Heterozygous Mapping Strategy (HetMappS) for High Resolution Genotyping-By-Sequencing Markers: A Case Study in
Katie E Hyma1, Paola Barba2, Minghui Wang3
1Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America; Genomic Diversity Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America.
Plos One
|August 6, 2015
Summary
We developed HetMappS, a new tool for creating genetic maps in highly heterozygous species using genotyping by sequencing (GBS). This method overcomes missing data and heterozygote undercalling, enabling accurate genetic mapping for diverse plant families.
Area of Science:
- Genetics
- Genomics
- Bioinformatics
Background:
- Genotyping by sequencing (GBS) offers cost-effective, high-resolution genetic mapping.
- Highly heterozygous species present challenges like missing data and undercalled heterozygotes in GBS genetic map creation.
Purpose of the Study:
- To develop a publicly available, modular approach (HetMappS) to overcome GBS limitations in highly heterozygous species.
- To enable accurate genetic map creation independent of parental genotypes and correct for heterozygosity-associated errors.
Main Methods:
- Developed HetMappS with reference-guided synteny and reference-independent de novo pipelines.
- Applied pipelines to five diverse Vitis spp. half-sib F1 families, analyzing over 116,466 SNPs per family.
- Generated phased pseudo-testcross (Pt) markers and high-confidence genetic maps.
Main Results:
- Identified 10,440–17,267 phased Pt markers per family, generating parental maps (1,047–1,696 cM) with high marker density.
- Demonstrated strong correlation between marker number and family size (r = 0.92–0.91).
- Validated map accuracy by correctly localizing the flower sex locus and showing high correlation between genetic and physical order.
Conclusions:
- HetMappS successfully generates high-confidence genetic maps in highly heterozygous species, overcoming common GBS challenges.
- The pipeline's modularity allows adaptation for various family types, genotyping methods, and applications.
- HetMappS is a valuable tool for genetic mapping in under-characterized or diverse plant populations.
