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Dada AO, Oresanya A, Akinyosoye ST, Arogundade O. The first report of bean common mosaic virus (BCMV) infection of African yam bean (Sphenostylis stenocarpa) in Nigeria. Mol Biol Rep 2022; 49:10133-10136. [PMID: 36028731 DOI: 10.1007/s11033-022-07883-3] [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: 05/05/2022] [Accepted: 08/17/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND African yam bean (Sphenostylis stenocarpa) is an underutilized crop that has the potential to contribute to sustainable food security. In October 2021, more than 90% African Yam Bean (AYB) plants showed typical virus symptoms of mosaic and necrosis in the grain legumes field of the Institute of Agricultural Research and Training (IAR&T), Nigeria. METHODS AND RESULTS Subsequently, leaf samples were collected and tested by ELISA and PCR to identify the virus species. Anti-BCMV and anti-potyvirus antibodies both gave positive results when symptomatic leaves were tested, and PCR using primers designed to the coat protein gene of BCMV amplified a band of the expected size (469 bp). The sequence of the PCR product was deposited in GenBank with the accession No. OL763314. The nucleotide sequence of the coat protein gene had 99% identity with BCMV isolate TN2 (KY044818). The identities of the nucleotide and amino acid sequence of the partial CP gene of the isolated virus relative to those of other potyviruses were 82.96-99.12% and 87.33-100%,, respectively. Phylogenetic analyses of the partial CP-nucleotide sequences grouped the isolate from this study (BCMV-IART-AYB) and BCMV-TN2 in the same cluster with other BCMV strains of the peanut stripe (PSt) and the blackeye cowpea (BlC) strains. CONCLUSIONS In this study, we identified Bean commom mosaic virus (BCMV) infecting AYB for the first time in Nigeria and show that it has high nucleotide and amino acid identity with an Isolate of cowpea-infecting BCMV in India and China respectively than isolate in Nigeria.
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Affiliation(s)
- A O Dada
- Institute of Agriculture Research and Training (IAR&T), Moor Plantation, PMB 5029, Ibadan, Nigeria
| | - A Oresanya
- International Institute of Tropical Agriculture (IITA), Oyo Road, PMB 5320, Ibadan, Nigeria
| | - S T Akinyosoye
- National Horticultural Research Institute (NIHORT), Jericho Reservation Area, Idi-Ishiin, PMB 5432, Ibadan, Nigeria
| | - O Arogundade
- National Horticultural Research Institute (NIHORT), Jericho Reservation Area, Idi-Ishiin, PMB 5432, Ibadan, Nigeria.
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Li B, Karthikeyan A, Wang L, Yin J, Jin T, Liu H, Li K, Gai J, Zhi H. Discovery and characterization of differentially expressed soybean miRNAs and their targets during soybean mosaic virus infection unveils novel insight into Soybean-SMV interaction. BMC Genomics 2022; 23:171. [PMID: 35236286 PMCID: PMC8889786 DOI: 10.1186/s12864-022-08385-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 02/07/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Soybean mosaic virus (SMV) is one of the most devastating pathogens of soybean. MicroRNAs (miRNAs) are a class of non-coding RNAs (21-24 nucleotides) which are endogenously produced by the plant host as part of a general gene expression regulatory mechanisms, but also play roles in regulating plant defense against pathogens. However, miRNA-mediated plant response to SMV in soybean is not as well documented. RESULT In this study, we analyzed 18 miRNA libraries, including three biological replicates from two soybean lines (Resistant and susceptible lines to SMV strain SC3 selected from the near-isogenic lines of Qihuang No. 1 × Nannong1138-2) after virus infection at three different time intervals (0 dpi, 7 dpi and 14 dpi). A total of 1,092 miRNAs, including 608 known miRNAs and 484 novel miRNAs were detected. Differential expression analyses identified the miRNAs profile changes during soybean-SMV interaction. Then, miRNAs potential target genes were predicted via data mining, and functional annotation was done by Gene Ontology (GO) analysis. The expression patterns of several miRNAs were validated by quantitative real-time PCR. We also validated the miRNA-target gene interaction by agrobacterium-mediated transient expression in Nicotiana benthamiana. CONCLUSION We have identified a large number of miRNAs and their target genes and also functional annotations. We found that multiple miRNAs were differentially expressed in the two lines and targeted a series of NBS-LRR resistance genes. It is worth mentioning that many of these genes exist in the previous fine-mapping interval of the resistance gene locus. Our study provides additional information on soybean miRNAs and an insight into the role of miRNAs during SMV-infection in soybean.
