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Terefe TG, Boshoff WHP, Park RF, Pretorius ZA, Visser B. Wheat Stem Rust Surveillance Reveals Two New Races of Puccinia graminis f. sp. tritici in South Africa During 2016 to 2020. Plant Dis 2024; 108:20-29. [PMID: 37580885 DOI: 10.1094/pdis-06-23-1120-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is an important disease of wheat in South Africa (SA) and is primarily controlled using resistant cultivars. Understanding virulence diversity of Pgt is essential for successful breeding of resistant cultivars. Samples of infected wheat stems were collected across the major wheat-growing regions of SA from 2016 to 2020 to determine the pathogenic variability of Pgt isolates. Seven races were identified from 517 isolates pathotyped. The most frequently found races were 2SA104 (BPGSC + Sr9h,27,Kw) (35% frequency) and 2SA88 (TTKSF + Sr8b) (33%). Race 2SA42 (PTKSK + Sr8b), which was found in 2017, and 2SA5 (BFGSF + Sr9h), identified in 2017, are new races. The Ug99 variant race 2SA42 is similar in its virulence to 2SA107 (PTKST + Sr8b) except for avirulence to Sr24 and virulence to Sr8155B1. Race 2SA5 is closely related in its virulence to existing races that commonly infect triticale. Certain races showed limited geographical distribution. Races 2SA5, 2SA105, and 2SA108 were found only in the Western Cape, whereas 2SA107 and 2SA42 were detected only in the Free State province. The new and existing races were compared using microsatellite (SSR) marker analysis and their virulence on commercial cultivars was also determined. Seedling response of 113 wheat entries against the new races, using 2SA88, 2SA88+9h, 2SA106, and 2SA107 as controls, revealed 2SA107 as the most virulent (67 entries susceptible), followed by 2SA42 (64), 2SA106 (60), 2SA88+9h (59), 2SA88 (25), and 2SA5 (17). Thus, 2SA5 may not pose a significant threat to local wheat production. SSR genotyping revealed that 2SA5 is genetically distinct from all other SA Pgt races.
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Affiliation(s)
- Tarekegn G Terefe
- Agricultural Research Council-Small Grain, Bethlehem 9700, South Africa
| | - Willem H P Boshoff
- Department of Plant Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Robert F Park
- Plant Breeding Institute Cobbitty, The University of Sydney, Narellan, NSW 2567, Australia
| | - Zacharias A Pretorius
- Department of Plant Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Botma Visser
- Department of Plant Sciences, University of the Free State, Bloemfontein 9300, South Africa
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Chen C, Jost M, Outram MA, Friendship D, Chen J, Wang A, Periyannan S, Bartoš J, Holušová K, Doležel J, Zhang P, Bhatt D, Singh D, Lagudah E, Park RF, Dracatos PM. A pathogen-induced putative NAC transcription factor mediates leaf rust resistance in barley. Nat Commun 2023; 14:5468. [PMID: 37673864 PMCID: PMC10482968 DOI: 10.1038/s41467-023-41021-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 08/21/2023] [Indexed: 09/08/2023] Open
Abstract
Leaf rust, caused by Puccinia hordei, is one of the most widespread and damaging foliar diseases affecting barley. The barley leaf rust resistance locus Rph7 has been shown to have unusually high sequence and haplotype divergence. In this study, we isolate the Rph7 gene using a fine mapping and RNA-Seq approach that is confirmed by mutational analysis and transgenic complementation. Rph7 is a pathogen-induced, non-canonical resistance gene encoding a protein that is distinct from other known plant disease resistance proteins in the Triticeae. Structural analysis using an AlphaFold2 protein model suggests that Rph7 encodes a putative NAC transcription factor with a zinc-finger BED domain with structural similarity to the N-terminal DNA-binding domain of the NAC transcription factor (ANAC019) from Arabidopsis. A global gene expression analysis suggests Rph7 mediates the activation and strength of the basal defence response. The isolation of Rph7 highlights the diversification of resistance mechanisms available for engineering disease control in crops.
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Affiliation(s)
- Chunhong Chen
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Matthias Jost
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Megan A Outram
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Dorian Friendship
- The University of Sydney, Faculty of Science, Plant Breeding Institute, Cobbitty, NSW, 2570, Australia
| | - Jian Chen
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Aihua Wang
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Sambasivam Periyannan
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
- The University of Southern Queensland, School of Agriculture and Environmental Science, Centre for Crop Health, Toowoomba, QLD, 4350, Australia
| | - Jan Bartoš
- Institute of Experimental Botany, Centre of Plant Structural and Functional Genomics, Olomouc, CZ-77900, Czech Republic
| | - Kateřina Holušová
- Institute of Experimental Botany, Centre of Plant Structural and Functional Genomics, Olomouc, CZ-77900, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of Plant Structural and Functional Genomics, Olomouc, CZ-77900, Czech Republic
| | - Peng Zhang
- The University of Sydney, Faculty of Science, Plant Breeding Institute, Cobbitty, NSW, 2570, Australia
| | - Dhara Bhatt
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Davinder Singh
- The University of Sydney, Faculty of Science, Plant Breeding Institute, Cobbitty, NSW, 2570, Australia
| | - Evans Lagudah
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia.
| | - Robert F Park
- The University of Sydney, Faculty of Science, Plant Breeding Institute, Cobbitty, NSW, 2570, Australia.
| | - Peter M Dracatos
- The University of Sydney, Faculty of Science, Plant Breeding Institute, Cobbitty, NSW, 2570, Australia.
- La Trobe Institute for Sustainable Agriculture & Food (LISAF), Department of Animal, Plant and Soil Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.
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Hayashibara CADA, Lopes MDS, Tobias PA, dos Santos IB, Figueredo EF, Ferrarezi JA, Marques JPR, Marcon J, Park RF, Teixeira PJPL, Quecine MC. In Planta Study Localizes an Effector Candidate from Austropuccinia psidii Strain MF-1 to the Nucleus and Demonstrates In Vitro Cuticular Wax-Dependent Differential Expression. J Fungi (Basel) 2023; 9:848. [PMID: 37623619 PMCID: PMC10455828 DOI: 10.3390/jof9080848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023] Open
Abstract
Austropuccinia psidii is a biotrophic fungus that causes myrtle rust. First described in Brazil, it has since spread to become a globally important pathogen that infects more than 480 myrtaceous species. One of the most important commercial crops affected by A. psidii is eucalypt, a widely grown forestry tree. The A. psidii-Eucalyptus spp. interaction is poorly understood, but pathogenesis is likely driven by pathogen-secreted effector molecules. Here, we identified and characterized a total of 255 virulence effector candidates using a genome assembly of A. psidii strain MF-1, which was recovered from Eucalyptus grandis in Brazil. We show that the expression of seven effector candidate genes is modulated by cell wax from leaves sourced from resistant and susceptible hosts. Two effector candidates with different subcellular localization predictions, and with specific gene expression profiles, were transiently expressed with GFP-fusions in Nicotiana benthamiana leaves. Interestingly, we observed the accumulation of an effector candidate, Ap28303, which was upregulated under cell wax from rust susceptible E. grandis and described as a peptidase inhibitor I9 domain-containing protein in the nucleus. This was in accordance with in silico analyses. Few studies have characterized nuclear effectors. Our findings open new perspectives on the study of A. psidii-Eucalyptus interactions by providing a potential entry point to understand how the pathogen manipulates its hosts in modulating physiology, structure, or function with effector proteins.
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Affiliation(s)
- Carolina Alessandra de Almeida Hayashibara
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (C.A.d.A.H.); (M.d.S.L.); (I.B.d.S.); (J.A.F.); (J.M.)
| | - Mariana da Silva Lopes
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (C.A.d.A.H.); (M.d.S.L.); (I.B.d.S.); (J.A.F.); (J.M.)
| | - Peri A. Tobias
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW 2006, Australia;
| | - Isaneli Batista dos Santos
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (C.A.d.A.H.); (M.d.S.L.); (I.B.d.S.); (J.A.F.); (J.M.)
| | | | - Jessica Aparecida Ferrarezi
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (C.A.d.A.H.); (M.d.S.L.); (I.B.d.S.); (J.A.F.); (J.M.)
| | - João Paulo Rodrigues Marques
- Department of Basic Sciences, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga 13635-900, SP, Brazil;
| | - Joelma Marcon
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (C.A.d.A.H.); (M.d.S.L.); (I.B.d.S.); (J.A.F.); (J.M.)
| | - Robert F. Park
- School of Life and Environmental Sciences, Plant Breeding Institute, The University of Sydney, Cobbitty, NSW 2570, Australia;
| | - Paulo José Pereira Lima Teixeira
- Department of Biological Sciences, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil;
| | - Maria Carolina Quecine
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (C.A.d.A.H.); (M.d.S.L.); (I.B.d.S.); (J.A.F.); (J.M.)
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Arifuzzaman M, Jost M, Wang M, Chen X, Perovic D, Park RF, Rouse M, Forrest K, Hayden M, Khan GA, Dracatos PM. Mining the Australian Grains Gene Bank for Rust Resistance in Barley. Int J Mol Sci 2023; 24:10860. [PMID: 37446042 DOI: 10.3390/ijms241310860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
Global barley production is threatened by plant pathogens, especially the rusts. In this study we used a targeted genotype-by-sequencing (GBS) assisted GWAS approach to identify rust resistance alleles in a collection of 287 genetically distinct diverse barley landraces and historical cultivars available in the Australian Grains Genebank (AGG) and originally sourced from Eastern Europe. The accessions were challenged with seven US-derived cereal rust pathogen races including Puccinia hordei (Ph-leaf rust) race 17VA12C, P. coronata var. hordei (Pch-crown rust) race 91NE9305 and five pathogenically diverse races of P. striiformis f. sp. hordei (Psh-stripe rust) (PSH-33, PSH-48, PSH-54, PSH-72 and PSH-100) and phenotyped quantitatively at the seedling stage. Novel resistance factors were identified on chromosomes 1H, 2H, 4H and 5H in response to Pch, whereas a race-specific QTL on 7HS was identified that was effective only to Psh isolates PSH-72 and PSH-100. A major effect QTL on chromosome 5HL conferred resistance to all Psh races including PSH-72, which is virulent on all 12 stripe rust differential tester lines. The same major effect QTL was also identified in response to leaf rust (17VA12C) suggesting this locus contains several pathogen specific rust resistance genes or the same gene is responsible for both leaf rust and stripe rust resistance. Twelve accessions were highly resistant to both leaf and stripe rust diseases and also carried the 5HL QTL. We subsequently surveyed the physical region at the 5HL locus for across the barley pan genome variation in the presence of known resistance gene candidates and identified a rich source of high confidence protein kinase and antifungal genes in the QTL region.
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Affiliation(s)
- Md Arifuzzaman
- Department of Genetics and Plant Breeding, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh
| | - Matthias Jost
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
- Agricultural Research Service, United States Department of Agriculture Wheat Health, Genetics and Quality Research Unit, Pullman, WA 99164-6430, USA
| | - Dragan Perovic
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Erwin-Baur-Strasse 27, 06484 Quedlinburg, Germany
| | - Robert F Park
- Plant Breeding Institute, Faculty of Science, The University of Sydney, Cobbitty, NSW 2570, Australia
| | - Matthew Rouse
- USDA-ARS Cereal Disease Laboratory and Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
| | - Kerrie Forrest
- Agriculture Victoria Research, AgriBio, Melbourne, VIC 3083, Australia
| | - Matthew Hayden
- Agriculture Victoria Research, AgriBio, Melbourne, VIC 3083, Australia
| | - Ghazanfar Abbas Khan
- Department of Animal, Plant and Soil Sciences, La Trobe University, AgriBio, Bundoora, VIC 3086, Australia
| | - Peter M Dracatos
- Department of Animal, Plant and Soil Sciences, La Trobe University, AgriBio, Bundoora, VIC 3086, Australia
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Ziems LA, Singh L, Dracatos PM, Dieters MJ, Sanchez-Garcia M, Amri A, Verma RPS, Park RF, Singh D. Characterization of Leaf Rust Resistance in International Barley Germplasm Using Genome-Wide Association Studies. Plants (Basel) 2023; 12:862. [PMID: 36840210 PMCID: PMC9963359 DOI: 10.3390/plants12040862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/09/2023] [Accepted: 02/11/2023] [Indexed: 06/18/2023]
Abstract
A panel of 114 genetically diverse barley lines were assessed in the greenhouse and field for resistance to the pathogen Puccinia hordei, the causal agent of barley leaf rust. Multi-pathotype tests revealed that 16.6% of the lines carried the all-stage resistance (ASR) gene Rph3, followed by Rph2 (4.4%), Rph1 (1.7%), Rph12 (1.7%) or Rph19 (1.7%). Five lines (4.4%) were postulated to carry the gene combinations Rph2+9.am, Rph2+19 and Rph8+19. Three lines (2.6%) were postulated to carry Rph15 based on seedling rust tests and genotyping with a marker linked closely to this gene. Based on greenhouse seedling tests and adult-plant field tests, 84 genotypes (73.7%) were identified as carrying APR, and genotyping with molecular markers linked closely to three known APR genes (Rph20, Rph23 and Rph24) revealed that 48 of the 84 genotypes (57.1%) likely carry novel (uncharacterized) sources of APR. Seven lines were found to carry known APR gene combinations (Rph20+Rph23, Rph23+Rph24 and Rph20+Rph24), and these lines had higher levels of field resistance compared to those carrying each of these three APR genes singly. GWAS identified 12 putative QTLs; strongly associated markers located on chromosomes 1H, 2H, 3H, 5H and 7H. Of these, the QTL on chromosome 7H had the largest effect on resistance response to P. hordei. Overall, these studies detected several potentially novel genomic regions associated with resistance. The findings provide useful information for breeders to support the utilization of these sources of resistance to diversify resistance to leaf rust in barley and increase resistance durability.
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Affiliation(s)
- Laura A. Ziems
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2570, Australia
| | - Lovepreet Singh
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2570, Australia
| | - Peter M. Dracatos
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2570, Australia
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Bundoora, VIC 3086, Australia
| | - Mark J. Dieters
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4067, Australia
| | - Miguel Sanchez-Garcia
- International Centre for Agriculture Research in Dry Areas (ICARDA), Rabat 10170, Morocco
| | - Ahmed Amri
- International Centre for Agriculture Research in Dry Areas (ICARDA), Rabat 10170, Morocco
| | - Ramesh Pal Singh Verma
- International Centre for Agriculture Research in Dry Areas (ICARDA), Rabat 10170, Morocco
- Indian Institute of Wheat and Barley Research, Karnal 132001, India
| | - Robert F. Park
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2570, Australia
| | - Davinder Singh
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2570, Australia
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Park RF, Boshoff WHP, Cabral AL, Chong J, Martinelli JA, McMullen MS, Fetch JWM, Paczos-Grzęda E, Prats E, Roake J, Sowa S, Ziems L, Singh D. Breeding oat for resistance to the crown rust pathogen Puccinia coronata f. sp. avenae: achievements and prospects. Theor Appl Genet 2022; 135:3709-3734. [PMID: 35665827 PMCID: PMC9729147 DOI: 10.1007/s00122-022-04121-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 05/01/2022] [Indexed: 05/05/2023]
Abstract
Crown rust, caused by Puccinia coronata f. sp. avenae (Pca), is a significant impediment to global oat production. Some 98 alleles at 92 loci conferring resistance to Pca in Avena have been designated; however, allelic relationships and chromosomal locations of many of these are unknown. Long-term monitoring of Pca in Australia, North America and elsewhere has shown that it is highly variable even in the absence of sexual recombination, likely due to large pathogen populations that cycle between wild oat communities and oat crops. Efforts to develop cultivars with genetic resistance to Pca began in the 1950s. Based almost solely on all all-stage resistance, this has had temporary benefits but very limited success. The inability to eradicate wild oats, and their common occurrence in many oat growing regions, means that future strategies to control Pca must be based on the assumption of a large and variable prevailing pathogen population with high evolutionary potential, even if cultivars with durable resistance are deployed and grown widely. The presence of minor gene, additive APR to Pca in hexaploid oat germplasm opens the possibility of pyramiding several such genes to give high levels of resistance. The recent availability of reference genomes for diploid and hexaploid oat will undoubtedly accelerate efforts to discover, characterise and develop high throughput diagnostic markers to introgress and pyramid resistance to Pca in high yielding adapted oat germplasm.
