Genotyping by multiplexed sequencing (GMS): A customizable platform for genomic selection.

Autor: Ruff TM; Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America.; USDA-ARS Wheat Health, Genetics and Quality Research Unit, Pullman, Washington, United States of America., Marston EJ; Department of Plant Pathology, Washington State University, Pullman, Washington, United States of America., Eagle JD; Department of Plant Pathology, Washington State University, Pullman, Washington, United States of America., Sthapit SR; Department of Plant Pathology, Washington State University, Pullman, Washington, United States of America., Hooker MA; Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America., Skinner DZ; Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America.; USDA-ARS Wheat Health, Genetics and Quality Research Unit, Pullman, Washington, United States of America., See DR; USDA-ARS Wheat Health, Genetics and Quality Research Unit, Pullman, Washington, United States of America.; Department of Plant Pathology, Washington State University, Pullman, Washington, United States of America.
Jazyk: angličtina
Zdroj: PloS one [PLoS One] 2020 May 01; Vol. 15 (5), pp. e0229207. Date of Electronic Publication: 2020 May 01 (Print Publication: 2020).
DOI: 10.1371/journal.pone.0229207
Abstrakt: As genotyping technologies continue to evolve, so have their throughput and multiplexing capabilities. In this study, we demonstrate a new PCR-based genotyping technology that multiplexes thousands of single nucleotide polymorphism (SNP) markers with high-throughput capabilities in a simple protocol using a two-step PCR approach. The bioinformatic pipeline is user friendly and yields results that are intuitive to interpret. This method was tested on two recombinant inbred line (RIL) populations that had previous genotyping data from the Illumina Infinium assay for Triticum aestivum L. and the two data sets were found to be 100% in agreement. The genotyping by multiplexed sequencing (GMS) protocol multiplexes 1,656 wheat SNP markers, 207 syntenic barley SNP markers, and 49 known informative markers, which generate a possible 2,433 data points (including homoeoalleles and paralogs). This genotyping approach has the flexibility of being sequenced on either the Ion Torrent or Illumina next generation sequencing (NGS) platforms. Products are the result of direct sequencing and are therefore more reliable than scatter plot analysis which is the output of other genotyping methods such as the Illumina Infinium assay, komeptitive allele specific PCR and other like technologies.
Competing Interests: The authors have declared that no competing interests exist.
Databáze: MEDLINE
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