Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping
By G. W. Peterson, Yibo Dong, Carolee Horbach, Yong‐Bi Fu. 2014
110 citations recorded by the source corpus.
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.
Subfields: Genetics, Molecular Biology, Plant Science
View Paper: https://www.semanticscholar.org/paper/f6cba7cc25725e8e00be464fbb226c941a26bbe1
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In Genetics
In Molecular Biology
In Plant Science
Citations in the corpus
- The Vulnerability of Plant Genetic Resources Conserved Ex Situ (2017, background): “Molecular characterization of conserved germplasm is useful and technically more feasible than before, thanks to the advances in next-generation sequencing (Kilian and Graner, 2012; Peterson et al., 2014).”
- Using nuclear gene data for plant phylogenetics: Progress and prospects II. Next‐gen approaches (2015, unknown): “Genotyping by sequencing (GBS) is a related, highly costeffective, genotyping procedure (Elshire et al., 2011; Poland et al., 2012; Peterson et al., 2014).”