Animal genetics.
Publisher:
Published by Blackwell Scientific Publications for the International Society for Animal Blood Group Research,. Oxford, England : Wiley-Blackwell
Frequency: Bimonthly,
Country: England
Language: English
Author(s):
International Society for Animal Blood Group Research., International Society for Animal Genetics.
Start Year:1986 -
ISSN:
0268-9146 (Print)
1365-2052 (Electronic)
0268-9146 (Linking)
1365-2052 (Electronic)
0268-9146 (Linking)
Impact Factor
2.4
2022
| NLM ID: | 8605704 |
| (DNLM): | SR0056566(s) |
| (OCoLC): | 13459823 |
| Coden: | ANGEE3 |
| LCCN: | sf 93095318 |
| Classification: | W1 AN228P |
Candidate gene analysis of osteochondrosis in Spanish Purebred horses. Equine osteochondrosis (OC) is a frequent developmental orthopaedic disease with high economic impact on the equine industry and may lead to premature retirement of the animal as a result of chronic pain and lameness. The genetic background of OC includes different genes affecting several locations; however, these genetic associations have been tested in only one or few populations, lacking the validation in others. The aim of this study was to identify the genetic determinants of OC in the Spanish Purebred horse breed. For that purpose, we used a candidate gene approach to study the associati...
Comparison of DMRT3 genotypes among American Saddlebred horses with reference to gait. Horse owners choose whether or not to train American Saddlebred horses (ASHs) to perform the 4-beat gaits called rack and slow gait. The rack and slow gait are similar to ambling gaits shown to be associated with variation in the DMRT3 gene in other breeds but are trained rather than naturally occurring gaits. A premature stop codon in the DMRT3 gene (DMRT3_Ser301STOP) caused by the Ch23:g.22999655C>A SNP has an effect on the pattern of locomotion in horses and allows for the pacing gait and strong association with performance of ambling gaits in diverse breeds. We used horse show records to i...
Analysis of genomic copy number variation in equine recurrent airway obstruction (heaves). We explored the involvement of genomic copy number variants (CNVs) in susceptibility to recurrent airway obstruction (RAO), or heaves-an asthmalike inflammatory disease in horses. Analysis of 16 RAO-susceptible (cases) and six RAO-resistant (control) horses on a custom-made whole-genome 400K equine tiling array identified 245 CNV regions (CNVRs), 197 previously known and 48 new, distributed on all horse autosomes and the X chromosome. Among the new CNVRs, 30 were exclusively found in RAO cases and were further analyzed by quantitative PCR, including additional cases and controls. Suggestive as...
Selection signatures in Shetland ponies. Shetland ponies were selected for numerous traits including small stature, strength, hardiness and longevity. Despite the different selection criteria, Shetland ponies are well known for their small stature. We performed a selection signature analysis including genome-wide SNPs of 75 Shetland ponies and 76 large-sized horses. Based upon this dataset, we identified a selection signature on equine chromosome (ECA) 1 between 103.8 Mb and 108.5 Mb. A total of 33 annotated genes are located within this interval including the IGF1R gene at 104.2 Mb and the ADAMTS17 gene at 105.4 Mb. These two ge...
Genome-wide association studies based on sequence-derived genotypes reveal new QTL associated with conformation and performance traits in the Franches-Montagnes horse breed. To identify novel quantitative trait loci (QTL) within horses, we performed genome-wide association studies (GWAS) based on sequence-level genotypes for conformation and performance traits in the Franches-Montagnes (FM) horse breed. Sequence-level genotypes of FM horses were derived by re-sequencing 30 key founders and imputing 50K data of genotyped horses. In total, we included 1077 FM horses genotyped for ~4 million SNPs and their respective de-regressed breeding values of the traits in the analysis. Based on this dataset, we identified a total of 14 QTL associated with 18 conformation trai...
