Thesis
Molecular marker identification in Oculimacula yallundae using next-generation sequencing
Washington State University
Master of Science (MS), Washington State University
05/2016
Handle:
https://hdl.handle.net/2376/102579
Abstract
Eyespot is a stem base disease primarily of fall-sown wheat caused by two fungal pathogens, Oculimacula yallundae (OY) and O. acuformis. This disease is characterized by eyeshaped, elliptical lesions that form on lower stem internodes of the host plant. Wheat yield reductions of up to 50% have been observed in fields with severe eyespot disease. This study was undertaken to identify a set of simple sequence repeat (SSR) markers for genotyping OY isolates for use in population genetic studies. Two OY isolates (90-45-7 and 90- 49-1) were used as parents and crossed in vitro to produce a segregating progeny population. Whole genome sequences of the parental isolates were obtained using Pacific Biosciences RS sequencing technology at the WSU Core Genomics Lab. After de novo assembly, isolate 90-45-7 was placed in 89 contigs and contained 47.5 Mbp and isolate 90-49-1 was placed in 91 contigs and contained 45.9 Mbp. There were 2,018 and 2,020 true SSR loci found in the genomes of OY isolates 90-45-7 and 90-49-1, respectively. Penta-nucleotide repeats were the most abundant, representing on average 39% of SSR identified. Penta- and hexa-nucleotide repeats were more abundant than shorter repeated SSR markers. In silico analyses revealed that 33 SSR loci were determined to be polymorphic between the parental isolates. PCR primers were designed for these loci for amplification of SSR- containing regions in the segregating progeny population. Fifteen reproducibly amplified SSR were used for validation in the progeny population. Ten primer pairs successfully amplified SSR loci that were polymorphic, unlinked and segregated 1:1 in the progeny of parental isolates 90-49- 1 and 90-45-7. The SSR markers reported in this study are the first reported for OY. These markers will be used in a phylogeographic study of OY to indicate migration patterns between global regions and to identify a location and time of origin for this pathogen. Population genetics approaches may inform researchers about the modes of pathogen introductions and assist in preventing further introductions. Also, understanding diversity and origin of a pathogen can inform breeders as to which resistant germplasm might be effective for use in breeding programs.
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Details
- Title
- Molecular marker identification in Oculimacula yallundae using next-generation sequencing
- Creators
- Staci Lynne Koberstein
- Contributors
- Timothy D. Murray (Chair)Weidong Chen (Committee Member) - Washington State University, Plant Pathology, Department ofDaniel Z Skinner (Committee Member) - Washington State University, Crop and Soil Sciences, Department ofTOBIN PEEVER (Committee Member)Deven Robert See (Committee Member) - 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; [Pullman, Washington] :
- Number of pages
- 75
- Identifiers
- 99900525201301842
- Language
- English
- Resource Type
- Thesis