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Nguyen DT, Henningsen EC, Lewis D, Mago R, McNeil M, Suchecki R, Boden S, Sperschneider J, Kianian SF, Dodds PN, Figueroa M. Genotypic and Resistance Profile Analysis of Two Oat Crown Rust Differential Sets Urge Coordination and Standardization. PHYTOPATHOLOGY 2024:PHYTO10230353R. [PMID: 38114076 DOI: 10.1094/phyto-10-23-0353-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Puccinia coronata f. sp. avenae is the causal agent of the disease known as crown rust, which represents a bottleneck in oat production worldwide. Characterization of pathogen populations often involves race (pathotype) assignments using differential sets, which are not uniform across countries. This study compared the virulence profiles of 25 P. coronata f. sp. avenae isolates from Australia using two host differential sets, one from Australia and one from the United States. These differential sets were also genotyped using diversity arrays technology sequencing technology. Phenotypic and genotypic discrepancies were detected on 8 out of 29 common lines between the two sets, indicating that pathogen race assignments based on those lines are not comparable. To further investigate molecular markers that could assist in the stacking of rust resistance genes important for Australia, four published Pc91-linked markers were validated across the differential sets and then screened across a collection of 150 oat cultivars. Drover, Aladdin, and Volta were identified as putative carriers of the Pc91 locus. This is the first report to confirm that the cultivar Volta carries Pc91 and demonstrates the value of implementing molecular markers to characterize materials in breeding pools of oat. Overall, our findings highlight the necessity of examining seed stocks using pedigree and molecular markers to ensure seed uniformity and bring robustness to surveillance methodologies. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Duong T Nguyen
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Adelaide, SA 5064, Australia
| | - Eva C Henningsen
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - David Lewis
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Rohit Mago
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Meredith McNeil
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, St. Lucia, QLD 4067, Australia
| | - Radoslaw Suchecki
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Adelaide, SA 5064, Australia
| | - Scott Boden
- School of Agriculture, Food & Wine, Faculty of Sciences, Waite Research Institute, University of Adelaide, Adelaide, SA 5064, Australia
| | - Jana Sperschneider
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Shahryar F Kianian
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN, U.S.A
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia
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Moreau ELP, Riddle JM, Nazareno ES, Kianian SF. Three Decades of Rust Surveys in the United States Reveal Drastic Virulence Changes in Oat Crown Rust. PLANT DISEASE 2024; 108:1298-1307. [PMID: 37953229 DOI: 10.1094/pdis-09-23-1956-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
To better understand how the pathogenicity of the oat crown rust pathogen Puccinia coronata f. sp. avenae (Pca) has changed in the United States, 30 years of United States Department of Agriculture (USDA) survey isolates (n = 5,456) tested on 30 to 40 differential lines were analyzed for overall and Pc-resistance-gene-specific virulence trends and correlations. Pca is incredibly pathologically diverse, with 88% of races represented by a single isolate. There are a slightly higher proportion of unique races from the Northern region of the United States, and for one fourth of the years, Northern region isolates were significantly more virulent than Southern isolates, which supports the idea that sexual recombination in this region is mediated by the alternate host as a major factor in creating new races. However, there is also support for regular isolate movement between North and South regions as isolates in the United States are steadily accumulating virulences at a rate of 0.35 virulences per year. Virulence significantly increased for 23 and decreased for four of the 40 differential lines. In the past few years, virulence has reached 90% or greater for 16 differential lines. There were also strong correlations in virulence for certain Pc genes that are likely identical, allelic, or target the same or closely linked pathogen effectors (e.g., Pc39, Pc55, and Pc71), and the results were largely in concordance with recent genome-wide association study (GWAS) effector studies using USDA isolate subsets. Understanding changes in Pca pathogenicity is essential for the responsible deployment and management of Pc resistance genes for sustainable and profitable oat production.
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Affiliation(s)
- Erin L P Moreau
- Cereal Disease Laboratory, USDA-Agricultural Research Service, St. Paul, MN 55108
| | - Jakob M Riddle
- Cereal Disease Laboratory, USDA-Agricultural Research Service, St. Paul, MN 55108
| | - Eric S Nazareno
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Shahryar F Kianian
- Cereal Disease Laboratory, USDA-Agricultural Research Service, St. Paul, MN 55108
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Mohaimin AZ, Krishnamoorthy S, Shivanand P. A critical review on bioaerosols-dispersal of crop pathogenic microorganisms and their impact on crop yield. Braz J Microbiol 2024; 55:587-628. [PMID: 38001398 PMCID: PMC10920616 DOI: 10.1007/s42770-023-01179-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Bioaerosols are potential sources of pathogenic microorganisms that can cause devastating outbreaks of global crop diseases. Various microorganisms, insects and viroids are known to cause severe crop diseases impeding global agro-economy. Such losses threaten global food security, as it is estimated that almost 821 million people are underfed due to global crisis in food production. It is estimated that global population would reach 10 billion by 2050. Hence, it is imperative to substantially increase global food production to about 60% more than the existing levels. To meet the increasing demand, it is essential to control crop diseases and increase yield. Better understanding of the dispersive nature of bioaerosols, seasonal variations, regional diversity and load would enable in formulating improved strategies to control disease severity, onset and spread. Further, insights on regional and global bioaerosol composition and dissemination would help in predicting and preventing endemic and epidemic outbreaks of crop diseases. Advanced knowledge of the factors influencing disease onset and progress, mechanism of pathogen attachment and penetration, dispersal of pathogens, life cycle and the mode of infection, aid the development and implementation of species-specific and region-specific preventive strategies to control crop diseases. Intriguingly, development of R gene-mediated resistant varieties has shown promising results in controlling crop diseases. Forthcoming studies on the development of an appropriately stacked R gene with a wide range of resistance to crop diseases would enable proper management and yield. The article reviews various aspects of pathogenic bioaerosols, pathogen invasion and infestation, crop diseases and yield.
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Affiliation(s)
- Abdul Zul'Adly Mohaimin
- Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Bandar Seri Begawan, BE1410, Brunei Darussalam
| | - Sarayu Krishnamoorthy
- Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Bandar Seri Begawan, BE1410, Brunei Darussalam
| | - Pooja Shivanand
- Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Bandar Seri Begawan, BE1410, Brunei Darussalam.
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Hewitt TC, Henningsen EC, Pereira D, McElroy K, Nazareno ES, Dugyala S, Nguyen-Phuc H, Li F, Miller ME, Visser B, Pretorius ZA, Boshoff WHP, Sperschneider J, Stukenbrock EH, Kianian SF, Dodds PN, Figueroa M. Genome-Enabled Analysis of Population Dynamics and Virulence-Associated Loci in the Oat Crown Rust Fungus Puccinia coronata f. sp. avenae. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:290-303. [PMID: 37955552 DOI: 10.1094/mpmi-09-23-0126-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Puccinia coronata f. sp. avenae (Pca) is an important fungal pathogen causing crown rust that impacts oat production worldwide. Genetic resistance for crop protection against Pca is often overcome by the rapid virulence evolution of the pathogen. This study investigated the factors shaping adaptive evolution of Pca using pathogen populations from distinct geographic regions within the United States and South Africa. Phenotypic and genome-wide sequencing data of these diverse Pca collections, including 217 isolates, uncovered phylogenetic relationships and established distinct genetic composition between populations from northern and southern regions from the United States and South Africa. The population dynamics of Pca involve a bidirectional movement of inoculum between northern and southern regions of the United States and contributions from clonality and sexuality. The population from South Africa is solely clonal. A genome-wide association study (GWAS) employing a haplotype-resolved Pca reference genome was used to define 11 virulence-associated loci corresponding to 25 oat differential lines. These regions were screened to determine candidate Avr effector genes. Overall, the GWAS results allowed us to identify the underlying genetic factors controlling pathogen recognition in an oat differential set used in the United States to assign pathogen races (pathotypes). Key GWAS findings support complex genetic interactions in several oat lines, suggesting allelism among resistance genes or redundancy of genes included in the differential set, multiple resistance genes recognizing genetically linked Avr effector genes, or potentially epistatic relationships. A careful evaluation of the composition of the oat differential set accompanied by the development or implementation of molecular markers is recommended. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Tim C Hewitt
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2600, Australia
| | - Eva C Henningsen
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2600, Australia
| | - Danilo Pereira
- Christian Albrechts University of Kiel, 24118 Kiel, Germany
- Max Planck Institute of Evolutionary Biology, 24306 Plön, Germany
| | - Kerensa McElroy
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2600, Australia
| | - Eric S Nazareno
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Sheshanka Dugyala
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Hoa Nguyen-Phuc
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Feng Li
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Marisa E Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Botma Visser
- Department of Plant Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Zacharias A Pretorius
- Department of Plant Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Willem H P Boshoff
- Department of Plant Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Jana Sperschneider
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2600, Australia
| | - Eva H Stukenbrock
- Christian Albrechts University of Kiel, 24118 Kiel, Germany
- Max Planck Institute of Evolutionary Biology, 24306 Plön, Germany
| | - Shahryar F Kianian
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
- USDA-ARS Cereal Disease Laboratory, St. Paul, MN 55108, U.S.A
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2600, Australia
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2600, Australia
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Greatens N, Jin Y, Olivera Firpo PD. Aecial and Telial Host Specificity of Puccinia coronata var. coronata, a Eurasian Crown Rust Fungus of Two Highly Invasive Wetland Species in North America. PLANT DISEASE 2024; 108:175-181. [PMID: 37606959 DOI: 10.1094/pdis-04-23-0776-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
The Eurasian crown rust fungus Puccinia coronata var. coronata (Pcc) was recently reported in North America and is widespread across the Midwest and Northeast United States. Pcc is a close relative of major pathogens of oats, barley, and turfgrasses. It infects two highly invasive wetland plants, glossy buckthorn (Frangula alnus) and reed canarygrass (Phalaris arundinacea), and could be useful as an augmentative biological control agent. We conducted large greenhouse trials to assess the host specificity of Pcc and determine any threat to cultivated cereals, turfgrasses, or native North American species. A total of 1,830 accessions of cereal crop species and 783 accessions of 110 other gramineous species were evaluated. Young plants were first inoculated with a composite uredinial inoculum derived from aecia. Accessions showing sporulation were further tested with pure urediniospore isolates. Sixteen potential aecial hosts in the families Rhamnaceae and Elaeagnaceae were tested for susceptibility through inoculation with germinating teliospores. Thirteen grass species within five genera in the tribe Poeae (Apera, Calamagrostis, Lamarckia, Phalaris, and Puccinellia) and four species in Rhamnaceae (Frangula alnus, F. californica, F. caroliniana, and Rhamnus lanceolata) were found to be susceptible to Pcc, with some species native to North America. All assessed crop species and turfgrasses were resistant. Limited sporulation, however, was observed on some resistant species within Poeae and four other tribes: Brachypodieae, Bromeae, Meliceae, and Triticeae. Among these species are oats, barley, and Brachypodium distachyon, suggesting the possible use of Pcc in studies of nonhost resistance.
