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The American Quarter Horse: Population Structure and Relationship to the Thoroughbred
Abstract
A breed known for its versatility, the American Quarter Horse (QH), is increasingly bred for performance in specific disciplines. The impact of selective breeding on the diversity and structure of the QH breed was evaluated using pedigree analysis and genome-wide SNP data from horses representing 6 performance groups (halter, western pleasure, reining, working cow, cutting, and racing). Genotype data (36 037 single nucleotide polymorphisms [SNPs]) from 36 Thoroughbreds were also evaluated with those from the 132 performing QHs to evaluate the Thoroughbred's influence on QH diversity. Results showed significant population structure among all QH performance groups excepting the comparison between the cutting and working cow horses; divergence was greatest between the cutting and racing QHs, the latter of which had a large contribution of Thoroughbred ancestry. Significant coancestry and the potential for inbreeding exist within performance groups, especially when considering the elite performers. Relatedness within performance groups is increasing with popular sires contributing disproportionate levels of variation to each discipline. Expected heterozygosity, inbreeding, F ST, cluster, and haplotype analyses suggest these QHs can be broadly classified into 3 categories: stock, racing, and pleasure/halter. Although the QH breed as a whole contains substantial genetic diversity, current breeding practices have resulted in this variation being sequestered into subpopulations.
... Quarter Horses (QH) are the fastest horses in the world in shortdistance races (Nielsen et al., 2006) and the most versatile (Petersen et al., 2014). In addition, this breed represents the largest population of registered horses in Brazil (514,316 animals) (ABQM, 2019) and in the world (2,906,070 animals) (AQHA, 2015). ...
... In addition, this breed represents the largest population of registered horses in Brazil (514,316 animals) (ABQM, 2019) and in the world (2,906,070 animals) (AQHA, 2015). The QH breed comprises three groups (lines) of genetically distinct animals (Petersen et al., 2014), which are defined based on their performance: stock horses (working livestock and Western competitions), halter/pleasure horses, and racing horses. ...
... Studies evaluating the genetic diversity and most influential ancestors of all animals of the QH breed (considering the three lines) based on genealogical data were conducted in the United States (Tunnell et al., 1983) and Brazil (Faria et al., 2018a). However, no emphasis was given considering each line separately, as reported by Marchiori et al. (2019) and Petersen et al. (2014). ...
The aims of this study were to evaluate the genetic diversity of the racing line Quarter Horse breed in Brazil and to provide data on the most influential ancestors by pedigree analysis. All horses that had participated in sprint races in Brazil between 1978 and 2016 were evaluated. There were 5,861 athletes horses (2,474 males and 3,387 females) born between 1971 and 2014. These animals were referred to as the racing population (Pr), which was divided into three subpopulations to evaluate three complete decades (84.5% of Pr). These subpopulations consisted of 1,712, 1,604 and 1,461 animals born in the 1980s (sP80), 1990s (sP90) and 2000s (sP00), respectively. The quality of the pedigree was assessed based on the number of complete equivalent generation traced. There were 5.4 (Pr), 4.7 (sP80), 5.7 (sP90) and 6.3 (sP00) generations, which permitted accuracy of the conclusions reported. The generation intervals were long, with 13.2 (sire-son/daughter) and 10.6 (dams-son/daughter) years (Pr). The coefficients of inbreeding and average relatedness were 0.95% and 1.84% for Pr and 1.60% and 2.56% for sP00, respectively. In Pr and sP00, the effective population size (Ne) based on ΔFi was 215 and 144, respectively, with 68 and 41 animals per generation. The probability of gene origin given by the effective number of founders (fe), ancestors (fa) and founder genome equivalents (fge) was 192, 61 and 34, respectively, for Pr, with considerable losses of genetic diversity over the last decades evaluated. The number of ancestors (founders or not) that explained the total genetic diversity was 1,587. This number is considered high; however, only 32 and 9 ancestors explained 50% of the genetic diversity of Pr and sP00, respectively. The 10 most influential ancestors of sP00 explained 52.2% of the total genetic diversity. The loss of genetic diversity and concentration in a reduced number of breeding animals indicate failures in the breeding and conservation programs of the racing line. Mating designs in conjunction with the selection of breeding animals should be promoted and goals should be defined for racing line of the Quarter Horse breed in Brazil.
... Notably, over 70% of Quarter Horse samples included in this study were heterozygous for these SNPs ( Table 1). The Quarter Horse has an open stud book, and higher genetic diversity than the Thoroughbred population 65 , making the high frequency of a potentially lethal haplotype at first surprising. The Quarter Horse dataset reportedly did not contain full or half siblings 65 , but the collection of samples from one geographical area may not fully reflect the diversity of the worldwide population. ...
... The Quarter Horse has an open stud book, and higher genetic diversity than the Thoroughbred population 65 , making the high frequency of a potentially lethal haplotype at first surprising. The Quarter Horse dataset reportedly did not contain full or half siblings 65 , but the collection of samples from one geographical area may not fully reflect the diversity of the worldwide population. An average relatedness analysis of these samples noted the large genetic influence of one particular Thoroughbred stallion 65 , which may explain the high frequency of heterozygotes observed in this population. ...
... The Quarter Horse dataset reportedly did not contain full or half siblings 65 , but the collection of samples from one geographical area may not fully reflect the diversity of the worldwide population. An average relatedness analysis of these samples noted the large genetic influence of one particular Thoroughbred stallion 65 , which may explain the high frequency of heterozygotes observed in this population. However, the extremely high frequency of heterozygotes in this breed may be due to selective breeding favouring these individuals. ...
Domestic animal populations are often characterised by high rates of inbreeding and low effective population sizes due to selective breeding practices. These practices can result in otherwise rare recessive deleterious alleles drifting to high frequencies, resulting in reduced fertility rates. This study aimed to identify potential recessive lethal haplotypes in the Thoroughbred horse breed, a closed population that has been selectively bred for racing performance. In this study, we identified a haplotype in the LY49B gene that shows strong evidence of being homozygous lethal, despite having high frequencies of heterozygotes in Thoroughbreds and other domestic horse breeds. Variant analysis of whole-genome sequence data identified two SNPs in the 3′UTR of the LY49B gene that may result in loss of function. Analysis of transcriptomic data from equine embryonic tissue revealed that LY49B is expressed in the trophoblast during placentation stage of development. These findings suggest that LY49B may have an essential, but as yet unknown function in the implantation stage of equine development. Further investigation of this region may allow for the development of a genetic test to improve fertility rates in horse populations. Identification of other lethal variants could assist in improving natural levels of fertility in horse populations.
... Struktura genetyczna koni rasy American Quarter była przedmiotem badań w USA [21,30], zaś w Niemczech badano konie rasy American Paint [25], które w większości posiadają geny rasy AQ, a tylko ze względu na srokatą maść nie były zaliczane do tej rasy. Natomiast struktura genetyczna koni rasy American Quarter w Polsce nie była dotąd badana. ...
... Również Petersen i wsp. [21], w późniejszym opracowaniu dotyczącym rasy American Quarter, wymieniają ogiera DOC BAR jako przodka mającego największy udział alleli w genotypach koni startujących w kategoriach: reining (brak polskiego odpowiednika nazwy), Tabela 3 -Table 3 Ogólna Zechner i wsp. [35], badając konie lipicańskie stwierdzili, iż zróżnicowanie przodków występujące w rodowodach nie zawsze znajduje odzwierciedlenie w zróżnicowaniu genetycznym, co częściowo potwierdziło się również u badanych koni rasy AQ, u których przodkowie i założyciele o najwyższych udziałach byli niejednokrotnie dla siebie bliższymi lub dalszymi krewnymi (rys. ...
... Rys. 3. Zależności genealogiczne między założycielem i jego potomkami będącymi przodkami o najwyższych udziałach alleli (ich nazwy wytłuszczono i umieszczono w ramkach) Fig. 3. Genealogical relations between the founder and its progeny -most influential ancestors (names are in bold and enclosed in boxes) Rys. 4. Zależności genealogiczne między przodkami o najwyższych udziałach alleli (ich nazwy wytłuszczono i umieszczono w ramkach) Fig. 4. Genealogical relations between the most influential ancestors (names are in bold and enclosed in boxes) ♂ W tabeli 4. przedstawiono uzyskane przez różnych autorów wyniki dotyczące inbredu i pokrewieństwa dla różnych ras koni, w tabeli 5. umieszczono natomiast efektywną liczbę założycieli i przodków uzyskaną w badaniach różnych ras koni przez różnych autorów. Table 4 Współczynniki inbredu (F X ) i pokrewieństwa (R XY ) u różnych ras koniowatych Inbreeding (F X ) and relationship (R XY ) coefficients in different Eqiudae breeds Porównując otrzymane wyniki własne dotyczące inbredu oraz pokrewieństwa z danymi zamieszczonymi w literaturze dla tej samej i innych ras koni można stwierdzić, iż oszacowane w niniejszej pracy wartości F X są podobne lub niekiedy znacznie niższe niż uzyskane przez większość autorów cytowanych w tabeli 4. Szczególnie porównanie wyników dla tej samej rasy, uzyskanych przez autorów amerykańskich [21,30], wypada zdecydowanie na korzyść badanego stada, ponieważ tak współczynniki inbredu, jak i pokrewieństwa są niższe dla koni z Roleski Ranch. ...
The study investigated inbreeding and relationship in American Quarter Horses (AQ) kept or
bred on the Roleski Ranch stud farm (Stare Żukowice, Małopolska region). The data consisted of
pedigrees of 76 AQ horses (40 stallions and 36 mares) born in 1993-2012. Coefficients of inbreeding
(FX) and relationship (RXY) were calculated according to Tier. The effective number of founders (fe)
and effective number of ancestors (fa) were calculated as well. Almost 91% of horses were found to be
inbred – 90% of stallions and 91.67% of mares. In sex groups, FX averaged 0.0132 and 0.0142 for all
stallions and all mares, and 0.0146 and 0.0155 for inbred stallions and inbred mares. About 97.37% of
animal pairs were found to be related. Over 99% of male pairs were related, with RXY for all and inbred
males averaging 0.0610 and 0.0641, respectively. In females, nearly 95% of pairs were related, but RXY
values were slightly lower, averaging 0.0590 and 0.0591 for all and related pairs, respectively. Among
mixed male-female pairs 97.5% were related, with RXY values averaging 0.0607 and 0.0622 for all
and related pairs, respectively. The fe was 121 and the fa = 26. Half of the genetic pool was explained
by contributions of only 10 ancestors, and 90% of alleles originated in 39 ancestors. Due to steady
importation of stock AQ horses and careful mating plans, the inbreeding and relationship coefficients
on the Roleski Ranch stud farm are relatively low
... The Arabian cluster is also broad, particularly in the PC1 dimension, suggesting a high level of genetic diversity within the global Arabian population. The other breed with a similarly broad cluster across the PCA was the American Quarter Horse, a breed notable for its division into several subgroups that also cluster separately in PCA 23 and differ in the frequency of alleles determining susceptibility to recessive inherited diseases 24 . In our analysis, the Quarter Horse samples displayed diversity across PC2. ...
... This finding agrees with the written histories of these groups, characterized by closely controlled breeding of these lineages over the past 200 years 6 . A similar sub-breed structure has been described in the American Quarter Horse, a registry notable for its functional division into several subgroups that also cluster separately in PC space 23 . ...
The Arabian horse, one of the world’s oldest breeds of any domesticated animal, is characterized by natural beauty, graceful movement, athletic endurance, and, as a result of its development in the arid Middle East, the ability to thrive in a hot, dry environment. Here we studied 378 Arabian horses from 12 countries using equine single nucleotide polymorphism (SNP) arrays and whole-genome re-sequencing to examine hypotheses about genomic diversity, population structure, and the relationship of the Arabian to other horse breeds. We identified a high degree of genetic variation and complex ancestry in Arabian horses from the Middle East region. Also, contrary to popular belief, we could detect no significant genomic contribution of the Arabian breed to the Thoroughbred racehorse, including Y chromosome ancestry. However, we found strong evidence for recent interbreeding of Thoroughbreds with Arabians used for flat-racing competitions. Genetic signatures suggestive of selective sweeps across the Arabian breed contain candidate genes for combating oxidative damage during exercise, and within the “Straight Egyptian” subgroup, for facial morphology. Overall, our data support an origin of the Arabian horse in the Middle East, no evidence for reduced global genetic diversity across the breed, and unique genetic adaptations for both physiology and conformation.
... In cattle and in horses, genetic stratification within breeds, resulting from selection for different purposes, was shown by using Principal Component Analysis (PCA) and Discriminant Analysis of Principal Component (DAPC) [5][6][7]. Petersen et al., (2014) used fixation index (FST), PCA and haplotype analyses, to find genomic differences across six performance groups of Quarter Horse, caused by increased specialization over the past 75 years [8]. The presence of signatures of selection within Quarter Horse subpopulations was confirmed in a more recent study [9]. ...
