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Cao C, Hu B, Li H, Wei Z, Li L, Zhang H, Chen J, Sun Z, Xu Z, Li Y. Metatranscriptome and small RNA sequencing revealed a mixed infection of newly identified bymovirus and bean yellow mosaic virus on peas. Virology 2024; 596:110116. [PMID: 38788336 DOI: 10.1016/j.virol.2024.110116] [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: 03/19/2024] [Revised: 05/11/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024]
Abstract
Peas (Pisum sativum L.) are widely cultivated in temperate regions and are susceptible hosts for various viruses across different families. The discovery and identification of new viruses in peas has significant implications for field disease management. Here, we identified a mixed infection of two viruses from field-collected peas exhibiting virus-like symptoms using metatranscriptome and small RNA sequencing techniques. Upon identification, one of the viruses was determined to be a newly isolated and discovered bymovirus from peas, named "pea bymovirus 1 (PBV1)". The other was identified as a novel variant of bean yellow mosaic virus (BYMV-HZ1). Subsequently, mechanical inoculation and RT-PCR assays confirmed that both viruses could be inoculated back onto peas and tobaccos, showing mixed infection by PBV1 and BYMV-HZ1. To our knowledge, this is the first isolation of a bymovirus from pea and the first documented case of mixed infection of peas by PBV1 and BYMV-HZ1 in China.
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Affiliation(s)
- Chen Cao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Biao Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Huajuan Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Zhongyan Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Lulu Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Hehong Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Zongtao Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Zhongtian Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
| | - Yanjun Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
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Chen D, Zhang HY, Hu SM, He Z, Wu YQ, Zhang ZY, Wang Y, Han CG. The P2 protein of wheat yellow mosaic virus acts as a viral suppressor of RNA silencing in Nicotiana benthamiana to facilitate virus infection. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39016637 DOI: 10.1111/pce.15041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/18/2024] [Accepted: 07/08/2024] [Indexed: 07/18/2024]
Abstract
Wheat yellow mosaic virus (WYMV) causes severe viral wheat disease in Asia. The WYMV P1 protein encoded by RNA2 has viral suppressor of RNA silencing (VSR) activity to facilitate virus infection, however, VSR activity has not been identified for P2 protein encoded by RNA2. In this study, P2 protein exhibited strong VSR activity in Nicotiana benthamiana at the four-leaf stage, and point mutants P70A and G230A lost VSR activity. Protein P2 interacted with calmodulin (CaM) protein, a gene-silencing associated protein, while point mutants P70A and G230A did not interact with it. Competitive bimolecular fluorescence complementation and competitive co-immunoprecipitation experiments showed that P2 interfered with the interaction between CaM and calmodulin-binding transcription activator 3 (CAMTA3), but the point mutants P70A and G230A could not. Mechanical inoculation of wheat with in vitro transcripts of WYMV infectious cDNA clone further confirmed that VSR-deficient mutants P70A and G230A decreased WYMV infection in wheat plants compared with the wild type. In addition, RNA silencing, temperature, ubiquitination and autophagy had significant effects on accumulation of P2 protein in N. benthamiana leaves. In conclusion, WYMV P2 plays a VSR role in N. benthamiana and promotes virus infection by interfering with calmodulin-related antiviral RNAi defense.
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Affiliation(s)
- Dao Chen
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and College of Plant Protection, China Agricultural University, Beijing, China
| | - Hui-Ying Zhang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and College of Plant Protection, China Agricultural University, Beijing, China
| | - Shu-Ming Hu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and College of Plant Protection, China Agricultural University, Beijing, China
| | - Zheng He
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and College of Plant Protection, China Agricultural University, Beijing, China
| | - Yong Qi Wu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and College of Plant Protection, China Agricultural University, Beijing, China
| | - Zong-Ying Zhang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and College of Plant Protection, China Agricultural University, Beijing, China
| | - Ying Wang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and College of Plant Protection, China Agricultural University, Beijing, China
| | - Cheng-Gui Han
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and College of Plant Protection, China Agricultural University, Beijing, China
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Mishina K, Kai H, Hamada M, Haraguchi Y, Oono Y, Ordon F, Komatsuda T. Series of Resistance Genes in Barley ( Hordeum vulgare) that Control Barley Yellow Mosaic Virus Multiplication and the Root-to-Leaf Systemic Movement. PLANT DISEASE 2024; 108:1719-1728. [PMID: 38173257 DOI: 10.1094/pdis-07-23-1451-re] [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: 01/05/2024]
Abstract
The infection of young winter barley (Hordeum vulgare L.) root system in winter by barley yellow mosaic virus (BaYMV) can lead to high yield losses. Resistance breeding is critical for managing this virus, but there are only a few reports on resistance genes that describe how the genes control BaYMV propagation and the systemic movement from the roots to the leaves. Here we report a real-time quantitative PCR analysis of the virus in barley roots and leaves carrying BaYMV resistance genes (rym1 to rym15 and an unknown gene) to elucidate the molecular mechanisms underlying the barley response to BaYMV. The resistance mechanism directly targets the virus. Moreover, the resistance genes/cultivars were classified into the following three groups according to their BaYMV titer: (i) immune (BaYMV was undetectable in the roots or leaves), (ii) partially immune (BaYMV was detected in the roots but not in the leaves), and (iii) susceptible (BaYMV was detected in the roots and leaves). Our results clarified the functions of the resistance genes in barley roots and leaves following a BaYMV infection. We anticipate our analysis to be a starting point for more understanding of the correspondence between resistance genes of Triticeae and the soil-borne viruses.
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Affiliation(s)
- Kohei Mishina
- National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
| | - Hiroomi Kai
- Fukuoka Agricultural Research Center, Chikushino, Fukuoka 818-8577, Japan
| | - Michio Hamada
- Fukuoka Agricultural Research Center, Chikushino, Fukuoka 818-8577, Japan
| | - Yuhi Haraguchi
- Fukuoka Agricultural Research Center, Chikushino, Fukuoka 818-8577, Japan
| | - Youko Oono
- National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Quedlinburg, Germany
| | - Takao Komatsuda
- National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
- Crop Research Institute, Shandong Academy of Agricultural Sciences (SAAS), Ji'nan, 250100 Shandong, China
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Zhu H, Okiyama T, Mishina K, Kikuchi S, Sassa H, Komatsuda T, Kato T, Oono Y. Identification of Barley yellow mosaic virus Isolates Breaking rym3 Resistance in Japan. Genes (Basel) 2024; 15:697. [PMID: 38927633 PMCID: PMC11203024 DOI: 10.3390/genes15060697] [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: 04/14/2024] [Revised: 05/17/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
In early spring 2018, significant mosaic disease symptoms were observed for the first time on barley leaves (Hordeum vulgare L., cv. New Sachiho Golden) in Takanezawa, Tochigi Prefecture, Japan. This cultivar carries the resistance gene rym3 (rym; resistance to yellow mosaic). Through RNA-seq analysis, Barley yellow mosaic virus (BaYMV-Takanezawa) was identified in the roots of all five plants (T01-T05) in the field. Phylogenetic analysis of RNA1, encompassing known BaYMV pathotypes I through V, revealed that it shares the same origin as isolate pathotype IV (BaYMV-Ohtawara pathotype). However, RNA2 analysis of isolates revealed the simultaneous presence of two distinct BaYMV isolates, BaYMV-Takanezawa-T01 (DRR552862, closely related to pathotype IV) and BaYMV-Takanezawa-T02 (DRR552863, closely related to pathotype III). The amino acid sequences of the BaYMV-Takanezawa isolates displayed variations, particularly in the VPg and N-terminal region of CP, containing mutations not found in other domains of the virus genome. Changes in the CI (RNA1 amino acid residue 459) and CP (RNA1 amino acid residue 2138) proteins correlated with pathogenicity. These findings underscore the importance of monitoring and understanding the genetic diversity of BaYMV for effective disease management strategies in crop breeding.
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Affiliation(s)
- Hongjing Zhu
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba 305-8602, Japan; (H.Z.); (K.M.)
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo 271-8510, Japan; (S.K.); (H.S.)
| | - Takeshi Okiyama
- Tochigi Prefectural Agricultural Experiment Station, Kawaraya-cho 1080, Utsunomiya 320-0002, Japan; (T.O.); (T.K.)
| | - Kohei Mishina
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba 305-8602, Japan; (H.Z.); (K.M.)
| | - Shinji Kikuchi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo 271-8510, Japan; (S.K.); (H.S.)
| | - Hidenori Sassa
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo 271-8510, Japan; (S.K.); (H.S.)
| | - Takao Komatsuda
- Shandong Academy of Agricultural Sciences (SAAS), Crop Research Institute, 202 Gongyebei Road, Licheng District, Jinan 250100, China;
| | - Tsuneo Kato
- Tochigi Prefectural Agricultural Experiment Station, Kawaraya-cho 1080, Utsunomiya 320-0002, Japan; (T.O.); (T.K.)
| | - Youko Oono
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba 305-8602, Japan; (H.Z.); (K.M.)