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Affiliation(s)
- R F Park
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia.
| | - W H P Boshoff
- Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - A L Cabral
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, Canada
| | - J Chong
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Canada
| | - J A Martinelli
- Department of Crop Science, Agronomy School, Federal University of Rio Grande Do Sul (UFRGS), Av. Bento Gonçalves, 7712, Porto Alegre, RS, 91501-970, Brazil
| | - M S McMullen
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58105-5051, USA
| | - J W Mitchell Fetch
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, Canada
| | - E Paczos-Grzęda
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, 20-950, Lublin, Poland
| | - E Prats
- CSIC-Institute for Sustainable Agriculture, Avda. Menéndez Pidal s/n. , 14004, Córdoba, Spain
| | - J Roake
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
| | - S Sowa
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, 20-950, Lublin, Poland
| | - L Ziems
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
| | - D Singh
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
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Mehnaz M, Dracatos PM, Dinh HX, Forrest K, Rouse MN, Park RF, Singh D. A novel locus conferring resistance to Puccinia hordei maps to the genomic region corresponding to Rph14 on barley chromosome 2HS. Front Plant Sci 2022; 13:980870. [PMID: 36275572 PMCID: PMC9583899 DOI: 10.3389/fpls.2022.980870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Barley leaf rust (BLR), caused by Puccinia hordei, is best controlled through genetic resistance. An efficient resistance breeding program prioritizes the need to identify, characterize, and map new sources of resistance as well as understanding the effectiveness, structure, and function of resistance genes. In this study, three mapping populations were developed by crossing Israelian barley lines "AGG-396," "AGG-397," and "AGG-403" (carrying unknown leaf rust resistance) with a susceptible variety "Gus" to characterize and map resistance. Genetic analysis of phenotypic data from rust testing F3s with a P. hordei pathotype 5457 P+ revealed monogenic inheritance in all three populations. Targeted genotyping-by-sequencing of the three populations detected marker trait associations in the same genomic region on the short arm of chromosome 2H between 39 and 57 Mb (AGG-396/Gus), 44 and 64 Mb (AGG-397/Gus), and 31 and 58 Mb (AGG-403/Gus), suggesting that the resistance in all three lines is likely conferred by the same locus (tentatively designated RphAGG396). Two Kompetitive allele-specific PCR (KASP) markers, HvGBSv2-902 and HvGBSv2-932, defined a genetic distance of 3.8 cM proximal and 7.1 cM distal to RphAGG396, respectively. To increase the marker density at the RphAGG396 locus, 75 CAPS markers were designed between two flanking markers. Integration of marker data resulted in the identification of two critical recombinants and mapping RphAGG396 between markers- Mloc-28 (40.75 Mb) and Mloc-41 (41.92 Mb) narrowing the physical window to 1.17 Mb based on the Morex v2.0 reference genome assembly. To enhance map resolution, 600 F2s were genotyped with markers- Mloc-28 and Mloc-41 and nine recombinants were identified, placing the gene at a genetic distance of 0.5 and 0.2 cM between the two markers, respectively. Two annotated NLR (nucleotide-binding domain leucine-rich repeat) genes (r2.2HG0093020 and r2.2HG0093030) were identified as the best candidates for RphAGG396. A closely linked marker was developed for RphAGG396 that can be used for marker-assisted selection.
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Affiliation(s)
- Mehnaz Mehnaz
- School of Life and Environmental Sciences, Plant Breeding Institute, University of Sydney, Sydney, NSW, Australia
| | - Peter M. Dracatos
- Department of Animal, Plant and Soil Sciences, La Trobe University, AgriBio, Bundoora, VIC, Australia
| | - Hoan X. Dinh
- School of Life and Environmental Sciences, Plant Breeding Institute, University of Sydney, Sydney, NSW, Australia
| | - Kerrie Forrest
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Matthew N. Rouse
- USDA-ARS Cereal Disease Laboratory, Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Robert F. Park
- School of Life and Environmental Sciences, Plant Breeding Institute, University of Sydney, Sydney, NSW, Australia
| | - Davinder Singh
- School of Life and Environmental Sciences, Plant Breeding Institute, University of Sydney, Sydney, NSW, Australia
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Dinh HX, Pourkheirandish M, Park RF, Singh D. The genetic basis and interaction of genes conferring resistance to Puccinia hordei in an ICARDA barley breeding line GID 5779743. Front Plant Sci 2022; 13:988322. [PMID: 36051292 PMCID: PMC9425046 DOI: 10.3389/fpls.2022.988322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Leaf rust of barley causes significant losses in crops of susceptible cultivars. Deploying host resistance is the most cost-effective and eco-sustainable strategy to protect the harvest. However, most known leaf rust resistance genes have been overcome by the pathogen due to the pathogen's evolution and adaptation. The discovery of novel sources of genetic resistance is vital to keep fighting against pathogen evolution. In this study, we investigated the genetic basis of resistance in barley breeding line GID 5779743 (GID) from ICARDA, found to carry high levels of seedling resistance to prevalent Australian pathotypes of Puccinia hordei. Multipathotype tests, genotyping, and marker-trait associations revealed that the resistance in GID is conferred by two independent genes. The first gene, Rph3, was detected using a linked CAPS marker and QTL analysis. The second gene was detected by QTL analysis and mapped to the same location as that of the Rph5 locus on the telomeric region of chromosome 3HS. The segregating ratio in F2 (conforming to 9 resistant: 7 susceptible genetic ratio; p > 0.8) and F3 (1 resistant: 8 segregating: 7 susceptible; p > 0.19) generations of the GID × Gus population, when challenged with pathotype 5477 P- (virulent on Rph3 and Rph5) suggested the interaction of two genes in a complementary fashion. This study demonstrated that Rph3 interacts with Rph5 or an additional locus closely linked to Rph5 (tentatively designated RphGID) in GID to produce an incompatible response when challenged with a pathotype virulent on Rph3+Rph5.
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Affiliation(s)
- Hoan X. Dinh
- Faculty of Science, Plant Breeding Institute, The University of Sydney, Sydney, NSW, Australia
| | - Mohammad Pourkheirandish
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Robert F. Park
- Faculty of Science, Plant Breeding Institute, The University of Sydney, Sydney, NSW, Australia
| | - Davinder Singh
- Faculty of Science, Plant Breeding Institute, The University of Sydney, Sydney, NSW, Australia
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Dinh HX, Singh D, Gomez de la Cruz D, Hensel G, Kumlehn J, Mascher M, Stein N, Perovic D, Ayliffe M, Moscou MJ, Park RF, Pourkheirandish M. The barley leaf rust resistance gene Rph3 encodes a predicted membrane protein and is induced upon infection by avirulent pathotypes of Puccinia hordei. Nat Commun 2022; 13:2386. [PMID: 35501307 PMCID: PMC9061838 DOI: 10.1038/s41467-022-29840-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 04/03/2022] [Indexed: 01/04/2023] Open
Abstract
Leaf rust, caused by Puccinia hordei, is an economically significant disease of barley, but only a few major resistance genes to P. hordei (Rph) have been cloned. In this study, gene Rph3 was isolated by positional cloning and confirmed by mutational analysis and transgenic complementation. The Rph3 gene, which originated from wild barley and was first introgressed into cultivated Egyptian germplasm, encodes a unique predicted transmembrane resistance protein that differs from all known plant disease resistance proteins at the amino acid sequence level. Genetic profiles of diverse accessions indicated limited genetic diversity in Rph3 in domesticated germplasm, and higher diversity in wild barley from the Eastern Mediterranean region. The Rph3 gene was expressed only in interactions with Rph3-avirulent P. hordei isolates, a phenomenon also observed for transcription activator-like effector-dependent genes known as executors conferring resistance to Xanthomonas spp. Like known transmembrane executors such as Bs3 and Xa7, heterologous expression of Rph3 in N. benthamiana induced a cell death response. The isolation of Rph3 highlights convergent evolutionary processes in diverse plant-pathogen interaction systems, where similar defence mechanisms evolved independently in monocots and dicots. Leaf rust is an economically significant disease of barley. Here the authors describe cloning of the barley Rph3 leaf rust resistance gene and reveal it encodes a predicted transmembrane protein that is expressed upon infection by Rph3-avirulent Puccinia hordei isolates.
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10
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Abstract
Sexual reproduction, mutation, and reassortment of nuclei increase genotypic diversity in rust fungi. Sexual reproduction is inherent to rust fungi, coupled with their coevolved plant hosts in native pathosystems. Rust fungi are hypothesised to exchange nuclei by somatic hybridisation with an outcome of increased genotypic diversity, independent of sexual reproduction. We provide criteria to demonstrate whether somatic exchange has occurred, including knowledge of parental haplotypes and rejection of fertilisation in normal rust life cycles.
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Affiliation(s)
- Alistair R. McTaggart
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Dutton Park, Queensland, Australia
| | - Timothy Y. James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Alexander Idnurm
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Robert F. Park
- Plant Breeding Institute, The University of Sydney, Cobbitty, New South Wales, Australia
| | - Louise S. Shuey
- Queensland Department of Agriculture and Fisheries, Ecosciences Precinct, Dutton Park, Queensland, Australia
| | - Michelle N. K. Demers
- Plant Breeding Institute, The University of Sydney, Cobbitty, New South Wales, Australia
| | - M. Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail:
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11
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Ding Y, Gardiner DM, Powell JJ, Colgrave ML, Park RF, Kazan K. Adaptive defence and sensing responses of host plant roots to fungal pathogen attack revealed by transcriptome and metabolome analyses. Plant Cell Environ 2021; 44:3526-3544. [PMID: 34591319 DOI: 10.1111/pce.14195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 09/15/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Plant root-produced constitutive and inducible defences inhibit pathogenic microorganisms within roots and in the rhizosphere. However, regulatory mechanisms underlying host responses during root-pathogen interactions are largely unexplored. Using the model species Brachypodium distachyon (Bd), we studied transcriptional and metabolic responses altered in Bd roots following challenge with Fusarium graminearum (Fg), a fungal pathogen that causes diseases in diverse organs of cereal crops. Shared gene expression patterns were found between Bd roots and spikes during Fg infection associated with the mycotoxin deoxynivalenol (DON). Overexpression of BdMYB78, an up-regulated transcription factor, significantly increased root resistance during Fg infection. We show that Bd roots recognize encroaching Fg prior to physical contact by altering transcription of genes associated with multiple cellular processes such as reactive oxygen species and cell development. These changes coincide with altered levels of secreted host metabolites detected by an untargeted metabolomic approach. The secretion of Bd metabolites was suppressed by Fg as enhanced levels of defence-associated metabolites were found in roots during pre-contact with a Fg mutant defective in host perception and the ability to cause disease. Our results help to understand root defence strategies employed by plants, with potential implications for improving the resistance of cereal crops to soil pathogens.
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Affiliation(s)
- Yi Ding
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, St Lucia, Queensland, Australia
- The Plant Breeding Institute, School of Life & Environmental Sciences, Faculty of Science, The University of Sydney, Cobbitty, New South Wales, Australia
| | - Donald M Gardiner
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, St Lucia, Queensland, Australia
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, St Lucia, Queensland, Australia
| | - Jonathan J Powell
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, St Lucia, Queensland, Australia
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, St Lucia, Queensland, Australia
| | - Michelle L Colgrave
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, St Lucia, Queensland, Australia
- Australian Research Council, Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Robert F Park
- The Plant Breeding Institute, School of Life & Environmental Sciences, Faculty of Science, The University of Sydney, Cobbitty, New South Wales, Australia
| | - Kemal Kazan
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, St Lucia, Queensland, Australia
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, St Lucia, Queensland, Australia
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12
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Quade A, Ash GJ, Park RF, Stodart B. Resistance in Maize ( Zea mays) to Isolates of Puccinia sorghi from Eastern Australia. Phytopathology 2021; 111:1751-1757. [PMID: 33620235 DOI: 10.1094/phyto-11-20-0524-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The causal agent of maize common rust (CR), Puccinia sorghi, has increased in incidence and severity in Australia in recent years, prompting the assessment of sources of resistance and a preliminary survey of the diversity of P. sorghi populations. The maize commercial hybrids tested carried no resistance to 14 isolates of P. sorghi and had infection types comparable with that of a susceptible check. The resistance gene Rp1_D that remained effective in the United States for 35 years was ineffective against 7 of the 14 isolates. Maize lines carrying known "resistance to Puccinia" (Rp) genes were inoculated with the five isolates considered most diverse based on year of collection (2018 or 2019), location (Queensland or Victoria), and host from which they were isolated (maize or sweet corn). Lines carrying the resistance genes RpG, Rp5, Rp1_E, Rp1_I, Rp1_L, RpGDJ, RpGJF, and Rp5GCJ were resistant to all five isolates and to isolates collected in many agroecological regions. These lines were recommended as donors of effective resistance for maize breeding programs in Australia. Lines carrying no known resistance or resistance genes Rp8_A, Rp8_B, Rp1_J, Rp1_M, Rp7, and Rpp9 (conferring resistance to P. polysora) were susceptible to all five isolates. Differential lines carrying resistance genes Rp1_B, Rp1_C, Rp1_D, Rp1_F, Rp1_K, Rp3_D, or Rp4_A were either resistant or susceptible depending upon the isolate used, showing that the isolates varied in virulence for these genes. Urediniospore production was reduced on adult compared with juvenile plants, presumably due to changes in plant physiology associated with age or the presence of adult plant resistance.
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Affiliation(s)
- Aurelie Quade
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, QLD 4350, Australia
| | - Gavin J Ash
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, QLD 4350, Australia
- Graham Centre for Agricultural Innovation (Charles Sturt University and NSW Department of Primary Industries), School of Agricultural and Wine Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Robert F Park
- Plant Breeding Institute, University of Sydney, Cobbitty, NSW 2570, Australia
| | - Benjamin Stodart
- Graham Centre for Agricultural Innovation (Charles Sturt University and NSW Department of Primary Industries), School of Agricultural and Wine Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
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13
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Ding Y, Cuddy WS, Wellings CR, Zhang P, Thach T, Hovmøller MS, Qutob D, Brar GS, Kutcher HR, Park RF. Incursions of divergent genotypes, evolution of virulence and host jumps shape a continental clonal population of the stripe rust pathogen Puccinia striiformis. Mol Ecol 2021; 30:6566-6584. [PMID: 34543497 DOI: 10.1111/mec.16182] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 08/22/2021] [Accepted: 09/13/2021] [Indexed: 11/30/2022]
Abstract
Long-distance migration and host adaptation by transboundary plant pathogens often brings detrimental effects to important agroecosystems. Efficient surveillance as a basis for responding to the dynamics of such pathogens is often hampered by a lack of information on incursion origin, evolutionary pathways and the genetic basis of rapidly evolving virulence across larger timescales. Here, we studied these genetic features by using historical isolates of the obligate biotrophic pathogen Puccinia striiformis f. sp. tritici (Pst), which causes one of the most widespread and devastating diseases, stripe (yellow) rust, of wheat. Through a combination of genotypic, phenotypic and genomic analyses, we assigned eight Pst isolates representing putative exotic Pst incursions into Australia to four previously defined genetic groups, PstS0, PstS1, PstS10 and PstS13. We showed that isolates of an additional incursion of P. striiformis, known locally as P. striiformis f. sp. pseudo-hordei, had a new and unique multilocus SSR genotype (MLG). We provide results of overall genomic variation of representative Pst isolates from each genetic group by comparative genomic analyses. We showed that isolates within the PstS1 and PstS13 genetic groups are most distinct at the whole-genome variant level from isolates belonging to genetic group PstS0, whereas the isolate from the PstS10 genetic group is intermediate. We further explored variable gene content, including putative effectors, representing both shared but also unique genetic changes that have occurred following introduction, some of which may additionally account for local adaptation of these isolates to triticale. Our genotypic and genomic data revealed new genetic insights into the evolution of diverse phenotypes of rust pathogens following incursion into a geographically isolated continental region.
