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Kumar S, Singh A, Bist CMS, Sharma M. Advancements in genetic techniques and functional genomics for enhancing crop traits and agricultural sustainability. Brief Funct Genomics 2024; 23:607-623. [PMID: 38679487 DOI: 10.1093/bfgp/elae017] [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: 02/08/2024] [Revised: 04/03/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
Genetic variability is essential for the development of new crop varieties with economically beneficial traits. The traits can be inherited from wild relatives or induced through mutagenesis. Novel genetic elements can then be identified and new gene functions can be predicted. In this study, forward and reverse genetics approaches were described, in addition to their applications in modern crop improvement programs and functional genomics. By using heritable phenotypes and linked genetic markers, forward genetics searches for genes by using traditional genetic mapping and allele frequency estimation. Despite recent advances in sequencing technology, omics and computation, genetic redundancy remains a major challenge in forward genetics. By analyzing close-related genes, we will be able to dissect their functional redundancy and predict possible traits and gene activity patterns. In addition to these predictions, sophisticated reverse gene editing tools can be used to verify them, including TILLING, targeted insertional mutagenesis, gene silencing, gene targeting and genome editing. By using gene knock-down, knock-up and knock-out strategies, these tools are able to detect genetic changes in cells. In addition, epigenome analysis and editing enable the development of novel traits in existing crop cultivars without affecting their genetic makeup by increasing epiallelic variants. Our understanding of gene functions and molecular dynamics of various biological phenomena has been revised by all of these findings. The study also identifies novel genetic targets in crop species to improve yields and stress tolerances through conventional and non-conventional methods. In this article, genetic techniques and functional genomics are specifically discussed and assessed for their potential in crop improvement.
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Affiliation(s)
- Surender Kumar
- Department of Biotechnology, College of Horticulture, Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan-173230, Himachal Pradesh, India
| | - Anupama Singh
- Department of Biotechnology, College of Horticulture, Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan-173230, Himachal Pradesh, India
| | - Chander Mohan Singh Bist
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla-171001, Himachal Pradesh, India
| | - Munish Sharma
- Department of Plant Sciences, Central University of Himachal Pradesh, Dharamshala-176215, Himachal Pradesh, India
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2
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Ouyang H, Sun G, Li K, Wang R, Lv X, Zhang Z, Zhao R, Wang Y, Shu H, Jiang H, Zhang S, Wu J, Zhang Q, Chen X, Liu T, Ye W, Wang Y, Wang Y. Profiling of Phakopsora pachyrhizi transcriptome revealed co-expressed virulence effectors as prospective RNA interference targets for soybean rust management. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 39225562 DOI: 10.1111/jipb.13772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024]
Abstract
Soybean rust (SBR), caused by an obligate biotrophic pathogen Phakopsora pachyrhizi, is a devastating disease of soybean worldwide. However, the mechanisms underlying plant invasion by P. pachyrhizi are poorly understood, which hinders the development of effective control strategies for SBR. Here we performed detailed histological characterization on the infection cycle of P. pachyrhizi in soybean and conducted a high-resolution transcriptional dissection of P. pachyrhizi during infection. This revealed P. pachyrhizi infection leads to significant changes in gene expression with 10 co-expressed gene modules, representing dramatic transcriptional shifts in metabolism and signal transduction during different stages throughout the infection cycle. Numerous genes encoding secreted protein are biphasic expressed, and are capable of inhibiting programmed cell death triggered by microbial effectors. Notably, three co-expressed P. pachyrhizi apoplastic effectors (PpAE1, PpAE2, and PpAE3) were found to suppress plant immune responses and were essential for P. pachyrhizi infection. Double-stranded RNA coupled with nanomaterials significantly inhibited SBR infection by targeting PpAE1, PpAE2, and PpAE3, and provided long-lasting protection to soybean against P. pachyrhizi. Together, this study revealed prominent changes in gene expression associated with SBR and identified P. pachyrhizi virulence effectors as promising targets of RNA interference-based soybean protection strategy against SBR.
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Affiliation(s)
- Haibing Ouyang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory (ZBBL), Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, 210095, China
| | - Guangzheng Sun
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory (ZBBL), Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, 210095, China
| | - Kainan Li
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory (ZBBL), Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, 210095, China
| | - Rui Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory (ZBBL), Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoyu Lv
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory (ZBBL), Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhichao Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory (ZBBL), Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, 210095, China
| | - Rong Zhao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory (ZBBL), Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haidong Shu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory (ZBBL), Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, 210095, China
| | - Haibin Jiang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory (ZBBL), Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, 210095, China
| | - Sicong Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory (ZBBL), Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinbin Wu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory (ZBBL), Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, 210095, China
| | - Qi Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory (ZBBL), Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, 210095, China
| | - Xi Chen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory (ZBBL), Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, 210095, China
| | - Tengfei Liu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory (ZBBL), Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory (ZBBL), Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, 210095, China
| | - Yan Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory (ZBBL), Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory (ZBBL), Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, 210095, China
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3
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Aoyagi LN, Ferreira EGC, da Silva DCG, Dos Santos AB, Avelino BB, Lopes-Caitar VS, de Oliveira MF, Abdelnoor RV, de Souto ER, Arias CA, Belzile F, Marcelino-Guimarães FC. Allelic variability in the Rpp1 locus conferring resistance to Asian soybean rust revealed by genome-wide association. BMC PLANT BIOLOGY 2024; 24:743. [PMID: 39095733 PMCID: PMC11297723 DOI: 10.1186/s12870-024-05454-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024]
Abstract
Soybean is a crucial crop for the Brazilian economy, but it faces challenges from the biotrophic fungus Phakopsora pachyrhizi, which causes Asian Soybean Rust (ASR). In this study, we aimed to identify SNPs associated with resistance within the Rpp1 locus, which is effective against Brazilian ASR populations. We employed GWAS and re-sequencing analyzes to pinpoint SNP markers capable of differentiating between soybean accessions harboring the Rpp1, Rpp1-b and other alternative alleles in the Rpp1 locus and from susceptible soybean cultivars. Seven SNP markers were found to be associated with ASR resistance through GWAS, with three of them defining haplotypes that efficiently distinguished the accessions based on their ASR resistance and source of the Rpp gene. These haplotypes were subsequently validated using a bi-parental population and a diverse set of Rpp sources, demonstrating that the GWAS markers co-segregate with ASR resistance. We then examined the presence of these haplotypes in a diverse set of soybean genomes worldwide, finding a few new potential sources of Rpp1/Rpp1-b. Further genomic sequence analysis revealed nucleotide differences within the genes present in the Rpp1 locus, including the ULP1-NBS-LRR genes, which are potential R gene candidates. These results provide valuable insights into ASR resistance in soybean, thus helping the development of resistant soybean varieties through genetic breeding programs.
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Affiliation(s)
- Luciano Nobuhiro Aoyagi
- National Agriculture and Food Research Organization (NARO), 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604, Japan
- Maringá State University (UEM), Colombo Avenue, No. 5790, Maringá, PR, Brazil
| | | | - Danielle C Gregorio da Silva
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Carlos João Strass Road, Warta County, Londrina, PR, Brazil
| | - Adriana Brombini Dos Santos
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Carlos João Strass Road, Warta County, Londrina, PR, Brazil
| | - Bruna Barbosa Avelino
- Department of Computer Science, Federal University of Technology of Paraná (UTFPR), Paraná, Brazil
| | | | - Marcelo Fernandes de Oliveira
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Carlos João Strass Road, Warta County, Londrina, PR, Brazil
| | - Ricardo V Abdelnoor
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Carlos João Strass Road, Warta County, Londrina, PR, Brazil
| | | | - Carlos Arrabal Arias
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Carlos João Strass Road, Warta County, Londrina, PR, Brazil
| | - François Belzile
- Department of Plant Sciences and Institute of Integrative Biology and Systems (IBIS), Université Laval, Quebec City, Quebec, G1V 0A6, Canada
| | - Francismar C Marcelino-Guimarães
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Carlos João Strass Road, Warta County, Londrina, PR, Brazil.
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4
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Rodrigues JCM, Carrijo J, Anjos RM, Cunha NB, Grynberg P, Aragão FJL, Vianna GR. The role of microRNAs in NBS-LRR gene expression and its implications for plant immunity and crop development. Transgenic Res 2024; 33:159-174. [PMID: 38856866 DOI: 10.1007/s11248-024-00387-9] [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: 12/01/2023] [Accepted: 05/15/2024] [Indexed: 06/11/2024]
Abstract
Plants evolved, over millions of years, complex defense systems against pathogens. Once infected, the interaction between pathogen effector molecules and host receptors triggers plant immune responses, which include apoptosis, systemic immune response, among others. An important protein family responsible for pathogen effector recognition is the nucleotide binding site-leucine repeat rich (NBS-LRR) proteins. The NBS-LRR gene family is the largest disease resistance gene class in plants. These proteins are widely distributed in vascular plants and have a complex multigenic cluster distribution in plant genomes. To counteract the genetic load of such a large gene family on fitness cost, plants evolved a mechanism using post transcriptional gene silencing induced by small RNAs, particularly microRNAs. For the NBS-LRR gene family, the small RNAs involved in this silencing mechanism are mainly the microRNA482/2118 superfamily. This suppression mechanism is relieved upon pathogen infection, thus allowing increased NBS-LRR expression and triggering plant immunity. In this review, we will discuss the biogenesis of microRNAs and secondary RNAs involved in this silencing mechanism, biochemical and structural features of NBS-LRR proteins in response to pathogen effectors and the evolution of microRNA-based silencing mechanism with a focus on the miR482/2118 family. Furthermore, the biotechnological manipulation of microRNA expression, using both transgenic or genome editing approaches to improve cultivated plants will be discussed, with a focus on the miR482/2118 family in soybean.
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Affiliation(s)
- J C M Rodrigues
- Embrapa Genetic Resources and Biotechnology, Brasília, Brazil.
| | - J Carrijo
- Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
| | - R M Anjos
- University of Brasília, Brasília, Brazil
| | - N B Cunha
- University of Brasília, Brasília, Brazil
| | - P Grynberg
- Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
| | - F J L Aragão
- Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
| | - G R Vianna
- Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
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5
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Bhunjun C, Chen Y, Phukhamsakda C, Boekhout T, Groenewald J, McKenzie E, Francisco E, Frisvad J, Groenewald M, Hurdeal VG, Luangsa-ard J, Perrone G, Visagie C, Bai F, Błaszkowski J, Braun U, de Souza F, de Queiroz M, Dutta A, Gonkhom D, Goto B, Guarnaccia V, Hagen F, Houbraken J, Lachance M, Li J, Luo K, Magurno F, Mongkolsamrit S, Robert V, Roy N, Tibpromma S, Wanasinghe D, Wang D, Wei D, Zhao C, Aiphuk W, Ajayi-Oyetunde O, Arantes T, Araujo J, Begerow D, Bakhshi M, Barbosa R, Behrens F, Bensch K, Bezerra J, Bilański P, Bradley C, Bubner B, Burgess T, Buyck B, Čadež N, Cai L, Calaça F, Campbell L, Chaverri P, Chen Y, Chethana K, Coetzee B, Costa M, Chen Q, Custódio F, Dai Y, Damm U, Santiago A, De Miccolis Angelini R, Dijksterhuis J, Dissanayake A, Doilom M, Dong W, Álvarez-Duarte E, Fischer M, Gajanayake A, Gené J, Gomdola D, Gomes A, Hausner G, He M, Hou L, Iturrieta-González I, Jami F, Jankowiak R, Jayawardena R, Kandemir H, Kiss L, Kobmoo N, Kowalski T, Landi L, Lin C, Liu J, Liu X, Loizides M, Luangharn T, Maharachchikumbura S, Mkhwanazi GM, Manawasinghe I, Marin-Felix Y, McTaggart A, Moreau P, Morozova O, Mostert L, Osiewacz H, Pem D, Phookamsak R, Pollastro S, Pordel A, Poyntner C, Phillips A, Phonemany M, Promputtha I, Rathnayaka A, Rodrigues A, Romanazzi G, Rothmann L, Salgado-Salazar C, Sandoval-Denis M, Saupe S, Scholler M, Scott P, Shivas R, Silar P, Silva-Filho A, Souza-Motta C, Spies C, Stchigel A, Sterflinger K, Summerbell R, Svetasheva T, Takamatsu S, Theelen B, Theodoro R, Thines M, Thongklang N, Torres R, Turchetti B, van den Brule T, Wang X, Wartchow F, Welti S, Wijesinghe S, Wu F, Xu R, Yang Z, Yilmaz N, Yurkov A, Zhao L, Zhao R, Zhou N, Hyde K, Crous P. What are the 100 most cited fungal genera? Stud Mycol 2024; 108:1-411. [PMID: 39100921 PMCID: PMC11293126 DOI: 10.3114/sim.2024.108.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 03/17/2024] [Indexed: 08/06/2024] Open
Abstract
The global diversity of fungi has been estimated between 2 to 11 million species, of which only about 155 000 have been named. Most fungi are invisible to the unaided eye, but they represent a major component of biodiversity on our planet, and play essential ecological roles, supporting life as we know it. Although approximately 20 000 fungal genera are presently recognised, the ecology of most remains undetermined. Despite all this diversity, the mycological community actively researches some fungal genera more commonly than others. This poses an interesting question: why have some fungal genera impacted mycology and related fields more than others? To address this issue, we conducted a bibliometric analysis to identify the top 100 most cited fungal genera. A thorough database search of the Web of Science, Google Scholar, and PubMed was performed to establish which genera are most cited. The most cited 10 genera are Saccharomyces, Candida, Aspergillus, Fusarium, Penicillium, Trichoderma, Botrytis, Pichia, Cryptococcus and Alternaria. Case studies are presented for the 100 most cited genera with general background, notes on their ecology and economic significance and important research advances. This paper provides a historic overview of scientific research of these genera and the prospect for further research. Citation: Bhunjun CS, Chen YJ, Phukhamsakda C, Boekhout T, Groenewald JZ, McKenzie EHC, Francisco EC, Frisvad JC, Groenewald M, Hurdeal VG, Luangsa-ard J, Perrone G, Visagie CM, Bai FY, Błaszkowski J, Braun U, de Souza FA, de Queiroz MB, Dutta AK, Gonkhom D, Goto BT, Guarnaccia V, Hagen F, Houbraken J, Lachance MA, Li JJ, Luo KY, Magurno F, Mongkolsamrit S, Robert V, Roy N, Tibpromma S, Wanasinghe DN, Wang DQ, Wei DP, Zhao CL, Aiphuk W, Ajayi-Oyetunde O, Arantes TD, Araujo JC, Begerow D, Bakhshi M, Barbosa RN, Behrens FH, Bensch K, Bezerra JDP, Bilański P, Bradley CA, Bubner B, Burgess TI, Buyck B, Čadež N, Cai L, Calaça FJS, Campbell LJ, Chaverri P, Chen YY, Chethana KWT, Coetzee B, Costa MM, Chen Q, Custódio FA, Dai YC, Damm U, de Azevedo Santiago ALCM, De Miccolis Angelini RM, Dijksterhuis J, Dissanayake AJ, Doilom M, Dong W, Alvarez-Duarte E, Fischer M, Gajanayake AJ, Gené J, Gomdola D, Gomes AAM, Hausner G, He MQ, Hou L, Iturrieta-González I, Jami F, Jankowiak R, Jayawardena RS, Kandemir H, Kiss L, Kobmoo N, Kowalski T, Landi L, Lin CG, Liu JK, Liu XB, Loizides M, Luangharn T, Maharachchikumbura SSN, Makhathini Mkhwanazi GJ, Manawasinghe IS, Marin-Felix Y, McTaggart AR, Moreau PA, Morozova OV, Mostert L, Osiewacz HD, Pem D, Phookamsak R, Pollastro S, Pordel A, Poyntner C, Phillips AJL, Phonemany M, Promputtha I, Rathnayaka AR, Rodrigues AM, Romanazzi G, Rothmann L, Salgado-Salazar C, Sandoval-Denis M, Saupe SJ, Scholler M, Scott P, Shivas RG, Silar P, Souza-Motta CM, Silva-Filho AGS, Spies CFJ, Stchigel AM, Sterflinger K, Summerbell RC, Svetasheva TY, Takamatsu S, Theelen B, Theodoro RC, Thines M, Thongklang N, Torres R, Turchetti B, van den Brule T, Wang XW, Wartchow F, Welti S, Wijesinghe SN, Wu F, Xu R, Yang ZL, Yilmaz N, Yurkov A, Zhao L, Zhao RL, Zhou N, Hyde KD, Crous PW (2024). What are the 100 most cited fungal genera? Studies in Mycology 108: 1-411. doi: 10.3114/sim.2024.108.01.
