Full pedigree quantitative trait locus analysis in commercial pigs using variance components.
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In commercial livestock populations, QTL detection methods often use existing half-sib family structures and ignore additional relationships within and between families. We reanalyzed the data from a large QTL confirmation experiment with 10 pig lines and 10 chromosome regions using identity-by-descent (IBD) scores and variance component analyses. The IBD scores were obtained using a Monte Carlo Markov Chain method, as implemented in the LOKI software, and were used to model a putative QTL in a mixed animal model. The analyses revealed 61 QTL at a nominal 5% level (out of 650 tests). Twenty-seven QTL mapped to areas where QTL have been reported, and eight of these exceeded the threshold to claim confirmed linkage (P < 0.01). Forty-two of the putative QTL were detected previously using half-sib analyses, whereas 46 QTL previously identified by half-sib analyses could not be confirmed using the variance component approach. Some of the differences could be traced back to the underlying assumptions between the two methods. Using a deterministic approach to estimate IBD scores on a subset of the data gave very similar results to LOKI. We have demonstrated the feasibility of applying variance component QTL analysis to a large amount of data, equivalent to a genome scan. In many situations, the deterministic IBD approach offers a fast alternative to LOKI.
author list (cited authors)
de Koning, D. J., Pong-Wong, R., Varona, L., Evans, G. J., Giuffra, E., Sanchez, A., ... Haley, C. S.
complete list of authors
de Koning, DJ||Pong-Wong, R||Varona, L||Evans, GJ||Giuffra, E||Sanchez, A||Plastow, G||Noguera, JL||Andersson, L||Haley, CS