Evidence for the effect of serotonin receptor 1A gene (HTR1A) polymorphism on tractability in Thoroughbred horses. Tractability, or how easily animals can be trained and controlled, is an important behavioural trait for the management and training of domestic animals, but its genetic basis remains unclear. Polymorphisms in the serotonin receptor 1A gene (HTR1A) have been associated with individual variability in anxiety-related traits in several species. In this study, we examined the association between HTR1A polymorphisms and tractability in Thoroughbred horses. We assessed the tractability of 167 one-year-old horses reared at a training centre for racehorses using a questionnaire consisting of 17 items....
Variant in the RFWD3 gene associated with PATN1, a modifier of leopard complex spotting. Leopard complex spotting (LP), the result of an incompletely dominant mutation in TRPM1, produces a collection of unique depigmentation patterns in the horse. Although the LP mutation allows for expression of the various patterns, other loci are responsible for modification of the extent of white. Pedigree analysis of families segregating for high levels of patterning indicated a single dominant gene, named Pattern-1 (PATN1), as a major modifier of LP. Linkage analysis in two half-sibling families segregating for PATN1 identified a 15-Mb region on ECA3p that warranted further investigation. Wh...
An application of MeSH enrichment analysis in livestock. An integral part of functional genomics studies is to assess the enrichment of specific biological terms in lists of genes found to be playing an important role in biological phenomena. Contrasting the observed frequency of annotated terms with those of the background is at the core of overrepresentation analysis (ORA). Gene Ontology (GO) is a means to consistently classify and annotate gene products and has become a mainstay in ORA. Alternatively, Medical Subject Headings (MeSH) offers a comprehensive life science vocabulary including additional categories that are not covered by GO. Although...
The DMRT3 gene mutation in Chinese horse breeds. The research focuses on investigating whether a specific gene mutation, called DMRT3, in Chinese horse breeds affects periods of disease incubation in classical scrapie, a transmissible brain condition. Scrapie and […]
Two variants in the KIT gene as candidate causative mutations for a dominant white and a white spotting phenotype in the donkey. White spotting phenotypes have been intensively studied in horses, and although similar phenotypes occur in the donkey, little is known about the molecular genetics underlying these patterns in donkeys. White spotting in donkeys can range from only a few white areas to almost complete depigmentation and is characterised by a loss of pigmentation usually progressing from a white spot in the hip area. Completely white-born donkeys are rare, and the phenotype is characterised by the complete absence of pigment resulting in pink skin and a white coat. A dominant mode of inheritance has been demons...
DMRT3 is associated with gait type in Mangalarga Marchador horses, but does not control gait ability. The Mangalarga Marchador (MM) is a Brazilian horse breed known for a uniquely smooth gait. A recent publication described a mutation in the DMRT3 gene that the authors claim controls the ability to perform lateral patterned gaits (Andersson et al. 2012). We tested 81 MM samples for the DMRT3 mutation using extracted DNA from hair bulbs using a novel RFLP. Horses were phenotypically categorized by their gait type (batida or picada), as recorded by the Brazilian Mangalarga Marchador Breeders Association (ABCCMM). Statistical analysis using the plink toolset (Purcell, 2007) revealed significant a...
Genome-wide association study for jumping performances in French sport horses. A genome-wide association study was performed to identify single nucleotide polymorphisms (SNPs) associated with jumping performances of warmbloods in France. The 999 horses included in the study for jumping performances were sport horses [mostly Selle Français (68%), Anglo-Arabians (13%) and horses from the other European studbooks]. Horses were genotyped using the Illumina EquineSNP50 BeadChip. Of the 54,602 SNPs available on this chip, 44,424 were retained after quality testing. Phenotypes were obtained by deregressing official breeding values for jumping competitions to use all available ...
