Modelling genetic evaluation for dressage in Pura Raza Español horses with focus on the rider effect

The most popular use of the Pura Raza Español horse in sport is for dressage competitions. Tests on young sport horses were first established in 2004 in Spain to collect data for the genetic evaluation of this breed's suitability for dressage. The aim of this study was to compare eight different models to find out the most appropriate way to include the rider in the genetic evaluation of dressage. A progressive removal of systematic effects from model was also analysed. A total of 8867 performance records collected between 2004 and 2011 from 1234 horses aged between 4 and 6 years old were used. The final score in the dressage test was used as the performance trait. The pedigree matrix contained 8487 individuals. A BLUP animal model was applied using a Bayesian approach with TM software. The horse's age, gender, travelling time, training level, stud of birth and event were included as systematic effects in all the models. Apart from the animal and residual effects that were present in all models, different models were compared combining random effects such as the rider, match (i.e. rider–horse interaction) and permanent environmental effects. A cross‐validation approach was used to evaluate the models' prediction ability. The best model included the permanent environmental, rider and match random effects. As far as systematic effects are concerned, the event or the stud of birth was essential effects needed to fit the data.     

Genetic inbreeding depression load for fertility traits in Pura Raza Española mares

Fertility is a key factor in the economic success of horse farms. However, it has received little attention due to the difficulty of measuring fertility objectively. Since its studbook creation (1912), the Pura Raza Española (PRE) breed has been a closed population and become high in-bred resulting in inbreeding depression (poor phenotypic values). Nevertheless, heterogeneous effects of inbreeding depression have been detected among founders and nonfounders. The aims of this study were (1) to analyze the genetic parameters for reproductive traits in mares of the PRE horse breed and (2) to estimate, for the first time, the inbreeding depression load associated with common ancestors of the breed. A total of 22,799 mares were analyzed. Heritability estimates ranged from 0.05 (interval between first and second foaling) to 0.16 (age at first foaling), whereas inbreeding depression load ratios ranged from 0.06 (parturition efficiency at 6th foaling) to 0.17 (age at first foaling), for a partial inbreeding coefficient of 10%. Although heritability is related to the variability expressed in the population, inbreeding depression load ratios measure the potential variability, whether expressed in the population or not. Most correlations between additive and inbreeding depression load genetic values were significant (P < 0.001) and of low to moderate magnitude. Our results confirm that individual inbreeding depression loads allow us to select horses that have a genetic value resistant to the deleterious effects of inbreeding.     

Morphological and genetic diversity of Pura Raza Español horse with regard to the coat colour

Gene mutations influencing melanocytes also impact on physiological and behavioural functions. In this study, we investigated their association with four different coat colours in the Pura Raza Español (PRE) horse using morphological traits and molecular datasets. Four different subpopulations were identified according to individual coat colour: grey, bay, chestnut and black. Coat colour significantly associated with morphological measurements. Observed and expected heterozygosity values were low in grey compared with the other three subpopulations, suggesting the presence of unique ancestral alleles probably arisen by genetic drift and selection mechanism effects. Nei's distance demonstrated a clear division among subpopulations, the grey being the most divergent group. Gene flow estimates were similar, showing the lowest values in grey. Divergence times among subpopulations assessed with the average square distance suggested that grey was the original PRE population which diverged from bay, chestnut and black. Our results also demonstrated a clear morphological differentiation according to coat colour. The close genetic structure of bay and chestnut PRE subpopulations and the clear differences in most morphological traits of grey and chestnut PRE mares would suggest the pleiotropic effect of genomic regions determining coat colour in horses. However, further analysis including genomic information would be necessary to elucidate the mechanisms involved.     

Estimation of genetic parameters of conformation traits in Iranian Thoroughbred horses

The aim of this study was to estimate the genetic parameters of conformation traits in Iranian Thoroughbred race horses. The data set included the conformation records of 607 Thoroughbred horses. In this study, 10 conformation traits were recorded. The effect of sex was significant for length of back line (P < 0.05), withers height (P < 0.05), circumference of front cannon (P < 0.001), and circumference of hind cannon (P < 0.001). The effect of age was significant for all traits (P < 0.01). The genetic parameters were estimated by the restricted maximum likelihood (REML) method using DFREML program. The heritability estimates were for head length 0.39, length of back line 0.41, length of shoulder 0.24, heart girth 0.49, chest width 0.22, withers height 0.38, front cannon height 0.27, circumference of front cannon 0.30, hind cannon height 0.29 and circumference of hind cannon 0.34. The estimates of genetic correlation ranged from 0.18 to 0.96 and those of phenotypic correlation varied from 0.16 to 0.83.     