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Affiliation(s)
- Nicholas Greatens
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Yue Jin
- USDA-ARS Cereal Disease Laboratory, St. Paul, MN 55108
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Sperschneider J, Hewitt T, Lewis DC, Periyannan S, Milgate AW, Hickey LT, Mago R, Dodds PN, Figueroa M. Nuclear exchange generates population diversity in the wheat leaf rust pathogen Puccinia triticina. Nat Microbiol 2023; 8:2130-2141. [PMID: 37884814 PMCID: PMC10627818 DOI: 10.1038/s41564-023-01494-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 09/11/2023] [Indexed: 10/28/2023]
Abstract
In clonally reproducing dikaryotic rust fungi, non-sexual processes such as somatic nuclear exchange are postulated to play a role in diversity but have been difficult to detect due to the lack of genome resolution between the two haploid nuclei. We examined three nuclear-phased genome assemblies of Puccinia triticina, which causes wheat leaf rust disease. We found that the most recently emerged Australian lineage was derived by nuclear exchange between two pre-existing lineages, which originated in Europe and North America. Haplotype-specific phylogenetic analysis reveals that repeated somatic exchange events have shuffled haploid nuclei between long-term clonal lineages, leading to a global P. triticina population representing different combinations of a limited number of haploid genomes. Thus, nuclear exchange seems to be the predominant mechanism generating diversity and the emergence of new strains in this otherwise clonal pathogen. Such genomics-accelerated surveillance of pathogen evolution paves the way for more accurate global disease monitoring.
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Affiliation(s)
- Jana Sperschneider
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, GPO, Canberra, Australian Capital Territory, Australia.
| | - Tim Hewitt
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, GPO, Canberra, Australian Capital Territory, Australia
| | - David C Lewis
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, GPO, Canberra, Australian Capital Territory, Australia
| | - Sambasivam Periyannan
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, GPO, Canberra, Australian Capital Territory, Australia
- School of Agriculture and Environmental Science, Centre for Crop Health, The University of Southern Queensland, Toowoomba, Queensland, Australia
| | - Andrew W Milgate
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, New South Wales, Australia
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Queensland, Australia
| | - Rohit Mago
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, GPO, Canberra, Australian Capital Territory, Australia
| | - Peter N Dodds
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, GPO, Canberra, Australian Capital Territory, Australia.
| | - Melania Figueroa
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, GPO, Canberra, Australian Capital Territory, Australia.
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Holden S, Bakkeren G, Hubensky J, Bamrah R, Abbasi M, Qutob D, de Graaf ML, Kim SH, Kutcher HR, McCallum BD, Randhawa HS, Iqbal M, Uloth K, Burlakoti RR, Brar GS. Uncovering the history of recombination and population structure in western Canadian stripe rust populations through mating type alleles. BMC Biol 2023; 21:233. [PMID: 37880702 PMCID: PMC10601111 DOI: 10.1186/s12915-023-01717-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/27/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND The population structure of crop pathogens such as Puccinia striiformis f. sp. tritici (Pst), the cause of wheat stripe rust, is of interest to researchers looking to understand these pathogens on a molecular level as well as those with an applied focus such as disease epidemiology. Cereal rusts can reproduce sexually or asexually, and the emergence of novel lineages has the potential to cause serious epidemics such as the one caused by the 'Warrior' lineage in Europe. In a global context, Pst lineages in Canada were not well-characterized and the origin of foreign incursions was not known. Additionally, while some Pst mating type genes have been identified in published genomes, there has been no rigorous assessment of mating type diversity and distribution across the species. RESULTS We used a whole-genome/transcriptome sequencing approach for the Canadian Pst population to identify lineages in their global context and evidence tracing foreign incursions. More importantly: for the first time ever, we identified nine alleles of the homeodomain mating type locus in the worldwide Pst population and show that previously identified lineages exhibit a single pair of these alleles. Consistently with the literature, we find only two pheromone receptor mating type alleles. We show that the recent population shift from the 'PstS1' lineage to the 'PstS1-related' lineage is also associated with the introduction of a novel mating type allele (Pst-b3-HD) to the Canadian population. We also show evidence for high levels of mating type diversity in samples associated with the Himalayan center of diversity for Pst, including a single Canadian race previously identified as 'PstPr' (probable recombinant) which we identify as a foreign incursion, most closely related to isolates sampled from China circa 2015. CONCLUSIONS These data describe a recent shift in the population of Canadian Pst field isolates and characterize homeodomain-locus mating type alleles in the global Pst population which can now be utilized in testing several research questions and hypotheses around sexuality and hybridization in rust fungi.
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Affiliation(s)
- Samuel Holden
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, BC, Canada.
| | - Guus Bakkeren
- Agriculture and Agri-Food Canada (AAFC), Summerland Research and Development Center, Summerland, BC, Canada
| | - John Hubensky
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, BC, Canada
| | - Ramandeep Bamrah
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, BC, Canada
| | - Mehrdad Abbasi
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, BC, Canada
| | - Dinah Qutob
- Kent State University, Stark Campus, North Canton, OH, USA
| | - Mei-Lan de Graaf
- Agriculture and Agri-Food Canada (AAFC), Summerland Research and Development Center, Summerland, BC, Canada
| | - Sang Hu Kim
- Agriculture and Agri-Food Canada (AAFC), Summerland Research and Development Center, Summerland, BC, Canada
| | - Hadley R Kutcher
- Department of Plant Science/Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Brent D McCallum
- Agriculture and Agri-Food Canada (AAFC), Brandon Research and Development Center, Brandon, MB, Canada
| | - Harpinder S Randhawa
- Agriculture and Agri-Food Canada (AAFC), Lethbridge Research and Development Center, Lethbridge, AB, Canada
| | - Muhammad Iqbal
- Faculty of Agricultural, Life & Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Keith Uloth
- British Columbia Pest Monitoring Network, Dawson Creek, BC, Canada
| | - Rishi R Burlakoti
- Agriculture and Agri-Food Canada (AAFC), Agassiz Research and Development Center, Agassiz, BC, Canada
| | - Gurcharn S Brar
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, BC, Canada.
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Nazareno ES, Fiedler JD, Ardayfio NK, Miller ME, Figueroa M, Kianian SF. Genetic Analysis and Physical Mapping of Oat Adult Plant Resistance Loci Against Puccinia coronata f. sp. avenae. PHYTOPATHOLOGY 2023; 113:1307-1316. [PMID: 36721375 DOI: 10.1094/phyto-10-22-0395-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Six quantitative trait loci (QTLs) for adult plant resistance against oat crown rust (Puccinia coronata f. sp. avenae) were identified from mapping three recombinant inbred populations. Using genotyping-by-sequencing with markers called against the OT3098 v1 reference genome, the QTLs were mapped on six different chromosomes: Chr1D, Chr4D, Chr5A, Chr5D, Chr7A, and Chr7C. Composite interval mapping with marker cofactor selection showed that the phenotypic variance explained by all identified QTLs for coefficient of infection range from 12.2 to 46.9%, whereas heritability estimates ranged from 0.11 to 0.38. The significant regions were narrowed down to intervals of 3.9 to 25 cM, equivalent to physical distances of 11 to 133 Mb. At least two flanking single-nucleotide polymorphism markers were identified within 10 cM of each QTL that could be used in marker-assisted introgression, pyramiding, and selection. The additive effects of the QTLs in each population were determined using single-nucleotide polymorphism haplotype data, which showed a significantly lower coefficient of infection in lines homozygous for the resistant alleles. Analysis of pairwise linkage disequilibrium also revealed high correlation of markers and presence of linkage blocks in the significant regions. To further facilitate marker-assisted breeding, polymerase chain reaction allelic competitive extension (PACE) markers for the adult plant resistance loci were developed. Putative candidate genes were also identified in each of the significant regions, which include resistance gene analogs that encode for kinases, ligases, and predicted receptors of avirulence proteins from pathogens.