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Affiliation(s)
- C.S. Bhunjun
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Y.J. Chen
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - C. Phukhamsakda
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - T. Boekhout
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- The Yeasts Foundation, Amsterdam, the Netherlands
| | - J.Z. Groenewald
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - E.H.C. McKenzie
- Landcare Research Manaaki Whenua, Private Bag 92170, Auckland, New Zealand
| | - E.C. Francisco
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- Laboratório Especial de Micologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - J.C. Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - V. G. Hurdeal
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - J. Luangsa-ard
- BIOTEC, National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - G. Perrone
- Institute of Sciences of Food Production, National Research Council (CNR-ISPA), Via G. Amendola 122/O, 70126 Bari, Italy
| | - C.M. Visagie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - F.Y. Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - J. Błaszkowski
- Laboratory of Plant Protection, Department of Shaping of Environment, West Pomeranian University of Technology in Szczecin, Słowackiego 17, PL-71434 Szczecin, Poland
| | - U. Braun
- Martin Luther University, Institute of Biology, Department of Geobotany and Botanical Garden, Neuwerk 21, 06099 Halle (Saale), Germany
| | - F.A. de Souza
- Núcleo de Biologia Aplicada, Embrapa Milho e Sorgo, Empresa Brasileira de Pesquisa Agropecuária, Rodovia MG 424 km 45, 35701–970, Sete Lagoas, MG, Brazil
| | - M.B. de Queiroz
- Programa de Pós-graduação em Sistemática e Evolução, Universidade Federal do Rio Grande do Norte, Campus Universitário, Natal-RN, 59078-970, Brazil
| | - A.K. Dutta
- Molecular & Applied Mycology Laboratory, Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Jalukbari, Guwahati - 781014, Assam, India
| | - D. Gonkhom
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - B.T. Goto
- Programa de Pós-graduação em Sistemática e Evolução, Universidade Federal do Rio Grande do Norte, Campus Universitário, Natal-RN, 59078-970, Brazil
| | - V. Guarnaccia
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Largo Braccini 2, 10095 Grugliasco, TO, Italy
| | - F. Hagen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, the Netherlands
| | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - M.A. Lachance
- Department of Biology, University of Western Ontario London, Ontario, Canada N6A 5B7
| | - J.J. Li
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, P.R. China
| | - K.Y. Luo
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, P.R. China
| | - F. Magurno
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland
| | - S. Mongkolsamrit
- BIOTEC, National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - V. Robert
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - N. Roy
- Molecular & Applied Mycology Laboratory, Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Jalukbari, Guwahati - 781014, Assam, India
| | - S. Tibpromma
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan 655011, P.R. China
| | - D.N. Wanasinghe
- Center for Mountain Futures, Kunming Institute of Botany, Honghe 654400, Yunnan, China
| | - D.Q. Wang
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, P.R. China
| | - D.P. Wei
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, P.R. China
| | - C.L. Zhao
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, P.R. China
| | - W. Aiphuk
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - O. Ajayi-Oyetunde
- Syngenta Crop Protection, 410 S Swing Rd, Greensboro, NC. 27409, USA
| | - T.D. Arantes
- Laboratório de Micologia, Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, 74605-050, Goiânia, GO, Brazil
| | - J.C. Araujo
- Mykocosmos - Mycology and Science Communication, Rua JP 11 Qd. 18 Lote 13, Jd. Primavera 1ª etapa, Post Code 75.090-260, Anápolis, Goiás, Brazil
- Secretaria de Estado da Educação de Goiás (SEDUC/ GO), Quinta Avenida, Quadra 71, número 212, Setor Leste Vila Nova, Goiânia, Goiás, 74643-030, Brazil
| | - D. Begerow
- Organismic Botany and Mycology, Institute of Plant Sciences and Microbiology, Ohnhorststraße 18, 22609 Hamburg, Germany
| | - M. Bakhshi
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - R.N. Barbosa
- Micoteca URM-Department of Mycology Prof. Chaves Batista, Federal University of Pernambuco, Av. Prof. Moraes Rego, s/n, Center for Biosciences, University City, Recife, Pernambuco, Zip Code: 50670-901, Brazil
| | - F.H. Behrens
- Julius Kühn-Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Geilweilerhof, D-76833 Siebeldingen, Germany
| | - K. Bensch
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - J.D.P. Bezerra
- Laboratório de Micologia, Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, 74605-050, Goiânia, GO, Brazil
| | - P. Bilański
- Department of Forest Ecosystems Protection, Faculty of Forestry, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425 Krakow, Poland
| | - C.A. Bradley
- Department of Plant Pathology, University of Kentucky, Princeton, KY 42445, USA
| | - B. Bubner
- Johan Heinrich von Thünen-Institut, Bundesforschungsinstitut für Ländliche Räume, Wald und Fischerei, Institut für Forstgenetik, Eberswalder Chaussee 3a, 15377 Waldsieversdorf, Germany
| | - T.I. Burgess
- Harry Butler Institute, Murdoch University, Murdoch, 6150, Australia
| | - B. Buyck
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 39, 75231, Paris cedex 05, France
| | - N. Čadež
- University of Ljubljana, Biotechnical Faculty, Food Science and Technology Department Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - L. Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - F.J.S. Calaça
- Mykocosmos - Mycology and Science Communication, Rua JP 11 Qd. 18 Lote 13, Jd. Primavera 1ª etapa, Post Code 75.090-260, Anápolis, Goiás, Brazil
- Secretaria de Estado da Educação de Goiás (SEDUC/ GO), Quinta Avenida, Quadra 71, número 212, Setor Leste Vila Nova, Goiânia, Goiás, 74643-030, Brazil
- Laboratório de Pesquisa em Ensino de Ciências (LabPEC), Centro de Pesquisas e Educação Científica, Universidade Estadual de Goiás, Campus Central (CEPEC/UEG), Anápolis, GO, 75132-903, Brazil
| | - L.J. Campbell
- School of Veterinary Medicine, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - P. Chaverri
- Centro de Investigaciones en Productos Naturales (CIPRONA) and Escuela de Biología, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
- Department of Natural Sciences, Bowie State University, Bowie, Maryland, U.S.A
| | - Y.Y. Chen
- Guizhou Key Laboratory of Agricultural Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - K.W.T. Chethana
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - B. Coetzee
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
- School for Data Sciences and Computational Thinking, University of Stellenbosch, South Africa
| | - M.M. Costa
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - Q. Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - F.A. Custódio
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa-MG, Brazil
| | - Y.C. Dai
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - U. Damm
- Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806 Görlitz, Germany
| | - A.L.C.M.A. Santiago
- Post-graduate course in the Biology of Fungi, Department of Mycology, Federal University of Pernambuco, Av. Prof. Moraes Rego, s/n, 50740-465, Recife, PE, Brazil
| | | | - J. Dijksterhuis
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - A.J. Dissanayake
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - M. Doilom
- Innovative Institute for Plant Health/Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, P.R. China
| | - W. Dong
- Innovative Institute for Plant Health/Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, P.R. China
| | - E. Álvarez-Duarte
- Mycology Unit, Microbiology and Mycology Program, Biomedical Sciences Institute, University of Chile, Chile
| | - M. Fischer
- Julius Kühn-Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Geilweilerhof, D-76833 Siebeldingen, Germany
| | - A.J. Gajanayake
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - J. Gené
- Unitat de Micologia i Microbiologia Ambiental, Facultat de Medicina i Ciències de la Salut & IURESCAT, Universitat Rovira i Virgili (URV), Reus, Catalonia Spain
| | - D. Gomdola
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - A.A.M. Gomes
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife-PE, Brazil
| | - G. Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB, R3T 5N6
| | - M.Q. He
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - L. Hou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Space Nutrition and Food Engineering, China Astronaut Research and Training Center, Beijing, 100094, China
| | - I. Iturrieta-González
- Unitat de Micologia i Microbiologia Ambiental, Facultat de Medicina i Ciències de la Salut & IURESCAT, Universitat Rovira i Virgili (URV), Reus, Catalonia Spain
- Department of Preclinic Sciences, Medicine Faculty, Laboratory of Infectology and Clinical Immunology, Center of Excellence in Translational Medicine-Scientific and Technological Nucleus (CEMT-BIOREN), Universidad de La Frontera, Temuco 4810296, Chile
| | - F. Jami
- Plant Health and Protection, Agricultural Research Council, Pretoria, South Africa
| | - R. Jankowiak
- Department of Forest Ecosystems Protection, Faculty of Forestry, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425 Krakow, Poland
| | - R.S. Jayawardena
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, South Korea
| | - H. Kandemir
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - L. Kiss
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, QLD 4350 Toowoomba, Australia
- Centre for Research and Development, Eszterházy Károly Catholic University, H-3300 Eger, Hungary
| | - N. Kobmoo
- BIOTEC, National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - T. Kowalski
- Department of Forest Ecosystems Protection, Faculty of Forestry, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425 Krakow, Poland
| | - L. Landi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - C.G. Lin
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - J.K. Liu
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - X.B. Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, P.R. China
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Temesvári krt. 62, Szeged H-6726, Hungary
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | | | - T. Luangharn
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - S.S.N. Maharachchikumbura
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - G.J. Makhathini Mkhwanazi
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - I.S. Manawasinghe
- Innovative Institute for Plant Health/Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, P.R. China
| | - Y. Marin-Felix
- Department Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, 38106, Braunschweig, Germany
| | - A.R. McTaggart
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Dutton Park 4102, Queensland, Australia
| | - P.A. Moreau
- Univ. Lille, ULR 4515 - LGCgE, Laboratoire de Génie Civil et géo-Environnement, F-59000 Lille, France
| | - O.V. Morozova
- Komarov Botanical Institute of the Russian Academy of Sciences, 2, Prof. Popov Str., 197376 Saint Petersburg, Russia
- Tula State Lev Tolstoy Pedagogical University, 125, Lenin av., 300026 Tula, Russia
| | - L. Mostert
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - H.D. Osiewacz
- Faculty for Biosciences, Institute for Molecular Biosciences, Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany
| | - D. Pem
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - R. Phookamsak
- Center for Mountain Futures, Kunming Institute of Botany, Honghe 654400, Yunnan, China
| | - S. Pollastro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - A. Pordel
- Plant Protection Research Department, Baluchestan Agricultural and Natural Resources Research and Education Center, AREEO, Iranshahr, Iran
| | - C. Poyntner
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - A.J.L. Phillips
- Faculdade de Ciências, Biosystems and Integrative Sciences Institute (BioISI), Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal
| | - M. Phonemany
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - I. Promputtha
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - A.R. Rathnayaka
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - A.M. Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
| | - G. Romanazzi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - L. Rothmann
- Plant Pathology, Department of Plant Sciences, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, 9301, South Africa
| | - C. Salgado-Salazar
- Mycology and Nematology Genetic Diversity and Biology Laboratory, U.S. Department of Agriculture, Agriculture Research Service (USDA-ARS), 10300 Baltimore Avenue, Beltsville MD, 20705, USA
| | - M. Sandoval-Denis
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - S.J. Saupe
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS Université de Bordeaux, 1 rue Camille Saint Saëns, 33077 Bordeaux cedex, France
| | - M. Scholler
- Staatliches Museum für Naturkunde Karlsruhe, Erbprinzenstraße 13, 76133 Karlsruhe, Germany
| | - P. Scott
- Harry Butler Institute, Murdoch University, Murdoch, 6150, Australia
- Sustainability and Biosecurity, Department of Primary Industries and Regional Development, Perth WA 6000, Australia
| | - R.G. Shivas
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, QLD 4350 Toowoomba, Australia
| | - P. Silar
- Laboratoire Interdisciplinaire des Energies de Demain, Université de Paris Cité, 75205 Paris Cedex, France
| | - A.G.S. Silva-Filho
- IFungiLab, Departamento de Ciências e Matemática (DCM), Instituto Federal de Educação, Ciência e Tecnologia de São Paulo (IFSP), São Paulo, BraziI
| | - C.M. Souza-Motta
- Micoteca URM-Department of Mycology Prof. Chaves Batista, Federal University of Pernambuco, Av. Prof. Moraes Rego, s/n, Center for Biosciences, University City, Recife, Pernambuco, Zip Code: 50670-901, Brazil
| | - C.F.J. Spies
- Agricultural Research Council - Plant Health and Protection, Private Bag X5017, Stellenbosch, 7599, South Africa
| | - A.M. Stchigel
- Unitat de Micologia i Microbiologia Ambiental, Facultat de Medicina i Ciències de la Salut & IURESCAT, Universitat Rovira i Virgili (URV), Reus, Catalonia Spain
| | - K. Sterflinger
- Institute of Natural Sciences and Technology in the Arts (INTK), Academy of Fine Arts Vienna, Augasse 2–6, 1090, Vienna, Austria
| | - R.C. Summerbell
- Sporometrics, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - T.Y. Svetasheva
- Tula State Lev Tolstoy Pedagogical University, 125, Lenin av., 300026 Tula, Russia
| | - S. Takamatsu
- Mie University, Graduate School, Department of Bioresources, 1577 Kurima-Machiya, Tsu 514-8507, Japan
| | - B. Theelen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - R.C. Theodoro
- Laboratório de Micologia Médica, Instituto de Medicina Tropical do RN, Universidade Federal do Rio Grande do Norte, 59078-900, Natal, RN, Brazil
| | - M. Thines
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt Am Main, Germany
| | - N. Thongklang
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - R. Torres
- IRTA, Postharvest Programme, Edifici Fruitcentre, Parc Agrobiotech de Lleida, Parc de Gardeny, 25003, Lleida, Catalonia, Spain
| | - B. Turchetti
- Department of Agricultural, Food and Environmental Sciences and DBVPG Industrial Yeasts Collection, University of Perugia, Italy
| | - T. van den Brule
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- TIFN, P.O. Box 557, 6700 AN Wageningen, the Netherlands
| | - X.W. Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - F. Wartchow
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, Paraiba, João Pessoa, Brazil
| | - S. Welti
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, 38106, Braunschweig, Germany
| | - S.N. Wijesinghe
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - F. Wu
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - R. Xu
- School of Food Science and Engineering, Yangzhou University, Yangzhou 225127, China
- Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun 130118, China
| | - Z.L. Yang
- Syngenta Crop Protection, 410 S Swing Rd, Greensboro, NC. 27409, USA
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | - N. Yilmaz
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - A. Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - L. Zhao
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - R.L. Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - N. Zhou
- Department of Biological Sciences and Biotechnology, Botswana University of Science and Technology, Private Bag, 16, Palapye, Botswana
| | - K.D. Hyde
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Innovative Institute for Plant Health/Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, P.R. China
- Key Laboratory of Economic Plants and Biotechnology and the Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - P.W. Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht
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Bish MD, Ramachandran SR, Wright A, Lincoln LM, Whitham SA, Graham MA, Pedley KF. The Soybean Rpp3 Gene Encodes a TIR-NBS-LRR Protein that Confers Resistance to Phakopsora pachyrhizi. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:561-570. [PMID: 38569009 DOI: 10.1094/mpmi-01-24-0007-r] [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: 04/05/2024]
Abstract
Soybean rust is an economically significant disease caused by the fungus Phakopsora pachyrhizi that negatively impacts soybean (Glycine max [L.] Merr.) production throughout the world. Susceptible plants infected by P. pachyrhizi develop tan-colored lesions on the leaf surface that give rise to funnel-shaped uredinia as the disease progresses. While most soybean germplasm is susceptible, seven genetic loci (Rpp1 to Rpp7) that provide race-specific resistance to P. pachyrhizi (Rpp) have been identified. Rpp3 was first discovered and characterized in the soybean accession PI 462312 (Ankur), and it was also determined to be one of two Rpp genes present in PI 506764 (Hyuuga). Genetic crosses with PI 506764 were later used to fine-map the Rpp3 locus to a 371-kb region on chromosome 6. The corresponding region in the susceptible Williams 82 (Wm82) reference genome contains several homologous nucleotide binding site-leucine rich repeat (NBS-LRR) genes. To identify Rpp3, we designed oligonucleotide primers to amplify Rpp3 candidate (Rpp3C) NBS-LRR genes at this locus from PI 462312, PI 506764, and Wm82 using polymerase chain reaction (PCR). Five Rpp3C genes were identified in both Rpp3-resistant soybean lines, and co-silencing these genes compromised resistance to P. pachyrhizi. Gene expression analysis and sequence comparisons of the Rpp3C genes in PI 462312 and PI 506764 suggest that a single candidate gene, Rpp3C3, is responsible for Rpp3-mediated resistance. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2024.
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Affiliation(s)
- Mandy D Bish
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Fort Detrick, MD 21702, U.S.A
| | - Sowmya R Ramachandran
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Fort Detrick, MD 21702, U.S.A
- Oak Ridge Institute for Science and Education, ARS Research Participation Program, Oak Ridge, TN, U.S.A
| | - Amy Wright
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Fort Detrick, MD 21702, U.S.A
| | - Lori M Lincoln
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011, U.S.A
| | - Steven A Whitham
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Michelle A Graham
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011, U.S.A
- Department of Agronomy, Iowa State University, Ames, IA 50011, U.S.A
| | - Kerry F Pedley
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Fort Detrick, MD 21702, U.S.A
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7
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Chakraborty J. A comprehensive review of soybean RNL and TIR domain proteins. PLANT MOLECULAR BIOLOGY 2024; 114:78. [PMID: 38922375 DOI: 10.1007/s11103-024-01473-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 05/29/2024] [Indexed: 06/27/2024]
Abstract
Both prokaryotic and eukaryotic organisms use the nucleotide-binding domain/leucine-rich repeat (NBD/LRR)-triggered immunity (NLR-triggered immunity) signaling pathway to defend against pathogens. Plant NLRs are intracellular immune receptors that can bind to effector proteins secreted by pathogens. Dicotyledonous plants express a type of NLR known as TIR domain-containing NLRs (TNLs). TIR domains are enzymes that catalyze the production of small molecules that are essential for immune signaling and lead to plant cell death. The activation of downstream TNL signaling components, such as enhanced disease susceptibility 1 (EDS1), phytoalexin deficient 4 (PAD4), and senescence-associated gene 101 (SAG101), is facilitated by these small molecules. Helper NLRs (hNLRs) and the EDS1-PAD4/SAG101 complex associate after activation, causing the hNLRs to oligomerize, translocate to the plasma membrane (PM), and produce cation-selective channels. According to a recent theory, cations enter cells through pores created by oligomeric hNLRs and trigger cell death. Occasionally, TNLs can self-associate to create higher-order oligomers. Here, we categorized soybean TNLs based on the protein domains that they possess. We believe that TNLs may help soybean plants effectively fight pathogens by acting as a source of genetic resistance. In summary, the purpose of this review is to elucidate the range of TNLs that are expressed in soybean.
