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Title:   Author  item
                                            HYMA, KATIE - Cornell Universityitem
                                            BARBA, PAOLA - Cornell Universityitem
                                            WANG, MINGHUI - Cornell Universityitem
                                            Londo, Jasonitem
                                            HARE, MATTHEW - Cornell Universityitem
                                            ACHARYA, CHARLOTTE - Cornell Universityitem
                                            MITCHELL, SHARON - Cornell Universityitem
                                            SUN, QI - Cornell Universityitem
                                            REISCH, BRUCE - Cornell Universityitem
                                            Cadle-Davidson, Lance
  Submitted to: Annual International Plant & Animal Genome Conference
                                    Publication Type: Abstract Only
                                    Publication Acceptance Date: 11/15/2014
                                    Publication  Date: 1/1/2015
                                    Citation: Hyma, K., Barba, P., Wang, M., Londo, J.P., Hare, M., Acharya, C., Mitchell, S., Sun, Q., Reisch, B., Cadle Davidson, L.E. 2015. HetMappsS: Heterozygous mapping strategy for high resolution Genotyping-by-Sequencing Markers. Annual International Plant & Animal Genome Conference, San Diego, CA.Interpretive Summary:
                                Technical Abstract: 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.


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