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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.


Localization of the flower sex locus using de novo maps from three families.The PN40024 version 12X.2 reference surrounding the sex locus is shown. Numbers above blue and orange sections indicate scaffold id. Blue scaffolds were located in chromosome 2 and orange scaffolds were located in “unknown” chromosomes in the previous version 12X.0 of PN40024. Connecting lines indicate physical position for SNPs in three de novo maps: A) ‘Horizon’ x Illinois 547–1, B) ‘Horizon’ x V. cinerea B9, and C) ‘Chardonnay’ x V. cinerea B9. For each map, localization of flower sex locus is shown. Shaded areas indicating 1.8 LOD confidence intervals and solid red areas indicate position of the maximum LOD.
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pone.0134880.g008: Localization of the flower sex locus using de novo maps from three families.The PN40024 version 12X.2 reference surrounding the sex locus is shown. Numbers above blue and orange sections indicate scaffold id. Blue scaffolds were located in chromosome 2 and orange scaffolds were located in “unknown” chromosomes in the previous version 12X.0 of PN40024. Connecting lines indicate physical position for SNPs in three de novo maps: A) ‘Horizon’ x Illinois 547–1, B) ‘Horizon’ x V. cinerea B9, and C) ‘Chardonnay’ x V. cinerea B9. For each map, localization of flower sex locus is shown. Shaded areas indicating 1.8 LOD confidence intervals and solid red areas indicate position of the maximum LOD.

Mentions: Among the five interrelated families, flower sex segregated as a major locus following the current genetic model of dominance M > H > f for three families: ‘Horizon’ x Illinois 547–1, ‘Horizon’ x V. cinerea B9 and ‘Chardonnay’ x V. cinerea B9, with a 1:1 ratio of male:hermaphrodite (χ2(1) = 3.1935, 0.7042 and 2.3478, respectively). Crosses made with the female parent V. rupestris B38 (f f) showed no segregation of flower sex with all progeny being hermaphroditic, indicating that that ‘Chardonnay’ [54] and ‘Horizon’ are homozygous for the hermaphrodite allele (HH). In all three crosses and both pipelines, the flower sex locus consistently mapped to a physical position between 4.75 Mb to 5.39 Mb of the PN40024 version 12X.0 (Table 7), further supporting previous genetic analyses of flower sex [33–35]. Combining the genetic maps from these three families in alignment with the reference genome provided a higher resolution of the flower sex locus (Fig 8).


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)

Localization of the flower sex locus using de novo maps from three families.The PN40024 version 12X.2 reference surrounding the sex locus is shown. Numbers above blue and orange sections indicate scaffold id. Blue scaffolds were located in chromosome 2 and orange scaffolds were located in “unknown” chromosomes in the previous version 12X.0 of PN40024. Connecting lines indicate physical position for SNPs in three de novo maps: A) ‘Horizon’ x Illinois 547–1, B) ‘Horizon’ x V. cinerea B9, and C) ‘Chardonnay’ x V. cinerea B9. For each map, localization of flower sex locus is shown. Shaded areas indicating 1.8 LOD confidence intervals and solid red areas indicate position of the maximum LOD.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0134880.g008: Localization of the flower sex locus using de novo maps from three families.The PN40024 version 12X.2 reference surrounding the sex locus is shown. Numbers above blue and orange sections indicate scaffold id. Blue scaffolds were located in chromosome 2 and orange scaffolds were located in “unknown” chromosomes in the previous version 12X.0 of PN40024. Connecting lines indicate physical position for SNPs in three de novo maps: A) ‘Horizon’ x Illinois 547–1, B) ‘Horizon’ x V. cinerea B9, and C) ‘Chardonnay’ x V. cinerea B9. For each map, localization of flower sex locus is shown. Shaded areas indicating 1.8 LOD confidence intervals and solid red areas indicate position of the maximum LOD.
Mentions: Among the five interrelated families, flower sex segregated as a major locus following the current genetic model of dominance M > H > f for three families: ‘Horizon’ x Illinois 547–1, ‘Horizon’ x V. cinerea B9 and ‘Chardonnay’ x V. cinerea B9, with a 1:1 ratio of male:hermaphrodite (χ2(1) = 3.1935, 0.7042 and 2.3478, respectively). Crosses made with the female parent V. rupestris B38 (f f) showed no segregation of flower sex with all progeny being hermaphroditic, indicating that that ‘Chardonnay’ [54] and ‘Horizon’ are homozygous for the hermaphrodite allele (HH). In all three crosses and both pipelines, the flower sex locus consistently mapped to a physical position between 4.75 Mb to 5.39 Mb of the PN40024 version 12X.0 (Table 7), further supporting previous genetic analyses of flower sex [33–35]. Combining the genetic maps from these three families in alignment with the reference genome provided a higher resolution of the flower sex locus (Fig 8).

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.