Genetic parameters and purebred–crossbred genetic correlations for growth,meat quality,and carcass traits in pigs

Growth, meat quality, and carcass traits are of economic importance in swine breeding. Understanding their genetic basis in purebred (PB) and commercial crossbred (CB) pigs is necessary for a successful breeding program because, although the breeding goal is to improve CB performance, phenotype collection and selection are usually carried out in PB populations housed in biosecure nucleus herds. Thus, the selection is indirect, and the accuracy of selection depends on the genetic correlation between PB and CB performance (rpc). The objectives of this study were to 1) estimate genetic parameters for growth, meat quality, and carcass traits in a PB sire line and related commercial CB pigs and 2) estimate the corresponding genetic correlations between purebred and crossbred performance (rpc). Both objectives were investigated by using pedigree information only (PBLUP) and by combining pedigree and genomic information in a single-step genomic BLUP (ssGBLUP) procedure. Growth rate showed moderate estimates of heritability for both PB and CB based on PBLUP, while estimates were higher in CB based on ssGBLUP. Heritability estimates for meat quality traits were diverse and slightly different based on PB and CB data with both methods. Carcass traits had higher heritability estimates based on PB compared with CB data based on PBLUP and slightly higher estimates for CB data based on ssGBLUP. A wide range of estimates of genetic correlations were obtained among traits within the PB and CB data. In the PB population, estimates of heritabilities and genetic correlations were similar based on PBLUP and ssGBLUP for all traits, while based on the CB data, ssGBLUP resulted in different estimates of genetic parameters with lower SEs. With some exceptions, estimates of rpc were moderate to high. The SE on the rpc estimates was generally large when based on PBLUP due to limited sample size, especially for CBs. In contrast, estimates of rpc based on ssGBLUP were not only more precise but also more consistent among pairs of traits, considering their genetic correlations within the PB and CB data. The wide range of estimates of rpc (less than 0.70 for 7 out of 13 traits) indicates that the use of CB phenotypes recorded on commercial farms, along with genomic information, for selection in the PB population has potential to increase the genetic progress of CB performance.     

Genetic associations between accumulated productivity, and reproductive and growth traits in Nelore cattle

The total meat yield in a beef cattle production cycle is economically very important and depends on the number of calves born per year or birth season, being directly related to reproductive potential. Accumulated Productivity (ACP) is an index that expresses a cow's capacity to give birth regularly at a young age and to wean animals of greater body weight. Using data from cattle participating in the “Program for Genetic Improvement of the Nelore Breed” (PMGRN — Nelore Brasil), bi-trait analyses were performed using the Restricted Maximum Likelihood method based on an ACP animal model and the following traits: age at first calving (AFC), female body weight adjusted for 365 (BW365) and 450 (BW450) days of age, and male scrotal circumference adjusted for 365 (SC365), 450 (SC450), 550 (SC550) and 730 (SC730) days of age. Median estimated ACP heritability was 0.19 and the genetic correlations with AFC, BW365, BW450, SC365, SC450, SC550 and SC730 were 0.33, 0.70, 0.65, 0.08, 0.07, 0.12 and 0.16, respectively. ACP increased and AFC decreased over time, revealing that the selection criteria genetically improved these traits. Selection based on ACP appears to favor the heaviest females at 365 and 450 days of age who showed better reproductive performance as regards AFC. Scrotal circumference was not genetically associated with ACP.     

Genetic correlations between dressage,show jumping and studbook‐entry inspection traits in a process of specialization in Dutch Warmblood horses

Sport performance in dressage and show jumping are two important traits in the breeding goals of many studbooks. To determine the optimum selection scheme for jumping and dressage, knowledge is needed on the genetic correlation between both disciplines and between traits measured early in life and performance in competition in each discipline. This study aimed to estimate genetic parameters to support decision‐making on specialization of breeding horses for dressage and show jumping in Dutch warmblood horses. Genetic correlations between performance of horses in dressage and show jumping were estimated as well as the genetic correlation between traits recorded during studbook‐entry inspections and performance in dressage and show jumping competitions. The information on competition comprised the performance of 82 694 horses in dressage and 62 072 horses in show jumping, recorded in the period 1993–2012. For 26 056 horses, information was available for both disciplines. The information on traits recorded at studbook‐entry inspections comprised 62 628 horses, recorded in the period 1992–2013. Genetic parameters were estimated from the whole dataset and from a subset without horses recorded in both disciplines. Additionally, the genetic parameters were estimated in three different time periods defined by horses' birth year. The genetic correlation between dressage and show jumping in the whole dataset was ?0.23, and it was ?0.03 when it was estimated from horses recorded in only one discipline. The genetic correlation between dressage and show jumping was more negative in the most recent time period in all the cases. The more negative correlation between disciplines in more recent time periods was not reflected in changes in the correlations between competitions traits and the traits recorded in the studbook‐first inspection. These results suggest that a breeding programme under specialization might be most effective defining two separate aggregate breeding goals for each of the disciplines.     