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo 271-8510, Japan; (S.K.); (H.S.)
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Chen D, Zhang HY, Hu SM, Tian MY, Zhang ZY, Wang Y, Sun LY, Han CG. The P1 protein of wheat yellow mosaic virus exerts RNA silencing suppression activity to facilitate virus infection in wheat plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1717-1736. [PMID: 37751381 DOI: 10.1111/tpj.16461] [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: 04/15/2023] [Revised: 08/07/2023] [Accepted: 08/29/2023] [Indexed: 09/28/2023]
Abstract
Wheat yellow mosaic virus (WYMV) causes severe wheat viral disease in Asia. However, the viral suppressor of RNA silencing (VSR) encoded by WYMV has not been identified. Here, the P1 protein encoded by WYMV RNA2 was shown to suppress RNA silencing in Nicotiana benthamiana. Mutagenesis assays revealed that the alanine substitution mutant G175A of P1 abolished VSR activity and mutant Y10A VSR activity remained only in younger leaves. P1, but not G175A, interacted with gene silencing-related protein, N. benthamiana calmodulin-like protein (NbCaM), and calmodulin-binding transcription activator 3 (NbCAMTA3), and Y10A interacted with NbCAMTA3 only. Competitive Bimolecular fluorescence complementation and co-immunoprecipitation assays showed that the ability of P1 disturbing the interaction between NbCaM and NbCAMTA3 was stronger than Y10A, Y10A was stronger than G175A. In vitro transcript inoculation of infectious WYMV clones further demonstrated that VSR-defective mutants G175A and Y10A reduced WYMV infection in wheat (Triticum aestivum L.), G175A had a more significant effect on virus accumulation in upper leaves of wheat than Y10A. Moreover, RNA silencing, temperature, and autophagy have significant effects on the accumulation of P1 in N. benthamiana. Taken together, WYMV P1 acts as VSR by interfering with calmodulin-associated antiviral RNAi defense to facilitate virus infection in wheat, which has provided clear insights into the function of P1 in the process of WYMV infection.
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Affiliation(s)
- Dao Chen
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, and State Key Laboratory of Agricultural Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Hui-Ying Zhang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, and State Key Laboratory of Agricultural Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Shu-Ming Hu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, and State Key Laboratory of Agricultural Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Meng-Yuan Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang, 712100, China
| | - Zong-Ying Zhang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, and State Key Laboratory of Agricultural Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Ying Wang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, and State Key Laboratory of Agricultural Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Li-Ying Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang, 712100, China
| | - Cheng-Gui Han
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, and State Key Laboratory of Agricultural Biotechnology, China Agricultural University, Beijing, 100193, China
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Liu P, Shi C, Liu S, Lei J, Lu Q, Hu H, Ren Y, Zhang N, Sun C, Chen L, Jiang Y, Feng L, Zhang T, Zhong K, Liu J, Zhang J, Zhang Z, Sun B, Chen J, Tang Y, Chen F, Yang J. A papain-like cysteine protease-released small signal peptide confers wheat resistance to wheat yellow mosaic virus. Nat Commun 2023; 14:7773. [PMID: 38012219 PMCID: PMC10682394 DOI: 10.1038/s41467-023-43643-y] [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: 07/02/2022] [Accepted: 11/15/2023] [Indexed: 11/29/2023] Open
Abstract
Wheat yellow mosaic virus (WYMV), a soil-borne pathogen, poses a serious threat to global wheat production. Here, we identify a WYMV resistance gene, TaRD21A, that belongs to the papain-like cysteine protease family. Through genetic manipulation of TaRD21A expression, we establish its positive role in the regulation of wheat to WYMV resistance. Furthermore, our investigation shows that the TaRD21A-mediated plant antiviral response relies on the release of a small peptide catalyzed by TaRD21A protease activity. To counteract wheat resistance, WYMV-encoded nuclear inclusion protease-a (NIa) suppress TaRD21A activity to promote virus infection. In resistant cultivars, a natural variant of TaRD21A features a glycine-to-threonine substitution and this substitution enables the phosphorylation of threonine, thereby weakening the interaction between NIa and TaRD21A, reinforcing wheat resistance against WYMV. Our study not only unveils a WYMV resistance gene but also offers insights into the intricate mechanisms underpinning resistance against WYMV.
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Affiliation(s)
- Peng Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Chaonan Shi
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, 450002, China
| | - Shuang Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Jiajia Lei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Qisen Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Haichao Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Yan Ren
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, 450002, China
| | - Ning Zhang
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, 450002, China
| | - Congwei Sun
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, 450002, China
| | - Lu Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Yaoyao Jiang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Lixiao Feng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Tianye Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Kaili Zhong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Jiaqian Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Juan Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Zhuo Zhang
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, 410152, China
| | - Bingjian Sun
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
| | - Yimiao Tang
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Feng Chen
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Jian Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
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7
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Zhang M, Hong Y, Zhu J, Pan Y, Zhou H, Lv C, Guo B, Wang F, Xu R. Molecular insights into the responses of barley to yellow mosaic disease through transcriptome analysis. BMC PLANT BIOLOGY 2023; 23:267. [PMID: 37208619 DOI: 10.1186/s12870-023-04276-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/09/2023] [Indexed: 05/21/2023]
Abstract
BACKGROUND Barley (Hordeum vulgare L.) represents the fourth most essential cereal crop in the world, vulnerable to barley yellow mosaic virus (BaYMV) and/or barley mild mosaic virus (BaMMV), leading to the significant yield reduction. To gain a better understanding of the mechanisms regarding barley crop tolerance to virus infection, we employed a transcriptome sequencing approach and investigated global gene expression among three barley varieties under both infected and control conditions. RESULTS High-throughput sequencing outputs revealed massive genetic responses, reflected by the barley transcriptome after BaYMV and/or BaMMV infection. Significant enrichments in peptidase complex and protein processing in endoplasmic reticulum were clustered through Gene ontology and KEGG analysis. Many genes were identified as transcription factors, antioxidants, disease resistance genes and plant hormones and differentially expressed between infected and uninfected barley varieties. Importantly, general response genes, variety-specific and infection-specific genes were also discovered. Our results provide useful information for future barley breeding to resist BaYMV and BaMMV. CONCLUSIONS Our study elucidates transcriptomic adaptations in barley response to BaYMV/BaMMV infection through high-throughput sequencing technique. The analysis outcome from GO and KEGG pathways suggests that BaYMV disease induced regulations in multiple molecular-biology processes and signalling pathways. Moreover, critical DEGs involved in defence and stress tolerance mechanisms were displayed. Further functional investigations focusing on these DEGs contributes to understanding the molecular mechanisms of plant response to BaYMV disease infection, thereby offering precious genetic resources for breeding barley varieties resistant to BaYMV disease.
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Affiliation(s)
- Mengna Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Yi Hong
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Juan Zhu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Yuhan Pan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Hui Zhou
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Chao Lv
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Baojian Guo
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Feifei Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Rugen Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
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8
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Kan J, Cai Y, Cheng C, Chen S, Jiang C, He Z, Yang P. CRISPR/Cas9-guided knockout of eIF4E improves Wheat yellow mosaic virus resistance without yield penalty. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:893-895. [PMID: 36628413 PMCID: PMC10106853 DOI: 10.1111/pbi.14002] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/27/2022] [Accepted: 12/29/2022] [Indexed: 05/04/2023]
Affiliation(s)
- Jinhong Kan
- Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Yu Cai
- Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Chunyuan Cheng
- Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Shiqiang Chen
- Agricultural Sciences Institute in Jiangsu Lixiahe AreaYangzhouChina
| | - Congcong Jiang
- Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Zhentian He
- Agricultural Sciences Institute in Jiangsu Lixiahe AreaYangzhouChina
| | - Ping Yang
- Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingChina
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9
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Jin Y, Chen S, Xu X, Jiang C, He Z, Shen H, Ji W, Yang P. Host Specificity of Soilborne Pathogens in Hordeum Species and Their Relatives. PLANT DISEASE 2023; 107:1044-1053. [PMID: 36089682 DOI: 10.1094/pdis-04-22-0760-re] [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: 06/15/2023]
Abstract
Soilborne pathogens destabilize the yields of Triticeae crops, including barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.). Although genetic resistance derived from relatives of these species has been utilized to prevent rust diseases (i.e., in the wheat-rye 1BL-1RS translocation line), research on resistance against soilborne pathogens remains limited. Here, we performed field trials using 76 genotypes representing 28 Hordeum, six Triticum, and two Aegilops species to examine resistance against three soilborne bymoviruses: barley yellow mosaic virus (BaYMV), barley mild mosaic virus (BaMMV), and wheat yellow mosaic virus (WYMV). We also performed greenhouse tests using the soilborne fungal pathogen Fusarium pseudograminearum, which causes Fusarium crown rot (FCR). Using RT-PCR, we detected BaMMV and BaYMV in several Hordeum species, whereas WYMV induced systemic infection in the Triticum and Aegilops species. The identification of FCR susceptibility in all species examined suggests that F. pseudograminearum is a facultative fungal pathogen in Triticeae. Intraspecies variation in FCR disease severity was observed for several species, pointing to the possibility of exploring host resistance mechanisms. Therefore, by unlocking the host specificity of four soilborne pathogens in Hordeum species and their relatives, we obtained insights for the further exploration of wild sources of soilborne pathogen resistance for future wheat and barley improvement programs.
