypes, respectively, in terms of aggressiveness of symptoms. The accumulation of BCMV was analyzed in the resistant and susceptible genotypes 3, 6, and 9 days following the inoculation by the newly developed qRT-PCR. The mean cycle threshold (Ct) values showed that the viral titer was significantly lower in YLV-14, which was evident in both root and leaf 3 days after the inoculation. The qRT-PCR thus facilitated an accurate, specific, and feasible assessment of BCMV accumulation in bean tissues even in low virus titers, allowing novel clues in selecting resistant genotypes in the early stages of infection, which is critical for disease management. To the best of our knowledge, this is the first study of a successfully performed qRT-PCR to estimate BCMV quantification.
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Affiliation(s)
- Ali Çelik
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Türkiye
- *Correspondence: Ali Çelik, ; Göksel Özer, ; Faheem Shehzad Baloch, ; Yong Suk Chung,
| | - Orkun Emiralioğlu
- Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Türkiye
| | - Mehmet Zahit Yeken
- Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Türkiye
| | - Vahdettin Çiftçi
- Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Türkiye
| | - Göksel Özer
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Türkiye
- *Correspondence: Ali Çelik, ; Göksel Özer, ; Faheem Shehzad Baloch, ; Yong Suk Chung,
| | - Yoonha Kim
- Laboratory of Crop Production, Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
- *Correspondence: Ali Çelik, ; Göksel Özer, ; Faheem Shehzad Baloch, ; Yong Suk Chung,
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, Republic of Korea
- *Correspondence: Ali Çelik, ; Göksel Özer, ; Faheem Shehzad Baloch, ; Yong Suk Chung,
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Wainaina JM, Kubatko L, Harvey J, Ateka E, Makori T, Karanja D, Boykin LM, Kehoe MA. Evolutionary insights of Bean common mosaic necrosis virus and Cowpea aphid-borne mosaic virus. PeerJ 2019; 7:e6297. [PMID: 30783563 PMCID: PMC6377593 DOI: 10.7717/peerj.6297] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 12/18/2018] [Indexed: 11/20/2022] Open
Abstract
Plant viral diseases are one of the major limitations in legume production within sub-Saharan Africa (SSA), as they account for up to 100% in production losses within smallholder farms. In this study, field surveys were conducted in the western highlands of Kenya with viral symptomatic leaf samples collected. Subsequently, next-generation sequencing was carried out to gain insights into the molecular evolution and evolutionary relationships of Bean common mosaic necrosis virus (BCMNV) and Cowpea aphid-borne mosaic virus (CABMV) present within symptomatic common bean and cowpea. Eleven near-complete genomes of BCMNV and two for CABMV were obtained from western Kenya. Bayesian phylogenomic analysis and tests for differential selection pressure within sites and across tree branches of the viral genomes were carried out. Three well-supported clades in BCMNV and one supported clade for CABMNV were resolved and in agreement with individual gene trees. Selection pressure analysis within sites and across phylogenetic branches suggested both viruses were evolving independently, but under strong purifying selection, with a slow evolutionary rate. These findings provide valuable insights on the evolution of BCMNV and CABMV genomes and their relationship to other viral genomes globally. The results will contribute greatly to the knowledge gap involving the phylogenomic relationship of these viruses, particularly for CABMV, for which there are few genome sequences available, and inform the current breeding efforts towards resistance for BCMNV and CABMV.