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Affiliation(s)
- Eric S Nazareno
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, U.S.A
| | - Jason D Fiedler
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Fargo, ND, U.S.A
| | - Naa Korkoi Ardayfio
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Fargo, ND, U.S.A
| | - Marisa E Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, U.S.A
- Pairwise Plants, LLC, 807 East Main Street, Suite 4-100, Durham, NC, U.S.A
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Shahryar F Kianian
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN, U.S.A
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Avasthi S, Gautam AK, Niranjan M, Verma RK, Karunarathna SC, Kumar A, Suwannarach N. Insights into Diversity, Distribution, and Systematics of Rust Genus Puccinia. J Fungi (Basel) 2023; 9:639. [PMID: 37367575 DOI: 10.3390/jof9060639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/21/2023] [Accepted: 05/29/2023] [Indexed: 06/28/2023] Open
Abstract
Puccinia, which comprises 4000 species, is the largest genus of rust fungi and one of the destructive plant pathogenic rust genera that are reported to infect both agricultural and nonagricultural plants with severe illnesses. The presence of bi-celled teliospores is one of the major features of these rust fungi that differentiated them from Uromyces, which is another largest genus of rust fungi. In the present study, an overview of the current knowledge on the general taxonomy and ecology of the rust genus Puccinia is presented. The status of the molecular identification of this genus along with updated species numbers and their current statuses in the 21st century are also presented, in addition to their threats to both agricultural and nonagricultural plants. Furthermore, a phylogenetic analysis based on ITS and LSU DNA sequence data available in GenBank and the published literature was performed to examine the intergeneric relationships of Puccinia. The obtained results revealed the worldwide distribution of Puccinia. Compared with other nations, a reasonable increase in research publications over the current century was demonstrated in Asian countries. The plant families Asteraceae and Poaceae were observed as the most infected in the 21st century. The phylogenetic studies of the LSU and ITS sequence data revealed the polyphyletic nature of Puccinia. In addition, the presences of too short, too lengthy, and incomplete sequences in the NCBI database demonstrate the need for extensive DNA-based analyses for a better understanding of the taxonomic placement of Puccinia.
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Affiliation(s)
- Shubhi Avasthi
- School of Studies in Botany, Jiwaji University, Gwalior 474011, India
| | - Ajay Kumar Gautam
- School of Agriculture, Abhilashi University, Mandi 175028, India
- Patanjali Herbal Research Department, Patanjali Research Institute, Haridwar 249405, India
| | - Mekala Niranjan
- Department of Botany, Rajiv Gandhi University, Rono Hills, Doimukh, Itanagar 791112, India
- Fungal Biotechnology Lab, Department of Biotechnology, School of Life Sciences, Pondicherry University, Kalapet 605014, India
| | - Rajnish Kumar Verma
- Department of Plant Pathology, Punjab Agricultural University, Ludhiana 141004, India
| | - Samantha C Karunarathna
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
- National Institute of Fundamental Studies (NIFS), Hantana Road, Kandy 20000, Sri Lanka
| | - Ashwani Kumar
- Patanjali Herbal Research Department, Patanjali Research Institute, Haridwar 249405, India
| | - Nakarin Suwannarach
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
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Nemati Z, Dadkhodaie A, Mostowfizadeh-Ghalamfarsa R, Mehrabi R, Cacciola SO. Genetic Variation of Puccinia triticina Populations in Iran from 2010 to 2017 as Revealed by SSR and ISSR Markers. J Fungi (Basel) 2023; 9:jof9030388. [PMID: 36983556 PMCID: PMC10056552 DOI: 10.3390/jof9030388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Puccinia triticina is a major wheat pathogen worldwide. Although Iran is within the Fertile Crescent, which is supposed to be the center of origin of both wheat and P. triticina, the knowledge of the genetic variability of local populations of this basidiomycete is limited. We analyzed 12 inter simple sequence repeats (ISSRs) and 18 simple sequence repeats (SSRs) of 175 P. triticina isolates sampled between 2010 and 2017 from wheat and other Poaceae in 14 provinces of Iran. SSRs revealed more polymorphisms than ISSRs, indicating they were more effective in differentiating P. triticina populations. Based on a dissimilarity matrix with a variable mutation rate for SSRs and a Dice coefficient for ISSRs, the isolates were separated into three large groups, each including isolates from diverse geographic origins and hosts. The grouping of SSR genotypes in UPGMA dendrograms was consistent with the grouping inferred from the Bayesian approach. However, isolates with a common origin clustered into separate subgroups within each group. The high proportion of heterozygous alleles suggests that in Iran clonal reproduction prevails over sexual reproduction of the pathogen. A significant correlation was found between SSR and ISSR genotypes and the virulence phenotypes of the isolates, as determined in a previous study.
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Affiliation(s)
- Zahra Nemati
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Ali Dadkhodaie
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | | | - Rahim Mehrabi
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan 81431-53784, Iran
| | - Santa Olga Cacciola
- Department of Agriculture, Food and Environment (Di3A), University of Catania, 95123 Catania, Italy
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11
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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. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 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] [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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12
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Nazareno ES, Fiedler J, Miller ME, Figueroa M, Kianian SF. A reference-anchored oat linkage map reveals quantitative trait loci conferring adult plant resistance to crown rust (Puccinia coronata f. sp. avenae). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3307-3321. [PMID: 36029319 DOI: 10.1007/s00122-022-04128-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
We mapped three adult plant resistance (APR) loci on oat chromosomes 4D and 6C and developed flanking KASP/PACE markers for marker-assisted selection and gene pyramiding. Using sequence orthology search and the available oat genomic and transcriptomic data, we surveyed these genomic regions for genes that may control disease resistance. Sources of durable disease resistance are needed to minimize yield losses in cultivated oat caused by crown rust (Puccinia coronata f. sp. avenae). In this study, we developed five oat recombinant inbred line mapping populations to identify sources of adult plant resistance from crosses between five APR donors and Otana, a susceptible variety. The preliminary bulk segregant mapping based on allele frequencies showed two regions in linkage group Mrg21 (Chr4D) that are associated with the APR phenotype in all five populations. Six markers from these regions in Chr4D were converted to high-throughput allele specific PCR assays and were used to genotype all individuals in each population. Simple interval mapping showed two peaks in Chr4D, named QPc.APR-4D.1 and QPc.APR-4D.2, which were detected in the OtanaA/CI4706-2 and OtanaA/CI9416-2 and in the Otana/PI189733, OtanaD/PI260616, and OtanaA/CI8000-4 populations, respectively. These results were validated by mapping two entire populations, Otana/PI189733 and OtanaA/CI9416, genotyped using Illumina HiSeq, in which polymorphisms were called against the OT3098 oat reference genome. Composite interval mapping results confirmed the presence of the two quantitative trait loci (QTL) located on oat chromosome 4D and an additional QTL with a smaller effect located on chromosome 6C. This mapping approach also narrowed down the physical intervals to between 5 and 19 Mb, and indicated that QPc.APR-4D.1, QPc.APR-4D.2, and QPc.APR-6C explained 43.4%, 38.5%, and 21.5% of the phenotypic variation, respectively. In a survey of the gene content of each QTL, several clusters of disease resistance genes that may contribute to APR were found. The allele specific PCR markers developed for these QTL regions would be beneficial for marker-assisted breeding, gene pyramiding, and future cloning of resistance genes from oat.
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Affiliation(s)
- Eric S Nazareno
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - Jason Fiedler
- US Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Fargo, ND, USA
| | - Marisa E Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
- Pairwise Plants, LLC. 807 East Main Street, Suite 4-100, Durham, NC, USA
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Shahryar F Kianian
- US Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN, USA.
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13
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Carlson CH, Fiedler JD, Naraghi SM, Nazareno ES, Ardayfio NK, McMullen MS, Kianian SF. Archetypes of inflorescence: genome-wide association networks of panicle morphometric, growth, and disease variables in a multiparent oat population. Genetics 2022; 223:6700642. [PMID: 36106985 PMCID: PMC9910404 DOI: 10.1093/genetics/iyac128] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
There is limited information regarding the morphometric relationships of panicle traits in oat (Avena sativa) and their contribution to phenology and growth, physiology, and pathology traits important for yield. To model panicle growth and development and identify genomic regions associated with corresponding traits, 10 diverse spring oat mapping populations (n = 2,993) were evaluated in the field and 9 genotyped via genotyping-by-sequencing. Representative panicles from all progeny individuals, parents, and check lines were scanned, and images were analyzed using manual and automated techniques, resulting in over 60 unique panicle, rachis, and spikelet variables. Spatial modeling and days to heading were used to account for environmental and phenological variances, respectively. Panicle variables were intercorrelated, providing reproducible archetypal and growth models. Notably, adult plant resistance for oat crown rust was most prominent for taller, stiff stalked plants having a more open panicle structure. Within and among family variance for panicle traits reflected the moderate-to-high heritability and mutual genome-wide associations (hotspots) with numerous high-effect loci. Candidate genes and potential breeding applications are discussed. This work adds to the growing genetic resources for oat and provides a unique perspective on the genetic basis of panicle architecture in cereal crops.
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Affiliation(s)
- Craig H Carlson
- Corresponding author: Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, USDA-ARS, Fargo, ND, 58102, USA.
| | - Jason D Fiedler
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, USDA-ARS, Fargo, ND 58102, USA
| | | | - Eric S Nazareno
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
| | - Naa Korkoi Ardayfio
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58105, USA
| | - Michael S McMullen
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58105, USA
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14
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Sowa S, Sozoniuk M, Toporowska J, Kowalczyk K, Paczos-Grzęda E. Validation of reference genes as an internal control for studying Avena sativa-Puccinia coronata interaction by RT-qPCR. Sci Rep 2022; 12:14601. [PMID: 36028746 PMCID: PMC9418433 DOI: 10.1038/s41598-022-18746-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/18/2022] [Indexed: 11/11/2022] Open
Abstract
In this study we evaluated eleven candidate reference genes in Avena sativa during compatible and incompatible interactions with two different pathotypes of Puccinia coronata f. sp. avenae in six time points post-inoculation. The identification of genes with high expression stability was performed by four algorithms (geNorm, NormFinder, BestKeeper and ΔCt method). The results obtained confirmed that the combination of two genes would be sufficient for reliable normalization of the expression data. In general, the most stable in the tested plant-pathogen system were HNR (heterogeneous nuclear ribonucleoprotein 27C) and EF1A (elongation factor 1-alpha). ARF (ADP-ribosylation factor) and EIF4A (eukaryotic initiation factor 4A-3) could also be considered as exhibiting high expression stability. CYP (cyclophilin) was shown by all assessment methods to be the worst candidate for normalization in this dataset. To date, this is the first report of reference genes selection in A. sativa–P. coronata interaction system. Identified reference genes enable reliable and comprehensive RT-qPCR analysis of oat gene expression in response to crown rust infection. Understanding the molecular mechanisms involved in the host–pathogen interactions may expand knowledge of durable resistance strategies beneficial to modern oat breeding.