... In cattle and in horses, genetic stratification within breeds, resulting from selection for different purposes, was shown by using Principal Component Analysis (PCA) and Discriminant Analysis of Principal Component (DAPC) [5][6][7]. Petersen et al., (2014) used fixation index (FST), PCA and haplotype analyses, to find genomic differences across six performance groups of Quarter Horse, caused by increased specialization over the past 75 years [8]. The presence of signatures of selection within Quarter Horse subpopulations was confirmed in a more recent study [9]. ...
The equestrian sport horse Swedish Warmblood (SWB) originates from versatile cavalry horses. Most modern SWB breeders have specialized their breeding either towards show jumping or dressage disciplines. The aim of this study was to explore the genomic structure of SWB horses to evaluate the presence of genomic subpopulations, and to search for signatures of selection in subgroups of SWB with high or low breeding values (EBVs) for show jumping. We analyzed high density genotype information from 380 SWB horses born in the period 2010–2011, and used Principal Coordinates Analysis and Discriminant Analysis of Principal Components to detect population stratification. Fixation index and Cross Population Extended Haplotype Homozygosity scores were used to scan the genome for potential signatures of selection. In accordance with current breeding practice, this study highlights the development of two separate breed subpopulations with putative signatures of selection in eleven chromosomes. These regions involve genes with known function in, e.g., mentality, endogenous reward system, development of connective tissues and muscles, motor control, body growth and development. This study shows genetic divergence, due to specialization towards different disciplines in SWB horses. This latter evidence can be of interest for SWB and other horse studbooks encountering specialized breeding.
... This information has also been useful to analyze the dynamic changes in gene pools during a certain period. These methodologies have been already used to describe the genetic structure of horse breeds and populations worldwide (Maccluer et al., 1983;Poncet et al., 2006;Bartolomé et al., 2011;Pjontek et al., 2012;Vicente et al., 2012;Borowska and Szwaczkowski, 2014;Petersen et al., 2014). Additionally, these results could be particularly interesting as an auxiliary tool in breeding decisions since in this species management and mating policies are normally decided by breeders in an artisanal way (Medeiros et al., 2014;Giontella et al., 2018). ...
... Moureaux et al. (1996) and GI=10.62, Bokor et al. (2013)), Hanoverian (GI ranging from 8.9 to 11.1, Hamann and Distl (2008)), American Quarter Horse (GI = 10.5, Petersen et al. (2014)), Spanish Sport Horse (GI = 10.8, Bartolomé et al. (2011)), French sport horse (GI=12; Dubois and Ricard (2007)), Selle Français (GI = 11.7, ...
The Argentine Polo Horse (AP), an autochthonous breed officially created in Argentina in the early 1980s, is globally recognized as the best equid for playing polo. Their breeding is characterized by the use of cutting-edge assisted reproductive techniques such as large-scale embryo transfer (ET) programs and cloning. The aim of this study was to determine the impact of the use of those reproductive biotechnologies on the genetic structure, variability and reproductive parameters of the AP breed using genealogical data (81,633 pedigree records). In total, 18,077 animals drawn from the last generation (2006–2015) were employed as the reference population (WP), which was further divided into two subsets: animals produced (ET; n = 13,478) and not produced by ET (NOT-ET; n = 4,599). Horses produced by ET showed a significant decrease in generation interval compared with NOT-ET. On the other hand, the number of foals per stallion and broodmare as well as inbreeding (F = 0.89%) and average relatedness (AR=1%) were higher in ET compared with NOT-ET (F = 0.6%; AR = 0.54%), depicting an increased selective intensity. Our analysis also revealed that the effective number of founders and ancestors in ET showed a disproportionate gene contribution and a strong genetic bottleneck as well as the inter-herd fixation index (FST) revealed an increased genetic flow among herds and higher internal relatedness values within ET horses. In conclusion, the use of large-scale ET programs decreased genetic variability (lower effective population size and number of founders and ancestors and higher F, AR and coancestry), increased the genetic flow among herds and decreased the generation interval, contributing to the possibility of higher rates of genetic progress in the AP.
... The Quarter Horse (QH) breed originated in the United States in the 17th century from the crossing of stallions from Arabia and Turkey, characterized by resistance and elegance, with fast and muscular English Thoroughbred dams, resulting in a compact and muscular horse that is agile when used as a working horse and fast in short-distance races (ABQM, 2017). The versatility of the QH breed was investigated recently in the genomic study of Petersen et al. (2014), who described six groups (halter, western pleasure, reining, working cow, cutting, and racing short distances) within the breed. In Brazil, the first animals were imported from the state of Texas (MacCluer et al., 1983), generation interval (GI), inbreeding coefficient (Wright, 1931) and the probability of gene origin (Boichard et al., 1997) are important to design an animal breeding program. ...
... tic gain probably because of the use of artificial insemination and/or embryo transfer, techniques that permit the reproductive use of deceased or older animals. The high standard deviations indicate differences in the GI within the population. Long GI as obtained in the present study have been reported in the literature for different horse breeds.Petersen et al. (2014) found a similar mean GI (9.5 years) for QH in the United States.Vicente et al. (2012) reported a longer GI (10.5 years) for Lusitano horses. The GI is a parameter that is monitored in breeding programs because its reduction promotes an increase in genetic gain. However, the QH of most Brazilian breeders have long GI, reducing the rate o ...
This study aimed to evaluate population parameters and to describe the genetic diversity of Quarter Horse breed (QH) in Brazil, reported for the first time in the literature. The pedigree data comprised 131,716 animals representing the total population (TP), with records of animals born between 1747 and 2008. The reference population (RP) representing the last generation was applied in this study considering 47,861 animals born between 2000 and 2008. The average generation interval was 9.6 and 10.8 years in TP and RP, respectively. The average equivalent complete generations (EG) were 5.09 (TP) and 6.24 (RP). The inbreeding coefficient (F), average relatedness (AR) and the increase in inbreeding by generation (ΔF) was 1.07%, 0.95% and 0.24%, respectively, for TP. The effective population size (Ne) based on ΔF was 195 and 164 for TP and RP, respectively. The effective number of founders (fe) was 1045 and 811 for TP and RP, respectively, that of ancestors (fa) was 156 and 113, and that of founder genomes (fg) was 105 and 66. The fe/fa and fe/fg ratios in TP were 6.70 and 9.95, respectively, and an increase was observed in RP, indicated a strong bottleneck effect. The total genetic diversity of the QH breed was explained by 4780 ancestors, with 50% of diversity being explained by only 121 and 72 ancestors in TP and RP, respectively. The thoroughbred stallion Three Bars is the most influential ancestor with the largest marginal genetic contribution for TP (5.73) and RP (5.94%). The results demonstrate a large number of founders and ancestors, but a small ancestor group was responsible for the continuity of the QH breed in Brazil. These finding highlight the importance of monitoring genetic diversity, including follow-up by breeding programs, to permit control of the next generations.
... These results suggest that this MSTN polymorphism has been under selective pressure in Quarter Horses. Indeed, a recent study involving 33 breeds (n ¼ 744) detected a selection signature in the region of the MSTN gene in Paint Horses and Quarter Horses [24]. Sequencing and histologic analysis showed that the SNP studied (g.66493737C>T), located in intron 1, and a highly correlated (95%) variation in the promoter region (227-bp SINE insertion) were significantly associated with the volume of type IIx (fast glycolytic) muscle fibers [24]. ...
... Indeed, a recent study involving 33 breeds (n ¼ 744) detected a selection signature in the region of the MSTN gene in Paint Horses and Quarter Horses [24]. Sequencing and histologic analysis showed that the SNP studied (g.66493737C>T), located in intron 1, and a highly correlated (95%) variation in the promoter region (227-bp SINE insertion) were significantly associated with the volume of type IIx (fast glycolytic) muscle fibers [24]. ...
Single nucleotide polymorphisms (SNPs) in the equine myostatin (MSTN) (g.66493737C>T) and creatine kinase muscle (CKM) (g.22999655C>A) genes have been associated with optimum racing distance and muscle development and racing performance in Thoroughbred horses, respectively. Considering that, since its formation, the Quarter Horse breed has received important genetic influence from the English breed, the genes cited become important candidates for athletic performance in the racing line of the American breed. An SNP in the equine doublesex and mab-3-related transcription factor 3 (DMRT3) gene (g.22999655C>A) has been described, which is responsible for the gait phenotype in homozygous individuals. Using a sample of 296 Quarter Horses of the racing line and 68 animals of the cutting line, the objective of this study was to compare the frequencies of the three SNPs cited above between a random subsample of animals of the cutting line (n = 20) and animals with extreme phenotypes for racing performance (n = 20 per extreme phenotype). The MSTN SNP showed practically no variation, with the observation of only one heterozygous animal (CT) in the cutting line, suggesting that this gene has been under great selective pressure within the racing segment. The CKM gene variant studied was found to be polymorphic, but no significant associates were observed between its alleles and the different lines or groups. Two animals carrying the CA heterozygous DMRT3 genotype were identified in the group with poor racing performance and one in the cutting line, indicating that this variant can be a limiting factor for the development of greater speeds.
... Advances in molecular genetics have contributed to population studies analyzing the history of the origin of mammalian species, the genetic composition and origin of animal breeds, as well as the molecular causes of the formation of various traits [11]. The number of publications on the population genetics of horses is growing, which include several fundamental studies covering various breeds [7, [12][13][14], as well as many studies on one breed or group of related breeds: the American Quarter horse [15][16][17][18], Hanoverian and German warm-blooded breeds [19,20], Arabic and related Middle Eastern breeds [21,22], Chinese aboriginal horses [23], Japanese aboriginal horse [24], Yakut horse [25], Puerto Rican horse [26]. Despite the large number of studies of the genetic structure of horses, their conclusions are quite similar to each other, namely, that modern horse breeds are characterized by high interbreed and low intrabreed genetic diversity [12,13]. ...
The article presents significant variations in the coding sequences of the genome associated with the productive qualities of the Kazakh breed of the jabe type, identified on the basis of genotyping with a wide genome coverage. A genome-wide analysis of the association of SNP markers with measurements and live weight of a horse was performed for all animals with available phenotypic data, with the exception of horses under the age of three years and distant genotypes identified during the analysis of the genetic structure. The total number of selected animals was 1 533. To ensure that there is no influence of age as covariates in the study sample, all phenotypic variables were tested for Pearson's correlation with age. Standard measurements of physique, height at the withers and oblique body length showed no significant correlation at a threshold value of p < 0.05 (p-values 0.8388 and 0.4211, respectively). Only weak correlations were found for chest circumference (0.0841, p-value 0.000507), pastern circumference (0.1011, p-value 2.922•10-5) and body weight (0.1121, p-value 3.496•10-6). Four body measurements were combined into a single variable using PCA after normalization; the first main component, describing 81% of the total variation, was selected as the new size variable. The results of the analysis of the genetic structure were taken into account when selecting samples for GWAS. The analysis of the connection was carried out by live weight and measurements. The Pearson correlation test was used to ensure the independence of phenotypic variables from age. The size variable was determined using measurements of height at the withers (HW), oblique body length (OBL), chest (CC) circumference, cannon bone circumference (CBC), and body weight (BW). These parameters were normalized by subtracting the average value and dividing by the standard deviation, then the analysis of the main components was carried out.
... 6) Racinghorses race over distances from 201 to 796 metres. The classic distance is 402 metres (0.25 miles) (Petersen et al. 2014). Reining is the only Western event recognized by the FEI (www.fei.org). ...
The study aimed to compare the level of discomfort behaviour in dressage and reining horses. The research material consisted of video recordings of 60 dressage and 40 reining rides. The duration of discomfort behaviours (tail swishing, mouth opening, rearing, head banging, and bucking/kicking) during the performance of each figure and the total time spent performing each figure were measured. Dressage horses were found to swish their tails and open their mouths more often than reining horses. In dressage, this was associated with constant contact with the muzzle and a high neck position, as well as inappropriate use of the Weymouth bit. When performing a flying change in canter, dressage horses opened their mouths more often and for longer periods. Irrespective of the riding style, horses were most likely to swish their tails during flying changes, which may have been due to balance disturbances. This was observed more often in dressage horses than in reining horses. Neck hyperflexion practiced in dressage horses at a collected canter and a lack of relaxation at an extended canter resulted in more frequent mouth opening and tail swishing. Rein back was the most difficult figure for horses in both styles.
... Los caballos de la raza Cuarto de Milla (QH, por sus siglas en inglés) se consideran los más veloces en carreras de distancias cortas y este rasgo es un criterio de selección para progresos en programas de mejoramiento genético de ésta raza, lo que ha permitido aumentar el número de crías de los garañones mejor evaluados (Petersen et al., 2014). El QH es la raza más numerosa en México, en el año 2019 existían 47,719 ejemplares, lo que ubica al país como el tercer lugar de caballos con registro de raza a nivel mundial (HorsesMx, 2021). ...
