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Diversity 2014, 6(4), 665-680; doi:10.3390/d6040665

Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping

Plant Gene Resources of Canada, Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK S7N 0X2, Canada
These authors contributed equally to this work.
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Received: 25 August 2014 / Revised: 11 October 2014 / Accepted: 13 October 2014 / Published: 20 October 2014
(This article belongs to the Special Issue Genetic Diversity and Molecular Evolution)
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Abstract

Genotyping-by-sequencing (GBS) has recently emerged as a promising genomic approach for exploring plant genetic diversity on a genome-wide scale. However, many uncertainties and challenges remain in the application of GBS, particularly in non-model species. Here, we present a GBS protocol we developed and use for plant genetic diversity analysis. It uses two restriction enzymes to reduce genome complexity, applies Illumina multiplexing indexes for barcoding and has a custom bioinformatics pipeline for genotyping. This genetic diversity-focused GBS (gd-GBS) protocol can serve as an easy-to-follow lab guide to assist a researcher through every step of a GBS application with five main components: sample preparation, library assembly, sequencing, SNP calling and diversity analysis. Specifically, in this presentation, we provide a brief overview of the GBS approach, describe the gd-GBS procedures, illustrate it with an application to analyze genetic diversity in 20 flax (Linum usitatissimum L.) accessions and discuss related issues in GBS application. Following these lab bench procedures and using the custom bioinformatics pipeline, one could generate genome-wide SNP genotype data for a conventional genetic diversity analysis of a non-model plant species. View Full-Text
Keywords: next generation sequencing; genotyping-by-sequencing; SNP genotyping; non-model plant; plant genetic diversity analysis; contig assembly; genome reduction next generation sequencing; genotyping-by-sequencing; SNP genotyping; non-model plant; plant genetic diversity analysis; contig assembly; genome reduction
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Peterson, G.W.; Dong, Y.; Horbach, C.; Fu, Y.-B. Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping. Diversity 2014, 6, 665-680.

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