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Affiliation(s)
- Sylwia Sowa
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 13, 20-950, Lublin, Poland.
| | - Magdalena Sozoniuk
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 13, 20-950, Lublin, Poland
| | - Joanna Toporowska
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 13, 20-950, Lublin, Poland
| | - Krzysztof Kowalczyk
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 13, 20-950, Lublin, Poland
| | - Edyta Paczos-Grzęda
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 13, 20-950, Lublin, Poland
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15
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Xia C, Qiu A, Wang M, Liu T, Chen W, Chen X. Current Status and Future Perspectives of Genomics Research in the Rust Fungi. Int J Mol Sci 2022; 23:ijms23179629. [PMID: 36077025 PMCID: PMC9456177 DOI: 10.3390/ijms23179629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/22/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Rust fungi in Pucciniales have caused destructive plant epidemics, have become more aggressive with new virulence, rapidly adapt to new environments, and continually threaten global agriculture. With the rapid advancement of genome sequencing technologies and data analysis tools, genomics research on many of the devastating rust fungi has generated unprecedented insights into various aspects of rust biology. In this review, we first present a summary of the main findings in the genomics of rust fungi related to variations in genome size and gene composition between and within species. Then we show how the genomics of rust fungi has promoted our understanding of the pathogen virulence and population dynamics. Even with great progress, many questions still need to be answered. Therefore, we introduce important perspectives with emphasis on the genome evolution and host adaptation of rust fungi. We believe that the comparative genomics and population genomics of rust fungi will provide a further understanding of the rapid evolution of virulence and will contribute to monitoring the population dynamics for disease management.
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Affiliation(s)
- Chongjing Xia
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: (C.X.); (X.C.); Tel.: +86-13880134318 (C.X.); +1-509-335-8086 (X.C.)
| | - Age Qiu
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
| | - Taiguo Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
- Wheat Health, Genetics, and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, WA 99164-6430, USA
- Correspondence: (C.X.); (X.C.); Tel.: +86-13880134318 (C.X.); +1-509-335-8086 (X.C.)
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16
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Henningsen EC, Hewitt T, Dugyala S, Nazareno ES, Gilbert E, Li F, Kianian SF, Steffenson BJ, Dodds PN, Sperschneider J, Figueroa M. A chromosome-level, fully phased genome assembly of the oat crown rust fungus Puccinia coronata f. sp. avenae: a resource to enable comparative genomics in the cereal rusts. G3 (BETHESDA, MD.) 2022; 12:6613142. [PMID: 35731221 PMCID: PMC9339303 DOI: 10.1093/g3journal/jkac149] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/19/2022] [Indexed: 12/12/2022]
Abstract
Advances in sequencing technologies as well as development of algorithms and workflows have made it possible to generate fully phased genome references for organisms with nonhaploid genomes such as dikaryotic rust fungi. To enable discovery of pathogen effectors and further our understanding of virulence evolution, we generated a chromosome-scale assembly for each of the 2 nuclear genomes of the oat crown rust pathogen, Puccinia coronata f. sp. avenae (Pca). This resource complements 2 previously released partially phased genome references of Pca, which display virulence traits absent in the isolate of historic race 203 (isolate Pca203) which was selected for this genome project. A fully phased, chromosome-level reference for Pca203 was generated using PacBio reads and Hi-C data and a recently developed pipeline named NuclearPhaser for phase assignment of contigs and phase switch correction. With 18 chromosomes in each haplotype and a total size of 208.10 Mbp, Pca203 has the same number of chromosomes as other cereal rust fungi such as Puccinia graminis f. sp. tritici and Puccinia triticina, the causal agents of wheat stem rust and wheat leaf rust, respectively. The Pca203 reference marks the third fully phased chromosome-level assembly of a cereal rust to date. Here, we demonstrate that the chromosomes of these 3 Puccinia species are syntenous and that chromosomal size variations are primarily due to differences in repeat element content.
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Affiliation(s)
- Eva C Henningsen
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA.,Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia.,Present address: Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Tim Hewitt
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Sheshanka Dugyala
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
| | - Eric S Nazareno
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
| | | | - Feng Li
- eGenesis Inc., Cambridge, MA 02139, USA
| | - Shahryar F Kianian
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA.,USDA-ARS Cereal Disease Laboratory, St. Paul, MN 55108, USA
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Jana Sperschneider
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia
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17
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McNish IG, Smith KP. Oat Crown Rust Disease Severity Estimated at Many Time Points Using Multispectral Aerial Photos. PHYTOPATHOLOGY 2022; 112:682-690. [PMID: 34384242 DOI: 10.1094/phyto-09-20-0442-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
All plant breeding programs are dependent on plant phenotypic and genotypic data, but the development of phenotyping technology has been slow relative to that of genotyping. Crown rust (Puccinia coronata f. sp. avenae Erikss.) is the most important disease of cultivated oat (Avena sativa L.), making the development of disease-resistant oat cultivars an important breeding objective. Visual observation is the most common scoring method, but it can be laborious and subjective. We visually scored a diverse collection of 256 oat lines at a total of 27 time points in three disease nursery environments. Multispectral aerial photos were collected using an unmanned aerial vehicle at the same time points as the visual observations. The photos were analyzed, and subsets of the spectral properties of each plot were measured. Random forest modeling was used to model the relationship between the spectral properties of the plots and visually observed disease severity. The ability of the photo data and the random forest model to estimate visually observed disease severity was evaluated using three different cross-validation analyses. We specifically addressed the issue of assessing phenotyping accuracy across and within time points. The accuracy of the photo estimates was greatest for adult plants shortly before they began to senesce. Accuracy outside of that time frame was generally low but statistically significant. Unmanned aerial vehicle-mounted sensors could increase disease scoring efficiency, but additional investigation into the spectral signature of disease severity at all plant growth stages may be necessary to automate accurate full-season measurements.
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Affiliation(s)
| | - Kevin P Smith
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108
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18
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Discovery and Chromosomal Location a Highly Effective Oat Crown Rust Resistance Gene Pc50-5. Int J Mol Sci 2021; 22:ijms222011183. [PMID: 34681841 PMCID: PMC8540790 DOI: 10.3390/ijms222011183] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 01/15/2023] Open
Abstract
Crown rust, caused by Puccinia coronata f. sp. avenae, is one of the most destructive fungal diseases of oat worldwide. Growing disease-resistant oat cultivars is the preferred method of preventing the spread of rust and potential epidemics. The object of the study was Pc50-5, a race-specific seedling crown rust resistant gene, highly effective at all growth stages, selected from the differential line Pc50 (Avena sterilis L. CW 486-1 × Pendek). A comparison of crown rust reaction as well as an allelism test showed the distinctiveness of Pc50-5, whereas the proportions of phenotypes in segregating populations derived from a cross with two crown rust-susceptible Polish oat cultivars, Kasztan × Pc50-5 and Bingo × Pc50-5, confirmed monogenic inheritance of the gene, indicating its usefulness in oat breeding programs. Effective gene introgression depends on reliable gene identification in the early stages of plant development; thus, the aim of the study was to develop molecular markers that are tightly linked to Pc50-5. Segregating populations of Kasztan × Pc50-5 were genotyped using DArTseq technology based on next-generation Illumina short-read sequencing. Markers associated with Pc50-5 were located on chromosome 6A of the current version of the oat reference genome (Avena sativa OT3098 v2, PepsiCo) in the region between 434,234,214 and 440,149,046 bp and subsequently converted to PCR-based SCAR (sequence-characterized amplified region) markers. Furthermore, 5426978_SCAR and 24031809_SCAR co-segregated with the Pc50-5 resistance allele and were mapped to the partial linkage group at 0.6 and 4.0 cM, respectively. The co-dominant 58163643_SCAR marker was the best diagnostic and it was located closest to Pc50-5 at 0.1 cM. The newly discovered, very strong monogenic crown rust resistance may be useful for oat improvement. DArTseq sequences converted into specific PCR markers will be a valuable tool for marker-assisted selection in breeding programs.
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19
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Havrlentová M, Šliková S, Gregusová V, Kovácsová B, Lančaričová A, Nemeček P, Hendrichová J, Hozlár P. The Influence of Artificial Fusarium Infection on Oat Grain Quality. Microorganisms 2021; 9:2108. [PMID: 34683429 PMCID: PMC8538375 DOI: 10.3390/microorganisms9102108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/29/2021] [Accepted: 10/04/2021] [Indexed: 11/16/2022] Open
Abstract
Adverse environmental conditions, such as various biotic and abiotic stresses, are the primary reason for decreased crop productivity. Oat, as one of the world's major crops, is an important cereal in human nutrition. The aim of this work was to analyze the effect of inoculation with two species of the genus Fusarium on the selected qualitative parameters of oat grain intended for the food industry. Artificial inoculation caused a statistically significant decrease in the content of starch, oleic, linoleic, and α-linolenic acids in oat grains compared to the control. Moreover, artificial inoculation had no statistically significant effect on the content of β-D-glucans, total dietary fiber, total lipids, palmitic, stearic, and cis-vaccenic acids. An increase in the content of polyunsaturated fatty acids in oat grains was observed after inoculation. The most important indicator of Fusarium infection was the presence of the mycotoxin deoxynivalenol in the grain. The content of β-D-glucans, as a possible protective barrier in the cell wall, did not have a statistically significant effect on the inoculation manifestation in the grain.
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Affiliation(s)
- Michaela Havrlentová
- Department of Biotechnologies, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, 917 01 Trnava, Slovakia; (V.G.); (B.K.)
