Genetic relationships between breeds of horses and ponies in the Netherlands

An investigation on the genetic relationships between 12 horse and pony breeds was performed, using blood protein variants as genetic markers. The relationships were established by the use of 5 different numerical taxonomic methods, 4 of which yielded very similar results. The relationships as estimated were evaluated on the basis of the breeds' historical development.     

Genetic analysis of insect bite hypersensitivity (summer eczema) in Icelandic horses

There is a lack of knowledge about the genetic background of eczema due to insect bite hypersensitivity, also called summer eczema, in horses. The condition is known in several horse breeds and countries and it causes reduced welfare of the horse and economic losses to the owner. The aim of this study was to estimate genetic parameters for summer eczema in Swedish-born Icelandic horses. A questionnaire was sent to owners of horses sired by stallions with more than 50 offspring born in Sweden between 1991 and 2001. Variance components of summer eczema classified as healthy, mild, moderate or severe were estimated using the threshold methodology with sire models. In addition, summer eczema was analysed as a binary trait (healthy v. affected). The analyses included 1250 horses sired by 33 stallions. The prevalence of summer eczema was 8%, with a range of 0% to 30% in different paternal half-sib groups. Offspring of dams suffering from eczema had a higher risk of developing eczema. The heritability for severity of summer eczema was estimated at 0.3 (s.d. < 0.2) with a threshold sire model. In contrast to the age of the horse, different geographic areas and gender were significantly associated with severity of the eczema. We conclude that genetic selection could decrease the prevalence of summer eczema among Swedish-born Icelandic horses. The amount and quality of data are, however, crucial for the possibility to introduce a genetic evaluation of summer eczema. The symptoms should be classified in several classes according to severity, and this classification could be made by the horse owner.     

Genetic parameters of eventing horse competition in France

Genetic parameters of eventing horse competitions were estimated. About 13 000 horses, 30 000 annual results during 17 years and 110 000 starts in eventing competitions during 8 years were recorded. The measures of performance were logarithmic transformations of annual earnings, annual earnings per start, and annual earnings per place, and underlying variables responsible for ranks in each competition. Heritabilities were low (0.11/0.17 for annual results, 0.07 for ranks). Genetic correlations between criteria were high (greater than 0.90) except between ranks and earnings per place (0.58) or per start (0.67). Genetic correlations between ages (from 5 to 10 years old) were also high (more than 0.85) and allow selection on early performances. The genetic correlation between the results in different levels of competition (high/international and low/amateur) was near 1. Genetic correlations of eventing with other disciplines, which included partial aptitude needed for eventing, were very low for steeplechase races (0.18) and moderate with sport: jumping (0.45), dressage (0.58). The results suggest that selection on jumping performance will lead to some positive correlated response for eventing performance, but much more response could be obtained if a specific breeding objective and selection criteria were developed for eventing.     

Genetic and environmental influences on self-reported and parent-reported behavior problems in young adult adoptees

The aim of the present study was to estimate the genetic, shared and nonshared environmental contributions to self-reported and parent-reported internalizing and externalizing problems in a follow-up study of intercountry adopted young adults. Young Adult Self-Report ratings were obtained from 1475 adoptees aged 22–32 years and Young Adult Behavior Checklist ratings from 1115 adoptive parents. For the genetic analyses, a subset of 143 adopted biologically related and 295 unrelated siblings was used. The data were subjected to model fitting decomposing three sources of variance: genetic factors (A) shared environment (C) and nonshared environment (E). Genetic factors were of more importance in both self-reported ( A ²= 54%, C ²= 0, and E ²= 46%) and parent-reported ( A ²= 76%, C ²= 15% and E ²= 9%) internalizing problems. Environmental factors were of more importance in both self-reported ( A ²= 33%, C ²= 17% and E ²= 50%) and parent-reported ( A ²= 28%, C ²= 27% and E ²= 45%) externalizing problems. This was in contrast with findings from the first and second assessments in the same sample during adolescence when genetic factors were more important in explaining externalizing problems compared with internalizing problems. Our results suggest a developmental reversal in genetic and environmental influences on behavior problems from early adolescence into adulthood, which could be related to different underlying developmental trajectories.     