Heritability of racing performance in the Australian Thoroughbred racing population. Performance data for 164,046 Thoroughbreds entered in a race or official barrier trial in Australia were provided by Racing Information Services Australia. Analyses estimating the heritability for a range of racing performance traits using a single-trait animal model were performed using ASREML-R. Log of cumulative earnings (LCE; 0.19 ± 0.01), log of earnings per race start (0.23 ± 0.02) and best race distance (0.61 ± 0.03) were all significantly heritable. Fixed effects for sex were significant (P < 0.001) for all performance traits aside from LCE (P = 0.382). With the exception of annual ...
Haplotype diversity in the equine myostatin gene with focus on variants associated with race distance propensity and muscle fiber type proportions. Two variants in the equine myostatin gene (MSTN), including a T/C SNP in the first intron and a 227-bp SINE insertion in the promoter, are associated with muscle fiber type proportions in the Quarter Horse (QH) and with the prediction of race distance propensity in the Thoroughbred (TB). Genotypes from these loci, along with 18 additional variants surrounding MSTN, were examined in 301 horses of 14 breeds to evaluate haplotype relationships and diversity. The C allele of intron 1 was found in 12 of 14 breeds at a frequency of 0.27; the SINE was observed in five breeds, but common in only the T...
A missense mutation in melanocortin 1 receptor is associated with the red coat colour in donkeys. The seven donkey breeds recognised by the French studbook are characterised by few coat colours: black, bay and grey. Normand bay donkeys seldom give birth to red foals, a colour more commonly seen and recognised in American miniature donkeys. Red resembles the equine chestnut colour, previously attributed to a mutation in the melanocortin 1 receptor gene (MC1R). We used a panel of 124 donkeys to identify a recessive missense c.629T>C variant in MC1R that showed a perfect association with the red coat colour. This variant leads to a methionine to threonine substitution at position 210 in th...
Genetic analysis of seven Italian horse breeds based on mitochondrial DNA D-loop variation. To understand the origin and genetic diversity of Italian horses, mitochondrial DNA D-loop sequences were generated for 163 horses from seven breeds. Sequence analysis of a 480-bp segment revealed a total of 84 haplotypes with 57 polymorphic sites, indicating multiple maternal origins and high genetic diversity. Comparison of the haplotypes with the equine mtDNA haplotype/haplogroup nomenclature showed a haplogroup distribution in the Italian breeds more similar to that found in the Middle East breeds than in the European breeds, probably due to the economic and cultural relationship with the ...
Genetic risk factors for insidious equine recurrent uveitis in Appaloosa horses. Appaloosa horses are predisposed to equine recurrent uveitis (ERU), an immune-mediated disease characterized by recurring inflammation of the uveal tract in the eye, which is the leading cause of blindness in horses. Nine genetic markers from the ECA1 region responsible for the spotted coat color of Appaloosa horses, and 13 microsatellites spanning the equine major histocompatibility complex (ELA) on ECA20, were evaluated for association with ERU in a group of 53 Appaloosa ERU cases and 43 healthy Appaloosa controls. Three markers were significantly associated (corrected P-value <0.05): a SNP ...
Worldwide frequency distribution of the ‘Gait keeper’ mutation in the DMRT3 gene. For centuries, domestic horses have represented an important means of transport and served as working and companion animals. Although their role in transportation is less important today, many horse breeds are still subject to intense selection based on their pattern of locomotion. A striking example of such a selected trait is the ability of a horse to perform additional gaits other than the common walk, trot and gallop. Those could be four-beat ambling gaits, which are particularly smooth and comfortable for the rider, or pace, used mainly in racing. Gaited horse breeds occur around the glob...
Equine developmental orthopaedic diseases–a genome-wide association study of first phalanx plantar osteochondral fragments in Standardbred trotters. Palmar/plantar osteochondral fragments (POF) in fetlock joints commonly affect and influence the athletic performance of horses. In this study, we used the Equine SNP50 BeadChip® to perform a genome-wide association study of metatarsophalangeal POF in 176 Norwegian Standardbred trotter yearlings. Putative quantitative trait loci (QTL) for medial and/or lateral POF, and medial POF only were identified on ECA1, 2, 7, 9 and 31, whereas for lateral POF, only on ECA7, 11, 27 and X. The moderate number of QTL evidences a complex inheritance and suggests various genes controlling POF development in ...