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Affiliation(s)
- Yi Ding
- School of Life and Environmental Sciences, Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, Australia
| | - Will S Cuddy
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - Colin R Wellings
- School of Life and Environmental Sciences, Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, Australia.,NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - Peng Zhang
- School of Life and Environmental Sciences, Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, Australia
| | - Tine Thach
- Department of Agroecology, Global Rust Reference Center, Aarhus University, Slagelse, Denmark
| | - Mogens S Hovmøller
- Department of Agroecology, Global Rust Reference Center, Aarhus University, Slagelse, Denmark
| | - Dinah Qutob
- Department of Biological Sciences, Kent State University at Stark, North Canton, ON, USA
| | - Gurcharn S Brar
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Hadley R Kutcher
- College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, Canada
| | - Robert F Park
- School of Life and Environmental Sciences, Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, Australia
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14
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Wu JQ, Song L, Ding Y, Dong C, Hasan M, Park RF. A Chromosome-Scale Assembly of the Wheat Leaf Rust Pathogen Puccinia triticina Provides Insights Into Structural Variations and Genetic Relationships With Haplotype Resolution. Front Microbiol 2021; 12:704253. [PMID: 34394053 PMCID: PMC8358450 DOI: 10.3389/fmicb.2021.704253] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 07/12/2021] [Indexed: 11/24/2022] Open
Abstract
Despite the global economic importance of the wheat leaf rust pathogen Puccinia triticina (Pt), genomic resources for Pt are limited and chromosome-level assemblies of Pt are lacking. Here, we present a complete haplotype-resolved genome assembly at a chromosome-scale for Pt using the Australian pathotype 64-(6),(7),(10),11 (Pt64; North American race LBBQB) built upon the newly developed technologies of PacBio and Hi-C sequencing. PacBio reads with ∼200-fold coverage (29.8 Gb data) were assembled by Falcon and Falcon-unzip and subsequently scaffolded with Hi-C data using Falcon-phase and Proximo. This approach allowed us to construct 18 chromosome pseudomolecules ranging from 3.5 to 12.3 Mb in size for each haplotype of the dikaryotic genome of Pt64. Each haplotype had a total length of ∼147 Mb, scaffold N50 of ∼9.4 Mb, and was ∼93% complete for BUSCOs. Each haplotype had ∼29,800 predicted genes, of which ∼2,000 were predicted as secreted proteins (SPs). The investigation of structural variants (SVs) between haplotypes A and B revealed that 10% of the total genome was spanned by SVs, highlighting variations previously undetected by short-read based assemblies. For the first time, the mating type (MAT) genes on each haplotype of Pt64 were identified, which showed that MAT loci a and b are located on two chromosomes (chromosomes 7 and 14), representing a tetrapolar type. Furthermore, the Pt64 assembly enabled haplotype-based evolutionary analyses for 21 Australian Pt isolates, which highlighted the importance of a haplotype resolved reference when inferring genetic relationships using whole genome SNPs. This Pt64 assembly at chromosome-scale with full phase information provides an invaluable resource for genomic and evolutionary research, which will accelerate the understanding of molecular mechanisms underlying Pt-wheat interactions and facilitate the development of durable resistance to leaf rust in wheat and sustainable control of rust disease.
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Affiliation(s)
- Jing Qin Wu
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Long Song
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Yi Ding
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Chongmei Dong
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Mafruha Hasan
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Robert F Park
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
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15
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Mehnaz M, Dracatos P, Pham A, March T, Maurer A, Pillen K, Forrest K, Kulkarni T, Pourkheirandish M, Park RF, Singh D. Discovery and fine mapping of Rph28: a new gene conferring resistance to Puccinia hordei from wild barley. Theor Appl Genet 2021; 134:2167-2179. [PMID: 33774682 DOI: 10.1007/s00122-021-03814-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 03/10/2021] [Indexed: 06/12/2023]
Abstract
A new gene Rph28 conferring resistance to barley leaf rust was discovered and fine-mapped on chromosome 5H from wild barley. Leaf rust is a highly destructive disease of barley caused by the fungal pathogen Puccinia hordei. Genetic resistance is considered to be the most effective, economical and eco-friendly approach to minimize losses caused by this disease. A study was undertaken to characterize and fine map a seedling resistance gene identified in a Hordeum vulgare ssp. spontaneum-derived barley line, HEB-04-101, that is broadly effective against a diverse set of Australian P. hordei pathotypes. Genetic analysis of an F3 population derived from a cross between HEB-04-101 and the H. vulgare cultivar Flagship (seedling susceptible) confirmed the presence of a single dominant gene for resistance in HEB-04-101. Selective genotyping was performed on representative plants from non-segregating homozygous resistant and homozygous susceptible F3 families using the targeted genotyping-by-sequencing (tGBS) assay. Putatively linked SNP markers with complete fixation were identified on the long arm of chromosome 5H spanning a physical interval between 622 and 669 Mb based on the 2017 Morex barley reference genome assembly. Several CAPS (cleaved amplified polymorphic sequences) markers were designed from the pseudomolecule sequence of the Morex assembly (v1.0 and v2.0), and 16 polymorphic markers were able to delineate the RphHEB locus to a 0.05 cM genetic interval spanning 98.6 kb. Based on its effectiveness and wild origin, RphHEB is distinct from all other designated Rph genes located on chromosome 5H and therefore the new locus symbol Rph28 is recommended for RphHEB in accordance with the rules and cataloguing system of barley gene nomenclature.
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Affiliation(s)
- M Mehnaz
- Plant Breeding Institute Cobbitty, School of Life and Environmental Sciences, University of Sydney, Narellan, NSW, Australia
| | - P Dracatos
- Plant Breeding Institute Cobbitty, School of Life and Environmental Sciences, University of Sydney, Narellan, NSW, Australia
| | - A Pham
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - T March
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - A Maurer
- Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120, Halle/Saale, Germany
| | - K Pillen
- Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120, Halle/Saale, Germany
| | - K Forrest
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, 3083, Australia
| | - T Kulkarni
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, 3083, Australia
| | - M Pourkheirandish
- Faculty of Veterinary and Agriculture, The University of Melbourne, Parkville, 3010, Australia
| | - R F Park
- Plant Breeding Institute Cobbitty, School of Life and Environmental Sciences, University of Sydney, Narellan, NSW, Australia
| | - D Singh
- Plant Breeding Institute Cobbitty, School of Life and Environmental Sciences, University of Sydney, Narellan, NSW, Australia.
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16
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Zhang J, Hewitt TC, Boshoff WHP, Dundas I, Upadhyaya N, Li J, Patpour M, Chandramohan S, Pretorius ZA, Hovmøller M, Schnippenkoetter W, Park RF, Mago R, Periyannan S, Bhatt D, Hoxha S, Chakraborty S, Luo M, Dodds P, Steuernagel B, Wulff BBH, Ayliffe M, McIntosh RA, Zhang P, Lagudah ES. A recombined Sr26 and Sr61 disease resistance gene stack in wheat encodes unrelated NLR genes. Nat Commun 2021; 12:3378. [PMID: 34099713 PMCID: PMC8184838 DOI: 10.1038/s41467-021-23738-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 05/10/2021] [Indexed: 12/25/2022] Open
Abstract
The re-emergence of stem rust on wheat in Europe and Africa is reinforcing the ongoing need for durable resistance gene deployment. Here, we isolate from wheat, Sr26 and Sr61, with both genes independently introduced as alien chromosome introgressions from tall wheat grass (Thinopyrum ponticum). Mutational genomics and targeted exome capture identify Sr26 and Sr61 as separate single genes that encode unrelated (34.8%) nucleotide binding site leucine rich repeat proteins. Sr26 and Sr61 are each validated by transgenic complementation using endogenous and/or heterologous promoter sequences. Sr61 orthologs are absent from current Thinopyrum elongatum and wheat pan genome sequences, contrasting with Sr26 where homologues are present. Using gene-specific markers, we validate the presence of both genes on a single recombinant alien segment developed in wheat. The co-location of these genes on a small non-recombinogenic segment simplifies their deployment as a gene stack and potentially enhances their resistance durability. The tall wheat grass-derived stem rust resistance genes Sr26 and Sr61 are among a few ones that are effective to all current dominant races of stem rust, including Ug99. Here, the authors show that the two genes are present in a small non-recombinogenic segment but encode two unrelated NLR proteins.
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Affiliation(s)
- Jianping Zhang
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia.,CSIRO Agriculture & Food, Canberra, ACT, Australia
| | - Timothy C Hewitt
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia.,CSIRO Agriculture & Food, Canberra, ACT, Australia
| | - Willem H P Boshoff
- Department of Plant Sciences, University of the Free State, Bloemfontein, South Africa
| | - Ian Dundas
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | | | - Jianbo Li
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia
| | - Mehran Patpour
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | | | - Zacharias A Pretorius
- Department of Plant Sciences, University of the Free State, Bloemfontein, South Africa
| | | | | | - Robert F Park
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia
| | - Rohit Mago
- CSIRO Agriculture & Food, Canberra, ACT, Australia
| | | | - Dhara Bhatt
- CSIRO Agriculture & Food, Canberra, ACT, Australia
| | - Sami Hoxha
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia
| | | | - Ming Luo
- CSIRO Agriculture & Food, Canberra, ACT, Australia
| | - Peter Dodds
- CSIRO Agriculture & Food, Canberra, ACT, Australia
| | | | | | | | - Robert A McIntosh
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia
| | - Peng Zhang
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia.
| | - Evans S Lagudah
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia. .,CSIRO Agriculture & Food, Canberra, ACT, Australia.
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17
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Chen C, Jost M, Clark B, Martin M, Matny O, Steffenson BJ, Franckowiak JD, Mascher M, Singh D, Perovic D, Richardson T, Periyannan S, Lagudah ES, Park RF, Dracatos PM. BED domain-containing NLR from wild barley confers resistance to leaf rust. Plant Biotechnol J 2021; 19:1206-1215. [PMID: 33415836 PMCID: PMC8196641 DOI: 10.1111/pbi.13542] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 12/20/2020] [Accepted: 12/26/2020] [Indexed: 05/22/2023]
Abstract
Leaf rust, caused by Puccinia hordei, is a devastating fungal disease affecting barley (Hordeum vulgare subsp. vulgare) production globally. Despite the effectiveness of genetic resistance, the deployment of single genes often compromises durability due to the emergence of virulent P. hordei races, prompting the search for new sources of resistance. Here we report on the cloning of Rph15, a resistance gene derived from barley's wild progenitor H. vulgare subsp. spontaneum. We demonstrate using introgression mapping, mutation and complementation that the Rph15 gene from the near-isogenic line (NIL) Bowman + Rph15 (referred to as BW719) encodes a coiled-coil nucleotide-binding leucine-rich repeat (NLR) protein with an integrated Zinc finger BED (ZF-BED) domain. A predicted KASP marker was developed and validated across a collection of Australian cultivars and a series of introgression lines in the Bowman background known to carry the Rph15 resistance. Rph16 from HS-680, another wild barley derived leaf rust resistance gene, was previously mapped to the same genomic region on chromosome 2H and was assumed to be allelic with Rph15 based on genetic studies. Both sequence analysis, race specificity and the identification of a knockout mutant in the HS-680 background suggest that Rph15- and Rph16-mediated resistances are in fact the same and not allelic as previously thought. The cloning of Rph15 now permits efficient gene deployment and the production of resistance gene cassettes for sustained leaf rust control.
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Affiliation(s)
- Chunhong Chen
- Agriculture & FoodCommonwealth Scientific and Industrial Research OrganisationCanberraACTAustralia
| | - Matthias Jost
- Agriculture & FoodCommonwealth Scientific and Industrial Research OrganisationCanberraACTAustralia
| | - Bethany Clark
- Plant Breeding InstituteThe University of SydneyCobbittyNSWAustralia
| | - Matthew Martin
- Department of Plant PathologyUniversity of MinnesotaSt. PaulMNUSA
| | - Oadi Matny
- Department of Plant PathologyUniversity of MinnesotaSt. PaulMNUSA
| | | | | | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
| | - Davinder Singh
- Plant Breeding InstituteThe University of SydneyCobbittyNSWAustralia
| | - Dragan Perovic
- Institute for Resistance Research and Stress ToleranceFederal Research Centre for Cultivated PlantsJulius Kühn‐Institute (JKI)QuedlinburgGermany
| | - Terese Richardson
- Agriculture & FoodCommonwealth Scientific and Industrial Research OrganisationCanberraACTAustralia
| | - Sambasivam Periyannan
- Agriculture & FoodCommonwealth Scientific and Industrial Research OrganisationCanberraACTAustralia
| | - Evans S. Lagudah
- Agriculture & FoodCommonwealth Scientific and Industrial Research OrganisationCanberraACTAustralia
| | - Robert F. Park
- Plant Breeding InstituteThe University of SydneyCobbittyNSWAustralia
| | - Peter M. Dracatos
- Plant Breeding InstituteThe University of SydneyCobbittyNSWAustralia
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18
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Tobias PA, Schwessinger B, Deng CH, Wu C, Dong C, Sperschneider J, Jones A, Lou Z, Zhang P, Sandhu K, Smith GR, Tibbits J, Chagné D, Park RF. Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements. G3 (Bethesda) 2021; 11:jkaa015. [PMID: 33793741 PMCID: PMC8063080 DOI: 10.1093/g3journal/jkaa015] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 10/26/2020] [Indexed: 02/06/2023]
Abstract
Austropuccinia psidii, originating in South America, is a globally invasive fungal plant pathogen that causes rust disease on Myrtaceae. Several biotypes are recognized, with the most widely distributed pandemic biotype spreading throughout the Asia-Pacific and Oceania regions over the last decade. Austropuccinia psidii has a broad host range with more than 480 myrtaceous species. Since first detected in Australia in 2010, the pathogen has caused the near extinction of at least three species and negatively affected commercial production of several Myrtaceae. To enable molecular and evolutionary studies into A. psidii pathogenicity, we assembled a highly contiguous genome for the pandemic biotype. With an estimated haploid genome size of just over 1 Gb (gigabases), it is the largest assembled fungal genome to date. The genome has undergone massive expansion via distinct transposable element (TE) bursts. Over 90% of the genome is covered by TEs predominantly belonging to the Gypsy superfamily. These TE bursts have likely been followed by deamination events of methylated cytosines to silence the repetitive elements. This in turn led to the depletion of CpG sites in TEs and a very low overall GC content of 33.8%. Compared to other Pucciniales, the intergenic distances are increased by an order of magnitude indicating a general insertion of TEs between genes. Overall, we show how TEs shaped the genome evolution of A. psidii and provide a greatly needed resource for strategic approaches to combat disease spread.
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Affiliation(s)
- Peri A Tobias
- School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW 2006, Australia
- Plant & Food Research Australia, SA 5064, Australia
| | - Benjamin Schwessinger
- Australia Research School of Biology, The Australian National University, Acton, ACT 2601, Australia
| | - Cecilia H Deng
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
| | - Chen Wu
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
| | - Chongmei Dong
- Plant Breeding Institute, University of Sydney, Narellan, NSW 2567, Australia
| | - Jana Sperschneider
- Biological Data Science Institute, The Australian National University, Canberra, ACT, 2600, Australia
| | - Ashley Jones
- Australia Research School of Biology, The Australian National University, Acton, ACT 2601, Australia
| | - Zhenyan Lou
- Australia Research School of Biology, The Australian National University, Acton, ACT 2601, Australia
| | - Peng Zhang
- Plant Breeding Institute, University of Sydney, Narellan, NSW 2567, Australia
| | - Karanjeet Sandhu
- Plant Breeding Institute, University of Sydney, Narellan, NSW 2567, Australia
| | - Grant R Smith
- The New Zealand Institute for Plant and Food Research Limited, Christchurch 8140, New Zealand
| | - Josquin Tibbits
- Agriculture Victoria Department of Jobs, Precincts and Regions, Bundoora, VIC 3083, Australia
| | - David Chagné
- The New Zealand Institute for Plant & Food Research, Palmerston North 4442, New Zealand
| | - Robert F Park
- Plant Breeding Institute, University of Sydney, Narellan, NSW 2567, Australia
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19
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Abstract
Improving resistance to barley leaf rust (caused by Puccinia hordei) is an important breeding objective in most barley growing regions worldwide. The development and subsequent utilization of high-throughput PCR-based codominant molecular markers remains an effective approach to select genotypes with multiple effective resistance genes, permitting efficient gene deployment and stewardship. The genes Rph20 and Rph24 confer widely effective adult plant resistance (APR) to leaf rust, are common in European and Australian barley germplasm (often in combination), and act interactively to confer high levels of resistance. Here we report on the development and validation of codominant insertion-deletion (indel) based PCR markers that are highly predictive for the resistance alleles Rph20.ai and Rph24.an (both referred to as Rph20 and Rph24).
