Model and Algorithm for Linkage Disequilibrium Analysis in a Non-equilibrium Population
The multilocus analysis of polymorphisms has emerged as a vital ingredient of population genetics and evolutionary biology. A fundamental assumption used for existing multilocus analysis approaches is Hardy-Weinberg equilibrium (HWE) at which maternally- and paternally-derived gametes combine random...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2012-07-01
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| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fgene.2012.00078/full |
| _version_ | 1818268684875988992 |
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| author | Jingyuan eLiu Zhong eWang Yaqun eWang Runze eLi Rongling eWu |
| author_facet | Jingyuan eLiu Zhong eWang Yaqun eWang Runze eLi Rongling eWu |
| author_sort | Jingyuan eLiu |
| collection | DOAJ |
| description | The multilocus analysis of polymorphisms has emerged as a vital ingredient of population genetics and evolutionary biology. A fundamental assumption used for existing multilocus analysis approaches is Hardy-Weinberg equilibrium (HWE) at which maternally- and paternally-derived gametes combine randomly during fertilization. Given the fact that natural populations are rarely panmictic, these approaches will have a significant limitation for practical use. We present a robust model for multilocus linkage disequilibrium analysis which does not rely on the assumption of random mating. This new disequilibrium model capitalizes on Weir’s definition of zygotic disequilibria and is based on an open-pollinated design in which multiple maternal individuals and their half-sib families are sampled from a natural population. This design captures two levels of associations: one is at the upper level that describes the pattern of co-segregation between different loci in the parental population and the other is at the lower level that specifies the extent of co-transmission of non-alleles at different loci from parents to their offspring. An MCMC method was implemented to estimate genetic parameters that define these associations. Simulation studies were used to validate the statistical behavior of the new model. |
| first_indexed | 2024-12-12T20:42:25Z |
| format | Article |
| id | doaj.art-aaaded22244a4101912a8df12d20d595 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-12T20:42:25Z |
| publishDate | 2012-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-aaaded22244a4101912a8df12d20d5952022-12-22T00:12:40ZengFrontiers Media S.A.Frontiers in Genetics1664-80212012-07-01310.3389/fgene.2012.0007816882Model and Algorithm for Linkage Disequilibrium Analysis in a Non-equilibrium PopulationJingyuan eLiu0Zhong eWang1Yaqun eWang2Runze eLi3Rongling eWu4Pennsylvania State UniversityPennsylvania State UniversityPennsylvania State UniversityPennsylvania State UniversityPennsylvania State UniversityThe multilocus analysis of polymorphisms has emerged as a vital ingredient of population genetics and evolutionary biology. A fundamental assumption used for existing multilocus analysis approaches is Hardy-Weinberg equilibrium (HWE) at which maternally- and paternally-derived gametes combine randomly during fertilization. Given the fact that natural populations are rarely panmictic, these approaches will have a significant limitation for practical use. We present a robust model for multilocus linkage disequilibrium analysis which does not rely on the assumption of random mating. This new disequilibrium model capitalizes on Weir’s definition of zygotic disequilibria and is based on an open-pollinated design in which multiple maternal individuals and their half-sib families are sampled from a natural population. This design captures two levels of associations: one is at the upper level that describes the pattern of co-segregation between different loci in the parental population and the other is at the lower level that specifies the extent of co-transmission of non-alleles at different loci from parents to their offspring. An MCMC method was implemented to estimate genetic parameters that define these associations. Simulation studies were used to validate the statistical behavior of the new model.http://journal.frontiersin.org/Journal/10.3389/fgene.2012.00078/fullgametic linkage disequilibriumzygotic linkage disequilibriumHardy-Weinberg equilibriumnon-equilibrium populationmolecular marker |
| spellingShingle | Jingyuan eLiu Zhong eWang Yaqun eWang Runze eLi Rongling eWu Model and Algorithm for Linkage Disequilibrium Analysis in a Non-equilibrium Population Frontiers in Genetics gametic linkage disequilibrium zygotic linkage disequilibrium Hardy-Weinberg equilibrium non-equilibrium population molecular marker |
| title | Model and Algorithm for Linkage Disequilibrium Analysis in a Non-equilibrium Population |
| title_full | Model and Algorithm for Linkage Disequilibrium Analysis in a Non-equilibrium Population |
| title_fullStr | Model and Algorithm for Linkage Disequilibrium Analysis in a Non-equilibrium Population |
| title_full_unstemmed | Model and Algorithm for Linkage Disequilibrium Analysis in a Non-equilibrium Population |
| title_short | Model and Algorithm for Linkage Disequilibrium Analysis in a Non-equilibrium Population |
| title_sort | model and algorithm for linkage disequilibrium analysis in a non equilibrium population |
| topic | gametic linkage disequilibrium zygotic linkage disequilibrium Hardy-Weinberg equilibrium non-equilibrium population molecular marker |
| url | http://journal.frontiersin.org/Journal/10.3389/fgene.2012.00078/full |
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