Con el objetivo de estudiar el efecto del clima a través del índice global del bulbo húmedo (íTGBH), sobre la calidad seminal de garañones Cuarto de Milla, en un criadero de los Tuxtlas, Veracruz, en ambiente tropical. Se evaluaron las variables meteorológicas temperatura ambiental y humedad relativa durante nueve años (2013-2021), para determinar el íTGBH diario y promedio mensual y relacionarlo con las características macroscópicas (volumen) y microscópicas (porcentaje de movilidad, vitalidad, espermatozoides normales y la concentración espermática) del semen obtenido de cinco sementales. Hubo un ambiente de confort térmico de diciembre a febrero (íTGBH≤26.99), dentro de la zona termo-neutral de los caballos; mientras que de abril a julio fue térmicamente estresante (íTGBH=32.99 a 36.80); con diferencia significativa (p≤0.05) en el porcentaje de movilidad (75.21±2.58 vs 62.79±2.51), vitalidad (80.50±2.03 vs 71.10±3.42) y espermatozoides normales (68.80±1.55 vs 58.02±2.0), siendo menor durante el periodo más caluroso. El volumen y concentración espermática no se vieron influenciadas por el aumento del índice pero sí por la estacionalidad. Se concluye que el incremento del calor, medido en términos de íTGBH tuvo un efecto negativo sobre la calidad seminal de los garañones.
... La raza Cuarto de Milla se destaca por su velocidad, resistencia y versatilidad, características que han atraído el interés de criadores y amantes de los caballos a nivel mundial (Petersen et al., 2014); no obstante, la doma tradicional empleada en la capital del Ariari sobre estos caballos ha sido un proceso menos explorado en términos académicos, lo que resalta la importancia de este estudio en el contexto internacional de la cultura equina. ...
Contextualización: La interacción entre humanos y caballos ha sido fundamental a lo largo de la historia, siendo la doma tradicional un aspecto crucial en el manejo equino; este estudio, se enfoca en comprender las respuestas de los caballos Cuarto de Milla a las diferentes técnicas o métodos de la doma tradicional empleada en el municipio de Granada Meta. Vacío de Conocimiento: A pesar de la relevancia histórica de la doma, existe un vacío en la comprensión detallada de cómo los diferentes métodos empleados durante la doma afectan el bienestar de los caballos, por lo que este estudio contribuye al campo, al explorar estas respuestas y sus implicaciones en el bienestar equino. Propósito: El objetivo principal es caracterizar las respuestas de los caballos Cuarto de Milla a distintos métodos usados dentro de la doma tradicional, buscando identificar el impacto de estas prácticas en el comportamiento y bienestar de los equinos. Metodología: Se empleó una metodología de investigación cualitativa, utilizando una Checklist diseñada específicamente para este estudio, se obtuvo información complementaria desde referentes antrópicos experimentados y en tiempo real se observaron las respuestas de los caballos a lineamientos como la monta inicial en bruto, uso de riendas sin embocaduras y entrenamiento en libertad. Resultados y Conclusiones: Los resultados revelaron variaciones significativas en las respuestas de los caballos a los diferentes métodos usados durante la doma y se observó que el trato suave y respetuoso, el uso de riendas sin embocaduras y las ayudas del talón sin espuelas generó una adaptación más rápida y una menor manifestación de estrés en comparación con otros métodos. Estos hallazgos destacan la importancia de considerar el bienestar animal al emplear diferentes métodos de doma tradicional y resaltan la necesidad de técnicas más suaves y progresivas para mejorar la adaptación de los caballos Cuarto de Milla.
... By definition, members of a sire line trace back to a single, often renowned, foundation individual in their paternal line of inheritance. Due to intensive selection of stallions, the predominance of a few sire lines is the rule rather than the exception in intensively managed horse breeds [10,11]. The English Thoroughbreds, with a well-documented closed studbook first published in 1791 [12], provides a compelling example of this sex bias in horse breeding with the tail-male lineages of only three foundation sires being retained today [13,14]. ...
The Y chromosome is a valuable genetic marker for studying the origin and influence of paternal lineages in populations. In this study, we conducted Y-chromosomal lineage-tracing in Arabian horses. First, we resolved a Y haplotype phylogeny based on the next generation sequencing data of 157 males from several breeds. Y-chromosomal haplotypes specific for Arabian horses were inferred by genotyping a collection of 145 males representing most Arabian sire lines that are active around the globe. These lines formed three discrete haplogroups, and the same haplogroups were detected in Arabian populations native to the Middle East. The Arabian haplotypes were clearly distinct from the ones detected in Akhal Tekes, Turkoman horses, and the progeny of two Thoroughbred foundation sires. However, a haplotype introduced into the English Thoroughbred by the stallion Byerley Turk (1680), was shared among Arabians, Turkomans, and Akhal Tekes, which opens a discussion about the historic connections between Oriental horse types. Furthermore, we genetically traced Arabian sire line breeding in the Western World over the past 200 years. This confirmed a strong selection for relatively few male lineages and uncovered incongruences to written pedigree records. Overall, we demonstrate how fine-scaled Y-analysis contributes to a better understanding of the historical development of horse breeds.
... A SNP in the noncoding region of MSTN gene is associated with the athletic performance of the elite horse (VAN DEN HOVEN et al., 2015). Genotyping revealed that Paint and Quarter horses are associated with different muscle fibers and increased sprint (PETERSEN, MICKELSON, CLEARY, and MCCUE, 2013). Two SNPs in the promoter sequence at 646 bp upstream g.26T> C and 516bp upstream g.156T> C to start codon and Five SNPs were identified in the intronic sequences,4 in intron 1 and 1 in intron 2 which has an association with racing (DALL' OLIO et al., 2010). ...
Myostatin is a protein translated by the the MSTN gene (also known as GDF8),
is responsible for limiting muscle growth and strength. In thoroughbred
horse (Equus Caballus), limited studies have been designed to examine the
variants in the coding region of MSTN gene. However, no data is available
regarding the single nucleotide polymorphisms (SNPs) of the MSTN about
racing performance in thoroughbred horses of Pakistan. In this study blood
samples of fifteen Pakistani thoroughbred horses were collected from Race
Club Lahore and immediately transferred into the ice box. The DNA was
extracted by using phenol-chloroform method. Primers were designed for the
amplification of all exons of the MSTN gene. The amplified PCR products were
precipitated and sequenced for the identification of SNPs. SNPs were
identified by visualizing the peaks of sequenced data by using Chromas
Software. Phylogenetic analysis of MSTN gene in Pak-thoroughbred with racing
species and some breeds of horses like Marwari Indian breed, Sindhi breed,
Kathlawari breed, Italian breed and Chines breed was done separately by
using MEGA 6 software. The analysis of identified SNPs were carried out by
software SNPator. The sequenced data with altered protein was published in
GenBank with accession number MN604194. Results have shown a total of 3
single nucleotide polymorphisms through Blast with reference sequences. Two
SNPs were found in exon 2 at position of 2406 (C/T) and 2408 (C/T)
respectively. One SNP (T/C) was detected in exon 3 at the position of 4661.
In conclusion, Pak-thoroughbred horse population has 3 polymorphisms in
their coding region which can be used as a biological marker for athletic
abilities in Pak- thoroughbred.
... Similarly, horses used in working equitation must be easy to train and relatively unreactive to novel stimuli or unfamiliar places, have low anxiety and be explorative [26]. Successful working cow horses are said to need good manners, smooth rideability, good cow sense and responsiveness to rein cues [57]. Working cow horses are often started younger, usually around 18 months of age to make them competitive for futurities at three years old [58]. ...
Simple Summary
Some treatments for common problem behaviours in domestic horses can compromise horse welfare. Such behaviours can be the manifestation of pain, confusion and conflict. In contrast, among the desirable attributes in horses, boldness and independence are two important behavioural traits that affect the fearfulness, assertiveness and sociability of horses when interacting with their environment, objects, conspecifics and humans. Shy and socially dependent horses are generally more difficult to manage and train than their bold and independent counterparts. Previous studies have shown how certain basic temperament traits predict the behavioural output of horses, but few have investigated how the age of the horse and the age it was when started being trained under saddle affect behaviour. Using 1940 responses to the Equine Behaviour Assessment and Research Questionnaire (E-BARQ), the current study explored the behavioural evidence of boldness and independence in horses and how these related to the age of the horse. Results revealed age-related effects on boldness and independence of horses. Older horses were bolder than younger horses, but horses started under saddle at an older age were less bold and independent than those started at a younger age. Additionally, significant differences in boldness and independence relating to specific breeds and primary equestrian disciplines also emerged. Finally, riders with eight or more years of riding experience reported having more independent horses than those who had ridden their whole lives. Understanding how horses’ ages affect behavioural traits can improve horse–rider matching and potentially also optimise welfare.
Abstract
The broad traits of boldness and independence in domestic horses can affect their usefulness and, indirectly, their welfare. The objective of the current study was to explore associations between attributes that reflect equine boldness and independence with both the age of horses and the age at which they were started under saddle, as well as other variables including breed, colour and primary equestrian discipline. All data were sourced from responses (n = 1940) to the 97-question online Equine Behaviour Assessment and Research Questionnaire (E-BARQ). Twenty E-BARQ items from the dataset were selected to reflect boldness and independence and were tested for univariate significance at p < 0.2. Multivariable modelling of the effect of age on remaining traits was assessed by an ordinal logistic regression, using a cumulative log odds model. This revealed that older horses were bolder (p = 0.012). However, horses started under saddle at an older age were less bold and less independent (p = 0.040 and p = 0.010, respectively). Australian Stock Horses were bolder and more independent (p = 0.014 and p = 0.007, respectively) than crossbreed horses. Horses used for breeding conformation (p = 0.039), working equitation (p = 0.045), eventing (p = 0.044) and traditional working horses (p = 0.034) were bolder than those used for other disciplines. Dressage (p = 0.039) and therapy (p = 0.040) horses were less bold than horses used for other disciplines. Stallions were bolder (p = −0.034) than geldings. Brown (p = 0.049) and chestnut (p = 0.027) horses were less bold than bay horses. Compared to crossbreed horses, Thoroughbreds (p = 0.000) and companion horses (p = 0.017) were less bold whilst heavy horses (p = 0.029) and ponies (p = 0.044) were bolder. Compared to pleasure horses, mounted games horses (p = 0.033) were less independent whereas working equitation horses (p = 0.020) were more independent. Riders with more than eight years’ experience reported more independence in their horses (p = 0.015) than those who had ridden their whole lives. The study findings suggest that boldness and independence are separate traits and only boldness was associated with the age of the horse. Factors that relate to desirable boldness and independence are important in ridden horses because they can affect rider safety. Results from this study should improve horse–rider matching and thereby potentially enhance horse welfare.
... In recent years there has been substantial interest in quantifying the genetic diversity of equine breeds using pedigree [1], molecular data [2] or a combination of both sources [3] in order to implement effective breed management strategies. The effectiveness of the use of both data types in the understanding and management of rare and native equine breeds have been investigated using both theoretical modelling, and studies of closed studbooks. ...
The Cleveland Bay horse is one of the oldest equines in the United Kingdom, with pedigree data going back almost 300 years. The studbook is essentially closed and because of this, there are concerns about loss of genetic variation across generations. The breed is one of five equine breeds listed as "critical" (<300 registered adult breeding females) by the UK Rare Breeds Survival Trust in their annual Watchlist. Due to their critically endangered status , the current breadth of their genetic diversity is of concern, and assessment of this can lead to improved breed management strategies. Herein, both genealogical and molecular methods are combined in order to assess founder representation, lineage, and allelic diversity. Data from 15 microsatellite loci from a reference population of 402 individuals determined a loss of 91% and 48% of stallion and dam lines, respectively. Only 3 ancestors determine 50% of the genome in the living population, with 70% of maternal lineage being derived from 3 founder females, and all paternal lineages traced back to a single founder stallion. Methods and theory are described in detail in order to demonstrate the scope of this analysis for wider conservation strategies. We quantitatively demonstrate the critical nature of the genetic resources within the breed and offer a perspective on implementing this data in considered breed management strategies.
... In recent years there has been substantial interest in quantifying the genetic diversity of equine breeds using pedigree [1], molecular data [2] or a combination of both sources [3] in order to implement effective breed management strategies. The effectiveness of the use of both data types in the understanding and management of rare and native equine breeds have been investigated using both theoretical modelling, and studies of closed studbooks. ...
