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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

Comparison of the distribution of minor tag frequency (MTF) and minor allele frequencies (MAF) in final and spurious SNPs.MTF (continuous line) and MAF (dotted line) distributions are shown for A) the final map (9,876 SNPs) and B) markers removed during curation (1,204 SNPs) in ‘Horizon’ x Illinois 547–1 de novo map.
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pone.0134880.g007: Comparison of the distribution of minor tag frequency (MTF) and minor allele frequencies (MAF) in final and spurious SNPs.MTF (continuous line) and MAF (dotted line) distributions are shown for A) the final map (9,876 SNPs) and B) markers removed during curation (1,204 SNPs) in ‘Horizon’ x Illinois 547–1 de novo map.

Mentions: While the minor allele frequency (MAF) in the final maps showed a normal distribution centered near 0.25 (Fig 7), the minor tag frequency (MTF, measured at read depth level of alleles) suggested a bimodal distribution with peak modes of 0.25 and 0.125 (Fig 7). In contrast, markers removed during the map curation process were distributed across all MTFs with a peak lower than 0.125 and with no correlation to the MAF distribution (Fig 7).


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)

Comparison of the distribution of minor tag frequency (MTF) and minor allele frequencies (MAF) in final and spurious SNPs.MTF (continuous line) and MAF (dotted line) distributions are shown for A) the final map (9,876 SNPs) and B) markers removed during curation (1,204 SNPs) in ‘Horizon’ x Illinois 547–1 de novo map.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0134880.g007: Comparison of the distribution of minor tag frequency (MTF) and minor allele frequencies (MAF) in final and spurious SNPs.MTF (continuous line) and MAF (dotted line) distributions are shown for A) the final map (9,876 SNPs) and B) markers removed during curation (1,204 SNPs) in ‘Horizon’ x Illinois 547–1 de novo map.
Mentions: While the minor allele frequency (MAF) in the final maps showed a normal distribution centered near 0.25 (Fig 7), the minor tag frequency (MTF, measured at read depth level of alleles) suggested a bimodal distribution with peak modes of 0.25 and 0.125 (Fig 7). In contrast, markers removed during the map curation process were distributed across all MTFs with a peak lower than 0.125 and with no correlation to the MAF distribution (Fig 7).

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