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Shao W, Shi G, Chu H, Du W, Zhou Z, Wuriyanghan H. Development of an NLR-ID Toolkit and Identification of Novel Disease-Resistance Genes in Soybean. PLANTS (BASEL, SWITZERLAND) 2024; 13:668. [PMID: 38475513 DOI: 10.3390/plants13050668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/16/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024]
Abstract
The recognition of pathogen effectors through the nucleotide-binding leucine-rich repeat receptor (NLR) family is an important component of plant immunity. In addition to typical domains such as TIR, CC, NBS, and LRR, NLR proteins also contain some atypical integrated domains (IDs), the roles of which are rarely investigated. Here, we carefully screened the soybean (Glycine max) genome and identified the IDs that appeared in the soybean TNL-like proteins. Our results show that multiple IDs (36) are widely present in soybean TNL-like proteins. A total of 27 Gm-TNL-ID genes (soybean TNL-like gene encoding ID) were cloned and their antiviral activity towards the soybean mosaic virus (SMV)/tobacco mosaic virus (TMV) was verified. Two resistance (R) genes, SRA2 (SMV resistance gene contains AAA_22 domain) and SRZ4 (SMV resistance gene contains zf-RVT domain), were identified to possess broad-spectrum resistance characteristics towards six viruses including SMV, TMV, plum pox virus (PPV), cabbage leaf curl virus (CaLCuV), barley stripe mosaic virus (BSMV), and tobacco rattle virus (TRV). The effects of Gm-TNL-IDX (the domain of the Gm-TNL-ID gene after the TN domain) on the antiviral activity of a R protein SRC7TN (we previously reported the TN domain of the soybean broad-spectrum resistance gene SRC7) were validated, and most of Gm-TNL-IDX inhibits antiviral activity mediated by SRC7TN, possibly through intramolecular interactions. Yeast-two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays showed that seven Gm-TNL-IDX interacted with SMV-component proteins. Truncation analysis on a broad-spectrum antiviral protein SRZ4 indicated that SRZ4TIR is sufficient to mediate antiviral activity against SMV. Soybean cDNA library screening on SRZ4 identified 48 interacting proteins. In summary, our results indicate that the integration of IDs in soybean is widespread and frequent. The NLR-ID toolkit we provide is expected to be valuable for elucidating the functions of atypical NLR proteins in the plant immune system and lay the foundation for the development of engineering NLR for plant-disease control in the future.
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Affiliation(s)
- Wei Shao
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Gongfu Shi
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Han Chu
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Wenjia Du
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Zikai Zhou
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Hada Wuriyanghan
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
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Brabham HJ, Gómez De La Cruz D, Were V, Shimizu M, Saitoh H, Hernández-Pinzón I, Green P, Lorang J, Fujisaki K, Sato K, Molnár I, Šimková H, Doležel J, Russell J, Taylor J, Smoker M, Gupta YK, Wolpert T, Talbot NJ, Terauchi R, Moscou MJ. Barley MLA3 recognizes the host-specificity effector Pwl2 from Magnaporthe oryzae. THE PLANT CELL 2024; 36:447-470. [PMID: 37820736 PMCID: PMC10827324 DOI: 10.1093/plcell/koad266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023]
Abstract
Plant nucleotide-binding leucine-rich repeat (NLRs) immune receptors directly or indirectly recognize pathogen-secreted effector molecules to initiate plant defense. Recognition of multiple pathogens by a single NLR is rare and usually occurs via monitoring for changes to host proteins; few characterized NLRs have been shown to recognize multiple effectors. The barley (Hordeum vulgare) NLR gene Mildew locus a (Mla) has undergone functional diversification, and the proteins encoded by different Mla alleles recognize host-adapted isolates of barley powdery mildew (Blumeria graminis f. sp. hordei [Bgh]). Here, we show that Mla3 also confers resistance to the rice blast fungus Magnaporthe oryzae in a dosage-dependent manner. Using a forward genetic screen, we discovered that the recognized effector from M. oryzae is Pathogenicity toward Weeping Lovegrass 2 (Pwl2), a host range determinant factor that prevents M. oryzae from infecting weeping lovegrass (Eragrostis curvula). Mla3 has therefore convergently evolved the capacity to recognize effectors from diverse pathogens.
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Affiliation(s)
- Helen J Brabham
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
- 2Blades, Evanston, IL 60201, USA
| | - Diana Gómez De La Cruz
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Vincent Were
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Motoki Shimizu
- Iwate Biotechnology Research Centre, Kitakami 024-0003, Japan
| | - Hiromasa Saitoh
- Department of Molecular Microbiology, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | | | - Phon Green
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jennifer Lorang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Koki Fujisaki
- Iwate Biotechnology Research Centre, Kitakami 024-0003, Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| | - István Molnár
- Institute of Experimental Botany of the Czech Academy of Sciences, 779 00 Olomouc, Czech Republic
| | - Hana Šimková
- Institute of Experimental Botany of the Czech Academy of Sciences, 779 00 Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, 779 00 Olomouc, Czech Republic
| | - James Russell
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jodie Taylor
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Matthew Smoker
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Yogesh Kumar Gupta
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
- 2Blades, Evanston, IL 60201, USA
| | - Tom Wolpert
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Nicholas J Talbot
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Ryohei Terauchi
- Iwate Biotechnology Research Centre, Kitakami 024-0003, Japan
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Kyoto 617-0001, Japan
| | - Matthew J Moscou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
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Tong C, Zhang Y, Shi F. Genome-wide identification and analysis of the NLR gene family in Medicago ruthenica. Front Genet 2023; 13:1088763. [PMID: 36704335 PMCID: PMC9871256 DOI: 10.3389/fgene.2022.1088763] [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: 11/03/2022] [Accepted: 12/22/2022] [Indexed: 01/11/2023] Open
Abstract
Medicago ruthenica, important forage in the legume family, possesses high nutritional value and carries abundant tolerance genes. This study used whole-genome data of M. ruthenica to perform a genome-wide analysis of the nucleotide-binding site-leucine-rich repeat receptor (NLR) gene family, which is the largest family of plant disease resistance genes (R genes). A total of 338 NLR genes were identified in the M. ruthenica genome, including 160 typical genes that contained 80 coiled-coil (CC)-NBS-LRR (CNL) genes, 76 toll/interleukin-1 receptor (TIR)-NBS-LRR (TNL) genes, four resistance to powdery mildew 8 (RPW8)-NBS-LRR (RNL) subclass genes, and 178 atypical NLR genes encoding proteins without at least one important domain. Among its eight chromosomes, M. ruthenica chromosomes 3 and 8 contained most of the NLR genes. More than 40% of all NLR genes were located on these two chromosomes, mainly in multigene clusters. The NLR proteins of M. ruthenica had six highly conserved motifs: P-loop, GLPL, RNBS-D, kinase-2, RNBS-C, and MHDV. Phylogenetic analysis revealed that the NLR genes of M. ruthenica formed three deeply separated clades according to the N-terminal domain of the proteins encoded by these genes. Gene duplication and syntenic analysis suggested four gene duplication types in the NLR genes of M. ruthenica, namely, tandem, proximal, dispersed, and segmental duplicates, which involved 189, 49, 59, and 41 genes, respectively. A total of 41 segmental duplication genes formed 23 NLR gene pairs located on syntenic chromosomal blocks mainly between chromosomes 6 and 7. In addition, syntenic analysis between M. truncatula and M. ruthenica revealed 193 gene pairs located on syntenic chromosomal blocks of the two species. The expression analysis of M. ruthenica NLR genes showed that 303 (89.6%) of the NLR genes were expressed in different varieties. Overall, this study described the full NLR profile of the M. ruthenica genome to provide an important resource for mining disease-resistant genes and disease-resistant breeding.
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Affiliation(s)
- Chunyan Tong
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China,Key Laboratory of Grassland Resources (IMAU), Ministry of Education, Hohhot, China
| | - Yutong Zhang
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China,Key Laboratory of Grassland Resources (IMAU), Ministry of Education, Hohhot, China
| | - Fengling Shi
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China,Key Laboratory of Grassland Resources (IMAU), Ministry of Education, Hohhot, China,*Correspondence: Fengling Shi,
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Xi Y, Cesari S, Kroj T. Insight into the structure and molecular mode of action of plant paired NLR immune receptors. Essays Biochem 2022; 66:513-526. [PMID: 35735291 PMCID: PMC9528088 DOI: 10.1042/ebc20210079] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/16/2022] [Accepted: 05/30/2022] [Indexed: 11/17/2022]
Abstract
The specific recognition of pathogen effectors by intracellular nucleotide-binding domain and leucine-rich repeat receptors (NLRs) is an important component of plant immunity. NLRs have a conserved modular architecture and can be subdivided according to their signaling domain that is mostly a coiled-coil (CC) or a Toll/Interleukin1 receptor (TIR) domain into CNLs and TNLs. Single NLR proteins are often sufficient for both effector recognition and immune activation. However, sometimes, they act in pairs, where two different NLRs are required for disease resistance. Functional studies have revealed that in these cases one NLR of the pair acts as a sensor (sNLR) and one as a helper (hNLR). The genes corresponding to such resistance protein pairs with one-to-one functional co-dependence are clustered, generally with a head-to-head orientation and shared promoter sequences. sNLRs in such functional NLR pairs have additional, non-canonical and highly diverse domains integrated in their conserved modular architecture, which are thought to act as decoys to trap effectors. Recent structure-function studies on the Arabidopsis thaliana TNL pair RRS1/RPS4 and on the rice CNL pairs RGA4/RGA5 and Pik-1/Pik-2 are unraveling how such protein pairs function together. Focusing on these model NLR pairs and other recent examples, this review highlights the distinctive features of NLR pairs and their various fascinating mode of action in pathogen effector perception. We also discuss how these findings on NLR pairs pave the way toward improved plant disease resistance.
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Affiliation(s)
- Yuxuan Xi
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Stella Cesari
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Thomas Kroj
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
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Huang Z, Qiao F, Yang B, Liu J, Liu Y, Wulff BBH, Hu P, Lv Z, Zhang R, Chen P, Xing L, Cao A. Genome-wide identification of the NLR gene family in Haynaldia villosa by SMRT-RenSeq. BMC Genomics 2022; 23:118. [PMID: 35144544 PMCID: PMC8832786 DOI: 10.1186/s12864-022-08334-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 01/24/2022] [Indexed: 01/19/2023] Open
Abstract
Background Nucleotide-binding and leucine-rich repeat (NLR) genes have attracted wide attention due to their crucial role in protecting plants from pathogens. SMRT-RenSeq, combining PacBio sequencing after resistance gene enrichment sequencing (RenSeq), is a powerful method for selectively capturing and sequencing full-length NLRs. Haynaldia villosa, a wild grass species with a proven potential for wheat improvement, confers resistance to multiple diseases. So, genome-wide identification of the NLR gene family in Haynaldia villosa by SMRT-RenSeq can facilitate disease resistance genes exploration. Results In this study, SMRT-RenSeq was performed to identify the genome-wide NLR complement of H. villosa. In total, 1320 NLRs were annotated in 1169 contigs, including 772 complete NLRs. All the complete NLRs were phylogenetically analyzed and 11 main clades with special characteristics were derived. NLRs could be captured with high efficiency when aligned with cloned R genes, and cluster expansion in some specific gene loci was observed. The physical location of NLRs to individual chromosomes in H. villosa showed a perfect homoeologous relationship with group 1, 2, 3, 5 and 6 of other Triticeae species, however, NLRs physically located on 4VL were largely in silico predicted to be located on the homoeologous group 7. Fifteen types of integrated domains (IDs) were integrated in 52 NLRs, and Kelch and B3 NLR-IDs were found to have expanded in H. villosa, while DUF948, NAM-associated and PRT_C were detected as unique integrated domains implying the new emergence of NLR-IDs after H. villosa diverged from other species. Conclusion SMRT-RenSeq is a powerful tool to identify NLR genes from wild species using the baits of the evolutionary related species with reference sequences. The availability of the NLRs from H. villosa provide a valuable library for R gene mining and transfer of disease resistance into wheat. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08334-w.
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Affiliation(s)
- Zhenpu Huang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Fangyuan Qiao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Boming Yang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Jiaqian Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Yangqi Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Brande B H Wulff
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Ping Hu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Zengshuai Lv
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Ruiqi Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Peidu Chen
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Liping Xing
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China.
| | - Aizhong Cao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China.
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Upadhaya A, Upadhaya SG, Brueggeman R. The Wheat Stem Rust ( Puccinia graminis f. sp. tritici) Population from Washington Contains the Most Virulent Isolates Reported on Barley. PLANT DISEASE 2022; 106:223-230. [PMID: 34546770 DOI: 10.1094/pdis-06-21-1195-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A diverse sexual population of wheat stem rust, Puccinia graminis f. sp. tritici, exists in the Pacific Northwest region of the United States because of the natural presence of Mahonia spp. that serves as alternate hosts to complete its sexual life cycle. The region appears to be a center of stem rust diversity in North America where novel virulence gene combinations can emerge that could overcome deployed barley and wheat stem rust resistances. A total of 100 single pustule isolates derived from stem rust samples collected from barley in Eastern Washington during the 2019 growing season were assayed for virulence on the two known effective barley stem rust resistance genes/loci, Rpg1 and the rpg4/5-mediated resistance locus (RMRL) at the seedling stage. Interestingly, 99% of the P. graminis f. sp. tritici isolates assayed were virulent on barley variety Morex carrying the Rpg1 gene, and 62% of the isolates were virulent on the variety Golden Promise transformant (H228.2c) that carries a single-copy insertion of the Rpg1 gene from Morex and is more resistant than Morex to many Rpg1 avirulent isolates. Also, 16% of the isolates were virulent on the near isogenic line HQ-1, which carries the RMRL introgression from the barley line Q21861 in the susceptible Harrington background. Alarmingly, 10% of the isolates were virulent on barley line Q21861, which contains both Rpg1 and RMRL. Thus, we report on the first P. graminis f. sp. tritici isolates worldwide with virulence on both Rpg1 and RMRL when stacked together, representing the most virulent P. graminis f. sp. tritici isolates reported on barley.