- National Agricultural and Food Centre, Research Institute of Plant Production in Piešťany, 921 68 Piešťany, Slovakia; (S.Š.); (A.L.); (J.H.)
| | - Svetlana Šliková
- National Agricultural and Food Centre, Research Institute of Plant Production in Piešťany, 921 68 Piešťany, Slovakia; (S.Š.); (A.L.); (J.H.)
| | - Veronika Gregusová
- Department of Biotechnologies, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, 917 01 Trnava, Slovakia; (V.G.); (B.K.)
| | - Bernadett Kovácsová
- Department of Biotechnologies, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, 917 01 Trnava, Slovakia; (V.G.); (B.K.)
| | - Andrea Lančaričová
- National Agricultural and Food Centre, Research Institute of Plant Production in Piešťany, 921 68 Piešťany, Slovakia; (S.Š.); (A.L.); (J.H.)
| | - Peter Nemeček
- Department of Chemistry, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, 917 01 Trnava, Slovakia;
| | - Jana Hendrichová
- National Agricultural and Food Centre, Research Institute of Plant Production in Piešťany, 921 68 Piešťany, Slovakia; (S.Š.); (A.L.); (J.H.)
| | - Peter Hozlár
- National Agricultural and Food Centre, Research Institute of Plant Production in Piešťany, Research and Breeding Station at Vígľaš-Pstruša, 962 12 Pstruša, Slovakia;
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20
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Sowa S, Paczos-Grzęda E. Virulence Structure of Puccinia coronata f. sp. avenae and Effectiveness of Pc Resistance Genes in Poland During 2017-2019. PHYTOPATHOLOGY 2021; 111:1158-1165. [PMID: 33225832 DOI: 10.1094/phyto-10-20-0457-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Crown rust caused by Puccinia coronata f. sp. avenae is one of the most destructive diseases of oat, regularly occurring worldwide and leading to significant yield losses. This article characterizes the pathotype structure of P. coronata in Poland and evaluates the potential of crown rust race-specific resistance genes for use in practical breeding conditions in this region. A total of 466 isolates were derived from four locations of intensive oat breeding in Poland in 2017 to 2019, representing P. coronata populations from West, East, South, and Central Poland. Their virulence structure was determined on 35 Pc differential lines in laboratory conditions. In each year and location, high pathotype diversity was observed. In total, 347 (75%) pathotypes were detected. On average P. coronata isolates collected in 2017 and 2018 were virulent to 11% of the oat differentials. In 2019 isolates from East and South of Poland were able to overcome 18.3 and 18.5% of the oat differentials, respectively. There was no isolate virulent against Pc51, Pc52, and Pc91 crown rust resistance genes. P. coronata isolates displayed modest virulence levels, high diversity, and no prevailing pathotype. The information provided here may be helpful for development of resistance breeding strategies and in choosing the most effective major genes for pyramiding into cultivars.
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Affiliation(s)
- Sylwia Sowa
- University of Life Sciences in Lublin, Institute of Plant Genetics, Breeding and Biotechnology, 20-950 Lublin, Poland
| | - Edyta Paczos-Grzęda
- University of Life Sciences in Lublin, Institute of Plant Genetics, Breeding and Biotechnology, 20-950 Lublin, Poland
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21
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Hage H, Rosso MN, Tarrago L. Distribution of methionine sulfoxide reductases in fungi and conservation of the free-methionine-R-sulfoxide reductase in multicellular eukaryotes. Free Radic Biol Med 2021; 169:187-215. [PMID: 33865960 DOI: 10.1016/j.freeradbiomed.2021.04.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 12/17/2022]
Abstract
Methionine, either as a free amino acid or included in proteins, can be oxidized into methionine sulfoxide (MetO), which exists as R and S diastereomers. Almost all characterized organisms possess thiol-oxidoreductases named methionine sulfoxide reductase (Msr) enzymes to reduce MetO back to Met. MsrA and MsrB reduce the S and R diastereomers of MetO, respectively, with strict stereospecificity and are found in almost all organisms. Another type of thiol-oxidoreductase, the free-methionine-R-sulfoxide reductase (fRMsr), identified so far in prokaryotes and a few unicellular eukaryotes, reduces the R MetO diastereomer of the free amino acid. Moreover, some bacteria possess molybdenum-containing enzymes that reduce MetO, either in the free or protein-bound forms. All these Msrs play important roles in the protection of organisms against oxidative stress. Fungi are heterotrophic eukaryotes that colonize all niches on Earth and play fundamental functions, in organic matter recycling, as symbionts, or as pathogens of numerous organisms. However, our knowledge on fungal Msrs is still limited. Here, we performed a survey of msr genes in almost 700 genomes across the fungal kingdom. We show that most fungi possess one gene coding for each type of methionine sulfoxide reductase: MsrA, MsrB, and fRMsr. However, several fungi living in anaerobic environments or as obligate intracellular parasites were devoid of msr genes. Sequence inspection and phylogenetic analyses allowed us to identify non-canonical sequences with potentially novel enzymatic properties. Finaly, we identified several ocurences of msr horizontal gene transfer from bacteria to fungi.
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Affiliation(s)
- Hayat Hage
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France
| | - Marie-Noëlle Rosso
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France
| | - Lionel Tarrago
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France.
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22
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Farner JE, Spear ER, Mordecai EA. Habitat type and interannual variation shape unique fungal pathogen communities on a California native bunchgrass. FUNGAL ECOL 2021; 48. [PMID: 33408755 DOI: 10.1016/j.funeco.2020.100983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The role of infectious disease in regulating host populations is increasingly recognized, but how environmental conditions affect pathogen communities and infection levels remains poorly understood. Over 3 y, we compared foliar disease burden, fungal pathogen community composition, and foliar chemistry in the perennial bunchgrass Stipa pulchra occurring in adjacent serpentine and nonserpentine grassland habitats with distinct soil types and plant communities. We found that serpentine and nonserpentine S. pulchra experienced consistent, low disease pressure associated with distinct fungal pathogen communities with high interannual species turnover. Additionally, plant chemistry differed with habitat type. The results indicate that this species experiences minimal foliar disease associated with diverse fungal communities that are structured across landscapes by spatially and temporally variable conditions. Distinct fungal communities associated with different growing conditions may shield S. pulchra from large disease outbreaks, contributing to the low disease burden observed on this and other Mediterranean grassland species.
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Affiliation(s)
- Johannah E Farner
- Biology Department, Stanford University, Stanford, California 94305 USA
| | - Erin R Spear
- Biology Department, Stanford University, Stanford, California 94305 USA.,Smithsonian Tropical Research Institute, Panama City, Panama, Republic of Panama
| | - Erin A Mordecai
- Biology Department, Stanford University, Stanford, California 94305 USA
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Miller ME, Nazareno ES, Rottschaefer SM, Riddle J, Dos Santos Pereira D, Li F, Nguyen-Phuc H, Henningsen EC, Persoons A, Saunders DGO, Stukenbrock E, Dodds PN, Kianian SF, Figueroa M. Increased virulence of Puccinia coronata f. sp.avenae populations through allele frequency changes at multiple putative Avr loci. PLoS Genet 2020; 16:e1009291. [PMID: 33370783 PMCID: PMC7793281 DOI: 10.1371/journal.pgen.1009291] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 01/08/2021] [Accepted: 12/04/2020] [Indexed: 12/17/2022] Open
Abstract
Pathogen populations are expected to evolve virulence traits in response to resistance deployed in agricultural settings. However, few temporal datasets have been available to characterize this process at the population level. Here, we examined two temporally separated populations of Puccinia coronata f. sp. avenae (Pca), which causes crown rust disease in oat (Avena sativa) sampled from 1990 to 2015. We show that a substantial increase in virulence occurred from 1990 to 2015 and this was associated with a genetic differentiation between populations detected by genome-wide sequencing. We found strong evidence for genetic recombination in these populations, showing the importance of the alternate host in generating genotypic variation through sexual reproduction. However, asexual expansion of some clonal lineages was also observed within years. Genome-wide association analysis identified seven Avr loci associated with virulence towards fifteen Pc resistance genes in oat and suggests that some groups of Pc genes recognize the same pathogen effectors. The temporal shift in virulence patterns in the Pca populations between 1990 and 2015 is associated with changes in allele frequency in these genomic regions. Nucleotide diversity patterns at a single Avr locus corresponding to Pc38, Pc39, Pc55, Pc63, Pc70, and Pc71 showed evidence of a selective sweep associated with the shift to virulence towards these resistance genes in all 2015 collected isolates.
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Affiliation(s)
- Marisa E. Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Eric S. Nazareno
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Susan M. Rottschaefer
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Jakob Riddle
- USDA-ARS Cereal Disease Laboratory, St. Paul, Minnesota, United States of America
| | - Danilo Dos Santos Pereira
- Environmental Genomics Group, Max Planck Institute for Evolutionary Biology, Plon, Germany
- Christian-Albrechts University of Kiel, Kiel Germany
| | - Feng Li
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Hoa Nguyen-Phuc
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Eva C. Henningsen
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Antoine Persoons
- INRA/Universite de Lorraine Interactions Abres/Microorganismes, Champenoux, France
| | | | - Eva Stukenbrock
- Environmental Genomics Group, Max Planck Institute for Evolutionary Biology, Plon, Germany
- Christian-Albrechts University of Kiel, Kiel Germany
| | - Peter N. Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australia
| | - Shahryar F. Kianian
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
- USDA-ARS Cereal Disease Laboratory, St. Paul, Minnesota, United States of America
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australia
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Gallego-Sánchez LM, Canales FJ, Montilla-Bascón G, Prats E. RUST: A Robust, User-Friendly Script Tool for Rapid Measurement of Rust Disease on Cereal Leaves. PLANTS 2020; 9:plants9091182. [PMID: 32932900 PMCID: PMC7576472 DOI: 10.3390/plants9091182] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 11/30/2022]
Abstract
Recently, phenotyping has become one of the main bottlenecks in plant breeding and fundamental plant science. This is particularly true for plant disease assessment, which has to deal with time-consuming evaluations and the subjectivity of visual assessments. In this work, we have developed an open source Robust, User-friendy Script Tool (RUST) for semi-automated evaluation of leaf rust diseases. RUST runs under the free Fiji imaging software (developed from ImageJ), which is a well-recognized software among the scientific community. The script enables the evaluation of leaf rust diseases using a color transformation tool and provides three different automation modes. The script opens images sequentially and records infection frequency (pustules per area) (semi-)automatically for high-throughput analysis. Furthermore, it can manage several scanned leaf segments in the same image, consecutively selecting the desired segments. The script has been validated with nearly 900 samples from 80 oat genotypes ranging from resistant to susceptible and from very light to heavily infected leaves showing a high accuracy with a Lin’s concordance correlation coefficient of 0.99. The analysis show a high repeatability as indicated by the low variation coefficients obtained when repeating the measurement of the same samples. The script also has optional steps for calibration and training to ensure accuracy, even in low-resolution images. This script can evaluate efficiently hundreds of leaves facilitating the screening of novel sources of resistance to this important cereal disease.
