Genetics, selection, evolution : GSE.
Periodical
Biology
Genetics
Animals
Domestic
Selection
Genetic
Publisher:
Elsevier,. London : BioMed Central
Frequency: Bimonthly, 1991-
Country: France
Language: English
Author(s):
Institut national de la recherche agronomique (France), Centre national de la recherche scientifique (France)
Start Year:1989 -
ISSN:
0999-193X (Print)
1297-9686 (Electronic)
0999-193X (Linking)
1297-9686 (Electronic)
0999-193X (Linking)
Impact Factor
4.1
2022
| NLM ID: | 9114088 |
| (DNLM): | SR0070931(s) |
| (OCoLC): | 19963483 |
| Coden: | GSEVE9 |
| Classification: | W1 GE293T |
A mutation in the MATP gene causes the cream coat colour in the horse.
Genetics, selection, evolution : GSE
February 28, 2003
Volume 35, Issue 1 119-133 doi: 10.1186/1297-9686-35-1-119
Mariat D, Taourit S, Guérin G.In horses, basic colours such as bay or chestnut may be partially diluted to buckskin and palomino, or extremely diluted to cream, a nearly white colour with pink skin and blue eyes. This dilution is expected to be controlled by one gene and we used both candidate gene and positional cloning strategies to identify the "cream mutation". A horse panel including reference colours was established and typed for different markers within or in the neighbourhood of two candidate genes. Our data suggest that the causal mutation, a G to A transition, is localised in exon 2 of the MATP gene leading to an... Read More
37
History of Lipizzan horse maternal lines as revealed by mtDNA analysis.
Genetics, selection, evolution : GSE
November 13, 2002
Volume 34, Issue 5 635-648 doi: 10.1186/1297-9686-34-5-635
Kavar T, Brem G, Habe F, Sölkner J, Dovc P.Sequencing of the mtDNA control region (385 or 695 bp) of 212 Lipizzans from eight studs revealed 37 haplotypes. Distribution of haplotypes among studs was biased, including many private haplotypes but only one haplotype was present in all the studs. According to historical data, numerous Lipizzan maternal lines originating from founder mares of different breeds have been established during the breed's history, so the broad genetic base of the Lipizzan maternal lines was expected. A comparison of Lipizzan sequences with 136 sequences of domestic- and wild-horses from GenBank showed a clusterin... Read More
12
Genetic diversity in Spanish donkey breeds using microsatellite DNA markers.
Genetics, selection, evolution : GSE
September 18, 2001
Volume 33, Issue 4 433-442 doi: 10.1186/1297-9686-33-4-433
Aranguren-Méndez J, Jordana J, Gomez M.Genetic diversity at 13 equine microsatellite loci was compared in five endangered Spanish donkey breeds: Andaluza, Catalana, Mallorquina, Encartaciones and Zamorano-Leonesa. All of the equine microsatellites used in this study were amplified and were polymorphic in the domestic donkey breeds with the exception of HMS1, which was monomorphic, and ASB2, which failed to amplify. Allele number, frequency distributions and mean heterozygosities were very similar among the Spanish donkey breeds. The unbiased expected heterozygosity (H(E)) over all the populations varied between 0.637 and 0.684 in t... Read More
13
Genetic parameters of eventing horse competition in France.
Genetics, selection, evolution : GSE
May 3, 2001
Volume 33, Issue 2 175-190 doi: 10.1186/1297-9686-33-2-175
Ricard A, Chanu I.Genetic parameters of eventing horse competitions were estimated. About 13 000 horses, 30 000 annual results during 17 years and 110 000 starts in eventing competitions during 8 years were recorded. The measures of performance were logarithmic transformations of annual earnings, annual earnings per start, and annual earnings per place, and underlying variables responsible for ranks in each competition. Heritabilities were low (0.11 / 0.17 for annual results, 0.07 for ranks). Genetic correlations between criteria were high (greater than 0.90) except between ranks and earnings per place (0.58) o... Methods to estimate effective population size using pedigree data: Examples in dog, sheep, cattle and horse.