The Cleveland Bay horse is one of the oldest equines in the United Kingdom, with pedigree data going back almost 300 years. The studbook is essentially closed and because of this, there are concerns about loss of genetic variation across generations. The breed is one of five equine breeds listed as “critical” (<300 registered adult breeding females) by the UK Rare Breeds Survival Trust in their annual Watchlist. Due to their critically endangered status, the current breadth of their genetic diversity is of concern, and assessment of this can lead to improved breed management strategies. Herein, both genealogical and molecular methods are combined in order to assess founder representation, lineage, and allelic diversity. Data from 15 microsatellite loci from a reference population of 402 individuals determined a loss of 91% and 48% of stallion and dam lines, respectively. Only 3 ancestors determine 50% of the genome in the living population, with 70% of maternal lineage being derived from 3 founder females, and all paternal lineages traced back to a single founder stallion. Methods and theory are described in detail in order to demonstrate the scope of this analysis for wider conservation strategies. We quantitatively demonstrate the critical nature of the genetic resources within the breed and offer a perspective on implementing this data in considered breed management strategies.
... On the other hand, substructuring of a breed and relationships between subpopulations can also be inferred by analyzing either pedigree information or different types of genetic markers, and this has often been reported by either one of the (Leroy et al., 2009b;Conant et al., 2011;Vicente et al., 2012;Petersen et al., 2013;Pinheiro et al., 2013;Pirault et al., 2013;Petersen et al., 2014). Moreover, the combination of the two methods has been proposed as a way to improve the reliability of estimation of relationships among animals (Bömcke et al., 2011). ...
An in-depth study of characterization and evaluation of selection strategies in the Lusitano horse breed was conducted to identify factors affecting the genetic variability of the breed and provide baseline information for the establishment of a sustainable genetic improvement program. Pedigree records collected in 53417 animals born from 1824 to 2009 were used. The mean generation interval was 11.33±5.23 and 9.71±4.48 years for sires and dams, respectively. For animals born between 2005 and 2009, the mean number of equivalent generations was 11.20±0.71 and the average inbreeding was 11.34±7.48%. The rate of inbreeding per year was 0.173±0.070, and the corresponding effective population size was about 28. The effective number of founders, ancestors and studs was 27.5, 11.7 and 5.4, respectively. These results reflect a strong emphasis placed on a few sire-families and raise concerns regarding the conservation of genetic diversity for the future.
Mixed model procedures were used to estimate genetic parameters, fixed effects and genetic trends for morpho-functional traits in Lusitano horses by uni- and multivariate animal models. Morphological traits included were partial scores attributed to more than 18000 horses at the time of registration in the studbook and included the classification of head/neck, shoulder/withers, chest/thorax, back/loin, croup, legs and overall impression, plus a final score (FS) and a score for gaits (GA) and the measurement of height at withers (HW). For functionality, the traits considered were scores obtained in dressage (WEDT) and maneability (WEMT) trials of working equitation (WE, about 1500 records by 200 horses), and classical dressage (CD, about 12130 records by nearly 760 horses). Fixed effects considered in the analyses of morphology, GA and FS were stud, year, sex, inbreeding and age. For functionally traits, the fixed effects were event, level of competition, sex, inbreeding and age. Heritability (h2) estimates for all partial morphological scores ranged between 0.12 and 0.18, except for legs (0.07), and were 0.18 for FS, 0.61 for HW and 0.17 for GA. For performance, h2 was 0.32 for WEDT and CD and 0.18 for WEMT. The genetic correlations among partial components of morphology were positive but widely different (0.08 to 0.77). The favourable genetic relationships existing between morphology and performance indicate that morphology and gaits traits can be used to enhance selection response when the improvement of WE or CD is intended. The magnitude of inbreeding depression was small for all the traits analyzed. The estimated breeding values for morphology, gaits and WE presented a large variability, indicating that selection can be effective, but the genetic trend observed over the last few years was positive but moderate for all traits.
The assessment of genetic diversity and population structure obtained by either pedigree data or microsatellite markers was compared. The same pedigree database was used and, in addition, data on either 6 or 8 microsatellite markers genotyped in more than 19000 horses, from 1998-2007. Genealogical inbreeding was a better predictor of molecular inbreeding than the opposite, but it had a modest correlation with multilocus heterozygosity (6% of its variability). Still, the rates of inbreeding per generation estimated by the two methods were very similar. Genetic distances among the major studs producing Lusitano horses were comparable when they were estimated from pedigree or molecular information, with a correlation between FST distances of 0.82, and similar dendrograms were obtained in both cases. Overall, estimates derived from a reduced number of microsatellites or from pedigrees are poorly correlated when considered at the individual level, but parameters derived from pedigree are better predictors of molecular-derived indicators. However, when considered at the breed-level, the estimated diversity parameters, time trends and population substructure are very similar when genealogical data or microsatellite markers are considered.
... physiological changes associated with individual growth, development, and health status) [52]. Indeed, the modern American Quarter Horse exhibits high genetic diversity, which is the result of increased gene flow during domestication and wide geographical spread due to its historical use in transportation [53,54]. Thus, just as in humans, diverse genetic variants in the American Quarter Horse may be linked to significant variation of gut microbiome profiles between individuals at very specific taxonomic groups [55,56]. ...
Background: Although contributions of the equine gut microbiome to forage utilization are well recognized, the impact of alfalfa lignification on the equine gut microbiome remains unknown. Here, we characterized microbial community dynamics in the equine distal gut when feeding reduced lignin (RL) and reference alfalfa hays (CON-control) ( Medicago sativa L.) to adult stock-type horses. Hay from RL and CON cultivars were similar in crude protein, neutral detergent fiber, and equine digestible energy, but differed in acid detergent lignin content (RL:74 g kg -1 vs. CON: 81 g kg -1 ). Dietary treatments were fed to six horses in a crossover study. Experimental periods consisted of a 9-d dietary adaptation phase followed by a 5-d total fecal collection phase, during which horses were housed in individual box stalls and manure was removed on a continuous 24-h basis. At 12-h intervals, feces were thoroughly mixed, frozen, and used for bacterial community composition analyses via V4, 16S rRNA amplicon MiSeq sequencing.
Results: RL alfalfa did not result in specific fecal microbiome composition across all horses. However, upon incorporating individual horse in the model, it was shown that the microbiome of each subject did respond to hay lignin content in an individualized manner over time, in terms of alpha and beta diversity. Closer inspection of specific taxonomic changes upon feeding the two diets also revealed horse-specific trends, with unique amplicon sequence variants classified as Akkermansia , Fibrobacter succinogenes , Treponema, and Paludibacter fluctuating significantly in abundance when RL alfalfa was fed, depending on horse. Along these lines, horse-specific associations between individual gut microbiome traits and characteristics of the digested CON or RL alfalfa were observed, mainly in regards to dry matter digestibility and mean feed particle size.
Conclusions: These results indicate that the horse gut microbiome responds in an individualized manner to small changes in the amount of acid detergent lignin in alfalfa hay, potentially impacting several feed digestibility characteristics. The implications of horse-specific responses to forage quality in regards to metabolic health and performance remain to be elucidated.
... Selective breeding can lead to population stratification within breeds [39], and not accounting for this population stratification can lead to spurious associations on GWA [40]. For this data, principal components analysis revealed population stratification in the Welsh pony cohort based on clustering of the registered sections ( Figure A1). ...
Equine metabolic syndrome (EMS) is a complex trait for which few genetic studies have been published. Our study objectives were to perform within breed genome-wide association analyses (GWA) to identify associated loci in two high-risk breeds, coupled with meta-analysis to identify shared and unique loci between breeds. GWA for 12 EMS traits identified 303 and 142 associated genomic regions in 264 Welsh ponies and 286 Morgan horses, respectively. Meta-analysis demonstrated that 65 GWA regions were shared across breeds. Region boundaries were defined based on a fixed-size or the breakdown of linkage disequilibrium, and prioritized if they were: shared between breeds or across traits (high priority), identified in a single GWA cohort (medium priority), or shared across traits with no SNPs reaching genome-wide significance (low priority), resulting in 56 high, 26 medium, and seven low priority regions including 1853 candidate genes in the Welsh ponies; and 39 high, eight medium, and nine low priority regions including 1167 candidate genes in the Morgans. The prioritized regions contained protein-coding genes which were functionally enriched for pathways associated with inflammation, glucose metabolism, or lipid metabolism. These data demonstrate that EMS is a polygenic trait with breed-specific risk alleles as well as those shared across breeds.
... Owing to the wealth of available genome-wide tools and resources (see above), these breeds can now be studied in detail for genetic makeup, signatures of selection and relatedness to other breeds. The number of publications in the field is growing almost exponentially and these include a few seminal studies encompassing a global collection of breeds ( McCue et al. 2012;Petersen et al. 2013a,b;Jagannathan et al. 2019), and many studies specializing in a single breed or a group of related breeds, for example, the American Quarter Horse ( Petersen et al. 2014a;Avila et al. 2018;Marchiori et al. 2019;Pereira et al. 2019), the Hanoverian and other German Warmblood breeds ( Nanaei et al. 2019;Nolte et al. 2019), the Arabian and related Middle Eastern breeds ( Almarzook et al. 2017;Sadeghi et al. 2019), and some native/primitive breeds such as Hucul and Konik (Gurgul et al. 2019), Chinese native horses ( Zhang et al. 2018), Japanese native breeds ( Tozaki et al. 2019), the Yakutian Horse ( Librado et al. 2015) and Korean horses ( Seong et al. 2019). This is by no means an exhaustive list and it is even longer when including breeds that have recently been studied based on a genome-wide collection of microsatellite markers, such as Estonian horse breeds ( Sild et al. 2019) or Konik ( Szwaczkowski et al. 2016). ...
The horse reference genome from the Thoroughbred mare Twilight has been available for a decade and, together with advances in genomics technologies, has led to unparalleled developments in equine genomics. At the core of this progress is the continuing improvement of the quality, contiguity and completeness of the reference genome, and its functional annotation. Recent achievements include the release of the next version of the reference genome (EquCab3.0) and generation of a reference sequence for the Y chromosome. Horse satellite‐free centromeres provide unique models for mammalian centromere research. Despite extremely low genetic diversity of the Y chromosome, it has been possible to trace patrilines of breeds and pedigrees and show that Y variation was lost in the past approximately 2300 years owing to selective breeding. The high‐quality reference genome has led to the development of three different SNP arrays and WGSs of almost 2000 modern individual horses. The collection of WGS of hundreds of ancient horses is unique and not available for any other domestic species. These tools and resources have led to global population studies dissecting the natural history of the species and genetic makeup and ancestry of modern breeds. Most importantly, the available tools and resources, together with the discovery of functional elements, are dissecting molecular causes of a growing number of Mendelian and complex traits. The improved understanding of molecular underpinnings of various traits continues to benefit the health and performance of the horse whereas also serving as a model for complex disease across species.
... This has been demonstrated in recent analyses of genetic relatedness among performance subgroups of QHs, including 6 groups (not including barrel racing) examined in the present study of E321G MYH1 variant frequency. 17 Our investigation supports previous suggestions that it is incorrect to assume without a confirmatory genetic survey that the frequency of a disease allele in 1 performance subgroup of QHs is similar to that in a different subgroup or the whole breed. 4 On average, the prevalence of the E321G MYH1 variant was 54% different in magnitude among the 5 performance subgroups in this survey. ...
Background
Immune‐mediated myositis (IMM) in American Quarter Horses (QHs) causes acute muscle atrophy and lymphocytic infiltration of myofibers. Recently, an E321G mutation in a highly conserved region of the myosin heavy chain 1 (MYH1) gene was associated with susceptibility to IMM and nonexertional rhabdomyolysis.
Objectives
To estimate prevalence of the E321G MYH1 variant in the QH breed and performance subgroups.
Animals
Three‐hundred seven elite performance QHs and 146 random registered QH controls.
Methods
Prospective genetic survey. Elite QHs from barrel racing, cutting, halter, racing, reining, Western Pleasure, and working cow disciplines and randomly selected registered QHs were genotyped for the E321G MYH1 variant and allele frequencies were calculated.
Results
The E321G MYH1 variant allele frequency was 0.034 ± 0.011 in the general QH population (6.8% of individuals in the breed) and the highest among the reining (0.135 ± 0.040; 24.3% of reiners), working cow (0.085 ± 0.031), and halter (0.080 ± 0.027) performance subgroups. The E321G MYH1 variant was present in cutting (0.044 ± 0.022) and Western Pleasure (0.021 ± 0.015) QHs at lower frequency and was not observed in barrel racing or racing QHs.
Conclusions and Clinical Importance
Knowing that reining and working cow QHs have the highest prevalence of the E321G MYH1 variant and that the variant is more prevalent than the alleles for hereditary equine regional dermal asthenia and hyperkalemic periodic paralysis in the general QH population will guide the use of genetic testing for diagnostic and breeding purposes.
