Thesis
Method of deducing genotypes using curated and uncurated SNP data
Washington State University
Master of Science (MS), Washington State University
05/2020
DOI:
https://doi.org/10.7273/000004114
Handle:
https://hdl.handle.net/2376/125319
Abstract
Tree fruit breeders, collection curators, and other germplasm users require genetic information to effectively manage their material. Single Nucleotide Polymorphism (SNP) arrays have become the preferred platform to efficiently provide genome-wide genetic information for elite germplasm and could also provide information at specific positions in the genome ("loci") such as those associated with valuable traits. However, genotypic information for loci of interest across the genome is not yet readily extracted from SNP array data. This study aimed to establish a method for associating available SNP array data with the alleles of any locus of interest. The objective of the first experiment was to establish the method for any locus, extrapolating reference information for only a few cultivars from previous genetic studies to a large germplasm set. Using apple 8K SNP array data and sweet cherry 6K SNP array data, unique SNP allele patterns (haplotypes) spanning target loci were identified and allocated to specific alleles reported for important breeding parents and their ancestors. These haplotypes were then compared to those of other cultivars and selections important to U.S. apple and cherry breeding programs to deduce locus alleles in this new test germplasm. At least one allele was deduced for 64% to 93% of test cultivars. The objective of the second study was to demonstrate applicability of the method for several reported fruit quality trait loci of apple. Unambiguous haplotypes were able to be associated with each allele for these loci. For trait all loci, at least one allele was deduced for 86% of 121 cultivars. The objective of the third study was to demonstrate applicability of method using unphased SNP data. Allele deduction was successful for 58% to 98% of the individuals, depending on the locus. The method established and information obtained from this study can be used by germplasm users to reveal alleles carried by their germplasm and can also be applied to other loci of other crops that have SNP arrays developed.
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Details
- Title
- Method of deducing genotypes using curated and uncurated SNP data
- Creators
- Alexander J. Schaller
- Contributors
- Cameron Peace (Advisor) - Washington State University, Horticulture, Department of
- Awarding Institution
- Washington State University
- Academic Unit
- Horticulture, Department of
- Theses and Dissertations
- Master of Science (MS), Washington State University
- Publisher
- Washington State University
- Identifiers
- 99900890785101842
- Language
- English
- Resource Type
- Thesis