Thesis
Genotyping by multiplexed sequencing in barley and stripe rust resistance in wheat
Washington State University
Master of Science (MS), Washington State University
05/2021
DOI:
https://doi.org/10.7273/000004275
Handle:
https://hdl.handle.net/2376/125204
Abstract
Genotyping by sequencing (GBS) and single nucleotide polymorphism (SNP) chip technologies are the primary SNP genotyping technologies used today. However, these genotyping technologies have some drawbacks that limit their usefulness in analysis. We have developed a robust protocol called genotyping by multiplexed sequencing (GMS) using SNP markers that provide informative genotypic data and greater flexibility. The genotypes derived from direct sequence reads reduce ambiguity in genetic analysis. The advantages of this protocol include: 1) This PCR-based direct sequencing protocol generates information from markers of interest and provides a more streamlined and accurate analysis process, by multiplexing hundreds of informative markers into a single sequencing run. 2) The marker sets are easily customized to the species of interest and can readily be changed. In this study we used the GMS protocol developed in wheat and adapted it to barley. We have identified 577 SNP markers that work well using this protocol providing adequate genome coverage for genomic selection and tag 267 QTLs for genes of interest. Good markers have a read depth of at least 5 amplicons and are reliably present across the population. Puccinia striiformis Westend. f. sp. tritici Erikss, causing wheat stripe rust, is an economically important pathogen of wheat (Triticum aestivum L.). The hexaploid club spring wheat cultivar JD contains both all-stage and adult plant resistance genes and is very resistant to stripe rust in the field. The objective of this study was to identify quantitative trait loci (QTL) for stripe rust resistance using a BC1F7 recombinant inbred line (RIL) population from parental line JD and backcross parent Avocet Susceptible (AvS). The population was phenotyped in field plots in Washington State at Pullman and Mount Vernon in 2014, 2015, and 2016. A major QTL conferring all-stage resistance from the JD background was identified on chromosome 1B using GBS markers. This QTL was further characterized with SSR markers and found to have the greatest effect at SSR marker WMC798, approximately 12 cM distal of WMC406. Additional QTL for adult-plant resistance were identified in the JD background on chromosomes 3A, 3B, 4A, 6B, and 7A having smaller effects.
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Details
- Title
- Genotyping by multiplexed sequencing in barley and stripe rust resistance in wheat
- Creators
- Jonathan Duran Eagle
- Contributors
- Deven Robert See (Advisor) - Washington State University, Plant Pathology, Department of
- 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
- Identifiers
- 99900896413801842
- Language
- English
- Resource Type
- Thesis