Dissertation
GENETIC DIVERSITY, POPULATION STRUCTURE, AND SECRETED PROTEIN GENE-BASED SNP (SP-SNP) MARKERS ASSOCIATED TO VIRULENCE PHENOTYPES OF STRIPE RUST PATHOGEN PUCCINIA STRIIFORMIS
Washington State University
Doctor of Philosophy (PhD), Washington State University
01/2022
DOI:
https://doi.org/10.7273/000004341
Handle:
https://hdl.handle.net/2376/123426
Abstract
Puccinia striiformis caused stripe rust is an important disease in wheat and barley production around the world. This research project was conducted to characterize the stripe rust collections from the USA and eight other countries using molecular markers to determine the population structure and understand evolutionary mechanisms of the pathogen. In the first study, 2,247 isolates of P. striiformis f. sp. tritici (Pst), the wheat stripe rust pathogen collected in the USA from 2010–2017, were genotyped using 14 simple sequencing repeat markers (SSR). From the collections, more multilocus genotypes (MLGs) and greater genotypic diversity were identified in western than eastern regions. The comparison of the 2010–2017 populations with those of 1968–2009, showed fast evolution of Pst populations in the USA. In the second study, using a similar approach, 567 Pst isolates from nine countries collected from 2010–2018 were genotyped. All isolates clustered into 10 Molecular Groups (MGs) based on hierarchical clustering analysis, with some of the MGs present in all countries, indicating that there have been Pst migrations among countries. In the third study, 447 isolates of P. striiformis f. sp. hordei (Psh), the barley stripe rust pathogen, collected from 1993–2017 in the USA, were genotyped with the same SSR markers. The results indicated that the Psh populations changed rapidly from year to year, with the most significant changes around 2000 and 2010. In the fourth study, we developed >200 secreted protein gene-based single nucleotide polymorphism (SP-SNP) markers to re-characterize the Pst isolates in the USA and other countries from the first two studies based on geographic origin, race, and genotype, to identify SP-SNP markers associated with avirulence genes through association analysis. Nineteen SP-SNP markers were significantly associated with 12 avirulence genes: AvYr1, AvYr6, AvYr7, AvYr9, AvYr10, AvYr24, AvYr27, AvYr32, AvYr43, AvYr44, AvYrSP, and AvYr76. These studies have established a molecular marker system for P. striiformis and provided genetic resources for monitoring changes in the pathogen population, determining genetic relationships of the pathogen populations in the USA and other countries, identifying candidate avirulence genes for functional characterization, and improving our understanding of pathogen evolutionary mechanisms.
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Details
- Title
- GENETIC DIVERSITY, POPULATION STRUCTURE, AND SECRETED PROTEIN GENE-BASED SNP (SP-SNP) MARKERS ASSOCIATED TO VIRULENCE PHENOTYPES OF STRIPE RUST PATHOGEN PUCCINIA STRIIFORMIS
- Creators
- Qing Bai
- Contributors
- Xianming XMC Chen (Advisor)Weidong Chen (Committee Member)Scot Hulbert (Committee Member)Tobin Peever (Committee Member)Deven See (Committee Member)
- Awarding Institution
- Washington State University
- Academic Unit
- Plant Pathology, Department of
- Theses and Dissertations
- Doctor of Philosophy (PhD), Washington State University
- Publisher
- Washington State University
- Number of pages
- 228
- Identifiers
- OCLC#: 1365112515; 99900882929001842
- Language
- English
- Resource Type
- Dissertation