A rank-based nonparametric method for mapping quantitative trait loci in outbred half-sib pedigrees: application to milk production in a granddaughter design.
We describe the development of a multipoint nonparametric quantitative trait loci mapping method based on the Wilcoxon rank-sum test applicable to outbred half-sib pedigrees. The method has been evaluated on a simulated dataset and its efficiency compared with interval mapping by using regression. It was shown that the rank-based approach is slightly inferior to regression when the residual variance is homoscedastic normal; however, in three out of four other scenarios envisaged, i.e., residual variance heteroscedastic normal, homoscedastic skewed, and homoscedastic positively kurtosed, the latter outperforms the former one. Both methods were applied to a real data set analyzing the effect of bovine chromosome 6 on milk yield and composition by using a 125-cM map comprising 15 microsatellites and a granddaughter design counting 1158 Holstein-Friesian sires.
Coppieters
W
W
Department of Genetics, Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium.
Kvasz
A
A
Farnir
F
F
Arranz
J J
JJ
Grisart
B
B
Mackinnon
M
M
Georges
M
M
D000818:Animals; D001947:Breeding / Q000379:methods; D002417:Cattle / Q000235:genetics* / Q000502:physiology; D005260:Female; D005819:Genetic Markers; D008297:Male; D018895:Microsatellite Repeats; D008892:Milk; D008957:Models, Genetic; D015233:Models, Statistical; D010375:Pedigree; D019655:Quantitative Trait, Heritable; D012044:Regression Analysis; D018709:Statistics, Nonparametric
D005819:Genetic Markers