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 418155
Title QTL linkage analysis of connected populations using ancestral marker and pedigree information
Author(s) Bink, M.C.A.M.; Radu Totir, L.; Braak, C.J.F. ter; Winkler, C.R.; Boer, M.P.; Smith, O.S.
Source Theoretical and Applied Genetics 124 (2012)6. - ISSN 0040-5752 - p. 1097 - 1113.
DOI https://doi.org/10.1007/s00122-011-1772-8
Department(s) Biometris (PPO/PRI)
Biometris (WU MAT)
PE&RC
Publication type Refereed Article in a scientific journal
Publication year 2012
Keyword(s) quantitative trait loci - plant-populations - kernel hardness - dough strength - model - maize - selection - families - wheat - identity
Abstract The common assumption in quantitative trait locus (QTL) linkage mapping studies that parents of multiple connected populations are unrelated is unrealistic for many plant breeding programs. We remove this assumption and propose a Bayesian approach that clusters the alleles of the parents of the current mapping populations from locus-specific identity by descent (IBD) matrices that capture ancestral marker and pedigree information. Moreover, we demonstrate how the parental IBD data can be incorporated into a QTL linkage analysis framework by using two approaches: a Threshold IBD model (TIBD) and a Latent Ancestral Allele Model (LAAM). The TIBD and LAAM models are empirically tested via numerical simulation based on the structure of a commercial maize breeding program. The simulations included a pilot dataset with closely linked QTL on a single linkage group and 100 replicated datasets with five linkage groups harboring four unlinked QTL. The simulation results show that including parental IBD data (similarly for TIBD and LAAM) significantly improves the power and particularly accuracy of QTL mapping, e.g., position, effect size and individuals’ genotype probability without significantly increasing computational demand.
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