The role of polymorphisms of the MSTN, GRIN2B and DOCK8 genes in the performance of pace-racing Icelandic horses

This study investigated the association of single-nucleotide polymorphisms (SNPs) of three different genes with pace racing performance in the Icelandic horse. The SNPs chosen were PR3737, PR8604 and PR9482 of the Myostatin gene; SNPs g.41206762 C>T and g.41218272 T>C of the GRIN2B gene and SNP g.22496787 T>C of the DOCK8 gene. Icelandic horses that compete frequently in any of the three pace race disciplines (P1 over 250m, P2 over 100m and P3 over 150m) were genotyped for all SNPs mentioned above. The horses in the sample (n=131) were divided into “Speed groups” based on consistency of racing times and training schemes. Three groups were created: Fast (n=37), Average (n=75) and Slow (n=19). Differences in genotype distribution among the different Speed groups were evaluated using Fisher’s Exact Test. Significant differences were found for all SNPs except PR9482 when comparing only Fast versus Slow horses. Significant differences were also found between all three groups when comparing allele frequencies. Moreover, a drastic difference in allele frequency of the mutant allele for the DOCK8 SNP was found between horses of the Fast group (frequency of the mutant allele was of 0.70) and 280 Icelandic horses genotyped for other studies (mutant allele frequency ranging between 0.33 (n=95) and 0.43 (n=192)). This implies an important role of this SNP and its mutant allele in pace-racing performance. Additionally, horses were evaluated by owners in terms of three temperament traits: Nervousness, Focus and Motivation. Significant differences were found in the distribution of scores for these temperament traits between horses with the different genotypes of the GRIN2B SNPs, suggesting a beneficial effect of the mutant alleles on the horse’s temperament. An association analysis was also performed, where the genotypes were evaluated for association with life-time racing performance results for race times (P1, P2 and/or P3), Breeding Field Test (BFT) assessment scores for pace and estimated breeding values (EBV) for pace at BFTs. Additionally, the genotypes were evaluated for association with performance results obtained when the horses competed at the age of 13 years or under (n=117) and over 13 years of age (n=64). Significant associations were found for PR9482, where the C allele (stamina-related in other breeds) was beneficial to performance in the longer P1 races and the T allele (speed-related in other breeds) was beneficial to performance in P3 for horses of ages 13 and under. Associations were also found for the GRIN2B SNP, with the C (mutant) allele having a beneficial effect in the shorter P3 races for both lifetime career and performance in the age group of 13 years and under. As for DOCK8, associations were also found in relation to P2, with the mutant (T) allele having a positive effect on the performance. No associations were found with any of the studied polymorphisms with BFT assessment scores for pace or with estimated breeding values. This study concludes that a SNP at the DOCK8 gene may well be beneficial to performance in pace-racing Icelandic horses due to the associations found with racing times and, more interestingly, the difference found in mutant allele frequencies between an elite group of racers and the rest of the population. Additionally, the study showcases the importance of temperament traits as factors that affect performance in pace-racing, as evidenced by the associations found between the mutant allele of the GRIN2B polymorphism and temperament scores, along with racing times. Furthermore, the study concludes that Myostatin SNPs have little effect in pace-racing performance, seeing as only one polymorphism affected performance and only in one of the age groups. Moreover, comparing mutant allele frequencies between the elite racers and a large number of Icelandic horses that were not selected for pace racing showed no variation at all. This further indicates these mutations may not play a major role in performance as they do in other breeds, such as the Thoroughbreds