... Lusitano (10.28) and American Quarter Horse (10.5). (Valera et al., 2005;Vicente et al., 2012Petersen et al., 2014. Lower generation intervals were observed in Pantaneiro horse (8.20 years) and Slovak Sport Pony (9.96) (Pjontek et al., 2012;McManus et al., 2013). ...
The Maremmano is an autochthonous Italian horse breed, which probably descended from the native horses of the Etruscans (VI century B.C.); the Studbook was acknowledged in 1980, and it includes 12 368 horses born from that year up to 2015. The aim of this study was to evaluate the effect of the selection program on the genetic variability of the Maremmano population; the analysis was performed using both the ‘Endog v 4.8’ program available at http://webs.ucm.es/info/prodanim/html/JP_Web.htm and in-house software on official pedigree data. Four Reference Populations were considered, and the most important one was the population of the 12 368 Maremmano horses officially registered in the National Studbook. The pedigree completeness of this population was very good because it was more than 90% at the third parental generation and more than 70% at the fifth generation; the pedigree traced back to a maximum of 10.50 generations with an average of 3.30 complete generations and 5.70 equivalent complete generations. The average generation interval was 10.65±4.72 years, with stallions used for longer periods than mares. The intervals ranged from 10.15±4.45 (mother–daughter) to 10.99±4.93 (father–daughter). The effective number of founders ( fe ) was 74 and the effective number of ancestors ( fa ) was 30 so that the ratio fe / fa was 2.47. The founder genome equivalents ( fg ) was 13.72 with a ratio fg / fe equal to 0.18. The mean of the genetic conservation index was 5.55±3.37, and it ranged from 0.81 to 21.32. The average inbreeding coefficient was 2.94%, with an increase of 0.1%/year, and the average relatedness coefficient was 5.52%. The effective population size ( Ne ) computed by an individual increase in inbreeding was 68.1±13.00; the Ne on equivalent generations was 42.00, and this value slightly increased to 42.20 when computed by Log regression on equivalent generations. The analysis confirmed the presence of seven traditional male lines. The percentage of Thoroughbred blood in the foals born in 2015 was 20.30% and has increased 0.21%/year since 1980; in particular, it increased more than twice (0.51%/year) until 1993 and afterwards slightly fluctuated. The pedigree analysis confirmed the completeness of genealogical information and the traditional importance that breeders gave to the male lines; although the genetic diversity of Maremmano seemed to be not endangered by the selection program, some effects on the population structure were found and a more scientific approach to genetic conservation should be incorporated in the selection plans.
... Other subspecies of Equus ferus like tar pan (Equus ferus ferus) were undomesticated which are extinct now (Kavar and Dovc, 2008). Humans started to domesticate horse about 4000BC ago (Goodwin, 2007) in Eurasian steppes (Petersen et al., 2013). Two alternative hypotheses can be formulated for the origin of the domestic horse from wild populations. ...
In the current study, data of 930 horses was used and divided into four types of categories i.e. Draft, Wild, Sports and Race types. A set of ten microsatellite markers HTG10, ASB2, ASB17, HMS3, AHT4, HMS7, VHL20, AHT05, HTG4, and HMS6 were studied. Allelic frequency, total number of alleles, observed number of alleles, expected number of alleles, heterozygosity, Hardy-Weinberg equilibrium was calculated using GeneAIEX 6.502 software. Genetic structure of horse breeds was studied using STRUCTURE & STRUCTURE harvest software, while results were visualized by CLUMP and DISTRUCT software. Moreover, Phylogenetic analysis was performed using PHYLIP and data was visualized in MEGA 7. Maximum number of alleles was observed for sports category, and most polymorphic markers among all types of horses was ASB17. The maximum and minimum values of inbreeding coefficient was found in wild and race horses respectively. Maximum observed heterozygosity was found in case of race horses; however, highest value of expected heterozygosity was found for sports horses. Present study showed that even with limited number of markers considerable level of genetic diversity between and among all types of horses was observed.
... Other subspecies of Equus ferus like tar pan (Equus ferus ferus) were undomesticated which are extinct now (Kavar and Dovc, 2008). Humans started to domesticate horse about 4000BC ago (Goodwin, 2007) in Eurasian steppes (Petersen et al., 2013). Two alternative hypotheses can be formulated for the origin of the domestic horse from wild populations. ...
... These animals were later taken to New Mexico and California and eventually originated feral populations that were sometimes mixed with different European breeds in order to improve their original aptitudes (Clutton-Brock, 1992). For example, the Thoroughbred contributed to the Quarter Horse to increase its speed (Petersen, Mickelson, Cleary, & McCue, 2014), and also to the Rocky Mountain, Tennessee Walking and Saddlebred breeds, which originated in the same geographical area (Dutson, 2005). Thoroughbred, Arabian, Quarter Horse, Morgan and Standardbred influences have been documented in the Appaloosa (Appaloosa Horse Club), while all Morgan horses can trace back to a single stallion, figure, whose sire was probably a Thoroughbred (Appaloosa Horse Club). ...
Criollo horse populations descend from horses brought from the Iberian Peninsula over the period of colonization (15th to 17th century). They are spread throughout the Americas and have potentially undergone genetic hybridization with other breeds in the recent past. In this study, 25 autosomal microsatellites were genotyped in 50 horse breeds representing Criollo populations from 12 American countries (27 breeds), breeds from the Iberian Peninsula (19), one breed each from France and Morocco and two cosmopolitan horse breeds (Thoroughbred and Arabian). The genetic relationships among breeds identified five clusters: Celtic; Iberian; North American with Thoroughbred influence; most Colombian breeds; and nearly all other Criollo breeds. The group of "all other Criollo breeds" had the closest genetic relationship with breeds originating from the Iberian Peninsula, specifically with the Celtic group. For the whole set of Criollo breeds analysed, the estimated genetic contribution from other breeds was approximately 50%, 30% and 20% for the Celtic, Iberian and Arab-Thoroughbred groups, respectively. The spatial distribution of genetic diversity indicates that hotspots of genetic diversity are observed in populations from Colombia, Ecuador, Brazil, Paraguay and western United States, possibly indicating points of arrival and dispersion of Criollo horses in the American continent. These results indicate that Criollo breeds share a common ancestry, but that each breed has its own identity.
... The analysis showed a clear separation between these breeds (Fig. 1). The major genetic distance in these five breeds is between Arabian and Thoroughbred breeds, while the breeds which are closer from each other are Appaloosa and Quarter Horse, corroborating the historical data that indicate the time and the way of each horse breed arose [12][13][14][15][16][17][18][19][20][21]. Based on the largest publication and one of the most important on allelic frequencies of the seventeen STR markers present in our study [1], we compared the most frequent alleles at each locus in three horse breeds that are common in both works (Appaloosa, Arabian and Thoroughbred). ...
Allele frequencies and other forensic parameters for seventeen equine-specific STR loci (AHT4, AHT5, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG6, HTG7, HTG10, LEX3 and VHL20) were determined from a pool of 32,053 purebred horses, consisting of five breeds (Appaloosa, Arabian, Uruguayan Criollo, Thoroughbred and Quarter Horse) from Uruguayan equine population. The forensically informative parameters (Ho, He, HWE test, PIC, PD, PE and PID) as well as the coefficients of inbreeding (FIS), fixation indices (FST), and total inbreeding (FIT) were ascertained from this population sample. Based on genotypic frequencies of the seventeen STRs of this study, pairwise genetic distances were calculated among five breeds of Uruguayan horses, showing a clear separation between these breeds. The presentation of these data, with these set of genetic markers, for Uruguayan Criollo and Quarter Horse breeds, is one of the first publications in the scientific community.
... As expected, within the QH, where the haplotype containing the SINE and C allele of intron 1 is under selection (Petersen et al. 2013b), overall haplotype diversity in the breed was low. Haplotype diversity in the TB was also relatively low, likely as a result of selection for racing characteristics and due to generally low diversity present in the breed (Petersen et al. 2013a;Petersen et al. 2014). ...
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 TB and QH (0.73 and 0.48 respectively). Haplotype data suggest the SINE insertion is contemporary to and arose upon a haplotype containing the intron 1 C allele. Gluteal muscle biopsies of TBs showed a significant association of the intron 1 C allele and SINE with a higher proportion of Type 2B and lower proportion of Type 1 fibers. However, in the Belgian horse, in which the SINE is not present, the intron 1 SNP was not associated with fiber type proportions, and evaluation of fiber type proportions across the Belgian, TB and QH breeds shows the significant effect of breed on fiber type proportions is negated when evaluating horses without the SINE variant. These data suggest the SINE, rather than the intron 1 SNP, is driving the observed muscle fiber type characteristics and is the variant targeted by selection for short-distance racing.
... Analysis between the racing and cutting lines The mean value of parameter θ = F ST (± standard deviation) estimated for the 42 058 informative SNPs, considering both lines, was 0.0342 ( ±0.0403), with θ ranging from 0.0025 to 0.3556. The global F ST value obtained by Petersen et al. (2014), who used genome-wide SNP data from Quarter Horses represented by six performance groups (halter, western pleasure, reining, working cow, cutting and racing) to examine genetic diversity within the breed, was 0.035. With the exception of the working cow and cutting horses, pairwise F ST values show significant population structure among the six performance groups with the highest divergence observed between the cutting and racing (0.074). ...
Selection of Quarter Horses for different purposes has led to the formation of lines, including racing and cutting horses. The objective of this study was to identify genomic regions divergently selected in racing line of Quarter Horses in relation to cutting line applying relative extended haplotype homozygosity (REHH) analysis, an extension of extended haplotype homozygosity (EHH) analysis, and the fixation index (F ST) statistic. A total of 188 horses of both sexes, born between 1985 and 2009 and registered at the Brazilian Association of Quarter Horse Breeders, including 120 of the racing line and 68 of the cutting line, were genotyped using single nucleotide polymorphism arrays. On the basis of 27 genomic regions identified as selection signatures by REHH and F ST statistics, functional annotations of genes were made in order to identify those that could have been important during formation of the racing line and that could be used subsequently for the development of selection tools. Genes involved in muscle growth (n=8), skeletal growth (n=10), muscle energy metabolism (n=15), cardiovascular system (n=14) and nervous system (n=23) were identified, including the FKTN, INSR, GYS1, CLCN1, MYLK, SYK, ANG, CNTFR and HTR2B.
Background: Congenital myotonia is a genetic neuromuscular disorder characterized by delayed relaxation of the musculature following a strong contraction. Variants in the skeletal muscle chloride channel 1 gene (CLCN1) have been linked to this disorder across several species. The CLCN1_c.1775A>C, an autosomal recessive, variant was identified as a potential causative factor for congenital myotonia in New Forest Pony. While the CLCN1_c.1775A>C variant has been studied in different breeds of horses, it remains unexplored in Brazilian Quarter Horses. Therefore, this study aimed to assess the prevalence of the CLCN1_c.1775A>C variant among Brazilian Quarter Horses across various disciplines. Materials, Methods & Results: In this study, 96 DNA samples were obtained from athletic Brazilian Quarter Horses representing various disciplines, 24 each from cutting, reining, barrel racing, and bull-cacthing (“vaquejada”). DNA viability was assessed via PCR targeting the β-actin gene. Subsequently, a previously described set of specific primers was employed to amplify the region encompassing the CLCN1_c.1775A>C variant. The resulting purified PCR products underwent Sanger direct sequencing, and their electropherograms were analyzed. Notably, none of the horses in this cohort were found to carry the CLCN1_c.1775A>C variant. The inbreeding coefficient (F) was calculated using pedigree data sourced from the 96 Quarter Horses according to Brazilian Quarter Horse Breeders Association records, encompassing 4 generations. The average F value for the entire cohort was found to be 0.2%. However, when assessed across disciplines, the average F values varied, with cutting at 0.002 (0.2%), reining at 0.003 (0.3%), barrel racing at 0.0008 (0.08%), and bull-cacthing at 0.001 (0.1%), respectively. Notably, within this cohort, 48 horses were identified as inbred, exhibiting an average F of 1.5%. Discussion: Genetic variants associated with conditions such as hyperkalemic periodic paralysis, myosin heavy chain myopathy, and polysaccharide storage myopathy type 1 have been previously documented in Quarter Horses globally, including Brazil. However, as in the present study, the CLCN1 c.1775A>C variant was also not detected in American Quarter Horses affected by muscular disorders. Although this variant has been implicated as the cause of congenital myotonia in a New Forest pony, its correlation with cases of congenital myotonia in Quarter Horses has not been established yet. Although the inbreeding coefficient and the prevalence of endogamous horses observed in this study were lower compared to findings in other studies, the presence of inbreeding and shared ancestors within Quarter Horses lineages was evident. High rates of inbreeding may disseminate undesirable genetic variants, since popular stallions may improve the athletic performance of its progenies but also may transmit alleles with pathogenic variants, as seen in other genetic disorders in horses. Differently, since it was not observed in this group of evaluated Quarter Horses nor in other previous studies, it may be that the CLCN1 c.1775A>C is a 'de novo' variant related strictly to congenital myotonia in the New Forest pony. Nevertheless, it is imperative to highlight the potential for congenital myotonia to inflict significant harm upon horses. Investigations into new cases are essential to establish both clinical and etiological diagnoses, thereby enabling the assessment of the requisite preventive measures against this disorder. Keywords: CLCN1, equestrian industry, genotyping, variants.
