A New Lab Guide on Genotyping-by-Sequencing for Plant Genetic Diversity Analysis

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 GBS applications, particularly in non-model species. We develop a genetic diversity focused GBS (gd-GBS) protocol and present it as an easy-to-follow lab guide to assist a researcher through every step of a GBS application from sample preparation, library assembly, sequencing, SNP calling, to diversity analysis. It uses two restriction enzymes to reduce genome complexity, applies Illumina multiplexing indexes for barcoding, and has a custom bioinformatics pipeline (npGeno) for automatic SNP genotyping. In this presentation, I will introduce the new GBS lab guide, illustrate its application, discuss related application issues, and update our current efforts in GBS research. Following these lab bench procedures and using the npGeno pipeline, one could generate genome-wide SNP genotype data for a conventional genetic diversity analysis of a plant species.