Main Goal

We aim to develop a highly affordable whole-genome genotyping platform that offers extensive and rapid genotyping accessible to breeders in a fee-for-service basis.

The germplasm used in breeding programs is typically of two types: 1) elite materials already adapted to the targeted growing areas and 2) "exotic'" accessions that are sources of novel genetics that confer specific traits of interest. When developing efficient genotyping tools, both of these needs to be taken into account. The approach we propose relies on the combination of a very low-cost genotyping approach, genotyping-by-sequencing (GBS), and whole-genome re-sequencing of representative soybean lines that will then allow us to rapidly characterize any line at millions of SNPs.

The following sub-objectives will be instrumental to reach the main goal.

Act.1.1 Production of a haplotype map by whole-genome re-sequencing 

We will aim to capture the genetic diversity that exists on a genome-wide level within both elite short-season soybean lines and “exotic” accessions that are of interest to breeders in Canada (and elsewhere)

Act.1.2 Development of an integrated haplotype map for short-season soybean

The purpose of this sub-objective is to first impute any missing data in our GBS-derived set of SNPs (typically 50-60K markers; depending on sequencing depth) and then to integrate these GBS SNP data with other existing SNP datasets derived from other genotyping approaches.

Act.1.3 Production of a "universal" GBS database to allow for rapid genotyping 

This sub-objective aims at developing a highly efficient genotyping pipeline to more rapidly extract a catalogue of SNPs directly from GBS read data

Act.1.4 Private and public breeder training on the handling of these data sets 

Our objective here is to ensure active, hands-on end-user engagement in the use of large-scale genotypic datasets through training workshops coinciding with our yearly research workshops.

1) Complete catalogue of SNPs from re-sequencing up to 200 soybean lines

2) Haplotype map for lines of interest to Canadian breeders

3) Universal GBS-database of SNPs for use with TASSEL-GBSv2 pipeline