Mangalarga Marchador (MM) is the most important Brazilian horse breed, with 600 thousand animals registered. The aim of this study carry out the genetic characterization of the breed. Samples were collected from 355 horses [MM, n = 218; Andalusian n = 20; Purebred Lusitano n = 21; Sorraia (SOR) n = 16; Thoroughbred n = 21; Campolina (CAM) n = 21, and Mangalarga (MAN) n = 38] and genotyped with the SNP 70K BeadChip. Parameters were calculated, such as expected heterozygosities (He), Hardy-Weinberg equilibrium (HWE), linkage disequilibrium (r²), genetic differentiation, and principal component analysis (PCA); and haplotypes in common and population structure was assessed by Bayesian methods. The MM breed obtained reasonable He and deviations from HWE. The SOR breed had high r², and CAM and MM had low r². MAN and MM had a similar haplotype block. Analyses of population structure showed that, just as the other Brazilian breeds, the MM breed is not well defined, showing signs of substructure and possibly admixture. The analyses with PCA showed that Brazilian breeds clustered together, and well separated from the remaining breeds. A breeding program seeking to maximize the variability of MM and structure the breed as a more defined genetic entity should be implemented immediately.
The aim of this study was to evaluate the genetic diversity and to identify the most influential ancestors in the population of Brazilian Quarter Horses participating in cutting competitions. Data from 1,590 elite horses born between 1970 and 2015, which participated in cutting competitions between 1981 and 2018, were evaluated based on the pedigree file that contained 5,832 animals born since 1834. Evaluation of the quality of the pedigree data showed a mean number of known equivalent generations of 5.4 ± 1.5 and a mean generation interval of 11.7 ± 8.8 years. The inbreeding coefficient (1.98 ± 7.13%), relatedness coefficient (2.18 ± 0.01%), and individual increase in inbreeding (0.43 ± 0.01%) were low. The effective population size (Ne) was 136 animals. The probability of gene origin indicated effective numbers of founders, ancestors and founder genomes of 255, 37 and 23 animals, respectively. The number of founders and ancestors was 1,852 and 899 animals, respectively, with 10, 50 and 100 ancestors explaining 39.2%, 67.9% and 91.6%, respectively, of the genetic diversity of the population. The five most influential ancestors were Doc Bar, Peppy San Badger, Freckles Playboy, Poco Lena and High Brow Cat, accumulating 30.7% of the marginal genetic contributions of the population. Few ancestors were responsible for the genetic diversity, resulting in the narrowing of the initial genetic base. Breeders depend on a small group of ancestors, which could be corrected by increasing the number of breeding animals and by directed mating using ancestors of different origins.
The elongated, distally tapered limbs of horses are adapted for high‐speed locomotion. Because these traits are artificially selected for in modern racehorses, they operate at a morphological extreme with a high risk of fracture. Racehorses are subject to different training and racing regimes depending on their breed and gait, and are therefore an interesting model to examine bone functional adaptation under variable biomechanically intense conditions. This study compares bone structural properties in the third metacarpal (MCIII) of Thoroughbred (n = 9) and Quarter Horse (n = 11) racehorses, using feral Assateague Island ponies (n = 6) as an untrained/unraced outgroup, to determine whether structural properties reflect variable racing and training regimes. Geometric section properties and bone mineral densities were determined using peripheral quantitative CT at two diaphyseal sites and through the distal epiphysis. Diaphyseal strength of the MCIII in all three breeds does not differ relative to body size, but in the mid‐diaphyseal region Thoroughbreds have higher antero‐posterior relative to medio‐lateral bending strength than Quarter Horses, as well as higher bone mineral densities in left MCIII epiphyses (particularly in the lateral condyle). Interestingly, all breeds have lower bone mineral densities in the lateral versus medial condyle, an inherent structural feature that may influence predisposition to fracture when running around turns. Our results suggest that despite subtle differences in bone structure between different racehorse breeds, basic morphology of the third metacarpus is relatively similar among racing and non‐racing horses, possibly reflecting intense selection (natural and artificial) across domestic equids for similar structural features within distal limb elements.
The Cleveland Bay horse is one of the oldest equines in the United Kingdom, with pedigree data going back almost 300 years. The studbook is essentially closed and because of this, there are concerns about loss of genetic variation across generations. The breed is one of five equine breeds listed as critical (<300 registered adult breeding females) by the UK Rare Breeds Survival Trust in their annual Watchlist. Due to their critically endangered status, the current breadth of their genetic diversity is of concern, and assessment of this can lead to improved breed management strategies. Herein, both genealogical and molecular methods are combined in order to assess founder representation, lineage, and allelic diversity. Data from 16 microsatellite loci from a reference population of 402 individuals determined a loss of 91% and 48% of stallion and dam lines, respectively in the reference population. Only 3 ancestors determine 50% of the genome in the living population, with 70% of maternal lineage being derived from 3 founder females, and all paternal lineages traced back to a single founder stallion. Methods and theory are described in detail in order to demonstrate the scope of this analysis for wider conservation strategies. We quantitatively demonstrate the critical nature of the genetic resources within the breed, and offer a perspective on implementing this data in considered breed management strategies.
The aim of the study was to analyze the results of Quarter Horse (QM) speed racing in Brazil, prioritizing discussions of race pattern, genetic diversity, main ancestors, parameters and genetic trends of the characteristics derived from earning, final time and velocity. The data contained 23,482 sprint records, belonging to 5,861 animals (42.2% males) and a total pedigree of 11,425 horses. Five distances 275, 301, 320, 365 and 402 meters (m) were evaluated, with 1,072, 6,579, 2,726, 5,682 and 7,423 records, respectively. Changes in animal genetic diversity were evaluated by 3 subpopulations in three complete decades, from 1980 (sP80), 1990 (sP90) and 2000 (sP00), evaluating 84.5% of the total data. The characteristics monetary profitability at the age of two horse age (RM2), best time and distance class 301 and 402 m (BT301, BT402, CT301 and CT402) were used to estimate genetic parameters. The beginning of the career of the 5,861 horses indicated that 29.4% and 27.9% of the animals performed their first race in the distances of 301 m and 402 m, respectively, and 75.2% of the animals started at 2 years of age. horse riding. At the main distance (402 m), the non-breeding male animals that started the races at 4 years were the fastest and the ones that contributed the most to the phenotypic evolution of the final time and speed characteristics. Inbreeding and kinship coefficients were low, ranging from 0.49% to 1.60% and from 1.12% to 2.56%, respectively. The effective population size (Ne) values ranged from 144 to 369 (ΔFi) and 41 to 117 (generation). The totality of genetic diversity was explained by 1,587 ancestors (founders or not), considered high, but with only 50 (sP80) and 9 (sP00) ancestors it is possible to explain 50% of the total genetic diversity. The loss of genetic diversity in the QM race lineage in Brazil is evident and undeniable, and regular evaluation programs are necessary to prevent the continuation of the loss of genetic diversity observed in animals born in the 21st century. The heritability traits obtained in the traits were low to moderate in magnitude and the means ranged from 0.11 ± 0.05 (R2) to 0.35 ± 0.05 (CT301). The estimates of the bi-characteristics were moderate to high and, higher than the uni values, the bi-characteristics ranged from 0.19 ± 0.06 (CT301) to 0.76 ± 0.02 (BT402) in the interaction with RM2. The additive genetic, residual and phenotypic correlations showed positive values between RM2 with CT301 and CT301 and negative between RM2 with BT301. The study proved to be a good indicator for tracking changes in traits earnings, best time and speed, providing information on genetic diversity as well as animal models that can be used in breeding evaluation and selection for breeding programs of the Quarter Horse racing line in Brazil.
Different selection goals in the Quarter Horse breed have led to the formation of lines. These lines have different skills such as working with cattle or running and differ in morphology, physiology and inbreeding. The aim of this study was to characterize the linkage disequilibrium (LD, r²) in the cutting and racing lines of Quarter Horses bred in Brazil using large-scale SNP genotyping. Additionally, the effective population size (Ne) of the two populations (lines) was determined, as well as their structure and relationships. A total of 428 Quarter Horses (both sexes) of the two lines (cutting: 68; racing: 360), registered in the Stud book of the Brazilian Association of Quarter Horse Breeders (ABQM), were used. The animals had blood collected in the Sorocaba Jockey Club (Sorocaba/SP) and in dozens rural properties across the state of São Paulo, Brazil. In 2011, 188 horses (cutting: 68; racing: 120) were genotyped using a 54k SNP chip. The remaining animals (n = 240) were genotyped in 2015 using a 65k SNP chip. The average genomic r² between marker pairs was 0.22 for the cutting line and 0.27 for the racing line. In the cutting line, the r² was less than 0.20 between 100 and 150 kb, while the same threshold (0.20) was found between 300 and 350 kb in the racing line. The Ne was 60 and 50 effective animals in the last generation of the cutting and racing line, respectively. The greater extent of LD and smaller Ne in the racing line may be explained by the structure of the population, which is more closed because of the more rigorous registration process and greater influence of the Thoroughbred breed on the formation of this line. The results point to marked differences between the lines of this breed. In addition, subpopulations were found in the racing line, which may be related to the formation of families descending from important sires.
Selective breeding for athletic performance in various disciplines has resulted in population stratification within the American Quarter Horse (QH) breed. The goals of this study were to utilize high density genotype data to: (1) identify genomic regions undergoing positive selection within and among QH subpopulations; (2) investigate haplotype structure within each QH subpopulation; and (3) identify candidate genes within genomic regions of interest (ROI), as well as biological pathways, predicted to play a role in elite performance in each group. For that, 65K SNP genotyping data on 143 elite individuals from 6 QH subpopulations (cutting, halter, racing, reining, western pleasure, and working cow) were imputed to 2M SNPs. Signatures of selection were identified using FST-based (di) and haplotype-based (hapFLK) analyses, accompanied by identification of local haplotype structure and sharing within subpopulations (hapQTL). Regions undergoing positive selection were identified on all 31 autosomes, and ROI on 2 chromosomes were identified by all 3 methods combined. Genes within each ROI were retrieved and used to identify pathways and genes that might contribute to performance in each subpopulation. These included, among others, candidate genes associated with skeletal muscle development, metabolism, and central nervous system development. This work improves our understanding of equine breed development, and provides breeders with a better understanding of how selective breeding impacts the performance of QH populations.
Within the scope of current genetic diversity analyses, population structure and homozygosity measures are independently analysed and interpreted. To enhance analytical power, we combined the visualization of recently described high-resolution population networks with runs of homozygosity (ROH). In this study, we demonstrate that this approach enabled us to reveal important aspects of the breeding history of the Haflinger horse. We collected high-density genotype information of 531 horses originating from seven populations which were involved in the formation of the Haflinger, namely 32 Italian Haflingers, 78 Austrian Haflingers, 190 Noriker, 23 Bosnian Mountain Horses, 20 Gidran, 33 Shagya Arabians, and 155 Purebred Arabians. Model-based cluster analysis identified substructures within Purebred Arabian, Haflinger and Noriker that reflected distinct genealogy (Purebred Arabian), geographic origin (Haflinger) and coat colour patterns (Noriker). Analysis of ROH revealed that the two Arabian populations (Purebred and Shagya Arabians), Gidran and the Bosnian Mountain Horse had the highest genome proportion covered by ROH segments (306Mb - 397Mb). The Noriker and the Austrian Haflinger showed the lowest ROH coverage (228Mb, 282Mb). Our combined visualization approach made it feasible to clearly identify outbred (admixture) and inbred (ROH segments) horses. Genomic inbreeding coefficients (FROH) ranged from 10.1% (Noriker) to 17.7% (Purebred Arabian). Finally it could be demonstrated, that the Austrian Haflinger sample has a lack of longer ROH segments and a deviating ROH spectrum, which is associated with past bottleneck events and the recent mating strategy favouring out-crosses within the breed.