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Affiliation(s)
- Arjun Upadhaya
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164
| | - Sudha Gc Upadhaya
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164
| | - Robert Brueggeman
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164
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Richards JK, Kariyawasam GK, Seneviratne S, Wyatt NA, Xu SS, Liu Z, Faris JD, Friesen TL. A triple threat: the Parastagonospora nodorum SnTox267 effector exploits three distinct host genetic factors to cause disease in wheat. THE NEW PHYTOLOGIST 2022; 233:427-442. [PMID: 34227112 PMCID: PMC9292537 DOI: 10.1111/nph.17601] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/27/2021] [Indexed: 05/21/2023]
Abstract
Parastagonospora nodorum is a fungal pathogen of wheat. As a necrotrophic specialist, it deploys effector proteins that target dominant host susceptibility genes to elicit programmed cell death (PCD). Here we identify and functionally validate the effector targeting the host susceptibility genes Snn2, Snn6 and Snn7. We utilized whole-genome sequencing, association mapping, gene-disrupted mutants, gain-of-function transformants, virulence assays, bioinformatics and quantitative PCR to characterize these interactions. A single proteinaceous effector, SnTox267, targeted Snn2, Snn6 and Snn7 to trigger PCD. Snn2 and Snn6 functioned cooperatively to trigger PCD in a light-dependent pathway, whereas Snn7-mediated PCD functioned in a light-independent pathway. Isolates harboring 20 SnTox267 protein isoforms quantitatively varied in virulence. The diversity and distribution of isoforms varied between populations, indicating adaptation to local selection pressures. SnTox267 deletion resulted in the upregulation of effector genes SnToxA, SnTox1 and SnTox3. We validated a novel effector operating in an inverse-gene-for-gene manner to target three genetically distinct host susceptibility genes and elicit PCD. The discovery of the complementary gene action of Snn2 and Snn6 indicates their potential function in a guard or decoy model. Additionally, differences in light dependency in the elicited pathways and upregulation of unlinked effectors sheds new light onto a complex fungal necrotroph-host interaction.
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Affiliation(s)
- Jonathan K. Richards
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLA70803USA
| | | | | | - Nathan A. Wyatt
- Cereal Crops Research UnitEdward T. Schaffer Agricultural Research CenterUSDA‐ARSFargoND58102USA
| | - Steven S. Xu
- Department of Plant SciencesNorth Dakota State UniversityFargoND58102USA
- Cereal Crops Research UnitEdward T. Schaffer Agricultural Research CenterUSDA‐ARSFargoND58102USA
| | - Zhaohui Liu
- Department of Plant PathologyNorth Dakota State UniversityFargoND58102USA
| | - Justin D. Faris
- Department of Plant SciencesNorth Dakota State UniversityFargoND58102USA
- Cereal Crops Research UnitEdward T. Schaffer Agricultural Research CenterUSDA‐ARSFargoND58102USA
| | - Timothy L. Friesen
- Department of Plant PathologyNorth Dakota State UniversityFargoND58102USA
- Cereal Crops Research UnitEdward T. Schaffer Agricultural Research CenterUSDA‐ARSFargoND58102USA
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Sun Y, Zhong M, Li Y, Zhang R, Su L, Xia G, Wang H. GhADF6-mediated actin reorganization is associated with defence against Verticillium dahliae infection in cotton. MOLECULAR PLANT PATHOLOGY 2021; 22:1656-1667. [PMID: 34515397 PMCID: PMC8578822 DOI: 10.1111/mpp.13137] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/28/2021] [Accepted: 08/19/2021] [Indexed: 05/07/2023]
Abstract
Several studies have revealed that actin depolymerizing factors (ADFs) participate in plant defence responses; however, the functional mechanisms appear intricate and need further exploration. In this study, we identified an ADF6 gene in upland cotton (designated as GhADF6) that is evidently involved in cotton's response to the fungal pathogen Verticillium dahliae. GhADF6 binds to actin filaments and possesses actin severing and depolymerizing activities in vitro and in vivo. When cotton root (the site of the fungus invasion) was inoculated with the pathogen, the expression of GhADF6 was markedly down-regulated in the epidermal cells. By virus-induced gene silencing analysis, the down-regulation of GhADF6 expression rendered the cotton plants tolerant to V. dahliae infection. Accordingly, the abundance of actin filaments and bundles in the root cells was significantly higher than that in the control plant, which phenocopied that of the V. dahliae-challenged wild-type cotton plant. Altogether, our results provide evidence that an increase in filament actin (F-actin) abundance as well as dynamic actin remodelling are required for plant defence against the invading pathogen, which are likely to be fulfilled by the coordinated expressional regulation of the actin-binding proteins, including ADF.
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Affiliation(s)
- Yongduo Sun
- Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- State Key Laboratory of Plant GenomicsBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Mengmeng Zhong
- Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- State Key Laboratory of Plant GenomicsBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yuanbao Li
- Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- State Key Laboratory of Plant GenomicsBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Ruihui Zhang
- University of Chinese Academy of SciencesBeijingChina
- Institute of BotanyChinese Academy of SciencesBeijingChina
| | - Lei Su
- Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- State Key Laboratory of Plant GenomicsBeijingChina
| | - Guixian Xia
- Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- State Key Laboratory of Plant GenomicsBeijingChina
| | - Haiyun Wang
- Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- State Key Laboratory of Plant GenomicsBeijingChina
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Haghdoust R, Singh D, Park RF, Dracatos PM. Characterizing the Genetic Architecture of Nonhost Resistance in Barley Using Pathogenically Diverse Puccinia Isolates. PHYTOPATHOLOGY 2021; 111:684-694. [PMID: 32931394 DOI: 10.1094/phyto-05-20-0193-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Barley is an intermediate or near nonhost to many cereal rust pathogens that infect grasses, making it a highly suitable model to understand the evolution and genetic basis of nonhost resistance (NHR) in plants. To characterize the genetic architecture of NHR in barley, we used the Oregon Wolfe Barley doubled haploid and Morex × SusPtrit recombinant inbred line mapping populations. To elicit a wide array of NHR responses, we tested 492 barley accessions and both mapping populations with pathogenically diverse cereal rust isolates representing distinct formae speciales adapted to Avena, Hordeum, Triticum, and Lolium spp.: P. coronata f. sp. avenae (oat crown rust pathogen) and P. coronata f. sp. lolii (ryegrass crown rust pathogen), P. graminis f. sp. avenae (oat stem rust pathogen) and P. graminis f. sp. lolii (the ryegrass stem rust pathogen), and P. striiformis f. sp. tritici (wheat stripe rust pathogen) and P. striiformis f. sp. pseudo-hordei (barley grass stripe rust pathogen). With the exception of P. coronata f. sp. lolii and P. coronata f. sp. avenae, susceptibility and segregation for NHR was observed in the barley accessions and both mapping populations. Quantitative trait loci (QTLs) for NHR were mapped on all seven chromosomes. NHR in barley to the heterologous rusts tested was attributable to a combination of QTLs with either or both overlapping and distinct specificities. Across both mapping populations, broadly effective NHR loci were also identified that likely play a role in host specialization.
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Affiliation(s)
- R Haghdoust
- Plant Breeding Institute, University of Sydney, Cobbitty, Narellan, New South Wales 2567, Australia
| | - D Singh
- Plant Breeding Institute, University of Sydney, Cobbitty, Narellan, New South Wales 2567, Australia
| | - R F Park
- Plant Breeding Institute, University of Sydney, Cobbitty, Narellan, New South Wales 2567, Australia
| | - P M Dracatos
- Plant Breeding Institute, University of Sydney, Cobbitty, Narellan, New South Wales 2567, Australia
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Hatta MAM, Arora S, Ghosh S, Matny O, Smedley MA, Yu G, Chakraborty S, Bhatt D, Xia X, Steuernagel B, Richardson T, Mago R, Lagudah ES, Patron NJ, Ayliffe M, Rouse MN, Harwood WA, Periyannan S, Steffenson BJ, Wulff BB. The wheat Sr22, Sr33, Sr35 and Sr45 genes confer resistance against stem rust in barley. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:273-284. [PMID: 32744350 PMCID: PMC7868974 DOI: 10.1111/pbi.13460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 06/17/2020] [Indexed: 05/16/2023]
Abstract
In the last 20 years, stem rust caused by the fungus Puccinia graminis f. sp. tritici (Pgt), has re-emerged as a major threat to wheat and barley production in Africa and Europe. In contrast to wheat with 60 designated stem rust (Sr) resistance genes, barley's genetic variation for stem rust resistance is very narrow with only ten resistance genes genetically identified. Of these, only one complex locus consisting of three genes is effective against TTKSK, a widely virulent Pgt race of the Ug99 tribe which emerged in Uganda in 1999 and has since spread to much of East Africa and parts of the Middle East. The objective of this study was to assess the functionality, in barley, of cloned wheat Sr genes effective against race TTKSK. Sr22, Sr33, Sr35 and Sr45 were transformed into barley cv. Golden Promise using Agrobacterium-mediated transformation. All four genes were found to confer effective stem rust resistance. The barley transgenics remained susceptible to the barley leaf rust pathogen Puccinia hordei, indicating that the resistance conferred by these wheat Sr genes was specific for Pgt. Furthermore, these transgenic plants did not display significant adverse agronomic effects in the absence of disease. Cloned Sr genes from wheat are therefore a potential source of resistance against wheat stem rust in barley.
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Affiliation(s)
- M. Asyraf Md Hatta
- John Innes CentreNorwich Research ParkNorwichUK
- Department of Agriculture TechnologyFaculty of AgricultureUniversiti Putra MalaysiaSerdangMalaysia
| | - Sanu Arora
- John Innes CentreNorwich Research ParkNorwichUK
| | - Sreya Ghosh
- John Innes CentreNorwich Research ParkNorwichUK
| | - Oadi Matny
- Department of Plant PathologyStakman Borlaug Center for Sustainable Plant HealthUniversity of MinnesotaSt. PaulMNUSA
| | | | - Guotai Yu
- John Innes CentreNorwich Research ParkNorwichUK
| | - Soma Chakraborty
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Dhara Bhatt
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Xiaodi Xia
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | | | - Terese Richardson
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Rohit Mago
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Evans S. Lagudah
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | | | - Michael Ayliffe
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Matthew N. Rouse
- Department of Plant PathologyStakman Borlaug Center for Sustainable Plant HealthUniversity of MinnesotaSt. PaulMNUSA
- USDA‐ARS Cereal Disease LaboratorySt. PaulMNUSA
| | | | - Sambasivam Periyannan
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Brian J. Steffenson
- Department of Plant PathologyStakman Borlaug Center for Sustainable Plant HealthUniversity of MinnesotaSt. PaulMNUSA
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11
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Jaswal R, Kiran K, Rajarammohan S, Dubey H, Singh PK, Sharma Y, Deshmukh R, Sonah H, Gupta N, Sharma TR. Effector Biology of Biotrophic Plant Fungal Pathogens: Current Advances and Future Prospects. Microbiol Res 2020; 241:126567. [PMID: 33080488 DOI: 10.1016/j.micres.2020.126567] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 07/21/2020] [Accepted: 07/25/2020] [Indexed: 12/13/2022]
Abstract
The interaction of fungal pathogens with their host requires a novel invading mechanism and the presence of various virulence-associated components responsible for promoting the infection. The small secretory proteins, explicitly known as effector proteins, are one of the prime mechanisms of host manipulation utilized by the pathogen to disarm the host. Several effector proteins are known to translocate from fungus to the plant cell for host manipulation. Many fungal effectors have been identified using genomic, transcriptomic, and bioinformatics approaches. Most of the effector proteins are devoid of any conserved signatures, and their prediction based on sequence homology is very challenging, therefore by combining the sequence consensus based upon machine learning features, multiple tools have also been developed for predicting apoplastic and cytoplasmic effectors. Various post-genomics approaches like transcriptomics of virulent isolates have also been utilized for identifying active consortia of effectors. Significant progress has been made in understanding biotrophic effectors; however, most of it is underway due to their complex interaction with host and complicated recognition and signaling networks. This review discusses advances, and challenges in effector identification and highlighted various features of the potential effector proteins and approaches for understanding their genetics and strategies for regulation.
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Affiliation(s)
- Rajdeep Jaswal
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India; Department of Microbiology, Panjab University, Chandigarh, Punjab, 160014, India
| | - Kanti Kiran
- ICAR-National Institute for Plant Biotechnology, Pusa Campus New Delhi, 110012, India
| | | | - Himanshu Dubey
- ICAR-National Institute for Plant Biotechnology, Pusa Campus New Delhi, 110012, India
| | - Pankaj Kumar Singh
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India
| | - Yogesh Sharma
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India
| | - Naveen Gupta
- Department of Microbiology, Panjab University, Chandigarh, Punjab, 160014, India.
| | - T R Sharma
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India.