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Affiliation(s)
- Yanlong Jin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Shiqiang Chen
- Lixiahe Institute of Agriculture Sciences in Jiangsu Province, Yangzhou 225007, China
| | - Xiao Xu
- Institute of Agricultural Sciences of Coastal Area Jiangsu, Yancheng 224002, China
| | - Congcong Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Zhentian He
- Lixiahe Institute of Agriculture Sciences in Jiangsu Province, Yangzhou 225007, China
| | - Huiquan Shen
- Institute of Agricultural Sciences of Coastal Area Jiangsu, Yancheng 224002, China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Ping Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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10
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Okada K, Xu W, Mishina K, Oono Y, Kato T, Namai K, Komatsuda T. Genetic resistance in barley against Japanese soil-borne wheat mosaic virus functions in the roots. FRONTIERS IN PLANT SCIENCE 2023; 14:1149752. [PMID: 36968424 PMCID: PMC10036763 DOI: 10.3389/fpls.2023.1149752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Infection by the Japanese soil-borne wheat mosaic virus (JSBWMV) can lead to substantial losses in the grain yield of barley and wheat crops. While genetically based resistance to this virus has been documented, its mechanistic basis remains obscure. In this study, the deployment of a quantitative PCR assay showed that the resistance acts directly against the virus rather than by inhibiting the colonization of the roots by the virus' fungal vector Polymyxa graminis. In the susceptible barley cultivar (cv.) Tochinoibuki, the JSBWMV titre was maintained at a high level in the roots during the period December-April, and the virus was translocated from the root to the leaf from January onwards. In contrast, in the roots of both cv. Sukai Golden and cv. Haruna Nijo, the titre was retained at a low level, and translocation of the virus to the shoot was strongly suppressed throughout the host's entire life cycle. The roots of wild barley (Hordeum vulgare ssp. spontaneum) accession H602 responded in the early stages of infection similarly to those of the resistant cultivated forms, but the host was unable to suppress the translocation of the virus to the shoot from March onwards. The virus titre in the root was presumed to have been restricted by the action of the gene product of Jmv1 (on chromosome 2H), while the stochastic nature of the infection was suppressed by the action of that of Jmv2 (on chromosome 3H), a gene harbored by cv. Sukai Golden but not by either cv. Haruna Nijo or accession H602.
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Affiliation(s)
- Kaori Okada
- Tochigi Prefectural Agricultural Experiment Station, Utsunomiya, Tochigi, Japan
| | - Wenjing Xu
- Crop Research Institute, Shandong Academy of Agricultural Sciences (SAAS), Ji’nan, Shandong, China
| | - Kohei Mishina
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Kan-non-dai, Ibaraki, Japan
| | - Youko Oono
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Kan-non-dai, Ibaraki, Japan
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
| | - Tsuneo Kato
- Tochigi Prefectural Agricultural Experiment Station, Utsunomiya, Tochigi, Japan
| | - Kiyoshi Namai
- Tochigi Prefectural Agricultural Experiment Station, Utsunomiya, Tochigi, Japan
| | - Takao Komatsuda
- Crop Research Institute, Shandong Academy of Agricultural Sciences (SAAS), Ji’nan, Shandong, China
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Kan-non-dai, Ibaraki, Japan
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
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11
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Kondo H, Sugahara H, Fujita M, Hyodo K, Andika IB, Hisano H, Suzuki N. Discovery and Genome Characterization of a Closterovirus from Wheat Plants with Yellowing Leaf Symptoms in Japan. Pathogens 2023; 12:pathogens12030358. [PMID: 36986280 PMCID: PMC10053543 DOI: 10.3390/pathogens12030358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023] Open
Abstract
Many aphid-borne viruses are important pathogens that affect wheat crops worldwide. An aphid-transmitted closterovirus named wheat yellow leaf virus (WYLV) was found to have infected wheat plants in Japan in the 1970s; however, since then, its viral genome sequence and occurrence in the field have not been investigated. We observed yellowing leaves in the 2018/2019 winter wheat-growing season in an experimental field in Japan where WYLV was detected five decades ago. A virome analysis of those yellow leaf samples lead to the discovery of a closterovirus together with a luteovirus (barley yellow dwarf virus PAV variant IIIa). The complete genomic sequence of this closterovirus, named wheat closterovirus 1 isolate WL19a (WhCV1-WL19a), consisted of 15,452 nucleotides harboring nine open reading frames. Additionally, we identified another WhCV1 isolate, WL20, in a wheat sample from the winter wheat-growing season of 2019/2020. A transmission test indicated that WhCV1-WL20 was able to form typical filamentous particles and transmissible by oat bird-cherry aphid (Rhopalosiphum pad). Sequence and phylogenetic analyses showed that WhCV1 was distantly related to members of the genus Closterovirus (family Closteroviridae), suggesting that the virus represents a novel species in the genus. Furthermore, the characterization of WhCV1-WL19a-derived small RNAs using high-throughput sequencing revealed highly abundant 22-nt-class small RNAs potentially derived from the 3′-terminal end of the WhCV1 negative-strand genomic RNA, indicating that this terminal end of the WhCV1 genome is likely particularly targeted for the synthesis of viral small RNAs in wheat plants. Our results provide further knowledge on closterovirus diversity and pathogenicity and suggest that the impact of WhCV1 on wheat production warrants further investigations.
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Affiliation(s)
- Hideki Kondo
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
- Correspondence: ; Tel./Fax: +81-(86)-434-1232
| | - Hitomi Sugahara
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Miki Fujita
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Kiwamu Hyodo
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Ida Bagus Andika
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Hiroshi Hisano
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
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12
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Hoffie RE, Perovic D, Habekuß A, Ordon F, Kumlehn J. Novel resistance to the Bymovirus BaMMV established by targeted mutagenesis of the PDIL5-1 susceptibility gene in barley. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:331-341. [PMID: 36221782 PMCID: PMC9884012 DOI: 10.1111/pbi.13948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 08/24/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
The Potyviridae are the largest family of plant-pathogenic viruses. Members of this family are the soil-borne bymoviruses barley yellow mosaic virus (BaYMV) and barley mild mosaic virus (BaMMV), which, upon infection of young winter barley seedlings in autumn, can cause yield losses as high as 50%. Resistance breeding plays a major role in coping with these pathogens. However, some viral strains have overcome the most widely used resistance. Thus, there is a need for novel sources of resistance. In ancient landraces and wild relatives of cultivated barley, alleles of the susceptibility factor PROTEIN DISULFIDE ISOMERASE LIKE 5-1 (PDIL5-1) were identified to confer resistance to all known strains of BaYMV and BaMMV. Although the gene is highly conserved throughout all eukaryotes, barley is thus far the only species for which PDIL5-1-based virus resistance has been reported. Whereas introgression by crossing to the European winter barley breeding pool is tedious, time-consuming and additionally associated with unwanted linkage drag, the present study exemplifies an approach to targeted mutagenesis of two barley cultivars employing CRISPR-associated endonuclease technology to induce site-directed mutations similar to those described for PDIL5-1 alleles that render certain landraces resistant. Homozygous primary mutants were produced in winter barley, and transgene-free homozygous M2 mutants were produced in spring barley. A variety of mutants carrying novel PDIL5-1 alleles were mechanically inoculated with BaMMV, by which all frameshift mutations and certain in-frame mutations were demonstrated to confer resistance to this virus. Under greenhouse conditions, virus-resistant mutants showed no adverse effects in terms of growth and yield.