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Affiliation(s)
- Bowen Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Adhimoolam Karthikeyan
- Subtropical Horticulture Research Institute, Jeju National University, Jeju, 63243, South Korea
| | - Liqun Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Jinlong Yin
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Tongtong Jin
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Hui Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Kai Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Junyi Gai
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
| | - Haijian Zhi
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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Liu XT, Wu XY, Wu WP, Wu M, Chen JQ, Wang B. A bean common mosaic virus-resistance gene in the soybean variant V94-5152 was mapped to the Rsv4 locus conferring resistance to soybean mosaic virus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2367-2377. [PMID: 33997918 DOI: 10.1007/s00122-021-03829-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/30/2021] [Indexed: 06/12/2023]
Abstract
KEY MESSAGE In the soybean variant V94-5152, a BCMV-resistance gene was mapped near to the region of SMV-resistance Rsv4 locus, raising a possibility that V94-5152 may rely on Rsv4 locus to resist against both SMV and BCMV. Both Soybean mosaic virus (SMV) and Bean common mosaic virus (BCMV) can induce soybean mosaic diseases, but few studies have explored soybean resistance against BCMV so far. In this study, V94-5152, a soybean variant resistant to BCMV and SMV, was crossed with a susceptible cultivar, Williams 82 to map the resistance gene. By inoculating 292 F2 individuals with a BCMV isolate HZZB011, a segregation ratio of 3 resistant: 1 susceptible was observed, suggesting that V94-5152 possesses a single-dominant resistance gene against BCMV-HZZB011. Bulk segregation analysis (BSA) then revealed that the resistance gene is closely linked to BARCSOYSSR_02_0617, a simple sequence repeat (SSR) marker on chromosome 2. Genotyping neighboring SSR markers among the 292 F2 individuals enabled us to draw a genetic linkage map, which indicated that the BCMV-resistance gene is located 0.2 cM downstream of BARCSOYSSR_02_0617. Amplification and sequencing ten candidate genes (Glyma02g121300 to Glyma02g122200) around this marker then revealed four genes containing nonsynonymous changes or indels. Also, this location is near to the recently cloned SMV-resistance Rsv4 locus from the cultivar Peking. By obtaining ten more sequences of Rsv4 locus from cultivated and wild soybean materials, we further investigated the variation and evolutionary patterns of this virus-resistance locus. It was evident that positive selections had been acting on this locus, with one critical amino acid change (R55P) shared by all resistance soybeans tested.
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Affiliation(s)
- Xue-Ting Liu
- School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China
| | - Xiao-Yi Wu
- School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China
| | - Wen-Ping Wu
- School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China
| | - Mian Wu
- School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China.
| | - Jian-Qun Chen
- School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China.
| | - Bin Wang
- School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China.
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Tirnaz S, Zhang Y, Batley J. Genome-Wide Mining of Disease Resistance Gene Analogs Using Conserved Domains. Methods Mol Biol 2020; 2107:365-375. [PMID: 31893459 DOI: 10.1007/978-1-0716-0235-5_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The production of legume crop species is severely affected by disease, imposing a significant yield loss annually worldwide. Plant resistance gene analogs (RGAs) play specific roles in plant resistance responses, and their identification and subsequent application in breeding programs help to reduce this yield loss. RGAs contain conserved domains and motifs, which can be used for their identification and classification. Nucleotide-binding site-leucine-rich repeat (NLR), receptor like kinase (RLK), and receptor like protein (RLP) genes are the main types of RGAs. Computational identification and characterization of RGAs has been performed successfully among different plant species. Here, we explain the computational workflow for genome-wide RGA identification in legumes.
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Affiliation(s)
- Soodeh Tirnaz
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - Yueqi Zhang
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia.
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Wu M, Liu YN, Zhang C, Liu XT, Liu CC, Guo R, Niu KX, Zhu AQ, Yang JY, Chen JQ, Wang B. Molecular mapping of the gene(s) conferring resistance to Soybean mosaic virus and Bean common mosaic virus in the soybean cultivar Raiden. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:3101-3114. [PMID: 31432199 DOI: 10.1007/s00122-019-03409-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 07/29/2019] [Indexed: 05/29/2023]
Abstract
KEY MESSAGE In the soybean cultivar Raiden, both a SMV-resistance gene and a BCMV-resistance gene were fine-mapped to a common region within the Rsv1 complex locus on chromosome 13, in which two CC-NBS-LRR resistance genes (Glyma.13g184800 and Glyma.13g184900) exhibited significant divergence between resistant and susceptible cultivars and were subjected to positive selection. Both Soybean mosaic virus (SMV) and Bean common mosaic virus (BCMV) can induce soybean mosaic diseases. To date, few studies have explored soybean resistance against these two viruses simultaneously. In this work, Raiden, a cultivar resistant to both SMV and BCMV, was crossed with a susceptible cultivar, Williams 82, to fine-map the resistance genes. After inoculating ~ 200 F2 individuals with either SMV (SC6-N) or BCMV (HZZB011), a segregation ratio of 3 resistant:1 susceptible was observed, indicating that for either virus, a single dominant gene confers resistance. Bulk segregation analysis (BSA) revealed that the BCMV-resistance gene is also linked to the SMV-resistance Rsv1 complex locus. Genotyping the F2 individuals with 12 simple sequence repeat (SSR) markers across the Rsv1 complex locus then preliminarily mapped the SMV-resistance gene, Rsv1-r, between SSR markers BARCSOYSSR_13_1075 and BARCSOYSSR_13_1161 and the BCMV-resistance gene between BARCSOYSSR_13_1084 and BARCSOYSSR_13_1115. Furthermore, a population of 1009 F2 individuals was screened with markers BARCSOYSSR_13_1075 and BARCSOYSSR_13_1161, and 32 recombinant F2 individuals were identified. By determining the genotypes of these F2 individuals on multiple internal SSR and single nucleotide polymorphism (SNP) markers and assaying the phenotypes of selected recombinant F2:3 lines, both the SMV- and BCMV-resistance genes were fine-mapped to a common region ( ~ 154.5 kb) between two SNP markers: SNP-38 and SNP-50. Within the mapped region, two CC-NBS-LRR genes exhibited significant divergence between Raiden and Williams 82, and their evolution has been affected by positive selection.