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12
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Yu Y, Qiao L, Chen J, Rong Y, Zhao Y, Cui X, Xu J, Hou X, Dong CH. Arabidopsis REM16 acts as a B3 domain transcription factor to promote flowering time via directly binding to the promoters of SOC1 and FT. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1386-1398. [PMID: 32391591 DOI: 10.1111/tpj.14807] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 04/22/2020] [Accepted: 05/01/2020] [Indexed: 05/25/2023]
Abstract
Actin depolymerizing factor (ADF) is a key modulator for dynamic organization of actin cytoskeleton. Interestingly, it was found that the ADF1 gene silencing delays flowering, but its mechanism remains unclear. In this study, ADF1 was used as a bait to screen its interacting proteins by the yeast two-hybrid (Y2H) system. One of them, the REM16 transcription factor was identified. As one of the AP2/B3-like transcriptional factor family members, the REM16 contains two B3 domains and its transcript levels kept increasing during the floral transition stage. Overexpression of REM16 accelerates flowering while silencing of REM16 delays flowering. Gene expression analysis indicated that the key flowering activation genes such as CONSTANS (CO), FLOWERING LOCUS T (FT), LEAFY (LFY) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS (SOC1) were upregulated in the REM16 overexpression lines, while the transcription of the flowering suppression gene FLOWERING LOCUS C (FLC) was decreased. In contrast, the REM16 gene silencing lines contained lower transcript levels of the CO, FT, LFY and SOC1 but higher transcript levels of the FLC compared with the wild-type plants. It was proved that REM16 could directly bind to the promoter regions of SOC1 and FT by in vitro and in vivo assays. Genetic analysis supported that REM16 acts upstream of SOC1 and FT in flowering pathways. All these studies provided strong evidence demonstrating that REM16 promotes flowering by directly activating SOC1 and FT.
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Affiliation(s)
- Yanchong Yu
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Longfei Qiao
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Jiacai Chen
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Yongheng Rong
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Yuhang Zhao
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Xiankui Cui
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Jinpeng Xu
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Xiaomin Hou
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Chun-Hai Dong
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
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13
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Ren S, Sun M, Yan H, Wu B, Jing T, Huang L, Zeng B. Identification and Distribution of NBS-Encoding Resistance Genes of Dactylis glomerata L. and Its Expression Under Abiotic and Biotic Stress. Biochem Genet 2020; 58:824-847. [PMID: 32506157 DOI: 10.1007/s10528-020-09977-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 06/01/2020] [Indexed: 11/29/2022]
Abstract
Orchardgrass (Dactylis glomerata L.) is drought resistant and tolerant to barren landscapes, making it one of the most important forages for animal husbandry, as well as ecological restoration of rocky landscapes that are undergoing desertification. However, orchardgrass is susceptible to rust, which can significantly reduce its yield and quality. Therefore, understanding the genes that underlie resistance against rust in orchardgrass is critical. The evolution, cloning of plant disease resistance genes, and the analysis of pathogenic bacteria induced expression patterns are important contents in the study of interaction between microorganisms and plants. Genes with nucleotide binding site (NBS) structure are disease-resistant genes ubiquitous in plants and play an important role in plant attacks against various pathogens. Using sequence analysis and re-annotation, we identified 413 NBS resistance genes in orchardgrass. Similar to previous studies, NBS resistance genes containing TIR (toll/interleukin-1 receptor) domain were not found in orchardgrass. The NBS resistance genes can be divided into four types: NBS (up to 264 homologous genes, accounting for 64% of the total number of NBS genes in orchardgrass), NBS-LRR, CC-NBS, and CC-NBS-LRR (minimum of 26 homologous genes, only 6% of the total number of NBS genes in orchardgrass). These 413 NBS resistance genes were unevenly distributed across seven chromosomes where chromosome 5 had up to 99 NBS resistance genes. There were 224 (54%) NBS resistance genes expressed in different tissues (roots, stems, leaves, flowers, and spikes), and we did not detect expression for 45 genes (11%). The remaining 145 (35%) were expressed in some tissues. And we found that 11 NBS resistance genes were differentially expressed under waterlogging stress, 5 NBS resistance genes were differentially expressed under waterlogging and drought stress, and 1 NBS resistance was is differentially expressed under waterlogging and heat stress. Most importantly, we found that 65 NBS resistance genes were significantly expressed in different control groups. On the 7th day of inoculation, 23 NBS resistance genes were differentially expressed in high resistance materials alone, of which 7 NBS resistance genes regulate the "plant-pathogen interaction" pathway by encoding RPM1. At the same time, 2 NBS resistance genes that were differentially expressed in the high resistance material after inoculation were also differentially expressed in abiotic stress. In summary, the NBS resistance gene plays a crucial role in the resistance of orchardgrass to rust.
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Affiliation(s)
- Shuping Ren
- College of Animal Science, Southwest University, Rongchang Campus, Chongqing, 402460, China
| | - Min Sun
- Department of Grassland Science, Faculty of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Haidong Yan
- Department of Grassland Science, Faculty of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Bingchao Wu
- Department of Grassland Science, Faculty of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tingting Jing
- Department of Grassland Science, Faculty of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linkai Huang
- Department of Grassland Science, Faculty of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Bing Zeng
- College of Animal Science, Southwest University, Rongchang Campus, Chongqing, 402460, China.
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14
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Hernandez J, Del Blanco A, Filichkin T, Fisk S, Gallagher L, Helgerson L, Meints B, Mundt C, Steffenson B, Hayes P. A Genome-Wide Association Study of Resistance to Puccinia striiformis f. sp. hordei and P. graminis f. sp. tritici in Barley and Development of Resistant Germplasm. PHYTOPATHOLOGY 2020; 110:1082-1092. [PMID: 32023173 DOI: 10.1094/phyto-11-19-0415-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Stripe rust (incited by Puccinia striiformis f. sp. hordei) and stem rust (incited by P. graminis f. sp. tritici) are two of the most important diseases affecting barley. Building on prior work involving the introgression of the resistance genes rpg4/Rpg5 into diverse genetic backgrounds and the discovery of additional quantitative trait locus (QTLs) for stem rust resistance, we generated an array of germplasm in which we mapped resistance to stripe rust and stem rust. Stem rust races TTKSK and QCCJB were used for resistance mapping at the seedling and adult plant stages, respectively. Resistance to stripe rust, at the adult plant stage, was determined by QTLs on chromosomes 1H, 4H, and 5H that were previously reported in the literature. The rpg4/Rpg5 complex was validated as a source of resistance to stem rust at the seedling stage. Some parental germplasm, selected as potentially resistant to stem rust or susceptible but having other positive attributes, showed resistance at the seedling stage, which appears to be allelic to rpg4/Rpg5. The rpg4/Rpg5 complex, and this new allele, were not sufficient for adult plant resistance to stem rust in one environment. A QTL on 5H, distinct from Rpg5 and a previously reported resistance QTL, was required for resistance at the adult plant stage in all environments. This QTL is coincident with the QTL for stripe rust resistance. Germplasm with mapped genes/QTLs conferring resistance to stripe and stem rust was identified and is available as a resource to the research and breeding communities.
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Affiliation(s)
- Javier Hernandez
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Alicia Del Blanco
- Department of Plant Sciences, University of California-Davis, Davis, CA 95616
| | - Tanya Filichkin
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Scott Fisk
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Lynn Gallagher
- Department of Plant Sciences, University of California-Davis, Davis, CA 95616
| | - Laura Helgerson
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Brigid Meints
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Chris Mundt
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Brian Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Patrick Hayes
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
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15
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Sharma Poudel R, Richards J, Shrestha S, Solanki S, Brueggeman R. Transcriptome-wide association study identifies putative elicitors/suppressor of Puccinia graminis f. sp. tritici that modulate barley rpg4-mediated stem rust resistance. BMC Genomics 2019; 20:985. [PMID: 31842749 PMCID: PMC6915985 DOI: 10.1186/s12864-019-6369-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 12/04/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Stem rust is an economically important disease of wheat and barley. However, studies to gain insight into the molecular basis of these host-pathogen interactions have primarily focused on wheat because of its importance in human sustenance. This is the first extensive study utilizing a transcriptome-wide association mapping approach to identify candidate Puccinia graminis f. sp. tritici (Pgt) effectors/suppressors that elicit or suppress barley stem rust resistance genes. Here we focus on identifying Pgt elicitors that interact with the rpg4-mediated resistance locus (RMRL), the only effective source of Pgt race TTKSK resistance in barley. RESULTS Thirty-seven Pgt isolates showing differential responses on RMRL were genotyped using Restriction Site Associated DNA-Genotyping by Sequencing (RAD-GBS), identifying 24 diverse isolates that were used for transcript analysis during the infection process. In planta RNAseq was conducted with the 24 diverse isolates on the susceptible barley variety Harrington, 5 days post inoculation. The transcripts were mapped to the Pgt race SCCL reference genome identifying 114 K variants in predicted genes that would result in nonsynonymous amino acid substitutions. Transcriptome wide association analysis identified 33 variants across 28 genes that were associated with dominant RMRL virulence, thus, representing candidate suppressors of resistance. Comparative transcriptomics between the 9 RMRL virulent -vs- the 15 RMRL avirulent Pgt isolates identified 44 differentially expressed genes encoding candidate secreted effector proteins (CSEPs), among which 38 were expressed at lower levels in virulent isolates suggesting that they may represent RMRL avirulence genes. Barley transcript analysis after colonization with 9 RMRL virulent and 15 RMRL avirulent isolates inoculated on the susceptible line Harrington showed significantly lower expression of host biotic stress responses specific to RMRL virulent isolates suggesting virulent isolates harbor effectors that suppress resistance responses. CONCLUSIONS This transcriptomic study provided novel findings that help fill knowledge gaps in the understanding of stem rust virulence/avirulence and host resistance in barley. The pathogen transcriptome analysis suggested RMRL virulence might depend on the lack of avirulence genes, but evidence from pathogen association mapping analysis and host transcriptional analysis also suggested the alternate hypothesis that RMRL virulence may be due to the presence of suppressors of defense responses.
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Affiliation(s)
| | - Jonathan Richards
- Department of Plant Pathology and Crop Physiology, Louisiana State University, Baton Rouge, LA, USA
| | - Subidhya Shrestha
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA
| | - Shyam Solanki
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Robert Brueggeman
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA.
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16
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Ma YQ, Li Q, Pu ZQ, Lu MX, Yao JW, Feng JC, Xu ZQ. Constitutive expression of NtabSPL6-1 in tobacco and Arabidopsis could change the structure of leaves and promote the development of trichomes. JOURNAL OF PLANT PHYSIOLOGY 2019; 240:152991. [PMID: 31207459 DOI: 10.1016/j.jplph.2019.152991] [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: 02/04/2019] [Revised: 06/04/2019] [Accepted: 06/04/2019] [Indexed: 06/09/2023]
Abstract
The coding sequence of NtabSPL6-1 was cloned by high-fidelity PCR with specific primers and was used in construction of a binary vector for overexpression. Wild-type Col-0 Arabidopsis plants and Qinyan95 tobacco leaves were transformed using floral dip and leaf disc methods, respectively. Phenotypic observation showed that constitutive expression of NtabSPL6-1 in Arabidopsis could promote the development of trichomes on leaf epidermis and influence the growth pattern of cauline leaves. In tobacco, ectopic expression of NtabSPL6-1 led to dwarfism of the plants and alteration of the leaf structure, accompanied by changes of the glandular trichomes in development. At the same time, the self-regulation capability of NtabSPL6-1 was determined by yeast two-hybrid system. The results indicated that SBP-C terminal domain and C terminal domain of NtabSPL6-1 possessed strong transcriptional activation ability; the intact protein, N terminal domain, and the first peptide fragment in N terminal domain possessed weak transcriptional activation ability; and the second and the third peptide fragments in N terminal domain had no transcriptional activation ability, suggesting the N terminal domain of NtabSPL6-1 could block the activity of the C terminal domain. NtabSPL6-1 may affect the resistance of plants to biotic stress factors indirectly by regulation of the trichome growth.
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Affiliation(s)
- Yan-Qin Ma
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, People's Republic of China
| | - Qi Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, People's Republic of China
| | - Zuo-Qian Pu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, People's Republic of China
| | - Meng-Xin Lu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, People's Republic of China
| | - Jing-Wen Yao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, People's Republic of China
| | - Jia-Chun Feng
- Key Laboratory of Molecular Engineering of Polymers of Ministry of Education, Department of Macromolecular Science and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, People's Republic of China
| | - Zi-Qin Xu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, People's Republic of China.
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17
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Solanki S, Richards J, Ameen G, Wang X, Khan A, Ali H, Stangel A, Tamang P, Gross T, Gross P, Fetch TG, Brueggeman RS. Characterization of genes required for both Rpg1 and rpg4-mediated wheat stem rust resistance in barley. BMC Genomics 2019; 20:495. [PMID: 31200635 PMCID: PMC6570958 DOI: 10.1186/s12864-019-5858-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 05/29/2019] [Indexed: 01/20/2023] Open
Abstract
Background Puccinia graminis f. sp. tritici (Pgt) race TTKSK and its lineage pose a threat to barley production world-wide justifying the extensive efforts to identify, clone, and characterize the rpg4-mediated resistance locus (RMRL), the only effective resistance to virulent Pgt races in the TTKSK lineage. The RMRL contains two nucleotide-binding domain and leucine-rich repeat (NLR) resistance genes, Rpg5 and HvRga1, which are required for resistance. The two NLRs have head-to-head genome architecture with one NLR, Rpg5, containing an integrated C-terminal protein kinase domain, characteristic of an “integrated sensory domain” resistance mechanism. Fast neutron mutagenesis of line Q21861 was utilized in a forward genetics approach to identify genetic components that function in the RMRL or Rpg1 resistance mechanisms, as Q21861 contains both genes. A mutant was identified that compromises both RMRL and Rpg1-mediated resistances and had stunted seedling roots, designated required for P. graminis resistance 9 (rpr9). Results The rpr9 mutant generated in the Q21861 background was crossed with the Swiss landrace Hv584, which carries RMRL but contains polymorphism across the genome compared to Q21861. To map Rpr9, a Hv584 x rpr9 F6:7 recombinant inbred line (RIL) population was developed. The RIL population was phenotyped with Pgt race QCCJB. The Hv584 x rpr9 RIL population was genotyped with the 9 k Illumina Infinium iSelect marker panel, producing 2701 polymorphic markers. A robust genetic map consisting of 563 noncosegregating markers was generated and used to map Rpr9 to an ~ 3.4 cM region on barley chromosome 3H. The NimbleGen barley exome capture array was utilized to capture rpr9 and wild type Q21861 exons, followed by Illumina sequencing. Comparative analysis, resulting in the identification of a 1.05 Mbp deletion at the chromosome 3H rpr9 locus. The identified deletion contains ten high confidence annotated genes with the best rpr9 candidates encoding a SKP1-like 9 protein and a F-box family protein. Conclusion Genetic mapping and exome capture rapidly identified candidate gene/s that function in RMRL and Rpg1 mediated resistance pathway/s. One or more of the identified candidate rpr9 genes are essential in the only two known effective stem rust resistance mechanisms, present in domesticated barley. Electronic supplementary material The online version of this article (10.1186/s12864-019-5858-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shyam Solanki
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Jonathan Richards
- Department of Plant Pathology and Crop Physiology, Louisiana State University AgCenter, Baton Rouge, LA, 70803, USA
| | - Gazala Ameen
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Xue Wang
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Atiya Khan
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Harris Ali
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Alex Stangel
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Prabin Tamang
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Thomas Gross
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Patrick Gross
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Thomas G Fetch
- Cereal Research Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - Robert S Brueggeman
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA.