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Affiliation(s)
- Joydeep Chakraborty
- School of Plant Sciences and Food Security, Tel Aviv University, Tel-Aviv, Israel.
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8
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Hao Q, Yang H, Chen S, Zhang C, Chen L, Cao D, Yuan S, Guo W, Yang Z, Huang Y, Qu Y, Qin L, Sheng X, Wang X, Mitra C, Zhong H, Dawson J, Bumann E, Wang W, Jiang Y, Tang G, Carlin R, Chen H, Liu Q, Shan Z, Zhou X. An pair of an atypical NLR encoding genes confer Asian soybean rust resistance in soybean. Nat Commun 2024; 15:3310. [PMID: 38632249 PMCID: PMC11023949 DOI: 10.1038/s41467-024-47611-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
Asian soybean rust (ASR), caused by Phakopsora pachyrhizi, is a devastating disease that is present in all major soybean-producing regions. The limited availability of resistant germplasm has resulted in a scarcity of commercial soybean cultivars that are resistant to the disease. To date, only the Chinese soybean landrace SX6907 has demonstrated an immune response to ASR. In this study, we present the isolation and characterization of Rpp6907-7 and Rpp6907-4, a gene pair that confer broad-spectrum resistance to ASR. Rpp6907-7 and Rpp6907-4 encode atypic nucleotide-binding leucine-rich repeat (NLR) proteins that are found to be required for NLR-mediated immunity. Genetic analysis shows that only Rpp6907-7 confers resistance, while Rpp6907-4 regulates Rpp6907-7 signaling activity by acting as a repressor in the absence of recognized effectors. Our work highlights the potential value of using Rpp6907 in developing resistant soybean cultivars.
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Affiliation(s)
- Qingnan Hao
- Soybean Genetics and breeding team, Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
- Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Hongli Yang
- Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Shuilian Chen
- Soybean Collaborative Innovation Center, Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Chanjuan Zhang
- Soybean Genetics and breeding team, Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Limiao Chen
- Soybean Genetics and breeding team, Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Dong Cao
- Soybean Genetics and breeding team, Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Songli Yuan
- Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Wei Guo
- Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Zhonglu Yang
- Soybean Collaborative Innovation Center, Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Yi Huang
- Soybean Collaborative Innovation Center, Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Yanhui Qu
- The Graduate School of Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Lucy Qin
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Xiaoyan Sheng
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Xueyan Wang
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Chandrani Mitra
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Heng Zhong
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - John Dawson
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Eric Bumann
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Wenling Wang
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Yaping Jiang
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Guozhu Tang
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Ryan Carlin
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Haifeng Chen
- Soybean Collaborative Innovation Center, Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan, 430062, China.
| | - Qingli Liu
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA.
| | - Zhihui Shan
- Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China.
| | - Xinan Zhou
- Soybean Genetics and breeding team, Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan, 430062, China.
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9
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Kohlhase DR, O’Rourke JA, Graham MA. GmGLU1 and GmRR4 contribute to iron deficiency tolerance in soybean. FRONTIERS IN PLANT SCIENCE 2024; 15:1295952. [PMID: 38476685 PMCID: PMC10927968 DOI: 10.3389/fpls.2024.1295952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 02/02/2024] [Indexed: 03/14/2024]
Abstract
Iron deficiency chlorosis (IDC) is a form of abiotic stress that negatively impacts soybean yield. In a previous study, we demonstrated that the historical IDC quantitative trait locus (QTL) on soybean chromosome Gm03 was composed of four distinct linkage blocks, each containing candidate genes for IDC tolerance. Here, we take advantage of virus-induced gene silencing (VIGS) to validate the function of three high-priority candidate genes, each corresponding to a different linkage block in the Gm03 IDC QTL. We built three single-gene constructs to target GmGLU1 (GLUTAMATE SYNTHASE 1, Glyma.03G128300), GmRR4 (RESPONSE REGULATOR 4, Glyma.03G130000), and GmbHLH38 (beta Helix Loop Helix 38, Glyma.03G130400 and Glyma.03G130600). Given the polygenic nature of the iron stress tolerance trait, we also silenced the genes in combination. We built two constructs targeting GmRR4+GmGLU1 and GmbHLH38+GmGLU1. All constructs were tested on the iron-efficient soybean genotype Clark grown in iron-sufficient conditions. We observed significant decreases in soil plant analysis development (SPAD) measurements using the GmGLU1 construct and both double constructs, with potential additive effects in the GmRR4+GmGLU1 construct. Whole genome expression analyses (RNA-seq) revealed a wide range of affected processes including known iron stress responses, defense and hormone signaling, photosynthesis, and cell wall structure. These findings highlight the importance of GmGLU1 in soybean iron stress responses and provide evidence that IDC is truly a polygenic trait, with multiple genes within the QTL contributing to IDC tolerance. Finally, we conducted BLAST analyses to demonstrate that the Gm03 IDC QTL is syntenic across a broad range of plant species.
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Affiliation(s)
| | - Jamie A. O’Rourke
- United States Department of Agriculture, Agricultural Research Service, Corn Insects and Crop Genetics Research Unit and Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Michelle A. Graham
- United States Department of Agriculture, Agricultural Research Service, Corn Insects and Crop Genetics Research Unit and Department of Agronomy, Iowa State University, Ames, IA, United States
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10
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Chicowski AS, Bredow M, Utiyama AS, Marcelino‐Guimarães FC, Whitham SA. Soybean-Phakopsora pachyrhizi interactions: towards the development of next-generation disease-resistant plants. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:296-315. [PMID: 37883664 PMCID: PMC10826999 DOI: 10.1111/pbi.14206] [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: 07/06/2023] [Revised: 09/19/2023] [Accepted: 10/08/2023] [Indexed: 10/28/2023]
Abstract
Soybean rust (SBR), caused by the obligate biotrophic fungus Phakopsora pachyrhizi, is a devastating foliar disease threatening soybean production. To date, no commercial cultivars conferring durable resistance to SBR are available. The development of long-lasting SBR resistance has been hindered by the lack of understanding of this complex pathosystem, encompassing challenges posed by intricate genetic structures in both the host and pathogen, leading to a gap in the knowledge of gene-for-gene interactions between soybean and P. pachyrhizi. In this review, we focus on recent advancements and emerging technologies that can be used to improve our understanding of the P. pachyrhizi-soybean molecular interactions. We further explore approaches used to combat SBR, including conventional breeding, transgenic approaches and RNA interference, and how advances in our understanding of plant immune networks, the availability of new molecular tools, and the recent sequencing of the P. pachyrhizi genome could be used to aid in the development of better genetic resistance against SBR. Lastly, we discuss the research gaps of this pathosystem and how new technologies can be used to shed light on these questions and to develop durable next-generation SBR-resistant soybean plants.
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Affiliation(s)
- Aline Sartor Chicowski
- Department of Plant Pathology, Entomology and MicrobiologyIowa State UniversityAmesIowaUSA
| | - Melissa Bredow
- Department of Plant Pathology, Entomology and MicrobiologyIowa State UniversityAmesIowaUSA
| | - Alice Satiko Utiyama
- Brazilian Agricultural Research Corporation – National Soybean Research Center (Embrapa Soja)LondrinaParanáBrazil
- Department of AgronomyFederal University of ViçosaViçosaMinas GeraisBrazil
| | | | - Steven A. Whitham
- Department of Plant Pathology, Entomology and MicrobiologyIowa State UniversityAmesIowaUSA
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11
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McCabe CE, Lincoln LM, O’Rourke JA, Graham MA. Virus induced gene silencing confirms oligogenic inheritance of brown stem rot resistance in soybean. FRONTIERS IN PLANT SCIENCE 2024; 14:1292605. [PMID: 38259908 PMCID: PMC10801082 DOI: 10.3389/fpls.2023.1292605] [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: 09/11/2023] [Accepted: 12/11/2023] [Indexed: 01/24/2024]
Abstract
Brown Stem Rot (BSR), caused by the soil borne fungal pathogen Phialophora gregata, can reduce soybean yields by as much as 38%. Previous allelism studies identified three Resistant to brown stem Rot genes (Rbs1, Rbs2, and Rbs3), all mapping to large, overlapping regions on soybean chromosome 16. However, recent fine-mapping and genome wide association studies (GWAS) suggest Rbs1, Rbs2, and Rbs3 are alleles of a single Rbs locus. To address this conflict, we characterized the Rbs locus using the Williams82 reference genome (Wm82.a4.v1). We identified 120 Receptor-Like Proteins (RLPs), with hallmarks of disease resistance receptor-like proteins (RLPs), which formed five distinct clusters. We developed virus induced gene silencing (VIGS) constructs to target each of the clusters, hypothesizing that silencing the correct RLP cluster would result in a loss of resistance phenotype. The VIGS constructs were tested against P. gregata resistant genotypes L78-4094 (Rbs1), PI 437833 (Rbs2), or PI 437970 (Rbs3), infected with P. gregata or mock infected. No loss of resistance phenotype was observed. We then developed VIGS constructs targeting two RLP clusters with a single construct. Construct B1a/B2 silenced P. gregata resistance in L78-4094, confirming at least two genes confer Rbs1-mediated resistance to P. gregata. Failure of B1a/B2 to silence resistance in PI 437833 and PI 437970 suggests additional genes confer BSR resistance in these lines. To identify differentially expressed genes (DEGs) responding to silencing, we conducted RNA-seq of leaf, stem and root samples from B1a/B2 and empty vector control plants infected with P. gregata or mock infected. B1a/B2 silencing induced DEGs associated with cell wall biogenesis, lipid oxidation, the unfolded protein response and iron homeostasis and repressed numerous DEGs involved in defense and defense signaling. These findings will improve integration of Rbs resistance into elite germplasm and provide novel insights into fungal disease resistance.
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Affiliation(s)
- Chantal E. McCabe
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Corn Insects and Crop Genetics Research Unit, Ames, IA, United States
| | - Lori M. Lincoln
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Corn Insects and Crop Genetics Research Unit, Ames, IA, United States
| | - Jamie A. O’Rourke
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Corn Insects and Crop Genetics Research Unit, Ames, IA, United States
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Michelle A. Graham
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Corn Insects and Crop Genetics Research Unit, Ames, IA, United States
- Department of Agronomy, Iowa State University, Ames, IA, United States
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12
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Hao Q, Yang H, Chen S, Qu Y, Zhang C, Chen L, Cao D, Yuan S, Guo W, Yang Z, Huang Y, Shan Z, Chen H, Zhou X. RNA-Seq and Comparative Transcriptomic Analyses of Asian Soybean Rust Resistant and Susceptible Soybean Genotypes Provide Insights into Identifying Disease Resistance Genes. Int J Mol Sci 2023; 24:13450. [PMID: 37686258 PMCID: PMC10487414 DOI: 10.3390/ijms241713450] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/26/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
Asian soybean rust (ASR), caused by Phakopsora pachyrhizi, is one of the most destructive foliar diseases that affect soybeans. Developing resistant cultivars is the most cost-effective, environmentally friendly, and easy strategy for controlling the disease. However, the current understanding of the mechanisms underlying soybean resistance to P. pachyrhizi remains limited, which poses a significant challenge in devising effective control strategies. In this study, comparative transcriptomic profiling using one resistant genotype and one susceptible genotype was performed under infected and control conditions to understand the regulatory network operating between soybean and P. pachyrhizi. RNA-Seq analysis identified a total of 6540 differentially expressed genes (DEGs), which were shared by all four genotypes. The DEGs are involved in defense responses, stress responses, stimulus responses, flavonoid metabolism, and biosynthesis after infection with P. pachyrhizi. A total of 25,377 genes were divided into 33 modules using weighted gene co-expression network analysis (WGCNA). Two modules were significantly associated with pathogen defense. The DEGs were mainly enriched in RNA processing, plant-type hypersensitive response, negative regulation of cell growth, and a programmed cell death process. In conclusion, these results will provide an important resource for mining resistant genes to P. pachyrhizi infection and valuable resources to potentially pyramid quantitative resistance loci for improving soybean germplasm.
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Affiliation(s)
- Qingnan Hao
- Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan 430062, China; (Q.H.); (H.Y.); (S.C.); (Y.Q.); (C.Z.); (L.C.); (D.C.); (S.Y.); (W.G.); (Z.Y.); (Y.H.); (X.Z.)
- Key Laboratory for Biological Sciences of Oil Crops, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Hongli Yang
- Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan 430062, China; (Q.H.); (H.Y.); (S.C.); (Y.Q.); (C.Z.); (L.C.); (D.C.); (S.Y.); (W.G.); (Z.Y.); (Y.H.); (X.Z.)
- Key Laboratory for Biological Sciences of Oil Crops, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Shuilian Chen
- Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan 430062, China; (Q.H.); (H.Y.); (S.C.); (Y.Q.); (C.Z.); (L.C.); (D.C.); (S.Y.); (W.G.); (Z.Y.); (Y.H.); (X.Z.)
- Key Laboratory for Biological Sciences of Oil Crops, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Yanhui Qu
- Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan 430062, China; (Q.H.); (H.Y.); (S.C.); (Y.Q.); (C.Z.); (L.C.); (D.C.); (S.Y.); (W.G.); (Z.Y.); (Y.H.); (X.Z.)
- The Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chanjuan Zhang
- Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan 430062, China; (Q.H.); (H.Y.); (S.C.); (Y.Q.); (C.Z.); (L.C.); (D.C.); (S.Y.); (W.G.); (Z.Y.); (Y.H.); (X.Z.)
- Key Laboratory for Biological Sciences of Oil Crops, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Limiao Chen
- Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan 430062, China; (Q.H.); (H.Y.); (S.C.); (Y.Q.); (C.Z.); (L.C.); (D.C.); (S.Y.); (W.G.); (Z.Y.); (Y.H.); (X.Z.)
- Key Laboratory for Biological Sciences of Oil Crops, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Dong Cao
- Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan 430062, China; (Q.H.); (H.Y.); (S.C.); (Y.Q.); (C.Z.); (L.C.); (D.C.); (S.Y.); (W.G.); (Z.Y.); (Y.H.); (X.Z.)
- Key Laboratory for Biological Sciences of Oil Crops, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Songli Yuan
- Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan 430062, China; (Q.H.); (H.Y.); (S.C.); (Y.Q.); (C.Z.); (L.C.); (D.C.); (S.Y.); (W.G.); (Z.Y.); (Y.H.); (X.Z.)
- Key Laboratory for Biological Sciences of Oil Crops, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Wei Guo
- Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan 430062, China; (Q.H.); (H.Y.); (S.C.); (Y.Q.); (C.Z.); (L.C.); (D.C.); (S.Y.); (W.G.); (Z.Y.); (Y.H.); (X.Z.)
- Key Laboratory for Biological Sciences of Oil Crops, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Zhonglu Yang
- Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan 430062, China; (Q.H.); (H.Y.); (S.C.); (Y.Q.); (C.Z.); (L.C.); (D.C.); (S.Y.); (W.G.); (Z.Y.); (Y.H.); (X.Z.)
- Key Laboratory for Biological Sciences of Oil Crops, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Yi Huang
- Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan 430062, China; (Q.H.); (H.Y.); (S.C.); (Y.Q.); (C.Z.); (L.C.); (D.C.); (S.Y.); (W.G.); (Z.Y.); (Y.H.); (X.Z.)
- Key Laboratory for Biological Sciences of Oil Crops, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Zhihui Shan
- Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan 430062, China; (Q.H.); (H.Y.); (S.C.); (Y.Q.); (C.Z.); (L.C.); (D.C.); (S.Y.); (W.G.); (Z.Y.); (Y.H.); (X.Z.)
- Key Laboratory for Biological Sciences of Oil Crops, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Haifeng Chen
- Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan 430062, China; (Q.H.); (H.Y.); (S.C.); (Y.Q.); (C.Z.); (L.C.); (D.C.); (S.Y.); (W.G.); (Z.Y.); (Y.H.); (X.Z.)
- Key Laboratory for Biological Sciences of Oil Crops, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Xinan Zhou
- Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan 430062, China; (Q.H.); (H.Y.); (S.C.); (Y.Q.); (C.Z.); (L.C.); (D.C.); (S.Y.); (W.G.); (Z.Y.); (Y.H.); (X.Z.)
- Key Laboratory for Biological Sciences of Oil Crops, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
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13
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Mena E, Reboledo G, Stewart S, Montesano M, Ponce de León I. Comparative analysis of soybean transcriptional profiles reveals defense mechanisms involved in resistance against Diaporthe caulivora. Sci Rep 2023; 13:13061. [PMID: 37567886 PMCID: PMC10421924 DOI: 10.1038/s41598-023-39695-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 07/29/2023] [Indexed: 08/13/2023] Open
Abstract
Soybean stem canker (SSC) caused by the fungal pathogen Diaporthe caulivora is an important disease affecting soybean production worldwide. However, limited information related to the molecular mechanisms underlying soybean resistance to Diaporthe species is available. In the present work, we analyzed the defense responses to D. caulivora in the soybean genotypes Williams and Génesis 5601. The results showed that compared to Williams, Génesis 5601 is more resistant to fungal infection evidenced by significantly smaller lesion length, reduced disease severity and pathogen biomass. Transcriptional profiling was performed in untreated plants and in D. caulivora-inoculated and control-treated tissues at 8 and 48 h post inoculation (hpi). In total, 2.322 and 1.855 genes were differentially expressed in Génesis 5601 and Williams, respectively. Interestingly, Génesis 5601 exhibited a significantly higher number of upregulated genes compared to Williams at 8 hpi, 1.028 versus 434 genes. Resistance to D. caulivora was associated with defense activation through transcriptional reprogramming mediating perception of the pathogen by receptors, biosynthesis of phenylpropanoids, hormone signaling, small heat shock proteins and pathogenesis related (PR) genes. These findings provide novel insights into soybean defense mechanisms leading to host resistance against D. caulivora, and generate a foundation for the development of resistant SSC varieties within soybean breeding programs.