Genetics, selection, evolution : GSE
January 2, 2013
Volume 45, Issue 1 1 doi: 10.1186/1297-9686-45-1
Leroy G, Mary-Huard T, Verrier E, Danvy S, Charvolin E, Danchin-Burge C.Effective population sizes of 140 populations (including 60 dog breeds, 40 sheep breeds, 20 cattle breeds and 20 horse breeds) were computed using pedigree information and six different computation methods. Simple demographical information (number of breeding males and females), variance of progeny size, or evolution of identity by descent probabilities based on coancestry or inbreeding were used as well as identity by descent rate between two successive generations or individual identity by descent rate. Results: Depending on breed and method, effective population sizes ranged from 15 to 133 ... Read More
68
A mutation in the MATP gene causes the cream coat colour in the horse.
Genetics, selection, evolution : GSE
February 28, 2003
Volume 35, Issue 1 119-133 doi: 10.1186/1297-9686-35-1-119
Mariat D, Taourit S, Guérin G.In horses, basic colours such as bay or chestnut may be partially diluted to buckskin and palomino, or extremely diluted to cream, a nearly white colour with pink skin and blue eyes. This dilution is expected to be controlled by one gene and we used both candidate gene and positional cloning strategies to identify the "cream mutation". A horse panel including reference colours was established and typed for different markers within or in the neighbourhood of two candidate genes. Our data suggest that the causal mutation, a G to A transition, is localised in exon 2 of the MATP gene leading to an... Read More
37
Two recessive mutations in FGF5 are associated with the long-hair phenotype in donkeys.
Genetics, selection, evolution : GSE
September 25, 2014
Volume 46, Issue 1 65 doi: 10.1186/s12711-014-0065-5
Legrand R, Tiret L, Abitbol M.Seven donkey breeds are recognized by the French studbook. Individuals from the Pyrenean, Provence, Berry Black, Normand, Cotentin and Bourbonnais breeds are characterized by a short coat, while those from the Poitou breed (Baudet du Poitou) are characterized by a long-hair phenotype. We hypothesized that loss-of-function mutations in the FGF5 (fibroblast growth factor 5) gene, which are associated with a long-hair phenotype in several mammalian species, may account for the special coat feature of Poitou donkeys. To the best of our knowledge, mutations in FGF5 have never been described in Equi... Read More
25
Genome-wide association study of insect bite hypersensitivity in two horse populations in the Netherlands.
Genetics, selection, evolution : GSE
October 30, 2012
Volume 44, Issue 1 31 doi: 10.1186/1297-9686-44-31
Schurink A, Wolc A, Ducro BJ, Frankena K, Garrick DJ, Dekkers JC, van Arendonk JA.Insect bite hypersensitivity is a common allergic disease in horse populations worldwide. Insect bite hypersensitivity is affected by both environmental and genetic factors. However, little is known about genes contributing to the genetic variance associated with insect bite hypersensitivity. Therefore, the aim of our study was to identify and quantify genomic associations with insect bite hypersensitivity in Shetland pony mares and Icelandic horses in the Netherlands. Methods: Data on 200 Shetland pony mares and 146 Icelandic horses were collected according to a matched case-control design. C... Read More
20
A comparison of methods for whole-genome QTL mapping using dense markers in four livestock species.
Genetics, selection, evolution : GSE
February 12, 2015
Volume 47, Issue 1 6 doi: 10.1186/s12711-015-0087-7
Legarra A, Croiseau P, Sanchez MP, Teyssèdre S, Sallé G, Allais S, Fritz S, Moreno CR, Ricard A, Elsen JM.With dense genotyping, many choices exist for methods to detect quantitative trait loci (QTL) in livestock populations. However, no across-species study has been conducted on the performance of different methods using real data. We compared three methods that correct for relatedness either implicitly or explicitly: linkage and linkage disequilibrium haplotype-based analysis (LDLA), efficient mixed-model association (EMMA) analysis, and Bayesian whole-genome regression (BayesC). We analyzed one chromosome in each of five datasets (dairy cattle, beef cattle, sheep, horses, and pigs) using real g... Read More
19
Genetic diversity of a large set of horse breeds raised in France assessed by microsatellite polymorphism.
