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

Authors: XIA, CHONGJING - Washington State University; LEI, YU - Washington State University; WANG, MEINAN - Washington State University; CHEN, WANQUAN - Chinese Academy Of Agricultural Sciences; Chen, Xianming

Submitted to: mSphere
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/27/2020
Publication Date: 7/3/2020
Citation: Xia, C., Lei, Y., Wang, M., Chen, W., Chen, X. 2020. 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. 5(3). https://doi.org/10.1128/mSphere.00128-20.
DOI: https://doi.org/10.1128/mSphere.00128-20

Interpretive Summary: Stripe rust is a destructive disease of wheat worldwide, and the causal agent is an obligate, biotrophic fungus that has been difficult to study its genetics due to the lack of sexual reproduction. The recent discovery of alternate hosts for the rust fungus makes it possible to study the inheritance and map genes involved in its interaction with plant host. To identify avirulence (Avr) genes, we developed a sexual population of the fungus on barberry plants under controlled conditions. The progeny isolate segregated for avirulent/virulent phenotypes on nine wheat lines representing nine resistance genes. The progeny isolates were whole-genome sequenced. A total of 8027 genome-wide high-quality molecular markers were used to construct a genetic map of six linkage groups covering 76 Mb of the reference genome. Quantitative trait locus (QTL) analysis mapped six Avr gene loci to the genetic map, including an Avr cluster harboring four of the Avr genes. Aligning the genetic map to the reference genome identified Avr candidates and narrowed them to a small genomic region (<200 kb). The identification of candidate genes set the first important step towards cloning Avr genes for studying molecular mechanisms of the pathogen-host interactions. The information of 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 the devastating disease.

Technical Abstract: Puccinia striiformis f. sp. tritici (Pst), 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 the rust fungus makes it possible to study the inheritance and map genes involved in its interaction with plant host. To identify avirulence (Avr) genes in Pst, we developed a segregating population by self-fertilizing isolate 12-368 (race PSTv-4) on barberry (Berberis vulgaris) plants under controlled conditions. Virulence testing of the progeny isolates showed that the sexual population segregated for avirulent/virulent phenotypes on nine wheat lines representing nine resistance genes. The 117 progeny isolates were whole-genome sequenced at >30X coverage using the Illumina HiSeq PE 150 technology. A total of 8027 genome-wide high-quality molecular markers were used to construct a genetic map, which was comprised of six linkage groups, spanning 47306 cM and covering 76 Mb of the reference genome. The recombination rate was estimated as 2.90±2.89 cM/10 kb. Quantitative trait locus (QTL) analysis mapped six Avr gene loci to the genetic map, including an Avr cluster harboring four of the 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 the pathogen evolution, and the identification of candidate genes set the first important step towards cloning Avr genes for studying molecular mechanisms of the 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 control of the disease. However, Pst 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 Pst 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 the pathogen pathogenicity and adaptation to different environments and crop cultivars carrying different resistance genes. The information of 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 the devastating disease.