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18
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Hernandez J, Steffenson BJ, Filichkin T, Fisk SP, Helgerson L, Meints B, Vining KJ, Marshall D, Del Blanco A, Chen X, Hayes PM. Introgression of rpg4/ Rpg5 Into Barley Germplasm Provides Insights Into the Genetics of Resistance to Puccinia graminis f. sp. tritici Race TTKSK and Resources for Developing Resistant Cultivars. PHYTOPATHOLOGY 2019; 109:1018-1028. [PMID: 30714882 DOI: 10.1094/phyto-09-18-0350-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Stem rust (incited by Puccinia graminis f. sp. tritici) is a devastating disease of wheat and barley in many production areas. The widely virulent African P. graminis f. sp. tritici race TTKSK is of particular concern, because most cultivars are susceptible. To prepare for the possible arrival of race TTKSK in North America, we crossed a range of barley germplasm-representing different growth habits and end uses-with donors of stem rust resistance genes Rpg1 and rpg4/Rpg5. The former confers resistance to prevalent races of P. graminis f. sp. tritici in North America, and the latter confers resistance to TTKSK and other closely related races from Africa. We produced doubled haploids from these crosses and determined their allele type at the Rpg loci and haplotype at 7,864 single-nucleotide polymorphism loci. The doubled haploids were phenotyped for TTKSK resistance at the seedling stage. Integration of genotype and phenotype data revealed that (i) Rpg1 was not associated with TTKSK resistance, (ii) rpg4/Rpg5 was necessary but was not sufficient for resistance, and (iii) specific haplotypes at two quantitative trait loci were required for rpg4/Rpg5 to confer resistance to TTKSK. To confirm whether lines found resistant to TTKSK at the seedling resistance were also resistant at the adult plant stage, a subset of doubled haploids was evaluated in Kenya. Additionally, adult plant resistance to leaf rust and stripe rust (incited by Puccinia hordei and Puccinia striiformis f. sp. hordei, respectively) was also assessed on the doubled haploids in field trials at three locations in the United States over a 2-year period. Doubled haploids were identified with adult plant resistance to all three rusts, and this germplasm is available to the research and breeding communities.
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Affiliation(s)
- Javier Hernandez
- 1 Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Brian J Steffenson
- 2 Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Tanya Filichkin
- 1 Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Scott P Fisk
- 1 Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Laura Helgerson
- 1 Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Brigid Meints
- 1 Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Kelly J Vining
- 3 Department of Horticulture, Oregon State University, Corvallis, OR 97331
| | - David Marshall
- 4 U.S. Department of Agriculture Agricultural Research Service, Raleigh, NC 27695
| | - Alicia Del Blanco
- 5 Department of Plant Sciences, University of California, Davis, CA 95616
| | - Xianming Chen
- 6 U.S. Department of Agriculture Agricultural Research Service Wheat Health, Genetics, and Quality Research Unit and Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430
| | - Patrick M Hayes
- 1 Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
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Solanki S, Ameen G, Borowicz P, Brueggeman RS. Shedding Light on Penetration of Cereal Host Stomata by Wheat Stem Rust Using Improved Methodology. Sci Rep 2019; 9:7939. [PMID: 31138873 PMCID: PMC6538696 DOI: 10.1038/s41598-019-44280-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 05/08/2019] [Indexed: 11/09/2022] Open
Abstract
Asexual urediniospore infection of primary cereal hosts by Puccinia graminis f. sp. tritici (Pgt), the wheat stem rust pathogen, was considered biphasic. The first phase, spore germination and appressoria formation, requires a dark period and moisture. The second phase, host entry by the penetration peg originating from the appressoria formed over the guard cells, was thought to require light to induce natural stomata opening. Previous studies concluded that inhibition of colonization by the dark was due to lack of penetration through closed stomata. A sensitive WGA-Alexa Fluor 488 fungal staining, surface creation and biovolume analysis method was developed enabling visualization and quantification of fungal growth in planta at early infection stages surpassing visualization barriers using previous methods. The improved method was used to investigate infection processes of Pgt during stomata penetration and colonization in barley and wheat showing that penetration is light independent. Based on the visual growth and fungal biovolume analysis it was concluded that the differences in pathogen growth dynamics in both resistant and susceptible genotypes was due to light induced pathogen growth after penetration into the substomatal space. Thus, light induced plant or pathogen cues triggers pathogen growth in-planta post penetration.
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Affiliation(s)
- Shyam Solanki
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Gazala Ameen
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Pawel Borowicz
- Department of Animal Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Robert S Brueggeman
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA.
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20
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Kapos P, Devendrakumar KT, Li X. Plant NLRs: From discovery to application. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 279:3-18. [PMID: 30709490 DOI: 10.1016/j.plantsci.2018.03.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 03/01/2018] [Accepted: 03/02/2018] [Indexed: 05/09/2023]
Abstract
Plants require a complex immune system to defend themselves against a wide range of pathogens which threaten their growth and development. The nucleotide-binding leucine-rich repeat proteins (NLRs) are immune sensors that recognize effectors delivered by pathogens. The first NLR was cloned more than twenty years ago. Since this initial discovery, NLRs have been described as key components of plant immunity responsible for pathogen recognition and triggering defense responses. They have now been described in most of the well-studied mulitcellular plant species, with most having large NLR repertoires. As research has progressed so has the understanding of how NLRs interact with their recognition substrates and how they in turn activate downstream signalling. It has also become apparent that NLR regulation occurs at the transcriptional, post-transcriptional, translational, and post-translational levels. Even before the first NLR was cloned, breeders were utilising such genes to increase crop performance. Increased understanding of the mechanistic details of the plant immune system enable the generation of plants resistant against devastating pathogens. This review aims to give an updated summary of the NLR field.
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Affiliation(s)
- Paul Kapos
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada; Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Karen Thulasi Devendrakumar
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada; Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada; Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
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Sharma Poudel R, Al-Hashel AF, Gross T, Gross P, Brueggeman R. Pyramiding rpg4- and Rpg1-Mediated Stem Rust Resistance in Barley Requires the Rrr1 Gene for Both to Function. FRONTIERS IN PLANT SCIENCE 2018; 9:1789. [PMID: 30568667 PMCID: PMC6290389 DOI: 10.3389/fpls.2018.01789] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/19/2018] [Indexed: 05/20/2023]
Abstract
Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt) is an economically important disease of wheat and barley. Rpg1 is the only resistance gene deployed in Midwestern US barley varieties and provides remarkable resistance to most North American races, except Pgt race QCCJB. Rpg1 is also ineffective against Pgt race TTKSK and its lineage that originated in Africa. The barley rpg4-mediated resistance locus (RMRL) conferring resistance to Pgt races QCCJB and TTKSK was isolated from line Q21861, which is resistant to all known Pgt races due to Rpg1 and RMRL. To develop elite barley varieties RMRL was pyramided into the varieties, Pinnacle and Conlon (both contain Rpg1), producing the near isogenic lines (NILs), Pinnacle RMRL-NIL (PRN) and Conlon RMRL-NIL (CRN). The CRN was resistant to Pgt races QCCJB (RMRL specific) and HKHJC (Rpg1 specific) at the seedling stage and Pgt race TTKSK (RMRL specific) at the adult stage. In contrast, PRN was susceptible to QCCJB and HKHJC at the seedling stage and TTKSK at the adult stage. Interestingly, PRN's susceptibility to QCCJB and HKHJC showed that RMRL was non-functional in the Pinnacle background but its presence also suppressed Rpg1-mediated resistance. Thus, in the absence of a gene/s found in the Q21861 background, Rpg1 becomes non-functional if RMRL is present, suggesting that another polymorphic gene, that we designated Rrr1 (required for rpg4-mediated resistance 1), is required for RMRL resistance and Rpg1-mediated resistance in the presence of RMRL. Utilizing a PRN/Q21861 derived recombinant inbred line (RIL) population, Rrr1 was delimited to a ∼0.5 MB physical region, slightly proximal (∼1.8 MB) of RMRL on barley chromosome 5H. A second gene, designated required for Rpg1-mediated resistance 2 (Rrr2), with duplicate gene action to Rrr1 in Rpg1-mediated resistance function, was genetically delimited to a physical region of ∼0.7 MB, slightly distal (∼3.1 MB) to Rpg1 on the short arm of barley chromosome 7H. Thus, Rrr1 is required for RMRL resistance and Rrr1 or Rrr2 is required for functional Rpg1-mediated resistance in the presence of the RMRL introgression. Candidate Rrr1 and Rrr2 genes were identified that need to be considered when pyramiding Rpg1 and RMRL in barley.
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Affiliation(s)
| | | | | | | | - Robert Brueggeman
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
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22
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Case AJ, Bhavani S, Macharia G, Pretorius Z, Coetzee V, Kloppers F, Tyagi P, Brown-Guedira G, Steffenson BJ. Mapping adult plant stem rust resistance in barley accessions Hietpas-5 and GAW-79. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2245-2266. [PMID: 30109391 DOI: 10.1007/s00122-018-3149-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/23/2018] [Indexed: 06/08/2023]
Abstract
Key message Major stem rust resistance QTLs proposed to be Rpg2 from Hietpas-5 and Rpg3 from GAW-79 were identified in chromosomes 2H and 5H, respectively, and will enhance the diversity of stem rust resistance in barley improvement programs. Stem rust is a devastating disease of cereal crops worldwide. In barley (Hordeum vulgare ssp. vulgare), the disease is caused by two pathogens: Puccinia graminis f. sp. secalis (Pgs) and Puccinia graminis f. sp. tritici (Pgt). In North America, the stem rust resistance gene Rpg1 has protected barley from serious losses for more than 60 years; however, widely virulent Pgt races from Africa in the Ug99 group threaten the crop. The accessions Hietpas-5 (CIho 7124) and GAW-79 (PI 382313) both possess moderate-to-high levels of adult plant resistance to stem rust and are the sources of the resistance genes Rpg2 and Rpg3, respectively. To identify quantitative trait loci (QTL) for stem rust resistance in Hietpas-5 and GAW-79, two biparental populations were developed with Hiproly (PI 60693), a stem rust-susceptible accession. Both populations were phenotyped to the North American Pgt races of MCCFC, QCCJB, and HKHJC in St. Paul, Minnesota, and to African Pgt races (predominately TTKSK in the Ug99 group) in Njoro, Kenya. In the Hietpas-5/Hiproly population, a major effect QTL was identified in chromosome 2H, which is proposed as the location for Rpg2. In the GAW-79/Hiproly population, a major effect QTL was identified in chromosome 5H and is the proposed location for Rpg3. These QTLs will enhance the diversity of stem rust resistance in barley improvement programs.
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Affiliation(s)
- Austin J Case
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - Sridhar Bhavani
- Centro Internacional de Mejoramiento de Maíz y Trigo (CIMMYT), Nairobi, Kenya
| | - Godwin Macharia
- Kenya Agriculture and Livestock Research Organization (KALRO), Njoro, Kenya
| | - Zacharias Pretorius
- Department of Plant Sciences, University of the Free State, Bloemfontein, Republic of South Africa
| | - Vicky Coetzee
- Pannar Seed (Pyt) Ltd, Greytown, Republic of South Africa
| | | | - Priyanka Tyagi
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | | | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA.
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23
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Nicolis V, Venter E. Silencing of a Unique Integrated Domain Nucleotide-Binding Leucine-Rich Repeat Gene in Wheat Abolishes Diuraphis noxia Resistance. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018. [PMID: 29533135 DOI: 10.1094/mpmi-11-17-0262-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Plants respond in a similar manner to aphid feeding as to pathogen attack. Diuraphis noxia is a specialist aphid, feeding only on selected grasses that include wheat, barley, and oats. The wheat-Diuraphis noxia interaction is characterized by responses very similar to those seen in wheat-pathogen interactions with none of the underlying resistance pathways and genes characterized yet. From wheat harboring the Dn1 resistance gene, we have identified a nucleotide-binding leucine-rich repeat (NLR) gene containing two integrated domains (IDs). These are three C-terminus ankyrin repeat domains and an N-terminus WRKY domain. The NLR core of the gene can be traced through speciation events within the grass family, with a recent WRKY domain integration that is Triticum-specific. Virus-induced gene silencing of the gene in a resistant wheat line resulted in the abolishment of the resistance response and induced a highly susceptible phenotype. Silenced plants supported a higher number of aphids, similar to the susceptible near-isogenic line (NIL), and the intrinsic rate of increase of the aphids matched that of aphids feeding on the susceptible NIL. The presence of the gene is necessary for Dn1 resistance and we have named the gene Associated with Dn resistance 1 (Adnr1) to reflect this function.
