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Heterozygous Mapping Strategy (HetMappS) for High Resolution Genotyping-By-Sequencing Markers: A Case Study in Grapevine.

Hyma KE, Barba P, Wang M, Londo JP, Acharya CB, Mitchell SE, Sun Q, Reisch B, Cadle-Davidson L - PLoS ONE (2015)

Bottom Line: To overcome these issues, we developed a publicly available, modular approach called HetMappS, which functions independently of parental genotypes and corrects for genotyping errors associated with heterozygosity.Flower sex was mapped in three families and correctly localized to the known sex locus in all cases.The HetMappS pipeline could have wide application for genetic mapping in highly heterozygous species, and its modularity provides opportunities to adapt portions of the pipeline to other family types, genotyping technologies or applications.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics 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.

ABSTRACT
Genotyping by sequencing (GBS) provides opportunities to generate high-resolution genetic maps at a low genotyping cost, but for highly heterozygous species, missing data and heterozygote undercalling complicate the creation of GBS genetic maps. To overcome these issues, we developed a publicly available, modular approach called HetMappS, which functions independently of parental genotypes and corrects for genotyping errors associated with heterozygosity. For linkage group formation, HetMappS includes both a reference-guided synteny pipeline and a reference-independent de novo pipeline. The de novo pipeline can be utilized for under-characterized or high diversity families that lack an appropriate reference. We applied both HetMappS pipelines in five half-sib F1 families involving genetically diverse Vitis spp. Starting with at least 116,466 putative SNPs per family, the HetMappS pipelines identified 10,440 to 17,267 phased pseudo-testcross (Pt) markers and generated high-confidence maps. Pt marker density exceeded crossover resolution in all cases; up to 5,560 non-redundant markers were used to generate parental maps ranging from 1,047 cM to 1,696 cM. The number of markers used was strongly correlated with family size in both de novo and synteny maps (r = 0.92 and 0.91, respectively). Comparisons between allele and tag frequencies suggested that many markers were in tandem repeats and mapped as single loci, while markers in regions of more than two repeats were removed during map curation. Both pipelines generated similar genetic maps, and genetic order was strongly correlated with the reference genome physical order in all cases. Independently created genetic maps from shared parents exhibited nearly identical results. Flower sex was mapped in three families and correctly localized to the known sex locus in all cases. The HetMappS pipeline could have wide application for genetic mapping in highly heterozygous species, and its modularity provides opportunities to adapt portions of the pipeline to other family types, genotyping technologies or applications.

No MeSH data available.


Related in: MedlinePlus

Separation of chromosomes into linkage groups (LGs) in the HetMappS synteny pipeline.This dendrogram was created from hierarchical clustering of a topological overlap matrix (as implemented by WGCNA) for markers on chromosome 2 in the F1 family ‘Horizon’ x Illinois 547–1. LGs result from cutting the dendrogram with height 0.9 and minimum cluster size 30, creating one LG for each parent.
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pone.0134880.g003: Separation of chromosomes into linkage groups (LGs) in the HetMappS synteny pipeline.This dendrogram was created from hierarchical clustering of a topological overlap matrix (as implemented by WGCNA) for markers on chromosome 2 in the F1 family ‘Horizon’ x Illinois 547–1. LGs result from cutting the dendrogram with height 0.9 and minimum cluster size 30, creating one LG for each parent.

Mentions: Markers from each chromosome were further separated into linkage groups (LGs) corresponding to the minor allele contribution from each parent, through hierarchical clustering and dendrogram cutting (Fig 3). A static cut of the dendrogram with height 0.9 for the VitisGen families and 0.825 for the V. rupestris B38 x ‘Chardonnay’ family, with a minimum cluster size of 30, resolved two or more LGs per chromosome. For all VitisGen families, a static cut height of 0.9 resolved at least one LG per chromosome per parent. In some cases, chromosomal groups were split into more than one LG per parent, resulting in a larger number of LGs than the expected 38 per grapevine family (Table 3). These extra groups can be fused together at the ordering step if the true classification can be determined, either by looking for recombination fractions lower than 0.5 [51] among groups or by reference to the parental contribution of the minor allele (S3 File). Results shown here were based on the latter approach.