Genetics, selection, evolution : GSE
January 5, 2009
Volume 41, Issue 1 5 doi: 10.1186/1297-9686-41-5
Leroy G, Callède L, Verrier E, Mériaux JC, Ricard A, Danchin-Burge C, Rognon X.The genetic diversity and structure of horses raised in France were investigated using 11 microsatellite markers and 1679 animals belonging to 34 breeds. Between-breed differences explained about ten per cent of the total genetic diversity (Fst = 0.099). Values of expected heterozygosity ranged from 0.43 to 0.79 depending on the breed. According to genetic relationships, multivariate and structure analyses, breeds could be classified into four genetic differentiated groups: warm-blooded, draught, Nordic and pony breeds. Using complementary maximisation of diversity and aggregate diversity appr... Read More
18
A new view on dam lines in Polish Arabian horses based on mtDNA analysis.
Genetics, selection, evolution : GSE
September 27, 2007
Volume 39, Issue 5 609-619 doi: 10.1186/1297-9686-39-5-609
Głazewska I, Wysocka A, Gralak B, Sell J.Polish Arabian horses are one of the oldest and the most important Arab populations in the world. The Polish Arabian Stud Book and the Genealogical Charts by Skorkowski are the main sources of information on the ancestors of Polish Arabs. Both publications were viewed as credible sources of information until the 1990s when the data regarding one of the dam lines was questioned. The aim of the current study was to check the accuracy of the pedigree data of Polish dam lines using mtDNA analysis. The analyses of a 458 bp mtDNA D-loop fragment from representatives of 15 Polish Arabian dam lines re... Read More
14
The utility of low-density genotyping for imputation in the Thoroughbred horse.
Genetics, selection, evolution : GSE
February 4, 2014
Volume 46, Issue 1 9 doi: 10.1186/1297-9686-46-9
Corbin LJ, Kranis A, Blott SC, Swinburne JE, Vaudin M, Bishop SC, Woolliams JA.Despite the dramatic reduction in the cost of high-density genotyping that has occurred over the last decade, it remains one of the limiting factors for obtaining the large datasets required for genomic studies of disease in the horse. In this study, we investigated the potential for low-density genotyping and subsequent imputation to address this problem. Results: Using the haplotype phasing and imputation program, BEAGLE, it is possible to impute genotypes from low- to high-density (50K) in the Thoroughbred horse with reasonable to high accuracy. Analysis of the sources of variation in imput... Read More
14
Genetic diversity in Spanish donkey breeds using microsatellite DNA markers.
Genetics, selection, evolution : GSE
September 18, 2001
Volume 33, Issue 4 433-442 doi: 10.1186/1297-9686-33-4-433
Aranguren-Méndez J, Jordana J, Gomez M.Genetic diversity at 13 equine microsatellite loci was compared in five endangered Spanish donkey breeds: Andaluza, Catalana, Mallorquina, Encartaciones and Zamorano-Leonesa. All of the equine microsatellites used in this study were amplified and were polymorphic in the domestic donkey breeds with the exception of HMS1, which was monomorphic, and ASB2, which failed to amplify. Allele number, frequency distributions and mean heterozygosities were very similar among the Spanish donkey breeds. The unbiased expected heterozygosity (H(E)) over all the populations varied between 0.637 and 0.684 in t... Read More
13
History of Lipizzan horse maternal lines as revealed by mtDNA analysis.
Genetics, selection, evolution : GSE
November 13, 2002
Volume 34, Issue 5 635-648 doi: 10.1186/1297-9686-34-5-635
Kavar T, Brem G, Habe F, Sölkner J, Dovc P.Sequencing of the mtDNA control region (385 or 695 bp) of 212 Lipizzans from eight studs revealed 37 haplotypes. Distribution of haplotypes among studs was biased, including many private haplotypes but only one haplotype was present in all the studs. According to historical data, numerous Lipizzan maternal lines originating from founder mares of different breeds have been established during the breed's history, so the broad genetic base of the Lipizzan maternal lines was expected. A comparison of Lipizzan sequences with 136 sequences of domestic- and wild-horses from GenBank showed a clusterin... Read More
12
Imputation of sequence level genotypes in the Franches-Montagnes horse breed.