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Affiliation(s)
- James M Wainaina
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, Australia
| | - Laura Kubatko
- Ohio State University, Columbus, OH, United States of America
| | - Jagger Harvey
- Feed the Future Innovation Lab for the Reduction of Post-Harvest Loss, Kansas State University, Manhattan, KS, United States of America
| | - Elijah Ateka
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Timothy Makori
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - David Karanja
- Kenya Agricultural and Livestock Research Organization (KARLO), Machakos, Kenya
| | - Laura M Boykin
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, Australia
| | - Monica A Kehoe
- Plant Pathology, Department of Primary Industries and Regional Development Diagnostic Laboratory Service, South Perth, Australia
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Worrall EA, Hayward AC, Fletcher SJ, Mitter N. Molecular characterization and analysis of conserved potyviral motifs in bean common mosaic virus (BCMV) for RNAi-mediated protection. Arch Virol 2018; 164:181-194. [DOI: 10.1007/s00705-018-4065-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 09/21/2018] [Indexed: 01/01/2023]
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Martin K, Singh J, Hill JH, Whitham SA, Cannon SB. Dynamic transcriptome profiling of Bean Common Mosaic Virus (BCMV) infection in Common Bean (Phaseolus vulgaris L.). BMC Genomics 2016; 17:613. [PMID: 27515794 PMCID: PMC4982238 DOI: 10.1186/s12864-016-2976-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 07/28/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bean common mosaic virus (BCMV) is widespread, with Phaseolus species as the primary host plants. Numerous BCMV strains have been identified on the basis of a panel of bean varieties that distinguish the pathogenicity types with respect to the viral strains. The molecular responses in Phaseolus to BCMV infection have not yet been well characterized. RESULTS We report the transcriptional responses of a widely susceptible variety of common bean (Phaseolus vulgaris L., cultivar 'Stringless green refugee') to two BCMV strains, in a time-course experiment. We also report the genome sequence of a previously unreported BCMV strain. The interaction with the known strain NL1-Iowa causes moderate symptoms and large transcriptional responses, and the newly identified strain (Strain 2 or S2) causes severe symptoms and moderate transcriptional responses. The transcriptional profiles of host plants infected with the two isolates are distinct, and involve numerous differences in splice forms in particular genes, and pathway specific expression patterns. CONCLUSIONS We identified differential host transcriptome response after infection of two different strains of Bean common mosaic virus (BCMV) in common bean (Phaseolus vulgaris L.). Virus infection initiated a suite of changes in gene expression level and patterns in the host plants. Pathways related to defense, gene regulation, metabolic processes, photosynthesis were specifically altered after virus infection. Results presented in this study can increase the understanding of host-pathogen interactions and provide resources for further investigations of the biological mechanisms in BCMV infection and defense.
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Affiliation(s)
- Kathleen Martin
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
| | - Jugpreet Singh
- ORISE Fellow, USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011 USA
| | - John H. Hill
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, 50011 USA
| | - Steven A. Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, 50011 USA
| | - Steven B. Cannon
- Department of Agronomy, Iowa State University, Ames, IA 50011 USA
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Crop Genome Informatics Laboratory, Iowa State University, Ames, IA 50011 USA
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Worrall EA, Wamonje FO, Mukeshimana G, Harvey JJ, Carr JP, Mitter N. Bean Common Mosaic Virus and Bean Common Mosaic Necrosis Virus: Relationships, Biology, and Prospects for Control. Adv Virus Res 2015; 93:1-46. [PMID: 26111585 DOI: 10.1016/bs.aivir.2015.04.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The closely related potyviruses Bean common mosaic virus (BCMV) and Bean common mosaic necrosis virus (BCMNV) are major constraints on common bean (Phaseolus vulgaris) production. Crop losses caused by BCMV and BCMNV impact severely not only on commercial scale cultivation of this high-value crop but also on production by smallholder farmers in the developing world, where bean serves as a key source of dietary protein and mineral nutrition. In many parts of the world, progress has been made in combating BCMV through breeding bean varieties possessing the I gene, a dominant gene conferring resistance to most BCMV strains. However, in Africa, and in particular in Central and East Africa, BCMNV is endemic and this presents a serious problem for deployment of the I gene because this virus triggers systemic necrosis (black root disease) in plants possessing this resistance gene. Information on these two important viruses is scattered throughout the literature from 1917 onward, and although reviews on resistance to BCMV and BCMNV exist, there is currently no comprehensive review on the biology and taxonomy of BCMV and BCMNV. In this chapter, we discuss the current state of our knowledge of these two potyviruses including fundamental aspects of classification and phylogeny, molecular biology, host interactions, transmission through seed and by aphid vectors, geographic distribution, as well as current and future prospects for the control of these important viruses.
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