Effect of family relatedness on characteristics of estimated IBD probabilities in relation to precision of QTL estimates

Hernandez Sanchez, J., Freyer, G., & Vukasinovic, N. (2010) Effect of family relatedness on characteristics of estimated IBD probabilities in relation to precision of QTL estimates. BMC Genetics, 11(85).

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Abstract

Background: A random QTL effects model uses a function of probabilities that two alleles in the same or in different animals at a particular genomic position are identical by descent (IBD). Estimates of such IBD probabilities and therefore, modeling and estimating QTL variances, depend on marker polymorphism, strength of linkage and linkage disequilibrium of markers and QTL, and the relatedness of animals in the pedigree. The effect of relatedness of animals in a pedigree on IBD probabilities and their characteristics was examined in a simulation study. Results: The study based on nine multi-generational family structures, similar to a pedigree structure of a real dairy population, distinguished by an increased level of inbreeding from zero to 28 % across the studied population. Highest inbreeding level in the pedigree, connected with highest relatedness, was accompanied by highest IBD probabilities of two alleles at the same locus, and by lower relative variation coefficients. Profiles of correlation coefficients of IBD probabilities along the marked chromosomal segment with those at the true QTL position were steepest when the inbreeding coefficient in the pedigree was highest. Precision of estimated QTL location increased with increasing inbreeding and pedigree relatedness. A method to assess the optimum level of inbreeding for QTL detection is proposed, depending on population parameters. Conclusions: An increased overall relationship in a QTL mapping design has positive effects on precision of QTL position estimates. But the relationship of inbreeding level and the capacity for QTL detection depending on the recombination rate of QTL and adjacent informative marker is not linear. © 2010 Freyer et al., licensee BioMed Central Ltd.

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ID Code: 58106
Item Type: Journal Article
Refereed: Yes
Additional URLs:
Keywords: Animalia, allele, dairy cattle, gene linkage disequilibrium, gene locus, genetic variability, genomics, identical by descent, inbreeding, pedigree, quantitative trait locus, quantitative trait locus mapping, simulation
DOI: 10.1186/1471-2156-11-85
ISSN: 1471-2156
Subjects: Australian and New Zealand Standard Research Classification > AGRICULTURAL AND VETERINARY SCIENCES (070000) > ANIMAL PRODUCTION (070200) > Animal Breeding (070201)
Divisions: Current > Institutes > Institute of Health and Biomedical Innovation
Copyright Owner: Copyright 2010 The authors; licensee BioMed Central Ltd.
Copyright Statement: This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Deposited On: 11 Mar 2013 22:45
Last Modified: 19 Sep 2013 00:04

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