Family-Based Haplotype Estimation and Allele Dosage Correction for Polyploids Using Short Sequence Reads
DNA sequence reads contain information about the genomic variants located on a single chromosome. By extracting and extending this information using the overlaps between the reads, the haplotypes of an individual can be obtained. Using parent-offspring relationships in a population can considerably...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-04-01
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| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2019.00335/full |
| _version_ | 1818206290964381696 |
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| author | Ehsan Motazedi Ehsan Motazedi Chris Maliepaard Richard Finkers Richard Visser Dick de Ridder |
| author_facet | Ehsan Motazedi Ehsan Motazedi Chris Maliepaard Richard Finkers Richard Visser Dick de Ridder |
| author_sort | Ehsan Motazedi |
| collection | DOAJ |
| description | DNA sequence reads contain information about the genomic variants located on a single chromosome. By extracting and extending this information using the overlaps between the reads, the haplotypes of an individual can be obtained. Using parent-offspring relationships in a population can considerably improve the quality of the haplotypes obtained from short reads, as pedigree information can be used to correct for spurious overlaps (due to sequencing errors) and insufficient overlaps (due to short read lengths, low genomic variation and shallow coverage). We developed a novel method, PopPoly, to estimate polyploid haplotypes in an F1-population from short sequence data by taking into consideration the transmission of the haplotypes from the parents to the offspring. In addition, this information is employed to improve genotype dosage estimation and to call missing genotypes in the population. Through simulations, we compare PopPoly to other haplotyping methods and show its better performance. We evaluate PopPoly by applying it to a tetraploid potato cross at nine genomic regions involved in tuber formation. |
| first_indexed | 2024-12-12T04:10:41Z |
| format | Article |
| id | doaj.art-a6d79dd4d66647cf9245f3a328047e84 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-12T04:10:41Z |
| publishDate | 2019-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-a6d79dd4d66647cf9245f3a328047e842022-12-22T00:38:37ZengFrontiers Media S.A.Frontiers in Genetics1664-80212019-04-011010.3389/fgene.2019.00335442980Family-Based Haplotype Estimation and Allele Dosage Correction for Polyploids Using Short Sequence ReadsEhsan Motazedi0Ehsan Motazedi1Chris Maliepaard2Richard Finkers3Richard Visser4Dick de Ridder5Bioinformatics Group, Wageningen University & Research, Wageningen, NetherlandsPlant Breeding, Wageningen University & Research, Wageningen, NetherlandsPlant Breeding, Wageningen University & Research, Wageningen, NetherlandsPlant Breeding, Wageningen University & Research, Wageningen, NetherlandsPlant Breeding, Wageningen University & Research, Wageningen, NetherlandsBioinformatics Group, Wageningen University & Research, Wageningen, NetherlandsDNA sequence reads contain information about the genomic variants located on a single chromosome. By extracting and extending this information using the overlaps between the reads, the haplotypes of an individual can be obtained. Using parent-offspring relationships in a population can considerably improve the quality of the haplotypes obtained from short reads, as pedigree information can be used to correct for spurious overlaps (due to sequencing errors) and insufficient overlaps (due to short read lengths, low genomic variation and shallow coverage). We developed a novel method, PopPoly, to estimate polyploid haplotypes in an F1-population from short sequence data by taking into consideration the transmission of the haplotypes from the parents to the offspring. In addition, this information is employed to improve genotype dosage estimation and to call missing genotypes in the population. Through simulations, we compare PopPoly to other haplotyping methods and show its better performance. We evaluate PopPoly by applying it to a tetraploid potato cross at nine genomic regions involved in tuber formation.https://www.frontiersin.org/article/10.3389/fgene.2019.00335/fullhaplotypepolyploidsequence datafamilyestimation |
| spellingShingle | Ehsan Motazedi Ehsan Motazedi Chris Maliepaard Richard Finkers Richard Visser Dick de Ridder Family-Based Haplotype Estimation and Allele Dosage Correction for Polyploids Using Short Sequence Reads Frontiers in Genetics haplotype polyploid sequence data family estimation |
| title | Family-Based Haplotype Estimation and Allele Dosage Correction for Polyploids Using Short Sequence Reads |
| title_full | Family-Based Haplotype Estimation and Allele Dosage Correction for Polyploids Using Short Sequence Reads |
| title_fullStr | Family-Based Haplotype Estimation and Allele Dosage Correction for Polyploids Using Short Sequence Reads |
| title_full_unstemmed | Family-Based Haplotype Estimation and Allele Dosage Correction for Polyploids Using Short Sequence Reads |
| title_short | Family-Based Haplotype Estimation and Allele Dosage Correction for Polyploids Using Short Sequence Reads |
| title_sort | family based haplotype estimation and allele dosage correction for polyploids using short sequence reads |
| topic | haplotype polyploid sequence data family estimation |
| url | https://www.frontiersin.org/article/10.3389/fgene.2019.00335/full |
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