Genetics, selection, evolution : GSE
October 1, 2014
Volume 46, Issue 1 63 doi: 10.1186/s12711-014-0063-7
Frischknecht M, Neuditschko M, Jagannathan V, Drögemüller C, Tetens J, Thaller G, Leeb T, Rieder S.A cost-effective strategy to increase the density of available markers within a population is to sequence a small proportion of the population and impute whole-genome sequence data for the remaining population. Increased densities of typed markers are advantageous for genome-wide association studies (GWAS) and genomic predictions. Methods: We obtained genotypes for 54 602 SNPs (single nucleotide polymorphisms) in 1077 Franches-Montagnes (FM) horses and Illumina paired-end whole-genome sequencing data for 30 FM horses and 14 Warmblood horses. After variant calling, the sequence-derived SNP geno... Read More
12
Genetic inbreeding depression load for morphological traits and defects in the Pura Raza Española horse.
Genetics, selection, evolution : GSE
October 20, 2020
Volume 52, Issue 1 62 doi: 10.1186/s12711-020-00582-2
Poyato-Bonilla J, Perdomo-González DI, Sánchez-Guerrero MJ, Varona L, Molina A, Casellas J, Valera M.Inbreeding is caused by mating between related individuals and is associated with reduced fitness and performance (inbreeding depression). Several studies have detected heterogeneity in inbreeding depression among founder individuals. Recently, a procedure was developed to predict hidden inbreeding depression load that is associated with founders using the Mendelian sampling of non-founders. The objectives of this study were to: (1) analyse the population structure and general inbreeding, and (2) test this recent approach for predicting hidden inbreeding depression load for four morphological ... Read More
11
A missense variant in the coil1A domain of the keratin 25 gene is associated with the dominant curly hair coat trait (Crd) in horse.
Genetics, selection, evolution : GSE
November 15, 2017
Volume 49, Issue 1 85 doi: 10.1186/s12711-017-0359-5
Morgenthaler C, Diribarne M, Capitan A, Legendre R, Saintilan R, Gilles M, Esquerré D, Juras R, Khanshour A, Schibler L, Cothran G.Curly horses present a variety of curl phenotypes that are associated with various degrees of curliness of coat, mane, tail and ear hairs. Their origin is still a matter of debate and several genetic hypotheses have been formulated to explain the diversity in phenotype, including the combination of autosomal dominant and recessive alleles. Our purpose was to map the autosomal dominant curly hair locus and identify the causal variant using genome-wide association study (GWAS) and whole-genome sequencing approaches. Results: A GWAS was performed using a Bayesian sparse linear mixed model, based ... Read More
11
A mutation in the LAMC2 gene causes the Herlitz junctional epidermolysis bullosa (H-JEB) in two French draft horse breeds.
Genetics, selection, evolution : GSE
March 14, 2003
Volume 35, Issue 2 249-256 doi: 10.1186/1297-9686-35-2-249
Milenkovic D, Chaffaux S, Taourit S, Guérin G.Epidermolysis bullosa (EB) is a heterogeneous group of inherited diseases characterised by skin blistering and fragility. In humans, one of the most severe forms of EB known as Herlitz-junctional EB (H-JEB), is caused by mutations in the laminin 5 genes. EB has been described in several species, like cattle, sheep, dogs, cats and horses where the mutation, a cytosine insertion in exon 10 of the LAMC2 gene, was very recently identified in Belgian horses as the mutation responsible for JEB. In this study, the same mutation was found to be totally associated with the JEB phenotype in two French d... Read More
10
Does heterozygosity at the DMRT3 gene make French trotters better racers?
Genetics, selection, evolution : GSE
February 26, 2015
Volume 47, Issue 1 10 doi: 10.1186/s12711-015-0095-7
Ricard A.Recently, a mutation was discovered in the DMRT3 gene that controls pacing in horses. The mutant allele A is fixed in the American Standardbred trotter breed, while in the French trotter breed, the frequency of the wild-type allele C is still 24%. This study aimed at measuring the effect of DMRT3 genotypes on the performance of French trotters and explaining why the polymorphism still occurs in this breed. Using a mixed animal model, genetic parameters and environmental effects on performance traits were estimated from data on 173 176 French trotter races. The effect of the DMRT3 gene was then... Read More
10
Genetic parameters of eventing horse competition in France.