The role of Myostatin polymorphisms in the Finnhorse and Shetland pony breeds

Myostatin, encoded by the MSTN gene, is a member of the transforming growth factor β that normally acts to limit skeletal muscle mass by regulating both the number and growth of muscle fibers. Natural mutations that decrease the amounts of myostatin and/or inhibit its function have been identified in several cattle, sheep and dog breeds, where loss-of-function mutations cause increased skeletal muscle mass and produce a phenotype known as “double-muscling”. This gene has also been associated with racing performance in Thoroughbreds, where studies have found two Myostatin polymorphisms (PR3737 and PR8604) to be strongly associated with genetic potential and athletic phenotype, affecting both speed and muscularity, although no such associations have been found in harness-racing breeds such as the Swedish-Norwegian Coldblooded trotter. Single nucleotide polymorphisms have also been shown to have an effect on conformation, where these SNPs have been found to have different genotype distributions between horse breeds with different origin, morphology and uses. Such is the case with Icelandic horses, where significantly different genotype distributions for another SNP, PR5826, were observed between horses used for different purposes. This study investigated the association of these MSTN polymorphisms with harness racing performance in the Finnhorse and body conformation in the Shetland pony. Finnhorses used for different disciplines were genotyped for three SNPs (PR5826, PR3737 and PR8604) and were divided into three categories based on their use: harness racing horses (n=223), representing those horses with at least one start in harness racing; riding horses (n=79) used for recreational riding of which owner questionnaire information was available and horses with no performance data (n=112). An association analysis was performed on the raced group, where the genotypes were evaluated for association with life-time racing performance results for: number of starts, victories, placings (1-3) and unplaced, along with proportions for each of these traits, as well as earnings, earnings per start and race times for volt- and autostart. Additionally, the genotypes were evaluated for association with these performance results obtained between 3 and 6 years of age (n=207) and 7 to 10 years of age (n=183). Significant associations were found in the 3 to 6 years of age group as well as the 7 to 10 group. In both cases, TT horses for PR3737 earned more money, were faster for both racing methods and presented a lower number of disqualifications than the CT horses. Concerning PR8604, a similar effect was observed, where the TT horses also earned more money, were faster in auto start racing method and presented a lower number of disqualifications. This study concluded that MSTN sequence polymorphisms seem to have an effect on harness racing performance in the Finnhorse. Concerning body conformation on the Shetland pony, a breed which presents a “Heavy” body type and a “Light” body type, no significant associations were found between conformation and MSTN genotype. However, further investigation is needed before drawing the conclusion that MSTN has no effect on Shetland pony conformation. This is due to the small sample size and classification method, which could be expanded to include morphological measurements

The genetic consequences of dog breed formation-Accumulation of deleterious genetic variation and fixation of mutations associated with myxomatous mitral valve disease in cavalier King Charles spaniels

Selective breeding for desirable traits in strictly controlled populations has generated an extraordinary diversity in canine morphology and behaviour, but has also led to loss of genetic variation and random entrapment of disease alleles. As a consequence, specific diseases are now prevalent in certain breeds, but whether the recent breeding practice led to an overall increase in genetic load remains unclear. Here we generate whole genome sequencing (WGS) data from 20 dogs per breed from eight breeds and document a similar to 10% rise in the number of derived alleles per genome at evolutionarily conserved sites in the heavily bottlenecked cavalier King Charles spaniel breed (cKCs) relative to in most breeds studied here. Our finding represents the first clear indication of a relative increase in levels of deleterious genetic variation in a specific breed, arguing that recent breeding practices probably were associated with an accumulation of genetic load in dogs. We then use the WGS data to identify candidate risk alleles for the most common cause for veterinary care in cKCs-the heart disease myxomatous mitral valve disease (MMVD). We verify a potential link to MMVD for candidate variants near the heart specific NEBL gene in a dachshund population and show that two of the NEBL candidate variants have regulatory potential in heartderived cell lines and are associated with reduced NEBL isoform nebulette expression in papillary muscle (but not in mitral valve, nor in left ventricular wall). Alleles linked to reduced nebulette expression may hence predispose cKCs and other breeds to MMVD via loss of papillary muscle integrity

Association of IL4R single-nucleotide polymorphisms with rheumatoid nodules in African Americans with rheumatoid arthritis