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Affiliation(s)
- P M Dracatos
- Sydney Institute of Agriculture, Plant Breeding Institute, The University of Sydney, Narellan 2567, NSW, Australia
| | - R F Park
- Sydney Institute of Agriculture, Plant Breeding Institute, The University of Sydney, Narellan 2567, NSW, Australia
| | - D Singh
- Sydney Institute of Agriculture, Plant Breeding Institute, The University of Sydney, Narellan 2567, NSW, Australia
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20
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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Wang E, Dong C, Zhang P, Roberts TH, Park RF. Carotenoid biosynthesis and the evolution of carotenogenesis genes in rust fungi. Fungal Biol 2020; 125:400-411. [PMID: 33910681 DOI: 10.1016/j.funbio.2020.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 11/17/2020] [Accepted: 12/21/2020] [Indexed: 11/30/2022]
Abstract
Diseases caused by rust fungi pose a significant threat to global plant production. Although carotenoid pigments are produced in spores of nearly all rust species, the corresponding biosynthesis pathway(s) have not been investigated. Here, candidate genes for carotenoid biosynthesis in Puccinia graminis f. sp. tritici (Pgt) were identified, cloned and functionally complemented using specifically engineered strains of Escherichia coli. A part of the carotenoid biosynthesis pathway in rust fungi was elucidated, with only two genes, CrtYB and CrtI, catalysing the reactions from geranyl-geranyl diphosphate (GGPP) to γ-carotene. The CrtYB gene encodes a bi-functional lycopene cyclase/phytoene synthase, which catalyses the condensation of two GGPP into phytoene, as well as the cyclisation of the ψ-end of lycopene to form γ-carotene. The CrtI gene encodes a phytoene desaturase that carries out four successive desaturations of phytoene, through the intermediates phytofluene and neurosporene to lycopene. The evolution of carotenoid pigmentation in rust fungi, including Pgt, P. graminis avenae, P. graminis secalis (Pgs), P. graminis lolli, P. striiformis f. sp. tritici, P. striiformis f. sp. pseudohordei, P. striiformis f. sp. hordei, the "scabrum" rust (putative hybrids between Pgt and Pgs), P. triticina, and P. hordei, was investigated by phylogenetic analysis. Both CrtYB and CrtI were found to be closely related among rust fungi, other pathogenic fungi, and some aphids. Our results provide a springboard to increase the understanding of the physiological role(s) of carotenoid pigments in rust fungi, to better understand evolution within the Pucciniales, and to develop robust molecular diagnostics for rust fungi.
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Affiliation(s)
- Erpei Wang
- Plant Breeding Institute, Sydney Institute of Agriculture, University of Sydney, NSW, 2570, Australia
| | - Chongmei Dong
- Plant Breeding Institute, Sydney Institute of Agriculture, University of Sydney, NSW, 2570, Australia
| | - Peng Zhang
- Plant Breeding Institute, Sydney Institute of Agriculture, University of Sydney, NSW, 2570, Australia
| | - Thomas H Roberts
- Plant Breeding Institute, Sydney Institute of Agriculture, University of Sydney, NSW, 2570, Australia
| | - Robert F Park
- Plant Breeding Institute, Sydney Institute of Agriculture, University of Sydney, NSW, 2570, Australia.
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22
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Zhang N, Yuan S, Zhao C, Park RF, Wen X, Yang W, Zhang N, Liu D. TaNAC35 acts as a negative regulator for leaf rust resistance in a compatible interaction between common wheat and Puccinia triticina. Mol Genet Genomics 2020; 296:279-287. [PMID: 33245431 DOI: 10.1007/s00438-020-01746-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/10/2020] [Indexed: 02/03/2023]
Abstract
NAC (NAM, AFAT1/2, and CUC2) transcription factors play important roles in plant growth and in resistance to abiotic and biotic stresses. Here, we show that the TaNAC35 gene negatively regulates leaf rust resistance in the wheat line Thatcher + Lr14b (TcLr14b) when challenged with a virulent isolate of Puccinia triticina (Pt). The TaNAC35 gene was cloned from this line, and blastp results showed that its open reading frame (ORF) was 96.16% identical to the NAC35-like sequence reported from Aegilops tauschii, and that it encoded a protein with 387 amino acids (aa) including a conserved NAM domain with 145 aa at the N-terminal alongside the transcriptional activation domain with 220 aa in the C-terminal. Yeast-one-hybrid analysis proved that the C-terminal of the TaNAC35 protein was responsible for transcriptional activation. A 250-bp fragment from the 3'-end of this target gene was introduced to a BSMV-VIGS vector and used to infect the wheat line Thatcher + Lr14b (TcLr14b). The BSMV-VIGS/TaNAC35-infected plant material showed enhanced resistance (infection type "1") to Pt pathotype THTT, which was fully virulent (infection type "4") on BSMV-VIGS only infected TcLr14b plants. Histological studies showed that inhibition of TaNAC35 reduced the formation of haustorial mother cells (HMC) and mycelial growth, implying that the TaNAC35 gene plays a negative role in the response of TcLr14b to Pt pathotype THTT. These results provide molecular insight into the interaction between Pt and its wheat host, and identify a potential target for engineering resistance in wheat to this damaging pathogen.
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Affiliation(s)
- Na Zhang
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, 289 Lingyusi Street, Baoding, 071001, Hebei, China
| | - Shengliang Yuan
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, 289 Lingyusi Street, Baoding, 071001, Hebei, China
| | - Chenguang Zhao
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, 289 Lingyusi Street, Baoding, 071001, Hebei, China
| | - Robert F Park
- Plant Breeding Institute, The University of Sydney, New South Wales, 2006, Australia
| | - Xiaolei Wen
- Hebei Normal University of Science & Technology, Qinhuangdao, 066000, Hebei, China
| | - Wenxiang Yang
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, 289 Lingyusi Street, Baoding, 071001, Hebei, China
| | - Na Zhang
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, 289 Lingyusi Street, Baoding, 071001, Hebei, China.
| | - Daqun Liu
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, 289 Lingyusi Street, Baoding, 071001, Hebei, China.
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23
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Pathan AK, Cuddy W, Kimberly MO, Adusei-Fosu K, Rolando CA, Park RF. Efficacy of Fungicides Applied for Protectant and Curative Activity Against Myrtle Rust. Plant Dis 2020; 104:2123-2129. [PMID: 32539594 DOI: 10.1094/pdis-10-19-2106-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Myrtle rust, caused by the pathogen Austropuccinia psidii, affects species of the Myrtaceae, many of which are endemic to Australia and New Zealand. Originating from South America, A. psidii is now present in both countries, necessitating effective chemical control for disease management. Using an artificial inoculation protocol, the efficacy of eight fungicides (tebuconazole/trifloxystrobin, cyproconazole/azoxystrobin, fosetyl aluminum, triforine, triadimenol, oxycarboxin, copper, and tebuconazole) applied as curative or protectant treatments was tested on two native New Zealand species (Lophomyrtus × ralphii and Metrosideros excelsa). The impacts of rate (×2), frequency (single or double), and timing (pre- or postinfection) of fungicide application were investigated. Overall, the most effective fungicides tested across both species were those that included a demethylation inhibitor and strobilurin mix, notably tebuconazole/trifloxystrobin (Scorpio) and cyproconazole/azoxystrobin (Amistar Xtra). These fungicides significantly reduced infection of host plants relative to the water control. Timing of application significantly affected bioefficacy, with applications made 7 days before inoculation or 7 days after inoculation being generally the most effective. The rate of fungicide application was not significant for both host species, with few interaction terms showing overall significance. Key findings from this study will set the foundation for further fungicide bioefficacy research conducted to evaluate formulations and adjuvant mixtures, determine suitable application methods for enhanced retention and coverage, and derive optimum application time for effective protection of native and exotic Myrtaceae species in New Zealand.
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Affiliation(s)
- Amin K Pathan
- Ministry for Primary Industries, Rotorua, New Zealand
| | - William Cuddy
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle NSW 2568, Australia
| | | | | | | | - Robert F Park
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Narellan, NSW 2567, Australia
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24
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Dinh HX, Singh D, Periyannan S, Park RF, Pourkheirandish M. Molecular genetics of leaf rust resistance in wheat and barley. Theor Appl Genet 2020; 133:2035-2050. [PMID: 32128617 DOI: 10.1007/s00122-020-03570-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/18/2020] [Indexed: 06/10/2023]
Abstract
The demand for cereal grains as a main source of energy continues to increase due to the rapid increase in world population. The leaf rust diseases of cereals cause significant yield losses, posing challenges for global food security. The deployment of resistance genes has long been considered as the most effective and sustainable way to control cereal leaf rust diseases. While genetic resistance has reduced the impact of these diseases in agriculture, losses still occur due to the ability of the respective rust pathogens to change and render resistance genes ineffective plus the slow pace at which resistance genes are discovered and characterized. This article highlights novel recently developed strategies based on advances in genome sequencing that have accelerated gene isolation by overcoming the complexity of cereal genomes. The leaf rust resistance genes cloned so far from wheat and barley belong to various protein families, including nucleotide binding site/leucine-rich repeat receptors and transporters. We review recent studies that are beginning to reveal the defense mechanisms conferred by the leaf rust resistance genes identified to date in cereals and their roles in either pattern-triggered immunity or effector-triggered immunity.
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Affiliation(s)
- Hoan X Dinh
- Plant Breeding Institute, Faculty of Science, The University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Davinder Singh
- Plant Breeding Institute, Faculty of Science, The University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Sambasivam Periyannan
- CSIRO Agriculture and Food, Box 1700, Clunies Ross Street, Canberra, 2601, Australia
| | - Robert F Park
- Plant Breeding Institute, Faculty of Science, The University of Sydney, Cobbitty, NSW, 2570, Australia.
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25
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Wu JQ, Dong C, Song L, Park RF. Long-Read-Based de novo Genome Assembly and Comparative Genomics of the Wheat Leaf Rust Pathogen Puccinia triticina Identifies Candidates for Three Avirulence Genes. Front Genet 2020; 11:521. [PMID: 32582280 PMCID: PMC7287177 DOI: 10.3389/fgene.2020.00521] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/29/2020] [Indexed: 11/18/2022] Open
Abstract
Leaf rust, caused by Puccinia triticina (Pt), is one of the most devastating diseases of wheat, affecting production in nearly all wheat-growing regions worldwide. Despite its economic importance, genomic resources for Pt are very limited. In the present study, we have used long-read sequencing (LRS) and the pipeline of FALCON and FALCON-Unzip (v4.1.0) to carry out the first LRS-based de novo genome assembly for Pt. Using 22.4-Gb data with an average read length of 11.6 kb and average coverage of 150-fold, we generated a genome assembly for Pt104 [strain 104-2,3,(6),(7),11; isolate S423], considered to be the founding isolate of a clonal lineage of Pt in Australia. The Pt104 genome contains 162 contigs with a total length of 140.5 Mb and N50 of 2 Mb, with the associated haplotigs providing haplotype information for 91% of the genome. This represents the best quality of Pt genome assembly to date, which reduces the contig number by 91-fold and improves the N50 by 4-fold as compared to the previous Pt race1 assembly. An annotation pipeline that combined multiple lines of evidence including the transcriptome assemblies derived from RNA-Seq, previously identified expressed sequence tags and Pt race 1 protein sequences predicted 29,043 genes for Pt104 genome. Based on the presence of a signal peptide, no transmembrane segment, and no target location to mitochondria, 2,178 genes were identified as secreted proteins (SPs). Whole-genome sequencing (Illumina paired-end) was performed for Pt104 and six additional strains with differential virulence profile on the wheat leaf rust resistance genes Lr26, Lr2a, and Lr3ka. To identify candidates for the corresponding avirulence genes AvrLr26, AvrLr2a, and AvrLr3ka, genetic variation within each strain was first identified by mapping to the Pt104 genome. Variants within predicted SP genes between the strains were then correlated to the virulence profiles, identifying 38, 31, and 37 candidates for AvrLr26, AvrLr2a, and AvrLr3ka, respectively. The identification of these candidate genes lays a good foundation for future studies on isolating these avirulence genes, investigating the molecular mechanisms underlying host-pathogen interactions, and the development of new diagnostic tools for pathogen monitoring.
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Affiliation(s)
| | | | | | - Robert F. Park
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
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26
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Jost M, Singh D, Lagudah E, Park RF, Dracatos P. Fine mapping of leaf rust resistance gene Rph13 from wild barley. Theor Appl Genet 2020; 133:1887-1895. [PMID: 32123957 DOI: 10.1007/s00122-020-03564-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 02/14/2020] [Indexed: 06/10/2023]
Abstract
Fine mapping of the barley leaf rust resistance locus Rph13 on chromosome 3HL facilitates its use in breeding programs through marker-assisted selection. Barley leaf rust (BLR-caused by Puccinia hordei) is a widespread fungal disease that can be effectively controlled by genetic resistance. There is an ongoing need to both diversify and genetically characterise resistance loci to provide effective and durable control given the ongoing threat of rapidly evolving P. hordei populations. Here, we report on the molecular genetic characterisation of the Rph13 locus, originally derived from wild barley and transferred to barley accession Berac (then referred to as PI 531849). The 2017 reference genome of cv. Morex was used as a road map to rapidly narrow both a genetic and physical intervals around the Rph13 resistance locus. Using recombination-based mapping, we narrowed the physical interval to 116.6 kb on chromosome 3H in a segregating population of a cross of the Rph13 carrying resistant line PI 531849 with the leaf rust-susceptible cultivar Gus. We identified two nucleotide-binding leucine-rich repeat genes as likely candidates for the Rph13 resistance. Sequences from the candidate genes enabled the development of a KASP marker that distinguished resistant and susceptible progeny and was found to be predictive and useful for MAS.
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Affiliation(s)
- Matthias Jost
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Davinder Singh
- Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Evans Lagudah
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Robert F Park
- Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Peter Dracatos
- Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, 2570, Australia.
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27
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Rothwell CT, Singh D, Dracatos PM, Park RF. Inheritance and Characterization of Rph27: A Third Race-Specific Resistance Gene in the Barley Cultivar Quinn. Phytopathology 2020; 110:1067-1073. [PMID: 32096696 DOI: 10.1094/phyto-12-19-0470-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The barley cultivar Quinn was previously reported to carry two genes for resistance to Puccinia hordei, viz. Rph2 and Rph5. In this study, we characterized and mapped a third resistance gene (RphCRQ3) in cultivar Quinn. Multipathotype testing in the greenhouse on a panel of barley genotypes previously postulated to carry Rph2 revealed rare race specificity in four genotypes in response to P. hordei pathotype (pt.) 222 P+ (virulent on Rph2 and Rph5). This suggested either the presence of a race-specific allele variant of Rph2 or the presence of an independent uncharacterized leaf rust resistance locus. A test of allelism on 1,271 F2 Peruvian (Rph2)/Quinn (Rph2 + Rph5) derived seedlings with P. hordei pt. 220 P+ (avirulent on Rph2 and virulent on Rph5) revealed no susceptible segregants. To determine whether the race-specific resistance in Quinn was due to an allele of Rph2 on chromosome 5H or a third uncharacterized resistance gene, we tested the Peruvian/Quinn F3 population with 222 P+ and observed monogenic inheritance. Subsequent bulked segregant analysis indicated the presence of complete in-phase marker fixation near the telomere on the short arm of chromosome 4H, confirming the presence of a third resistance locus in Quinn in addition to Rph2 and Rph5. In accordance with the rules and numbering system of barley gene nomenclature, RphCRQ3 has been designated Rph27.
