Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 542166
Title Recursive algorithms for modeling genomic ancestral origins in a fixed pedigree
Author(s) Zheng, Chaozhi; Boer, Martin P.; Eeuwijk, Fred A. van
Source G3 : Genes Genomes Genetics 8 (2018)10. - ISSN 2160-1836 - p. 3231 - 3245.
DOI https://doi.org/10.1534/g3.118.200340
Department(s) Biometris (PPO/PRI)
PE&RC
Biometris (WU MAT)
Publication type Refereed Article in a scientific journal
Publication year 2018
Keyword(s) Ancestral inference - Collaborative cross (CC) - Identical by descent - Junction theory - Multiparent advanced generation intercross (MAGIC) - Multiparental populations mpp - QTL mapping - Recombinant inbred line (RIL) - Resolution
Abstract

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.

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