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Affiliation(s)
- Vittorio Nicolis
- Department of Botany and Plant Biotechnology, University of Johannesburg, Auckland Park, Johannesburg, 2006, South Africa
| | - Eduard Venter
- Department of Botany and Plant Biotechnology, University of Johannesburg, Auckland Park, Johannesburg, 2006, South Africa
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24
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Li J, Staiger CJ. Understanding Cytoskeletal Dynamics During the Plant Immune Response. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:513-533. [PMID: 29975609 DOI: 10.1146/annurev-phyto-080516-035632] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The plant cytoskeleton is a dynamic framework of cytoplasmic filaments that rearranges as the needs of the cell change during growth and development. Incessant turnover mechanisms allow these networks to be rapidly redeployed in defense of host cytoplasm against microbial invaders. Both chemical and mechanical stimuli are recognized as danger signals to the plant, and these are perceived and transduced into cytoskeletal dynamics and architecture changes through a collection of well-recognized, previously characterized players. Recent advances in quantitative cell biology approaches, along with the powerful molecular genetics techniques associated with Arabidopsis, have uncovered two actin-binding proteins as key intermediaries in the immune response to phytopathogens and defense signaling. Certain bacterial phytopathogens have adapted to the cytoskeletal-based defense mechanism during the basal immune response and have evolved effector proteins that target actin filaments and microtubules to subvert transcriptional reprogramming, secretion of defense-related proteins, and cell wall-based defenses. In this review, we describe current knowledge about host cytoskeletal dynamics operating at the crossroads of the molecular and cellular arms race between microbes and plants.
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Affiliation(s)
- Jiejie Li
- Department of Biological Sciences and Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA;
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Science, Beijing Normal University, Beijing 100875, China
| | - Christopher J Staiger
- Department of Biological Sciences and Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA;
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25
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Mondal S, Badigannavar AM. Mapping of a dominant rust resistance gene revealed two R genes around the major Rust_QTL in cultivated peanut (Arachis hypogaea L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1671-1681. [PMID: 29744525 DOI: 10.1007/s00122-018-3106-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 05/02/2018] [Indexed: 05/16/2023]
Abstract
A consensus rust QTL was identified within a 1.25 cM map interval of A03 chromosome in cultivated peanut. This map interval contains a TIR-NB-LRR R gene and four pathogenesis-related genes. Disease resistance in plants is manifested due to the specific interaction between the R gene product and its cognate avirulence gene product (AVR) in the pathogen. Puccinia arachidis Speg. causes rust disease and inflicts economic damages to peanut. Till now, no experimental evidence is known for the action of R gene in peanut for rust resistance. A fine mapping approach towards the development of closely linked markers for rust resistance gene was undertaken in this study. Phenotyping of an RIL population at five environments for field rust score and subsequent QTL analysis has identified a 1.25 cM map interval that harbored a consensus major Rust_QTL in A03 chromosome. This Rust_QTL is flanked by two SSR markers: FRS72 and SSR_GO340445. Both the markers clearly identified strong association of the mapped region with rust reaction in both resistant and susceptible genotypes from a collection of 95 cultivated peanut germplasm. This 1.25 cM map interval contained 331.7 kb in the physical map of A. duranensis and had a TIR-NB-LRR category R gene (Aradu.Z87JB) and four glucan endo-1,3 β glucosidase genes (Aradu.RKA6 M, Aradu.T44NR, Aradu.IWV86 and Aradu.VG51Q). Another resistance gene analog was also found in the vicinity of mapped Rust_QTL. The sequence between SSR markers, FRS72 and FRS49, contains an LRR-PK (Aradu.JG217) which is equivalent to RHG4 in soybean. Probably, the protein kinase domain in AhRHG4 acts as an integrated decoy for the cognate AVR from Puccinia arachidis and helps the TIR-NB-LRR R-protein to initiate a controlled program cell death in resistant peanut plants.
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Affiliation(s)
- Suvendu Mondal
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India.
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094, India.
| | - Anand M Badigannavar
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094, India
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26
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Haghdoust R, Singh D, Garnica DP, Park RF, Dracatos PM. Isolate Specificity and Polygenic Inheritance of Resistance in Barley to Diverse Heterologous Puccinia striiformis Isolates. PHYTOPATHOLOGY 2018; 108:617-626. [PMID: 29271300 DOI: 10.1094/phyto-10-17-0345-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Barley is a host to Puccinia striiformis f. sp. hordei, and is an intermediate or near nonhost to the formae speciales adapted to wheat (P. striiformis f. sp. tritici) and to barley grass (P. striiformis f. sp. pseudo-hordei). The genetic basis of resistance to these forms of P. striiformis is not well understood. Accordingly, a recombinant inbred line (RIL) population was developed using a P. striiformis-susceptible accession (Biosaline-19) and the immune cultivar Pompadour. We investigated the genetic basis of resistance to four diverse P. striiformis isolates (P. striiformis f. sp. pseudo-hordei, and P. striiformis f. sp. tritici pathotypes 104 E137 A-, 134 E16 A+, and 64 E0 A-). and determined that the immunity in Pompadour at the seedling stage to the different P. striiformis isolates was due to quantitative trait loci (QTL) on chromosomes 1H, 3H, 5H, and 7H with both overlapping and distinct specificities. Further histological analysis confirmed the presence of isolate specificity. The RILs were also assessed in the field for resistance to P. striiformis f. sp. pseudo-hordei, P. striiformis f. sp. hordei, and the leaf rust pathogen (P. hordei) to identify pleiotropic QTL loci effective at the adult plant stage and determine whether the leaf rust resistance in Pompadour (Rph20) was also effective to P. striiformis. RILs that were seedling susceptible to P. striiformis f. sp. pseudo-hordei were resistant in the field, implicating the involvement of adult plant resistance (APR). Additional QTLs were identified on chromosome 7H at the same genetic position as Rph23 (APR to leaf rust), suggesting either pleiotropic resistance or the presence of a stripe rust resistance gene closely linked to or allelic with Rph23. Unlike many pleiotropic APR genes identified and isolated in wheat, our data suggest that the Rph20 locus does not confer resistance to the P. striiformis isolates used in this study (P. striiformis f. sp. hordei [χ2 (independence) = 2.47 P > 0.12] and P. striiformis f. sp. pseudo-hordei [χ2 (independence) = 0.42 P > 0.60]).
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Affiliation(s)
- R Haghdoust
- First, second, fourth, and fifth authors: The University of Sydney, Plant Breeding Institute, Cobbitty, Private Bag 4011, Narellan, NSW, 2567, Australia; and second author: CSIRO Plant Industries, GPO Box 1600, Canberra, ACT, 2601, Australia
| | - D Singh
- First, second, fourth, and fifth authors: The University of Sydney, Plant Breeding Institute, Cobbitty, Private Bag 4011, Narellan, NSW, 2567, Australia; and second author: CSIRO Plant Industries, GPO Box 1600, Canberra, ACT, 2601, Australia
| | - D P Garnica
- First, second, fourth, and fifth authors: The University of Sydney, Plant Breeding Institute, Cobbitty, Private Bag 4011, Narellan, NSW, 2567, Australia; and second author: CSIRO Plant Industries, GPO Box 1600, Canberra, ACT, 2601, Australia
| | - R F Park
- First, second, fourth, and fifth authors: The University of Sydney, Plant Breeding Institute, Cobbitty, Private Bag 4011, Narellan, NSW, 2567, Australia; and second author: CSIRO Plant Industries, GPO Box 1600, Canberra, ACT, 2601, Australia
| | - P M Dracatos
- First, second, fourth, and fifth authors: The University of Sydney, Plant Breeding Institute, Cobbitty, Private Bag 4011, Narellan, NSW, 2567, Australia; and second author: CSIRO Plant Industries, GPO Box 1600, Canberra, ACT, 2601, Australia
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27
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Chakraborty J, Jain A, Mukherjee D, Ghosh S, Das S. Functional diversification of structurally alike NLR proteins in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 269:85-93. [PMID: 29606220 DOI: 10.1016/j.plantsci.2018.01.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/14/2017] [Accepted: 01/15/2018] [Indexed: 06/08/2023]
Abstract
In due course of evolution many pathogens alter their effector molecules to modulate the host plants' metabolism and immune responses triggered upon proper recognition by the intracellular nucleotide-binding oligomerization domain containing leucine-rich repeat (NLR) proteins. Likewise, host plants have also evolved with diversified NLR proteins as a survival strategy to win the battle against pathogen invasion. NLR protein indeed detects pathogen derived effector proteins leading to the activation of defense responses associated with programmed cell death (PCD). In this interactive process, genome structure and plasticity play pivotal role in the development of innate immunity. Despite being quite conserved with similar biological functions in all eukaryotes, the intracellular NLR immune receptor proteins happen to be structurally distinct. Recent studies have made progress in identifying transcriptional regulatory complexes activated by NLR proteins. In this review, we attempt to decipher the intracellular NLR proteins mediated surveillance across the evolutionarily diverse taxa, highlighting some of the recent updates on NLR protein compartmentalization, molecular interactions before and after activation along with insights into the finer role of these receptor proteins to combat invading pathogens upon their recognition. Latest information on NLR sensors, helpers and NLR proteins with integrated domains in the context of plant pathogen interactions are also discussed.
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Affiliation(s)
- Joydeep Chakraborty
- Division of Plant Biology, Bose Institute, Centenary Campus, Kolkata, West Bengal, India.
| | - Akansha Jain
- Division of Plant Biology, Bose Institute, Centenary Campus, Kolkata, West Bengal, India.
| | - Dibya Mukherjee
- Division of Plant Biology, Bose Institute, Centenary Campus, Kolkata, West Bengal, India.
| | - Suchismita Ghosh
- Division of Plant Biology, Bose Institute, Centenary Campus, Kolkata, West Bengal, India; Department of Biotechnology, St. Xavier's College, Kolkata, West Bengal, India.
| | - Sampa Das
- Division of Plant Biology, Bose Institute, Centenary Campus, Kolkata, West Bengal, India.
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28
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Case AJ, Bhavani S, Macharia G, Steffenson BJ. Genome-wide association study of stem rust resistance in a world collection of cultivated barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:107-126. [PMID: 29177535 DOI: 10.1007/s00122-017-2989-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 09/19/2017] [Indexed: 05/20/2023]
Abstract
QTL conferring a 14-40% reduction in adult plant stem rust severity to multiple races of Pgt were found on chromosome 5H and will be useful in barley breeding. Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt) is an important disease of barley. The resistance gene Rpg1 has protected the crop against stem rust losses for over 70 years in North America, but is not effective against the African Pgt race TTKSK (and its variants) nor the domestic race QCCJB. To identify resistance to these Rpg1-virulent races, the Barley iCore Collection, held by the United States Department of Agriculture-Agricultural Research Service National Small Grains Collection was evaluated for adult plant resistance (APR) and seedling resistance to race TTKSK and APR to race QCCJB and the Pgt TTKSK composite of races TTKSK, TTKST, TTKTK, and TTKTT. Using a genome-wide association study approach based on 6224 single nucleotide polymorphic markers, seven significant loci for stem rust resistance were identified on chromosomes 1H, 2H, 3H, and 5H. The most significant markers detected were 11_11355 and SCRI_RS_177017 at 71-75 cM on chromosome 5H, conferring APR to QCCJB and TTKSK composite. Significant markers were also detected for TTKSK seedling resistance on chromosome 5H. All markers detected on 5H were independent of the rpg4/Rpg5 complex at 152-168 cM. This study verified the importance of the 11_11355 locus in conferring APR to races QCCJB and TTKSK and suggests that it may be effective against other races in the Ug99 lineage.
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Affiliation(s)
- Austin J Case
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - Sridhar Bhavani
- Centro Internacional de Mejoramiento de Maíz y Trigo (CIMMYT), Nairobi, Kenya
| | - Godwin Macharia
- Kenya Agriculture Livestock Research Organization (KALRO), Njoro, Kenya
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA.
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Kachroo A, Vincelli P, Kachroo P. Signaling Mechanisms Underlying Resistance Responses: What Have We Learned, and How Is It Being Applied? PHYTOPATHOLOGY 2017; 107:1452-1461. [PMID: 28609156 DOI: 10.1094/phyto-04-17-0130-rvw] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Plants have evolved highly specific mechanisms to resist pathogens including preformed barriers and the induction of elaborate signaling pathways. Induced signaling requires recognition of the pathogen either via conserved pathogen-derived factors or specific pathogen-encoded proteins called effectors. Recognition of these factors by host encoded receptor proteins can result in the elicitation of different tiers of resistance at the site of pathogen infection. In addition, plants induce a type of systemic immunity which is effective at the whole plant level and protects against a broad spectrum of pathogens. Advances in our understanding of pathogen-recognition mechanisms, identification of the underlying molecular components, and their significant conservation across diverse plant species has enabled the development of novel strategies to combat plant diseases. This review discusses key advances in plant defense signaling that have been adapted or have the potential to be adapted for plant protection against microbial diseases.
