Thesis
Development of SP-SNP markers and use them in studying population genetics and identifying markers associated with avirulence genes of Puccinia striiformis F. Sp. Tritici
Washington State University
Master of Science (MS), Washington State University
2014
Handle:
https://hdl.handle.net/2376/103030
Abstract
Stripe rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss. (Pst), is one of the most destructive diseases of wheat worldwide. Various molecular marker techniques have been used to study the genetic variation of different populations of the pathogen in the world, but none of the previous studies were to develop markers for tagging avirulence genes. The objectives of this study were intended to develop secreted protein - single nucleotide polymorphism (SP-SNP) markers identified in previous studies and use them for studying population genetics and avirulence genes of the pathogen. Firstly, we developed over a hundred SP- SNP markers in the Pst fungus. The development method of the potential non-neutral SP-SNP markers can be applied in other non- v model microorganisms and these markers should be useful to identify genomic regions or genes that are under different selections from both crop and pathogen populations. Secondly, a total of 352 Pst isolates and 23 P. striiformis f. sp. hordei (causing stripe rust on barley) isolates, collected over all stripe rust epidemiological regions in the US to represent a diverse virulence races, were genotyped at 97 SP-SNP loci to study the population diversity and differentiation. Significant differences were detected between the eastern and western US populations and some of the epidemiological regions. Isolates from western US were more diverse than isolates from eastern US. The population diversity and differentiation information from this study would be useful for wheat breeding programs and stripe rust management. Thirdly, 352 Pst isolates were genotyped at 97 SP-SNP loci to identify candidate avirulence (Avr) genes corresponding to various resistance genes using association analyses. Among 19 avirulence genes, significantly associated SP-SNP markers were detected for AvYr1, AvYr2, AvYr6, AvYr7, AvYr8, AvYr44, AvYrExp2, AvYrSP, and AvYrTye. These preliminary results indicated that association analysis is a powerful approach for linking virulence traits of Pst with genetic markers. More SP-SNPs from the whole genome sequences of multiple Pst isolates will be used to identify markers highly associated with avirulence genes using both natural and artificially made sexual populations.
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Details
- Title
- Development of SP-SNP markers and use them in studying population genetics and identifying markers associated with avirulence genes of Puccinia striiformis F. Sp. Tritici
- Creators
- Chongjing Xia
- Contributors
- Xianming Chen (Degree Supervisor)
- Awarding Institution
- Washington State University
- Academic Unit
- Plant Pathology, Department of
- Theses and Dissertations
- Master of Science (MS), Washington State University
- Publisher
- Washington State University; [Pullman, Washington] :
- Identifiers
- 99900525150201842
- Language
- English
- Resource Type
- Thesis