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Figueroa M, Dodds PN, Henningsen EC. Evolution of virulence in rust fungi - multiple solutions to one problem. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:20-27. [PMID: 32244171 DOI: 10.1016/j.pbi.2020.02.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/18/2020] [Accepted: 02/25/2020] [Indexed: 05/18/2023]
Abstract
Rust fungi are major pathogens that negatively affect crops and ecosystems. Recent rust disease epidemics driven by the emergence of strains with novel virulence profiles demand a better understanding of the evolutionary mechanisms of these organisms. Here, we review research advances in genome-scale analysis coupled with functional validation of effector candidate genes that have been instrumental to elucidate processes that contribute to changes in virulence phenotypes. We highlight how haplotype-phased genome references have paved the road to link these processes to the reproductive phases of rust fungi and have provided evidence for somatic exchange between strains as an important mechanism for generating diversity in asexual populations. With increasing data availability, we envision the future development of molecular virulence diagnostic tools.
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Affiliation(s)
- Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia.
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Eva C Henningsen
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
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26
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An Avirulence Gene Cluster in the Wheat Stripe Rust Pathogen (Puccinia striiformis f. sp. tritici) Identified through Genetic Mapping and Whole-Genome Sequencing of a Sexual Population. mSphere 2020; 5:5/3/e00128-20. [PMID: 32554716 PMCID: PMC7300351 DOI: 10.1128/msphere.00128-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe (yellow) rust, is an obligate, biotrophic fungus. It was difficult to study the genetics of the pathogen due to the lack of sexual reproduction. The recent discovery of alternate hosts for P. striiformis f. sp. tritici makes it possible to study inheritance and map genes involved in its interaction with plant hosts. To identify avirulence (Avr) genes in P. striiformis f. sp. tritici, we developed a segregating population by selfing isolate 12-368 on barberry (Berberis vulgaris) plants under controlled conditions. The dikaryotic sexual population segregated for avirulent/virulent phenotypes on nine Yr single-gene lines. The parental and progeny isolates were whole-genome sequenced at >30× coverage using Illumina HiSeq PE150 technology. A total of 2,637 high-quality markers were discovered by mapping the whole-genome sequencing (WGS) reads to the reference genome of strain 93-210 and used to construct a genetic map, consisting of 41 linkage groups, spanning 7,715.0 centimorgans (cM) and covering 68 Mb of the reference genome. The recombination rate was estimated to be 1.81 ± 2.32 cM/10 kb. Quantitative trait locus analysis mapped six Avr gene loci to the genetic map, including an Avr cluster harboring four Avr genes, AvYr7, AvYr43, AvYr44, and AvYrExp2 Aligning the genetic map to the reference genome identified Avr candidates and narrowed them to a small genomic region (<200 kb). The discovery of the Avr gene cluster is useful for understanding pathogen evolution, and the identification of candidate genes is an important step toward cloning Avr genes for studying molecular mechanisms of pathogen-host interactions.IMPORTANCE Stripe rust is a destructive disease of wheat worldwide. Growing resistant cultivars is the most effective, easy-to-use, economical, and environmentally friendly strategy for the control of the disease. However, P. striiformis f. sp. tritici can produce new virulent races that may circumvent race-specific resistance. Therefore, understanding the genetic basis of the interactions between wheat genes for resistance and P. striiformis f. sp. tritici genes for avirulence is useful for improving cultivar resistance for more effective control of the disease. This study developed a high-quality map that facilitates genomic and genetic studies of important traits related to pathogen pathogenicity and adaptation to different environments and crop cultivars carrying different resistance genes. The information on avirulence/virulence genes identified in this study can be used for guiding breeding programs to select combinations of genes for developing new cultivars with effective resistance to mitigate this devastating disease.
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Zhao J, Kebede AZ, Bekele WA, Menzies JG, Chong J, Mitchell Fetch JW, Tinker NA, Beattie AD, Peng YY, McCartney CA. Mapping of the Oat Crown Rust Resistance Gene Pc39 Relative to Single Nucleotide Polymorphism Markers. PLANT DISEASE 2020; 104:1507-1513. [PMID: 32150502 DOI: 10.1094/pdis-09-19-2002-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Crown rust, caused by Puccinia coronata f. sp. avenae Eriks. (Pca), is among the most important oat diseases resulting in significant yield losses in many growing regions. A gene-for-gene interaction is well established in this pathosystem and has been exploited by oat breeders to control crown rust. Pc39 is a seedling crown rust resistance gene that has been widely deployed in North American oat breeding. DNA markers are desired to accurately predict the specific Pc genes present in breeding germplasm. The objectives of the study were as follows: (i) to map Pc39 in two recombinant inbred line (RIL) populations (AC Assiniboia/MN841801 and AC Medallion/MN841801) and (ii) to identify single nucleotide polymorphism (SNP) markers for postulation of Pc39 in oat germplasm. Pc39 was mapped to a linkage group consisting of 16 SNP markers, which placed the gene on linkage group Mrg11 (chromosome 1C) of the oat consensus map. Pc39 cosegregated with SNP marker GMI_ES01_c12570_390 in the AC Assiniboia/MN841801 RIL population and was flanked by the SNP markers avgbs_126086.1.41 and GMI_ES15_c276_702, with genetic distances of 1.7 and 0.3 cM, respectively. In the AC Medallion/MN841801 RIL population, similar results were obtained but the genetic distances of the flanking markers were 0.4 and 0.4 cM, respectively. Kompetitive Allele-Specific PCR assays were successfully designed for Pc39-linked SNP loci. Two SNP loci defined a haplotype that accurately predicted Pc39 status in a diverse panel of oat germplasm and will be useful for marker-assisted selection in oat breeding.
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Affiliation(s)
- Jun Zhao
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Manitoba, Canada
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Aida Z Kebede
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Manitoba, Canada
| | - Wubishet A Bekele
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Jim G Menzies
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Manitoba, Canada
| | - James Chong
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Manitoba, Canada
| | - Jennifer W Mitchell Fetch
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, Manitoba, Canada
| | - Nicholas A Tinker
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Aaron D Beattie
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yuan-Ying Peng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Curt A McCartney
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Manitoba, Canada
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Sowa S, Paczos-Grzęda E. Identification of molecular markers for the Pc39 gene conferring resistance to crown rust in oat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1081-1094. [PMID: 31927607 PMCID: PMC7064627 DOI: 10.1007/s00122-020-03533-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 01/03/2020] [Indexed: 05/22/2023]
Abstract
KEY MESSAGE Six new PCR-based markers for the Pc39 crown rust resistance gene in Avena sativa L. were developed. Pc39 was mapped to Mrg11 of the oat consensus map using BLASTn analysis. The aim of this study was the identification of molecular markers for the Pc39 gene in cultivated oat (Avena sativa L.). Pc39 is a major race-specific crown rust resistance gene originally found in an Israeli accession of the wild hexaploid Avena sterilis. The effectiveness of this gene in Europe has decreased in recent years, but is still relatively high and breeding programs would benefit from the availability of molecular markers to aid in its mapping and deployment. The complexity of the oat genome poses a significant obstacle to genetic research. No oat rust resistance genes have yet been cloned, and even the number of relevant molecular markers is very limited. Here, genotyping of a segregating population derived from a cross 'Celer' (Pc39)/STH9210 (susceptible) was conducted using RAPD- and SRAP-PCR-based methods, as well as microarray-based DArT™ and next-generation sequencing DArTseq™ techniques. Markers associated with Pc39 were placed on the hexaploid oat consensus linkage group Mrg11 at 3.7-6.7 cM. Six new PCR-based markers were developed to allow identification of the resistant Pc39 allele. These tightly linked markers will be useful in marker-assisted selection, with the closest, SCAR_3456624, being within 0.37 cM of Pc39. The newly developed markers could find applications in the fine mapping or positional cloning of this gene. Moreover, easy-to-use PCR-based markers linked to Pc39 could facilitate the utilization of this gene in oat breeding programs, especially as a component of crown rust resistance gene pyramids.
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Affiliation(s)
- Sylwia Sowa
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Lublin, Poland
| | - Edyta Paczos-Grzęda
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Lublin, Poland.