Genetic correlations between conformation traits and radiographic findings in the limbs of German Warmblood riding horses

Studbook inspection (SBI) data of 20 768 German Warmblood mares and radiography results (RR) data of 5102 Hanoverian Warmblood horses were used for genetic correlation analyses. The scores on a scale from 0 to 10 were given for conformation and basic quality of gaits, resulting in 14 SBI traits which were used for the correlation analyses. The radiographic findings considered included osseous fragments in fetlock (OFF) and hock joints (OFH), deforming arthropathy in hock joints (DAH) and distinct radiographic findings in the navicular bones (DNB) which were analyzed as binary traits, and radiographic appearance of the navicular bones (RNB) which was analyzed as a quasi-linear trait. Genetic parameters were estimated multivariately in linear animal models with REML using information on 24 448 horses with SBI and/or RR records. The ranges of heritability estimates were h² = 0.14–0.34 for the RR traits and h² = 0.09–0.50 for the SBI traits. Negative additive genetic correlations of r_g = -0.19 to -0.56 were estimated between OFF and conformation of front and hind limbs and walk at hand, and between DNB and hind limb conformation. There were indications of negative additive genetic correlations between DAH and all SBI traits, but because of low prevalence and low heritability of DAH, these results require further scrutiny. Positive additive genetic correlations of r_g = 0.37–0.52 were estimated between OFF and withers height and between OFH and withers height, indicating that selection for taller horses will increase disposition to develop OFF and OFH. Selection of broodmares with regards to functional conformation will assist, but cannot replace possible selection against radiographic findings in the limbs of young Warmblood riding horses, particularly with regards to OFF.     

Genetic parameters for traits evaluated at field tests of 3- and 4-year-old Swedish Warmblood horses

There are two types of 1-day field tests available for young Swedish Warmblood sport horses; one test for 3-year olds and one more advanced test for 4-year olds. Conformation, gaits and jumping ability are evaluated at both tests. Studies on various genetic parameters were based on about 20 000 tested horses. The data for 4-year olds consisted of 30 years of testing. The aims of the study were to estimate genetic parameters for results from different time periods, and to estimate heritabilities for, and genetic correlations between, traits scored in the two tests. The judgement of traits was shown to have been changed during the 30 years of testing, resulting in changes in higher heritabilities in, and stronger genetic correlations between, later time periods. In the first time period, records showed higher residual and lower genetic variances than in the subsequent time periods. Genetic correlations between traits recorded in the first and last time period deviated considerably from unity. Further studies are needed to investigate how to treat data from the early period in genetic evaluations. Heritabilities were moderate to high for conformation traits (0.24 to 0.58) at both types of tests, except for correctness of legs (0.08). The heritabilities for gait traits were also moderate to high (0.37 to 0.53). For jumping traits, the heritabilities ranged between 0.17 and 0.33. The highly positive genetic correlations (0.82 to 0.99) between corresponding traits tested at the simpler test for 3-year olds and at the ridden test of 4-year olds implied that it would be desirable to include the test results of 3-year olds into the genetic evaluation as breeding values for Swedish Warmbloods for many years has only been based on results from 4-year olds.     