Abstract Introduction To determine whether IL4R single-nucleotide polymorphisms (SNPs) rs1805010 (I50V) and rs1801275 (Q551R), which have been associated with disease severity in rheumatoid arthritis (RA) patients of European ancestry, relate to the presence of rheumatoid nodules and radiographic erosions in African Americans. Methods Two IL4R SNPs, rs1805010 and rs1801275, were genotyped in 749 patients from the Consortium for Longitudinal Evaluation of African-Americans with Early Rheumatoid Arthritis (CLEAR) registries. End points were rheumatoid nodules defined as present either by physical examination or by chest radiography and radiographic erosions (radiographs of hands/wrists and feet were scored using the modified Sharp/van der Heijde system). Statistical analyses were performed by using logistic regression modeling adjusted for confounding factors. Results Of the 749 patients with RA, 156 (20.8%) had rheumatoid nodules, with a mean age of 47.0 years, 84.6% female gender, and median disease duration of 1.9 years. Of the 461 patients with available radiographic data, 185 (40.1%) had erosions (score >0); their mean age was 46.7 years; 83.3% were women; and median disease duration was 1.5 years. Patients positive for HLA-DRB1 shared epitope (SE) and autoantibodies (rheumatoid factor (RF) or anti-cyclic citrullinated peptide (CCP)) had a higher risk of developing rheumatoid nodules in the presence of the AA and AG alleles of rs1801275 (odds ratio (OR)adj = 8.08 (95% confidence interval (CI): 1.60-40.89), P = 0.01 and ORadj = 2.97 (95% CI, 1.08 to 8.17), P = 0.04, respectively). Likewise, patients positive for the HLA-DRB1 SE and RF alone had a higher risk of developing rheumatoid nodules in presence of the AA and AG alleles of rs1801275 (ORadj = 8.45 (95% CI, 1.57 to 45.44), P = 0.01, and ORadj = 3.57 (95% CI, 1.18 to 10.76), P = 0.02, respectively) and in the presence of AA allele of rs1805010 (ORadj = 4.52 (95% CI, 1.20 to 17.03), P = 0.03). No significant association was found between IL4R and radiographic erosions or disease susceptibility, although our statistical power was limited by relatively small numbers of cases and controls. Conclusions We found that IL4R SNPs, rs1801275 and rs1805010, are associated with rheumatoid nodules in autoantibody-positive African-American RA patients with at least one HLA-DRB1 allele encoding the SE. These findings highlight the need for analysis of genetic factors associated with clinical RA phenotypes in different racial/ethnic populations

Genome data uncover four synergistic key regulators for extremely small body size in horses

Abstract Background Miniature size in horses represents an extreme reduction of withers height that originated after domestication. In some breeds, it is a highly desired trait representing a breed- or subtype-specific feature. The genomic changes that emerged due to strong-targeted selection towards this distinct type remain unclear. Results Comparisons of whole-genome sequencing data from two Miniature Shetland ponies and one standard-sized Shetland pony, performed to elucidate genetic determinants for miniature size, revealed four synergistic variants, limiting withers height to 34.25 in. (87 cm). Runs of homozygosity regions were detected spanning these four variants in both the Miniature Shetland ponies and the standard-sized Shetland pony. They were shown to be characteristic of the Shetland pony breed, resulting in a miniature type under specific genotypic combinations. These four genetic variants explained 72% of the size variation among Shetland ponies and related breeds. The length of the homozygous regions indicate that they arose over 1000 years ago. In addition, a copy number variant was identified in DIAPH3 harboring a loss exclusively in ponies and donkeys and thus representing a potential height-associated variant. Conclusion This study reveals main drivers for miniature size in horses identified in whole genome data and thus provides relevant candidate genes for extremely short stature in mammals

Additional file 3 of Genome data uncover four synergistic key regulators for extremely small body size in horses

Comparison of ROH regions with Fst. The highest 1% Fst investigated for ROHs in the same region found in three Shetland ponies. In total 439 overlapping regions were identified. (XLSX 20 kb

Additional file 7 of Genome data uncover four synergistic key regulators for extremely small body size in horses

Characterization of potential Shetland pony-specific CNV regions. The size of the 97 CNV regions identified in the intersection of all four CNV detection runs for Shetland pony-specific CNVs is shown in base pairs (bp) per chromosome. The number and size of all CNV regions varies among the chromosomes. On eleven chromosomes, no CNV region could be found in the overlapping results. (TIFF 16611 kb

Additional file 1 of Genome data uncover four synergistic key regulators for extremely small body size in horses

Mapping statistics of whole-genome sequencing data. In total 32 samples of equids of different populations were analyzed in this study. Sequence read achieve ID, sequencing parameters and mean coverage are shown. (DOCX 15 kb

Additional file 12 of Genome data uncover four synergistic key regulators for extremely small body size in horses

Primers and assays for validation of variants in ROH regions. SNVs in ROH regions specifically filtered for their functional effects were genotyped using Kompetitive Allele Specific PCR (KASP). Primer sequences, annealing temperature and number of PCR cycles are shown. (DOCX 23 kb

Additional file 5 of Genome data uncover four synergistic key regulators for extremely small body size in horses

Functional classification of genes. Variants identified in ROH regions in the two Miniature Shetland ponies and one standard sized Shetland pony, which were estimated to be deleterious (SIFT prediction) were investigated for their genomic positions in genes. In addition, variants, which showed an exclusively homozygous mutant genotype in all three Shetland ponies, were added to the analysis. Human orthologue genes were functionally classified using DAVID Functional Annotation Tool. (XLSX 23 kb