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Affiliation(s)
- Aardra Kachroo
- Department of Plant Pathology, University of Kentucky, Lexington 40546
| | - Paul Vincelli
- Department of Plant Pathology, University of Kentucky, Lexington 40546
| | - Pradeep Kachroo
- Department of Plant Pathology, University of Kentucky, Lexington 40546
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Sallam AH, Tyagi P, Brown-Guedira G, Muehlbauer GJ, Hulse A, Steffenson BJ. Genome-Wide Association Mapping of Stem Rust Resistance in Hordeum vulgare subsp. spontaneum. G3 (BETHESDA, MD.) 2017; 7:3491-3507. [PMID: 28855281 PMCID: PMC5633397 DOI: 10.1534/g3.117.300222] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 08/24/2017] [Indexed: 01/06/2023]
Abstract
Stem rust was one of the most devastating diseases of barley in North America. Through the deployment of cultivars with the resistance gene Rpg1, losses to stem rust have been minimal over the past 70 yr. However, there exist both domestic (QCCJB) and foreign (TTKSK aka isolate Ug99) pathotypes with virulence for this important gene. To identify new sources of stem rust resistance for barley, we evaluated the Wild Barley Diversity Collection (WBDC) (314 ecogeographically diverse accessions of Hordeum vulgare subsp. spontaneum) for seedling resistance to four pathotypes (TTKSK, QCCJB, MCCFC, and HKHJC) of the wheat stem rust pathogen (Puccinia graminis f. sp. tritici, Pgt) and one isolate (92-MN-90) of the rye stem rust pathogen (P. graminis f. sp. secalis, Pgs). Based on a coefficient of infection, the frequency of resistance in the WBDC was low ranging from 0.6% with HKHJC to 19.4% with 92-MN-90. None of the accessions was resistant to all five cultures of P. graminis A genome-wide association study (GWAS) was conducted to map stem rust resistance loci using 50,842 single-nucleotide polymorphic markers generated by genotype-by-sequencing and ordered using the new barley reference genome assembly. After proper accounting for genetic relatedness and structure among accessions, 45 quantitative trait loci were identified for resistance to P. graminis across all seven barley chromosomes. Three novel loci associated with resistance to TTKSK, QCCJB, MCCFC, and 92-MN-90 were identified on chromosomes 5H and 7H, and two novel loci associated with resistance to HKHJC were identified on chromosomes 1H and 3H. These novel alleles will enhance the diversity of resistance available for cultivated barley.
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Affiliation(s)
- Ahmad H Sallam
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
| | - Priyanka Tyagi
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina 27695
| | - Gina Brown-Guedira
- United States Department of Agriculture-Agricultural Research Service, Raleigh, North Carolina 27695
| | - Gary J Muehlbauer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Alex Hulse
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
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Rodriguez-Moreno L, Song Y, Thomma BP. Transfer and engineering of immune receptors to improve recognition capacities in crops. CURRENT OPINION IN PLANT BIOLOGY 2017; 38:42-49. [PMID: 28472757 DOI: 10.1016/j.pbi.2017.04.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 04/05/2017] [Accepted: 04/10/2017] [Indexed: 05/23/2023]
Abstract
Immune receptors are pivotal elements of the plant immune system that act as sentinels for microbial invasion. Knowingly or unknowingly, breeding for resistance has largely relied on the transfer of immune receptor recognition specificities between plant genotypes. For decades such transfers were limited to crossable species. However, advents in transgene technologies have allowed overcoming species barriers. Novel strategies for mining of recognition specificities, combined with our recently increased understanding of immune receptor functioning, allows to increase and alter recognition specificities, which should ultimately increase the spectrum of recognition specificities that are available to control plant diseases in crops.
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Affiliation(s)
- Luis Rodriguez-Moreno
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Yin Song
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Bart Phj Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
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Periyannan S, Milne RJ, Figueroa M, Lagudah ES, Dodds PN. An overview of genetic rust resistance: From broad to specific mechanisms. PLoS Pathog 2017; 13:e1006380. [PMID: 28704545 PMCID: PMC5509339 DOI: 10.1371/journal.ppat.1006380] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Sambasivam Periyannan
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Canberra, Australian Capital Territory, Australia
- Research School of Biology, The Australian National University, Canberra Australian Capital Territory, Australia
| | - Ricky J. Milne
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Melania Figueroa
- Department of Plant Pathology and The Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Evans S. Lagudah
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Peter N. Dodds
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Canberra, Australian Capital Territory, Australia
- * E-mail:
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Tock AJ, Fourie D, Walley PG, Holub EB, Soler A, Cichy KA, Pastor-Corrales MA, Song Q, Porch TG, Hart JP, Vasconcellos RCC, Vicente JG, Barker GC, Miklas PN. Genome-Wide Linkage and Association Mapping of Halo Blight Resistance in Common Bean to Race 6 of the Globally Important Bacterial Pathogen. FRONTIERS IN PLANT SCIENCE 2017; 8:1170. [PMID: 28736566 PMCID: PMC5500643 DOI: 10.3389/fpls.2017.01170] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/19/2017] [Indexed: 05/11/2023]
Abstract
Pseudomonas syringae pv. phaseolicola (Psph) Race 6 is a globally prevalent and broadly virulent bacterial pathogen with devastating impact causing halo blight of common bean (Phaseolus vulgaris L.). Common bean lines PI 150414 and CAL 143 are known sources of resistance against this pathogen. We constructed high-resolution linkage maps for three recombinant inbred populations to map resistance to Psph Race 6 derived from the two common bean lines. This was complemented with a genome-wide association study (GWAS) of Race 6 resistance in an Andean Diversity Panel of common bean. Race 6 resistance from PI 150414 maps to a single major-effect quantitative trait locus (QTL; HB4.2) on chromosome Pv04 and confers broad-spectrum resistance to eight other races of the pathogen. Resistance segregating in a Rojo × CAL 143 population maps to five chromosome arms and includes HB4.2. GWAS detected one QTL (HB5.1) on chromosome Pv05 for resistance to Race 6 with significant influence on seed yield. The same HB5.1 QTL, found in both Canadian Wonder × PI 150414 and Rojo × CAL 143 populations, was effective against Race 6 but lacks broad resistance. This study provides evidence for marker-assisted breeding for more durable halo blight control in common bean by combining alleles of race-nonspecific resistance (HB4.2 from PI 150414) and race-specific resistance (HB5.1 from cv. Rojo).
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Affiliation(s)
- Andrew J. Tock
- School of Life Sciences, Faculty of Science, University of WarwickWellesbourne, United Kingdom
- Department of Plant Sciences, Faculty of Biology, University of CambridgeCambridge, United Kingdom
| | - Deidré Fourie
- ARC-Grain Crops InstitutePotchefstroom, South Africa
| | - Peter G. Walley
- Functional and Comparative Genomics, Institute of Integrative Biology, University of LiverpoolLiverpool, United Kingdom
| | - Eric B. Holub
- School of Life Sciences, Faculty of Science, University of WarwickWellesbourne, United Kingdom
| | - Alvaro Soler
- Grain Legume Genetics and Physiology Research Unit, Agricultural Research Service, US Department of AgricultureProsser, WA, United States
| | - Karen A. Cichy
- Sugarbeet and Bean Research Unit, Agricultural Research Service, US Department of AgricultureEast Lansing, MI, United States
| | - Marcial A. Pastor-Corrales
- Soybean Genomics and Improvement Laboratory, Agricultural Research Service, US Department of AgricultureBeltsville, MD, United States
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, Agricultural Research Service, US Department of AgricultureBeltsville, MD, United States
| | - Timothy G. Porch
- Tropical Agriculture Research Station, Agricultural Research Service, US Department of AgricultureMayagüez, Puerto Rico
| | - John P. Hart
- Tropical Agriculture Research Station, Agricultural Research Service, US Department of AgricultureMayagüez, Puerto Rico
| | | | - Joana G. Vicente
- School of Life Sciences, Faculty of Science, University of WarwickWellesbourne, United Kingdom
| | - Guy C. Barker
- School of Life Sciences, Faculty of Science, University of WarwickWellesbourne, United Kingdom
| | - Phillip N. Miklas
- Grain Legume Genetics and Physiology Research Unit, Agricultural Research Service, US Department of AgricultureProsser, WA, United States
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Yu G, Champouret N, Steuernagel B, Olivera PD, Simmons J, Williams C, Johnson R, Moscou MJ, Hernández-Pinzón I, Green P, Sela H, Millet E, Jones JDG, Ward ER, Steffenson BJ, Wulff BBH. Discovery and characterization of two new stem rust resistance genes in Aegilops sharonensis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1207-1222. [PMID: 28275817 PMCID: PMC5440502 DOI: 10.1007/s00122-017-2882-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/17/2017] [Indexed: 05/12/2023]
Abstract
KEY MESSAGE We identified two novel wheat stem rust resistance genes, Sr-1644-1Sh and Sr-1644-5Sh in Aegilops sharonensis that are effective against widely virulent African races of the wheat stem rust pathogen. Stem rust is one of the most important diseases of wheat in the world. When single stem rust resistance (Sr) genes are deployed in wheat, they are often rapidly overcome by the pathogen. To this end, we initiated a search for novel sources of resistance in diverse wheat relatives and identified the wild goatgrass species Aegilops sharonesis (Sharon goatgrass) as a rich reservoir of resistance to wheat stem rust. The objectives of this study were to discover and map novel Sr genes in Ae. sharonensis and to explore the possibility of identifying new Sr genes by genome-wide association study (GWAS). We developed two biparental populations between resistant and susceptible accessions of Ae. sharonensis and performed QTL and linkage analysis. In an F6 recombinant inbred line and an F2 population, two genes were identified that mapped to the short arm of chromosome 1Ssh, designated as Sr-1644-1Sh, and the long arm of chromosome 5Ssh, designated as Sr-1644-5Sh. The gene Sr-1644-1Sh confers a high level of resistance to race TTKSK (a member of the Ug99 race group), while the gene Sr-1644-5Sh conditions strong resistance to TRTTF, another widely virulent race found in Yemen. Additionally, GWAS was conducted on 125 diverse Ae. sharonensis accessions for stem rust resistance. The gene Sr-1644-1Sh was detected by GWAS, while Sr-1644-5Sh was not detected, indicating that the effectiveness of GWAS might be affected by marker density, population structure, low allele frequency and other factors.
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Affiliation(s)
- Guotai Yu
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- 2Blades Foundation, 1630 Chicago Avenue, Suite 1901, Evanston, IL, 60201, USA
| | - Nicolas Champouret
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
- J.R. Simplot Company, 5369 West Irving Street, Boise, ID, 83706, USA
| | | | - Pablo D Olivera
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Jamie Simmons
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Cole Williams
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Ryan Johnson
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Matthew J Moscou
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - Phon Green
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Hanan Sela
- Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Eitan Millet
- Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv, 69978, Israel
| | | | - Eric R Ward
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
- 2Blades Foundation, 1630 Chicago Avenue, Suite 1901, Evanston, IL, 60201, USA
- AgBiome Inc, 104 T. W. Alexander Drive, Building 1, Research Triangle Park, NC, 27709, USA
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Brande B H Wulff
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.
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35
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36
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Yeo FKS, Bouchon R, Kuijken R, Loriaux A, Boyd C, Niks RE, Marcel TC. High-resolution mapping of genes involved in plant stage-specific partial resistance of barley to leaf rust. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2017; 37:45. [PMID: 28356783 PMCID: PMC5352788 DOI: 10.1007/s11032-017-0624-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 01/20/2017] [Indexed: 05/30/2023]
Abstract
Partial resistance quantitative trait loci (QTLs) Rphq11 and rphq16 against Puccinia hordei isolate 1.2.1 were previously mapped in seedlings of the mapping populations Steptoe/Morex and Oregon Wolfe Barleys, respectively. In this study, QTL mapping was performed at adult plant stage for the two mapping populations challenged with the same rust isolate. The results suggest that Rphq11 and rphq16 are effective only at seedling stage, and not at adult plant stage. The cloning of several genes responsible for partial resistance of barley to P. hordei will allow elucidation of the molecular basis of this type of plant defence. A map-based cloning approach requires to fine-map the QTL in a narrow genetic window. In this study, Rphq11 and rphq16 were fine-mapped using an approach aiming at speeding up the development of plant material and simplifying its evaluation. The plant materials for fine-mapping were identified from early plant materials developed to produce QTL-NILs. The material was first selected to carry the targeted QTL in heterozygous condition and susceptibility alleles at other resistance QTLs in homozygous condition. This strategy took four to five generations to obtain fixed QTL recombinants (i.e., homozygous resistant at the Rphq11 or rphq16 QTL alleles, homozygous susceptible at the non-targeted QTL alleles). In less than 2 years, Rphq11 was fine-mapped into a 0.2-cM genetic interval and a 1.4-cM genetic interval for rphq16. The strongest candidate gene for Rphq11 is a phospholipid hydroperoxide glutathione peroxidase. Thus far, no candidate gene was identified for rphq16.
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Affiliation(s)
- F. K. S. Yeo
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, 6700 AJ Wageningen, the Netherlands
- Department of Plant Science and Environmental Ecology, Faculty of Resource Science and Technology, University Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
| | - R. Bouchon
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, 6700 AJ Wageningen, the Netherlands
| | - R. Kuijken
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, 6700 AJ Wageningen, the Netherlands
| | - A. Loriaux
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, 6700 AJ Wageningen, the Netherlands
| | - C. Boyd
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-4660 USA
| | - R. E. Niks
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, 6700 AJ Wageningen, the Netherlands
| | - T. C. Marcel
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, 6700 AJ Wageningen, the Netherlands
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850 Thiverval-Grignon, France
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Inada N. Plant actin depolymerizing factor: actin microfilament disassembly and more. JOURNAL OF PLANT RESEARCH 2017; 130:227-238. [PMID: 28044231 PMCID: PMC5897475 DOI: 10.1007/s10265-016-0899-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 11/14/2016] [Indexed: 05/19/2023]
Abstract
ACTIN DEPOLYMERIZING FACTOR (ADF) is a conserved protein among eukaryotes. The main function of ADF is the severing and depolymerizing filamentous actin (F-actin), thus regulating F-actin organization and dynamics and contributing to growth and development of the organisms. Mammalian genomes contain only a few ADF genes, whereas angiosperm plants have acquired an expanding number of ADFs, resulting in the differentiation of physiological functions. Recent studies have revealed functions of ADFs in plant growth and development, and various abiotic and biotic stress responses. In biotic stress responses, ADFs are involved in both susceptibility and resistance, depending on the pathogens. Furthermore, recent studies have highlighted a new role of ADF in the nucleus, possibly in the regulation of gene expression. In this review, I will summarize the current status of plant ADF research and discuss future research directions.
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Affiliation(s)
- Noriko Inada
- The Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma-shi, Nara, 630-0192, Japan.