Genetic analysis of protoplast regeneration ability in Brassica oleracea

In Brassica oleracea L., plant regeneration from protoplasts is genotype-dependent and colony formation can be obtained routinely. In order to identify genes for regenerability, we performed a genetic analysis of the characteristic in the F₂ generation of a cross between two accessions selected for high and low regenerability. Regeneration frequencies were obtained from protoplast culture of 248 individual F₂ plants after 5, 10, and 15 weeks of culture on regeneration medium. Broad-sense heritability estimate was 0.492 at the early stage and lower (0.046–0.149) at advanced stages. The frequency distribution observed during short-term culture can be explained by two independent loci with duplicate dominant genes controlling regeneration. In long-term culture, one additional dominant gene can confer regeneration; i.e., three independent loci are responsible for regenerability. The results suggest that selection for high regeneration response may be efficient at early stages because of the lower environmental influence on the characteristic, and because fewer genes are involved at this stage than at advanced stages. The control of regenerability by a few dominant genes facilitates incorporation of the trait into breeding material. Molecular markers linked to the genes may assist in the selection of genotypes with high regeneration percentage in the future. This revised version was published online in June 2006 with corrections to the Cover Date.     

Genetic linkage between the loci for phosphohexose isomerase (PHI) and a serum protein (Xk) in horses

Genetic linkage between the equine loci for phosphohexose isomerase (PHI) and serum Xk protein was demonstrated by means of segregation data from three sire families. The recombination frequency was estimated from pooled data to be 0.23 ± 0.02; a significant heterogeneity between sires for estimates of the recombination frequency was observed. No indication of linkage was detected between Xk and 14 other blood marker loci. Linkage between the Xk locus and the locus for soluble malic enzyme ( ME1 ) has recently been reported in horses. An equine linkage group designated LG IV comprising the three loci ME1, PH1 , and Xk has thus been established. The possibility that the linkage between PH1 and Xk is homologous to the linkage between the loci for PHI and a serum postalbumin (PO-2) in pigs was discussed.     

Genetic analysis of haematological and plasma biochemical parameters in the Spanish purebred horse exercised on a treadmill

The novel aim of this study was to describe the reference values of different haematological and biochemical parameters in the Spanish purebred horse (Andalusian, SPB) in each of the stages of a programmed exercise on a treadmill system, and to establish heritability and genetic correlations for these haematological and biochemical parameters. For this, 94 young SPB male horses (4.22 ± 2.27 years old) were used. An increasing intensity exercise test at 4, 5, 6 and 7 m/s was carried out on a treadmill (6% inclination). Total red blood cells, total white blood cells, neutrophils and lymphocytes counts; haematocrit, haemoglobin, lactate, uric acid, creatinine and total plasma proteins concentrations and aspartate transaminase, lactate dehydrogenase, creatine-quinase activities were determined. To conclude: (i) the reference values for each parameter were determined for each of the exercise test stages (ii) all the parameters analysed manifested a medium-high heritability and a high repeatability. These results will, in the near future, determine the measuring guidelines for improving the SPB horse's athletic ability on an objective treadmill system and for selecting these animals in response to those parameters.     

Genetic and environmental effects on secondary sex traits in guppies (Poecilia reticulata)

Male guppies (Poecilia reticulata) exhibit extreme phenotypic and genetic variability for several traits that are important to male fitness, and several lines of evidence suggest that resource level affects phenotypic expression of these traits in nature. We tested the hypothesis that genetic variation for male secondary sex traits could be maintained by genotype-specific effects of variable resource levels (genotype-environment interaction). To do this, we measured genetic variation and covariation under two environmental conditions--relatively low and relatively high food availability. We found high levels of genetic variation for most traits, but we only found a significant G x E interaction across food levels for one trait (body size) for one population. The across-environment correlations for size were large and positive, indicating that the reaction norms for size did not cross. We also found that male colour pattern elements had nearly an order of magnitude more genetic variation than did male size. Heritability estimates indicated that Y-linked genes are responsible for some of the genetic variation in male size and colour traits. We discuss implications of these results for theories of the maintenance of genetic variation in male secondary sexual traits in guppies.     