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Affiliation(s)
- Christopher T Rothwell
- Plant Breeding Institute, School of Life and Environmental Science, University of Sydney, NSW, Australia
| | - Davinder Singh
- Plant Breeding Institute, School of Life and Environmental Science, University of Sydney, NSW, Australia
| | - Peter M Dracatos
- Plant Breeding Institute, School of Life and Environmental Science, University of Sydney, NSW, Australia
| | - Robert F Park
- Plant Breeding Institute, School of Life and Environmental Science, University of Sydney, NSW, Australia
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28
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Talbot JJ, Subedi S, Halliday CL, Hibbs DE, Lai F, Lopez-Ruiz FJ, Harper L, Park RF, Cuddy WS, Biswas C, Cooley L, Carter D, Sorrell TC, Barrs VR, Chen SCA. Surveillance for azole resistance in clinical and environmental isolates of Aspergillus fumigatus in Australia and cyp51A homology modelling of azole-resistant isolates. J Antimicrob Chemother 2019; 73:2347-2351. [PMID: 29846581 DOI: 10.1093/jac/dky187] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/19/2018] [Indexed: 11/14/2022] Open
Abstract
Background The prevalence of azole resistance in Aspergillus fumigatus is uncertain in Australia. Azole exposure may select for resistance. We investigated the frequency of azole resistance in a large number of clinical and environmental isolates. Methods A. fumigatus isolates [148 human, 21 animal and 185 environmental strains from air (n = 6) and azole-exposed (n = 64) or azole-naive (n = 115) environments] were screened for azole resistance using the VIPcheck™ system. MICs were determined using the Sensititre™ YeastOne YO10 assay. Sequencing of the Aspergillus cyp51A gene and promoter region was performed for azole-resistant isolates, and cyp51A homology protein modelling undertaken. Results Non-WT MICs/MICs at the epidemiological cut-off value of one or more azoles were observed for 3/148 (2%) human isolates but not amongst animal, or environmental, isolates. All three isolates grew on at least one azole-supplemented well based on VIPcheck™ screening. For isolates 9 and 32, the itraconazole and posaconazole MICs were 1 mg/L (voriconazole MICs 0.12 mg/L); isolate 129 had itraconazole, posaconazole and voriconazole MICs of >16, 1 and 8 mg/L, respectively. Soil isolates from azole-exposed and azole-naive environments had similar geometric mean MICs of itraconazole, posaconazole and voriconazole (P > 0.05). A G54R mutation was identified in the isolates exhibiting itraconazole and posaconazole resistance, and the TR34/L98H mutation in the pan-azole-resistant isolate. cyp51A modelling predicted that the G54R mutation would prevent binding of itraconazole and posaconazole to the haem complex. Conclusions Azole resistance is uncommon in Australian clinical and environmental A. fumigatus isolates; further surveillance is indicated.
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Affiliation(s)
- Jessica J Talbot
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, New South Wales, Australia
| | - Shradha Subedi
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, New South Wales Health Pathology, Westmead Hospital, The University of Sydney, Westmead, New South Wales, Australia.,Department of Infectious Diseases, Sunshine Coast University Hospital, Queensland, Australia
| | - Catriona L Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, New South Wales Health Pathology, Westmead Hospital, The University of Sydney, Westmead, New South Wales, Australia
| | - David E Hibbs
- Faculty of Pharmacy, The University of Sydney, New South Wales, Australia
| | - Felcia Lai
- Faculty of Pharmacy, The University of Sydney, New South Wales, Australia
| | - Francisco J Lopez-Ruiz
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Lincoln Harper
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Robert F Park
- Judith & David Coffey Chair of Sustainable Agriculture, University of Sydney Plant Breeding Institute Cobbitty, The University of Sydney, New South Wales, Australia
| | - William S Cuddy
- NSW Department of Primary Industries, co-located at the Elizabeth Macarthur Agricultural Institute, Menangle and the University of Sydney's Plant Breeding Institute Cobbitty, The University of Sydney, New South Wales, Australia
| | - Chayanika Biswas
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, New South Wales Health Pathology, Westmead Hospital, The University of Sydney, Westmead, New South Wales, Australia.,The University of Sydney, Marie Bashir Institute for Infectious Diseases and Biosecurity and Westmead Clinical School and The Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Louise Cooley
- Department of Microbiology and Infectious Diseases, Royal Hobart Hospital, Hobart, Tasmania, Australia
| | - Dee Carter
- The University of Sydney, Marie Bashir Institute for Infectious Diseases and Biosecurity and Westmead Clinical School and The Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,School of Life and Environmental Sciences, The University of Sydney, New South Wales, Australia
| | - Tania C Sorrell
- The University of Sydney, Marie Bashir Institute for Infectious Diseases and Biosecurity and Westmead Clinical School and The Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Vanessa R Barrs
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, New South Wales, Australia.,The University of Sydney, Marie Bashir Institute for Infectious Diseases and Biosecurity and Westmead Clinical School and The Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Sharon C-A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, New South Wales Health Pathology, Westmead Hospital, The University of Sydney, Westmead, New South Wales, Australia.,The University of Sydney, Marie Bashir Institute for Infectious Diseases and Biosecurity and Westmead Clinical School and The Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
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Wang E, Dong C, Park RF, Roberts TH. Carotenoid complement of rust spores: Variation among species and pathotype. Phytochemistry 2019; 161:139-148. [PMID: 30836233 DOI: 10.1016/j.phytochem.2019.02.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 01/23/2019] [Accepted: 02/17/2019] [Indexed: 06/09/2023]
Abstract
Rust fungi, which are responsible for some of the world's most destructive plant diseases, are named for the distinctive rusty colour of one or more of their spore forms. Rust spore pigments are thought to provide protection against UV radiation and oxidative stress, and may act as virulence factors. However, with the exception of daisy rust spores, the identity and relative abundance of the carotenoids in the rust spore cytoplasm have not been investigated using modern analytical methods, and little is known about the dependence of the carotenoid complement on species, pathotype, spore-colour mutations and season. We developed and validated a method to separate, identify and quantify rust carotenoids by reversed-phase high-performance liquid chromatography (RP-HPLC) combined with mass spectrometry. The carotenoids identified were lycopene, γ-carotene, β-carotene and phytoene. Rates of carotenoid degradation depended greatly on spore storage conditions, with freezing at -80 °C providing optimal stability. Carotenoid profiles of 103 isolates from 14 rust species were compared, showing that the ratio γ-carotene:β-carotene varied substantially among species. Total carotenoid content was generally lower in spring than in autumn (Sydney, Australia)-possibly due to differences in solar exposure-but the percentage of individual carotenoids was relatively stable. Among the colour mutants tested, chocolate mutants of Puccinia graminis f. sp. tritici (wheat stem rust) contained no carotenoid pigments, while albino mutants of P. striiformis f. sp. tritici (wheat stripe rust) contained only phytoene, a colourless carotenoid. We discuss our results in terms of the biogenesis and biological functions of carotenoids in rust fungi.
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Affiliation(s)
- Erpei Wang
- Plant Breeding Institute, Sydney Institute of Agriculture, University of Sydney, NSW, 2006, Australia
| | - Chongmei Dong
- Plant Breeding Institute, Sydney Institute of Agriculture, University of Sydney, NSW, 2006, Australia
| | - Robert F Park
- Plant Breeding Institute, Sydney Institute of Agriculture, University of Sydney, NSW, 2006, Australia
| | - Thomas H Roberts
- Plant Breeding Institute, Sydney Institute of Agriculture, University of Sydney, NSW, 2006, Australia.
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Dracatos PM, Haghdoust R, Singh RP, Huerta Espino J, Barnes CW, Forrest K, Hayden M, Niks RE, Park RF, Singh D. High-Density Mapping of Triple Rust Resistance in Barley Using DArT-Seq Markers. Front Plant Sci 2019; 10:467. [PMID: 31105717 PMCID: PMC6498947 DOI: 10.3389/fpls.2019.00467] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 03/28/2019] [Indexed: 05/31/2023]
Abstract
The recent availability of an assembled and annotated genome reference sequence for the diploid crop barley (Hordeum vulgare L.) provides new opportunities to study the genetic basis of agronomically important traits such as resistance to stripe [Puccinia striiformis f. sp. hordei (Psh)], leaf [P. hordei (Ph)], and stem [P. graminis f. sp. tritici (Pgt)] rust diseases. The European barley cultivar Pompadour is known to possess high levels of resistance to leaf rust, predominantly due to adult plant resistance (APR) gene Rph20. We developed a barley recombinant inbred line (RIL) population from a cross between Pompadour and the leaf rust and stripe rust susceptible selection Biosaline-19 (B-19), and genotyped this population using DArT-Seq genotyping by sequencing (GBS) markers. In the current study, we produced a high-density linkage map comprising 8,610 (SNP and in silico) markers spanning 5957.6 cM, with the aim of mapping loci for resistance to leaf rust, stem rust, and stripe rust. The RIL population was phenotyped in the field with Psh (Mexico and Ecuador) and Ph (Australia) and in the greenhouse at the seedling stage with Australian Ph and Pgt races, and at Wageningen University with a European variant of Psh race 24 (PshWUR). For Psh, we identified a consistent field QTL on chromosome 2H across all South American field sites and years. Two complementary resistance genes were mapped to chromosomes 1H and 4H at the seedling stage in response to PshWUR, likely to be the loci rpsEm1 and rpsEm2 previously reported from the cultivar Emir from which Pompadour was bred. For leaf rust, we determined that Rph20 in addition to two minor-effect QTL on 1H and 3H were effective at the seedling stage, whilst seedling resistance to stem rust was due to QTL on chromosomes 3H and 7H conferred by Pompadour and B-19, respectively.
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Affiliation(s)
- Peter M. Dracatos
- Plant Breeding Institute Cobbitty, Sydney Institute of Agriculture, The University of Sydney, Sydney, NSW, Australia
| | - Rouja Haghdoust
- Plant Breeding Institute Cobbitty, Sydney Institute of Agriculture, The University of Sydney, Sydney, NSW, Australia
| | - Ravi P. Singh
- International Maize and Wheat Improvement Center, Texcoco, Mexico
- Campo Experimental Valle de México, INIFAP, Chapingo, Mexico
| | - Julio Huerta Espino
- International Maize and Wheat Improvement Center, Texcoco, Mexico
- Campo Experimental Valle de México, INIFAP, Chapingo, Mexico
| | - Charles W. Barnes
- Instituto Nacional de Investigaciones Agropecuarias (INIAP), Quito, Ecuador
| | - Kerrie Forrest
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, La Trobe University, Melbourne, VIC, Australia
| | - Matthew Hayden
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, La Trobe University, Melbourne, VIC, Australia
| | - Rients E. Niks
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Robert F. Park
- Plant Breeding Institute Cobbitty, Sydney Institute of Agriculture, The University of Sydney, Sydney, NSW, Australia
| | - Davinder Singh
- Plant Breeding Institute Cobbitty, Sydney Institute of Agriculture, The University of Sydney, Sydney, NSW, Australia
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31
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Dracatos PM, Bartoš J, Elmansour H, Singh D, Karafiátová M, Zhang P, Steuernagel B, Svačina R, Cobbin JCA, Clark B, Hoxha S, Khatkar MS, Doležel J, Wulff BB, Park RF. The Coiled-Coil NLR Rph1, Confers Leaf Rust Resistance in Barley Cultivar Sudan. Plant Physiol 2019; 179:1362-1372. [PMID: 30593453 PMCID: PMC6446784 DOI: 10.1104/pp.18.01052] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 12/18/2018] [Indexed: 05/18/2023]
Abstract
Unraveling and exploiting mechanisms of disease resistance in cereal crops is currently limited by their large repeat-rich genomes and the lack of genetic recombination or cultivar (cv)-specific sequence information. We cloned the first leaf rust resistance gene Rph1 (Rph1 a) from cultivated barley (Hordeum vulgare) using "MutChromSeq," a recently developed molecular genomics tool for the rapid cloning of genes in plants. Marker-trait association in the CI 9214/Stirling doubled haploid population mapped Rph1 to the short arm of chromosome 2H in a physical region of 1.3 megabases relative to the barley cv Morex reference assembly. A sodium azide mutant population in cv Sudan was generated and 10 mutants were confirmed by progeny-testing. Flow-sorted 2H chromosomes from Sudan (wild type) and six of the mutants were sequenced and compared to identify candidate genes for the Rph1 locus. MutChromSeq identified a single gene candidate encoding a coiled-coil nucleotide binding site Leucine-rich repeat (NLR) receptor protein that was altered in three different mutants. Further Sanger sequencing confirmed all three mutations and identified an additional two independent mutations within the same candidate gene. Phylogenetic analysis determined that Rph1 clustered separately from all previously cloned NLRs from the Triticeae and displayed highest sequence similarity (89%) with a homolog of the Arabidopsis (Arabidopsis thaliana) disease resistance protein 1 protein in Triticum urartu In this study we determined the molecular basis for Rph1-mediated resistance in cultivated barley enabling varietal improvement through diagnostic marker design, gene editing, and gene stacking technologies.
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Affiliation(s)
- Peter Michael Dracatos
- Sydney Institute of Agriculture, Plant Breeding Institute, The University of Sydney, Narellan, NSW 2567, Australia
| | - Jan Bartoš
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc CZ-78371, Czech Republic
| | - Huda Elmansour
- Sydney Institute of Agriculture, Plant Breeding Institute, The University of Sydney, Narellan, NSW 2567, Australia
| | - Davinder Singh
- Sydney Institute of Agriculture, Plant Breeding Institute, The University of Sydney, Narellan, NSW 2567, Australia
| | - Miroslava Karafiátová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc CZ-78371, Czech Republic
| | - Peng Zhang
- Sydney Institute of Agriculture, Plant Breeding Institute, The University of Sydney, Narellan, NSW 2567, Australia
| | | | - Radim Svačina
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc CZ-78371, Czech Republic
| | - Joanna C A Cobbin
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Bethany Clark
- Sydney Institute of Agriculture, Plant Breeding Institute, The University of Sydney, Narellan, NSW 2567, Australia
| | - Sami Hoxha
- Sydney Institute of Agriculture, Plant Breeding Institute, The University of Sydney, Narellan, NSW 2567, Australia
| | - Mehar S Khatkar
- Faculty of Veterinary Science, The University of Sydney, Camden, NSW 2570, Australia
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc CZ-78371, Czech Republic
| | | | - Robert F Park
- Sydney Institute of Agriculture, Plant Breeding Institute, The University of Sydney, Narellan, NSW 2567, Australia
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Visser B, Meyer M, Park RF, Gilligan CA, Burgin LE, Hort MC, Hodson DP, Pretorius ZA. Microsatellite Analysis and Urediniospore Dispersal Simulations Support the Movement of Puccinia graminis f. sp. tritici from Southern Africa to Australia. Phytopathology 2019; 109:133-144. [PMID: 30028232 DOI: 10.1094/phyto-04-18-0110-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The Australian wheat stem rust (Puccinia graminis f. sp. tritici) population was shaped by the introduction of four exotic incursions into the country. It was previously hypothesized that at least two of these (races 326-1,2,3,5,6 and 194-1,2,3,5,6 first detected in 1969) had an African origin and moved across the Indian Ocean to Australia on high-altitude winds. We provide strong supportive evidence for this hypothesis by combining genetic analyses and complex atmospheric dispersion modeling. Genetic analysis of 29 Australian and South African P. graminis f. sp. tritici races using microsatellite markers confirmed the close genetic relationship between the South African and Australian populations, thereby confirming previously described phenotypic similarities. Lagrangian particle dispersion model simulations using finely resolved meteorological data showed that long distance dispersal events between southern Africa and Australia are indeed possible, albeit rare. Simulated urediniospore transmission events were most frequent from central South Africa (viable spore transmission on approximately 7% of all simulated release days) compared with other potential source regions in southern Africa. The study acts as a warning of possible future P. graminis f. sp. tritici dispersal events from southern Africa to Australia, which could include members of the Ug99 race group, emphasizing the need for continued surveillance on both continents.