Genetic analysis of six production traits in Peruvian alpacas

In this study a total of 6499 records were obtained for fibre diameter (FD) and coefficient of variation of FD (CV), 3283 records for greasy fleece weight (GFW), staple length (SL) and shearing interval (SI) and 1802 records of textile value index (TV) obtained from an experimental herd of alpacas exploited in the Peruvian Altiplano.The estimated heritabilities were: 0.412 ± 0.015 (FD), 0.321 ± 0.013 (CV), 0.098 ± 0.016 (GFW), 0.070 ± 0.011 (SL), 0.061 ± 0.012 (SI) and 0.163 ± 0.017 (TV). No significant genetic correlation was found for the pairs FD-CV and CV-GFW whilst the pairs FD-GFW, FD-SI and FD-TV had significant genetic correlations of, respectively, 0.405 ± 0.081, − 0.395 ± 0.078 and − 0.746 ± 0.049. No significant correlations were found for SL except for the pair SL-SI (0.397 ± 0.099). The TV index also showed significant genetic correlations with CV of 0.125 ± 0.061 and with GFW of 0.490 ± 0.070. All estimates of permanent environmental effects (c²) associated with the six analysed traits were statistically significant ranging from 0.008 for SI to 0.259 for CV. Total repeatability for the analysed traits was low for SI (0.069) and SL (0.090), moderate for TV (0.299) and GFW (0.316) and high for FD (0.578) and CV (0.579). The permanent environmental effect associated with CV is significantly correlated with those of the other traits except for FD. The permanent environmental effects associated with GFW and SL seemed to be basically the same (estimated correlation of 0.916 ± 0.062). The permanent environmental effect for TV is highly correlated with those associated with GFW (0.498 ± 0.058) and SL (0.750 ± 0.137). Expected selection response for TV was higher when FD was considered as selection goal instead of TV itself.It would, therefore, be more efficient to use FD rather than empirical indices as selection criterion to increase textile value in Peruvian alpacas. The reported genetic parameters and correlation matrices can be useful to implement multitrait breeding value estimations for alpaca selection.     

Genetic connections between dressage and show-jumping horses in Dutch Warmblood horses

Abstract

During the last decades, the breeding practice within the Dutch Warmblood studbook (KWPN) has resulted in an increasing specialisation of horses into show-jumping (JH) and dressage (DH). The objective of this study was to describe the effect of the specialisation on the connectedness between the subpopulations of JH and DH horses registered by KWPN. The subpopulations comprised 23,800 JH horses and 18,125 DH horses, born between 1995 and 2009. Genetic similarity (GS), genetic pool in common (GC_x) based on the marginal genetic contribution of common ancestors and coefficient of relationship (r) between and within subpopulations were analysed in three periods of time to describe changes in genetic connectedness between subpopulations. A decline in GS (0.97–0.45), GC_0.5 (0.69–0.13) and r (0.018–0.014) in the recent years was observed. Both subpopulations have a common genetic pool; however, if the specialisation process continues, it will result in two unrelated (genetic) groups.     

Genetic parameters for litter traits at different parities in purebred Landrace and Yorkshire pigs

Comparison of the multi‐trait animal model and the traditional repeatability model was carried out using data obtained from 6,424 Landrace and 20,835 Yorkshire sows farrowed from January 2000 to April 2018 in order to estimate genetic parameters for litter traits at different parities. Specifically, records of the total number born (TNB), number born alive (NBA), total number of mortality (MORT), number of stillborn (NSB) and number of mummified pigs (MUM) were used. Although results showed the heterogeneity of heritability for litter traits at different parities, the mean heritability estimates from the multi‐trait model were found to be higher than those of the repeatability model for all traits in both pig breeds. In terms of genetic correlation between parities, a slight difference in genetic control in the first parity was noted for TNB and NBA in Landrace and Yorkshire pigs. The correlation between the first parity and later parities ranged from 0.48 to 0.74 for TNB and NBA in both breeds. Moreover, genetic correlation between parities for MORT and NSB was observed to be high for parities higher than 2 in Yorkshire pigs. For MUM, genetic correlation between the first and other parities was generally low in both breeds, indicating that culling pigs on the basis of MUM at the first parity could probably be unreasonable. Overall, the results of this study suggest that the multi‐trait approach for litter size traits is useful for the accurate estimation of genetic parameters.     