Genetic diversity in German draught horse breeds compared with a group of primitive, riding and wild horses by means of microsatellite DNA markers

We compared the genetic diversity and distance among six German draught horse breeds to wild (Przewalski's Horse), primitive (Icelandic Horse, Sorraia Horse, Exmoor Pony) or riding horse breeds (Hanoverian Warmblood, Arabian) by means of genotypic information from 30 microsatellite loci. The draught horse breeds included the South German Coldblood, Rhenish German Draught Horse, Mecklenburg Coldblood, Saxon Thuringa Coldblood, Black Forest Horse and Schleswig Draught Horse. Despite large differences in population sizes, the average observed heterozygosity (H(o)) differed little among the heavy horse breeds (0.64-0.71), but was considerably lower than in the Hanoverian Warmblood or Icelandic Horse population. The mean number of alleles (N(A)) decreased more markedly with declining population sizes of German draught horse breeds (5.2-6.3) but did not reach the values of Hanoverian Warmblood (N(A) = 6.7). The coefficient of differentiation among the heavy horse breeds showed 11.6% of the diversity between the heavy horse breeds, as opposed to 21.2% between the other horse populations. The differentiation test revealed highly significant genetic differences among all draught horse breeds except the Mecklenburg and Saxon Thuringa Coldbloods. The Schleswig Draught Horse was the most distinct draught horse breed. In conclusion, the study demonstrated a clear distinction among the German draught horse breeds and even among breeds with a very short history of divergence like Rhenish German Draught Horse and its East German subpopulations Mecklenburg and Saxon Thuringa Coldblood.     

The Dynamics of Genetic Draft in Rapidly Adapting Populations

The accumulation of beneficial mutations on competing genetic backgrounds in rapidly adapting populations has a striking impact on evolutionary dynamics. This effect, known as clonal interference, causes erratic fluctuations in the frequencies of observed mutations, randomizes the fixation times of successful mutations, and leaves distinct signatures on patterns of genetic variation. Here, we show how this form of “genetic draft” affects the forward-time dynamics of site frequencies in rapidly adapting asexual populations. We calculate the probability that mutations at individual sites shift in frequency over a characteristic timescale, extending Gillespie’s original model of draft to the case where many strongly selected beneficial mutations segregate simultaneously. We then derive the sojourn time of mutant alleles, the expected fixation time of successful mutants, and the site frequency spectrum of beneficial and neutral mutations. Finally, we show how this form of draft affects inferences in the McDonald–Kreitman test and how it relates to recent observations that some aspects of genetic diversity are described by the Bolthausen–Sznitman coalescent in the limit of very rapid adaptation.     

Genetic structure of populations of horses based on distribution of hemotypes

The distribution of hemotypes, that is, the juxtaposition of electrophoretic phenotypes at six blood protein and enzyme loci expressing the individual genetic traits of every member of a population, has been investigated in 15 populations belonging to nine breeds of horses. The total number of hemotypes recorded in a population was lower than the number expected on the basis of allelic frequencies. The mean number of individuals per hemotype varied from 1.5 in ponies to 18.6 in Thoroughbreds. Breeds or populations differ either qualitatively by the nature of hemotypes, or quantitatively by the proportions of repetitive hemotypes carried by several individuals, and of unique hemotypes, carried by single individuals. The so-called closed breeds of populations, such as Thoroughbreds, contain predominantly repetitive hemotypes, while the feral or rustic breeds present a large proportion of unique hemotypes.     

Genetic and environmental influences on shape variation in the European sea bass (Dicentrarchus labrax)

This paper demonstrates the contribution of both genetic and environmental effects on cultured European sea bass shape. We used the progeny of five populations of sea bass, in a partly diallel design, to investigate the genetics of shape (estimated with geometric morphometrics) in European sea bass. This was done using a common garden experiment with microsatellite markers assignment to parents and populations to avoid confusion between genetic and environmental effects. Additionally, one of the populations was studied over four different aquaculture facilities to investigate the effects of environment on shape. For the first time in this species, shape‐related traits were linked with genetic variation. The first relative warp analysis axis clearly differentiated rearing sites, demonstrating that the main shape/weight effects are related to culturing conditions, thereby accounting for ecomorphologically related differences. The second axis strongly differentiated groups by parental origins; there was a good correlation between shape differences and geographic distances between broodstock sampling locations. High heritabilities of axes scores (0.40–0.55) showed high genetic variation for shape within populations. This study shows that variation in shape has a high genetic component in sea bass, both at the population level and within populations. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 427–436.     