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Affiliation(s)
- Botma Visser
- First and eighth authors: Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa; second and fourth authors: Epidemiology and Modelling Group, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK; third author: Plant Breeding Institute Cobbitty, The University of Sydney, Private Mail Bag 11, Camden, NSW 2570, Australia; fifth and sixth authors: Atmospheric Dispersion and Air Quality (ADAQ), Met Office, Exeter, EX1 3PB, UK; and seventh author: International Maize and Wheat Improvement Center (CIMMYT), P.O. Box 5689, Addis Ababa, Ethiopia
| | - Marcel Meyer
- First and eighth authors: Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa; second and fourth authors: Epidemiology and Modelling Group, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK; third author: Plant Breeding Institute Cobbitty, The University of Sydney, Private Mail Bag 11, Camden, NSW 2570, Australia; fifth and sixth authors: Atmospheric Dispersion and Air Quality (ADAQ), Met Office, Exeter, EX1 3PB, UK; and seventh author: International Maize and Wheat Improvement Center (CIMMYT), P.O. Box 5689, Addis Ababa, Ethiopia
| | - Robert F Park
- First and eighth authors: Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa; second and fourth authors: Epidemiology and Modelling Group, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK; third author: Plant Breeding Institute Cobbitty, The University of Sydney, Private Mail Bag 11, Camden, NSW 2570, Australia; fifth and sixth authors: Atmospheric Dispersion and Air Quality (ADAQ), Met Office, Exeter, EX1 3PB, UK; and seventh author: International Maize and Wheat Improvement Center (CIMMYT), P.O. Box 5689, Addis Ababa, Ethiopia
| | - Christopher A Gilligan
- First and eighth authors: Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa; second and fourth authors: Epidemiology and Modelling Group, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK; third author: Plant Breeding Institute Cobbitty, The University of Sydney, Private Mail Bag 11, Camden, NSW 2570, Australia; fifth and sixth authors: Atmospheric Dispersion and Air Quality (ADAQ), Met Office, Exeter, EX1 3PB, UK; and seventh author: International Maize and Wheat Improvement Center (CIMMYT), P.O. Box 5689, Addis Ababa, Ethiopia
| | - Laura E Burgin
- First and eighth authors: Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa; second and fourth authors: Epidemiology and Modelling Group, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK; third author: Plant Breeding Institute Cobbitty, The University of Sydney, Private Mail Bag 11, Camden, NSW 2570, Australia; fifth and sixth authors: Atmospheric Dispersion and Air Quality (ADAQ), Met Office, Exeter, EX1 3PB, UK; and seventh author: International Maize and Wheat Improvement Center (CIMMYT), P.O. Box 5689, Addis Ababa, Ethiopia
| | - Matthew C Hort
- First and eighth authors: Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa; second and fourth authors: Epidemiology and Modelling Group, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK; third author: Plant Breeding Institute Cobbitty, The University of Sydney, Private Mail Bag 11, Camden, NSW 2570, Australia; fifth and sixth authors: Atmospheric Dispersion and Air Quality (ADAQ), Met Office, Exeter, EX1 3PB, UK; and seventh author: International Maize and Wheat Improvement Center (CIMMYT), P.O. Box 5689, Addis Ababa, Ethiopia
| | - David P Hodson
- First and eighth authors: Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa; second and fourth authors: Epidemiology and Modelling Group, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK; third author: Plant Breeding Institute Cobbitty, The University of Sydney, Private Mail Bag 11, Camden, NSW 2570, Australia; fifth and sixth authors: Atmospheric Dispersion and Air Quality (ADAQ), Met Office, Exeter, EX1 3PB, UK; and seventh author: International Maize and Wheat Improvement Center (CIMMYT), P.O. Box 5689, Addis Ababa, Ethiopia
| | - Zacharias A Pretorius
- First and eighth authors: Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa; second and fourth authors: Epidemiology and Modelling Group, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK; third author: Plant Breeding Institute Cobbitty, The University of Sydney, Private Mail Bag 11, Camden, NSW 2570, Australia; fifth and sixth authors: Atmospheric Dispersion and Air Quality (ADAQ), Met Office, Exeter, EX1 3PB, UK; and seventh author: International Maize and Wheat Improvement Center (CIMMYT), P.O. Box 5689, Addis Ababa, Ethiopia
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Gilbert B, Bettgenhaeuser J, Upadhyaya N, Soliveres M, Singh D, Park RF, Moscou MJ, Ayliffe M. Components of Brachypodium distachyon resistance to nonadapted wheat stripe rust pathogens are simply inherited. PLoS Genet 2018; 14:e1007636. [PMID: 30265668 PMCID: PMC6161853 DOI: 10.1371/journal.pgen.1007636] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 08/15/2018] [Indexed: 11/19/2022] Open
Abstract
Phytopathogens have a limited range of host plant species that they can successfully parasitise ie. that they are adapted for. Infection of plants by nonadapted pathogens often results in an active resistance response that is relatively poorly characterised because phenotypic variation in this response often does not exist within a plant species, or is too subtle for genetic dissection. In addition, complex polygenic inheritance often underlies these resistance phenotypes and mutagenesis often does not impact upon this resistance, presumably due to genetic or mechanistic redundancy. Here it is demonstrated that phenotypic differences in the resistance response of Brachypodium distachyon to the nonadapted wheat stripe rust pathogen Puccinia striiformis f. sp. tritici (Pst) are genetically tractable and simply inherited. Two dominant loci were identified on B. distachyon chromosome 4 that each reduce attempted Pst colonisation compared with sib and parent lines without these loci. One locus (Yrr1) is effective against diverse Australian Pst isolates and present in two B. distachyon mapping families as a conserved region that was reduced to 5 candidate genes by fine mapping. A second locus, Yrr2, shows Pst race-specificity and encodes a disease resistance gene family typically associated with host plant resistance. These data indicate that some components of resistance to nonadapted pathogens are genetically tractable in some instances and may mechanistically overlap with host plant resistance to avirulent adapted pathogens.
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Affiliation(s)
- Brian Gilbert
- CSIRO Agriculture and Food, Clunies Ross Drive, Canberra, ACT, Australia
| | - Jan Bettgenhaeuser
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Narayana Upadhyaya
- CSIRO Agriculture and Food, Clunies Ross Drive, Canberra, ACT, Australia
| | - Melanie Soliveres
- CSIRO Agriculture and Food, Clunies Ross Drive, Canberra, ACT, Australia
| | - Davinder Singh
- University of Sydney, Plant Breeding Institute, Cobbitty, NSW, Australia
| | - Robert F. Park
- University of Sydney, Plant Breeding Institute, Cobbitty, NSW, Australia
| | - Matthew J. Moscou
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
- University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Michael Ayliffe
- CSIRO Agriculture and Food, Clunies Ross Drive, Canberra, ACT, Australia
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Wang E, Dong C, Park RF, Roberts TH. Carotenoid pigments in rust fungi: Extraction, separation, quantification and characterisation. FUNGAL BIOL REV 2018. [DOI: 10.1016/j.fbr.2018.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Tobias PA, Guest DI, Külheim C, Park RF. De Novo Transcriptome Study Identifies Candidate Genes Involved in Resistance to Austropuccinia psidii (Myrtle Rust) in Syzygium luehmannii (Riberry). Phytopathology 2018; 108:627-640. [PMID: 29231777 DOI: 10.1094/phyto-09-17-0298-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Austropuccinia psidii, causal agent of myrtle rust, was discovered in Australia in 2010 and has since become established on a wide range of species within the family Myrtaceae. Syzygium luehmannii, endemic to Australia, is an increasingly valuable berry crop. Plants were screened for responses to A. psidii inoculation, and specific resistance, in the form of localized necrosis, was determined in 29% of individuals. To understand the molecular basis underlying this response, mRNA was sequenced from leaf samples taken preinoculation, and at 24 and 48 h postinoculation, from four resistant and four susceptible plants. Analyses, based on de novo transcriptome assemblies for all plants, identified significant expression changes in resistant plants (438 transcripts) 48 h after pathogen exposure compared with susceptible plants (three transcripts). Most significantly up-regulated in resistant plants were gene homologs for transcription factors, receptor-like kinases, and enzymes involved in secondary metabolite pathways. A putative G-type lectin receptor-like kinase was exclusively expressed in resistant individuals and two transcripts incorporating toll/interleukin-1, nucleotide binding site, and leucine-rich repeat domains were up-regulated in resistant plants. The results of this study provide the first early gene expression profiles for a plant of the family Myrtaceae in response to the myrtle rust pathogen.
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Affiliation(s)
- Peri A Tobias
- First and second authors: Sydney Institute of Agriculture, School of Life and Environmental Sciences, University of Sydney, Biomedical Building C81, 1 Central Ave., Australian Technology Park, Eveleigh, NSW 2015, Australia; third author: Research School of Biology, College of Sciences, Australian National University, Canberra, ACT 2601, Australia; and fourth author: Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Private Bag 4011, Narellan, NSW 2567, Australia
| | - David I Guest
- First and second authors: Sydney Institute of Agriculture, School of Life and Environmental Sciences, University of Sydney, Biomedical Building C81, 1 Central Ave., Australian Technology Park, Eveleigh, NSW 2015, Australia; third author: Research School of Biology, College of Sciences, Australian National University, Canberra, ACT 2601, Australia; and fourth author: Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Private Bag 4011, Narellan, NSW 2567, Australia
| | - Carsten Külheim
- First and second authors: Sydney Institute of Agriculture, School of Life and Environmental Sciences, University of Sydney, Biomedical Building C81, 1 Central Ave., Australian Technology Park, Eveleigh, NSW 2015, Australia; third author: Research School of Biology, College of Sciences, Australian National University, Canberra, ACT 2601, Australia; and fourth author: Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Private Bag 4011, Narellan, NSW 2567, Australia
| | - Robert F Park
- First and second authors: Sydney Institute of Agriculture, School of Life and Environmental Sciences, University of Sydney, Biomedical Building C81, 1 Central Ave., Australian Technology Park, Eveleigh, NSW 2015, Australia; third author: Research School of Biology, College of Sciences, Australian National University, Canberra, ACT 2601, Australia; and fourth author: Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Private Bag 4011, Narellan, NSW 2567, Australia
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36
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Nazareno ES, Li F, Smith M, Park RF, Kianian SF, Figueroa M. Puccinia coronata f. sp. avenae: a threat to global oat production. Mol Plant Pathol 2018; 19:1047-1060. [PMID: 28846186 PMCID: PMC6638059 DOI: 10.1111/mpp.12608] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/24/2017] [Accepted: 08/24/2017] [Indexed: 05/20/2023]
Abstract
UNLABELLED Puccinia coronata f. sp. avenae (Pca) causes crown rust disease in cultivated and wild oat (Avena spp.). The significant yield losses inflicted by this pathogen make crown rust the most devastating disease in the oat industry. Pca is a basidiomycete fungus with an obligate biotrophic lifestyle, and is classified as a typical macrocyclic and heteroecious fungus. The asexual phase in the life cycle of Pca occurs in oat, whereas the sexual phase takes place primarily in Rhamnus species as the alternative host. Epidemics of crown rust happens in areas with warm temperatures (20-25 °C) and high humidity. Infection by the pathogen leads to plant lodging and shrivelled grain of poor quality. Disease symptoms: Infection of susceptible oat varieties gives rise to orange-yellow round to oblong uredinia (pustules) containing newly formed urediniospores. Pustules vary in size and can be larger than 5 mm in length. Infection occurs primarily on the surfaces of leaves, although occasional symptoms develop in the oat leaf sheaths and/or floral structures, such as awns. Symptoms in resistant oat varieties vary from flecks to small pustules, typically accompanied by chlorotic halos and/or necrosis. The pycnial and aecial stages are mostly present in the leaves of Rhamnus species, but occasionally symptoms can also be observed in petioles, young stems and floral structures. Aecial structures display a characteristic hypertrophy and can differ in size, occasionally reaching more than 5 mm in diameter. Taxonomy: Pca belongs to the kingdom Fungi, phylum Basidiomycota, class Pucciniomycetes, order Pucciniales and family Pucciniaceae. Host range: Puccinia coronata sensu lato can infect 290 species of grass hosts. Pca is prevalent in all oat-growing regions and, compared with other cereal rusts, displays a broad telial host range. The most common grass hosts of Pca include cultivated hexaploid oat (Avena sativa) and wild relatives, such as bluejoint grass, perennial ryegrass and fescue. Alternative hosts include several species of Rhamnus, with R. cathartica (common buckthorn) as the most important alternative host in Europe and North America. CONTROL Most crown rust management strategies involve the use of rust-resistant crop varieties and the application of fungicides. The attainment of the durability of resistance against Pca is difficult as it is a highly variable pathogen with a great propensity to overcome the genetic resistance of varieties. Thus, adult plant resistance is often exploited in oat breeding programmes to develop new crown rust-resistant varieties. Useful website: https://www.ars.usda.gov/midwest-area/st-paul-mn/cereal-disease-lab/docs/cereal-rusts/race-surveys/.
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Affiliation(s)
- Eric S. Nazareno
- Department of Plant PathologyUniversity of MinnesotaSt. PaulMN 55108USA
| | - Feng Li
- Department of Plant PathologyUniversity of MinnesotaSt. PaulMN 55108USA
| | - Madeleine Smith
- Department of Plant PathologyUniversity of Minnesota‐Northwest Research and Outreach CenterCrookstonMN 56716USA
| | - Robert F. Park
- Plant Breeding InstituteThe University of SydneyNarellanNSW2567Australia
| | - Shahryar F. Kianian
- Cereal Disease Laboratory, US Department of Agriculture‐Agricultural Research ServiceSt. PaulMN 55108USA
| | - Melania Figueroa
- Department of Plant PathologyUniversity of MinnesotaSt. PaulMN 55108USA
- Stakman‐Borlaug Center for Sustainable Plant HealthUniversity of MinnesotaSt. PaulMN 55108USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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38
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Chen J, Upadhyaya NM, Ortiz D, Sperschneider J, Li F, Bouton C, Breen S, Dong C, Xu B, Zhang X, Mago R, Newell K, Xia X, Bernoux M, Taylor JM, Steffenson B, Jin Y, Zhang P, Kanyuka K, Figueroa M, Ellis JG, Park RF, Dodds PN. Loss of AvrSr50 by somatic exchange in stem rust leads to virulence for Sr50 resistance in wheat. Science 2018; 358:1607-1610. [PMID: 29269475 DOI: 10.1126/science.aao4810] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/03/2017] [Indexed: 01/03/2023]
Abstract
Race-specific resistance genes protect the global wheat crop from stem rust disease caused by Puccinia graminis f. sp. tritici (Pgt) but are often overcome owing to evolution of new virulent races of the pathogen. To understand virulence evolution in Pgt, we identified the protein ligand (AvrSr50) recognized by the Sr50 resistance protein. A spontaneous mutant of Pgt virulent to Sr50 contained a 2.5 mega-base pair loss-of-heterozygosity event. A haustorial secreted protein from this region triggers Sr50-dependent defense responses in planta and interacts directly with the Sr50 protein. Virulence alleles of AvrSr50 have arisen through DNA insertion and sequence divergence, and our data provide molecular evidence that in addition to sexual recombination, somatic exchange can play a role in the emergence of new virulence traits in Pgt.
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Affiliation(s)
- Jiapeng Chen
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia.,Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia.,Judith and David Coffey Life Lab, Charles Perkins Centre, University of Sydney
| | - Narayana M Upadhyaya
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Diana Ortiz
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Jana Sperschneider
- Centre for Environment and Life Sciences, Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Perth, WA, Australia
| | - Feng Li
- Department of Plant Pathology and The Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
| | - Clement Bouton
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Susan Breen
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Chongmei Dong
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia
| | - Bo Xu
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Xiaoxiao Zhang
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Rohit Mago
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Kim Newell
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Xiaodi Xia
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Maud Bernoux
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Jennifer M Taylor
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Brian Steffenson
- Department of Plant Pathology and The Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
| | - Yue Jin
- Department of Plant Pathology and The Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA.,United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Cereal Disease Laboratory, St. Paul, MN, USA
| | - Peng Zhang
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia
| | - Kostya Kanyuka
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Melania Figueroa
- Department of Plant Pathology and The Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
| | - Jeffrey G Ellis
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Robert F Park
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
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Schwessinger B, Sperschneider J, Cuddy WS, Garnica DP, Miller ME, Taylor JM, Dodds PN, Figueroa M, Park RF, Rathjen JP. A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity. mBio 2018; 9:e02275-17. [PMID: 29463659 PMCID: PMC5821087 DOI: 10.1128/mbio.02275-17] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 01/09/2018] [Indexed: 01/01/2023] Open
Abstract
A long-standing biological question is how evolution has shaped the genomic architecture of dikaryotic fungi. To answer this, high-quality genomic resources that enable haplotype comparisons are essential. Short-read genome assemblies for dikaryotic fungi are highly fragmented and lack haplotype-specific information due to the high heterozygosity and repeat content of these genomes. Here, we present a diploid-aware assembly of the wheat stripe rust fungus Puccinia striiformis f. sp. tritici based on long reads using the FALCON-Unzip assembler. Transcriptome sequencing data sets were used to infer high-quality gene models and identify virulence genes involved in plant infection referred to as effectors. This represents the most complete Puccinia striiformis f. sp. tritici genome assembly to date (83 Mb, 156 contigs, N50 of 1.5 Mb) and provides phased haplotype information for over 92% of the genome. Comparisons of the phase blocks revealed high interhaplotype diversity of over 6%. More than 25% of all genes lack a clear allelic counterpart. When we investigated genome features that potentially promote the rapid evolution of virulence, we found that candidate effector genes are spatially associated with conserved genes commonly found in basidiomycetes. Yet, candidate effectors that lack an allelic counterpart are more distant from conserved genes than allelic candidate effectors and are less likely to be evolutionarily conserved within the P. striiformis species complex and Pucciniales In summary, this haplotype-phased assembly enabled us to discover novel genome features of a dikaryotic plant-pathogenic fungus previously hidden in collapsed and fragmented genome assemblies.IMPORTANCE Current representations of eukaryotic microbial genomes are haploid, hiding the genomic diversity intrinsic to diploid and polyploid life forms. This hidden diversity contributes to the organism's evolutionary potential and ability to adapt to stress conditions. Yet, it is challenging to provide haplotype-specific information at a whole-genome level. Here, we take advantage of long-read DNA sequencing technology and a tailored-assembly algorithm to disentangle the two haploid genomes of a dikaryotic pathogenic wheat rust fungus. The two genomes display high levels of nucleotide and structural variations, which lead to allelic variation and the presence of genes lacking allelic counterparts. Nonallelic candidate effector genes, which likely encode important pathogenicity factors, display distinct genome localization patterns and are less likely to be evolutionary conserved than those which are present as allelic pairs. This genomic diversity may promote rapid host adaptation and/or be related to the age of the sequenced isolate since last meiosis.