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Affiliation(s)
- Eilyn Mena
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Guillermo Reboledo
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Silvina Stewart
- Programa Nacional de Cultivos de Secano, Instituto Nacional de Investigación Agropecuaria (INIA), La Estanzuela, Colonia, Uruguay
| | - Marcos Montesano
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
- Laboratorio de Fisiología Vegetal, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Inés Ponce de León
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay.
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14
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Yamanaka N, Aoyagi LN, Hossain MM, Aoyagi MBF, Muraki Y. Genetic Mapping of Seven Kinds of Locus for Resistance to Asian Soybean Rust. PLANTS (BASEL, SWITZERLAND) 2023; 12:2263. [PMID: 37375888 DOI: 10.3390/plants12122263] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/26/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023]
Abstract
Asian soybean rust (ASR), caused by Phakopsora pachyrhizi, is one of the most serious soybean (Glycine max) diseases in tropical and subtropical regions. To facilitate the development of resistant varieties using gene pyramiding, DNA markers closely linked to seven resistance genes, namely, Rpp1, Rpp1-b, Rpp2, Rpp3, Rpp4, Rpp5, and Rpp6, were identified. Linkage analysis of resistance-related traits and marker genotypes using 13 segregating populations of ASR resistance, including eight previously published by our group and five newly developed populations, identified the resistance loci with markers at intervals of less than 2.0 cM for all seven resistance genes. Inoculation was conducted of the same population with two P. pachyrhizi isolates of different virulence, and two resistant varieties, 'Kinoshita' and 'Shiranui,' previously thought to only harbor Rpp5, was found to also harbor Rpp3. Markers closely linked to the resistance loci identified in this study will be used for ASR-resistance breeding and the identification of the genes responsible for resistance.
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Affiliation(s)
- Naoki Yamanaka
- Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba 305-8686, Japan
| | - Luciano N Aoyagi
- Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba 305-8686, Japan
| | - Md Motaher Hossain
- Department of Plant Pathology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Salna, Gazipur 1706, Bangladesh
| | - Martina B F Aoyagi
- Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba 305-8686, Japan
| | - Yukie Muraki
- Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba 305-8686, Japan
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Xiong H, Chen Y, Pan YB, Wang J, Lu W, Shi A. A genome-wide association study and genomic prediction for Phakopsora pachyrhizi resistance in soybean. FRONTIERS IN PLANT SCIENCE 2023; 14:1179357. [PMID: 37313252 PMCID: PMC10258334 DOI: 10.3389/fpls.2023.1179357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 04/25/2023] [Indexed: 06/15/2023]
Abstract
Soybean brown rust (SBR), caused by Phakopsora pachyrhizi, is a devastating fungal disease that threatens global soybean production. This study conducted a genome-wide association study (GWAS) with seven models on a panel of 3,082 soybean accessions to identify the markers associated with SBR resistance by 30,314 high quality single nucleotide polymorphism (SNPs). Then five genomic selection (GS) models, including Ridge regression best linear unbiased predictor (rrBLUP), Genomic best linear unbiased predictor (gBLUP), Bayesian least absolute shrinkage and selection operator (Bayesian LASSO), Random Forest (RF), and Support vector machines (SVM), were used to predict breeding values of SBR resistance using whole genome SNP sets and GWAS-based marker sets. Four SNPs, namely Gm18_57,223,391 (LOD = 2.69), Gm16_29,491,946 (LOD = 3.86), Gm06_45,035,185 (LOD = 4.74), and Gm18_51,994,200 (LOD = 3.60), were located near the reported P. pachyrhizi R genes, Rpp1, Rpp2, Rpp3, and Rpp4, respectively. Other significant SNPs, including Gm02_7,235,181 (LOD = 7.91), Gm02_7234594 (LOD = 7.61), Gm03_38,913,029 (LOD = 6.85), Gm04_46,003,059 (LOD = 6.03), Gm09_1,951,644 (LOD = 10.07), Gm10_39,142,024 (LOD = 7.12), Gm12_28,136,735 (LOD = 7.03), Gm13_16,350,701(LOD = 5.63), Gm14_6,185,611 (LOD = 5.51), and Gm19_44,734,953 (LOD = 6.02), were associated with abundant disease resistance genes, such as Glyma.02G084100, Glyma.03G175300, Glyma.04g189500, Glyma.09G023800, Glyma.12G160400, Glyma.13G064500, Glyma.14g073300, and Glyma.19G190200. The annotations of these genes included but not limited to: LRR class gene, cytochrome 450, cell wall structure, RCC1, NAC, ABC transporter, F-box domain, etc. The GWAS based markers showed more accuracies in genomic prediction than the whole genome SNPs, and Bayesian LASSO model was the ideal model in SBR resistance prediction with 44.5% ~ 60.4% accuracies. This study aids breeders in predicting selection accuracy of complex traits such as disease resistance and can shorten the soybean breeding cycle by the identified markers.
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Affiliation(s)
- Haizheng Xiong
- Department of Horticulture, University of Arkansas, Fayetteville, AR, United States
| | - Yilin Chen
- Department of Horticulture, University of Arkansas, Fayetteville, AR, United States
| | - Yong-Bao Pan
- Sugarcane Research Unit, Untied State Department of Agriculture – Agriculture Research Service (USDA-ARS), Houma, LA, United States
| | - Jinshe Wang
- Henan Academy of Crops Molecular Breeding, National Centre for Plant Breeding, Zhengzhou, China
| | - Weiguo Lu
- Henan Academy of Crops Molecular Breeding, National Centre for Plant Breeding, Zhengzhou, China
| | - Ainong Shi
- Department of Horticulture, University of Arkansas, Fayetteville, AR, United States
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Barros LG, Avelino BB, da Silva DCG, Ferreira EGC, Castanho FM, Ferreira ME, Lopes-Caitar VS, Marin SRR, Arias CAA, de O. N. Lopes I, Abdelnoor RV, Marcelino-Guimarães FC. Mapping of a soybean rust resistance in PI 594756 at the Rpp1 locus. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:12. [PMID: 37313128 PMCID: PMC10248603 DOI: 10.1007/s11032-023-01358-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 01/31/2023] [Indexed: 06/15/2023]
Abstract
Asian soybean rust (ASR), caused by the fungus Phakopsora pachyrhizi, is the main disease affecting soybean in Brazil. This study aimed at investigating and mapping the resistance of the PI 594756 to P. pachyrhizi, by using Bulked Segregant Analysis (BSA). The PI 594756 and the susceptible PI 594891 were crossed and the resulting F2 and F2:3 populations (208 and 1770 plants, respectively) were tested against ASR. Also, these PIs and differential varieties were tested against a panel of monosporic isolates. Plants presenting tan lesions were classified as susceptible (S) while plants presenting reddish-brown (RB) lesions were classified as resistant. DNA bulks were genotyped with Infinium BeadChips and the genomic region identified was further analyzed in the F2 individuals with target GBS (tGBS). PI 594,56 presented a unique resistance profile compared to the differential varieties. The resistance was monogenic dominant; however, it was classified as incompletely dominant when quantitatively studied. Genetic and QTL mapping placed the PI 594756 gene between the genomic region located at 55,863,741 and 56,123,516 bp of chromosome 18. This position is slightly upstream mapping positions of Rpp1 (PI 200492) and Rpp1-b (PI 594538A). Finally, we performed a haplotype analysis in a whole genomic sequencing-SNP database composed of Brazilian historical germplasm and sources of Rpp genes. We found SNPs that successfully differentiated the new PI 594756 allele from Rpp1 and Rpp1-b sources. The haplotype identified can be used as a tool for marker-assisted selection (MAS). Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01358-4.
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Affiliation(s)
- Luciane G. Barros
- Department of General Biology, State University of Londrina (UEL), Londrina, Paraná Brazil
| | - Bruna B. Avelino
- Department of General Biology, State University of Londrina (UEL), Londrina, Paraná Brazil
| | - Danielle C. G. da Silva
- Brazilian Agricultural Research Corporation (Embrapa), Embrapa Soybean, Londrina, Paraná Brazil
| | - Everton G. C. Ferreira
- Department of General Biology, State University of Londrina (UEL), Londrina, Paraná Brazil
| | - Fernanda M. Castanho
- Department of General Biology, State University of Londrina (UEL), Londrina, Paraná Brazil
| | - Marcio E. Ferreira
- Brazilian Agricultural Research Coorporation, Embrapa Genetic Resources and Biotechnology, Brasilia, Distrito Federal Brazil
| | - Valeria S. Lopes-Caitar
- Brazilian Agricultural Research Corporation (Embrapa), Embrapa Soybean, Londrina, Paraná Brazil
| | - Silvana R. R. Marin
- Brazilian Agricultural Research Corporation (Embrapa), Embrapa Soybean, Londrina, Paraná Brazil
| | - Carlos A. A. Arias
- Brazilian Agricultural Research Corporation (Embrapa), Embrapa Soybean, Londrina, Paraná Brazil
| | - Ivani de O. N. Lopes
- Brazilian Agricultural Research Corporation (Embrapa), Embrapa Soybean, Londrina, Paraná Brazil
| | - Ricardo V. Abdelnoor
- Brazilian Agricultural Research Corporation (Embrapa), Embrapa Soybean, Londrina, Paraná Brazil
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17
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Mapping QTLs Controlling Soybean Rust Disease Resistance in Chiang Mai 5, an Induced Mutant Cultivar. Genes (Basel) 2022; 14:genes14010019. [PMID: 36672760 PMCID: PMC9858275 DOI: 10.3390/genes14010019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/12/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Soybean rust (SBR) caused by the fungus Phakopsora pachyrhizi is an important folia disease of soybean (Glycine max). In this study, we identified QTLs controlling SBR in Chiang Mai 5 (CM5), an SBR-resistant cultivar developed by induced mutation breeding. A recombinant inbred line (RIL) population of 108 lines developed from a cross between Sukhothai 2 (SKT2, a susceptible cultivar) and CM5 was evaluated for SBR resistance under field conditions in Thailand. QTL analysis for the resistance in the RIL population identified a single QTL, qSBR18.1, for resistance. qSBR18.1 was mapped to a 212-kb region on chromosome 18 between simple sequence repeat markers Satt288 and sc21_3420 and accounted for 21.31-35.09% depending on the traits evaluated for resistance. The qSBR18.1 interval overlapped with genomic regions containing resistance to P. pachyrhizi 4 (Rpp4), a locus for SBR resistance. Three tightly linked genes, Glyma.18G226250, Glyma.18G226300, and Glyma.18G226500, each encoding leucine-rich repeat-containing protein, were identified as candidate genes for SBR resistance at the qSRB18.1. The qSBR18.1 would be useful for breeding of SBR resistance.
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Molecular Breeding to Overcome Biotic Stresses in Soybean: Update. PLANTS 2022; 11:plants11151967. [PMID: 35956444 PMCID: PMC9370206 DOI: 10.3390/plants11151967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/16/2022] [Accepted: 07/25/2022] [Indexed: 11/17/2022]
Abstract
Soybean (Glycine max (L.) Merr.) is an important leguminous crop and biotic stresses are a global concern for soybean growers. In recent decades, significant development has been carried outtowards identification of the diseases caused by pathogens, sources of resistance and determination of loci conferring resistance to different diseases on linkage maps of soybean. Host-plant resistance is generally accepted as the bestsolution because of its role in the management of environmental and economic conditions of farmers owing to low input in terms of chemicals. The main objectives of soybean crop improvement are based on the identification of sources of resistance or tolerance against various biotic as well as abiotic stresses and utilization of these sources for further hybridization and transgenic processes for development of new cultivars for stress management. The focus of the present review is to summarize genetic aspects of various diseases caused by pathogens in soybean and molecular breeding research work conducted to date.
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Ambika, Aski MS, Gayacharan, Hamwieh A, Talukdar A, Kumar Gupta S, Sharma BB, Joshi R, Upadhyaya HD, Singh K, Kumar R. Unraveling Origin, History, Genetics, and Strategies for Accelerated Domestication and Diversification of Food Legumes. Front Genet 2022; 13:932430. [PMID: 35979429 PMCID: PMC9376740 DOI: 10.3389/fgene.2022.932430] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/15/2022] [Indexed: 11/24/2022] Open
Abstract
Domestication is a dynamic and ongoing process of transforming wild species into cultivated species by selecting desirable agricultural plant features to meet human needs such as taste, yield, storage, and cultivation practices. Human plant domestication began in the Fertile Crescent around 12,000 years ago and spread throughout the world, including China, Mesoamerica, the Andes and Near Oceania, Sub-Saharan Africa, and eastern North America. Indus valley civilizations have played a great role in the domestication of grain legumes. Crops, such as pigeon pea, black gram, green gram, lablab bean, moth bean, and horse gram, originated in the Indian subcontinent, and Neolithic archaeological records indicate that these crops were first domesticated by early civilizations in the region. The domestication and evolution of wild ancestors into today’s elite cultivars are important contributors to global food supply and agricultural crop improvement. In addition, food legumes contribute to food security by protecting human health and minimize climate change impacts. During the domestication process, legume crop species have undergone a severe genetic diversity loss, and only a very narrow range of variability is retained in the cultivars. Further reduction in genetic diversity occurred during seed dispersal and movement across the continents. In general, only a few traits, such as shattering resistance, seed dormancy loss, stem growth behavior, flowering–maturity period, and yield traits, have prominence in the domestication process across the species. Thus, identification and knowledge of domestication responsive loci were often useful in accelerating new species’ domestication. The genes and metabolic pathways responsible for the significant alterations that occurred as an outcome of domestication might aid in the quick domestication of novel crops. Further, recent advances in “omics” sciences, gene-editing technologies, and functional analysis will accelerate the domestication and crop improvement of new crop species without losing much genetic diversity. In this review, we have discussed about the origin, center of diversity, and seed movement of major food legumes, which will be useful in the exploration and utilization of genetic diversity in crop improvement. Further, we have discussed about the major genes/QTLs associated with the domestication syndrome in pulse crops and the future strategies to improve the food legume crops.
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Karhoff S, Vargas-Garcia C, Lee S, Mian MAR, Graham MA, Dorrance AE, McHale LK. Identification of Candidate Genes for a Major Quantitative Disease Resistance Locus From Soybean PI 427105B for Resistance to Phytophthora sojae. FRONTIERS IN PLANT SCIENCE 2022; 13:893652. [PMID: 35774827 PMCID: PMC9237613 DOI: 10.3389/fpls.2022.893652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
Phytophthora root and stem rot is a yield-limiting soybean disease caused by the soil-borne oomycete Phytophthora sojae. Although multiple quantitative disease resistance loci (QDRL) have been identified, most explain <10% of the phenotypic variation (PV). The major QDRL explaining up to 45% of the PV were previously identified on chromosome 18 and represent a valuable source of resistance for soybean breeding programs. Resistance alleles from plant introductions 427105B and 427106 significantly increase yield in disease-prone fields and result in no significant yield difference in fields with less to no disease pressure. In this study, high-resolution mapping reduced the QDRL interval to 3.1 cm, and RNA-seq analysis of near-isogenic lines (NILs) varying at QDRL-18 pinpointed a single gene of interest which was downregulated in inoculated NILs carrying the resistant allele compared to inoculated NILs with the susceptible allele. This gene of interest putatively encodes a serine-threonine kinase (STK) related to the AtCR4 family and may be acting as a susceptibility factor, based on the specific increase of jasmonic acid concentration in inoculated NILs. This work facilitates further functional analyses and marker-assisted breeding efforts by prioritizing candidate genes and narrowing the targeted region for introgression.
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Affiliation(s)
- Stephanie Karhoff
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States
- Center for Soybean Research, The Ohio State University, Columbus, OH, United States
| | - Christian Vargas-Garcia
- Center for Soybean Research, The Ohio State University, Columbus, OH, United States
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, United States
| | - Sungwoo Lee
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, United States
| | - M. A. Rouf Mian
- United States Department of Agriculture-Agricultural Research Service, Soybean Research Unit, Raleigh, NC, United States
| | - Michelle A. Graham
- Department of Agronomy, Iowa State University, Ames, IA, United States
- United States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Resources Unit, Ames, IA, United States
| | - Anne E. Dorrance
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States
- Center for Soybean Research, The Ohio State University, Columbus, OH, United States
- Department of Plant Pathology, The Ohio State University, Wooster, OH, United States
| | - Leah K. McHale
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States
- Center for Soybean Research, The Ohio State University, Columbus, OH, United States
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, United States
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21
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O’Rourke JA, Morrisey MJ, Merry R, Espina MJ, Lorenz AJ, Stupar RM, Graham MA. Mining Fiskeby III and Mandarin (Ottawa) Expression Profiles to Understand Iron Stress Tolerant Responses in Soybean. Int J Mol Sci 2021; 22:11032. [PMID: 34681702 PMCID: PMC8537376 DOI: 10.3390/ijms222011032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/06/2021] [Accepted: 10/10/2021] [Indexed: 12/13/2022] Open
Abstract
The soybean (Glycine max L. merr) genotype Fiskeby III is highly resistant to a multitude of abiotic stresses, including iron deficiency, incurring only mild yield loss during stress conditions. Conversely, Mandarin (Ottawa) is highly susceptible to disease and suffers severe phenotypic damage and yield loss when exposed to abiotic stresses such as iron deficiency, a major challenge to soybean production in the northern Midwestern United States. Using RNA-seq, we characterize the transcriptional response to iron deficiency in both Fiskeby III and Mandarin (Ottawa) to better understand abiotic stress tolerance. Previous work by our group identified a quantitative trait locus (QTL) on chromosome 5 associated with Fiskeby III iron efficiency, indicating Fiskeby III utilizes iron deficiency stress mechanisms not previously characterized in soybean. We targeted 10 of the potential candidate genes in the Williams 82 genome sequence associated with the QTL using virus-induced gene silencing. Coupling virus-induced gene silencing with RNA-seq, we identified a single high priority candidate gene with a significant impact on iron deficiency response pathways. Characterization of the Fiskeby III responses to iron stress and the genes underlying the chromosome 5 QTL provides novel targets for improved abiotic stress tolerance in soybean.