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Affiliation(s)
- Robert Eric Hoffie
- Plant Reproductive BiologyLeibniz‐Institute of Plant Genetics and Crop Plant Research (IPK)SeelandGermany
| | - Dragan Perovic
- Institute for Resistance Research and Stress ToleranceJulius Kuehn Institute (JKI)Federal Research Centre for Cultivated PlantsQuedlinburgGermany
| | - Antje Habekuß
- Institute for Resistance Research and Stress ToleranceJulius Kuehn Institute (JKI)Federal Research Centre for Cultivated PlantsQuedlinburgGermany
| | - Frank Ordon
- Institute for Resistance Research and Stress ToleranceJulius Kuehn Institute (JKI)Federal Research Centre for Cultivated PlantsQuedlinburgGermany
| | - Jochen Kumlehn
- Plant Reproductive BiologyLeibniz‐Institute of Plant Genetics and Crop Plant Research (IPK)SeelandGermany
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13
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Wu Q, Cui Y, Jin X, Wang G, Yan L, Zhong C, Yu M, Li W, Wang Y, Wang L, Wang H, Dang C, Zhang X, Chen Y, Zhang P, Zhao X, Wu J, Fu D, Xia L, Nevo E, Vogel J, Huo N, Li D, Gu YQ, Jackson AO, Zhang Y, Liu Z. The CC-NB-LRR protein BSR1 from Brachypodium confers resistance to Barley stripe mosaic virus in gramineous plants by recognising TGB1 movement protein. THE NEW PHYTOLOGIST 2022; 236:2233-2248. [PMID: 36059081 DOI: 10.1111/nph.18457] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/21/2022] [Indexed: 06/15/2023]
Abstract
Although some nucleotide binding, leucine-rich repeat immune receptor (NLR) proteins conferring resistance to specific viruses have been identified in dicot plants, NLR proteins involved in viral resistance have not been described in monocots. We have used map-based cloning to isolate the CC-NB-LRR (CNL) Barley stripe mosaic virus (BSMV) resistance gene barley stripe resistance 1 (BSR1) from Brachypodium distachyon Bd3-1 inbred line. Stable BSR1 transgenic Brachypodium line Bd21-3, barley (Golden Promise) and wheat (Kenong 199) plants developed resistance against BSMV ND18 strain. Allelic variation analyses indicated that BSR1 is present in several Brachypodium accessions collected from countries in the Middle East. Protein domain swaps revealed that the intact LRR domain and the C-terminus of BSR1 are required for resistance. BSR1 interacts with the BSMV ND18 TGB1 protein in planta and shows temperature-sensitive antiviral resistance. The R390 and T392 residues of TGB1ND (ND18 strain) and the G196 and K197 residues within the BSR1 P-loop motif are key amino acids required for immune activation. BSR1 is the first cloned virus resistance gene encoding a typical CNL protein in monocots, highlighting the utility of the Brachypodium model for isolation and analysis of agronomically important genes for crop improvement.
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Affiliation(s)
- Qiuhong Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Science, Beijing, 100101, China
| | - Yu Cui
- Institute of Crop Sciences, Chinese Academy of Agriculture Sciences, Beijing, 100081, China
| | - Xuejiao Jin
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Guoxin Wang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Lijie Yan
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Chenchen Zhong
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Meihua Yu
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Wenli Li
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yong Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ling Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Hao Wang
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Chen Dang
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xinyu Zhang
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yongxing Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Science, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Panpan Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Science, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaofei Zhao
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jiajie Wu
- College of Agronomy, Shandong Agriculture University, Taian, 271018, China
| | - Daolin Fu
- College of Agronomy, Shandong Agriculture University, Taian, 271018, China
| | - Lanqin Xia
- Institute of Crop Sciences, Chinese Academy of Agriculture Sciences, Beijing, 100081, China
| | - Eviatar Nevo
- Institute of Evolution, Haifa University, Haifa, 31905, Israel
| | - John Vogel
- Joint Genome Institute, DOE, Walnut Creek, CA, 94598, USA
| | - Naxin Huo
- USDA-ARS Western Regional Research Center, Albany, CA, 94710, USA
| | - Dawei Li
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yong Q Gu
- USDA-ARS Western Regional Research Center, Albany, CA, 94710, USA
| | - Andrew O Jackson
- Department of Plant and Microbiology, University of California, Berkeley, CA, 94720, USA
| | - Yongliang Zhang
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhiyong Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Science, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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14
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Okada K, Tanaka T, Fukuoka S, Oono Y, Mishina K, Oikawa T, Sato K, Kato T, Komatsuda T, Namai K. Two dominant genes in barley ( Hordeum vulgare L.) complementarily encode perfect resistance to Japanese soil-borne wheat mosaic virus. BREEDING SCIENCE 2022; 72:372-382. [PMID: 36776442 PMCID: PMC9895801 DOI: 10.1270/jsbbs.22046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/17/2022] [Indexed: 06/18/2023]
Abstract
Japanese soil-borne wheat mosaic virus (Furovirus) is a damaging pathogen of wheat and barley. This virus can survive in the soil for several decades, so the deployment of resistant cultivars represents the only practical control measure. Here, a genetic analysis has identified two regions of the barley genome-one on chromosome 2H and the other on chromosome 3H-as harboring gene(s) encoding resistance to this virus. The joint presence of both loci, termed Jmv1 and Jmv2, made the plants essentially immune, with resistance being dominant over susceptibility at each locus. Phylogenetic analysis showed that the virus is not closely related to the type Furovirus species Soil-borne wheat mosaic virus. There was a difference between the RNA1- and RNA2-based phylogenies of the virus species in Furovirus implying the independent segregation of the virus subgenomes.
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Affiliation(s)
- Kaori Okada
- Tochigi Prefectural Agricultural Experiment Station, 1080 Kawaraya-cho, Utsunomiya, Tochigi 320-0002, Japan
| | - Tsuyoshi Tanaka
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Kan-non-dai, Tsukuba, Ibaraki 305-8518, Japan
| | - Shuichi Fukuoka
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Kan-non-dai, Tsukuba, Ibaraki 305-8518, Japan
| | - Youko Oono
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Kan-non-dai, Tsukuba, Ibaraki 305-8518, Japan
| | - Kohei Mishina
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Kan-non-dai, Tsukuba, Ibaraki 305-8518, Japan
| | - Tetsuo Oikawa
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Kan-non-dai, Tsukuba, Ibaraki 305-8518, Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan
| | - Tsuneo Kato
- Tochigi Prefectural Agricultural Experiment Station, 1080 Kawaraya-cho, Utsunomiya, Tochigi 320-0002, Japan
| | - Takao Komatsuda
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Kan-non-dai, Tsukuba, Ibaraki 305-8518, Japan
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8510, Japan
- Crop Research Institute, Shandong Academy of Agricultural Sciences (SAAS), 202 Gongyebei Road, Licheng District, Ji’nan, 250100 Shandong, China
| | - Kiyoshi Namai
- Tochigi Prefectural Agricultural Experiment Station, 1080 Kawaraya-cho, Utsunomiya, Tochigi 320-0002, Japan
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15
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Cheng C, Kan J, Li S, Jiang C, He X, Shen H, Xu R, Li B, Feng Z, Yang P. Mutation of barley HvPDIL5-1 improves resistance to yellow mosaic virus disease without growth or yield penalties. FRONTIERS IN PLANT SCIENCE 2022; 13:1018379. [PMID: 36275526 PMCID: PMC9583009 DOI: 10.3389/fpls.2022.1018379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 09/20/2022] [Indexed: 06/15/2023]
Abstract
The soil-borne yellow mosaic virus disease, which is caused by the bymoviruses barley yellow mosaic virus (BaYMV) and/or barley mild mosaic virus (BaMMV), seriously threatens winter barley production in Europe and East Asia. Both viruses are transmitted by the soil-borne plasmodiophorid Polymyxa graminis and are difficult to eliminate through chemical or physical measures in the field, making breeding for resistant cultivars the optimal strategy for disease control. The resistance locus rym1/11 was cloned encoding the host factor gene Protein Disulfide Isomerase Like 5-1 (PDIL5-1), whose loss-of-function variants confer broad-spectrum resistance to multiple strains of BaMMV/BaYMV. Most resistance-conferring variants have been identified in six-rowed barley landraces/historic cultivars, and their introgression into modern two-rowed malting cultivars is difficult because PDIL5-1 is located in a peri-centromeric region with suppressed recombination. In this study, we used CRISPR/Cas9 genome editing to modify PDIL5-1 in the BaYMV/BaMMV-susceptible elite malting barley cv. 'Golden Promise' and obtained the mutants pdil5-1-a and pdil5-1-b. PDIL5-1 in the pdil5-1-a mutant encodes a protein lacking a cysteine residue, and pdil5-1-b contains a protein-coding frameshift. Both mutants were completely resistant to BaYMV. The knockout mutant pdil5-1-b showed complete BaMMV resistance, while pdil5-1-a showed decreased viral accumulation but no disease symptoms if compared to 'Golden Promise'. Both PDIL5-1 edited lines, as well as the previously produced EMS-induced pdil5-1 mutant '10253-1-5' in the elite malting barley cv. 'Barke' background, displayed no growth or yield penalties in garden experiments or bymovirus-free field trials. Line '10253-1-5' showed improved resistance and yield performance compared to the wild-type and its sibling line when grown in infectious fields. Therefore, genome editing of the host factor gene PDIL5-1 could facilitate the breeding of barley varieties with resistance to bymoviruses.
