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Mackenzie A, Norman M, Gessese M, Chen C, Sørensen C, Hovmøller M, Ma L, Forrest K, Hickey L, Bariana H, Bansal U, Periyannan S. Wheat stripe rust resistance locus YR63 is a hot spot for evolution of defence genes - a pangenome discovery. BMC PLANT BIOLOGY 2023; 23:590. [PMID: 38008766 PMCID: PMC10680240 DOI: 10.1186/s12870-023-04576-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 11/01/2023] [Indexed: 11/28/2023]
Abstract
BACKGROUND Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), poses a threat to global wheat production. Deployment of widely effective resistance genes underpins management of this ongoing threat. This study focused on the mapping of stripe rust resistance gene YR63 from a Portuguese hexaploid wheat landrace AUS27955 of the Watkins Collection. RESULTS YR63 exhibits resistance to a broad spectrum of Pst races from Australia, Africa, Asia, Europe, Middle East and South America. It was mapped to the short arm of chromosome 7B, between two single nucleotide polymorphic (SNP) markers sunCS_YR63 and sunCS_67, positioned at 0.8 and 3.7 Mb, respectively, in the Chinese Spring genome assembly v2.1. We characterised YR63 locus using an integrated approach engaging targeted genotyping-by-sequencing (tGBS), mutagenesis, resistance gene enrichment and sequencing (MutRenSeq), RNA sequencing (RNASeq) and comparative genomic analysis with tetraploid (Zavitan and Svevo) and hexaploid (Chinese Spring) wheat genome references and 10+ hexaploid wheat genomes. YR63 is positioned at a hot spot enriched with multiple nucleotide-binding and leucine rich repeat (NLR) and kinase domain encoding genes, known widely for defence against pests and diseases in plants and animals. Detection of YR63 within these gene clusters is not possible through short-read sequencing due to high homology between members. However, using the sequence of a NLR member we were successful in detecting a closely linked SNP marker for YR63 and validated on a panel of Australian bread wheat, durum and triticale cultivars. CONCLUSIONS This study highlights YR63 as a valuable source for resistance against Pst in Australia and elsewhere. The closely linked SNP marker will facilitate rapid introgression of YR63 into elite cultivars through marker-assisted selection. The bottleneck of this study reinforces the necessity for a long-read sequencing such as PacBio or Oxford Nanopore based techniques for accurate detection of the underlying resistance gene when it is part of a large gene cluster.
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Affiliation(s)
- Amy Mackenzie
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, Australian Capital Territory, 2601, Australia
- Centre for Crop Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Brisbane, Queensland, 4072, Australia
| | - Michael Norman
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, Australian Capital Territory, 2601, Australia
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, New South Wales, 2570, Australia
| | - Mesfin Gessese
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, New South Wales, 2570, Australia
- Present address:, Wolaita sodo University, Sodo, Ethiopia
| | - Chunhong Chen
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, Australian Capital Territory, 2601, Australia
| | - Chris Sørensen
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Mogens Hovmøller
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Lina Ma
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, Australian Capital Territory, 2601, Australia
| | - Kerrie Forrest
- Agriculture Victoria, Department of Energy, Environment and Climate Action, AgriBio, Centre for AgriBioscience, 5 Ring Rd, Bundoora, Victoria, 3083, Australia
| | - Lee Hickey
- Centre for Crop Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Brisbane, Queensland, 4072, Australia
| | - Harbans Bariana
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, New South Wales, 2570, Australia
- School of Science, Western Sydney University, Bourke Road, Richmond, New South Wales, 2753, Australia
| | - Urmil Bansal
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, New South Wales, 2570, Australia.
| | - Sambasivam Periyannan
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, Australian Capital Territory, 2601, Australia.
- Centre for Crop Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Brisbane, Queensland, 4072, Australia.
- School of Agriculture and Environmental Science & Centre for Crop Health, University of Southern Queensland, Toowoomba, Queensland, 4350, Australia.