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Affiliation(s)
| | | | - Ryan Merry
- Department of Genetics and Agronomy, University of Minnesota, St. Paul, MN 55108, USA; (R.M.); (M.J.E.); (A.J.L.); (R.M.S.)
| | - Mary Jane Espina
- Department of Genetics and Agronomy, University of Minnesota, St. Paul, MN 55108, USA; (R.M.); (M.J.E.); (A.J.L.); (R.M.S.)
| | - Aaron J. Lorenz
- Department of Genetics and Agronomy, University of Minnesota, St. Paul, MN 55108, USA; (R.M.); (M.J.E.); (A.J.L.); (R.M.S.)
| | - Robert M. Stupar
- Department of Genetics and Agronomy, University of Minnesota, St. Paul, MN 55108, USA; (R.M.); (M.J.E.); (A.J.L.); (R.M.S.)
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22
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Parmezan TR, Brito Júnior SL, Carvalho KD, Aquino MD, Birkett M, Pickett J, Nunes EDO, Abdelnor RV, Campo CBH, Marcelino-Guimarães FC. Transcriptional profile of genes involved in the production of terpenes and glyceollins in response to biotic stresses in soybean. Genet Mol Biol 2020; 43:e20190388. [PMID: 33174975 PMCID: PMC7644969 DOI: 10.1590/1678-4685-gmb-2019-0388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 07/08/2020] [Indexed: 11/21/2022] Open
Abstract
Terpenes produced by plants comprise a diverse range of secondary metabolites, including volatile organic compounds (VOCs). Terpene VOC production may be altered after damage or by biological stimuli such as bacterial, fungal and insects, and subsequent triggering of plant defense responses. These VOCs originate in plants from two independent pathways: the mevalonate and the methylerythritol phosphate pathways, which utilize dimethylallyl and isopentenyl diphosphates to form the terpenoidal precursors. Phakopsora pachyrhizi fungi causes Asian soybean rust, limiting soybean production and resulting in losses of up to 80% if no control strategies are applied. By using a transcriptome datasets, we investigated the regulation of genes of the mevalonate pathway under different biotic stresses. We studied the impact of P. pachyrhizi infection in vivo expression profile of genes involved in terpenoid and glyceollin biosynthesis in genotypes harboring different resistance genes (Rpp), and across the infection cycle. In addition, we used UPLC and UPGC analysis to evaluate glyceollin and VOC production, respectively, to identify metabolites associated with soybean responses to pathogen infection. The regulation of soybean genes involved in terpene production was influenced by genotypes, depending on the Rpp gene, while glyceollin was induced in all genotypes. Furthermore, a sesquiterpene was identified as a potential marker associated with rust symptoms on soybean.
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Affiliation(s)
- Talitta Regina Parmezan
- Universidade Estadual de Londrina, Departamento de Bioquímica e Biotecnologia, Londrina, PR, Brazil
| | | | - Kenia de Carvalho
- Universidade Estadual de Londrina, Departamento de Genética e Biologia Molecular, Londrina, PR, Brazil
| | - Moisés de Aquino
- Empresa Brasileira de Pesquisa Agropecuária-EMBRAPA Soja, Londrina, PR, Brazil
| | - Michael Birkett
- Rothamsted Research, Biointeractions and Crop Protection Department, Harpenden, UK
| | - John Pickett
- Cardiff University, School of Chemistry, Wales, UK
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23
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McCabe CE, Graham MA. New tools for characterizing early brown stem rot disease resistance signaling in soybean. THE PLANT GENOME 2020; 13:e20037. [PMID: 33217212 DOI: 10.1002/tpg2.20037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 05/11/2020] [Accepted: 05/26/2020] [Indexed: 05/12/2023]
Abstract
Brown stem rot (BSR) reduces soybean [Glycine max (L.) Merr.] yield by up to 38%. The BSR causal agent is Phialophora gregata f. sp. sojae, a slow-growing, necrotrophic fungus whose life cycle includes latent and pathogenic phases, each lasting several weeks. Brown stem rot foliar symptoms are often misdiagnosed as other soybean diseases or nutrient stress, making BSR resistance especially difficult to phenotype. To shed light on the genes and networks contributing to P. gregata resistance, we conducted RNA sequencing (RNA-seq) of a resistant genotype (PI 437970, Rbs3). Leaf, stem, and root tissues were collected 12, 24, and 36 h after stab inoculation with P. gregata, or mock infection, in the plant stem. By using multiple tissues and time points, we could see that leaves, stems, and roots use the same defense pathways. Our analyses suggest that P. gregata induces a biphasic defense response, with pathogen-associated molecular pattern (PAMP) triggered immunity observed in leaves at 12 and 24 h after infection (HAI) and effector triggered immunity detected at 36 h after infection in the stems. Gene networks associated with defense, photosynthesis, nutrient homeostasis, DNA replication, and growth are the hallmarks of resistance to P. gregata. While P. gregata is a slow-growing pathogen, our results demonstrate that pathogen recognition occurs hours after infection. By exploiting the genes and networks described here, we will be able to develop novel diagnostic tools to facilitate breeding and screening for BSR resistance.
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Affiliation(s)
- Chantal E McCabe
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011-1010, USA
| | - Michelle A Graham
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011-1010, USA
- Department of Agronomy, Iowa State University, Ames, IA, 50011-1010, USA
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24
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Hu D, Chen Z, Zhang C, Ganiger M. Reduction of Phakopsora pachyrhizi infection on soybean through host- and spray-induced gene silencing. MOLECULAR PLANT PATHOLOGY 2020; 21:794-807. [PMID: 32196911 PMCID: PMC7214474 DOI: 10.1111/mpp.12931] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/23/2020] [Accepted: 02/19/2020] [Indexed: 05/10/2023]
Abstract
Asian soybean rust (ASR), caused by the obligate fungal pathogen Phakopsora pachyrhizi, often leads to significant yield losses and can only be managed through fungicide applications currently. In the present study, eight urediniospore germination or appressorium formation induced P. pachyrhizi genes were investigated for their feasibility to suppress ASR through a bean pod mottle virus (BPMV)-based host-induced gene silencing (HIGS) strategy. Soybean plants expressing three of these modified BPMV vectors suppressed the expression of their corresponding target gene by 45%-80%, fungal biomass accumulation by 58%-80%, and significantly reduced ASR symptom development in soybean leaves after the plants were inoculated with P. pachyrhizi, demonstrating that HIGS can be used to manage ASR. In addition, when the in vitro synthesized double-stranded RNAs (dsRNAs) for three of the genes encoding an acetyl-CoA acyltransferase, a 40S ribosomal protein S16, and glycine cleavage system H protein were sprayed directly onto detached soybean leaves prior to P. pachyrhizi inoculation, they also resulted in an average of over 73% reduction of pustule numbers and 75% reduction in P. pachyrhizi biomass accumulation on the detached leaves compared to the controls. To the best of our knowledge, this is the first report of suppressing P. pachyrhizi infection in soybean through both HIGS and spray-induced gene silencing. It was demonstrated that either HIGS constructs targeting P. pachyrhizi genes or direct dsRNA spray application could be an effective strategy for reducing ASR development on soybean.
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Affiliation(s)
- Dongfang Hu
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLAUSA
| | - Zhi‐Yuan Chen
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLAUSA
| | - Chunquan Zhang
- Department of AgricultureAlcorn State UniversityLormanMSUSA
| | - Mala Ganiger
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLAUSA
- Present address:
Department of Plant PathologyUniversity of MinnesotaSt. PaulMNUSA
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25
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Vieira P, Mowery J, Eisenback JD, Shao J, Nemchinov LG. Cellular and Transcriptional Responses of Resistant and Susceptible Cultivars of Alfalfa to the Root Lesion Nematode, Pratylenchus penetrans. FRONTIERS IN PLANT SCIENCE 2019; 10:971. [PMID: 31417588 PMCID: PMC6685140 DOI: 10.3389/fpls.2019.00971] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 07/11/2019] [Indexed: 05/04/2023]
Abstract
The root lesion nematode (RLN), Pratylenchus penetrans, is a migratory species that attacks a broad range of crops, including alfalfa. High levels of infection can reduce alfalfa forage yields and lead to decreased cold tolerance. Currently, there are no commercially certified varieties with RLN resistance. Little information on molecular interactions between alfalfa and P. penetrans, that would shed light on mechanisms of alfalfa resistance to RLN, is available. To advance our understanding of the host-pathogen interactions and to gain biological insights into the genetics and genomics of host resistance to RLN, we performed a comprehensive assessment of resistant and susceptible interactions of alfalfa with P. penetrans that included root penetration studies, ultrastructural observations, and global gene expression profiling of host plants and the nematode. Several gene-candidates associated with alfalfa resistance to P. penetrans and nematode parasitism genes encoding nematode effector proteins were identified for potential use in alfalfa breeding programs or development of new nematicides. We propose that preformed or constitutive defenses, such as significant accumulation of tannin-like deposits in root cells of the resistant cultivar, could be a key to nematode resistance, at least for the specific case of alfalfa-P. penetrans interaction.
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Affiliation(s)
- Paulo Vieira
- Molecular Plant Pathology Laboratory, United States Department of Agriculture – Agricultural Research Service, Beltsville, MD, United States
- School of Plant and Environmental Science, Virginia Tech, Blacksburg, VA, United States
| | - Joseph Mowery
- Electron and Confocal Microscopy Unit, United States Department of Agriculture – Agricultural Research Service, Beltsville, MD, United States
| | - Jonathan D. Eisenback
- School of Plant and Environmental Science, Virginia Tech, Blacksburg, VA, United States
| | - Jonathan Shao
- Molecular Plant Pathology Laboratory, United States Department of Agriculture – Agricultural Research Service, Beltsville, MD, United States
| | - Lev G. Nemchinov
- Molecular Plant Pathology Laboratory, United States Department of Agriculture – Agricultural Research Service, Beltsville, MD, United States
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Pedley KF, Pandey AK, Ruck A, Lincoln LM, Whitham SA, Graham MA. Rpp1 Encodes a ULP1-NBS-LRR Protein That Controls Immunity to Phakopsora pachyrhizi in Soybean. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:120-133. [PMID: 30303765 DOI: 10.1094/mpmi-07-18-0198-fi] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Phakopsora pachyrhizi is the causal agent of Asian soybean rust. Susceptible soybean plants infected by virulent isolates of P. pachyrhizi are characterized by tan-colored lesions and erumpent uredinia on the leaf surface. Germplasm screening and genetic analyses have led to the identification of seven loci, Rpp1 to Rpp7, that provide varying degrees of resistance to P. pachyrhizi (Rpp). Two genes, Rpp1 and Rpp1b, map to the same region on soybean chromosome 18. Rpp1 is unique among the Rpp genes in that it confers an immune response (IR) to avirulent P. pachyrhizi isolates. The IR is characterized by a lack of visible symptoms, whereas resistance provided by Rpp1b to Rpp7 results in red-brown foliar lesions. Rpp1 maps to a region spanning approximately 150 kb on chromosome 18 between markers Sct_187 and Sat_064 in L85-2378 (Rpp1), an isoline developed from Williams 82 and PI 200492 (Rpp1). To identify Rpp1, we constructed a bacterial artificial chromosome library from soybean accession PI 200492. Sequencing of the Rpp1 locus identified three homologous nucleotide binding site-leucine rich repeat (NBS-LRR) candidate resistance genes between Sct_187 and Sat_064. Each candidate gene is also predicted to encode an N-terminal ubiquitin-like protease 1 (ULP1) domain. Cosilencing of the Rpp1 candidates abrogated the immune response in the Rpp1 resistant soybean accession PI 200492, indicating that Rpp1 is a ULP1-NBS-LRR protein and plays a key role in the IR.
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Affiliation(s)
- Kerry F Pedley
- 1 United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD 21702, U.S.A
| | - Ajay K Pandey
- 1 United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD 21702, U.S.A
- 3 Iowa State University, Department of Plant Pathology and Microbiology, Ames, IA 50011, U.S.A
| | - Amy Ruck
- 1 United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD 21702, U.S.A
| | - Lori M Lincoln
- 2 USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, U.S.A.; and
| | - Steven A Whitham
- 3 Iowa State University, Department of Plant Pathology and Microbiology, Ames, IA 50011, U.S.A
| | - Michelle A Graham
- 2 USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, U.S.A.; and
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Wu X, Li G, Wang B, Hu Y, Wu X, Wang Y, Lu Z, Xu P. Fine mapping Ruv2, a new rust resistance gene in cowpea (Vigna unguiculata), to a 193-kb region enriched with NBS-type genes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2709-2718. [PMID: 30225641 DOI: 10.1007/s00122-018-3185-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/08/2018] [Indexed: 05/07/2023]
Abstract
A new rust resistance gene Ruv2 was fine-mapped in cowpea to a 193-kb region on chromosome 2, which harboured 23 predicted gene models enriched with NBS-type genes. ZN016 is a landrace vegetable cowpea highly resistant to rust. Two previous studies using mixed-spores inoculation suggested different modes of inheritance of rust resistance in ZN016. In this study, we initially developed a detached leaf assay with a purified single-rust isolate (Auv-LS). Using this approach, we assessed the inheritance of rust resistance in a recombinant inbred line (RIL) population and an F2 population, both derived from the cross of "ZN016" and the susceptible cultivar "Zhijiang282." A single dominant gene mode against Auv-LS was revealed in both populations. QTL mapping showed that this gene was coincident with the Ruv2 locus on LG7, one of the three resistance QTLs previously mapped based on mixed-spores inoculation data. Therefore, Ruv2 was considered as specifically against the rust isolate Auv-LS. Through an analysis of the RIL recombinants at Ruv2, we fine-mapped the gene to an ~ 0.45-cM interval between SNP markers 2_09656 and 2_00973, which corresponded to an ~ 193-kb region on chromosome 2 that harboured 23 predicted gene models enriched with NBS-type genes. Re-sequencing of the two parents revealed polymorphisms in four genes predictively to cause substantial protein structural changes, rendering them valuable candidate genes for future validation. Cross-species syntenic analysis indicated that Ruv2 may represent a novel rust resistance gene in food legumes. A cleaved amplified polymorphic sequences marker tightly linked to Ruv2 was developed to facilitate breeding. This work establishes a basis for map-based cloning of Ruv2 and breeding for rust resistance in cowpea and other legume crops.
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Affiliation(s)
- Xinyi Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
| | - Guojing Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
- State Key Laboratory Breeding Base for Sustainable Control of Plant Pest and Disease, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
| | - Baogen Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
| | - Yaowen Hu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
| | - Xiaohua Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
| | - Ying Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
| | - Zhongfu Lu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
| | - Pei Xu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China.
- State Key Laboratory Breeding Base for Sustainable Control of Plant Pest and Disease, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China.
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Childs SP, King ZR, Walker DR, Harris DK, Pedley KF, Buck JW, Boerma HR, Li Z. Discovery of a seventh Rpp soybean rust resistance locus in soybean accession PI 605823. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:27-41. [PMID: 28980046 DOI: 10.1007/s00122-017-2983-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 09/14/2017] [Indexed: 05/28/2023]
Abstract
KEY MESSAGE A novel Rpp gene from PI 605823 for resistance to Phakopsora pachyrhizi was mapped on chromosome 19. Soybean rust, caused by the obligate biotrophic fungal pathogen Phakopsora pachyrhizi Syd. & P. Syd, is a disease threat to soybean production in regions of the world with mild winters. Host plant resistance conditioned by resistance to P. pachyrhizi (Rpp) genes has been found in numerous soybean accessions, and at least 10 Rpp genes or alleles have been mapped to six genetic loci. Identifying additional disease-resistance genes will facilitate development of soybean cultivars with durable resistance. PI 605823, a plant introduction from Vietnam, was previously identified as resistant to US populations of P. pachyrhizi in greenhouse and field trials. In this study, bulked segregant analysis using an F2 population derived from 'Williams 82' × PI 605823 identified a genomic region associated with resistance to P. pachyrhizi isolate GA12, which had been collected in the US State of Georgia in 2012. To further map the resistance locus, linkage mapping was carried out using single-nucleotide polymorphism markers and phenotypic data from greenhouse assays with an F2:3 population derived from Williams 82 × PI 605823 and an F4:5 population derived from '5601T' × PI 605823. A novel resistance gene, Rpp7, was mapped to a 154-kb interval (Gm19: 39,462,291-39,616,643 Glyma.Wm82.a2) on chromosome 19 that is different from the genomic locations of any previously reported Rpp genes. This new gene could be incorporated into elite breeding lines to help provide more durable resistance to soybean rust.
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Affiliation(s)
- Silas P Childs
- Department of Crop and Soil Sciences and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA
| | - Zachary R King
- Department of Crop and Soil Sciences and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA
| | - David R Walker
- Soybean/Maize Germplasm, Pathology and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Urbana, IL, USA.
