A genome-wide SNP-association study confirms a sequence variant (g.66493737C>T) in the equine myostatin (MSTN) gene as the most powerful predictor of optimum racing distance for Thoroughbred racehorses

Abstract

BackgroundThoroughbred horses have been selected for traits contributing to speed and stamina for centuries. It is widely recognized that inherited variation in physical and physiological characteristics is responsible for variation in individual aptitude for race distance, and that muscle phenotypes in particular are important.ResultsA genome-wide SNP-association study for optimum racing distance was performed using the EquineSNP50 Bead Chip genotyping array in a cohort of n = 118 elite Thoroughbred racehorses divergent for race distance aptitude. In a cohort-based association test we evaluated genotypic variation at 40,977 SNPs between horses suited to short distance (≤ 8 f) and middle-long distance (> 8 f) races. The most significant SNP was located on chromosome 18: BIEC2-417495 ~690 kb from the gene encoding myostatin (MSTN) [Punadj. = 6.96 × 10-6]. Considering best race distance as a quantitative phenotype, a peak of association on chromosome 18 (chr18:65809482-67545806) comprising eight SNPs encompassing a 1.7 Mb region was observed. Again, similar to the cohort-based analysis, the most significant SNP was BIEC2-417495 (Punadj. = 1.61 × 10-9; PBonf. = 6.58 × 10-5). In a candidate gene study we have previously reported a SNP (g.66493737C>T) in MSTN associated with best race distance in Thoroughbreds; however, its functional and genome-wide relevance were uncertain. Additional re-sequencing in the flanking regions of the MSTN gene revealed four novel 3' UTR SNPs and a 227 bp SINE insertion polymorphism in the 5' UTR promoter sequence. Linkage disequilibrium was highest between g.66493737C>T and BIEC2-417495 (r2 = 0.86).ConclusionsComparative association tests consistently demonstrated the g.66493737C>T SNP as the superior variant in the prediction of distance aptitude in racehorses (g.66493737C>T, P = 1.02 × 10-10; BIEC2-417495, Punadj. = 1.61 × 10-9). Functional investigations will be required to determine whether this polymorphism affects putative transcription-factor binding and gives rise to variation in gene and protein expression. Nonetheless, this study demonstrates that the g.66493737C>T SNP provides the most powerful genetic marker for prediction of race distance aptitude in Thoroughbreds.

The genetic origin and history of speed in the Thoroughbred racehorse

“…The 47 SNP-haplotypes (Fig. 1a) spanned the 1.9-Mb region at the MSTN gene locus that contained a set of eight SNPs with genome-wide significance of association with best race distance in a previous genome-wide association study 20 . The C-allele was observed on a single haplotypic background spanning 932 kb (that is, no variation was detected between BIEC2-417299 and BIEC-417453; ECA18: 66064660-66996871 bp; n = 17 SNPs that were present at MAF > 0.05 in Thoroughbreds; Supplementary Data 1, TB_C1) and only minimal variation was detected in a single proximal region (Block 1) upstream of the g.66493737C/T SNP (Fig.…”

“…Evaluation of retrospective racecourse performance, physical growth and stallion progeny performance has demonstrated that C/C and C/T horses are more likely to be physically precocious and enjoy greater racecourse success as 2-year-old racehorses than T/T horses 19,28 . These findings have been subsequently validated in three independent genome-wide association (GWA) studies 18,20,21 in populations of Thoroughbreds originating in Ireland, Great Britain, New Zealand 20 , USA 18 and Japan 21 . The singular, genomic influence on optimum race distance at the MSTN locus in the Thoroughbred is supported by a high heritability for race distance (h 2 = 0.94) 29 .…”

“…However, the 50-bp sequence surrounding the g.66493737C/T SNP is conserved between horse and human and there is minimal divergence in the 200-bp 5′-and 3′-flanking sequences (5 and 1.25%, respectively). The presence of a 227-bp SINE insertion polymorphism (Ins227bp) located in the promoter region sequence may also be considered a putative functional variant and linkage disequilibrium between the two polymorphisms is high (r 2 = 0.73) but not complete 20 . The g.66493737C/T and Ins227bp variants are polymorphic in the Thoroughbred population; however, in a re-sequencing study that included populations of European horse breeds, the g.66493737C/T SNP was not polymorphic (minor allele frequency (MAF) < 0.05) and the Ins227bp allele was not identified 22 .…”

“…Recently, variation at the MSTN locus has been found to be highly predictive of genetic potential for race distance aptitude in Thoroughbred racehorses [18][19][20][21] and contributes to morphological type in other horse breeds 22 . The MSTN locus is associated with muscle hypertrophy phenotypes in a range of mammalian species [23][24][25][26][27] and a single nucleotide polymorphism (SNP, g.66493737C/T) located in the first intron of the MSTN gene influences speed in the Thoroughbred 19 .…”

A genome-wide scan study identifies a single nucleotide substitution in ASIP associated with white versus non-white coat-colour variation in sheep (Ovis aries)

“…However, the results of the qualitative trait GWAS demonstrated that the sample size used was sufficient to detect a major genetic effect such as that manifested at the ASIP locus. As reported in earlier studies of population isolates (for example, Peltonen et al, 2000;Hill et al, 2010), the high levels of LD in the isolated Finnsheep population are a reflection of low effective population size, which enables detection of association with smaller sample sizes. However, in the analysis of only non-white colours that include less than half of the animals, the power of the test could be relatively low, and thus contributes partly to the lack of significant associations (see for example, Han et al, 2008;Hill et al, 2010).…”