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Rodriguez-Algaba J, Hovmøller MS, Schulz P, Hansen JG, Lezáun JA, Joaquim J, Randazzo B, Czembor P, Zemeca L, Slikova S, Hanzalová A, Holdgate S, Wilderspin S, Mascher F, Suffert F, Leconte M, Flath K, Justesen AF. Stem rust on barberry species in Europe: Host specificities and genetic diversity. Front Genet 2022; 13:988031. [PMID: 36246643 PMCID: PMC9554944 DOI: 10.3389/fgene.2022.988031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
The increased emergence of cereal stem rust in southern and western Europe, caused by the pathogen Puccinia graminis, and the prevalence of alternate (sexual) host, Berberis species, have regained attention as the sexual host may serve as source of novel pathogen variability that may pose a threat to cereal supply. The main objective of the present study was to investigate the functional role of Berberis species in the current epidemiological situation of cereal stem rust in Europe. Surveys in 11 European countries were carried out from 2018 to 2020, where aecial infections from five barberry species were collected. Phylogenetic analysis of 121 single aecial clusters of diverse origin using the elongation factor 1-α gene indicated the presence of different special forms (aka formae speciales) of P. graminis adapted to different cereal and grass species. Inoculation studies using aecial clusters from Spain, United Kingdom, and Switzerland resulted in 533 stem rust isolates sampled from wheat, barley, rye, and oat, which confirmed the presence of multiple special forms of P. graminis. Microsatellite marker analysis of a subset of 192 sexually-derived isolates recovered on wheat, barley and rye from the three populations confirmed the generation of novel genetic diversity revealed by the detection of 135 multilocus genotypes. Discriminant analysis of principal components resulted in four genetic clusters, which grouped at both local and country level. Here, we demonstrated that a variety of Berberis species may serve as functional alternate hosts for cereal stem rust fungi and highlights the increased risks that the sexual cycle may pose to cereal production in Europe, which calls for new initiatives within rust surveillance, epidemiological research and resistance breeding.
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Affiliation(s)
- Julian Rodriguez-Algaba
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Slagelse, Denmark
- *Correspondence: Julian Rodriguez-Algaba,
| | - Mogens S. Hovmøller
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Slagelse, Denmark
| | - Philipp Schulz
- Federal Research Centre for Cultivated Plants, Julius Kühn-Institut, Institute for Plant Protection in Field Crops and Grassland, Kleinmachnow, Germany
| | - Jens G. Hansen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Slagelse, Denmark
| | - Juan Antonio Lezáun
- INTIA, Institute for Agrifood Technology and Infrastructures of Navarra, Villava, Navarra, Spain
| | - Jessica Joaquim
- Agroscope, Crop Plant Breeding and Genetic Ressources, Nyon, Switzerland
| | | | - Paweł Czembor
- Plant Breeding and Acclimatization Institute-National Research Institute, Radzików, Poland
| | - Liga Zemeca
- Institute of Plant Protection Research “Agrihorts”, Latvia University of Life Sciences and Technologies, Jelgava, Latvia
| | | | - Alena Hanzalová
- Crop Research Institute, Department of Genetics and Plant Breeding Methods, Prague, Czech Republic
| | - Sarah Holdgate
- National Institute of Agricultural Botany (NIAB), Cambridge, United Kingdom
| | - Sarah Wilderspin
- National Institute of Agricultural Botany (NIAB), Cambridge, United Kingdom
| | - Fabio Mascher
- Agroscope, Crop Plant Breeding and Genetic Ressources, Nyon, Switzerland
| | - Frederic Suffert
- INRAE (French National Institute for Agriculture Food and Environment), Université Paris-Saclay, Thiverval-Grignon, France
| | - Marc Leconte
- INRAE (French National Institute for Agriculture Food and Environment), Université Paris-Saclay, Thiverval-Grignon, France
| | - Kerstin Flath
- Federal Research Centre for Cultivated Plants, Julius Kühn-Institut, Institute for Plant Protection in Field Crops and Grassland, Kleinmachnow, Germany
| | - Annemarie F. Justesen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Slagelse, Denmark