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Donna K Harris
- Department of Crop and Soil Sciences and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA
| | - Kerry F Pedley
- Foreign Disease-Weed Science Research Unit, USDA-ARS, Ft. Detrick, Frederick, MD, USA
| | - James W Buck
- Department of Plant Pathology, University of Georgia, Griffin, GA, USA
| | - H Roger Boerma
- Department of Crop and Soil Sciences and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA
| | - Zenglu Li
- Department of Crop and Soil Sciences and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA.
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Morriss SC, Studham ME, Tylka GL, MacIntosh GC. Validation of a hairy roots system to study soybean-soybean aphid interactions. PLoS One 2017; 12:e0174914. [PMID: 28358854 PMCID: PMC5373632 DOI: 10.1371/journal.pone.0174914] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 03/17/2017] [Indexed: 11/30/2022] Open
Abstract
The soybean aphid (Aphis glycines) is one of the main insect pests of soybean (Glycine max) worldwide. Genomics approaches have provided important data on transcriptome changes, both in the insect and in the plant, in response to the plant-aphid interaction. However, the difficulties to transform soybean and to rear soybean aphid on artificial media have hindered our ability to systematically test the function of genes identified by those analyses as mediators of plant resistance to the insect. An efficient approach to produce transgenic soybean material is the production of transformed hairy roots using Agrobacterium rhizogenes; however, soybean aphids colonize leaves or stems and thus this approach has not been utilized. Here, we developed a hairy root system that allowed effective aphid feeding. We show that this system supports aphid performance similar to that observed in leaves. The use of hairy roots to study plant resistance is validated by experiments showing that roots generated from cotyledons of resistant lines carrying the Rag1 or Rag2 resistance genes are also resistant to aphid feeding, while related susceptible lines are not. Our results demonstrate that hairy roots are a good system to study soybean aphid-soybean interactions, providing a quick and effective method that could be used for functional analysis of the resistance response to this insect.
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Affiliation(s)
- Stephanie C. Morriss
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Matthew E. Studham
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Gregory L. Tylka
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America
| | - Gustavo C. MacIntosh
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
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Whitham SA, Qi M, Innes RW, Ma W, Lopes-Caitar V, Hewezi T. Molecular Soybean-Pathogen Interactions. ANNUAL REVIEW OF PHYTOPATHOLOGY 2016; 54:443-68. [PMID: 27359370 DOI: 10.1146/annurev-phyto-080615-100156] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Soybean hosts a wide variety of pathogens that cause significant yield losses. The importance of soybean as a major oilseed crop has led to research focused on its interactions with pathogens, such as Soybean mosaic virus, Pseudomonas syringae, Phytophthora sojae, Phakopsora pachyrhizi, and Heterodera glycines. Pioneering work on soybean's interactions with these organisms, which represent the five major pathogen groups (viruses, bacteria, oomycetes, fungi, and nematodes), has contributed to our understanding of the molecular mechanisms underlying virulence and immunity. These mechanisms involve conserved and unique features that validate the need for research in both soybean and homologous model systems. In this review, we discuss identification of effectors and their functions as well as resistance gene-mediated recognition and signaling. We also point out areas in which model systems and recent advances in resources and tools have provided opportunities to gain deeper insights into soybean-pathogen interactions.
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Affiliation(s)
- Steven A Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011; ,
| | - Mingsheng Qi
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011; ,
| | - Roger W Innes
- Department of Biology, Indiana University, Bloomington, Indiana 47405;
| | - Wenbo Ma
- Department of Plant Pathology and Microbiology, University of California, Riverside, California 92521;
| | - Valéria Lopes-Caitar
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996; ,
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996; ,
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31
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Meziadi C, Blanchet S, Richard MMS, Pilet-Nayel ML, Geffroy V, Pflieger S. Bean pod mottle virus: a new powerful tool for functional genomics studies in Pisum sativum. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1777-87. [PMID: 26896301 PMCID: PMC5067550 DOI: 10.1111/pbi.12537] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 11/13/2015] [Accepted: 01/06/2016] [Indexed: 05/08/2023]
Abstract
Pea (Pisum sativum L.) is an important legume worldwide. The importance of pea in arable rotations and nutritional value for both human and animal consumption have fostered sustained production and different studies to improve agronomic traits of interest. Moreover, complete sequencing of the pea genome is currently underway and will lead to the identification of a large number of genes potentially associated with important agronomic traits. Because stable genetic transformation is laborious for pea, virus-induced gene silencing (VIGS) appears as a powerful alternative technology for determining the function of unknown genes. In this work, we present a rapid and efficient viral inoculation method using DNA infectious plasmids of Bean pod mottle virus (BPMV)-derived VIGS vector. Six pea genotypes with important genes controlling biotic and/or abiotic stresses were found susceptible to BPMV carrying a GFP reporter gene and showed fluorescence in both shoots and roots. In a second step, we investigated 37 additional pea genotypes and found that 30 were susceptible to BPMV and only 7 were resistant. The capacity of BPMV to induce silencing of endogenes was investigated in the most susceptible genotype using two visual reporter genes: PsPDS and PsKORRIGAN1 (PsKOR1) encoding PHYTOENE DESATURASE and a 1,4-β-D-glucanase, respectively. The features of the 'one-step' BPMV-derived VIGS vector include (i) the ease of rub-inoculation, without any need for biolistic or agro-inoculation procedures, (ii) simple cost-effective procedure and (iii) noninterference of viral symptoms with silencing. These features make BPMV the most adapted VIGS vector in pea to make low- to high-throughput VIGS studies.
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Affiliation(s)
- Chouaib Meziadi
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot Sorbonne Paris-Cité, Université Paris-Saclay, Orsay, France
| | - Sophie Blanchet
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot Sorbonne Paris-Cité, Université Paris-Saclay, Orsay, France
| | - Manon M S Richard
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot Sorbonne Paris-Cité, Université Paris-Saclay, Orsay, France
| | | | - Valérie Geffroy
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot Sorbonne Paris-Cité, Université Paris-Saclay, Orsay, France
| | - Stéphanie Pflieger
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot Sorbonne Paris-Cité, Université Paris-Saclay, Orsay, France
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32
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Rincker K, Lipka AE, Diers BW. Genome-Wide Association Study of Brown Stem Rot Resistance in Soybean across Multiple Populations. THE PLANT GENOME 2016; 9. [PMID: 27898824 DOI: 10.3835/plantgenome2015.08.0064] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 12/15/2015] [Indexed: 05/07/2023]
Abstract
Genetic resistance to brown stem rot (BSR) of soybean [ (L.) Merr.], caused by (Allington & D.W. Chamb.) T.C. Harr. & McNew, has been identified and mapped with biparental populations. Although nearly 400 accessions have been identified with BSR resistance, this trait has been mapped in only 12 sources, and just two, PI84946-2 and PI88788, have been used to develop BSR resistant cultivars. Thus, there is a serious need to improve our knowledge of the genetic basis of BSR resistance in soybean so that resistance genes in cultivars can be diversified and markers close to resistance genes can be identified and used in marker-assisted selection (MAS). To this end, we conducted a genome-wide association study (GWAS) to identify novel genomic loci associated with BSR resistance and to gain further insight into a previously reported chromosome 16 region containing BSR resistance () genes. A total of 52,041 single-nucleotide polymorphisms (SNPs) were tested for association with BSR in a set of 4735 accessions from four diversity panels evaluated for resistance from 1989 to 2003. Using a unified mixed linear model and stepwise model selection, we refined the signals within the interval on chromosome 16 by finding associations that explain a substantial proportion of the total variation of BSR resistance. In combination with significant GWAS signals found elsewhere in the genome, our study will aid efforts to improve BSR resistance by providing new targets for MAS.
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33
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Langenbach C, Campe R, Beyer SF, Mueller AN, Conrath U. Fighting Asian Soybean Rust. FRONTIERS IN PLANT SCIENCE 2016; 7:797. [PMID: 27375652 PMCID: PMC4894884 DOI: 10.3389/fpls.2016.00797] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 05/22/2016] [Indexed: 05/18/2023]
Abstract
Phakopsora pachyrhizi is a biotrophic fungus provoking SBR disease. SBR poses a major threat to global soybean production. Though several R genes provided soybean immunity to certain P. pachyrhizi races, the pathogen swiftly overcame this resistance. Therefore, fungicides are the only current means to control SBR. However, insensitivity to fungicides is soaring in P. pachyrhizi and, therefore, alternative measures are needed for SBR control. In this article, we discuss the different approaches for fighting SBR and their potential, disadvantages, and advantages over other measures. These encompass conventional breeding for SBR resistance, transgenic approaches, exploitation of transcription factors, secondary metabolites, and antimicrobial peptides, RNAi/HIGS, and biocontrol strategies. It seems that an integrating approach exploiting different measures is likely to provide the best possible means for the effective control of SBR.
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Affiliation(s)
- Caspar Langenbach
- Department of Plant Physiology, RWTH Aachen UniversityAachen, Germany
| | - Ruth Campe
- BASF Plant Science Company GmbHLimburgerhof, Germany
| | | | - André N. Mueller
- Department of Plant Physiology, RWTH Aachen UniversityAachen, Germany
| | - Uwe Conrath
- Department of Plant Physiology, RWTH Aachen UniversityAachen, Germany
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34
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Kawashima CG, Guimarães GA, Nogueira SR, MacLean D, Cook DR, Steuernagel B, Baek J, Bouyioukos C, Melo BDVA, Tristão G, de Oliveira JC, Rauscher G, Mittal S, Panichelli L, Bacot K, Johnson E, Iyer G, Tabor G, Wulff BBH, Ward E, Rairdan GJ, Broglie KE, Wu G, van Esse HP, Jones JDG, Brommonschenkel SH. A pigeonpea gene confers resistance to Asian soybean rust in soybean. Nat Biotechnol 2016; 34:661-5. [PMID: 27111723 DOI: 10.1038/nbt.3554] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 03/24/2016] [Indexed: 12/31/2022]
Abstract
Asian soybean rust (ASR), caused by the fungus Phakopsora pachyrhizi, is one of the most economically important crop diseases, but is only treatable with fungicides, which are becoming less effective owing to the emergence of fungicide resistance. There are no commercial soybean cultivars with durable resistance to P. pachyrhizi, and although soybean resistance loci have been mapped, no resistance genes have been cloned. We report the cloning of a P. pachyrhizi resistance gene CcRpp1 (Cajanus cajan Resistance against Phakopsora pachyrhizi 1) from pigeonpea (Cajanus cajan) and show that CcRpp1 confers full resistance to P. pachyrhizi in soybean. Our findings show that legume species related to soybean such as pigeonpea, cowpea, common bean and others could provide a valuable and diverse pool of resistance traits for crop improvement.
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Affiliation(s)
| | | | | | | | - Doug R Cook
- Department of Plant Pathology, University of California Davis, Davis, California, USA
| | | | - Jongmin Baek
- Department of Plant Pathology, University of California Davis, Davis, California, USA
| | | | | | - Gustavo Tristão
- Dep. de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | - Gilda Rauscher
- Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA
| | - Shipra Mittal
- Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA
| | - Lisa Panichelli
- Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA
| | - Karen Bacot
- Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA
| | - Ebony Johnson
- Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA
| | - Geeta Iyer
- Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA
| | - Girma Tabor
- Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA
| | | | - Eric Ward
- 2Blades Foundation, Evanston, Illinois, USA
| | - Gregory J Rairdan
- Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA
| | - Karen E Broglie
- Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA
| | - Gusui Wu
- Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA
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Kim KH, Lim S, Kang YJ, Yoon MY, Nam M, Jun TH, Seo MJ, Baek SB, Lee JH, Moon JK, Lee SH, Lee SH, Lim HS, Moon JS, Park CH. Optimization of a Virus-Induced Gene Silencing System with Soybean yellow common mosaic virus for Gene Function Studies in Soybeans. THE PLANT PATHOLOGY JOURNAL 2016; 32:112-22. [PMID: 27147931 PMCID: PMC4853101 DOI: 10.5423/ppj.oa.04.2015.0063] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 11/27/2015] [Accepted: 12/02/2015] [Indexed: 05/24/2023]
Abstract
Virus-induced gene silencing (VIGS) is an effective tool for the study of soybean gene function. Successful VIGS depends on the interaction between virus spread and plant growth, which can be influenced by environmental conditions. Recently, we developed a new VIGS system derived from the Soybean yellow common mosaic virus (SYCMV). Here, we investigated several environmental and developmental factors to improve the efficiency of a SYCMV-based VIGS system to optimize the functional analysis of the soybean. Following SYCMV: Glycine max-phytoene desaturase (GmPDS) infiltration, we investigated the effect of photoperiod, inoculation time, concentration of Agrobacterium inoculm, and growth temperature on VIGS efficiency. In addition, the relative expression of GmPDS between non-silenced and silenced plants was measured by qRT-PCR. We found that gene silencing efficiency was highest at a photoperiod of 16/8 h (light/dark) at a growth temperature of approximately 27°C following syringe infiltration to unrolled unifoliolate leaves in cotyledon stage with a final SYCMV:GmPDS optimal density (OD)600 of 2.0. Using this optimized protocol, we achieved high efficiency of GmPDS-silencing in various soybean germplasms including cultivated and wild soybeans. We also confirmed that VIGS occurred in the entire plant, including the root, stem, leaves, and flowers, and could transmit GmPDS to other soybean germplasms via mechanical inoculation. This optimized protocol using a SYCMV-based VIGS system in the soybean should provide a fast and effective method to elucidate gene functions and for use in large-scale screening experiments.
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Affiliation(s)
- Kil Hyun Kim
- National Institute of Crop Science, Rural Development Administration, Suwon 441-707,
Korea
| | - Seungmo Lim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806,
Korea
- Biosystems and Bioengineering Program, University of Science and Technology, Daejeon 305-350,
Korea
| | - Yang Jae Kang
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921,
Korea
| | - Min Young Yoon
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921,
Korea
| | - Moon Nam
- School of Applied Biosciences, Kyungpook National University, Daegu 702-701,
Korea
| | - Tae Hwan Jun
- Department of Plant Bioscience, College of Natural Resources & Life Science, Pusan National University, Pusan 627-706,
Korea
| | - Min-Jung Seo
- National Institute of Crop Science, Rural Development Administration, Suwon 441-707,
Korea
| | - Seong-Bum Baek
- National Institute of Crop Science, Rural Development Administration, Suwon 441-707,
Korea
| | - Jeom-Ho Lee
- National Institute of Crop Science, Rural Development Administration, Suwon 441-707,
Korea
| | - Jung-Kyung Moon
- National Institute of Crop Science, Rural Development Administration, Suwon 441-707,
Korea
| | - Suk-Ha Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921,
Korea
| | - Su-Heon Lee
- School of Applied Biosciences, Kyungpook National University, Daegu 702-701,
Korea
| | - Hyoun-Sub Lim
- Department of Applied Biology, Chungnam National University, Daejeon 305-764,
Korea
| | - Jae Sun Moon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806,
Korea
- Biosystems and Bioengineering Program, University of Science and Technology, Daejeon 305-350,
Korea
| | - Chang-Hwan Park
- National Institute of Crop Science, Rural Development Administration, Suwon 441-707,
Korea
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King ZR, Harris DK, Pedley KF, Song Q, Wang D, Wen Z, Buck JW, Li Z, Boerma HR. A novel Phakopsora pachyrhizi resistance allele (Rpp) contributed by PI 567068A. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:517-34. [PMID: 26704418 DOI: 10.1007/s00122-015-2645-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 11/30/2015] [Indexed: 06/05/2023]
Abstract
KEY MESSAGE The Rpp6 locus of PI 567102B was mapped from 5,953,237 to 5,998,461 bp (chromosome 18); and a novel allele at the Rpp6 locus or tightly linked gene Rpp[PI567068A] of PI 567068A was mapped from 5,998,461 to 6,160,481 bp. Soybean rust (SBR), caused by the obligate, fungal pathogen Phakopsora pachyrhizi is an economic threat to soybean production, especially in the Americas. Host plant resistance is an important management strategy for SBR. The most recently described resistance to P. pachyrhizi (Rpp) gene is Rpp6 contributed by PI 567102B. Rpp6 was previously mapped to an interval of over four million base pairs on chromosome 18. PI 567068A was recently demonstrated to possess a resistance gene near the Rpp6 locus, yet PI 567068A gave a differential isolate reaction to several international isolates of P. pachyrhizi. The goals of this research were to fine map the Rpp6 locus of PI 567102B and PI 567068A and determine whether or not PI 567068A harbors a novel Rpp6 allele or another allele at a tightly linked resistance locus. Linkage mapping in this study mapped Rpp6 from 5,953,237 to 5,998,461 bp (LOD score of 58.3) and the resistance from PI 567068A from 5,998,461 to 6,160,481 bp (LOD score of 4.4) (Wm82.a1 genome sequence). QTL peaks were 139,033 bp apart from one another as determined by the most significant SNPs in QTL mapping. The results of haplotype analysis demonstrated that PI 567102B and PI 567068A share the same haplotype in the resistance locus containing both Rpp alleles, which was designated as the Rpp6/Rpp[PI567068A] haplotype. The Rpp6/Rpp[PI567068A] haplotype identified in this study can be used as a tool to rapidly screen other genotypes that possess a Rpp gene(s) and detect resistance at the Rpp6 locus in diverse germplasm.