Genetic investigation of equine recurrent uveitis in Appaloosa horses

Equine recurrent uveitis (ERU) is characterized by intraocular inflammation that often leads to blindness in horses. Appaloosas are more likely than any other breed to develop insidious ERU, distinguished by low-grade chronic intraocular inflammation, suggesting a genetic predisposition. Appaloosas are known for their white coat spotting patterns caused by the leopard complex spotting allele (LP) and the modifier PATN1. A marker linked to LP on ECA1 and markers near MHC on ECA20 were previously associated with increased ERU risk. This study aims to further investigate these loci and identify additional genetic risk factors. A GWAS was performed using the Illumina Equine SNP70 BeadChip in 91 horses. Additive mixed model approaches were used to correct for relatedness. Although they do not reach a strict Bonferroni genome-wide significance threshold, two SNPs on ECA1 and one SNP each on ECA12 and ECA29 were among the highest ranking SNPs and thus warranted further analysis (P = 1.20 × 10⁻⁵, P = 5.91 × 10⁻⁶, P = 4.91 × 10⁻⁵, P = 6.46 × 10⁻⁵). In a second cohort (n = 98), only an association with the LP allele on ECA1 was replicated (P = 5.33 × 10⁻⁵). Modeling disease risk with LP, age and additional depigmentation factors (PATN1 genotype and extent of roaning) supports an additive role for LP and suggests an additive role for PATN1. Genotyping for LP and PATN1 may help predict ERU risk (AUC = 0.83). The functional role of LP and PATN1 in ERU development requires further investigation. Testing samples across breeds with leopard complex spotting patterns and a denser set of markers is warranted to further refine the genetic components of ERU.     

Body development in sows, feed intake and maternal capacity. Part 2: gilt body condition before and after lactation, reproductive performance and correlations with lactation feed intake

Data on sow body weight (BW) and fatness (n = ~2250 pregnant sows) and reproductive data (including historical: n = ~18 000) were used to examine the genetic and phenotypic associations between body condition before and after farrowing, gestational outcomes, lactation feed intake and the gilts' ability to survive unculled to farrow in the second parity. Within-trait genetic correlations were very high between weight (0.77 ± 0.06) and fat depth (0.91 ± 0.04) recorded before farrowing and at weaning. Litter size traits were generally uncorrelated genetically with aspects of sow BW and body condition. However, genetic correlations indicated that sows producing heavier piglets at birth had litters with increased gain (0.36 ± 0.16), and were characterised by greater weight (-0.72 ± 0.08) and fat change (-0.19 ± 0.15) during lactation, reflected to a lesser extent by lower weight (-0.12 ± 0.11) and fatness (-0.17 ± 0.10) at weaning. Genetic correlations (r(a)) between reproductive traits and lactation feed intake were generally low, but favourable. However, lactation intake was positively correlated with measures of sow size (r(a) = ~0.55), such that selection for lactation feed intake would likely be accompanied by increased mature sow size. Phenotypic correlations (r(p)) showed that sow survival to the second parity (FAR12) was positively influenced by litter size and fat depth at weaning, supporting attributes of increased fatness before farrowing, less weight loss during lactation and an increased lactation intake.     