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Affiliation(s)
- Benjamin Schwessinger
- Research School of Biology, the Australian National University, Acton, ACT, Australia
| | - Jana Sperschneider
- Centre for Environment and Life Sciences, CSIRO Agriculture and Food, Perth, WA, Australia
| | - William S Cuddy
- Plant Breeding Institute, Faculty of Agriculture and Environment, the University of Sydney, Narellan, NSW, Australia
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - Diana P Garnica
- Research School of Biology, the Australian National University, Acton, ACT, Australia
| | - Marisa E Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Jennifer M Taylor
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Peter N Dodds
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Melania Figueroa
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, Minnesota, USA
| | - Robert F Park
- Plant Breeding Institute, Faculty of Agriculture and Environment, the University of Sydney, Narellan, NSW, Australia
| | - John P Rathjen
- Research School of Biology, the Australian National University, Acton, ACT, Australia
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40
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Miller ME, Zhang Y, Omidvar V, Sperschneider J, Schwessinger B, Raley C, Palmer JM, Garnica D, Upadhyaya N, Rathjen J, Taylor JM, Park RF, Dodds PN, Hirsch CD, Kianian SF, Figueroa M. De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates of Puccinia coronata f. sp. avenae, the Causal Agent of Oat Crown Rust. mBio 2018; 9:e01650-17. [PMID: 29463655 PMCID: PMC5821079 DOI: 10.1128/mbio.01650-17] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 01/09/2018] [Indexed: 01/18/2023] Open
Abstract
Oat crown rust, caused by the fungus Pucinnia coronata f. sp. avenae, is a devastating disease that impacts worldwide oat production. For much of its life cycle, P. coronata f. sp. avenae is dikaryotic, with two separate haploid nuclei that may vary in virulence genotype, highlighting the importance of understanding haplotype diversity in this species. We generated highly contiguous de novo genome assemblies of two P. coronata f. sp. avenae isolates, 12SD80 and 12NC29, from long-read sequences. In total, we assembled 603 primary contigs for 12SD80, for a total assembly length of 99.16 Mbp, and 777 primary contigs for 12NC29, for a total length of 105.25 Mbp; approximately 52% of each genome was assembled into alternate haplotypes. This revealed structural variation between haplotypes in each isolate equivalent to more than 2% of the genome size, in addition to about 260,000 and 380,000 heterozygous single-nucleotide polymorphisms in 12SD80 and 12NC29, respectively. Transcript-based annotation identified 26,796 and 28,801 coding sequences for isolates 12SD80 and 12NC29, respectively, including about 7,000 allele pairs in haplotype-phased regions. Furthermore, expression profiling revealed clusters of coexpressed secreted effector candidates, and the majority of orthologous effectors between isolates showed conservation of expression patterns. However, a small subset of orthologs showed divergence in expression, which may contribute to differences in virulence between 12SD80 and 12NC29. This study provides the first haplotype-phased reference genome for a dikaryotic rust fungus as a foundation for future studies into virulence mechanisms in P. coronata f. sp. avenaeIMPORTANCE Disease management strategies for oat crown rust are challenged by the rapid evolution of Puccinia coronata f. sp. avenae, which renders resistance genes in oat varieties ineffective. Despite the economic importance of understanding P. coronata f. sp. avenae, resources to study the molecular mechanisms underpinning pathogenicity and the emergence of new virulence traits are lacking. Such limitations are partly due to the obligate biotrophic lifestyle of P. coronata f. sp. avenae as well as the dikaryotic nature of the genome, features that are also shared with other important rust pathogens. This study reports the first release of a haplotype-phased genome assembly for a dikaryotic fungal species and demonstrates the amenability of using emerging technologies to investigate genetic diversity in populations of P. coronata f. sp. avenae.
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Affiliation(s)
- Marisa E Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Ying Zhang
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota, USA
| | - Vahid Omidvar
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Jana Sperschneider
- Centre for Environment and Life Sciences, Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Perth, WA, Australia
| | - Benjamin Schwessinger
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Castle Raley
- Leidos Biomedical Research, Frederick, Maryland, USA
| | - Jonathan M Palmer
- Center for Forest Mycology Research, Northern Research Station, USDA Forest Service, Madison, Wisconsin, USA
| | - Diana Garnica
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, Australia
| | - Narayana Upadhyaya
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, Australia
| | - John Rathjen
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Jennifer M Taylor
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, Australia
| | - Robert F Park
- Plant Breeding Institute, Faculty of Agriculture and Environment, School of Life and Environmental Sciences, University of Sydney, Narellan, NSW, Australia
| | - Peter N Dodds
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, Australia
| | - Cory D Hirsch
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Shahryar F Kianian
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
- USDA-ARS Cereal Disease Laboratory, St. Paul, Minnesota, USA
| | - Melania Figueroa
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, Minnesota, USA
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41
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Watson A, Ghosh S, Williams MJ, Cuddy WS, Simmonds J, Rey MD, Asyraf Md Hatta M, Hinchliffe A, Steed A, Reynolds D, Adamski NM, Breakspear A, Korolev A, Rayner T, Dixon LE, Riaz A, Martin W, Ryan M, Edwards D, Batley J, Raman H, Carter J, Rogers C, Domoney C, Moore G, Harwood W, Nicholson P, Dieters MJ, DeLacy IH, Zhou J, Uauy C, Boden SA, Park RF, Wulff BBH, Hickey LT. Speed breeding is a powerful tool to accelerate crop research and breeding. Nat Plants 2018; 4:23-29. [PMID: 29292376 DOI: 10.1038/s41477-017-0083-8] [Citation(s) in RCA: 375] [Impact Index Per Article: 62.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 11/28/2017] [Indexed: 05/18/2023]
Abstract
The growing human population and a changing environment have raised significant concern for global food security, with the current improvement rate of several important crops inadequate to meet future demand 1 . This slow improvement rate is attributed partly to the long generation times of crop plants. Here, we present a method called 'speed breeding', which greatly shortens generation time and accelerates breeding and research programmes. Speed breeding can be used to achieve up to 6 generations per year for spring wheat (Triticum aestivum), durum wheat (T. durum), barley (Hordeum vulgare), chickpea (Cicer arietinum) and pea (Pisum sativum), and 4 generations for canola (Brassica napus), instead of 2-3 under normal glasshouse conditions. We demonstrate that speed breeding in fully enclosed, controlled-environment growth chambers can accelerate plant development for research purposes, including phenotyping of adult plant traits, mutant studies and transformation. The use of supplemental lighting in a glasshouse environment allows rapid generation cycling through single seed descent (SSD) and potential for adaptation to larger-scale crop improvement programs. Cost saving through light-emitting diode (LED) supplemental lighting is also outlined. We envisage great potential for integrating speed breeding with other modern crop breeding technologies, including high-throughput genotyping, genome editing and genomic selection, accelerating the rate of crop improvement.
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Affiliation(s)
- Amy Watson
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, Queensland, Australia
| | - Sreya Ghosh
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Matthew J Williams
- Plant Breeding Institute, University of Sydney, Cobbitty, New South Wales, Australia
| | - William S Cuddy
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales, Australia
| | | | | | - M Asyraf Md Hatta
- John Innes Centre, Norwich Research Park, Norwich, UK
- Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Malaysia
| | | | - Andrew Steed
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | | | | | - Tracey Rayner
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Laura E Dixon
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Adnan Riaz
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, Queensland, Australia
| | - William Martin
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, Queensland, Australia
| | - Merrill Ryan
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, Queensland, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, Western Australia, Australia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, Western Australia, Australia
| | - Harsh Raman
- Wagga Wagga Agricultural Institute, NSW Department of Primary Industries, Wagga Wagga, New South Wales, Australia
| | - Jeremy Carter
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | - Graham Moore
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Wendy Harwood
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Mark J Dieters
- School of Agriculture and Food Sciences, University of Queensland, St Lucia, Queensland, Australia
| | - Ian H DeLacy
- School of Agriculture and Food Sciences, University of Queensland, St Lucia, Queensland, Australia
| | - Ji Zhou
- John Innes Centre, Norwich Research Park, Norwich, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | | | - Scott A Boden
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Robert F Park
- Plant Breeding Institute, University of Sydney, Cobbitty, New South Wales, Australia
| | | | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, Queensland, Australia.
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42
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Watson A, Ghosh S, Williams MJ, Cuddy WS, Simmonds J, Rey MD, Asyraf Md Hatta M, Hinchliffe A, Steed A, Reynolds D, Adamski NM, Breakspear A, Korolev A, Rayner T, Dixon LE, Riaz A, Martin W, Ryan M, Edwards D, Batley J, Raman H, Carter J, Rogers C, Domoney C, Moore G, Harwood W, Nicholson P, Dieters MJ, DeLacy IH, Zhou J, Uauy C, Boden SA, Park RF, Wulff BBH, Hickey LT. Speed breeding is a powerful tool to accelerate crop research and breeding. Nat Plants 2018; 4:23-29. [PMID: 29292376 DOI: 10.1038/s41477-017-0083-88] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 11/28/2017] [Indexed: 05/20/2023]
Abstract
The growing human population and a changing environment have raised significant concern for global food security, with the current improvement rate of several important crops inadequate to meet future demand 1 . This slow improvement rate is attributed partly to the long generation times of crop plants. Here, we present a method called 'speed breeding', which greatly shortens generation time and accelerates breeding and research programmes. Speed breeding can be used to achieve up to 6 generations per year for spring wheat (Triticum aestivum), durum wheat (T. durum), barley (Hordeum vulgare), chickpea (Cicer arietinum) and pea (Pisum sativum), and 4 generations for canola (Brassica napus), instead of 2-3 under normal glasshouse conditions. We demonstrate that speed breeding in fully enclosed, controlled-environment growth chambers can accelerate plant development for research purposes, including phenotyping of adult plant traits, mutant studies and transformation. The use of supplemental lighting in a glasshouse environment allows rapid generation cycling through single seed descent (SSD) and potential for adaptation to larger-scale crop improvement programs. Cost saving through light-emitting diode (LED) supplemental lighting is also outlined. We envisage great potential for integrating speed breeding with other modern crop breeding technologies, including high-throughput genotyping, genome editing and genomic selection, accelerating the rate of crop improvement.
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Affiliation(s)
- Amy Watson
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, Queensland, Australia
| | - Sreya Ghosh
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Matthew J Williams
- Plant Breeding Institute, University of Sydney, Cobbitty, New South Wales, Australia
| | - William S Cuddy
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales, Australia
| | | | | | - M Asyraf Md Hatta
- John Innes Centre, Norwich Research Park, Norwich, UK
- Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Malaysia
| | | | - Andrew Steed
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | | | | | - Tracey Rayner
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Laura E Dixon
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Adnan Riaz
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, Queensland, Australia
| | - William Martin
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, Queensland, Australia
| | - Merrill Ryan
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, Queensland, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, Western Australia, Australia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, Western Australia, Australia
| | - Harsh Raman
- Wagga Wagga Agricultural Institute, NSW Department of Primary Industries, Wagga Wagga, New South Wales, Australia
| | - Jeremy Carter
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | - Graham Moore
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Wendy Harwood
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Mark J Dieters
- School of Agriculture and Food Sciences, University of Queensland, St Lucia, Queensland, Australia
| | - Ian H DeLacy
- School of Agriculture and Food Sciences, University of Queensland, St Lucia, Queensland, Australia
| | - Ji Zhou
- John Innes Centre, Norwich Research Park, Norwich, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | | | - Scott A Boden
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Robert F Park
- Plant Breeding Institute, University of Sydney, Cobbitty, New South Wales, Australia
| | | | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, Queensland, Australia.
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43
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Ziems LA, Franckowiak JD, Platz GJ, Mace ES, Park RF, Singh D, Jordan DR, Hickey LT. Investigating successive Australian barley breeding populations for stable resistance to leaf rust. Theor Appl Genet 2017; 130:2463-2477. [PMID: 28836114 DOI: 10.1007/s00122-017-2970-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 08/14/2017] [Indexed: 06/07/2023]
Abstract
Genome-wide association studies of barley breeding populations identified candidate minor genes for pairing with the adult plant resistance gene Rph20 to provide stable leaf rust resistance across environments. Stable resistance to barley leaf rust (BLR, caused by Puccinia hordei) was evaluated across environments in barley breeding populations (BPs). To identify genomic regions that can be combined with Rph20 to improve adult plant resistance (APR), two BPs genotyped with the Diversity Arrays Technology genotyping-by-sequencing platform (DArT-seq) were examined for reaction to BLR at both seedling and adult growth stages in Australian environments. An integrated consensus map comprising both first- and second-generation DArT platforms was used to integrate QTL information across two additional BPs, providing a total of four interrelated BPs and 15 phenotypic data sets. This enabled identification of key loci underpinning BLR resistance. The APR gene Rph20 was the only active resistance region consistently detected across BPs. Of the QTL identified, RphQ27 on chromosome 6HL was considered the best candidate for pairing with Rph20. RphQ27 did not align or share proximity with known genes and was detected in three of the four BPs. The combination of RphQ27 and Rph20 was of low frequency in the breeding material; however, strong resistance responses were observed for the lines carrying this pairing. This suggests that the candidate minor gene RphQ27 can interact additively with Rph20 to provide stable resistance to BLR across diverse environments.
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Affiliation(s)
- L A Ziems
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia.
| | - J D Franckowiak
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN, 55108, USA
| | - G J Platz
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - E S Mace
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - R F Park
- The University of Sydney, Plant Breeding Institute, Narellan, NSW, 2567, Australia
| | - D Singh
- The University of Sydney, Plant Breeding Institute, Narellan, NSW, 2567, Australia
| | - D R Jordan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - L T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
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Zhang J, Zhang P, Karaoglu H, Park RF. Molecular Characterization of Australian Isolates of Puccinia graminis f. sp. tritici Supports Long-Term Clonality but also Reveals Cryptic Genetic Variation. Phytopathology 2017; 107:1032-1038. [PMID: 28513283 DOI: 10.1094/phyto-09-16-0334-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Long-term surveys of pathogenicity in Puccinia graminis f. sp. tritici in Australia have implicated mutation as a major source of virulence, at times leading to the demise of stem-rust-resistant wheat cultivars and substantial yield losses. Since 1925, these surveys have identified at least four occasions on which exotic isolates of P. graminis f. sp. tritici appeared in Australia, with each acting as a founding isolate that gave rise sequentially to derivative pathotypes via presumed single-step mutation. The current study examined the relationship between virulence and molecular patterns using simple-sequence repeat (SSR) markers on selected isolates of P. graminis f. sp. tritici collected in Australia during a 52-year period in order to propose an evolutionary pathway involving these isolates. Studies of SSR variability among this collection of isolates within a putative clonal lineage based on pathotype 21-0, first detected in 1954 (the "21/34 lineage"), provided compelling evidence of clonality over the 52-year period, coupled with single-step acquisition of virulence for resistance genes. It also supported the postulation that two triticale-attacking pathotypes (34-2,12 and 34-2,12,13) detected in the early 1980s were derived from pathotype 21-0 via stepwise sequential acquisition of virulence for Sr5, Sr11, Sr27, and then SrSatu. Some of the isolates examined that were regarded as members of the race 21/34 lineage based on pathogenicity differed significantly in their SSR genotypes, indicating that they may have originated from processes more complex than simple mutation. This included two isolates of pathotype 21-0, which were collected in 1994 and 2006. Given that sexual recombination in P. graminis is rare or absent in Australia, the cryptic complexity observed could indicate that one or more of these isolates arose as a consequence of asexual recombination.