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Sukarta OCA, Slootweg EJ, Goverse A. Structure-informed insights for NLR functioning in plant immunity. Semin Cell Dev Biol 2016; 56:134-149. [PMID: 27208725 DOI: 10.1016/j.semcdb.2016.05.012] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 05/11/2016] [Accepted: 05/17/2016] [Indexed: 01/07/2023]
Abstract
To respond to foreign invaders, plants have evolved a cell autonomous multilayered immune system consisting of extra- and intracellular immune receptors. Nucleotide binding and oligomerization domain (NOD)-like receptors (NLRs) mediate recognition of pathogen effectors inside the cell and trigger a host specific defense response, often involving controlled cell death. NLRs consist of a central nucleotide-binding domain, which is flanked by an N-terminal CC or TIR domain and a C-terminal leucine-rich repeat domain (LRR). These multidomain proteins function as a molecular switch and their activity is tightly controlled by intra and inter-molecular interactions. In contrast to metazoan NLRs, the structural basis underlying NLR functioning as a pathogen sensor and activator of immune responses in plants is largely unknown. However, the first crystal structures of a number of plant NLR domains were recently obtained. In addition, biochemical and structure-informed analyses revealed novel insights in the cooperation between NLR domains and the formation of pre- and post activation complexes, including the coordinated activity of NLR pairs as pathogen sensor and executor of immune responses. Moreover, the discovery of novel integrated domains underscores the structural diversity of NLRs and provides alternative models for how these immune receptors function in plants. In this review, we will highlight these recent advances to provide novel insights in the structural, biochemical and molecular aspects involved in plant NLR functioning.
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Affiliation(s)
- Octavina C A Sukarta
- Dept. of Plant Sciences, Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
| | - Erik J Slootweg
- Dept. of Plant Sciences, Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
| | - Aska Goverse
- Dept. of Plant Sciences, Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
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Kroj T, Chanclud E, Michel‐Romiti C, Grand X, Morel J. Integration of decoy domains derived from protein targets of pathogen effectors into plant immune receptors is widespread. THE NEW PHYTOLOGIST 2016; 210:618-26. [PMID: 26848538 PMCID: PMC5067614 DOI: 10.1111/nph.13869] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 12/16/2015] [Indexed: 05/18/2023]
Abstract
Plant immune receptors of the class of nucleotide-binding and leucine-rich repeat domain (NLR) proteins can contain additional domains besides canonical NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4 (NB-ARC)) and leucine-rich repeat (LRR) domains. Recent research suggests that these additional domains act as integrated decoys recognizing effectors from pathogens. Proteins homologous to integrated decoys are suspected to be effector targets and involved in disease or resistance. Here, we scrutinized 31 entire plant genomes to identify putative integrated decoy domains in NLR proteins using the Interpro search. The involvement of the Zinc Finger-BED type (ZBED) protein containing a putative decoy domain, called BED, in rice (Oryza sativa) resistance was investigated by evaluating susceptibility to the blast fungus Magnaporthe oryzae in rice over-expression and knock-out mutants. This analysis showed that all plants tested had integrated various atypical protein domains into their NLR proteins (on average 3.5% of all NLR proteins). We also demonstrated that modifying the expression of the ZBED gene modified disease susceptibility. This study suggests that integration of decoy domains in NLR immune receptors is widespread and frequent in plants. The integrated decoy model is therefore a powerful concept to identify new proteins involved in disease resistance. Further in-depth examination of additional domains in NLR proteins promises to unravel many new proteins of the plant immune system.
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Affiliation(s)
- Thomas Kroj
- INRACIRADSupAgroUMR BGPI INRA/CIRAD/SupAgroCampus International de BaillarguetTA A 54/K34398MontpellierFrance
| | - Emilie Chanclud
- Université Montpellier2 Place Eugène Bataillon34095Montpellier Cedex 5France
| | - Corinne Michel‐Romiti
- INRACIRADSupAgroUMR BGPI INRA/CIRAD/SupAgroCampus International de BaillarguetTA A 54/K34398MontpellierFrance
| | - Xavier Grand
- INRACIRADSupAgroUMR BGPI INRA/CIRAD/SupAgroCampus International de BaillarguetTA A 54/K34398MontpellierFrance
| | - Jean‐Benoit Morel
- INRACIRADSupAgroUMR BGPI INRA/CIRAD/SupAgroCampus International de BaillarguetTA A 54/K34398MontpellierFrance
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40
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Śniegowska-Świerk K, Dubas E, Rapacz M. Actin microfilaments are involved in the regulation of HVA1 transcript accumulation in drought-treated barley leaves. JOURNAL OF PLANT PHYSIOLOGY 2016; 193:22-25. [PMID: 26930570 DOI: 10.1016/j.jplph.2016.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/18/2016] [Accepted: 02/09/2016] [Indexed: 06/05/2023]
Abstract
Drought is one of the stresses that limit the yield of barley. Despite extensive studies focused on the issue, the molecular mechanism of the response to drought is still not fully understood. In our previous study, we proposed drought-induced signal perception controlled by actin filaments (AFs). To test this hypothesis, we used a chemical inhibitor of AF polarization-latrunculin B. In drought-treated barley leaves, latrunculin B induced AF depolymerization and altered gene expression (mainly those controlling AF formation), notably inhibiting the expression of HVA1, a dehydrin encoding gene whose function in drought tolerance has been widely studied. These results suggest that AFs might be involved in water-deficit signal perception in plant cells.
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Affiliation(s)
| | - Ewa Dubas
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, Kraków 30-239, Poland.
| | - Marcin Rapacz
- Department of Plant Physiology, University of Agriculture in Krakow, Podłużna 3, Kraków 30-239, Poland.
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41
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Inada N, Higaki T, Hasezawa S. Nuclear Function of Subclass I Actin-Depolymerizing Factor Contributes to Susceptibility in Arabidopsis to an Adapted Powdery Mildew Fungus. PLANT PHYSIOLOGY 2016; 170:1420-34. [PMID: 26747284 PMCID: PMC4775110 DOI: 10.1104/pp.15.01265] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 01/05/2016] [Indexed: 05/19/2023]
Abstract
Actin-depolymerizing factors (ADFs) are conserved proteins that function in regulating the structure and dynamics of actin microfilaments in eukaryotes. In this study, we present evidence that Arabidopsis (Arabidopsis thaliana) subclass I ADFs, particularly ADF4, functions as a susceptibility factor for an adapted powdery mildew fungus. The null mutant of ADF4 significantly increased resistance against the adapted powdery mildew fungus Golovinomyces orontii. The degree of resistance was further enhanced in transgenic plants in which the expression of all subclass I ADFs (i.e. ADF1-ADF4) was suppressed. Microscopic observations revealed that the enhanced resistance of adf4 and ADF1-4 knockdown plants (ADF1-4Ri) was associated with the accumulation of hydrogen peroxide and cell death specific to G. orontii-infected cells. The increased resistance and accumulation of hydrogen peroxide in ADF1-4Ri were suppressed by the introduction of mutations in the salicylic acid- and jasmonic acid-signaling pathways but not by a mutation in the ethylene-signaling pathway. Quantification by microscopic images detected an increase in the level of actin microfilament bundling in ADF1-4Ri but not in adf4 at early G. orontii infection time points. Interestingly, complementation analysis revealed that nuclear localization of ADF4 was crucial for susceptibility to G. orontii. Based on its G. orontii-infected-cell-specific phenotype, we suggest that subclass I ADFs are susceptibility factors that function in a direct interaction between the host plant and the powdery mildew fungus.
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Affiliation(s)
- Noriko Inada
- Laboratory of Plant Function Analysis, Plant Global Educational Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (N.I.); andDepartment of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan (T.H., S.H.)
| | - Takumi Higaki
- Laboratory of Plant Function Analysis, Plant Global Educational Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (N.I.); andDepartment of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan (T.H., S.H.)
| | - Seiichiro Hasezawa
- Laboratory of Plant Function Analysis, Plant Global Educational Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (N.I.); andDepartment of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan (T.H., S.H.)
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Figueroa M, Upadhyaya NM, Sperschneider J, Park RF, Szabo LJ, Steffenson B, Ellis JG, Dodds PN. Changing the Game: Using Integrative Genomics to Probe Virulence Mechanisms of the Stem Rust Pathogen Puccinia graminis f. sp. tritici. FRONTIERS IN PLANT SCIENCE 2016; 7:205. [PMID: 26941766 PMCID: PMC4764693 DOI: 10.3389/fpls.2016.00205] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/06/2016] [Indexed: 05/03/2023]
Abstract
The recent resurgence of wheat stem rust caused by new virulent races of Puccinia graminis f. sp. tritici (Pgt) poses a threat to food security. These concerns have catalyzed an extensive global effort toward controlling this disease. Substantial research and breeding programs target the identification and introduction of new stem rust resistance (Sr) genes in cultivars for genetic protection against the disease. Such resistance genes typically encode immune receptor proteins that recognize specific components of the pathogen, known as avirulence (Avr) proteins. A significant drawback to deploying cultivars with single Sr genes is that they are often overcome by evolution of the pathogen to escape recognition through alterations in Avr genes. Thus, a key element in achieving durable rust control is the deployment of multiple effective Sr genes in combination, either through conventional breeding or transgenic approaches, to minimize the risk of resistance breakdown. In this situation, evolution of pathogen virulence would require changes in multiple Avr genes in order to bypass recognition. However, choosing the optimal Sr gene combinations to deploy is a challenge that requires detailed knowledge of the pathogen Avr genes with which they interact and the virulence phenotypes of Pgt existing in nature. Identifying specific Avr genes from Pgt will provide screening tools to enhance pathogen virulence monitoring, assess heterozygosity and propensity for mutation in pathogen populations, and confirm individual Sr gene functions in crop varieties carrying multiple effective resistance genes. Toward this goal, much progress has been made in assembling a high quality reference genome sequence for Pgt, as well as a Pan-genome encompassing variation between multiple field isolates with diverse virulence spectra. In turn this has allowed prediction of Pgt effector gene candidates based on known features of Avr genes in other plant pathogens, including the related flax rust fungus. Upregulation of gene expression in haustoria and evidence for diversifying selection are two useful parameters to identify candidate Avr genes. Recently, we have also applied machine learning approaches to agnostically predict candidate effectors. Here, we review progress in stem rust pathogenomics and approaches currently underway to identify Avr genes recognized by wheat Sr genes.
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Affiliation(s)
- Melania Figueroa
- Department of Plant Pathology and the Stakman-Borlaug Center for Sustainable Plant Health, University of MinnesotaSt. Paul, MN, USA
| | - Narayana M. Upadhyaya
- Agriculture, Commonwealth Scientific and Industrial Research OrganisationCanberra, ACT, Australia
| | - Jana Sperschneider
- Agriculture, Centre for Environment and Life Sciences, Commonwealth Scientific and Industrial Research OrganisationPerth, WA, Australia
| | - Robert F. Park
- Faculty of Agriculture and Environment, Plant Breeding Institute, The University of SydneyNarellan, NSW, Australia
| | - Les J. Szabo
- Department of Plant Pathology and the Stakman-Borlaug Center for Sustainable Plant Health, University of MinnesotaSt. Paul, MN, USA
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research ServiceSt. Paul, MN, USA
| | - Brian Steffenson
- Department of Plant Pathology and the Stakman-Borlaug Center for Sustainable Plant Health, University of MinnesotaSt. Paul, MN, USA
| | - Jeff G. Ellis
- Agriculture, Commonwealth Scientific and Industrial Research OrganisationCanberra, ACT, Australia
| | - Peter N. Dodds
- Agriculture, Commonwealth Scientific and Industrial Research OrganisationCanberra, ACT, Australia
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Turuspekov Y, Ormanbekova D, Rsaliev A, Abugalieva S. Genome-wide association study on stem rust resistance in Kazakh spring barley lines. BMC PLANT BIOLOGY 2016; 16 Suppl 1:6. [PMID: 26821649 PMCID: PMC4895317 DOI: 10.1186/s12870-015-0686-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
BACKGROUND Stem rust (SR) is one of the most economically devastating barley diseases in Kazakhstan, and in some years it causes up to 50 % of yield losses. Routine conventional breeding for resistance to stem rust is almost always in progress in all Kazakhstan breeding stations. However, molecular marker based approach towards new SR resistance genes identification and relevant marker-assisted selection had never been employed in Kazakhstan yet. In this study, as a preliminary step the GWAS (genome-wide association study) mapping was applied in attempt to identify reliable SNP markers and quantitative trait loci (QTL) associated with resistance to SR. RESULTS Barley collection of 92 commercial cultivars and promising lines was genotyped using a high-throughput single nucleotide polymorphism (9,000 SNP) Illumina iSelect array. 6,970 SNPs out of 9,000 total were polymorphic and scorable. 5,050 SNPs out of 6,970 passed filtering threshold and were used for association mapping (AM). All 92 accessions were phenotyped for resistance to SR by observing adult plants in artificially infected plots at the Research Institute for Biological Safety Problems in Dzhambul region of Kazakhstan. GLM analysis allowed the identification of 15 SNPs associated with the resistance at the heading time (HA) phase, and 2 SNPs at the seed's milky-waxy maturity (SM) phase. However, after application of 5 % Bonferroni multiple test correction, only 2 SNPs at the HA stage on the same position of chromosome 6H can be claimed as reliable markers for SR resistance. The MLM analysis after the Bonferroni correction did not reveal any associations in this study, although distribution lines in the quantile-quantile (QQ) plot indicates that overcorrection in the test due to both Q and K matrices usage. CONCLUSIONS Obtained data suggest that genome wide genotyping of 92 spring barley accessions from Kazakhstan with 9 K Illumina SNP array was highly efficient. Linkage disequilibrium based mapping approach allowed the identification of highly significant QTL for the SR resistance at the HA phase of growth on chromosome 6H. On the other hand, no significant QTL was detected at the SM phase, assuming that for a successful GWASmapping experiment a larger size population with more diverse genetic background should be tested. Obtained results provide additional information towards better understanding of SR resistance in barley.