Accurate measures of effective population sizes (Ne ) in livestock require good quality data and specialized skills for their computation and analysis. Ne can be estimated by Wright's equation Ne =4MF/(M+ F) (M, F being sires and dams, respectively), but this requires assumptions which are often not met. Total census sizes Nc of livestock breeds are collated globally. This paper investigates whether estimates of Ne can be made from Nc ; this would facilitate conservation monitoring. Some Ne methodologies avoid the assumptions of Wright's equation and permit measurement, rather than estimation, of Ne . Those considered here employ, respectively, linkage disequilibrium (LD) of single-nucleotide polymorphisms (yielding Ne (LD)), and genealogical analysis (rate of increase of inbreeding, DF), yielding Ne (DF). Considering breeds of cattle, sheep, horses, pigs and goats for which Nc and either Ne (LD) or N e(DF) are known (totals of 203 breeds and 321 breeds, respectively), proportionality has been investigated between Nc and these measures of Ne . Ne (LD) was found to increase with Nc , significantly in sheep and horses, less so in cattle, but not at all in pigs. Ne (DF) was correlated with log10(Nc ) in cattle, sheep and horses (53, 56, 43 breeds, respectively). Ne (LD) was correlated in cattle (73 breeds) and pigs (31 breeds) with the log10 transformation of Ne as calculated by Wright's equation. Further verification and refinement are needed, particularly of census data, but credible predictions of Ne are obtainable by applying the following multipliers to log10(Nc ): cattle 17.61, sheep 97.72, horse 70.78. For cattle and pigs, multiplying log10(Ne (Wright)) by, respectively, 40.69 and 60.09, also gives credible predictions. Such census-based estimates of Ne could in principle be generated by non-specialists and are likely to be suited to audits of conservation activity when financial resources or availability of data are limiting. The ratio Ne /Nc varied among species with an overall median value of 0.03, less than a tenth of that typically observed in wild mammals. Characteristics were also investigated of a distinct herdbook-based methodology, namely the development of Wright's equation to take into account variances of progeny numbers to yield what has been termed here Ne (Hill). Comparison of these values with Ne (Wright) could help to identify breeds with breeding structures conducive or inimical to genetic conservation. However, Ne (Hill) requires breed-specific values for these variances, and this restricts its applicability.
Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multilocus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3.
Pedigree structure and inbreeding levels were examined for 5207 Standardbred horses from six breeding farms in the northeastern United States and Canada. Inbreeding coefficients were calculated from pedigrees traced back as far as 30 ancestral generations. A detailed analysis of inbreeding and pedigree structure was done for the first 14 ancestral generations. Although Standardbred breeders tend to avoid very close inbreeding, nearly all horses with complete pedigrees are inbred within the first five ancestral generations. Standardbreds are shown to be interrelated in complex ways, through multiple remote ancestors. Inbreeding coefficients increase markedly with increasing pedigree depth, leveling off only after 10-12 generations. When completeness of pedigrees is taken into account, there is little evidence for an increase in inbreeding through time. A preliminary analysis of inbreeding as a function of gait suggests that trotters are more highly inbred than are pacers.
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 approaches, we conclude that particular efforts should be made to conserve five local breeds, namely the Boulonnais, Landais, Merens, Poitevin and Pottok breeds.
Horses were domesticated from the Eurasian steppes 5,000-6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. F(ST) calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection.
Recent studies in the literature have appliedphylogenetic methods based on genetic distancesto set priorities for conservation of domesticanimal breeds. While these methods may beappropriate for between-species conservation,they are clearly inappropriate forwithin-species breed conservation, because theyignore within-breed variation. In this paper weshow the basic tools to analyse geneticdiversity in subdivided populations withinspecies, and illustrate the errors incurred byapplying methods based exclusively on geneticdistances. We also show that maximisation ofgenetic diversity (minimisation of coancestryor kinship) is equivalent to maximisation ofeffective population size, as in undividedpopulations, and derive a generalisation ofprevious equations for the prediction ofeffective size. Finally, we discuss thestrategies for conservation in the light of thetheory.
An equine SNP genotyping array was developed and evaluated on a panel of samples representing 14 domestic horse breeds and 18 evolutionarily related species. More than 54,000 polymorphic SNPs provided an average inter-SNP spacing of ∼43 kb. The mean minor allele frequency across domestic horse breeds was 0.23, and the number of polymorphic SNPs within breeds ranged from 43,287 to 52,085. Genome-wide linkage disequilibrium (LD) in most breeds declined rapidly over the first 50-100 kb and reached background levels within 1-2 Mb. The extent of LD and the level of inbreeding were highest in the Thoroughbred and lowest in the Mongolian and Quarter Horse. Multidimensional scaling (MDS) analyses demonstrated the tight grouping of individuals within most breeds, close proximity of related breeds, and less tight grouping in admixed breeds. The close relationship between the Przewalski's Horse and the domestic horse was demonstrated by pair-wise genetic distance and MDS. Genotyping of other Perissodactyla (zebras, asses, tapirs, and rhinoceros) was variably successful, with call rates and the number of polymorphic loci varying across taxa. Parsimony analysis placed the modern horse as sister taxa to Equus przewalski. The utility of the SNP array in genome-wide association was confirmed by mapping the known recessive chestnut coat color locus (MC1R) and defining a conserved haplotype of ∼750 kb across all breeds. These results demonstrate the high quality of this SNP genotyping resource, its usefulness in diverse genome analyses of the horse, and potential use in related species.
Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multi-locus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3.
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 approaches, we conclude that particular efforts should be made to conserve five local breeds, namely the Boulonnais, Landais, Merens, Poitevin and Pottok breeds.
Genetic parameters widely used to monitor genetic variation in conservation programmes, such as effective number of founders, founder genome equivalents and effective population size, are interrelated in terms of coancestries and variances of contributions from ancestors to descendants. A new parameter, the effective number of non-founders, is introduced to describe the relation between effective number of founders and founder genome equivalents. Practical recommendations for the maintenance of genetic variation in small captive populations are discussed. To maintain genetic diversity, minimum coancestry among individuals should be sought. This minimizes the variances of contributions from ancestors to descendants in all previous generations. The method of choice of parents and the system of mating should be independent of each other because a clear-cut recommendation cannot be given on the latter.
The thoroughbred (TB) horse is one of the oldest breeds of domestic animals, with pedigree records spanning three centuries. Because the population is essentially closed, there is concern about loss of genetic variation. Here we report two parallel analyses. In the first, genetic variation in the current population is measured using data from 13 microsatellite loci in 211 horses with relationships calculated based on allele sharing. In the second analysis, pedigree information is used to calculate genetic relationships between animals based on shared ancestry. These two measures of relationship are compared and shown to be closely related. Together, they provide an estimate of the amount of genetic variation which existed in founder animals. This study confirms the narrow genetic base of the breed and provides comprehensive analysis of contributions of founder animals. Seventy-eight percent of alleles in the current population are derived from 30 founders, 27 of these male. Ten founder females account for 72% of maternal lineages, while one founder stallion is responsible for 95% of paternal lineages.
Clustering of individuals into populations on the basis of multilocus genotypes is informative in a variety of settings. In population-genetic clustering algorithms, such as BAPS, STRUCTURE and TESS, individual multilocus genotypes are partitioned over a set of clusters, often using unsupervised approaches that involve stochastic simulation. As a result, replicate cluster analyses of the same data may produce several distinct solutions for estimated cluster membership coefficients, even though the same initial conditions were used. Major differences among clustering solutions have two main sources: (1) 'label switching' of clusters across replicates, caused by the arbitrary way in which clusters in an unsupervised analysis are labeled, and (2) 'genuine multimodality,' truly distinct solutions across replicates.
To facilitate the interpretation of population-genetic clustering results, we describe three algorithms for aligning multiple replicate analyses of the same data set. We have implemented these algorithms in the computer program CLUMPP (CLUster Matching and Permutation Program). We illustrate the use of CLUMPP by aligning the cluster membership coefficients from 100 replicate cluster analyses of 600 chickens from 20 different breeds.
CLUMPP is freely available at http://rosenberglab.bioinformatics.med.umich.edu/clumpp.html.
We describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci. The new model accounts for the correlations between linked loci that arise in admixed populations (“admixture linkage disequilibium”). This modification has several advantages, allowing (1) detection of admixture events farther back into the past, (2) inference of the population of origin of chromosomal regions, and (3) more accurate estimates of statistical uncertainty when linked loci are used. It is also of potential use for admixture mapping. In addition, we describe a new prior model for the allele frequencies within each population, which allows identification of subtle population subdivisions that were not detectable using the existing method. We present results applying the new methods to study admixture in African-Americans, recombination in Helicobacter pylori, and drift in populations of Drosophila melanogaster. The methods are implemented in a program, structure, version 2.0, which is available at http://pritch.bsd.uchicago.edu.
We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci—e.g., seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/~pritch/home.html.
To investigate morphological and genomic differences between cutting and racing lines of Quarter Horses, 120 racing and 68 cutting animals of both sexes, registered at the Brazilian Association of Quarter Horse Breeders, were used. Blood samples were collected, and the following physical traits were measured: weight; height at withers; body length; length of the shank, pastern, rump, head, and neck; and chest, shank, and hoof circumference. For analysis of genomic differences, 54,602 single-nucleotide polymorphisms (SNPs) were genotyped using the Equine SNP50 BeadChip, and the quality of individual and SNP genotype data were evaluated. The fixation index, FST, was used to identify genome regions that were altered in the lines by selection. The results showed significant differences between the lines in all physical traits. Quality control led to the exclusion of four cutting animals with a call rate of <0.95. After filtering, 12,544, 13,815, and 13,370 SNPs were excluded for the whole population (n = 184), the 120 racing animals, and the 64 cutting animals, respectively. The number of informative polymorphisms detected in each line and in the whole population indicated that the Equine SNP50 BeadChip can be used in genetic studies of Quarter Horses. The fixation index, FST, identified 2,558 genome regions that may have been modified by divergent selection.
Genetic diversity and population structure were analyzed in the Lusitano horse breed based on pedigree information of animals registered in the Studbook, to identify factors which may have affected the genetic variability of the breed, and provide the bases for the establishment of sustainable utilization programs. Pedigree records collected from 1824 to 2009, including information on 53,411 animals, were used in the analyses. The mean generation interval was 11.33±5.23 and 9.71±4.48 years for sires and dams, respectively, while the mean number of offspring registered was 13.13±22.53 for stallions and 4.00±3.38 for mares. All great-grandparents were known for the animals in the reference population (registered foals born from 2005 to 2009, n=9712), which had a mean number of equivalent generations known of 11.20±0.71 and an average inbreeding of 11.34±7.48%. For this population, the rate of inbreeding per year was 0.173±0.070, and the effective population size computed from this rate was about 28. The mean relationship among animals from the same and from different studs was 0.31±0.16 and 0.15±0.10, respectively. In spite of the high within-stud relationship, inbreeding has been kept lower than expected due to restrictions imposed by breeders on selection and allocation of mates. The effective number of founders, ancestors and studs contributing to the current genetic pool was 27.5, 11.7 and 5.4, respectively. Over the last 30 years, contributions to the genetic pool of Lusitano have been decreasing, with a reduction to about one-half in the effective number of founders and ancestors. Of the 267 founder sires, only 9 Y-chromosome sources are currently represented, with an effective number of 2.23. The diversity of mt-DNA sources is broader, with 129 lineages represented and an effective number of 42.8. The results of our study reflect the intensive emphasis that has been placed on a few sire-families over the years, and raise concerns regarding the conservation of genetic diversity for the future. Methods designed to minimize inbreeding and maximize the maintenance of genetic contributions from different founders and ancestors should be envisaged, to prevent further losses of genetic variability in the Lusitano horse breed.
The aim of the study was to analyse the pedigree information of Thoroughbred horses which were participating in gallop races between 1998 and 2010 in Hungary. Among the 3043 individuals of the reference population there were imported animals from foreign countries (e.g. Germany, England or Ireland) and horses that were born in Hungary. The number of complete generations was 15.64 (varied between 0 for the founders and 25.20), the mean number of full generations was 6.69, and the mean maximum generations were 28.96. The number of founders was 1062, and the effective number of founders was 42. Two hundred and thirty-two founders were born before 1793 (when the stud book of the Thoroughbred breed was closed), therefore these founders are considered as true founders of the breed. These 232 founders were responsible for 88.58% of the gene pool in the reference genome. The significant difference between the number of founders and effective number of founders indicate that the genetic diversity decreased greatly from the founders to the reference population. The number of ancestors was 908 and only 6 of them were responsible for 50% of the genetic diversity in the examined population. The effective number of ancestors was 15.32. From the ratio of the effective number of founders and effective number of ancestors we concluded to a bottleneck effect that characterizes the pedigree under study. Generation interval was more than a year longer for stallions (12.17) than it was for mares (10.64). More than 94% of the individuals in the pedigree were inbred, and the average inbreeding of the population was 9.58%. Considering the changes of the inbreeding status of the examined population 4 large time periods were appointed. The first lasted until 1780, the second period was from 1780 until 1952, the third period was between 1946 and 1998 and the last one was from 1998 until 2008. Rate of inbreeding in the last generation was 0.3%, which forecasts further increase in inbreeding. The effective population size was above 100 in the last 30 generations, proving the genetic diversity did not decrease by a level that would make long-term selection impossible.