Genetics, selection, evolution : GSE
May 3, 2001
Volume 33, Issue 2 175-190 doi: 10.1186/1297-9686-33-2-175
Ricard A, Chanu I.Genetic parameters of eventing horse competitions were estimated. About 13 000 horses, 30 000 annual results during 17 years and 110 000 starts in eventing competitions during 8 years were recorded. The measures of performance were logarithmic transformations of annual earnings, annual earnings per start, and annual earnings per place, and underlying variables responsible for ranks in each competition. Heritabilities were low (0.11 / 0.17 for annual results, 0.07 for ranks). Genetic correlations between criteria were high (greater than 0.90) except between ranks and earnings per place (0.58) o... Mitochondrial D-loop sequence variation among Italian horse breeds.
Genetics, selection, evolution : GSE
October 22, 2004
Volume 36, Issue 6 663-672 doi: 10.1186/1297-9686-36-6-663
Cozzi MC, Strillacci MG, Valiati P, Bighignoli B, Cancedda M, Zanotti M.The genetic variability of the mitochondrial D-loop DNA sequence in seven horse breeds bred in Italy (Giara, Haflinger, Italian trotter, Lipizzan, Maremmano, Thoroughbred and Sarcidano) was analysed. Five unrelated horses were chosen in each breed and twenty-two haplotypes were identified. The sequences obtained were aligned and compared with a reference sequence and with 27 mtDNA D-loop sequences selected in the GenBank database, representing Spanish, Portuguese, North African, wild horses and an Equus asinus sequence as the outgroup. Kimura two-parameter distances were calculated and a clust... Genetic variability and history of a native Finnish horse breed.
Genetics, selection, evolution : GSE
July 1, 2019
Volume 51, Issue 1 35 doi: 10.1186/s12711-019-0480-8
Kvist L, Niskanen M, Mannermaa K, Wutke S, Aspi J.The Finnhorse was established as a breed more than 110 years ago by combining local Finnish landraces. Since its foundation, the breed has experienced both strong directional selection, especially for size and colour, and severe population bottlenecks that are connected with its initial foundation and subsequent changes in agricultural and forestry practices. Here, we used sequences of the mitochondrial control region and genomic single nucleotide polymorphisms (SNPs) to estimate the genetic diversity and differentiation of the four Finnhorse breeding sections: trotters, pony-sized horses, dr... Genomic measures of inbreeding in the Norwegian-Swedish Coldblooded Trotter and their associations with known QTL for reproduction and health traits.
Genetics, selection, evolution : GSE
May 27, 2019
Volume 51, Issue 1 22 doi: 10.1186/s12711-019-0465-7
Velie BD, Solé M, Fegraeus KJ, Rosengren MK, Røed KH, Ihler CF, Strand E, Lindgren G.Since the 1950s, the Norwegian-Swedish Coldblooded trotter (NSCT) has been intensively selected for harness racing performance. As a result, the racing performance of the NSCT has improved remarkably; however, this improved racing performance has also been accompanied by a gradual increase in inbreeding level. Inbreeding in NSCT has historically been monitored by using traditional methods that are based on pedigree analysis, but with recent advancements in genomics, the NSCT industry has shown interest in adopting molecular approaches for the selection and maintenance of this breed. Consequent... Validation of models for analysis of ranks in horse breeding evaluation.
Genetics, selection, evolution : GSE
January 28, 2010
Volume 42, Issue 1 3 doi: 10.1186/1297-9686-42-3
Ricard A, Legarra A.Ranks have been used as phenotypes in the genetic evaluation of horses for a long time through the use of earnings, normal score or raw ranks. A model, ("underlying model" of an unobservable underlying variable responsible for ranks) exists. Recently, a full Bayesian analysis using this model was developed. In addition, in reality, competitions are structured into categories according to the technical level of difficulty linked to the technical ability of horses (horses considered to be the "best" meet their peers). The aim of this article was to validate the underlying model through simulatio... Genomic prediction of unordered categorical traits: an application to subpopulation assignment in German Warmblood horses.
