Thesis
Genotyping by multiplexed sequencing: a robust and adaptable genotyping technology for wheat
Washington State University
Master of Science (MS), Washington State University
2019
Handle:
https://hdl.handle.net/2376/103522
Abstract
Genotyping of polyploid species, such as common wheat, has proven difficult with current technologies that combine high-throughput and multiplexing abilities that are suitable for genomic selection (GS). The most common methods for high-throughput genotyping of wheat samples have been with the Illumina Infinium 90K SNP chip and more recently genotyping-by-sequencing (GBS). While many researchers continue to use these genotyping technologies for genetic studies in wheat, each have issues. The key problems with GBS is that the data analysis requires in-depth bioinformatic knowledge and imputation is essential to fill in missing data. The main drawback with the Illumina Infinium 90K wheat SNP chip in polyploids is the co-hybridization of homoeoalleles resulting in improper heterozygous calls. To correct this issue with the SNP chip data, a researcher must manually annotate tens of thousands of results to fix these errors. In doing this, all real heterozygous samples are converted to homozygous samples, which lead to the loss of these heterozygous samples from the data set. Another issue with SNP chip technology is that it is expensive to customize. Genotyping by Multiplexed Sequencing (GMS) was developed to address the specific issues mentioned above. GMS is PCR based, multiplexes 1,709 SNP wheat markers, 248 syntenic barley markers and 60 known informative markers (KIMs) used for marker-assisted selection (MAS) in wheat. GMS amplicon libraries have the flexibility to be sequenced on either the Ion Torrent or Illumina next generation sequencing platforms. Direct sequencing of amplicon libraries confirms heterozygous samples, does not require broad bioinformatic knowledge or imputation, and allows researchers to customize GMS to fit their research needs.
Metrics
33 File views/ downloads
102 Record Views
Details
- Title
- Genotyping by multiplexed sequencing
- Creators
- Travis Merle Ruff
- Contributors
- Michael O. Pumphrey (Degree Supervisor)
- Awarding Institution
- Washington State University
- Academic Unit
- Crop and Soil Sciences, Department of
- Theses and Dissertations
- Master of Science (MS), Washington State University
- Publisher
- Washington State University; [Pullman, Washington] :
- Identifiers
- 99900525049201842
- Language
- English
- Resource Type
- Thesis