Genetic diversity and admixture analysis of Sanfratellano and three other Italian horse breeds assessed by microsatellite markers

Sanfratellano is a native Sicilian horse breed, mainly reared in the north east of the Island, developed in the 19th century from local dams and sires with a restricted introgression of Oriental, African and, more recently, Maremmano stallions. In this study, the genetic relationships and admixture among Sanfratellano, the other two Sicilian autochthonous breeds and Maremmano breed were assessed using a set of microsatellites. The main goals were to infer the impact of Maremmano breed in the current Sanfratellano horse and to provide genetic information useful to improve the selection strategies of the Sanfratellano horse. The whole sample included 384 horses (238 Sanfratellano, 50 Sicilian Oriental Purebred, 30 Sicilian Indigenous and 66 Maremmano), chosen avoiding closely related animals. A total of 111 alleles from 11 microsatellite loci were detected, from four at HTG7 to 15 at ASB2 locus. The mean number of alleles was the lowest in Oriental Purebred (6.7), the highest in Sanfratellano (8.3). All the breeds showed a high level of gene diversity (He) ranging from 0.71 ± 0.04 in Sicilian Oriental Purebred to 0.81 ± 0.02 in Sicilian Indigenous. The genetic differentiation index was low; only about 6% of the diversity was found among breeds. Nei's standards (DS) and Reynolds' (DR) genetic distances reproduced the same population ranking. Individual genetic distances and admixture analysis revealed that: (a) nowadays Maremmano breed does not significantly influence the current Sanfratellano breed; (b) within Sanfratellano breed, it is possible to distinguish two well-defined groups with different proportions of Indigenous blood.     

Genetic and environmental sources of covariance among internal reproductive traits in the yellow dung fly

Substantial inter- and intraspecific variation is found in reproductive traits, but the evolutionary implications of this variation remain unclear. One hypothesis is that natural selection favours female reproductive morphology that allows females to control mating and fertilization and that diverse male reproductive traits arise as counter adaptations to subvert this control. Such co-evolution predicts the establishment of genetic correlations between male and female reproductive traits that closely interact during mating. Therefore, we measured phenotypic and genetic correlations between male and female reproductive tract characteristics in the yellow dung fly, Scathophaga stercoraria (Diptera: Scathophagidae), using a nested half-sib breeding experiment. We found significant heritabilities for the size of most reproductive tract traits investigated in both females (spermathecae and their ducts, accessory glands and their ducts) and males (testis size but not sperm length). Within the sexes, phenotypic and genetic correlations were mostly nil or positive, suggesting functional integration of or condition-dependent investment in internal reproductive traits. Negative intrasexual genetic correlations, potentially suggestive of resource allocation trade-offs, were not evident. Intersexual genetic correlations were mostly positive, reflecting expected allometries between male and female morphologies. Most interestingly, testis size correlated positively with female accessory gland size and duct length, potentially indicative of a co-evolutionary arms race. We discuss these and alternative explanations for these patterns of genetic covariance.     

Evolutionary potential of Chamaecrista fasciculata in relation to climate change. II. Genetic architecture of three populations reciprocally planted along an environmental gradient in the great plains

Climate change will test the evolutionary potential of populations. Information regarding the genetic architecture within and among populations is essential for prediction of evolutionary outcomes. However, little is known about the distribution of genetic variation for relevant traits in natural populations or alteration of genetic architecture in a changing environment. In this study, pedigreed families from three populations of the annual prairie legume Chamaecrista fasciculata were reciprocally transplanted in three environments across a broad latitudinal range in the Great Plains. The underlying premise of this work is that northern populations will in the future experience climates similar to current-day climates further south. Estimates of narrow-sense heritability ranged from 0.053 to 0.481, suggesting the potential for evolutionary change is possible for most traits. In general, the northern population harbored less genetic variation and had lower heritability for traits than the southern population. This population also experienced large reductions in fitness, as measured by estimated lifetime fecundity, when raised in either the intermediate or the southern climate, whereas the difference between the intermediate and southern population was less extreme. For fecundity, the pattern of cross-environment additive genetic correlations was antagonistic to evolutionary change in four of six cases when native and nonnative sites were compared. Six additional antagonistic positive correlations were found for the rate of phenological development and leaf thickness. Overall, the data suggest that if climate changes as predicted, the northern population will face a severe evolutionary challenge in the future because of low heritabilities, cross-environment genetic correlations antagonistic to selection, and demographic instability due to lower seed production in a hotter and drier climate.