HetMappS: Heterozygous Mapping Strategy for High Resolution Genotyping-by-Sequencing Markers

Reduced representation genotyping approaches, such as genotyping-by-sequencing (GBS), provide opportunities to generate high-resolution genetic maps at a low per-sample cost. However, missing data and non-uniform sequence coverage can complicate map creation in highly heterozygous species. To facilitate the creation of high-resolution genetic maps in highly heterozygous species, we have developed a modular pipeline, HetMappS, with an initial focus on analysis of GBS data. The pipeline functions independently of parental genotypes and provides tools for correction of genotyping errors associated with heterozygosity. HetMappS includes both a reference-based synteny pipeline, for species with a reference genome, and a reference-free de novo pipeline for species without a reference. Here, we apply the HetMappS pipeline to four half-sib F₁ Vitis families, using both synteny and de novo pipelines, and an oyster mapping population with the de novo pipeline. For Vitis families, the HetMappS pipelines identified 10,440 to 15,464 phased pseudotestcross markers, of which 2,000 to 10,000 non-redundant markers were assembled into high-confidence genetic maps.  As expected, the number of non-redundant markers on each map was strongly correlated with number of progeny in the family (R² ~ 0.85).  Thus, with GBS and the HetMappS pipeline, family size has become the limiting factor to map resolution in Vitis and other heterozygous species.