Heterozygous Mapping Strategy (HetMappS) for High Resolution Genotyping-By-Sequencing Markers: A Case Study in Grapevine.

Hyma KE, Barba P, Wang M, Londo JP, Acharya CB, Mitchell SE, Sun Q, Reisch B, Cadle-Davidson L - PLoS ONE (2015)

Separation of chromosomes into linkage groups (LGs) in the HetMappS synteny pipeline.This dendrogram was created from hierarchical clustering of a topological overlap matrix (as implemented by WGCNA) for markers on chromosome 2 in the F1 family ‘Horizon’ x Illinois 547–1. LGs result from cutting the dendrogram with height 0.9 and minimum cluster size 30, creating one LG for each parent.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4526651&req=5

pone.0134880.g003: Separation of chromosomes into linkage groups (LGs) in the HetMappS synteny pipeline.This dendrogram was created from hierarchical clustering of a topological overlap matrix (as implemented by WGCNA) for markers on chromosome 2 in the F1 family ‘Horizon’ x Illinois 547–1. LGs result from cutting the dendrogram with height 0.9 and minimum cluster size 30, creating one LG for each parent.
Mentions: Markers from each chromosome were further separated into linkage groups (LGs) corresponding to the minor allele contribution from each parent, through hierarchical clustering and dendrogram cutting (Fig 3). A static cut of the dendrogram with height 0.9 for the VitisGen families and 0.825 for the V. rupestris B38 x ‘Chardonnay’ family, with a minimum cluster size of 30, resolved two or more LGs per chromosome. For all VitisGen families, a static cut height of 0.9 resolved at least one LG per chromosome per parent. In some cases, chromosomal groups were split into more than one LG per parent, resulting in a larger number of LGs than the expected 38 per grapevine family (Table 3). These extra groups can be fused together at the ordering step if the true classification can be determined, either by looking for recombination fractions lower than 0.5 [51] among groups or by reference to the parental contribution of the minor allele (S3 File). Results shown here were based on the latter approach.

Bottom Line: To overcome these issues, we developed a publicly available, modular approach called HetMappS, which functions independently of parental genotypes and corrects for genotyping errors associated with heterozygosity.Flower sex was mapped in three families and correctly localized to the known sex locus in all cases.The HetMappS pipeline could have wide application for genetic mapping in highly heterozygous species, and its modularity provides opportunities to adapt portions of the pipeline to other family types, genotyping technologies or applications.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics 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.

ABSTRACT
Genotyping by sequencing (GBS) provides opportunities to generate high-resolution genetic maps at a low genotyping cost, but for highly heterozygous species, missing data and heterozygote undercalling complicate the creation of GBS genetic maps. To overcome these issues, we developed a publicly available, modular approach called HetMappS, which functions independently of parental genotypes and corrects for genotyping errors associated with heterozygosity. For linkage group formation, HetMappS includes both a reference-guided synteny pipeline and a reference-independent de novo pipeline. The de novo pipeline can be utilized for under-characterized or high diversity families that lack an appropriate reference. We applied both HetMappS pipelines in five half-sib F1 families involving genetically diverse Vitis spp. Starting with at least 116,466 putative SNPs per family, the HetMappS pipelines identified 10,440 to 17,267 phased pseudo-testcross (Pt) markers and generated high-confidence maps. Pt marker density exceeded crossover resolution in all cases; up to 5,560 non-redundant markers were used to generate parental maps ranging from 1,047 cM to 1,696 cM. The number of markers used was strongly correlated with family size in both de novo and synteny maps (r = 0.92 and 0.91, respectively). Comparisons between allele and tag frequencies suggested that many markers were in tandem repeats and mapped as single loci, while markers in regions of more than two repeats were removed during map curation. Both pipelines generated similar genetic maps, and genetic order was strongly correlated with the reference genome physical order in all cases. Independently created genetic maps from shared parents exhibited nearly identical results. Flower sex was mapped in three families and correctly localized to the known sex locus in all cases. The HetMappS pipeline could have wide application for genetic mapping in highly heterozygous species, and its modularity provides opportunities to adapt portions of the pipeline to other family types, genotyping technologies or applications.

No MeSH data available.


Related in: MedlinePlus