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Affiliation(s)
- Chunyuan Cheng
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinhong Kan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shanshan Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Congcong Jiang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyan He
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Huiquan Shen
- Institute of Agricultural Science in Jiangsu Coastal Areas, Yancheng, China
| | - Rugen Xu
- College of Agronomy, Yangzhou University, Yangzhou, China
| | - Boqun Li
- Special Crops Institute, Chongqing Academy of Agricultural Sciences, Chongqing, China
| | - Zongyun Feng
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Ping Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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16
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Jiang C, Lei M, Luan H, Pan Y, Zhang L, Zhou S, Cai Y, Xu X, Shen H, Xu R, Feng Z, Zhang J, Yang P. Genomic and Pathogenic Diversity of Barley Yellow Mosaic Virus and Barley Mild Mosaic Virus Isolates in Fields of China and Their Compatibility with Resistance Genes of Cultivated Barley. PLANT DISEASE 2022; 106:2201-2210. [PMID: 35077235 DOI: 10.1094/pdis-11-21-2473-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Plant viruses transmitted by the soilborne plasmodiophorid Polymyxa graminis constantly threaten global production of cereal crops. Although the yellow mosaic virus disease of barley has been known to be present for a long time in China, the understanding of the diversity of the viral pathogens and their interactions with host resistance remains limited. In this study, we conducted a nationwide survey of P. graminis and the barley yellow mosaic virus (BaYMV) and barley mild mosaic virus (BaMMV) it transmits, followed by genomic and pathogenic diversity analyses of both viruses. BaYMV and BaMMV were found exclusively in the region downstream of the Yangtze River, despite the national distribution of its transmission vector P. graminis. Analysis of the genomic variations of BaYMV and BaMMV revealed an elevated rate of nonsynonymous substitutions in the viral genome-linked protein (VPg), in which most substitutions were located in its interaction surface with the host eukaryotic translation initiation factor 4E (eIF4E). VPg sequence diversity was associated with the divergence in virus pathogenicity that was identified through multiple field trials. The majority of the resistance genes, including the widely applied rym4 and rym5 (alleles of eIF4E), as well as the combination of rym1/11 and rym5, are not sufficient to protect cultivated barley against viruses in China. Collectively, these results provide insights into virulence specificity and interaction mode with host resistance in cultivated barley, which has significant implications in breeding for the broad-spectrum resistance barley varieties.
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Affiliation(s)
- Congcong Jiang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Miaomiao Lei
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Haiye Luan
- Institute of Agricultural Science in Jiangsu Coastal Areas, Yancheng 224002, China
| | - Yuhan Pan
- College of Agronomy, Yangzhou University, Yangzhou 225009, China
| | - Li Zhang
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shenghui Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yu Cai
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiao Xu
- Institute of Agricultural Science in Jiangsu Coastal Areas, Yancheng 224002, China
| | - Huiquan Shen
- Institute of Agricultural Science in Jiangsu Coastal Areas, Yancheng 224002, China
| | - Rugen Xu
- College of Agronomy, Yangzhou University, Yangzhou 225009, China
| | - Zongyun Feng
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Jing Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ping Yang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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17
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Wang Y, Habekuß A, Jayakodi M, Mascher M, Snowdon RJ, Stahl A, Fuß J, Ordon F, Perovic D. High-Resolution Mapping of Barley mild mosaic virus Resistance Gene rym15. FRONTIERS IN PLANT SCIENCE 2022; 13:908170. [PMID: 35720548 PMCID: PMC9201720 DOI: 10.3389/fpls.2022.908170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
Barley yellow mosaic virus (BaYMV) and Barley mild mosaic virus (BaMMV), which are transmitted by the soil-borne plasmodiophorid Polymyxa graminis, cause high yield losses in barley. In previous studies, the recessive BaMMV resistance gene rym15, derived from the Japanese landrace Chikurin Ibaraki 1, was mapped on chromosome 6HS of Hordeum vulgare. In this study, 423 F4 segmental recombinant inbred lines (RILs) were developed from crosses of Chikurin Ibaraki 1 with two BaMMV-susceptible cultivars, Igri (139 RILs) and Uschi (284 RILs). A set of 32 competitive allele-specific PCR (KASP) assays, designed using single nucleotide polymorphisms (SNPs) from the barley 50 K Illumina Infinium iSelect SNP chip, genotyping by sequencing (GBS) and whole-genome sequencing (WGS), was used as a backbone for construction of two high-resolution maps. Using this approach, the target locus was narrowed down to 0.161 cM and 0.036 cM in the Igri × Chikurin Ibaraki 1 (I × C) and Chikurin Ibaraki 1 × Uschi (C × U) populations, respectively. Corresponding physical intervals of 11.3 Mbp and 0.281 Mbp were calculated for I × C and C × U, respectively, according to the Morex v3 genome sequence. In the 0.281 Mbp target region, six high confidence (HC) and two low confidence (LC) genes were identified. Genome assemblies of BaMMV-susceptible cultivars Igri and Golden Promise from the barley pan-genome, and a HiFi assembly of Chikurin Ibaraki 1 together with re-sequencing data for the six HC and two LC genes in susceptible parental cultivar Uschi revealed functional SNPs between resistant and susceptible genotypes only in two of the HC genes. These SNPs are the most promising candidates for the development of functional markers and the two genes represent promising candidates for functional analysis.
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Affiliation(s)
- Yaping Wang
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kuehn-Institute (JKI), Quedlinburg, Germany
| | - Antje Habekuß
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kuehn-Institute (JKI), Quedlinburg, Germany
| | - Murukarthick Jayakodi
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Martin Mascher
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Rod J. Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Andreas Stahl
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kuehn-Institute (JKI), Quedlinburg, Germany
| | - Janina Fuß
- Institute for Clinical Molecular Biology, Competence Centre for Genomic Analysis (CCGA), Kiel University, Kiel, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kuehn-Institute (JKI), Quedlinburg, Germany
| | - Dragan Perovic
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kuehn-Institute (JKI), Quedlinburg, Germany
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Kan J, Cai Y, Cheng C, Jiang C, Jin Y, Yang P. Simultaneous editing of host factor gene TaPDIL5-1 homoeoalleles confers wheat yellow mosaic virus resistance in hexaploid wheat. THE NEW PHYTOLOGIST 2022; 234:340-344. [PMID: 35092005 DOI: 10.1111/nph.18002] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Jinhong Kan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Yu Cai
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Chunyuan Cheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Congcong Jiang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Yanlong Jin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Ping Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
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Pan Y, Zhu J, Hong Y, Zhang M, Lv C, Guo B, Shen H, Xu X, Xu R. Screening of stable resistant accessions and identification of resistance loci to Barley yellow mosaic virus disease. PeerJ 2022; 10:e13128. [PMID: 35317071 PMCID: PMC8934529 DOI: 10.7717/peerj.13128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 02/25/2022] [Indexed: 01/12/2023] Open
Abstract
Background The disease caused by Barley yellow mosaic virus (BaYMV) infection is a serious threat to autumn-sown barley (Hordeum vulgare L.) production in Europe, East Asia and Iran. Due to the rapid diversification of BaYMV strains, it is urgent to discover novel germplasm and genes to assist breeding new varieties with resistance to different BaYMV strains, thus minimizing the effect of BaYMV disease on barley cropping. Methods A natural population consisting of 181 barley accessions with different levels of resistance to BaYMV disease was selected for field resistance identification in two separate locations (Yangzhou and Yancheng, Jiangsu Province, China). Additive main effects and multiplicative interaction (AMMI) analysis was used to identify accessions with stable resistance. Genome-wide association study (GWAS) of BaYMV disease resistance was broadly performed by combining both single nucleotide polymorphisms (SNPs) and specific molecular markers associated with the reported BaYMV disease resistance genes. Furthermore, the viral protein genome linked (VPg) sequences of the virus were amplified and analyzed to assess the differences between the BaYMV strains sourced from the different experimental sites. Results Seven barley accessions with lower standardized Area Under the Disease Progress Steps (sAUDPS) index in every environment were identified and shown to have stable resistance to BaYMV disease in each assessed location. Apart from the reported BaYMV disease resistance genes rym4 and rym5, one novel resistance locus explaining 24.21% of the phenotypic variation was identified at the Yangzhou testing site, while two other novel resistance loci that contributed 19.23% and 19.79% of the phenotypic variation were identified at the Yancheng testing site, respectively. Further analysis regarding the difference in the VPg sequence of the predominant strain of BaYMV collected from these two testing sites may explain the difference of resistance loci differentially identified under geographically distinct regions. Our research provides novel genetic resources and resistance loci for breeding barley varieties for BaMYV disease resistance.
