Genome-wide analysis reveals selection for important traits in domestic horse breeds.
Intense selective pressures applied over short evolutionary time have resulted in homogeneity within, but substantial variation among, horse breeds. Utilizing this population structure, 744 individuals from 33 breeds, and a 54,000 SNP genotyping array, breed-specific targets of selection were identified using an F(ST)-based statistic calculated in 500-kb windows across the genome. A 5.5-Mb region of ECA18, in which the myostatin (MSTN) gene was centered, contained the highest signature of selection in both the Paint and Quarter Horse. Gene sequencing and histological analysis of gluteal muscle biopsies showed a promoter variant and intronic SNP of MSTN were each significantly associated with higher Type 2B and lower Type 1 muscle fiber proportions in the Quarter Horse, demonstrating a functional consequence of selection at this locus. Signatures of selection on ECA23 in all gaited breeds in the sample led to the identification of a shared, 186-kb haplotype including two doublesex related mab transcription factor genes (DMRT2 and 3). The recent identification of a DMRT3 mutation within this haplotype, which appears necessary for the ability to perform alternative gaits, provides further evidence for selection at this locus. Finally, putative loci for the determination of size were identified in the draft breeds and the Miniature horse on ECA11, as well as when signatures of selection surrounding candidate genes at other loci were examined. This work provides further evidence of the importance of MSTN in racing breeds, provides strong evidence for selection upon gait and size, and illustrates the potential for population-based techniques to find genomic regions driving important phenotypes in the modern horse.
College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA. jlpeters@umn.edu
Jessica L
JL
Petersen
James R
JR
Mickelson
Aaron K
AK
Rendahl
Stephanie J
SJ
Valberg
Lisa S
LS
Andersson
Jeanette
J
Axelsson
Ernie
E
Bailey
Danika
D
Bannasch
Matthew M
MM
Binns
Alexandre S
AS
Borges
Pieter
P
Brama
Artur
A
da Câmara Machado
Stefano
S
Capomaccio
Katia
K
Cappelli
E Gus
EG
Cothran
Ottmar
O
Distl
Laura
L
Fox-Clipsham
Kathryn T
KT
Graves
Gérard
G
Guérin
Bianca
B
Haase
Telhisa
T
Hasegawa
Karin
K
Hemmann
Emmeline W
EW
Hill
Tosso
T
Leeb
Gabriella
G
Lindgren
Hannes
H
Lohi
Maria Susana
MS
Lopes
Beatrice A
BA
McGivney
Sofia
S
Mikko
Nicholas
N
Orr
M Cecilia T
MC
Penedo
Richard J
RJ
Piercy
Marja
M
Raekallio
Stefan
S
Rieder
Knut H
KH
Røed
June
J
Swinburne
Teruaki
T
Tozaki
Mark
M
Vaudin
Claire M
CM
Wade
Molly E
ME
McCue
D000818:Animals; D005075:Biological Evolution; D001947:Breeding; D055106:Genome-Wide Association Study; D005838:Genotype; D006239:Haplotypes; D006736:Horses / Q000235:genetics*; D055435:Myostatin / Q000235:genetics*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic
D055435:Myostatin