Prediction of identity by descent probabilities from marker-haplotypes
<p>Abstract</p> <p>The prediction of identity by descent (IBD) probabilities is essential for all methods that map quantitative trait loci (QTL). The IBD probabilities may be predicted from marker genotypes and/or pedigree information. Here, a method is presented that predicts IBD...
| Main Authors: | , |
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| Format: | Article |
| Language: | deu |
| Published: |
BMC
2001-11-01
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| Series: | Genetics Selection Evolution |
| Subjects: | |
| Online Access: | http://www.gsejournal.org/content/33/6/605 |
| _version_ | 1818752297798205440 |
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| author | Goddard Mike E Meuwissen Theo HE |
| author_facet | Goddard Mike E Meuwissen Theo HE |
| author_sort | Goddard Mike E |
| collection | DOAJ |
| description | <p>Abstract</p> <p>The prediction of identity by descent (IBD) probabilities is essential for all methods that map quantitative trait loci (QTL). The IBD probabilities may be predicted from marker genotypes and/or pedigree information. Here, a method is presented that predicts IBD probabilities at a given chromosomal location given data on a haplotype of markers spanning that position. The method is based on a simplification of the coalescence process, and assumes that the number of generations since the base population and effective population size is known, although effective size may be estimated from the data. The probability that two gametes are IBD at a particular locus increases as the number of markers surrounding the locus with identical alleles increases. This effect is more pronounced when effective population size is high. Hence as effective population size increases, the IBD probabilities become more sensitive to the marker data which should favour finer scale mapping of the QTL. The IBD probability prediction method was developed for the situation where the pedigree of the animals was unknown (<it>i.e. </it>all information came from the marker genotypes), and the situation where, say <it>T</it>, generations of unknown pedigree are followed by some generations where pedigree and marker genotypes are known.</p> |
| first_indexed | 2024-12-18T04:49:14Z |
| format | Article |
| id | doaj.art-88e9ab1ae25b46e4b3fa322a8d8f43a0 |
| institution | Directory Open Access Journal |
| issn | 0999-193X 1297-9686 |
| language | deu |
| last_indexed | 2024-12-18T04:49:14Z |
| publishDate | 2001-11-01 |
| publisher | BMC |
| record_format | Article |
| series | Genetics Selection Evolution |
| spelling | doaj.art-88e9ab1ae25b46e4b3fa322a8d8f43a02022-12-21T21:20:28ZdeuBMCGenetics Selection Evolution0999-193X1297-96862001-11-0133660563410.1186/1297-9686-33-6-605Prediction of identity by descent probabilities from marker-haplotypesGoddard Mike EMeuwissen Theo HE<p>Abstract</p> <p>The prediction of identity by descent (IBD) probabilities is essential for all methods that map quantitative trait loci (QTL). The IBD probabilities may be predicted from marker genotypes and/or pedigree information. Here, a method is presented that predicts IBD probabilities at a given chromosomal location given data on a haplotype of markers spanning that position. The method is based on a simplification of the coalescence process, and assumes that the number of generations since the base population and effective population size is known, although effective size may be estimated from the data. The probability that two gametes are IBD at a particular locus increases as the number of markers surrounding the locus with identical alleles increases. This effect is more pronounced when effective population size is high. Hence as effective population size increases, the IBD probabilities become more sensitive to the marker data which should favour finer scale mapping of the QTL. The IBD probability prediction method was developed for the situation where the pedigree of the animals was unknown (<it>i.e. </it>all information came from the marker genotypes), and the situation where, say <it>T</it>, generations of unknown pedigree are followed by some generations where pedigree and marker genotypes are known.</p>http://www.gsejournal.org/content/33/6/605identity by descenthaplotype analysiscoalescence processlinkage disequilibriumQTL mapping |
| spellingShingle | Goddard Mike E Meuwissen Theo HE Prediction of identity by descent probabilities from marker-haplotypes Genetics Selection Evolution identity by descent haplotype analysis coalescence process linkage disequilibrium QTL mapping |
| title | Prediction of identity by descent probabilities from marker-haplotypes |
| title_full | Prediction of identity by descent probabilities from marker-haplotypes |
| title_fullStr | Prediction of identity by descent probabilities from marker-haplotypes |
| title_full_unstemmed | Prediction of identity by descent probabilities from marker-haplotypes |
| title_short | Prediction of identity by descent probabilities from marker-haplotypes |
| title_sort | prediction of identity by descent probabilities from marker haplotypes |
| topic | identity by descent haplotype analysis coalescence process linkage disequilibrium QTL mapping |
| url | http://www.gsejournal.org/content/33/6/605 |
| work_keys_str_mv | AT goddardmikee predictionofidentitybydescentprobabilitiesfrommarkerhaplotypes AT meuwissentheohe predictionofidentitybydescentprobabilitiesfrommarkerhaplotypes |