Abstract

The Next-Generation Sequencing Revolution in Soybean: GBS, SNP arrays, WGS and Beyond

Francois Belzile, Full Professor, Laval University

Next-generation sequencing technologies have revolutionized many areas in biological sciences. In the field of crop genomics, they have mostly provided researchers with reference genomes and major advances in genotyping. In our group, we are exploiting these tools in soybean and other crop species to develop efficient genotyping-by-sequencing (GBS) approaches and analytical tools to provide cost-effective genotyping solutions to breeders. In the first part of this talk, I will describe our latest pipeline (Fast-GBS) for calling SNPs from GBS read data and will provide an overview of its efficiency and accuracy. We will then explore how powerful imputation methods can be exploited to combine GBS data with publicly available SNP array and whole-genome sequencing (WGS) data, an approach that we call “scanning and filling”. In the second portion of my talk, I will illustrate how such dense genome-wide SNP coverage can facilitate the identification of QTLs that are highly relevant to a specific set of breeding materials. In another application, we will explore how these tools can greatly facilitate the identification of known and novel alleles at loci that are known to control maturity in soybean. In closing, I will provide a brief overview of the SoyaGen project, a large-scale applied genomics project focusing on short-season soybean in Canada.