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Wamalwa MN, Wanyera R, Rodriguez-Algaba J, Boyd LA, Owuoche J, Ogendo J, Bhavani S, Uauy C, Justesen AF, Hovmøller M. Distribution of Puccinia striiformis f. sp. tritici Races and Virulence in Wheat Growing Regions of Kenya from 1970 to 2014. PLANT DISEASE 2022; 106:701-710. [PMID: 34633239 DOI: 10.1094/pdis-11-20-2341-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici, is a major threat to wheat (Triticum spp.) production worldwide. The objective of this study was to determine the virulence of P. striiformis f. sp. tritici races prevalent in the main wheat growing regions of Kenya, which includes Mt. Kenya, Eastern Kenya, and the Rift Valley (Central, Southern, and Northern Rift). Fifty P. striiformis f. sp. tritici isolates collected from 1970 to 1992 and from 2009 to 2014 were virulence phenotyped with stripe rust differential sets, and 45 isolates were genotyped with sequence characterized amplified region (SCAR) markers to differentiate the isolates and identify aggressive strains PstS1 and PstS2. Virulence corresponding to stripe rust resistance genes Yr1, Yr2, Yr3, Yr6, Yr7, Yr8, Yr9, Yr17, Yr25, and Yr27 and the seedling resistance in genotype Avocet S were detected. Ten races were detected in the P. striiformis f. sp. tritici samples obtained from 1970 to 1992, and three additional races were detected from 2009 to 2014, with a single race being detected in both periods. The SCAR markers detected both Pst1 and Pst2 strains in the collection. Increasing P. striiformis f. sp. tritici virulence was found in the Kenyan P. striiformis f. sp. tritici population, and different P. striiformis f. sp. tritici race groups were found to dominate different wheat growing regions. Moreover, recent P. striiformis f. sp. tritici races in East Africa indicated possible migration of some race groups into Kenya from other regions. This study is important in elucidating P. striiformis f. sp. tritici evolution and virulence diversity and useful in breeding wheat cultivars with effective resistance to stripe rust.
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Affiliation(s)
| | - Ruth Wanyera
- Kenya Agricultural and Livestock Research Organization Njoro, Private Bag 20107, Kenya
| | | | - Lesley A Boyd
- National Institute of Agricultural Botany, Cambridge CB3 0LE, UK
| | | | | | | | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich NR4 UH, UK
| | - Annemarie F Justesen
- Global Rust Reference Center, Aarhus University, Flakkebjerg, Slagelse DK-4200, Denmark
| | - Mogens Hovmøller
- Global Rust Reference Center, Aarhus University, Flakkebjerg, Slagelse DK-4200, Denmark
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Analysis of Host-Specific Differentiation of Puccinia striiformis in the South and North-West of the European Part of Russia. PLANTS 2021; 10:plants10112497. [PMID: 34834861 PMCID: PMC8622514 DOI: 10.3390/plants10112497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/09/2021] [Accepted: 11/16/2021] [Indexed: 11/16/2022]
Abstract
Yellow (stripe) rust, caused by Puccinia striiformis Westend. (Pst), is a major disease of cereals worldwide. We studied Pst virulence phenotypes on Triticum aestivum, Triticum durum, and triticale in three geographically distant regions of the European part of Russia (Dagestan and Krasnodar in North Caucasus, and Northwest) with different climate and environmental conditions. Based on the set of twenty differential lines, a relatively high level of population diversity was determined with 67 different Pst pathotypes identified among 141 isolates. Only seven pathotypes were shared by at least two hosts or occurred in the different regions. No significant differentiation was found between regional Pst collections of pathotypes either from T. aestivum or from T. durum. A set of Pst pathotypes from triticale was subdivided into two groups. One of them was indistinguishable from most durum and common wheat pathotypes, whereas the second group differed greatly from all other pathotypes. All sampled Pst isolates were avirulent on lines with Yr5, Yr10, Yr15, and Yr24 genes. Significant variation in virulence frequency among all Pst collections was observed on lines containing Yr1, Yr3, Yr17, Yr27, and YrSp genes and cvs Strubes Dickkopf, Carstens V, and Nord Desprez. Relationships between Russian regional collections of Pst from wheat did not conform to those for P. triticina.
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