Genetics, selection, evolution : GSE
February 11, 2016
Volume 48 13 doi: 10.1186/s12711-016-0192-2
Heuer C, Scheel C, Tetens J, Kühn C, Thaller G.Categorical traits without ordinal representation of classes do not qualify for threshold models. Alternatively, the multinomial problem can be assessed by a sequence of independent binary contrasts using schemes such as one-vs-all or one-vs-one. Class probabilities can be arrived at by normalization or pair-wise coupling strategies. We assessed the predictive ability of whole-genome regression models and support vector machines for the classification of horses into four German Warmblood breeds. Results: Prediction accuracies of leave-one-out cross-validation were high and ranged from 0.75 to ... Association between the MHC gene region and variation of serum IgE levels against specific mould allergens in the horse.
Genetics, selection, evolution : GSE
August 21, 2003
Volume 35 Suppl 1, Issue Suppl 1 S177-S190 doi: 10.1186/1297-9686-35-S1-S177
Curik I, Fraser D, Eder C, Achmann R, Swinburne J, Crameri R, Brem G, Sölkner J, Marti E.To investigate whether the equine major histocompatibility complex (MHC) gene region influences the production of mould-specific immunoglobulin E antibodies (IgE), alleles of the equine leukocyte antigen (ELA-A) locus and three microsatellite markers (UM-011, HTG-05 and HMS-42) located on the same chromosome as the equine MHC were determined in 448 Lipizzan horses. Statistical analyses based on composite models, showed significant associations of the ELA-A and UM-011 loci with IgE titres against the recombinant Aspergillus fumigatus 7 antigen (rAsp f 7). UM-011 was also significantly associate... Performance of Swedish Warmblood fragile foal syndrome carriers and breeding prospects.
Genetics, selection, evolution : GSE
January 21, 2022
Volume 54, Issue 1 4 doi: 10.1186/s12711-021-00693-4
Ablondi M, Johnsson M, Eriksson S, Sabbioni A, Viklund ÅG, Mikko S.Warmblood fragile foal syndrome (WFFS) is a monogenetic defect caused by a recessive lethal missense point mutation in the procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1 gene (PLOD1, c.2032G>A). The majority of homozygous WFFS horses are aborted during gestation. Clinical signs of affected horses include fragile skin, skin and mucosa lacerations, hyperextension of the articulations, and hematomas. In spite of its harmful effect, a relatively high frequency of WFFS carriers has been found in Warmblood horses, suggesting a heterozygote advantage. Thus, in this study our aims were to: (1) est... Adjusted fence height: an improved phenotype for the genetic evaluation of show jumping performance in Warmblood horses.
Genetics, selection, evolution : GSE
February 23, 2023
Volume 55, Issue 1 12 doi: 10.1186/s12711-023-00786-2
Chapard L, Van Thillo A, Meyermans R, Gorssen W, Buys N, Janssens S.Show jumping is one of the most popular disciplines in the horse sector, which makes success in show jumping competitions an important breeding goal for many studbooks. Therefore, the genetic evaluation of show jumping performance is of major interest and this is the case for two Belgian Warmblood studbooks: the Belgian Warmblood horse and Zangersheide. In this study, first an improved phenotype for show jumping performance was developed, i.e. adjusted fence height based on a new non-arbitrary method to scale ranking and competition level, which are two major components of success in competiti... Challenging the selection for consistency in the rank of endurance competitions.
Genetics, selection, evolution : GSE
April 10, 2020
Volume 52, Issue 1 20 doi: 10.1186/s12711-020-00539-5
Cervantes I, Bodin L, Valera M, Molina A, Gutiérrez JP.Control of the environmental variability by genetic selection offers possibilities for new selection objectives for productive traits. This methodology aims at reducing heterogeneity in productive traits and has been applied to several traits and species for which animal homogeneity is profitable. In horse breeding programmes, rank in competitions is a common selection objective but has been challenging to model. In this study, the parameters of environmental variability for the rank of a horse were computed to analyse the capability of a horse to maintain the best ranking across competitions ... The costs of breed reconstruction from cryopreserved material in mammalian livestock species.
