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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.


Relatedness to parents and Mendelian errors in the F1 family 'Horizon' x Illinois 547–1.A) Analysis of progeny relatedness to parents demonstrated that most progeny had expected relatedness values near (0,0), whereas 8 individuals were more related to ‘Horizon’ (emasculated hermaphrodite parent) and less related to Illinois547-1 (pollen parent) and were thus removed for downstream analysis. B) Mendelian error analysis indicated that 7 of these same individuals were enriched for male incompatible genotypes.
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pone.0134880.g002: Relatedness to parents and Mendelian errors in the F1 family 'Horizon' x Illinois 547–1.A) Analysis of progeny relatedness to parents demonstrated that most progeny had expected relatedness values near (0,0), whereas 8 individuals were more related to ‘Horizon’ (emasculated hermaphrodite parent) and less related to Illinois547-1 (pollen parent) and were thus removed for downstream analysis. B) Mendelian error analysis indicated that 7 of these same individuals were enriched for male incompatible genotypes.

Mentions: All progeny were tested for relatedness to the parents and for Mendelian errors, in order to identify pollen contaminants, self-hybridization, and mislabeling. Individuals derived from pollen contamination or self-hybridization were more related to the mother and less to the father than true progeny, as shown for eight outliers in the ‘Horizon’ x Illinois 547–1 dataset (Fig 2). Additionally, seven of these eight individuals had a high ratio of male incompatible Mendelian errors compared to female incompatible Mendelian errors. From zero to eight individuals were removed from each family, 1.7% of progeny across the families, (S3 Fig) resulting in the filtered number of progeny (S6 Table). After removing individuals, SNPs that were invariant or missing in all remaining individuals were removed, resulting in the filtered number of SNPs (S6 Table).


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)

Relatedness to parents and Mendelian errors in the F1 family 'Horizon' x Illinois 547–1.A) Analysis of progeny relatedness to parents demonstrated that most progeny had expected relatedness values near (0,0), whereas 8 individuals were more related to ‘Horizon’ (emasculated hermaphrodite parent) and less related to Illinois547-1 (pollen parent) and were thus removed for downstream analysis. B) Mendelian error analysis indicated that 7 of these same individuals were enriched for male incompatible genotypes.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0134880.g002: Relatedness to parents and Mendelian errors in the F1 family 'Horizon' x Illinois 547–1.A) Analysis of progeny relatedness to parents demonstrated that most progeny had expected relatedness values near (0,0), whereas 8 individuals were more related to ‘Horizon’ (emasculated hermaphrodite parent) and less related to Illinois547-1 (pollen parent) and were thus removed for downstream analysis. B) Mendelian error analysis indicated that 7 of these same individuals were enriched for male incompatible genotypes.
Mentions: All progeny were tested for relatedness to the parents and for Mendelian errors, in order to identify pollen contaminants, self-hybridization, and mislabeling. Individuals derived from pollen contamination or self-hybridization were more related to the mother and less to the father than true progeny, as shown for eight outliers in the ‘Horizon’ x Illinois 547–1 dataset (Fig 2). Additionally, seven of these eight individuals had a high ratio of male incompatible Mendelian errors compared to female incompatible Mendelian errors. From zero to eight individuals were removed from each family, 1.7% of progeny across the families, (S3 Fig) resulting in the filtered number of progeny (S6 Table). After removing individuals, SNPs that were invariant or missing in all remaining individuals were removed, resulting in the filtered number of SNPs (S6 Table).

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.