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Affiliation(s)
- Jianping Zhang
- First, second, third, and fourth authors: University of Sydney, Plant Breeding Institute Cobbitty, Cobbitty, NSW 2570, Australia; first author: CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601, Australia; and first author: Henan Tianmin Seed Company Ltd., South Industrial District, Lankao, Henan, 475300, P. R. China
| | - Peng Zhang
- First, second, third, and fourth authors: University of Sydney, Plant Breeding Institute Cobbitty, Cobbitty, NSW 2570, Australia; first author: CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601, Australia; and first author: Henan Tianmin Seed Company Ltd., South Industrial District, Lankao, Henan, 475300, P. R. China
| | - Haydar Karaoglu
- First, second, third, and fourth authors: University of Sydney, Plant Breeding Institute Cobbitty, Cobbitty, NSW 2570, Australia; first author: CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601, Australia; and first author: Henan Tianmin Seed Company Ltd., South Industrial District, Lankao, Henan, 475300, P. R. China
| | - Robert F Park
- First, second, third, and fourth authors: University of Sydney, Plant Breeding Institute Cobbitty, Cobbitty, NSW 2570, Australia; first author: CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601, Australia; and first author: Henan Tianmin Seed Company Ltd., South Industrial District, Lankao, Henan, 475300, P. R. China
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Rinaldo A, Gilbert B, Boni R, Krattinger SG, Singh D, Park RF, Lagudah E, Ayliffe M. The Lr34 adult plant rust resistance gene provides seedling resistance in durum wheat without senescence. Plant Biotechnol J 2017; 15:894-905. [PMID: 28005310 PMCID: PMC5466443 DOI: 10.1111/pbi.12684] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/13/2016] [Accepted: 12/14/2016] [Indexed: 05/18/2023]
Abstract
The hexaploid wheat (Triticum aestivum) adult plant resistance gene, Lr34/Yr18/Sr57/Pm38/Ltn1, provides broad-spectrum resistance to wheat leaf rust (Lr34), stripe rust (Yr18), stem rust (Sr57) and powdery mildew (Pm38) pathogens, and has remained effective in wheat crops for many decades. The partial resistance provided by this gene is only apparent in adult plants and not effective in field-grown seedlings. Lr34 also causes leaf tip necrosis (Ltn1) in mature adult plant leaves when grown under field conditions. This D genome-encoded bread wheat gene was transferred to tetraploid durum wheat (T. turgidum) cultivar Stewart by transformation. Transgenic durum lines were produced with elevated gene expression levels when compared with the endogenous hexaploid gene. Unlike nontransgenic hexaploid and durum control lines, these transgenic plants showed robust seedling resistance to pathogens causing wheat leaf rust, stripe rust and powdery mildew disease. The effectiveness of seedling resistance against each pathogen correlated with the level of transgene expression. No evidence of accelerated leaf necrosis or up-regulation of senescence gene markers was apparent in these seedlings, suggesting senescence is not required for Lr34 resistance, although leaf tip necrosis occurred in mature plant flag leaves. Several abiotic stress-response genes were up-regulated in these seedlings in the absence of rust infection as previously observed in adult plant flag leaves of hexaploid wheat. Increasing day length significantly increased Lr34 seedling resistance. These data demonstrate that expression of a highly durable, broad-spectrum adult plant resistance gene can be modified to provide seedling resistance in durum wheat.
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Affiliation(s)
| | | | - Rainer Boni
- Department of Plant and Microbial BiologyUniversity of ZurichZurichSwitzerland
| | - Simon G. Krattinger
- Department of Plant and Microbial BiologyUniversity of ZurichZurichSwitzerland
| | - Davinder Singh
- Plant Breeding InstituteUniversity of SydneyNarellanNSWAustralia
| | - Robert F. Park
- Plant Breeding InstituteUniversity of SydneyNarellanNSWAustralia
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Ziems LA, Hickey LT, Platz GJ, Franckowiak JD, Dracatos PM, Singh D, Park RF. Characterization of Rph24: A Gene Conferring Adult Plant Resistance to Puccinia hordei in Barley. Phytopathology 2017; 107:834-841. [PMID: 28430019 DOI: 10.1094/phyto-08-16-0295-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
We identified Rph24 as a locus in barley (Hordeum vulgare L.) controlling adult plant resistance (APR) to leaf rust, caused by Puccinia hordei. The locus was previously reported as a quantitative trait locus in barley line ND24260-1 and named qRphND. We crossed ND24260-1 to the leaf-rust-susceptible standard Gus and determined inheritance patterns in the progeny. For the comparative marker frequency analysis (MFA), resistant and susceptible tails of the F2 were genotyped with Diversity Arrays Technology genotyping-by-sequencing (DArT-Seq) markers. The Rph24 locus was positioned at 55.5 centimorgans on chromosome 6H on the DArT-Seq consensus map. Evaluation of F2:3 families confirmed that a single locus from ND24260-1 conferred partial resistance. The haploblock strongly associated with the Rph24 locus was used to estimate the allele frequency in a collection of 282 international barley cultivars. Rph24 was frequently paired with APR locus Rph20 in cultivars displaying high levels of APR to leaf rust. The markers identified in this study for Rph24 should be useful for marker-assisted selection.
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Affiliation(s)
- Laura A Ziems
- First and second authors: The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St. Lucia, QLD 4072, Australia; third author: Department of Agriculture and Fisheries, Hermitage Research Facility, 604 Yangan Rd, Warwick, QLD 4370, Australia; fourth author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul 55108; and fifth and sixth authors: The University of Sydney, Plant Breeding Institute Cobbitty, Private Bag 4011, Narellan, NSW 2167, Australia
| | - Lee T Hickey
- First and second authors: The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St. Lucia, QLD 4072, Australia; third author: Department of Agriculture and Fisheries, Hermitage Research Facility, 604 Yangan Rd, Warwick, QLD 4370, Australia; fourth author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul 55108; and fifth and sixth authors: The University of Sydney, Plant Breeding Institute Cobbitty, Private Bag 4011, Narellan, NSW 2167, Australia
| | - Gregory J Platz
- First and second authors: The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St. Lucia, QLD 4072, Australia; third author: Department of Agriculture and Fisheries, Hermitage Research Facility, 604 Yangan Rd, Warwick, QLD 4370, Australia; fourth author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul 55108; and fifth and sixth authors: The University of Sydney, Plant Breeding Institute Cobbitty, Private Bag 4011, Narellan, NSW 2167, Australia
| | - Jerome D Franckowiak
- First and second authors: The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St. Lucia, QLD 4072, Australia; third author: Department of Agriculture and Fisheries, Hermitage Research Facility, 604 Yangan Rd, Warwick, QLD 4370, Australia; fourth author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul 55108; and fifth and sixth authors: The University of Sydney, Plant Breeding Institute Cobbitty, Private Bag 4011, Narellan, NSW 2167, Australia
| | - Peter M Dracatos
- First and second authors: The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St. Lucia, QLD 4072, Australia; third author: Department of Agriculture and Fisheries, Hermitage Research Facility, 604 Yangan Rd, Warwick, QLD 4370, Australia; fourth author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul 55108; and fifth and sixth authors: The University of Sydney, Plant Breeding Institute Cobbitty, Private Bag 4011, Narellan, NSW 2167, Australia
| | - Davinder Singh
- First and second authors: The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St. Lucia, QLD 4072, Australia; third author: Department of Agriculture and Fisheries, Hermitage Research Facility, 604 Yangan Rd, Warwick, QLD 4370, Australia; fourth author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul 55108; and fifth and sixth authors: The University of Sydney, Plant Breeding Institute Cobbitty, Private Bag 4011, Narellan, NSW 2167, Australia
| | - Robert F Park
- First and second authors: The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St. Lucia, QLD 4072, Australia; third author: Department of Agriculture and Fisheries, Hermitage Research Facility, 604 Yangan Rd, Warwick, QLD 4370, Australia; fourth author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul 55108; and fifth and sixth authors: The University of Sydney, Plant Breeding Institute Cobbitty, Private Bag 4011, Narellan, NSW 2167, Australia
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Wu JQ, Sakthikumar S, Dong C, Zhang P, Cuomo CA, Park RF. Comparative Genomics Integrated with Association Analysis Identifies Candidate Effector Genes Corresponding to Lr20 in Phenotype-Paired Puccinia triticina Isolates from Australia. Front Plant Sci 2017; 8:148. [PMID: 28232843 PMCID: PMC5298990 DOI: 10.3389/fpls.2017.00148] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 01/24/2017] [Indexed: 05/05/2023]
Abstract
Leaf rust is one of the most common and damaging diseases of wheat, and is caused by an obligate biotrophic basidiomycete, Puccinia triticina (Pt). In the present study, 20 Pt isolates from Australia, comprising 10 phenotype-matched pairs with contrasting pathogenicity for Lr20, were analyzed using whole genome sequencing. Compared to the reference genome of the American Pt isolate 1-1 BBBD Race 1, an average of 404,690 single nucleotide polymorphisms (SNPs) per isolate was found and the proportion of heterozygous SNPs was above 87% in the majority of the isolates, demonstrating a high level of polymorphism and a high rate of heterozygosity. From the genome-wide SNPs, a phylogenetic tree was inferred, which consisted of a large clade of 15 isolates representing diverse presumed clonal lineages including 14 closely related isolates and the more diverged isolate 670028, and a small clade of five isolates characterized by lower heterozygosity level. Principle component analysis detected three distinct clusters, corresponding exactly to the two major subsets of the small clade and the large clade comprising all 15 isolates without further separation of isolate 670028. While genome-wide association analysis identified 302 genes harboring at least one SNP associated with Lr20 virulence (p < 0.05), a Wilcoxon rank sum test revealed that 36 and 68 genes had significant (p < 0.05) and marginally significant (p < 0.1) differences in the counts of non-synonymous mutations between Lr20 avirulent and virulent groups, respectively. Twenty of these genes were predicted to have a signal peptide without a transmembrane segment, and hence identified as candidate effector genes corresponding to Lr20. SNP analysis also implicated the potential involvement of epigenetics and small RNA in Pt pathogenicity. Future studies are thus warranted to investigate the biological functions of the candidate effectors as well as the gene regulation mechanisms at epigenetic and post-transcription levels. Our study is the first to integrate phenotype-genotype association with effector prediction in Pt genomes, an approach that may circumvent some of the technical difficulties in working with obligate rust fungi and accelerate avirulence gene identification.
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Affiliation(s)
- Jing Qin Wu
- Faculty of Agriculture and Environment, Plant Breeding Institute, The University of SydneyNarellan, NSW, Australia
| | - Sharadha Sakthikumar
- Genome Sequencing and Analysis Program, Broad Institute of Massachusetts Institute of Technology (MIT) and HarvardCambridge, MA, USA
| | - Chongmei Dong
- Faculty of Agriculture and Environment, Plant Breeding Institute, The University of SydneyNarellan, NSW, Australia
| | - Peng Zhang
- Faculty of Agriculture and Environment, Plant Breeding Institute, The University of SydneyNarellan, NSW, Australia
| | - Christina A. Cuomo
- Genome Sequencing and Analysis Program, Broad Institute of Massachusetts Institute of Technology (MIT) and HarvardCambridge, MA, USA
| | - Robert F. Park
- Faculty of Agriculture and Environment, Plant Breeding Institute, The University of SydneyNarellan, NSW, Australia
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Dracatos PM, Nansamba M, Berlin A, Park RF, Niks RE. Isolate Specificity and Polygenic Inheritance of Resistance in Barley to the Heterologous Rust Pathogen Puccinia graminis f. sp. avenae. Phytopathology 2016; 106:1029-37. [PMID: 27111801 DOI: 10.1094/phyto-10-15-0264-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Barley is a near-nonhost to numerous heterologous (nonadapted) rust pathogens because a small proportion of genotypes are somewhat susceptible. We assessed 66 barley accessions and three mapping populations (Vada × SusPtrit, Cebada Capa × SusPtrit, and SusPtrit × Golden Promise) for response to three Swedish oat stem rust (Puccinia graminis f. sp. avenae) fungal isolates and determined that barley is a near-nonhost to P. graminis f. sp. avenae and that resistance was polygenically inherited. The parental genotypes Vada and Golden Promise were immune to all three isolates, whereas Cebada Capa was immune to two isolates and moderately resistant to the third. Phenotypic data from the Vada × SusPtrit mapping population and the barley accessions tested also demonstrated isolate-specific resistance. In particular, the SusPtrit parent and several other accessions allowed sporulation by isolate Ingeberga but were resistant to isolate Evertsholm. Nine chromosomal regions carried quantitative trait loci (QTL) (Rpgaq1 to Rpgaq9) of varying effect, most of which colocated to previously identified QTL for resistance to other heterologous rust pathogens. Rpgaq1 on chromosome 1H (Vada and Golden Promise) was effective toward all isolates tested. Microscopic examination indicated that resistance was prehaustorial in Vada whereas, in SusPtrit, both pre- and posthaustorial mechanisms play a role.
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Affiliation(s)
- P M Dracatos
- First and fourth authors: The University of Sydney, Plant Breeding Institute, Cobbitty, Private Bag 4011, Narellan, NSW, 2567, Australia; second and fifith authors: Wageningen University and Research Center (WUR), Laboratory of Plant Breeding, 6700 AJ Wageningen, The Netherlands; and third author: Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-750 07 Uppsala, Sweden
| | - M Nansamba
- First and fourth authors: The University of Sydney, Plant Breeding Institute, Cobbitty, Private Bag 4011, Narellan, NSW, 2567, Australia; second and fifith authors: Wageningen University and Research Center (WUR), Laboratory of Plant Breeding, 6700 AJ Wageningen, The Netherlands; and third author: Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-750 07 Uppsala, Sweden
| | - A Berlin
- First and fourth authors: The University of Sydney, Plant Breeding Institute, Cobbitty, Private Bag 4011, Narellan, NSW, 2567, Australia; second and fifith authors: Wageningen University and Research Center (WUR), Laboratory of Plant Breeding, 6700 AJ Wageningen, The Netherlands; and third author: Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-750 07 Uppsala, Sweden
| | - R F Park
- First and fourth authors: The University of Sydney, Plant Breeding Institute, Cobbitty, Private Bag 4011, Narellan, NSW, 2567, Australia; second and fifith authors: Wageningen University and Research Center (WUR), Laboratory of Plant Breeding, 6700 AJ Wageningen, The Netherlands; and third author: Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-750 07 Uppsala, Sweden
| | - R E Niks
- First and fourth authors: The University of Sydney, Plant Breeding Institute, Cobbitty, Private Bag 4011, Narellan, NSW, 2567, Australia; second and fifith authors: Wageningen University and Research Center (WUR), Laboratory of Plant Breeding, 6700 AJ Wageningen, The Netherlands; and third author: Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-750 07 Uppsala, Sweden
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Tobias PA, Guest DI, Külheim C, Hsieh JF, Park RF. A curious case of resistance to a new encounter pathogen: myrtle rust in Australia. Mol Plant Pathol 2016; 17:783-8. [PMID: 26575410 PMCID: PMC6638338 DOI: 10.1111/mpp.12331] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 10/07/2015] [Accepted: 10/07/2015] [Indexed: 05/28/2023]
Abstract
Resistance genes (R genes) in plants mediate a highly specific response to microbial pathogens, often culminating in localized cell death. Such resistance is generally pathogen race specific and believed to be the result of evolutionary selection pressure. Where a host and pathogen do not share an evolutionary history, specific resistance is expected to be absent or rare. Puccinia psidii, the causal agent of myrtle rust, was recently introduced to Australia, a continent rich in myrtaceous taxa. Responses within species to this new pathogen range from full susceptibility to resistance. Using the myrtle rust case study, we examine models to account for the presence of resistance to new encounter pathogens, such as the retention of ancient R genes through prolonged 'trench warfare', pairing of resistance gene products and the guarding of host integrity.
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Affiliation(s)
- Peri A Tobias
- Department of Plant and Food Sciences, Faculty of Agriculture and Environment, University of Sydney, Eveleigh, NSW, 2015, Australia
| | - David I Guest
- Department of Plant and Food Sciences, Faculty of Agriculture and Environment, University of Sydney, Eveleigh, NSW, 2015, Australia
| | - Carsten Külheim
- Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Ji-Fan Hsieh
- Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Robert F Park
- Department of Plant and Food Sciences, Faculty of Agriculture and Environment, University of Sydney, Plant Breeding Institute, Narellan, NSW, 2567, Australia
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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. Front Plant Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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