Genetics, selection, evolution : GSE
July 6, 2007
Volume 39, Issue 4 465-479 doi: 10.1186/1297-9686-39-4-465
Gandini G, Pizzi F, Stella A, Boettcher PJ.The aim of this work was to compare costs, in the horse, cattle, sheep, swine, and rabbit species, for the creation of gene banks for reconstruction of an extinct breed, using different strategies: embryos-only, embryos in combination with semen, and semen-only. Three cost measures were used: time required for population reconstruction, cost for creation of the gene bank, number of years-keeping-female to reach reconstruction. Semen costs were estimated across four scenarios: the presence or absence of a commercial market for semen, purchase of semen donors, and semen extracted from the epidid... Development and validation of a horse reference panel for genotype imputation.
Genetics, selection, evolution : GSE
July 4, 2022
Volume 54, Issue 1 49 doi: 10.1186/s12711-022-00740-8
Reich P, Falker-Gieske C, Pook T, Tetens J.Genotype imputation is a cost-effective method to generate sequence-level genotypes for a large number of animals. Its application can improve the power of genomic studies, provided that the accuracy of imputation is sufficiently high. The purpose of this study was to develop an optimal strategy for genotype imputation from genotyping array data to sequence level in German warmblood horses, and to investigate the effect of different factors on the accuracy of imputation. Publicly available whole-genome sequence data from 317 horses of 46 breeds was used to conduct the analyses. Results: Depend... Genetic characterisation of the Connemara pony and the Warmblood horse using a within-breed clustering approach.
Genetics, selection, evolution : GSE
August 17, 2023
Volume 55, Issue 1 60 doi: 10.1186/s12711-023-00827-w
Lindsay-McGee V, Sanchez-Molano E, Banos G, Clark EL, Piercy RJ, Psifidi A.The Connemara pony (CP) is an Irish breed that has experienced varied selection by breeders over the last fifty years, with objectives ranging from the traditional hardy pony to an agile athlete. We compared these ponies with well-studied Warmblood (WB) horses, which are also selectively bred for athletic performance but with a much larger census population. Using genome-wide single nucleotide polymorphism (SNP) and whole-genome sequencing data from 116 WB (94 UK WB and 22 European WB) and 36 CP (33 UK CP and 3 US CP), we studied the genomic diversity, inbreeding and population structure of th... Genetic correlations between conformation traits and radiographic findings in the limbs of German Warmblood riding horses.
Genetics, selection, evolution : GSE
November 28, 2006
Volume 38, Issue 6 657-671 doi: 10.1186/1297-9686-38-6-657
Stock KF, Distl O.Studbook inspection (SBI) data of 20 768 German Warmblood mares and radiography results (RR) data of 5102 Hanoverian Warmblood horses were used for genetic correlation analyses. The scores on a scale from 0 to 10 were given for conformation and basic quality of gaits, resulting in 14 SBI traits which were used for the correlation analyses. The radiographic findings considered included osseous fragments in fetlock (OFF) and hock joints (OFH), deforming arthropathy in hock joints (DAH) and distinct radiographic findings in the navicular bones (DNB) which were analyzed as binary traits, and radio... Genetic analysis of geometric morphometric 3D visuals of French jumping horses.
Genetics, selection, evolution : GSE
September 18, 2023
Volume 55, Issue 1 63 doi: 10.1186/s12711-023-00837-8
Ricard A, Crevier-Denoix N, Pourcelot P, Crichan H, Sabbagh M, Dumont-Saint-Priest B, Danvy S.For centuries, morphology has been the most commonly selected trait in horses. A 3D video recording enabled us to obtain the coordinates of 43 anatomical landmarks of 2089 jumping horses. Generalized Procrustes analysis provided centered and scaled coordinates that were independent of volume, i.e., centroid size. Genetic analysis of these coordinates (mixed model; 17,994 horses in the pedigree) allowed us to estimate a variance-covariance matrix. New phenotypes were then defined: the "summarized shapes". They were obtained by linear combinations of Procrustes coordinates with, as coefficients,...