The generation interval may be defined as the mean age of parents of all progeny born, or as the mean age of parents of only those progeny destined to be selected as replacements. If the mean age of parents of replacements is used, selection differentials must be calculated within parental age groups. If the mean age of parents of all progeny born is used, the selection differential contains a component due to disproportionate selection of replacements from different parental age groups.
In analysis of multilocus genotypes from structured populations, individual coefficients of membership in subpopulations are often estimated using programs such as structure. distruct provides a general method for visualizing these estimated membership coefficients. Subpopulations are represented as colours, and individuals are depicted as bars partitioned into coloured segments that correspond to membership coefficients in the subgroups. distruct, available at http://www.cmb.usc.edu/~noahr/distruct.html, can also be used to display subpopulation assignment probabilities when individuals are assumed to have ancestry in only one group.
Yearling quarter horse prices are dependent upon a number of characteristics. Quantifiable genetic and macroeconomic variables for 5,295 sales from 1982-92 are used in a hedonic price model. Marginal values and discrete incremental prices are determined for 23 characteristics, 21 of which are found to be significant. The model’s fit implies it may be helpful for maximizing breeder returns. Overall, buyers pay substantial premiums if the yearling’s first dam or sire was a champion and if the sire or first dam previously produced a champion. Likewise, yearlings whose second and third dams are winners and producers of winners receive higher prices. Prices paid for fillies and older yearlings exceed those paid for clots, geldings, and younger horses.
GENALEX is a user-friendly cross-platform package that runs within Microsoft Excel, enabling population genetic analyses of codominant, haploid and binary data. Allele frequency-based analyses include heterozygosity, F statistics, Nei's genetic distance, population assignment, probabilities of identity and pairwise relatedness. Distance-based calculations include AMOVA, principal coordinates analysis (PCA), Mantel tests, multivariate and 2D spatial autocorrelation and TWOGENER. More than 20 different graphs summarize data and aid exploration. Sequence and genotype data can be imported from automated sequencers, and exported to other software. Initially designed as tool for teaching, GENALEX 6 now offers features for researchers as well. Documentation and the program are available at http://www.anu.edu.au/BoZo/GenAlEx/
To estimate allele frequencies of the hyperkalaemic periodic paralysis (HYPP), lethal white foal syndrome (LWFS), glycogen branching enzyme deficiency (GBED), hereditary equine regional dermal asthenia (HERDA), and type 1 polysaccharide storage myopathy (PSSM) genes in elite performance subgroups of American Quarter Horses (AQHs).
Prospective genetic survey.
651 elite performance AQHs, 200 control AQHs, and 180 control American Paint Horses (APHs).
Elite performance AQHs successful in 7 competitive disciplines (barrel racing, cutting, halter, racing, reining, western pleasure, and working cow horse) were geno- typed for 5 disease-causing alleles. Age-matched control AQHs and APHs were used to establish comparative whole-breed estimates of allele frequencies.
Highest allele frequencies among control AQHs were for type 1 PSSM (0.055) and GBED (0.054), whereas HERDA (0.021) and HYPP (0.008) were less prevalent. Control APHs uniquely harbored LWFS (0.107) and had high prevalence of HYPP (0.025), relative to AQHs. Halter horse subgroups had significantly greater allele frequencies for HYPP (0.299) and PSSM (0.155). Glycogen branching enzyme deficiency, HERDA, and PSSM were found broadly throughout subgroups; cutting subgroups were distinct for HERDA (0.142), and western pleasure subgroups were distinct for GBED (0.132). Racing and barrel racing subgroups had the lowest frequencies of the 5 disease genes.
Accurate estimates of disease-causing alleles in AQHs and APHs may guide use of diagnostic genetic testing, aid management of genetic diseases, and help minimize production of affected foals.
Pedigrees of randomly selected Quarter Horses born in each of the years 1946, 1956, 1966 and 1976 and of winning halter, cutting and race horses born in the same years were evaluated and compared. Average inbreeding and inter se relationship levels and relationships of influential ancestors to the sample were calculated for each sample. The amount of Thoroughbred influence and the average generation interval were also determined for each random sample. The levels of inbreeding found in the random samples were low, ranging from 1.3% in 1956 to 2.6% in 1966; however, these levels were higher than would be expected if mating were random. Show and race winners born in 1976 appeared to be less inbred than random horses of the breed. The estimated average inter se relationship within the random samples increased from 0% in 1946 to 3% in 1966, decreasing again to 0% in 1976. Horses in the elite samples appeared to be more closely related to each other than those in the random samples. Fifteen ancestors of horses in the random samples were identified as influential to the Quarter Horse breed. Many of these same ancestors were influential in the halter and cutting samples, but only one was influential in the race samples. The percentage of pedigree lines in the random samples that contained a Thoroughbred ancestor were as follows; 1946, 27.5%; 1956, 19.2%; 1966, 23.2% and 1976, 31.4%. The average generation interval fluctuated from approximately 8 yr to approximately 10 yr for the random samples.
We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci-e.g. , seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/ approximately pritch/home. html.
We describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci. The new model accounts for the correlations between linked loci that arise in admixed populations ("admixture linkage disequilibium"). This modification has several advantages, allowing (1) detection of admixture events farther back into the past, (2) inference of the population of origin of chromosomal regions, and (3) more accurate estimates of statistical uncertainty when linked loci are used. It is also of potential use for admixture mapping. In addition, we describe a new prior model for the allele frequencies within each population, which allows identification of subtle population subdivisions that were not detectable using the existing method. We present results applying the new methods to study admixture in African-Americans, recombination in Helicobacter pylori, and drift in populations of Drosophila melanogaster. The methods are implemented in a program, structure, version 2.0, which is available at http://pritch.bsd.uchicago.edu.
The aim of this note is to describe the program ENDOG (v.3.0). The program handles pedigree information to conduct several demographic and genetic analyses including: (a) the individual inbreeding and average relatedness coefficients; (b) effective population size; (c) parameters characterizing the concentration of both gene and individuals origin such as the effective number of founders and ancestors, the effective number of founder herds; (d) F statistics and paired genetic distances for each subpopulation under study; (e) descriptors of the genetic importance of the herds in a population and (f) generation intervals. The program will help breeders and researchers to monitor the changes in genetic variability and population structure with limited costs of preparing datasets. The program, user's guide and example file can be down-loaded free of charge from the World Wide Web at http://www.ucm.es/ info/prodanim/Endog30.zip.
Genetic characterization helps to assure breed integrity and to assign individuals to defined populations. The objective of this study was to characterize genetic diversity in six horse breeds and to analyse the population structure of the Franches-Montagnes breed, especially with regard to the degree of introgression with Warmblood. A total of 402 alleles from 50 microsatellite loci were used. The average number of alleles per locus was significantly lower in Thoroughbreds and Arabians. Average heterozygosities between breeds ranged from 0.61 to 0.72. The overall average of the coefficient of gene differentiation because of breed differences was 0.100, with a range of 0.036-0.263. No significant correlation was found between this parameter and the number of alleles per locus. An increase in the number of homozygous loci with increasing inbreeding could not be shown for the Franches-Montagnes horses. The proportion of shared alleles, combined with the neighbour-joining method, defined clusters for Icelandic Horse, Comtois, Arabians and Franches-Montagnes. A more disparate clustering could be seen for European Warmbloods and Thoroughbreds, presumably from frequent grading-up of Warmbloods with Thoroughbreds. Grading-up effects were also observed when Bayesian and Monte Carlo resampling approaches were used for individual assignment to a given population. Individual breed assignments to defined reference populations will be very difficult when introgression has occurred. The Bayesian approach within the Franches-Montagnes breed differentiated individuals with varied proportions of Warmblood.
We present a statistical model for patterns of genetic variation in samples of unrelated individuals from natural populations. This model is based on the idea that, over short regions, haplotypes in a population tend to cluster into groups of similar haplotypes. To capture the fact that, because of recombination, this clustering tends to be local in nature, our model allows cluster memberships to change continuously along the chromosome according to a hidden Markov model. This approach is flexible, allowing for both "block-like" patterns of linkage disequilibrium (LD) and gradual decline in LD with distance. The resulting model is also fast and, as a result, is practicable for large data sets (e.g., thousands of individuals typed at hundreds of thousands of markers). We illustrate the utility of the model by applying it to dense single-nucleotide-polymorphism genotype data for the tasks of imputing missing genotypes and estimating haplotypic phase. For imputing missing genotypes, methods based on this model are as accurate or more accurate than existing methods. For haplotype estimation, the point estimates are slightly less accurate than those from the best existing methods (e.g., for unrelated Centre d'Etude du Polymorphisme Humain individuals from the HapMap project, switch error was 0.055 for our method vs. 0.051 for PHASE) but require a small fraction of the computational cost. In addition, we demonstrate that the model accurately reflects uncertainty in its estimates, in that probabilities computed using the model are approximately well calibrated. The methods described in this article are implemented in a software package, fastPHASE, which is available from the Stephens Lab Web site.
Franches-Montagnes is the only native horse breed in Switzerland, therefore special efforts should be made for ensuring its survival. The objectives of this study were to characterize the structure of this population as well as genetic variability with pedigree data, conformation traits and molecular markers. Studies were focused to clarify if this population is composed of a heavy- and a light-type subpopulation. Extended pedigree records of 3-year-old stallions (n = 68) and mares (n = 108) were available. Evaluations of body conformation traits as well as pedigree data and molecular markers did not support the two-subpopulation hypothesis. The generation interval ranged from 7.8 to 9.3 years. The complete generation equivalent was high (>12). The number of effective ancestors varied between 18.9 and 20.1, whereof 50% of the genetic variability was attributed to seven of them. Genetic contribution of Warmblood horses ranged from 36% to 42% and that of Coldblood horses from 4% to 6%. The average inbreeding coefficient reached 6%. Inbreeding effective population size was 114.5 when the average increase of the inbreeding coefficient per year since 1910 was taken. Our results suggest that bottleneck situations occurred because of selection of a small number of sire lines. Promotion of planned matings between parents that are less related is recommended in order to avoid a reduction of the genetic diversity.
There are three native Portuguese horse breeds: Lusitano, Sorraia and Garrano. This study compares diversity patterns of 17 protein and 12 microsatellite markers in these three as well as 30 other breeds to infer relationships among the breeds and to compare levels of polymorphism of these breeds for use in conservation efforts. The Garrano and the Lusitano showed a high level of genetic diversity, similar to that observed for most of the other analysed breeds, while the Sorraia and Friesian breeds showed low levels of variation for both genetic marker types. The combined protein and microsatellite data produced a tree that fit historical records well and with greater confidence levels than those for either data set alone. The combined genetic diversity and relationship information provides important baseline data for future breed conservation efforts, especially for a critically endangered breed such as the Sorraia.
Whole-genome association studies (WGAS) bring new computational, as well as analytic, challenges to researchers. Many existing genetic-analysis tools are not designed to handle such large data sets in a convenient manner and do not necessarily exploit the new opportunities that whole-genome data bring. To address these issues, we developed PLINK, an open-source C/C++ WGAS tool set. With PLINK, large data sets comprising hundreds of thousands of markers genotyped for thousands of individuals can be rapidly manipulated and analyzed in their entirety. As well as providing tools to make the basic analytic steps computationally efficient, PLINK also supports some novel approaches to whole-genome data that take advantage of whole-genome coverage. We introduce PLINK and describe the five main domains of function: data management, summary statistics, population stratification, association analysis, and identity-by-descent estimation. In particular, we focus on the estimation and use of identity-by-state and identity-by-descent information in the context of population-based whole-genome studies. This information can be used to detect and correct for population stratification and to identify extended chromosomal segments that are shared identical by descent between very distantly related individuals. Analysis of the patterns of segmental sharing has the potential to map disease loci that contain multiple rare variants in a population-based linkage analysis.
American Quarter Horse Stud Book and Registry: Vol 1 No 1. Amarillo (TX): American Quarter Horse Association. Denhardt RM. 1967. Quarter horses: a story of two centuries
- R Denhardt
Denhardt R. 1941. American Quarter Horse Stud Book and Registry: Vol 1 No 1. Amarillo (TX): American Quarter Horse Association. Denhardt RM. 1967. Quarter horses: a story of two centuries. Norman (OK): University of Oklahoma Press.
International Encyclopedia of horse breeds
- B L Hendricks
Hendricks BL. 2007. International Encyclopedia of horse breeds. Norman
(OK): University of Oklahoma Press.
Quarter horses: a story of two centuries
- R M Denhardt
Denhardt RM. 1967. Quarter horses: a story of two centuries. Norman
(OK): University of Oklahoma Press.
America’s quarter horses
- P Laune
Laune P. 1973. America's quarter horses. Garden City (NY): Doubleday.
American Quarter Horse Association
American Quarter Horse Association. 2010. 2012 Annual Report. Amarillo
(TX): American Quarter Horse Association.