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Affiliation(s)
- Zachary R King
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
| | - Donna K Harris
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
| | - Kerry F Pedley
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Foreign Disease-Weed Science Research Unit, Ft. Detrick, Frederick, MD, 21702, USA
| | - Qijian Song
- USDA-ARS Soybean Genomics and Improvement Laboratory, Beltsville, MD, 20705, USA
| | - Dechun Wang
- Soybean Genetics Lab, Michigan State University, East Lansing, MI, 48824, USA
| | - Zixiang Wen
- Soybean Genetics Lab, Michigan State University, East Lansing, MI, 48824, USA
| | - James W Buck
- Department of Plant Pathology, University of Georgia, Griffin, GA, 30223, USA
| | - Zenglu Li
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA.
| | - H Roger Boerma
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
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Expression of a synthetic rust fungal virus cDNA in yeast. Arch Virol 2015; 161:111-23. [PMID: 26497180 DOI: 10.1007/s00705-015-2639-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 10/03/2015] [Indexed: 10/22/2022]
Abstract
Mycoviruses are viruses that infect fungi. Recently, mycovirus-like RNAs were sequenced from the fungus Phakopsora pachyrhizi, the causal agent of soybean rust. One of the RNAs appeared to represent a novel mycovirus and was designated Phakopsora pachyrhizi virus 2383 (PpV2383). The genome of PpV2383 resembles Saccharomyces cerevisiae virus L-A, a double-stranded (ds) RNA mycovirus of yeast. PpV2383 encodes two major, overlapping open reading frames with similarity to gag (capsid protein) and pol (RNA-dependent RNA polymerase), and a -1 ribosomal frameshift is necessary for the translation of a gag-pol fusion protein. Phylogenetic analysis of pol relates PpV2383 to members of the family Totiviridae, including L-A. Because the obligate biotrophic nature of P. pachyrhizi makes it genetically intractable for in vivo analysis and because PpV2383 is similar to L-A, we synthesized a DNA clone of PpV2383 and tested its infectivity in yeast cells. PpV2383 RNA was successfully expressed in yeast, and mass spectrometry confirmed the translation of gag and gag-pol fusion proteins. There was, however, no production of PpV2383 dsRNA, the evidence of viral replication. Neither the presence of endogenous L-A nor the substitution of the 5' and 3' untranslated regions with those from L-A was sufficient to rescue replication of PpV2383. Nevertheless, the proof of transcription and translation from the clone in vivo are steps toward confirming that PpV2383 is a mycovirus. Further development of a surrogate biological system for the study of rust mycoviruses is necessary, and such research may facilitate biological control of rust diseases.
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Cai Y, Chen L, Liu X, Sun S, Wu C, Jiang B, Han T, Hou W. CRISPR/Cas9-Mediated Genome Editing in Soybean Hairy Roots. PLoS One 2015; 10:e0136064. [PMID: 26284791 PMCID: PMC4540462 DOI: 10.1371/journal.pone.0136064] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 07/29/2015] [Indexed: 12/29/2022] Open
Abstract
As a new technology for gene editing, the CRISPR (clustered regularly interspaced short palindromic repeat)/Cas (CRISPR-associated) system has been rapidly and widely used for genome engineering in various organisms. In the present study, we successfully applied type II CRISPR/Cas9 system to generate and estimate genome editing in the desired target genes in soybean (Glycine max (L.) Merrill.). The single-guide RNA (sgRNA) and Cas9 cassettes were assembled on one vector to improve transformation efficiency, and we designed a sgRNA that targeted a transgene (bar) and six sgRNAs that targeted different sites of two endogenous soybean genes (GmFEI2 and GmSHR). The targeted DNA mutations were detected in soybean hairy roots. The results demonstrated that this customized CRISPR/Cas9 system shared the same efficiency for both endogenous and exogenous genes in soybean hairy roots. We also performed experiments to detect the potential of CRISPR/Cas9 system to simultaneously edit two endogenous soybean genes using only one customized sgRNA. Overall, generating and detecting the CRISPR/Cas9-mediated genome modifications in target genes of soybean hairy roots could rapidly assess the efficiency of each target loci. The target sites with higher efficiencies can be used for regular soybean transformation. Furthermore, this method provides a powerful tool for root-specific functional genomics studies in soybean.
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Affiliation(s)
- Yupeng Cai
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Li Chen
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiujie Liu
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shi Sun
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Cunxiang Wu
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Bingjun Jiang
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Tianfu Han
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wensheng Hou
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Liu JZ, Graham MA, Pedley KF, Whitham SA. Gaining insight into soybean defense responses using functional genomics approaches. Brief Funct Genomics 2015; 14:283-90. [PMID: 25832523 DOI: 10.1093/bfgp/elv009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
Soybean pathogens significantly impact yield, resulting in over $4 billion dollars in lost revenue annually in the United States. Despite the deployment of improved soybean cultivars, pathogens continue to evolve to evade plant defense responses. Thus, there is an urgent need to identify and characterize gene networks controlling defense responses to harmful pathogens. In this review, we focus on major advances that have been made in identifying the genes and gene networks regulating defense responses with an emphasis on soybean-pathogen interactions that have been amenable to gene function analyses using gene silencing technologies. Further we describe new research striving to identify genes involved in durable broad-spectrum resistance. Finally, we consider future prospects for functional genomic studies in soybean and demonstrate that understanding soybean disease and stress tolerance will be expedited at an unprecedented pace.
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Chen H, Zhao S, Yang Z, Sha A, Wan Q, Zhang C, Chen L, Yuan S, Qiu D, Chen S, Shan Z, Zhou XA. Genetic analysis and molecular mapping of resistance gene to Phakopsora pachyrhizi in soybean germplasm SX6907. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:733-43. [PMID: 25673142 DOI: 10.1007/s00122-015-2468-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 01/23/2015] [Indexed: 06/04/2023]
Abstract
KEY MESSAGE In this study, Rpp6907, a novel resistance gene/allele to Phakopsora pachyrhizi in soybean, was mapped in a 111.9-kb region, including three NBS-LRR type predicted genes, on chromosome 18. Soybean rust caused by Phakopsora pachyrhizi Sydow has been reported in numerous soybean-growing regions worldwide. The development of rust-resistant varieties is the most economical and environmentally safe method to control the disease. The Chinese soybean germplasm SX6907 is resistant to P. pachyrhizi and exhibits immune reaction compared with the known Rpp genes. These characteristics suggest that SX6907 may carry at least one novel Rpp gene/allele. Three F2 populations from the crosses of SX6907 (resistant) and Tianlong 1, Zhongdou40, and Pudou11 (susceptible) were used to map the Rpp gene. Three resistance responses (immune, red-brown, and tan-colored lesion) were observed from the F2 individuals. The segregation follows a ratio of 1(resistance):2(heterozygous):1(susceptible), indicating that the resistance in SX6907 is controlled by a single incomplete dominant gene (designated as Rpp6907). Results showed that Rpp6907 was mapped on soybean chromosome 18 (molecular linkage group G, MLG G) flanked by simple sequence repeat (SSR) markers SSR24 and SSR40 at a distance of 111.9 kb. Among the ten genes marked within this 111.9-kb region between the two markers, three genes (Glyma18g51930, Glyma18g51950, and Glyma18g51960) are nucleotide-binding site and leucine-rich repeat-type genes. These genes may be involved in recognizing the presence of pathogens and ultimately conferring resistance. Based on resistance spectrum analysis and mapping results, we inferred that Rpp6907 is a novel gene different from Rpp1 in PI 200492, PI 561356, PI 587880A, PI 587886, and PI 594538A, or a new Rpp1-b allele.
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Affiliation(s)
- Haifeng Chen
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
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Yu N, Kim M, King ZR, Harris DK, Buck JW, Li Z, Diers BW. Fine mapping of the Asian soybean rust resistance gene Rpp2 from soybean PI 230970. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:387-96. [PMID: 25504467 DOI: 10.1007/s00122-014-2438-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 11/27/2014] [Indexed: 06/04/2023]
Abstract
KEY MESSAGE Asian soybean rust (ASR) resistance gene Rpp2 has been fine mapped into a 188.1 kb interval on Glyma.Wm82.a2, which contains a series of plant resistance ( R ) genes. Asian soybean rust (ASR), caused by the fungus Phakopsora pachyrihizi Syd. & P. Syd., is a serious disease in major soybean [Glycine max (L.) Merr.] production countries worldwide and causes yield losses up to 75 %. Defining the exact chromosomal position of ASR resistance genes is critical for improving the effectiveness of marker-assisted selection (MAS) for resistance and for cloning these genes. The objective of this study was to fine map the ASR resistance gene Rpp2 from the plant introduction (PI) 230970. Rpp2 was previously mapped within a 12.9-cM interval on soybean chromosome 16. The fine mapping was initiated by identifying recombination events in F2 and F3 plants using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers that flank the gene. Seventeen recombinant plants were identified and then tested with additional genetic markers saturating the gene region to localize the positions of each recombination. The progeny of these selected plants were tested for resistance to ASR and with SSR markers resulting in the mapping of Rpp2 to a 188.1 kb interval on the Williams 82 reference genome (Glyma.Wm82.a2). Twelve genes including ten toll/interleukin-1 receptor (TIR)-nucleotide-binding site (NBS)-leucine-rich repeat (LRR) genes were predicted to exist in this interval on the Glyma.Wm82.a2.v1 gene model map. Eight of these ten genes were homologous to the Arabidopsis TIR-NBS-LRR gene AT5G17680.1. The identified SSR and SNP markers close to Rpp2 and the candidate gene information presented in this study will be significant resources for MAS and gene cloning research.
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Affiliation(s)
- Neil Yu
- Department of Crop Sciences, University of Illinois, 1101 W. Peabody Drive, Urbana, IL, 61801, USA
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Shao ZQ, Zhang YM, Hang YY, Xue JY, Zhou GC, Wu P, Wu XY, Wu XZ, Wang Q, Wang B, Chen JQ. Long-term evolution of nucleotide-binding site-leucine-rich repeat genes: understanding gained from and beyond the legume family. PLANT PHYSIOLOGY 2014; 166:217-34. [PMID: 25052854 PMCID: PMC4149708 DOI: 10.1104/pp.114.243626] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Accepted: 07/11/2014] [Indexed: 05/18/2023]
Abstract
Proper utilization of plant disease resistance genes requires a good understanding of their short- and long-term evolution. Here we present a comprehensive study of the long-term evolutionary history of nucleotide-binding site (NBS)-leucine-rich repeat (LRR) genes within and beyond the legume family. The small group of NBS-LRR genes with an amino-terminal RESISTANCE TO POWDERY MILDEW8 (RPW8)-like domain (referred to as RNL) was first revealed as a basal clade sister to both coiled-coil-NBS-LRR (CNL) and Toll/Interleukin1 receptor-NBS-LRR (TNL) clades. Using Arabidopsis (Arabidopsis thaliana) as an outgroup, this study explicitly recovered 31 ancestral NBS lineages (two RNL, 21 CNL, and eight TNL) that had existed in the rosid common ancestor and 119 ancestral lineages (nine RNL, 55 CNL, and 55 TNL) that had diverged in the legume common ancestor. It was shown that, during their evolution in the past 54 million years, approximately 94% (112 of 119) of the ancestral legume NBS lineages experienced deletions or significant expansions, while seven original lineages were maintained in a conservative manner. The NBS gene duplication pattern was further examined. The local tandem duplications dominated NBS gene gains in the total number of genes (more than 75%), which was not surprising. However, it was interesting from our study that ectopic duplications had created many novel NBS gene loci in individual legume genomes, which occurred at a significant frequency of 8% to 20% in different legume lineages. Finally, by surveying the legume microRNAs that can potentially regulate NBS genes, we found that the microRNA-NBS gene interaction also exhibited a gain-and-loss pattern during the legume evolution.
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Affiliation(s)
- Zhu-Qing Shao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China (Z.-Q.S., Y.-M.Z., J.-Y.X., G.-C.Z., P.W., X.-Y.W., X.-Z.W., Q.W., B.W., J.-Q.C.); andJiangsu Province and Chinese Academy of Science, Institute of Botany, Nanjing 210014, China (Y.-M.Z., Y.-Y.H., J.-Y.X.)
| | - Yan-Mei Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China (Z.-Q.S., Y.-M.Z., J.-Y.X., G.-C.Z., P.W., X.-Y.W., X.-Z.W., Q.W., B.W., J.-Q.C.); andJiangsu Province and Chinese Academy of Science, Institute of Botany, Nanjing 210014, China (Y.-M.Z., Y.-Y.H., J.-Y.X.)
| | - Yue-Yu Hang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China (Z.-Q.S., Y.-M.Z., J.-Y.X., G.-C.Z., P.W., X.-Y.W., X.-Z.W., Q.W., B.W., J.-Q.C.); andJiangsu Province and Chinese Academy of Science, Institute of Botany, Nanjing 210014, China (Y.-M.Z., Y.-Y.H., J.-Y.X.)
| | - Jia-Yu Xue
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China (Z.-Q.S., Y.-M.Z., J.-Y.X., G.-C.Z., P.W., X.-Y.W., X.-Z.W., Q.W., B.W., J.-Q.C.); andJiangsu Province and Chinese Academy of Science, Institute of Botany, Nanjing 210014, China (Y.-M.Z., Y.-Y.H., J.-Y.X.)
| | - Guang-Can Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China (Z.-Q.S., Y.-M.Z., J.-Y.X., G.-C.Z., P.W., X.-Y.W., X.-Z.W., Q.W., B.W., J.-Q.C.); andJiangsu Province and Chinese Academy of Science, Institute of Botany, Nanjing 210014, China (Y.-M.Z., Y.-Y.H., J.-Y.X.)
| | - Ping Wu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China (Z.-Q.S., Y.-M.Z., J.-Y.X., G.-C.Z., P.W., X.-Y.W., X.-Z.W., Q.W., B.W., J.-Q.C.); andJiangsu Province and Chinese Academy of Science, Institute of Botany, Nanjing 210014, China (Y.-M.Z., Y.-Y.H., J.-Y.X.)
| | - Xiao-Yi Wu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China (Z.-Q.S., Y.-M.Z., J.-Y.X., G.-C.Z., P.W., X.-Y.W., X.-Z.W., Q.W., B.W., J.-Q.C.); andJiangsu Province and Chinese Academy of Science, Institute of Botany, Nanjing 210014, China (Y.-M.Z., Y.-Y.H., J.-Y.X.)
| | - Xun-Zong Wu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China (Z.-Q.S., Y.-M.Z., J.-Y.X., G.-C.Z., P.W., X.-Y.W., X.-Z.W., Q.W., B.W., J.-Q.C.); andJiangsu Province and Chinese Academy of Science, Institute of Botany, Nanjing 210014, China (Y.-M.Z., Y.-Y.H., J.-Y.X.)
| | - Qiang Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China (Z.-Q.S., Y.-M.Z., J.-Y.X., G.-C.Z., P.W., X.-Y.W., X.-Z.W., Q.W., B.W., J.-Q.C.); andJiangsu Province and Chinese Academy of Science, Institute of Botany, Nanjing 210014, China (Y.-M.Z., Y.-Y.H., J.-Y.X.)
| | - Bin Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China (Z.-Q.S., Y.-M.Z., J.-Y.X., G.-C.Z., P.W., X.-Y.W., X.-Z.W., Q.W., B.W., J.-Q.C.); andJiangsu Province and Chinese Academy of Science, Institute of Botany, Nanjing 210014, China (Y.-M.Z., Y.-Y.H., J.-Y.X.)
| | - Jian-Qun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China (Z.-Q.S., Y.-M.Z., J.-Y.X., G.-C.Z., P.W., X.-Y.W., X.-Z.W., Q.W., B.W., J.-Q.C.); andJiangsu Province and Chinese Academy of Science, Institute of Botany, Nanjing 210014, China (Y.-M.Z., Y.-Y.H., J.-Y.X.)
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Pflieger S, Blanchet S, Meziadi C, Richard MMS, Thareau V, Mary F, Mazoyer C, Geffroy V. The "one-step" Bean pod mottle virus (BPMV)-derived vector is a functional genomics tool for efficient overexpression of heterologous protein, virus-induced gene silencing and genetic mapping of BPMV R-gene in common bean (Phaseolus vulgaris L.). BMC PLANT BIOLOGY 2014; 14:232. [PMID: 25168520 PMCID: PMC4163167 DOI: 10.1186/s12870-014-0232-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/20/2014] [Indexed: 05/11/2023]
Abstract
BACKGROUND Over the last two years, considerable advances have been made in common bean (Phaseolus vulgaris L.) genomics, especially with the completion of the genome sequence and the availability of RNAseq data. However, as common bean is recalcitrant to stable genetic transformation, much work remains to be done for the development of functional genomics tools adapted to large-scale studies. RESULTS Here we report the successful implementation of an efficient viral vector system for foreign gene expression, virus-induced gene silencing (VIGS) and genetic mapping of a BPMV resistance gene in common bean, using a "one-step" BPMV vector originally developed in soybean. With the goal of developing this vector for high-throughput VIGS studies in common bean, we optimized the conditions for rub-inoculation of infectious BPMV-derived plasmids in common bean cv. Black Valentine. We then tested the susceptibility to BPMV of six cultivars, and found that only Black Valentine and JaloEEP558 were susceptible to BPMV. We used a BPMV-GFP construct to detect the spatial and temporal infection patterns of BPMV in vegetative and reproductive tissues. VIGS of the PHYTOENE DESATURASE (PvPDS) marker gene was successfully achieved with recombinant BPMV vectors carrying fragments ranging from 132 to 391 bp. Finally, we mapped a gene for resistance to BPMV (R-BPMV) at one end of linkage group 2, in the vicinity of a locus (I locus) previously shown to be involved in virus resistance. CONCLUSIONS The "one-step" BPMV vector system therefore enables rapid and simple functional studies in common bean, and could be suitable for large-scale analyses. In the post-genomic era, these advances are timely for the common bean research community.