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Affiliation(s)
| | | | - Aralbek Rsaliev
- Research Institute for Biological Safety Problems, Gvardeiskiy vil, Dzhambul region, Kazakhstan.
| | - Saule Abugalieva
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan.
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Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation. Sci Rep 2016; 6:18936. [PMID: 26729541 PMCID: PMC4733048 DOI: 10.1038/srep18936] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 12/01/2015] [Indexed: 11/12/2022] Open
Abstract
Gene expression variation largely contributes to phenotypic diversity and constructing pan-transcriptome is considered necessary for species with complex genomes. However, the regulation mechanisms and functional consequences of pan-transcriptome is unexplored systematically. By analyzing RNA-seq data from 368 maize diverse inbred lines, we identified almost one-third nuclear genes under expression presence and absence variation, which tend to play regulatory roles and are likely regulated by distant eQTLs. The ePAV was directly used as “genotype” to perform GWAS for 15 agronomic phenotypes and 526 metabolic traits to efficiently explore the associations between transcriptomic and phenomic variations. Through a modified assembly strategy, 2,355 high-confidence novel sequences with total 1.9 Mb lengths were found absent within reference genome. Ten randomly selected novel sequences were fully validated with genomic PCR, including another two NBS_LRR candidates potentially affect flavonoids and disease-resistance. A simulation analysis suggested that the pan-transcriptome of the maize whole kernel is approaching a maximum value of 63,000 genes, and through developing two test-cross populations and surveying several most important yield traits, the dispensable genes were shown to contribute to heterosis. Novel perspectives and resources to discover maize quantitative trait variations were provided to better understand the kernel regulation networks and to enhance maize breeding.
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Gill US, Lee S, Mysore KS. Host versus nonhost resistance: distinct wars with similar arsenals. PHYTOPATHOLOGY 2015; 105:580-7. [PMID: 25626072 DOI: 10.1094/phyto-11-14-0298-rvw] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Plants face several challenges by bacterial, fungal, oomycete, and viral pathogens during their life cycle. In order to defend against these biotic stresses, plants possess a dynamic, innate, natural immune system that efficiently detects potential pathogens and initiates a resistance response in the form of basal resistance and/or resistance (R)-gene-mediated defense, which is often associated with a hypersensitive response. Depending upon the nature of plant-pathogen interactions, plants generally have two main defense mechanisms, host resistance and nonhost resistance. Host resistance is generally controlled by single R genes and less durable compared with nonhost resistance. In contrast, nonhost resistance is believed to be a multi-gene trait and more durable. In this review, we describe the mechanisms of host and nonhost resistance against fungal and bacterial plant pathogens. In addition, we also attempt to compare host and nonhost resistance responses to identify similarities and differences, and their practical applications in crop improvement.
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Affiliation(s)
- Upinder S Gill
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401
| | - Seonghee Lee
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401
| | - Kirankumar S Mysore
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401
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Dracatos P, Singh D, Fetch T, Park R. Resistance to Puccinia graminis f. sp. avenae in Barley Is Associated with the Rpg5 Locus. PHYTOPATHOLOGY 2015; 105:490-494. [PMID: 25870923 DOI: 10.1094/phyto-08-14-0224-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In barley, gene Rpg5 was first identified for providing resistance to the rye stem rust pathogen (Puccinia graminis f. sp. secalis). A subsequent study determined that Rpg5 is required for rpg4-mediated resistance to the wheat stem rust pathogen (P. graminis f. sp. tritici) including pathotype TTKSK ("Ug99"), which poses a major threat to global wheat and barley production. Based on the effectiveness of Rpg5 against P. graminis f. sp. tritici and P. graminis f. sp. secalis, we assessed whether it also conferred resistance to the oat stem rust pathogen (P. graminis f. sp. avenae). A barley F8 recombinant inbred line (RIL) population was produced by crossing 'Q21861' (Rpg1 and Rpg5) with '73-G1' (Rpg1), which is susceptible to P. graminis f. sp. avenae, P. graminis f. sp. secalis, and some pathotypes of P. graminis f. sp. tritici. Seedling tests were performed on the F8 RIL population using Australian pathotypes of P. graminis f. sp. tritici, P. graminis f. sp. secalis, P. graminis f. sp. avenae, and a putative somatic hybrid between P. graminis f. sp. tritici and P. graminis f. sp. secalis known as the 'Scabrum' rust. Segregation in the responses to all rust isolates for the RILs was identical (50 resistant: 52 susceptible), and fitted a 1:1 ratio (X2=0.039, P=0.843), indicating that resistance to all isolates was monogenetically inherited. Screening of the RILs and the parental lines with perfect markers for the functional Rpg1 and Rpg5 resistance alleles indicated that Rpg1 was fixed, while Rpg5 was positive in all resistant lines and negative in all susceptible lines. This suggests that different formae speciales of P. graminis may share common effectors, and that the Rpg5 locus confers resistance to both P. graminis f. sp. tritici and P. graminis f. sp. secalis and the heterologous formae speciales of P. graminis, P. graminis f. sp. avenae.
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Affiliation(s)
- Peter Dracatos
- First, second, and fourth authors: The University of Sydney, Plant Breeding Institute Cobbitty, Private Bag 4011, Narellan, NSW, 2567, Australia; and third author: Cereal Research Centre, Agriculture & Agri-Food Canada, Winnipeg, MB, Canada
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Zhao J. Phospholipase D and phosphatidic acid in plant defence response: from protein-protein and lipid-protein interactions to hormone signalling. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1721-36. [PMID: 25680793 PMCID: PMC4669553 DOI: 10.1093/jxb/eru540] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 12/08/2014] [Accepted: 12/15/2014] [Indexed: 05/05/2023]
Abstract
Phospholipase Ds (PLDs) and PLD-derived phosphatidic acids (PAs) play vital roles in plant hormonal and environmental responses and various cellular dynamics. Recent studies have further expanded the functions of PLDs and PAs into plant-microbe interaction. The molecular diversities and redundant functions make PLD-PA an important signalling complex regulating lipid metabolism, cytoskeleton dynamics, vesicle trafficking, and hormonal signalling in plant defence through protein-protein and protein-lipid interactions or hormone signalling. Different PLD-PA signalling complexes and their targets have emerged as fast-growing research topics for understanding their numerous but not yet established roles in modifying pathogen perception, signal transduction, and downstream defence responses. Meanwhile, advanced lipidomics tools have allowed researchers to reveal further the mechanisms of PLD-PA signalling complexes in regulating lipid metabolism and signalling, and their impacts on jasmonic acid/oxylipins, salicylic acid, and other hormone signalling pathways that essentially mediate plant defence responses. This review attempts to summarize the progress made in spatial and temporal PLD/PA signalling as well as PLD/PA-mediated modification of plant defence. It presents an in-depth discussion on the functions and potential mechanisms of PLD-PA complexes in regulating actin filament/microtubule cytoskeleton, vesicle trafficking, and hormonal signalling, and in influencing lipid metabolism-derived metabolites as critical signalling components in plant defence responses. The discussion puts PLD-PA in a broader context in order to guide future research.
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Affiliation(s)
- Jian Zhao
- National Key Laboratory for Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, PR China
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Mamo BE, Smith KP, Brueggeman RS, Steffenson BJ. Genetic Characterization of Resistance to Wheat Stem Rust Race TTKSK in Landrace and Wild Barley Accessions Identifies the rpg4/Rpg5 Locus. PHYTOPATHOLOGY 2015; 105:99-109. [PMID: 25084303 DOI: 10.1094/phyto-12-13-0340-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Race TTKSK of the wheat stem rust pathogen (Puccinia graminis f. sp. tritici) threatens the production of wheat and barley worldwide because of its broad-spectrum virulence on many widely grown cultivars. Sources of resistance against race TTKSK were recently identified in several barley landraces (Hordeum vulgare subsp. vulgare) and wild barley accessions (H. vulgare subsp. spontaneum). The objectives of this study were to characterize the inheritance of resistance to wheat stem rust race TTKSK in four barley landraces (Hv501, Hv545, Hv602, and Hv612) and two wild barley (WBDC213 and WBDC345) accessions, map the resistance genes, and determine the allelic relationships among the genes in these accessions and the previously described rpg4/Rpg5 locus. Resistant accessions were crossed with the susceptible cv. Steptoe and resulting F3 populations were evaluated for resistance to race TTKSK at the seedling stage. Segregation of F3 families in populations involving the resistance sources of Hv501, Hv545, Hv612, WBDC213, and WBDC345 fit a 1:2:1 ratio for homozygous resistant (HR)/segregating (SEG)/homozygous susceptible (HS) progenies (with χ2=2.27 to 5.87 and P=0.053 to 0.321), indicating that a single gene confers resistance to race TTKSK. Segregation of F3 families in cross Steptoe/Hv602 did not fit a 1:2:1 ratio (HR/SEG/HS of 20:47:43 with χ2=11.95 and P=0.003), indicating that more than one gene is involved in imparting resistance to race TTKSK. Bulked segregant analysis using >1,500 single-nucleotide polymorphism markers positioned a resistance locus in all six populations on chromosome 5HL in very close proximity to the known location of the rpg4/Rpg5 complex locus. Allelism tests were conducted by making crosses among resistant accessions Hv501, Hv545, and Hv612 and also Q21861 with the rpg4/Rpg5 complex. No segregation was observed in F2 families inoculated with race TTKSK, demonstrating that all Hv lines carry the same allele for resistance and that it resides at or very near the rpg4/Rpg5 locus. Phenotype evaluations of the six barley accessions with wheat stem rust race QCCJ revealed resistant infection types (ITs) at a low incubation temperature and susceptible ITs at a high incubation temperature, similar to Q21861, which carries the temperature-sensitive gene rpg4. The accessions also exhibited low ITs against the rye stem rust isolate 92-MN-90, suggesting that they also carry Rpg5. This result was confirmed through molecular analysis, which revealed that all six barley accessions contain the serine threonine protein kinase domain that confers Rpg5 resistance. These results indicate that cultivated barley is extremely vulnerable to African stem rust races such as TTKSK because even these diverse selections of landrace and wild barley accessions carry only one locus for resistance.
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Bettgenhaeuser J, Gilbert B, Ayliffe M, Moscou MJ. Nonhost resistance to rust pathogens - a continuation of continua. FRONTIERS IN PLANT SCIENCE 2014; 5:664. [PMID: 25566270 PMCID: PMC4263244 DOI: 10.3389/fpls.2014.00664] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 11/07/2014] [Indexed: 05/25/2023]
Abstract
The rust fungi (order: Pucciniales) are a group of widely distributed fungal plant pathogens, which can infect representatives of all vascular plant groups. Rust diseases significantly impact several crop species and considerable research focuses on understanding the basis of host specificity and nonhost resistance. Like many pathogens, rust fungi vary considerably in the number of hosts they can infect, such as wheat leaf rust (Puccinia triticina), which can only infect species in the genera Triticum and Aegilops, whereas Asian soybean rust (Phakopsora pachyrhizi) is known to infect over 95 species from over 42 genera. A greater understanding of the genetic basis determining host range has the potential to identify sources of durable resistance for agronomically important crops. Delimiting the boundary between host and nonhost has been complicated by the quantitative nature of phenotypes in the transition between these two states. Plant-pathogen interactions in this intermediate state are characterized either by (1) the majority of accessions of a species being resistant to the rust or (2) the rust only being able to partially complete key components of its life cycle. This leads to a continuum of disease phenotypes in the interaction with different plant species, observed as a range from compatibility (host) to complete immunity within a species (nonhost). In this review we will highlight how the quantitative nature of disease resistance in these intermediate interactions is caused by a continuum of defense barriers, which a pathogen needs to overcome for successfully establishing itself in the host. To illustrate continua as this underlying principle, we will discuss the advances that have been made in studying nonhost resistance towards rust pathogens, particularly cereal rust pathogens.
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Affiliation(s)
| | - Brian Gilbert
- Commonwealth Scientific and Industrial Research Organisation, Agriculture FlagshipCanberra, ACT, Australia
| | - Michael Ayliffe
- Commonwealth Scientific and Industrial Research Organisation, Agriculture FlagshipCanberra, ACT, Australia
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Al-Daoude A, Shoaib A, Al-Shehadah E, Jawhar M, Arabi MIE. Transcriptome Analysis of the Barley-Rhynchosporium secalis Interaction. THE PLANT PATHOLOGY JOURNAL 2014; 30:425-431. [PMID: 25506307 PMCID: PMC4262295 DOI: 10.5423/ppj.nt.04.2014.0033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 07/17/2014] [Accepted: 08/14/2014] [Indexed: 06/04/2023]
Abstract
Leaf scald caused by the infection of Rhynchosporium secalis, is a worldwide crop disease resulting in significant loss of barley yield. In this study, a systematic sequencing of expressed sequence tags (ESTs) was chosen to obtain a global picture of the assembly of genes involved in pathogenesis. To identify a large number of plant ESTs, which are induced at different time points, an amplified fragment length polymorphism (AFLP) display of complementary DNA (cDNA) was utilized. Transcriptional changes of 140 ESTs were observed, of which 19 have no previously described function. Functional annotation of the transcripts revealed a variety of infection-induced host genes encoding classical pathogenesis-related (PR) or genes that play a role in the signal transduction pathway. The expression analyses by a semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) revealed that Rar1 and Rpg4 are defense inducible genes, and were consistent with the cDNA-AFLP data in their expression patterns. Hence, the here presented transcriptomic approach provides novel global catalogue of genes not currently represented in the EST databases.
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Affiliation(s)
- Antonious Al-Daoude
- Corresponding author. Phone) +00963-11-2132580, FAX) 00963-11-6112289, E-mail)
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