Novel variants in the KIT and PAX3 genes in horses with white-spotted coat colour phenotypes. Variants in the EDNRB, KIT, MITF, PAX3 and TRPM1 genes are known to cause white spotting phenotypes in horses, which can range from the common white markings up to completely white horses. In this study, we investigated these candidate genes in 169 horses with white spotting phenotypes not explained by the previously described variants. We identified a novel missense variant, PAX3:p.Pro32Arg, in Appaloosa horses with a splashed white phenotype in addition to their leopard complex spotting patterns. We also found three novel variants in the KIT gene. The splice site variant c.1346+1G>A occur...
A genome-wide association study indicates LCORL/NCAPG as a candidate locus for withers height in German Warmblood horses. A genome-wide association scan for loci affecting withers height was conducted in 782 German Warmblood stallions, which were genotyped using the Illumina EquineSNP50 Bead Chip. A principal components approach was applied to correct for population structure. The analysis revealed a single major QTL on ECA3 explaining ~18 per cent of the phenotypic variance, which is in concordance with recent reports from other horse populations. The LCORL/NCAPG locus represents a strong candidate gene for this QTL. This locus is among a small number that have consistently been identified to influence human hei...
Genome-wide association study of osteochondrosis in the tarsocrural joint of Dutch Warmblood horses identifies susceptibility loci on chromosomes 3 and 10. Equine osteochondrosis is a developmental joint disease that is a significant source of morbidity affecting multiple breeds of horse. The genetic variants underlying osteochondrosis susceptibility have not been established. Here, we describe the results of a genome-wide association study of osteochondrosis using 90 cases and 111 controls from a population of Dutch Warmblood horses. We report putative associations between osteochondrosis and loci on chromosome 3 (BIEC2-808543; P = 5.03 × 10(-7) ) and chromosome 10 (BIEC2-121323; P = 2.62 × 10(-7) ).
Microsatellite variation in the equine MHC. Genes within the major histocompatibility complex (MHC) encode proteins involved in innate and adaptive immune responses. Genetic variation in this region can influence the immune response of an individual animal to challenges from a variety of pathogens; however, a complete documentation of genetic variation in the MHC is lacking for most domestic animals, including horses. To provide additional genetic markers for study of the horse MHC, or ELA (equine lymphocyte antigen), we identified 37 polymorphic microsatellite repeats in ELA and used these variations separately and together with publis...
Mitochondrial DNA D-loop sequence variation in maternal lineages of Iranian native horses. To understand the origin and genetic diversity of Iranian native horses, mitochondrial DNA (mtDNA) D-loop sequences were generated for 95 horses from five breeds sampled in eight geographical locations in Iran. Sequence analysis of a 247-bp segment revealed a total of 27 haplotypes with 38 polymorphic sites. Twelve of 19 mtDNA haplogroups were identified in the samples. The most common haplotypes were found within haplogroup X2. Within-population haplotype and nucleotide diversities of the five breeds ranged from 0.838 ± 0.056 to 0.974 ± 0.022 and 0.011 ± 0.002 to 0.021 ± 0.001 res...
Pedigrees as a source of information in mtDNA studies of dogs and horses. The goal of this study was to demonstrate the usefulness of pedigree data in studies of mitochondrial DNA diversity in dogs and horses. Pedigree information allows for precisely choosing animals with distinct haplotypes for analysis, makes it possible to find rare haplotypes present exclusively in single individuals and helps to evaluate haplotype frequencies at the present and in the past. Estimating founder contributions to gene pools enables evaluating the parts of gene pools observed with the help of mtDNA analysis. An important aspect is also the financial benefits: using pedigree data, r...