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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.


Linkage group (LG) formation in the HetMappS de novo pipeline.A representative dendrogram is shown for the F1 family ‘Horizon’ x Illinois 547–1, created from hierarchical clustering of a topological overlap matrix (as implemented in WGCNA), and subsequent cutting of the dendrogram. A cut height of 0.925 and minimum LG size of 50 resulted in 91% of the initial markers (15,464) separating into 40 LGs. Two pairs of LGs were joined in subsequent steps to create 2 parental maps with 19 LGs each.
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pone.0134880.g005: Linkage group (LG) formation in the HetMappS de novo pipeline.A representative dendrogram is shown for the F1 family ‘Horizon’ x Illinois 547–1, created from hierarchical clustering of a topological overlap matrix (as implemented in WGCNA), and subsequent cutting of the dendrogram. A cut height of 0.925 and minimum LG size of 50 resulted in 91% of the initial markers (15,464) separating into 40 LGs. Two pairs of LGs were joined in subsequent steps to create 2 parental maps with 19 LGs each.

Mentions: The de novo pipeline was initiated using the HetMappS Pt output markers identified in Table 1. LGs were resolved by hierarchical clustering and dendrogram cutting of all Pt markers simultaneously, cutting the dendrogram (Fig 5) at a height that resulted in 38 or more LGs while maximizing the number of markers retained (S2 File) The optimal cut height varied slightly among the four VitisGen families, with values between 0.925 and 0.95, and the number of resulting LGs obtained also varied, between 39 and 43 (Table 4). 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 as shown in the tables ‘GENOvsPARENT’ (S2 File), where the sum of heterozygous (het) alleles should be much greater than the sum of homozygous (hom) alleles, and physical location on a reference genome (S2 File, GENOvsPARENT and CHRvLGtop tabs, respectively)). 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)

Linkage group (LG) formation in the HetMappS de novo pipeline.A representative dendrogram is shown for the F1 family ‘Horizon’ x Illinois 547–1, created from hierarchical clustering of a topological overlap matrix (as implemented in WGCNA), and subsequent cutting of the dendrogram. A cut height of 0.925 and minimum LG size of 50 resulted in 91% of the initial markers (15,464) separating into 40 LGs. Two pairs of LGs were joined in subsequent steps to create 2 parental maps with 19 LGs each.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0134880.g005: Linkage group (LG) formation in the HetMappS de novo pipeline.A representative dendrogram is shown for the F1 family ‘Horizon’ x Illinois 547–1, created from hierarchical clustering of a topological overlap matrix (as implemented in WGCNA), and subsequent cutting of the dendrogram. A cut height of 0.925 and minimum LG size of 50 resulted in 91% of the initial markers (15,464) separating into 40 LGs. Two pairs of LGs were joined in subsequent steps to create 2 parental maps with 19 LGs each.
Mentions: The de novo pipeline was initiated using the HetMappS Pt output markers identified in Table 1. LGs were resolved by hierarchical clustering and dendrogram cutting of all Pt markers simultaneously, cutting the dendrogram (Fig 5) at a height that resulted in 38 or more LGs while maximizing the number of markers retained (S2 File) The optimal cut height varied slightly among the four VitisGen families, with values between 0.925 and 0.95, and the number of resulting LGs obtained also varied, between 39 and 43 (Table 4). 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 as shown in the tables ‘GENOvsPARENT’ (S2 File), where the sum of heterozygous (het) alleles should be much greater than the sum of homozygous (hom) alleles, and physical location on a reference genome (S2 File, GENOvsPARENT and CHRvLGtop tabs, respectively)). 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.