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Affiliation(s)
- Mian Wu
- Laboratory of Plant Genetics and Molecular Evolution, Department of Genetics and Evolutionary Biology, School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China
| | - Ying-Na Liu
- Laboratory of Plant Genetics and Molecular Evolution, Department of Genetics and Evolutionary Biology, School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China
| | - Cong Zhang
- Laboratory of Plant Genetics and Molecular Evolution, Department of Genetics and Evolutionary Biology, School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China
| | - Xue-Ting Liu
- Laboratory of Plant Genetics and Molecular Evolution, Department of Genetics and Evolutionary Biology, School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China
| | - Cheng-Chen Liu
- Laboratory of Plant Genetics and Molecular Evolution, Department of Genetics and Evolutionary Biology, School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China
| | - Rui Guo
- Laboratory of Plant Genetics and Molecular Evolution, Department of Genetics and Evolutionary Biology, School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China
| | - Ke-Xin Niu
- Laboratory of Plant Genetics and Molecular Evolution, Department of Genetics and Evolutionary Biology, School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China
| | - An-Qi Zhu
- Laboratory of Plant Genetics and Molecular Evolution, Department of Genetics and Evolutionary Biology, School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China
| | - Jia-Yin Yang
- Huaiyin Institute of Agricultural Science of Xuhuai Region in Jiangsu, Huai'an, 223001, Jiangsu Province, China
| | - Jian-Qun Chen
- Laboratory of Plant Genetics and Molecular Evolution, Department of Genetics and Evolutionary Biology, School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China.
| | - Bin Wang
- Laboratory of Plant Genetics and Molecular Evolution, Department of Genetics and Evolutionary Biology, School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China.
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Gil J, Solarte D, Lobaton JD, Mayor V, Barrera S, Jara C, Beebe S, Raatz B. Fine-mapping of angular leaf spot resistance gene Phg-2 in common bean and development of molecular breeding tools. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2003-2016. [PMID: 30976830 PMCID: PMC6588644 DOI: 10.1007/s00122-019-03334-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 03/20/2019] [Indexed: 05/25/2023]
Abstract
KEY MESSAGE The Common Bean Angular Leaf Spot Resistance Gene Phg-2 was fine-mapped to a 409-Kbp region, and molecular markers for breeders were developed and validated in field experiments. Common bean (Phaseolus vulgaris L.) is an important food legume in Latin America, Asia and Africa. It is an important source of protein, carbohydrates and micro-minerals, particularly for smallholder farmers. Common bean productivity is affected by angular leaf spot (ALS) disease caused by the pathogenic fungus Pseudocercospora griseola, resulting in significant yield losses, particularly in low-input smallholder farming systems in the tropics. The ALS resistance gene Phg-2, which was found in several highly resistant common bean genotypes, was investigated in crosses between Mesoamerican pre-breeding lines and elite Andean breeding lines. Next-generation sequencing (NGS) data sets were used to design new SNP-based molecular markers. The Phg-2 locus was confirmed to be the major locus providing ALS resistance in these crosses. The locus was fine-mapped to a 409-Kbp region on chromosome 8. Two clusters of highly related LRR genes were identified in this region, which are the best candidate genes for Phg-2. Molecular markers were identified that are closely linked to the Phg-2 resistance gene and also highly specific to the donor germplasm. Marker-assisted selection (MAS) was used to introgress the Phg-2 resistance locus into Andean breeding germplasm using MAB lines. The usefulness of molecular markers in MAS was confirmed in several field evaluations in complex breeding crosses, under inoculation with different ALS pathotypes. This project demonstrates that NGS data are a powerful tool for the characterization of genetic loci and can be applied in the development of breeding tools.
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Affiliation(s)
| | | | - Juan David Lobaton
- Environmental and Rural Sciences School, University of New England, Armidale, Australia
| | | | - Santos Barrera
- Centro Internacional de Agricultura Tropical (CIAT), Bean Program, Palmira, Colombia
| | - Carlos Jara
- Centro Internacional de Agricultura Tropical (CIAT), Bean Program, Palmira, Colombia
| | - Steve Beebe
- Centro Internacional de Agricultura Tropical (CIAT), Bean Program, Palmira, Colombia
| | - Bodo Raatz
- Centro Internacional de Agricultura Tropical (CIAT), Bean Program, Palmira, Colombia
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