Genotyping and Admixture Mapping of North American Fragaria chiloensis Populations Public Deposited

http://ir.library.oregonstate.edu/concern/undergraduate_thesis_or_projects/cn69m609c

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  • Assembly and genotyping of polyploid genomes poses many problems due to the complex nature of polyploid data, including the inability to determine allelic dosage and mixed inheritance patterns. This study was the first application of POLiMAPS genotyping on whole genome sequences without using cross information. In this study, whole genome sequencing data from twenty samples of the octoploid Fragaria chiloensis, collected from the northwest coast of North America, were assembled using BBTools. The sequences were genotyped using a POLiMAPS script and analyzed using principal component analysis in the R programming language. STRUCTURE was used to analyze the degree of admixture of the F. chiloensis individuals with F. virginiana. Principal component analysis and admixture mapping results show clustering of individuals from the same geographical area. Differences in read depth likely account for observations inconsistent with the expected results from population and species boundaries. An increased number of SNPs were called in sequences with higher read depth, which can cause unrelated sequences to appear similar, and for individuals of the same population to show differing clustering patterns.
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