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Affiliation(s)
- Yuhan Pan
- Yangzhou University, Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Institutes of Agricultural Science, Yangzhou, Jiangsu, China
| | - Juan Zhu
- Yangzhou University, Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Institutes of Agricultural Science, Yangzhou, Jiangsu, China
| | - Yi Hong
- Yangzhou University, Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Institutes of Agricultural Science, Yangzhou, Jiangsu, China
| | - Mengna Zhang
- Yangzhou University, Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Institutes of Agricultural Science, Yangzhou, Jiangsu, China
| | - Chao Lv
- Yangzhou University, Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Institutes of Agricultural Science, Yangzhou, Jiangsu, China
| | - Baojian Guo
- Yangzhou University, Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Institutes of Agricultural Science, Yangzhou, Jiangsu, China
| | - Huiquan Shen
- Jiangsu Institute for Seaside Agricultural Sciences and Yancheng Academy of Agricultural Science, Yancheng, Jiangsu, China
| | - Xiao Xu
- Jiangsu Institute for Seaside Agricultural Sciences and Yancheng Academy of Agricultural Science, Yancheng, Jiangsu, China
| | - Rugen Xu
- Yangzhou University, Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Institutes of Agricultural Science, Yangzhou, Jiangsu, China
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20
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Zhang H, Wu C, Wang F, Wang H, Chen G, Cheng Y, Chen J, Yang J, Ge T. Wheat yellow mosaic enhances bacterial deterministic processes in a plant-soil system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 812:151430. [PMID: 34748834 DOI: 10.1016/j.scitotenv.2021.151430] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/30/2021] [Accepted: 10/31/2021] [Indexed: 06/13/2023]
Abstract
Understanding the mechanisms that govern microbial community assembly across soil-plant continuum is crucial for predicting the response of ecosystems to environmental changes. However, the impact of the health status of plant on microbial assembly across this continuum still remain poorly understood. Here, we investigated how wheat yellow mosaic (WYM), caused by the wheat mosaic virus transmitted by Polymyxa graminis, affected microbial assembly across soil (bulk soil, rhizosphere soil), and plant (roots and leaves) continuum in a winter wheat (Triticum aestivum L.) system in northern China, using null model analysis. The results showed that deterministic processes dominated the bacterial community assembly, whereas stochastic processes were primarily responsible for the assembly of the fungal communities. With increasing levels of WYM, deterministic processes were greatly enhanced for bacterial community assembly, accompanied by a decrease in community niche breadth. Intensified competition between bacteria and fungi and increased soil total nitrogen (TN) and soil organic carbon (SOC) contents were mainly responsible for the enhanced deterministic processes for bacterial community assembly. Random forest modeling indicated a strong potential of rhizosphere bacterial community assembly for predicting the pathological conditions of wheat. Structural equation modeling showed that disease level was positively correlated with SOC and TN contents, competitions between bacteria and fungi, and the contribution of variable selection processes to the bacterial community assembly in the wheat rhizosphere. Our study revealed the ecological mechanisms underlying the associations between microbial communities and soil-borne disease, and highlighted the significance of microbial community assembly for maintaining soil and plant health.
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Affiliation(s)
- Haoqing Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Chuanfa Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Fangyan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Haiting Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Guixian Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; School of Resources and Environmental Engineering, Jiangxi University of Science and Technology, Ganzhou 341000, China
| | - Ye Cheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China.
| | - Jian Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Tida Ge
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China.
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21
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Pasin F, Daròs JA, Tzanetakis IE. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6534904. [PMID: 35195244 PMCID: PMC9249622 DOI: 10.1093/femsre/fuac011] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 02/02/2022] [Accepted: 02/08/2022] [Indexed: 11/17/2022] Open
Abstract
Potyviridae, the largest family of known RNA viruses (realm Riboviria), belongs to the picorna-like supergroup and has important agricultural and ecological impacts. Potyvirid genomes are translated into polyproteins, which are in turn hydrolyzed to release mature products. Recent sequencing efforts revealed an unprecedented number of potyvirids with a rich variability in gene content and genomic layouts. Here, we review the heterogeneity of non-core modules that expand the structural and functional diversity of the potyvirid proteomes. We provide a family-wide classification of P1 proteinases into the functional Types A and B, and discuss pretty interesting sweet potato potyviral ORF (PISPO), putative zinc fingers, and alkylation B (AlkB)—non-core modules found within P1 cistrons. The atypical inosine triphosphate pyrophosphatase (ITPase/HAM1), as well as the pseudo tobacco mosaic virus-like coat protein (TMV-like CP) are discussed alongside homologs of unrelated virus taxa. Family-wide abundance of the multitasking helper component proteinase (HC-pro) is revised. Functional connections between non-core modules are highlighted to support host niche adaptation and immune evasion as main drivers of the Potyviridae evolutionary radiation. Potential biotechnological and synthetic biology applications of potyvirid leader proteinases and non-core modules are finally explored.
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Affiliation(s)
- Fabio Pasin
- Corresponding author: Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València (CSIC-UPV), UPV Building 8E, Ingeniero Fausto Elio, 46011 Valencia, Spain. E-mail:
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València (CSIC-UPV), 46011 Valencia, Spain
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, 72701 Fayetteville, AR, USA
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22
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Hoffie RE, Otto I, Perovic D, Budhagatapalli N, Habekuß A, Ordon F, Kumlehn J. Targeted Knockout of Eukaryotic Translation Initiation Factor 4E Confers Bymovirus Resistance in Winter Barley. Front Genome Ed 2021; 3:784233. [PMID: 34913048 PMCID: PMC8667817 DOI: 10.3389/fgeed.2021.784233] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/04/2021] [Indexed: 12/03/2022] Open
Abstract
The Eukaryotic Translation Initiation Factor 4E (EIF4E) is a well-known susceptibility factor for potyvirus infections in many plant species. The barley yellow mosaic virus disease, caused by the bymoviruses Barley yellow mosaic virus (BaYMV) and Barley mild mosaic virus (BaMMV), can lead to yield losses of up to 50% in winter barley. In autumn, the roots of young barley plants are infected by the soil-borne plasmodiophoraceous parasite Polymyxa graminis L. that serves as viral vector. Upon viral establishment and systemic spreading into the upper parts of the plants, yellow mosaics occur as first symptoms on leaves. In the further course of plant development, the disease entails leaf necrosis and increased susceptibility to frost damage. Thanks to the rym4 and rym5 allelic variants of the HvEIF4E gene, more than two thirds of current European winter barley cultivars are resistant to BaYMV and BaMMV. However, several strains of BaYMV and BaMMV have already overcome rym4- and rym5-mediated resistance. Accordingly, new resistance-conferring alleles are needed for barley breeding. Therefore, we performed targeted mutagenesis of the EIF4E gene by Cas9 endonuclease in BaMMV/BaYMV-susceptible winter barley cv. “Igri”. Small insertions were generated, resulting in a shift of the translational reading frame, thereby causing the loss-of-function of EIF4E. The mutations occurred in the homozygous state already in the primary mutants. Their progeny proved invariably homozygous and fully resistant to mechanical inoculation with BaMMV. EIF4E knockout plants showed normal growth habit and produced grains, yet exhibited a yield penalty.
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Affiliation(s)
- Robert Eric Hoffie
- Plant Reproductive Biology, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Ingrid Otto
- Plant Reproductive Biology, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Dragan Perovic
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn Institute (JKI), Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
| | - Nagaveni Budhagatapalli
- Plant Reproductive Biology, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Antje Habekuß
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn Institute (JKI), Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn Institute (JKI), Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
| | - Jochen Kumlehn
- Plant Reproductive Biology, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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23
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Wang Y, Habekuß A, Snowdon RJ, Ordon F, Perovic D. Delineating the elusive BaMMV resistance gene rym15 in barley by medium-resolution mapping. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:76. [PMID: 37309517 PMCID: PMC10236098 DOI: 10.1007/s11032-021-01270-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 11/23/2021] [Indexed: 06/14/2023]
Abstract
Barley mild mosaic virus (BaMMV), transmitted by the soil-borne protist Polymyxa graminis, has a serious impact on winter barley production. Previously, the BaMMV resistance gene rym15 was mapped on chromosome 6HS, but the order of flanking markers was non-collinear between different maps. To resolve the position of the flanking markers and to enable map-based cloning of rym15, two medium-resolution mapping populations Igri (susceptible) × Chikurin Ibaraki 1 (resistant) (I × C) and Chikurin Ibaraki 1 × Uschi (susceptible) (C × U), consisting of 342 and 180 F2 plants, respectively, were developed. Efficiency of the mechanical inoculation of susceptible standards varied from 87.5 to 100% and in F2 populations from 90.56 to 93.23%. Phenotyping of F2 plants and corresponding F3 families revealed segregation ratios of 250 s:92r (I × C, χ2 = 0.659) and 140 s:40r (C × U, χ2 = 0.741), suggesting the presence of a single recessive resistance gene. After screening the parents with the 50 K Infinium chip and anchoring corresponding SNPs to the barley reference genome, 8 KASP assays were developed and used to remap the gene. Newly constructed maps revealed a collinear order of markers, thereby allowing the identification of high throughput flanking markers. This study demonstrates how construction of medium-resolution mapping populations in combination with robust phenotyping can efficiently resolve conflicting marker ordering and reduce the size of the target interval. In the reference genome era and genome-wide genotyping era, medium-resolution mapping will help accelerate candidate gene identification for traits where phenotyping is difficult. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01270-9.