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Zhao J, Kebede AZ, Menzies JG, Paczos-Grzęda E, Chong J, Mitchell Fetch JW, Beattie AD, Peng YY, McCartney CA. Chromosomal location of the crown rust resistance gene Pc98 in cultivated oat (Avena sativa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1109-1122. [PMID: 31938813 DOI: 10.1007/s00122-020-03535-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 01/03/2020] [Indexed: 05/22/2023]
Abstract
SNP loci linked to the crown rust resistance gene Pc98 were identified by linkage analysis and KASP assays were developed for marker-assisted selection in breeding programs. Crown rust is among the most damaging diseases of oat and is caused by Puccinia coronata var. avenae f. sp. avenae (Urban and Marková) (Pca). Host resistance is the preferred method to prevent crown rust epidemics. Pc98 is a race-specific, seedling crown rust resistance gene obtained from the wild oat Avena sterilis accession CAV 1979 that is effective at all growth stages of oat. Virulence to Pc98 has been very low in the Pca populations that have been tested. The objectives of this study were to develop SNP markers linked to Pc98 for use in marker-assisted selection and to locate Pc98 on the oat consensus map. The Pc98 gene was mapped using F2:3 populations developed from the crosses Pc98/Bingo and Pc98/Kasztan, where Pc98 is a single-gene line carrying Pc98. Both populations were evaluated in seedling inoculation experiments. Pc98 was mapped relative to Kompetitive Allele-Specific PCR SNP markers in both populations, placing Pc98 on the Mrg20 linkage group of the consensus map. Pc98 was bracketed by two SNP markers GMI_ES22_c3052_382_kom399 and GMI_ES14_lrc18344_662_kom398 in the Pc98/Bingo mapping population with genetic distances of 0.9 cM and 0.3 cM, respectively. Pc98 co-segregated with four SNP markers in the Pc98/Kasztan population, and the closest flanking markers were GMI_DS_LB_6017_kom367 and avgbs2_153634.1.59_kom410 with genetic distances of 0.7 cM and 0.3 cM, respectively. Two SNP loci defined a haplotype that accurately predicted Pc98 status in a diverse group of oat germplasm, which will be valuable for marker-assisted selection of Pc98 in breeding of new oat cultivars.
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Affiliation(s)
- Jun Zhao
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Canada
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Aida Z Kebede
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Canada
| | - Jim G Menzies
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Canada
| | - Edyta Paczos-Grzęda
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences, Lublin, Poland
| | - James Chong
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Canada
| | | | - Aaron D Beattie
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, Canada
| | - Yuan-Ying Peng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Curt A McCartney
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Canada.
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Abstract
Among the thousands of rust species described, many are known for their devastating effects on their hosts, which include major agriculture crops and trees. Hence, for over a century, these basidiomycete pathogenic fungi have been researched and experimented with. However, due to their biotrophic nature, they are challenging organisms to work with and, needing their hosts for propagation, represent pathosystems that are not easily experimentally accessible. Indeed, efforts to perform genetics have been few and far apart for the rust fungi, though one study performed in the 1940s was famously instrumental in formulating the gene-for-gene hypothesis describing pathogen-host interactions. By taking full advantage of the molecular genetic tools developed in the 1980s, research on many plant pathogenic microbes thrived, yet similar work on the rusts remained very challenging though not without some successes. However, the genomics era brought real breakthrough research for the biotrophic fungi and with innovative experimentation and the use of heterologous systems, molecular genetic analyses over the last 2 decades have significantly advanced our insight into the function of many rust fungus genes and their role in the interaction with their hosts. This has allowed optimizing efforts for resistance breeding and the design and testing of various novel strategies to reduce the devastating diseases they cause.
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Affiliation(s)
- Guus Bakkeren
- Agriculture and Agri-Food Canada, Summerland Research & Development Centre, 4200 Hwy 97, Summerland, BC, Canada V0H 1Z0
| | - Les J Szabo
- U.S. Department of Agriculture-Agriculture Research Service, Cereal Disease Laboratory and University of Minnesota, 1551 Lindig Street, St. Paul, MN 55108, U.S.A
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31
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McNish IG, Zimmer CM, Susko AQ, Heuschele DJ, Tiede T, Case AJ, Smith KP. Mapping crown rust resistance at multiple time points in elite oat germplasm. THE PLANT GENOME 2020; 13:e20007. [PMID: 33016637 DOI: 10.1002/tpg2.20007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 10/22/2019] [Indexed: 06/11/2023]
Abstract
Crown rust, caused by Puccinia coronata f. sp. avenae Erikss., is the most important disease impacting cultivated oat (Avena sativa L.). Genetic resistance is the most desirable management strategy. The genetic architecture of crown rust resistance is not fully understood, and previous mapping investigations have mostly ignored temporal variation. A collection of elite oat lines sourced from oat breeding programs in the American Upper Midwest and Canada was genotyped using a high-density genotyping-by-sequencing system and evaluated for crown rust disease severity at multiple time points throughout the growing season in three disease nursery environments. Genome-wide association mapping was conducted for disease severity on each observation date of each trial, area under the disease progress curve for each trial, heading date for each trial, and area under the disease progress curve in a multi-environment model. Crown rust resistance quantitative trait loci (QTL) were detected on linkage groups Mrg05, Mrg12, Mrg15, Mrg18, Mrg20, and Mrg33. None of these QTL were coincident with a days-to-heading QTL detected on Mrg02. Only the QTL detected on Mrg15 was detected in multiple mapping models. The QTL on Mrg05, Mrg12, Mrg18, Mrg20, and Mrg33 were detected on only a single observation date and were not detected on observations just days before and after. This result uncovers the importance of temporal variation in mapping experiments which is usually ignored. It is possible that high density temporal data could be used to more precisely characterize the nature of plant resistance in other systems.
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Affiliation(s)
- Ian G McNish
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN, 55108
| | - Cristiano M Zimmer
- Dep. of Crop Science, Federal Univ. of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Alexander Q Susko
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN, 55108
| | - D Jo Heuschele
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN, 55108
| | | | | | - Kevin P Smith
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN, 55108
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Koutouleas A, Jørgen Lyngs Jørgensen H, Jensen B, Lillesø JB, Junge A, Ræbild A. On the hunt for the alternate host of Hemileia vastatrix. Ecol Evol 2019; 9:13619-13631. [PMID: 31871671 PMCID: PMC6912922 DOI: 10.1002/ece3.5755] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 08/12/2019] [Accepted: 09/24/2019] [Indexed: 12/14/2022] Open
Abstract
Coffee leaf rust (CLR), caused by the fungal pathogen Hemileia vastatrix, has plagued coffee production worldwide for over 150 years. Hemileia vastatrix produces urediniospores, teliospores, and the sexual basidiospores. Infection of coffee by basidiospores of H. vastatrix has never been reported and thus far, no alternate host, capable of supporting an aecial stage in the disease cycle, has been found. Due to this, some argue that an alternate host of H. vastatrix does not exist. Yet, to date, the plant pathology community has been puzzled by the ability of H. vastatrix to overcome resistance in coffee cultivars despite the apparent lack of sexual reproduction and an aecidial stage. The purpose of this study was to introduce a new method to search for the alternate host(s) of H. vastatrix. To do this, we present the novel hypothetical alternate host ranking (HAHR) method and an automated text mining (ATM) procedure, utilizing comprehensive biogeographical botanical data from the designated sites of interests (Ethiopia, Kenya and Sri Lanka) and plant pathology insights. With the HAHR/ATM methods, we produced prioritized lists of potential alternate hosts plant of coffee leaf rust. This is a first attempt to seek out an alternate plant host of a pathogenic fungus in this manner. The HAHR method showed the highest-ranking probable alternate host as Psychotria mahonii, Rubus apetalus, and Rhamnus prinoides. The cross-referenced results by the two methods suggest that plant genera of interest are Croton, Euphorbia, and Rubus. The HAHR and ATM methods may also be applied to other plant-rust interactions that include an unknown alternate host or any other biological system, which rely on data mining of published data.
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Affiliation(s)
- Athina Koutouleas
- Department of Geosciences and Natural Resource ManagementUniversity of CopenhagenFrederiksberg CDenmark
| | - Hans Jørgen Lyngs Jørgensen
- Department of Plant and Environmental Sciences and Copenhagen Plant Science CentreUniversity of CopenhagenFrederiksberg CDenmark
| | - Birgit Jensen
- Department of Plant and Environmental Sciences and Copenhagen Plant Science CentreUniversity of CopenhagenFrederiksberg CDenmark
| | | | - Alexander Junge
- Faculty of Health and Medical SciencesNovo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagen NDenmark
| | - Anders Ræbild
- Department of Geosciences and Natural Resource ManagementUniversity of CopenhagenFrederiksberg CDenmark
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Mondo SJ, Jiménez DJ, Hector RE, Lipzen A, Yan M, LaButti K, Barry K, van Elsas JD, Grigoriev IV, Nichols NN. Genome expansion by allopolyploidization in the fungal strain Coniochaeta 2T2.1 and its exceptional lignocellulolytic machinery. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:229. [PMID: 31572496 PMCID: PMC6757388 DOI: 10.1186/s13068-019-1569-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/13/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND Particular species of the genus Coniochaeta (Sordariomycetes) exhibit great potential for bioabatement of furanic compounds and have been identified as an underexplored source of novel lignocellulolytic enzymes, especially Coniochaeta ligniaria. However, there is a lack of information about their genomic features and metabolic capabilities. Here, we report the first in-depth genome/transcriptome survey of a Coniochaeta species (strain 2T2.1). RESULTS The genome of Coniochaeta sp. strain 2T2.1 has a size of 74.53 Mbp and contains 24,735 protein-encoding genes. Interestingly, we detected a genome expansion event, resulting ~ 98% of the assembly being duplicated with 91.9% average nucleotide identity between the duplicated regions. The lack of gene loss, as well as the high divergence and strong genome-wide signatures of purifying selection between copies indicates that this is likely a recent duplication, which arose through hybridization between two related Coniochaeta-like species (allopolyploidization). Phylogenomic analysis revealed that 2T2.1 is related Coniochaeta sp. PMI546 and Lecythophora sp. AK0013, which both occur endophytically. Based on carbohydrate-active enzyme (CAZy) annotation, we observed that even after in silico removal of its duplicated content, the 2T2.1 genome contains exceptional lignocellulolytic machinery. Moreover, transcriptomic data reveal the overexpression of proteins affiliated to CAZy families GH11, GH10 (endoxylanases), CE5, CE1 (xylan esterases), GH62, GH51 (α-l-arabinofuranosidases), GH12, GH7 (cellulases), and AA9 (lytic polysaccharide monoxygenases) when the fungus was grown on wheat straw compared with glucose as the sole carbon source. CONCLUSIONS We provide data that suggest that a recent hybridization between the genomes of related species may have given rise to Coniochaeta sp. 2T2.1. Moreover, our results reveal that the degradation of arabinoxylan, xyloglucan and cellulose are key metabolic processes in strain 2T2.1 growing on wheat straw. Different genes for key lignocellulolytic enzymes were identified, which can be starting points for production, characterization and/or supplementation of enzyme cocktails used in saccharification of agricultural residues. Our findings represent first steps that enable a better understanding of the reticulate evolution and "eco-enzymology" of lignocellulolytic Coniochaeta species.
