Full pedigree quantitative trait locus analysis in commercial pigs using variance components.
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.
de Koning
D J
DJ
Roslin Institute, Roslin, Midlothian EH25 9PS, U.K. dj.dekoning@bbsrc.ac.uk
Pong-Wong
R
R
Varona
L
L
Evans
G J
GJ
Giuffra
E
E
Sanchez
A
A
Plastow
G
G
Noguera
J L
JL
Andersson
L
L
Haley
C S
CS
D000704:Analysis of Variance; D000818:Animals; D003627:Data Interpretation, Statistical; D005260:Female; D008040:Genetic Linkage; D005838:Genotype; D008297:Male; D040641:Quantitative Trait Loci; D013552:Swine / Q000235:genetics*