Simultaneous mining of linkage and linkage disequilibrium to fine map quantitative trait loci in outbred half-sib pedigrees: revisiting the location of a quantitative trait locus with major effect on milk production on bovine chromosome 14.
A maximum-likelihood QTL mapping method that simultaneously exploits linkage and linkage disequilibrium and that is applicable in outbred half-sib pedigrees is described. The method is applied to fine map a QTL with major effect on milk fat content in a 3-cM marker interval on proximal BTA14. This proximal location is confirmed by applying a haplotype-based association method referred to as recombinant ancestral haplotype analysis. The origin of the discrepancy between the QTL position derived in this work and that of a previous analysis is examined and shown to be due to the existence of distinct marker haplotypes associated with QTL alleles having large substitution effects.
Farnir
Frédéric
F
Department of Genetics, Faculty of Veterinary Medicine, University of Liège (B43), 4000-Liège, Belgium.
Grisart
Bernard
B
Coppieters
Wouter
W
Riquet
Juliette
J
Berzi
Paulette
P
Cambisano
Nadine
N
Karim
Latifa
L
Mni
Myriam
M
Moisio
Sirja
S
Simon
Patricia
P
Wagenaar
Danny
D
Vilkki
Johanna
J
Georges
Michel
M
D000818:Animals; D002417:Cattle / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods* / Q000706:statistics & numerical data / Q000662:veterinary; D006239:Haplotypes; D007774:Lactation; D016013:Likelihood Functions; D015810:Linkage Disequilibrium; D008126:Lod Score; D008892:Milk / Q000378:metabolism; D010375:Pedigree; D019655:Quantitative Trait, Heritable