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Affiliation(s)
- Yaping Wang
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kuehn-Institute, Erwin-Baur-Strasse 27, 06484 Quedlinburg, Germany
| | - Antje Habekuß
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kuehn-Institute, Erwin-Baur-Strasse 27, 06484 Quedlinburg, Germany
| | - Rod J. Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kuehn-Institute, Erwin-Baur-Strasse 27, 06484 Quedlinburg, Germany
| | - Dragan Perovic
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kuehn-Institute, Erwin-Baur-Strasse 27, 06484 Quedlinburg, Germany
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Zhang H, Zhang X, Zhao J, Sun L, Wang H, Zhu Y, Xiao J, Wang X. Genome-Wide Identification of GDSL-Type Esterase/Lipase Gene Family in Dasypyrum villosum L. Reveals That DvGELP53 Is Related to BSMV Infection. Int J Mol Sci 2021; 22:ijms222212317. [PMID: 34830200 PMCID: PMC8624868 DOI: 10.3390/ijms222212317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 12/21/2022] Open
Abstract
GDSL-type esterase/lipase proteins (GELPs) characterized by a conserved GDSL motif at their N-terminus belong to the lipid hydrolysis enzyme superfamily. In plants, GELPs play an important role in plant growth, development and stress response. The studies of the identification and characterization of the GELP gene family in Triticeae have not been reported. In this study, 193 DvGELPs were identified in Dasypyrum villosum and classified into 11 groups (clade A–K) by means of phylogenetic analysis. Most DvGELPs contain only one GDSL domain, only four DvGELPs contain other domains besides the GDSL domain. Gene structure analysis indicated 35.2% DvGELP genes have four introns and five exons. In the promoter regions of the identified DvGELPs, we detected 4502 putative cis-elements, which were associated with plant hormones, plant growth, environmental stress and light responsiveness. Expression profiling revealed 36, 44 and 17 DvGELPs were highly expressed in the spike, the root and the grain, respectively. Further investigation of a root-specific expressing GELP, DvGELP53, indicated it was induced by a variety of biotic and abiotic stresses. The knockdown of DvGELP53 inhibited long-distance movement of BSMV in the tissue of D. villosum. This research provides a genome-wide glimpse of the D. villosum GELP genes and hints at the participation of DvGELP53 in the interaction between virus and plants.
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Affiliation(s)
- Heng Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to The Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (H.Z.); (Y.Z.)
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China; (X.Z.); (L.S.); (H.W.); (J.X.)
| | - Xu Zhang
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China; (X.Z.); (L.S.); (H.W.); (J.X.)
| | - Jia Zhao
- College of Agriculture, South China Agriculture University, Guangzhou 510642, China;
| | - Li Sun
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China; (X.Z.); (L.S.); (H.W.); (J.X.)
| | - Haiyan Wang
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China; (X.Z.); (L.S.); (H.W.); (J.X.)
| | - Ying Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to The Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (H.Z.); (Y.Z.)
| | - Jin Xiao
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China; (X.Z.); (L.S.); (H.W.); (J.X.)
| | - Xiue Wang
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China; (X.Z.); (L.S.); (H.W.); (J.X.)
- Correspondence: ; Tel.: +86-25-84395308
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25
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Tanokami M, Wang WQ, Yamamoto M, Hagiwara T, Yumoto M, Tomiyama A, Mine S, Tamura Y, Kobayashi S, Nakazawa Y, Kato T, Natsuaki T, Nishigawa H. Utility of a GFP-expressing Barley yellow mosaic virus for analyzing disease resistance genes. BREEDING SCIENCE 2021; 71:484-490. [PMID: 34912175 PMCID: PMC8661491 DOI: 10.1270/jsbbs.21017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 07/02/2021] [Indexed: 05/03/2023]
Abstract
The soil-borne plasmodiophorid Polymyxa graminis is a vector for Barley yellow mosaic virus (BaYMV), which can severely damage barley plants. Although 22 disease resistance genes have been identified, only a few have been used for breeding virus-resistant cultivars. Recently, BaYMV strains capable of overcoming the effects of some of these genes have been detected. In this study, green fluorescent protein (GFP)-expressing BaYMV was constructed and used to examine viral dynamics in inoculated barley plants. Leaf inoculations resulted in higher infection rates than root or crown inoculations. Additionally, inoculations of some resistant cultivars produced infections that were similar to those observed in a field test. The results of this study indicate that the GFP-expressing virus is a useful tool for visualizing virus replication and dynamics, and for understanding resistance mechanisms.
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Affiliation(s)
- Mai Tanokami
- Tochigi Prefectural Agricultural Experiment Station, Kawaraya-cho 1080, Utsunomiya, Tochigi 320-0002, Japan
| | - Wei Qin Wang
- School of Agriculture, Utsunomiya University, Mine-machi 350, Utsunomiya, Tochigi 321-8505, Japan
| | - Meimi Yamamoto
- School of Agriculture, Utsunomiya University, Mine-machi 350, Utsunomiya, Tochigi 321-8505, Japan
| | - Tomomi Hagiwara
- School of Agriculture, Utsunomiya University, Mine-machi 350, Utsunomiya, Tochigi 321-8505, Japan
| | - Mari Yumoto
- School of Agriculture, Utsunomiya University, Mine-machi 350, Utsunomiya, Tochigi 321-8505, Japan
| | - Aika Tomiyama
- School of Agriculture, Utsunomiya University, Mine-machi 350, Utsunomiya, Tochigi 321-8505, Japan
| | - Satoru Mine
- School of Agriculture, Utsunomiya University, Mine-machi 350, Utsunomiya, Tochigi 321-8505, Japan
| | - Yukiko Tamura
- Tochigi Prefectural Agricultural Experiment Station, Kawaraya-cho 1080, Utsunomiya, Tochigi 320-0002, Japan
| | - Shunichi Kobayashi
- Tochigi Prefectural Agricultural Experiment Station, Kawaraya-cho 1080, Utsunomiya, Tochigi 320-0002, Japan
| | - Yoshiko Nakazawa
- Tochigi Prefectural Agricultural Experiment Station, Kawaraya-cho 1080, Utsunomiya, Tochigi 320-0002, Japan
| | - Tsuneo Kato
- Tochigi Prefectural Agricultural Experiment Station, Kawaraya-cho 1080, Utsunomiya, Tochigi 320-0002, Japan
| | - Tomohide Natsuaki
- School of Agriculture, Utsunomiya University, Mine-machi 350, Utsunomiya, Tochigi 321-8505, Japan
| | - Hisashi Nishigawa
- School of Agriculture, Utsunomiya University, Mine-machi 350, Utsunomiya, Tochigi 321-8505, Japan
- Corresponding author (e-mail: )
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26
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Kondo H, Yoshida N, Fujita M, Maruyama K, Hyodo K, Hisano H, Tamada T, Andika IB, Suzuki N. Identification of a Novel Quinvirus in the Family Betaflexiviridae That Infects Winter Wheat. Front Microbiol 2021; 12:715545. [PMID: 34489904 PMCID: PMC8417474 DOI: 10.3389/fmicb.2021.715545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/14/2021] [Indexed: 11/13/2022] Open
Abstract
Yellow mosaic disease in winter wheat is usually attributed to the infection by bymoviruses or furoviruses; however, there is still limited information on whether other viral agents are also associated with this disease. To investigate the wheat viromes associated with yellow mosaic disease, we carried out de novo RNA sequencing (RNA-seq) analyses of symptomatic and asymptomatic wheat-leaf samples obtained from a field in Hokkaido, Japan, in 2018 and 2019. The analyses revealed the infection by a novel betaflexivirus, which tentatively named wheat virus Q (WVQ), together with wheat yellow mosaic virus (WYMV, a bymovirus) and northern cereal mosaic virus (a cytorhabdovirus). Basic local alignment search tool (BLAST) analyses showed that the WVQ strains (of which there are at least three) were related to the members of the genus Foveavirus in the subfamily Quinvirinae (family Betaflexiviridae). In the phylogenetic tree, they form a clade distant from that of the foveaviruses, suggesting that WVQ is a member of a novel genus in the Quinvirinae. Laboratory tests confirmed that WVQ, like WYMV, is potentially transmitted through the soil to wheat plants. WVQ was also found to infect rye plants grown in the same field. Moreover, WVQ-derived small interfering RNAs accumulated in the infected wheat plants, indicating that WVQ infection induces antiviral RNA silencing responses. Given its common coexistence with WYMV, the impact of WVQ infection on yellow mosaic disease in the field warrants detailed investigation.
