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Recursive Algorithms for Modeling Genomic Ancestral Origins in a Fixed Pedigree
The study of gene flow in pedigrees is of strong interest for the development of quantitative trait loci (QTL) mapping methods in multiparental populations. We developed a Markovian framework for modeling ancestral origins along two homologous chromosomes within individuals in fixed pedigrees. A hig...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Genetics Society of America
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6169389/ https://www.ncbi.nlm.nih.gov/pubmed/30068523 http://dx.doi.org/10.1534/g3.118.200340 |
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author | Zheng, Chaozhi Boer, Martin P. van Eeuwijk, Fred A. |
author_facet | Zheng, Chaozhi Boer, Martin P. van Eeuwijk, Fred A. |
author_sort | Zheng, Chaozhi |
collection | PubMed |
description | The study of gene flow in pedigrees is of strong interest for the development of quantitative trait loci (QTL) mapping methods in multiparental populations. We developed a Markovian framework for modeling ancestral origins along two homologous chromosomes within individuals in fixed pedigrees. A highly beneficial property of our method is that the size of state space depends linearly or quadratically on the number of pedigree founders, whereas this increases exponentially with pedigree size in alternative methods. To calculate the parameter values of the Markov process, we describe two novel recursive algorithms that differ with respect to the pedigree founders being assumed to be exchangeable or not. Our algorithms apply equally to autosomes and sex chromosomes, another desirable feature of our approach. We tested the accuracy of the algorithms by a million simulations on a pedigree. We demonstrated two applications of the recursive algorithms in multiparental populations: design a breeding scheme for maximizing the overall density of recombination breakpoints and thus the QTL mapping resolution, and incorporate pedigree information into hidden Markov models in ancestral inference from genotypic data; the conditional probabilities and the recombination breakpoint data resulting from ancestral inference can facilitate follow-up QTL mapping. The results show that the generality of the recursive algorithms can greatly increase the application range of genetic analysis such as ancestral inference in multiparental populations. |
format | Online Article Text |
id | pubmed-6169389 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Genetics Society of America |
record_format | MEDLINE/PubMed |
spelling | pubmed-61693892018-10-04 Recursive Algorithms for Modeling Genomic Ancestral Origins in a Fixed Pedigree Zheng, Chaozhi Boer, Martin P. van Eeuwijk, Fred A. G3 (Bethesda) Multiparental Populations The study of gene flow in pedigrees is of strong interest for the development of quantitative trait loci (QTL) mapping methods in multiparental populations. We developed a Markovian framework for modeling ancestral origins along two homologous chromosomes within individuals in fixed pedigrees. A highly beneficial property of our method is that the size of state space depends linearly or quadratically on the number of pedigree founders, whereas this increases exponentially with pedigree size in alternative methods. To calculate the parameter values of the Markov process, we describe two novel recursive algorithms that differ with respect to the pedigree founders being assumed to be exchangeable or not. Our algorithms apply equally to autosomes and sex chromosomes, another desirable feature of our approach. We tested the accuracy of the algorithms by a million simulations on a pedigree. We demonstrated two applications of the recursive algorithms in multiparental populations: design a breeding scheme for maximizing the overall density of recombination breakpoints and thus the QTL mapping resolution, and incorporate pedigree information into hidden Markov models in ancestral inference from genotypic data; the conditional probabilities and the recombination breakpoint data resulting from ancestral inference can facilitate follow-up QTL mapping. The results show that the generality of the recursive algorithms can greatly increase the application range of genetic analysis such as ancestral inference in multiparental populations. Genetics Society of America 2018-08-09 /pmc/articles/PMC6169389/ /pubmed/30068523 http://dx.doi.org/10.1534/g3.118.200340 Text en Copyright © 2018 Zheng et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Multiparental Populations Zheng, Chaozhi Boer, Martin P. van Eeuwijk, Fred A. Recursive Algorithms for Modeling Genomic Ancestral Origins in a Fixed Pedigree |
title | Recursive Algorithms for Modeling Genomic Ancestral Origins in a Fixed Pedigree |
title_full | Recursive Algorithms for Modeling Genomic Ancestral Origins in a Fixed Pedigree |
title_fullStr | Recursive Algorithms for Modeling Genomic Ancestral Origins in a Fixed Pedigree |
title_full_unstemmed | Recursive Algorithms for Modeling Genomic Ancestral Origins in a Fixed Pedigree |
title_short | Recursive Algorithms for Modeling Genomic Ancestral Origins in a Fixed Pedigree |
title_sort | recursive algorithms for modeling genomic ancestral origins in a fixed pedigree |
topic | Multiparental Populations |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6169389/ https://www.ncbi.nlm.nih.gov/pubmed/30068523 http://dx.doi.org/10.1534/g3.118.200340 |
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