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Affiliation(s)
- Stephen J. Mondo
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
- Bioagricultural Science and Pest Management Department, Colorado State University, Fort Collins, CO 80521 USA
| | - Diego Javier Jiménez
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Carrera 1 No 18A-12, Bogotá, Colombia
| | - Ronald E. Hector
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, IL 61604 USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Mi Yan
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Jan Dirk van Elsas
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720-3102 USA
| | - Nancy N. Nichols
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, IL 61604 USA
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Paczos-Grzęda E, Sowa S. Virulence Structure and Diversity of Puccinia coronata f. sp. avenae P. Syd. & Syd. in Poland During 2013 to 2015. PLANT DISEASE 2019; 103:1559-1564. [PMID: 31025903 DOI: 10.1094/pdis-10-18-1820-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The crown rust fungus Puccinia coronata f. sp. avenae P. Syd. & Syd. (Pca) attacks cultivated oat and its wild relatives, causing significant losses to the crop worldwide. Although understanding the origin and dynamics of the pathogen's diversity is critical to developing methods for its control, there are little relevant data on Pca virulence diversity in Europe, the global center of oat production. The goal of this study was to analyze the diversity of Pca populations in Poland in 2013 to 2015 based on their ability to overcome currently available host resistance Pc genes. Pca isolate virulence was evaluated on a panel of lines containing 26 major resistance genes of oat. The isolates were able to overcome from 1 to 16 resistance genes each, with most isolates being virulent on five to seven lines. In all years, a very high level of crown rust pathotype diversity was observed, with Simpson and Evenness indices of 0.99. In total, 156 different pathotypes were detected, with no prevalent pathotype in any of the 3 years analyzed. The results showed that the virulence level of P. coronata isolates was relatively low for each year studied (21% on average), most likely owing to the low take up of Pc genes in Polish oat cultivars, meaning that many sources of resistance are still effective against Pca races occurring in Poland. The long-range dispersal of Puccinia spores supported by the availability of wild, weedy, and cultivated Avena species makes it likely that the virulence profile seen in Poland is representative of much of central Europe and beyond.
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Affiliation(s)
- Edyta Paczos-Grzęda
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, 20-950 Lublin, Poland
| | - Sylwia Sowa
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, 20-950 Lublin, Poland
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Paczos-Grzęda E, Sowa S, Boczkowska M, Langdon T. Detached Leaf Assays for Resistance to Crown Rust Reveal Diversity Within Populations of Avena sterilis. PLANT DISEASE 2019; 103:832-840. [PMID: 30806576 DOI: 10.1094/pdis-06-18-1045-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Crown rust is the most widespread and damaging disease of oat (Avena species). Genetic resistance to the pathogen is the preferred method for crop protection but widespread deployment of limited numbers of major effect genes has promoted the rapid emergence and spread of pathogen races that are able to overcome these genes. Combining genes with even partial resistance may help develop durable cultivars that are less vulnerable to changes in pathogen virulence. Partial resistance is expected to be relatively common in populations of wild species where constant pathogen pressure encourages diversity in host resistance mechanisms, but it may be discarded in conventional screens for major gene resistance. Here, we used a detached leaf assay to detect resistance to the crown rust pathogen, Puccinia coronata Cda. f. sp. avenae, in previously uncharacterized collections of the hexaploid wild oat relative A. sterilis made by the Polish National Centre for Plant Genetic Resources. Many of the accessions were collected in Morocco, the center of diversity for the Avena genus. The detached leaf assessment allowed individual plants to be challenged with multiple pathotypes and their responses compared with 34 known differentials. Broad-spectrum resistance was identified within accession PL 51855, which behaved as a single major locus on crossing to three cultivars. The locus provided resistance to over 50 rust pathotypes, a greater range than seen for any of the known host resistance (Pc) genes. Strong resistance was identified in other accessions, and heterogeneity in response within accessions was common. Several accessions show multiple partial resistance responses that may be of value for developing durable resistance in cultivars. Because the sources of resistance in all but two differential lines were collected outside of Morocco, resistance in all accessions tested here are potentially novel. This study demonstrates that diversity within A. sterilis accessions collected in Morocco could be a very valuable source of resistance to crown rust, and it provides new germplasm for use in resistance breeding programs. Detached leaf assessment provides a valuable first step in the identification of promising candidates in complex gene bank accessions.
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Affiliation(s)
- Edyta Paczos-Grzęda
- 1 Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, 20-950 Lublin, Poland
| | - Sylwia Sowa
- 1 Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, 20-950 Lublin, Poland
| | - Maja Boczkowska
- 2 Polish Academy of Sciences Botanical Garden, Center for Biological Diversity Conservation in Powsin, 02-973 Warsaw, Poland
- 3 Plant Breeding and Acclimatization Institute, National Research Institute 05-870 Radzikow, Poland; and
| | - Tim Langdon
- 4 Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, SY23 3EE Aberystwyth, U.K
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Omidvar V, Dugyala S, Li F, Rottschaefer SM, Miller ME, Ayliffe M, Moscou MJ, Kianian SF, Figueroa M. Detection of Race-Specific Resistance Against Puccinia coronata f. sp. avenae in Brachypodium Species. PHYTOPATHOLOGY 2018; 108:1443-1454. [PMID: 29923800 DOI: 10.1094/phyto-03-18-0084-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Oat crown rust caused by Puccinia coronata f. sp. avenae is the most destructive foliar disease of cultivated oat. Characterization of genetic factors controlling resistance responses to Puccinia coronata f. sp. avenae in nonhost species could provide new resources for developing disease protection strategies in oat. We examined symptom development and fungal colonization levels of a collection of Brachypodium distachyon and B. hybridum accessions infected with three North American P. coronata f. sp. avenae isolates. Our results demonstrated that colonization phenotypes are dependent on both host and pathogen genotypes, indicating a role for race-specific responses in these interactions. These responses were independent of the accumulation of reactive oxygen species. Expression analysis of several defense-related genes suggested that salicylic acid and ethylene-mediated signaling but not jasmonic acid are components of resistance reaction to P. coronata f. sp. avenae. Our findings provide the basis to conduct a genetic inheritance study to examine whether effector-triggered immunity contributes to nonhost resistance to P. coronata f. sp. avenae in Brachypodium spp.
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Affiliation(s)
- Vahid Omidvar
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Sheshanka Dugyala
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Feng Li
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Susan M Rottschaefer
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Marisa E Miller
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Mick Ayliffe
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Matthew J Moscou
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Shahryar F Kianian
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Melania Figueroa
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
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Rines HW, Miller ME, Carson M, Chao S, Tiede T, Wiersma J, Kianian SF. Identification, introgression, and molecular marker genetic analysis and selection of a highly effective novel oat crown rust resistance from diploid oat, Avena strigosa. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:721-733. [PMID: 29222636 DOI: 10.1007/s00122-017-3031-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 11/25/2017] [Indexed: 06/07/2023]
Abstract
Oat crown rust is one of the most damaging diseases of oat. We identified a new source of resistance and developed KASP and TaqMan markers for selection in breeding programs. A new highly effective resistance to oat crown rust (Puccinia coronata f. sp. avenae) was identified in the diploid oat Avena strigosa PI 258731 and introgressed into hexaploid cultivated oat. Young plants with this resistance show moderate susceptibility, whereas older plant tissues and adult plants are resistant with no virulent isolates encountered in over 8 years of testing. Resistance was incorporated into hexaploid oat by embryo rescue, colchicine chromosome doubling followed by backcrosses with a hexaploid parent, and selection for stable transmission of resistance. To mitigate flag leaf and panicle chlorosis/necrosis associated with the resistance, crosses were made with derived resistant lines to breeding lines of divergent parentage followed by selection. Subsequently, two F2 sister lines, termed MNBT1020-1 and MNBT1021-1, were identified in which the chlorosis/necrosis was reduced. These two lines performed well in replicated multi-location state trials in 2015 and 2016 out-yielding all cultivar entries. Segregating F2:3 plants resulting from crosses of MNBT lines to susceptible parents were genotyped with the oat 6K SNP array, and SNP loci with close linkage to the resistance were identified. KASP assays generated from linked SNPs showed accurate discrimination of the resistance in derivatives of the resistant MNBT lines crossed to susceptible breeding lines. A TaqMan marker was developed and correctly identified homozygous resistance in over 95% of 379 F4 plants when rust was scored in F4:5 plants in the field. Thus, a novel highly effective resistance and associated molecular markers are available for use in breeding, genetic analysis, and functional studies.
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Affiliation(s)
- Howard W Rines
- USDA-ARS Plant Sciences Research Unit, St. Paul, MN, 55108, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Marisa E Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Martin Carson
- USDA-ARS Cereal Disease Laboratory, St. Paul, MN, 55108, USA
| | - Shiaoman Chao
- USDA-ARS, Cereal Crops Research Unit, Fargo, ND, 58102, USA
| | - Tyler Tiede
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Jochum Wiersma
- Department of Agronomy and Plant Genetics, University of Minnesota, Crookston, MN, 56716, USA
| | - Shahryar F Kianian
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA.
- USDA-ARS Cereal Disease Laboratory, St. Paul, MN, 55108, USA.
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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] [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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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] [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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