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Affiliation(s)
- Hideki Kondo
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
| | - Naoto Yoshida
- Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Japan
| | - Miki Fujita
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
| | - Kazuyuki Maruyama
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
| | - Kiwamu Hyodo
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
| | - Hiroshi Hisano
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
| | - Tetsuo Tamada
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
- Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Japan
| | - Ida Bagus Andika
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
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27
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Hahn F, Sanjurjo Loures L, Sparks CA, Kanyuka K, Nekrasov V. Efficient CRISPR/Cas-Mediated Targeted Mutagenesis in Spring and Winter Wheat Varieties. PLANTS (BASEL, SWITZERLAND) 2021; 10:1481. [PMID: 34371684 PMCID: PMC8309376 DOI: 10.3390/plants10071481] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 11/16/2022]
Abstract
CRISPR/Cas technology has recently become the molecular tool of choice for gene function studies in plants as well as crop improvement. Wheat is a globally important staple crop with a well annotated genome and there is plenty of scope for improving its agriculturally important traits using genome editing technologies, such as CRISPR/Cas. As part of this study we targeted three different genes in hexaploid wheat Triticum aestivum: TaBAK1-2 in the spring cultivar Cadenza as well as Ta-eIF4E and Ta-eIF(iso)4E in winter cultivars Cezanne, Goncourt and Prevert. Primary transgenic lines carrying CRISPR/Cas-induced indels were successfully generated for all targeted genes. While BAK1 is an important regulator of plant immunity and development, Ta-eIF4E and Ta-eIF(iso)4E act as susceptibility (S) factors required for plant viruses from the Potyviridae family to complete their life cycle. We anticipate the resultant homozygous tabak1-2 mutant lines will facilitate studies on the involvement of BAK1 in immune responses in wheat, while ta-eif4e and ta-eif(iso)4e mutant lines have the potential to become a source of resistance to wheat spindle streak mosaic virus (WSSMV) and wheat yellow mosaic virus (WYMV), both of which are important pathogens of wheat. As winter wheat varieties are generally less amenable to genetic transformation, the successful experimental methodology for transformation and genome editing in winter wheat presented in this study will be of interest to the research community working with this crop.
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Affiliation(s)
- Florian Hahn
- Plant Sciences Department, Rothamsted Research, Harpenden AL5 2JQ, UK; (F.H.); (L.S.L.); (C.A.S.)
| | - Laura Sanjurjo Loures
- Plant Sciences Department, Rothamsted Research, Harpenden AL5 2JQ, UK; (F.H.); (L.S.L.); (C.A.S.)
| | - Caroline A. Sparks
- Plant Sciences Department, Rothamsted Research, Harpenden AL5 2JQ, UK; (F.H.); (L.S.L.); (C.A.S.)
| | - Kostya Kanyuka
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden AL5 2JQ, UK;
| | - Vladimir Nekrasov
- Plant Sciences Department, Rothamsted Research, Harpenden AL5 2JQ, UK; (F.H.); (L.S.L.); (C.A.S.)
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28
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Gonzalez MY, Zhao Y, Jiang Y, Stein N, Habekuss A, Reif JC, Schulthess AW. Genomic prediction models trained with historical records enable populating the German ex situ genebank bio-digital resource center of barley (Hordeum sp.) with information on resistances to soilborne barley mosaic viruses. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2181-2196. [PMID: 33768281 PMCID: PMC8263548 DOI: 10.1007/s00122-021-03815-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/10/2021] [Indexed: 05/04/2023]
Abstract
Genomic prediction with special weight of major genes is a valuable tool to populate bio-digital resource centers. Phenotypic information of crop genetic resources is a prerequisite for an informed selection that aims to broaden the genetic base of the elite breeding pools. We investigated the potential of genomic prediction based on historical screening data of plant responses against the Barley yellow mosaic viruses for populating the bio-digital resource center of barley. Our study includes dense marker data for 3838 accessions of winter barley, and historical screening data of 1751 accessions for Barley yellow mosaic virus (BaYMV) and of 1771 accessions for Barley mild mosaic virus (BaMMV). Linear mixed models were fitted by considering combinations for the effects of genotypes, years, and locations. The best linear unbiased estimations displayed a broad spectrum of plant responses against BaYMV and BaMMV. Prediction abilities, computed as correlations between predictions and observed phenotypes of accessions, were low for the marker-assisted selection approach amounting to 0.42. In contrast, prediction abilities of genomic best linear unbiased predictions were high, with values of 0.62 for BaYMV and 0.64 for BaMMV. Prediction abilities of genomic prediction were improved by up to ~ 5% using W-BLUP, in which more weight is given to markers with significant major effects found by association mapping. Our results outline the utility of historical screening data and W-BLUP model to predict the performance of the non-phenotyped individuals in genebank collections. The presented strategy can be considered as part of the different approaches used in genebank genomics to valorize genetic resources for their usage in disease resistance breeding and research.
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Affiliation(s)
- Maria Y Gonzalez
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Yong Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
- Department of Crop Sciences, Center for Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Antje Habekuss
- Julius Kühn Institute (Federal Research Centre for Cultivated Plants), Quedlinburg, Germany
| | - Jochen C Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany.
| | - Albert W Schulthess
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
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29
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Pidon H, Wendler N, Habekuβ A, Maasberg A, Ruge-Wehling B, Perovic D, Ordon F, Stein N. High-resolution mapping of Rym14 Hb, a wild relative resistance gene to barley yellow mosaic disease. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:823-833. [PMID: 33263784 PMCID: PMC7925471 DOI: 10.1007/s00122-020-03733-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/18/2020] [Indexed: 05/11/2023]
Abstract
We mapped the Rym14Hb resistance locus to barley yellow mosaic disease in a 2Mbp interval. The co-segregating markers will be instrumental for marker-assisted selection in barley breeding. Barley yellow mosaic disease is caused by Barley yellow mosaic virus and Barley mild mosaic virus and leads to severe yield losses in barley (Hordeum vulgare) in Central Europe and East-Asia. Several resistance loci are used in barley breeding. However, cases of resistance-breaking viral strains are known, raising concerns about the durability of those genes. Rym14Hb is a dominant major resistance gene on chromosome 6HS, originating from barley's secondary genepool wild relative Hordeum bulbosum. As such, the resistance mechanism may represent a case of non-host resistance, which could enhance its durability. A susceptible barley variety and a resistant H. bulbosum introgression line were crossed to produce a large F2 mapping population (n = 7500), to compensate for a ten-fold reduction in recombination rate compared to intraspecific barley crosses. After high-throughput genotyping, the Rym14Hb locus was assigned to a 2Mbp telomeric interval on chromosome 6HS. The co-segregating markers developed in this study can be used for marker-assisted introgression of this locus into barley elite germplasm with a minimum of linkage drag.
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Affiliation(s)
- Hélène Pidon
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Seeland, Germany.
| | - Neele Wendler
- KWS SAAT SE & Co. KGaA, Grimsehlstr. 31, 37574, Einbeck, Germany
| | - Antje Habekuβ
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (JKI), Erwin-Baur-Straße 27, 06484, Quedlinburg, Germany
| | - Anja Maasberg
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Straße 5, 29303, Bergen, Germany
| | - Brigitte Ruge-Wehling
- Institute for Breeding Research On Agricultural Crops, Julius Kühn Institute (JKI), Groß Lüsewitz, Rudolf-Schick-Platz 3a, 18190, Sanitz, Germany
| | - Dragan Perovic
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (JKI), Erwin-Baur-Straße 27, 06484, Quedlinburg, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (JKI), Erwin-Baur-Straße 27, 06484, Quedlinburg, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Seeland, Germany.
- Center for Integrated Breeding Research (CiBreed), Georg-August University, Von Siebold Straße 8, 37075, Göttingen, Germany.
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30
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Okada K, Kato T, Oikawa T, Komatsuda T, Namai K. A genetic analysis of the resistance in barley to Soil-borne wheat mosaic virus. BREEDING SCIENCE 2020; 70:617-622. [PMID: 33603558 PMCID: PMC7878938 DOI: 10.1270/jsbbs.20071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/13/2020] [Indexed: 06/12/2023]
Abstract
Soil-borne wheat mosaic virus (SBWMV), a ubiquitous pathogen commonly encountered in temperate regions of the Northern hemisphere, can damage a number of economically important cereal crops, notably wheat and barley. Given that the plasmodiophorid cercozoan Polymyxa graminis, which acts as the vector of SBWMV, can survive in the soil for many decades, the only feasible control measure is the deployment of resistant cultivars. Here, a quantitative trait locus (QTL) approach was taken to characterize the genetic basis of the SBWMV resistance exhibited by the barley cultivar Haruna Nijo. The analysis revealed that between 33% and 41% of the variation for the measure chosen to represent resistance was under the control of a gene(s) mapping to a region at the distal end of the short arm of chromosome 2H. In contrast to most of the genes known to encode resistance to soil-borne mosaic viruses, the allele specifying resistance was dominant over those present in a susceptible genotype.
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Affiliation(s)
- Kaori Okada
- Tochigi Prefectural Agricultural Experiment Station, Utsunomiya, Tochigi 320-0002, Japan
| | - Tsuneo Kato
- Tochigi Prefectural Agricultural Experiment Station, Utsunomiya, Tochigi 320-0002, Japan
| | - Tetsuo Oikawa
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8518, Japan
| | - Takao Komatsuda
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8518, Japan
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8510, Japan
| | - Kiyoshi Namai
- Tochigi Prefectural Agricultural Experiment Station, Utsunomiya, Tochigi 320-0002, Japan
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31
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Zhang Q, Xu M, Xia X, Komatsuda T, Varshney RK, Shi K. Crop genetics research in Asia: improving food security and nutrition. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1339-1344. [PMID: 32306095 DOI: 10.1007/s00122-020-03597-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Affiliation(s)
- Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Mingliang Xu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xianchun Xia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Takao Komatsuda
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502324, India
| | - Kai Shi
- Department of Horticulture, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
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