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Affiliation(s)
- Stéphanie Pflieger
- />CNRS, Institut de Biologie des Plantes, UMR 8618, Université Paris Sud, Saclay Plant Sciences (SPS), 91405 Orsay, France
- />Univ Paris Diderot, Sorbonne Paris Cité, 75205 Paris, France
| | - Sophie Blanchet
- />CNRS, Institut de Biologie des Plantes, UMR 8618, Université Paris Sud, Saclay Plant Sciences (SPS), 91405 Orsay, France
| | - Chouaib Meziadi
- />CNRS, Institut de Biologie des Plantes, UMR 8618, Université Paris Sud, Saclay Plant Sciences (SPS), 91405 Orsay, France
| | - Manon MS Richard
- />CNRS, Institut de Biologie des Plantes, UMR 8618, Université Paris Sud, Saclay Plant Sciences (SPS), 91405 Orsay, France
| | - Vincent Thareau
- />CNRS, Institut de Biologie des Plantes, UMR 8618, Université Paris Sud, Saclay Plant Sciences (SPS), 91405 Orsay, France
| | - Fanny Mary
- />CNRS, Institut de Biologie des Plantes, UMR 8618, Université Paris Sud, Saclay Plant Sciences (SPS), 91405 Orsay, France
| | - Céline Mazoyer
- />CNRS, Institut de Biologie des Plantes, UMR 8618, Université Paris Sud, Saclay Plant Sciences (SPS), 91405 Orsay, France
| | - Valérie Geffroy
- />CNRS, Institut de Biologie des Plantes, UMR 8618, Université Paris Sud, Saclay Plant Sciences (SPS), 91405 Orsay, France
- />INRA, Unité Mixte de Recherche de Génétique Végétale, Université Paris Sud, IDEEV FR3284, Ferme du Moulon, 91190 Gif-sur-Yvette, France
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Abstract
While the role of viral variants has long been known to play a key role in causing variation in disease severity, it is also clear that host genetic variation plays a critical role in determining virus-induced disease responses. However, a variety of factors, including confounding environmental variables, rare genetic variants requiring extremely large cohorts, the temporal dynamics of infections, and ethical limitation on human studies, have made the identification and dissection of variant host genes and pathways difficult within human populations. This difficulty has led to the development of a variety of experimental approaches used to identify host genetic contributions to disease responses. In this chapter, we describe the history of genetic associations within the human population, the development of experimentally tractable systems, and the insights these specific approaches provide. We conclude with a discussion of recent advances that allow for the investigation of the role of complex genetic networks that underlie host responses to infection, with the goal of drawing connections to human infections. In particular, we highlight the need for robust animal models with which to directly control and assess the role of host genetics on viral infection outcomes.
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Chang S, Thurber CS, Brown PJ, Hartman GL, Lambert KN, Domier LL. Comparative mapping of the wild perennial Glycine latifolia and soybean (G. max) reveals extensive chromosome rearrangements in the genus Glycine. PLoS One 2014; 9:e99427. [PMID: 24937645 PMCID: PMC4061007 DOI: 10.1371/journal.pone.0099427] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/14/2014] [Indexed: 12/22/2022] Open
Abstract
Soybean (Glycine max L. Mer.), like many cultivated crops, has a relatively narrow genetic base and lacks diversity for some economically important traits. Glycine latifolia (Benth.) Newell & Hymowitz, one of the 26 perennial wild Glycine species related to soybean in the subgenus Glycine Willd., shows high levels of resistance to multiple soybean pathogens and pests including Alfalfa mosaic virus, Heterodera glycines Ichinohe and Sclerotinia sclerotiorum (Lib.) de Bary. However, limited information is available on the genomes of these perennial Glycine species. To generate molecular resources for gene mapping and identification, high-density linkage maps were constructed for G. latifolia using single nucleotide polymorphism (SNP) markers generated by genotyping by sequencing and evaluated in an F2 population and confirmed in an F5 population. In each population, greater than 2,300 SNP markers were selected for analysis and segregated to form 20 large linkage groups. Marker orders were similar in the F2 and F5 populations. The relationships between G. latifolia linkage groups and G. max and common bean (Phaseolus vulgaris L.) chromosomes were examined by aligning SNP-containing sequences from G. latifolia to the genome sequences of G. max and P. vulgaris. Twelve of the 20 G. latifolia linkage groups were nearly collinear with G. max chromosomes. The remaining eight G. latifolia linkage groups appeared to be products of multiple interchromosomal translocations relative to G. max. Large syntenic blocks also were observed between G. latifolia and P. vulgaris. These experiments are the first to compare genome organizations among annual and perennial Glycine species and common bean. The development of molecular resources for species closely related to G. max provides information into the evolution of genomes within the genus Glycine and tools to identify genes within perennial wild relatives of cultivated soybean that could be beneficial to soybean production.
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Affiliation(s)
- Sungyul Chang
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Carrie S. Thurber
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Patrick J. Brown
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Glen L. Hartman
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
- United States Department of Agriculture, Agricultural Research Service, Urbana, Illinois, United States of America
| | - Kris N. Lambert
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Leslie L. Domier
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
- United States Department of Agriculture, Agricultural Research Service, Urbana, Illinois, United States of America
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Atwood SE, O'Rourke JA, Peiffer GA, Yin T, Majumder M, Zhang C, Cianzio SR, Hill JH, Cook D, Whitham SA, Shoemaker RC, Graham MA. Replication protein A subunit 3 and the iron efficiency response in soybean. PLANT, CELL & ENVIRONMENT 2014; 37:213-34. [PMID: 23742135 DOI: 10.1111/pce.12147] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 05/09/2013] [Accepted: 05/28/2013] [Indexed: 05/20/2023]
Abstract
In soybean [Glycine max (L.) Merr.], iron deficiency results in interveinal chlorosis and decreased photosynthetic capacity, leading to stunting and yield loss. In this study, gene expression analyses investigated the role of soybean replication protein A (RPA) subunits during iron stress. Nine RPA homologs were significantly differentially expressed in response to iron stress in the near isogenic lines (NILs) Clark (iron efficient) and Isoclark (iron inefficient). RPA homologs exhibited opposing expression patterns in the two NILs, with RPA expression significantly repressed during iron deficiency in Clark but induced in Isoclark. We used virus induced gene silencing (VIGS) to repress GmRPA3 expression in the iron inefficient line Isoclark and mirror expression in Clark. GmRPA3-silenced plants had improved IDC symptoms and chlorophyll content under iron deficient conditions and also displayed stunted growth regardless of iron availability. RNA-Seq comparing gene expression between GmRPA3-silenced and empty vector plants revealed massive transcriptional reprogramming with differential expression of genes associated with defense, immunity, aging, death, protein modification, protein synthesis, photosynthesis and iron uptake and transport genes. Our findings suggest the iron efficient genotype Clark is able to induce energy controlling pathways, possibly regulated by SnRK1/TOR, to promote nutrient recycling and stress responses in iron deficient conditions.
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Affiliation(s)
- Sarah E Atwood
- Interdepartmental Genetics Program, Iowa State University, Ames, IA, 50011, USA
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Cooper B, Campbell KB, McMahon MB, Luster DG. Disruption of Rpp1-mediated soybean rust immunity by virus-induced gene silencing. PLANT SIGNALING & BEHAVIOR 2013; 8:e27543. [PMID: 24401541 PMCID: PMC4091232 DOI: 10.4161/psb.27543] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 12/16/2013] [Accepted: 12/16/2013] [Indexed: 05/23/2023]
Abstract
Phakopsora pachyrhizi, a fungus that causes rust disease on soybean, has potential to impart significant yield loss and disrupt food security and animal feed production. Rpp1 is a soybean gene that confers immunity to soybean rust, and it is important to understand how it regulates the soybean defense system and to use this knowledge to protect commercial crops. It was previously discovered that some soybean proteins resembling transcription factors accumulate in the nucleus of Rpp1 soybeans. To determine if they contribute to immunity, Bean pod mottle virus was used to attenuate or silence the expression of their genes. Rpp1 plants subjected to virus-induced gene silencing exhibited reduced amounts of RNA for 5 of the tested genes, and the plants developed rust-like symptoms after subsequent inoculation with fungal spores. Symptoms were associated with the accumulation of rust fungal RNA and protein. Silenced plants also had reduced amounts of RNA for the soybean Myb84 transcription factor and soybean isoflavone O-methyltransferase, both of which are important to phenylpropanoid biosynthesis and lignin formation, crucial components of rust resistance. These results help resolve some of the genes that contribute to Rpp1-mediated immunity and improve upon the knowledge of the soybean defense system. It is possible that these genes could be manipulated to enhance rust resistance in otherwise susceptible soybean cultivars.
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Affiliation(s)
- Bret Cooper
- Soybean Genomics and Improvement Laboratory; USDA-ARS; Beltsville, MD USA
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Pflieger SP, Richard MMS, Blanchet S, Meziadi C, Geffroy VR. VIGS technology: an attractive tool for functional genomics studies in legumes. FUNCTIONAL PLANT BIOLOGY : FPB 2013; 40:1234-1248. [PMID: 32481191 DOI: 10.1071/fp13089] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 06/14/2013] [Indexed: 05/20/2023]
Abstract
Legume species are among the most important crops worldwide. In recent years, six legume genomes have been completely sequenced, and there is now an urgent need for reverse-genetics tools to validate genes affecting yield and product quality. As most legumes are recalcitrant to stable genetic transformation, virus-induced gene silencing (VIGS) appears to be a powerful alternative technology for determining the function of unknown genes. VIGS technology is based on the property of plant viruses to trigger a defence mechanism related to post-transcriptional gene silencing (PTGS). Infection by a recombinant virus carrying a fragment of a plant target gene will induce homology-dependent silencing of the endogenous target gene. Several VIGS systems have been developed for legume species since 2004, including those based on Bean pod mottle virus, Pea early browning virus, and Apple latent spherical virus, and used in reverse-genetics studies of a wide variety of plant biological processes. In this work, we give an overview of the VIGS systems available for legumes, and present their successful applications in functional genomics studies. We also discuss the limitations of these VIGS systems and the future challenges to be faced in order to use VIGS to its full potential in legume species.
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Affiliation(s)
- St Phanie Pflieger
- Institut de Biologie des Plantes, UMR8618, CNRS Université Paris-Sud, Saclay Plant Sciences, Rue Noetzlin, 91405 Orsay, France
| | - Manon M S Richard
- Institut de Biologie des Plantes, UMR8618, CNRS Université Paris-Sud, Saclay Plant Sciences, Rue Noetzlin, 91405 Orsay, France
| | - Sophie Blanchet
- Institut de Biologie des Plantes, UMR8618, CNRS Université Paris-Sud, Saclay Plant Sciences, Rue Noetzlin, 91405 Orsay, France
| | - Chouaib Meziadi
- Institut de Biologie des Plantes, UMR8618, CNRS Université Paris-Sud, Saclay Plant Sciences, Rue Noetzlin, 91405 Orsay, France
| | - Val Rie Geffroy
- Institut de Biologie des Plantes, UMR8618, CNRS Université Paris-Sud, Saclay Plant Sciences, Rue Noetzlin, 91405 Orsay, France
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Morales AMAP, O Rourke JA, van de Mortel M, Scheider KT, Bancroft TJ, Bor M AZ, Nelson RT, Nettleton D, Baum TJ, Shoemaker RC, Frederick RD, Abdelnoor RV, Pedley KF, Whitham SA, Graham MA. Transcriptome analyses and virus induced gene silencing identify genes in the Rpp4-mediated Asian soybean rust resistance pathway. FUNCTIONAL PLANT BIOLOGY : FPB 2013; 40:1029-1047. [PMID: 32481171 DOI: 10.1071/fp12296] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 01/12/2013] [Indexed: 05/24/2023]
Abstract
Rpp4 (Resistance to Phakopsora pachyrhizi 4) confers resistance to Phakopsora pachyrhizi Sydow, the causal agent of Asian soybean rust (ASR). By combining expression profiling and virus induced gene silencing (VIGS), we are developing a genetic framework for Rpp4-mediated resistance. We measured gene expression in mock-inoculated and P. pachyrhizi-infected leaves of resistant soybean accession PI459025B (Rpp4) and the susceptible cultivar (Williams 82) across a 12-day time course. Unexpectedly, two biphasic responses were identified. In the incompatible reaction, genes induced at 12h after infection (hai) were not differentially expressed at 24 hai, but were induced at 72 hai. In contrast, genes repressed at 12 hai were not differentially expressed from 24 to 144 hai, but were repressed 216 hai and later. To differentiate between basal and resistance-gene (R-gene) mediated defence responses, we compared gene expression in Rpp4-silenced and empty vector-treated PI459025B plants 14 days after infection (dai) with P. pachyrhizi. This identified genes, including transcription factors, whose differential expression is dependent upon Rpp4. To identify differentially expressed genes conserved across multiple P. pachyrhizi resistance pathways, Rpp4 expression datasets were compared with microarray data previously generated for Rpp2 and Rpp3-mediated defence responses. Fourteen transcription factors common to all resistant and susceptible responses were identified, as well as fourteen transcription factors unique to R-gene-mediated resistance responses. These genes are targets for future P. pachyrhizi resistance research.
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Affiliation(s)
- Aguida M A P Morales
- Universidade Federal de Viçosa, Departamento de Fitotecnia, 36.570-000, Viçosa, MG, Brazil
| | - Jamie A O Rourke
- USDA-Agricultural Research Service, Plant Science Research Unit, Saint Paul, MN 55108, USA
| | - Martijn van de Mortel
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50014, USA
| | - Katherine T Scheider
- USDA- Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Fort Detrick, MA 21702, USA
| | | | - Alu Zio Bor M
- Universidade Federal de Viçosa, Departamento de Fitotecnia, 36.570-000, Viçosa, MG, Brazil
| | - Rex T Nelson
- USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50014, USA
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, IA 50014, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50014, USA
| | - Randy C Shoemaker
- USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50014, USA
| | - Reid D Frederick
- USDA- Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Fort Detrick, MA 21702, USA
| | - Ricardo V Abdelnoor
- Laboratório de Biotecnologia Vegetal e Bioinformática, Embrapa Soja, Rod. Carlos João Strass, 86001-970, Londrina - PR, Brazil
| | - Kerry F Pedley
- USDA- Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Fort Detrick, MA 21702, USA
| | - Steven A Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50014, USA
| | - Michelle A Graham
- USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50014, USA
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Tremblay A, Hosseini P, Li S, Alkharouf NW, Matthews BF. Analysis of Phakopsora pachyrhizi transcript abundance in critical pathways at four time-points during infection of a susceptible soybean cultivar using deep sequencing. BMC Genomics 2013; 14:614. [PMID: 24025037 PMCID: PMC3847679 DOI: 10.1186/1471-2164-14-614] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Accepted: 08/31/2013] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Phakopsora pachyrhizi, the causal agent responsible for soybean rust, is among the top hundred most virulent plant pathogens and can cause soybean yield losses of up to 80% when appropriate conditions are met. We used mRNA-Seq by Illumina to analyze pathogen transcript abundance at 15 seconds (s), 7 hours (h), 48 h, and 10 days (d) after inoculation (ai) of susceptible soybean leaves with P. pachyrhizi to gain new insights into transcript abundance in soybean and the pathogen at specific time-points during the infection including the uredinial stage. RESULTS Over three million five hundred thousand sequences were obtained for each time-point. Energy, nucleotide metabolism, and protein synthesis are major priorities for the fungus during infection and development as indicated by our transcript abundance studies. At all time-points, energy production is a necessity for P. pachyrhizi, as indicated by expression of many transcripts encoding enzymes involved in oxidative phosphorylation and carbohydrate metabolism (glycolysis, glyoxylate and dicarboxylate, pentose phosphate, pyruvate). However, at 15 sai, transcripts encoding enzymes involved in ATP production were highly abundant in order to provide enough energy for the spore to germinate, as observed by the expression of many transcripts encoding proteins involved in electron transport. At this early time-point, transcripts encoding proteins involved in RNA synthesis were also highly abundant, more so than transcripts encoding genes involved in DNA and protein synthesis. At 7 hai, shortly after germination during tube elongation and penetration, transcripts encoding enzymes involved in deoxyribonucleotide and DNA synthesis were highly abundant. At 48 hai, transcripts encoding enzymes involved in amino acid metabolism were highly abundant to provide for increased protein synthesis during haustoria maturation. During sporulation at 10 dai, the fungus still required carbohydrate metabolism, but there also was increased expression of transcripts encoding enzymes involved in fatty acid metabolism. CONCLUSION This information provides insight into molecular events and their timing throughout the life cycle of the P. pachyrhizi, and it may be useful in the development of new methods of broadening resistance of soybean to soybean rust.
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Affiliation(s)
- Arianne Tremblay
- Soybean Genomics & Improvement Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Beltsville, MD 20705, USA
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, BS411/412, Baltimore, MD 21250, USA
| | - Parsa Hosseini
- Bioinformatics/Computational Biology, George Mason University, 4400 University Dr. Manassas, Fairfax, VA 22030, USA
- Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - Shuxian Li
- USDA-ARS, Crop Genetics Research Unit, Stoneville, MS 38776, USA
| | - Nadim W Alkharouf
- Molecular Biology, Biochemistry and Bioinformatics, Fischer College of Science and Mathematics, Towson University, 8000 York Road, Towson, MD 21252, USA
| | - Benjamin F Matthews
- Soybean Genomics & Improvement Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Beltsville, MD 20705, USA
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