An Avirulence Gene Cluster in the Wheat Stripe Rust Pathogen (<named-content content-type="genus-species">Puccinia striiformis</named-content> f. sp. <italic toggle="yes">tritici</italic>) Identified through Genetic Mapping and Whole-Genome Sequencing of a Sexual Population
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 ma...
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2020-06-01
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| Series: | mSphere |
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| Online Access: | https://journals.asm.org/doi/10.1128/mSphere.00128-20 |
| _version_ | 1818936015186821120 |
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| author | Chongjing Xia Yu Lei Meinan Wang Wanquan Chen Xianming Chen |
| author_facet | Chongjing Xia Yu Lei Meinan Wang Wanquan Chen Xianming Chen |
| author_sort | Chongjing Xia |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-20T05:29:20Z |
| format | Article |
| id | doaj.art-1b9adc6a1b534176ac0225b1d85a7538 |
| institution | Directory Open Access Journal |
| issn | 2379-5042 |
| language | English |
| last_indexed | 2024-12-20T05:29:20Z |
| publishDate | 2020-06-01 |
| publisher | American Society for Microbiology |
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| spelling | doaj.art-1b9adc6a1b534176ac0225b1d85a75382022-12-21T19:51:48ZengAmerican Society for MicrobiologymSphere2379-50422020-06-015310.1128/mSphere.00128-20An Avirulence Gene Cluster in the Wheat Stripe Rust Pathogen (<named-content content-type="genus-species">Puccinia striiformis</named-content> f. sp. <italic toggle="yes">tritici</italic>) Identified through Genetic Mapping and Whole-Genome Sequencing of a Sexual PopulationChongjing Xia0Yu Lei1Meinan Wang2Wanquan Chen3Xianming Chen4Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, ChinaDepartment of Plant Pathology, Washington State University, Pullman, Washington, USADepartment of Plant Pathology, Washington State University, Pullman, Washington, USAState Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, ChinaDepartment of Plant Pathology, Washington State University, Pullman, Washington, USAABSTRACT 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.https://journals.asm.org/doi/10.1128/mSphere.00128-20avirulencegeneticshost-pathogen interactionPuccinia striiformisQTL mappingwheat stripe rust |
| spellingShingle | Chongjing Xia Yu Lei Meinan Wang Wanquan Chen Xianming Chen An Avirulence Gene Cluster in the Wheat Stripe Rust Pathogen (<named-content content-type="genus-species">Puccinia striiformis</named-content> f. sp. <italic toggle="yes">tritici</italic>) Identified through Genetic Mapping and Whole-Genome Sequencing of a Sexual Population mSphere avirulence genetics host-pathogen interaction Puccinia striiformis QTL mapping wheat stripe rust |
| title | An Avirulence Gene Cluster in the Wheat Stripe Rust Pathogen (<named-content content-type="genus-species">Puccinia striiformis</named-content> f. sp. <italic toggle="yes">tritici</italic>) Identified through Genetic Mapping and Whole-Genome Sequencing of a Sexual Population |
| title_full | An Avirulence Gene Cluster in the Wheat Stripe Rust Pathogen (<named-content content-type="genus-species">Puccinia striiformis</named-content> f. sp. <italic toggle="yes">tritici</italic>) Identified through Genetic Mapping and Whole-Genome Sequencing of a Sexual Population |
| title_fullStr | An Avirulence Gene Cluster in the Wheat Stripe Rust Pathogen (<named-content content-type="genus-species">Puccinia striiformis</named-content> f. sp. <italic toggle="yes">tritici</italic>) Identified through Genetic Mapping and Whole-Genome Sequencing of a Sexual Population |
| title_full_unstemmed | An Avirulence Gene Cluster in the Wheat Stripe Rust Pathogen (<named-content content-type="genus-species">Puccinia striiformis</named-content> f. sp. <italic toggle="yes">tritici</italic>) Identified through Genetic Mapping and Whole-Genome Sequencing of a Sexual Population |
| title_short | An Avirulence Gene Cluster in the Wheat Stripe Rust Pathogen (<named-content content-type="genus-species">Puccinia striiformis</named-content> f. sp. <italic toggle="yes">tritici</italic>) Identified through Genetic Mapping and Whole-Genome Sequencing of a Sexual Population |
| title_sort | avirulence gene cluster in the wheat stripe rust pathogen named content content type genus species puccinia striiformis named content f sp italic toggle yes tritici italic identified through genetic mapping and whole genome sequencing of a sexual population |
| topic | avirulence genetics host-pathogen interaction Puccinia striiformis QTL mapping wheat stripe rust |
| url | https://journals.asm.org/doi/10.1128/mSphere.00128-20 |
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