Genetic parameters of performance traits in horse endurance races

The objective of the study was to find a heritable trait measuring ability in endurance races from competition results in order to select endurance horses from them. The results of 90–160 km endurance races in France from 2002 to 2004 were available including 2795 horses, 3.2 races per horse, from which 2264 had a speed measured, i.e. 5252 measurements of speed and 9059 of placing (0 or 1 when the horse completed the race). The model included fixed effects of sex, age, month of birth (not significant), region of birth, breed, and random effects of permanent environmental effects and animal effect (20,854 horses). Heritabilities were 0.28 and 0.06 (0.10 on underlying scale) respectively for speed and placing. Repeatabilities were respectively 0.44 and 0.07 (0.12). The genetic correlation was 0.87. No genetic differences were found between the results in small distance races (90 km) and long distance races (120–160 km). Additional data on young horses in specific races (20–60 km) with controlled speed did not give a precocious criterion (genetic correlation between speed in adult races and maximum level of distance and difficulty in the young horse equal to 0.07) for selection. In conclusion, breeding values should be calculated from speed and placing in races ≥ 90 km. A higher genetic progress is expected than for other equestrian disciplines since heritability is considerably higher for a trait measured in a single event.     

Genetic parameters for body weights,egg traits and antibody response against Newcastle Disease Virus (NDV) vaccine among two Tanzania chicken ecotypes

Genetic parameters were estimated for production traits and primary antibody response (Ab) against Newcastle diseases virus (NDV) vaccine among two Tanzania chicken ecotypes viz. Kuchi and Tanzania Medium (Medium). Production traits studied were body weights at 8 (Bwt8), 12(Bwt12), 16(Bwt16), and 20 (Bwt20) weeks of age, age at first egg (AFE), egg number in the first 90 days after sexual maturity (EN-90), egg weight (EW), egg shell thickness (STH), and egg shape index (ESI). Heritability estimates for Bwt8, Bwt12, Bwt16, Bwt20, AFE, EN-90, EW, STH, ESI and Ab for Kuchi chicken were 0.38 ± 0.10, 0.41 ± 0.07, 0.44 ± 0.08, 0.45 ± 0.09, 0.42 ± 0.10, 0.31 ± 0.05, 0.43 ± 0.08, 0.53 ± 0.11, 0.48 ± 0.13 and 0.27 ± 0.06, respectively. Corresponding estimates for Medium ecotype were 0.39 ± 0.09, 0.43 ± 0.10, 0.42 ± 0.08, 0.43 ± 0.07, 0.52 ± 0.11, 0.32 ± 0.06, 0.50 ± 0.07, 0.61 ± 0.13, 0.52 ± 0.10 and 0.29 ± 0.05, respectively. Genetic (r _g) and phenotypic (r_p) correlations in both ecotypes were highest among body weights (i.e. r_g = 0.60 to 0.93 and r_p = 0.54 to 0.78), and were lowest (around 0.10 and below, ranging from positive to negative) among primary antibody response against NDV vaccine and production traits, and among eggshell thickness, egg shape index and other production traits. The magnitudes of heritability estimates obtained in this study indicate good prospects of improving these traits in both ecotypes through selection.     

Estimates of non-genetic effects and genetic parameters for body measures and subjectively scored traits in Finnhorse trotters

This study examined non-genetic effects and genetic parameters of body measures and subjectively scored traits in the Finnhorse trotter population. The data was based on studbook inspections from 1971 to 2004 covering observations on 6381 horses. There were five body measures – height at withers, height at croup, circumference of girth, length of body and circumference of cannon bone – and six subjectively scored traits – character, body conformation, leg stances, quality of legs, hooves and movements – included in the analyses. Multivariate mixed models were applied with year–sex and age as fixed effects and animal as a random effect. The year–sex effect had a significant influence on body measures and scored traits. Age at judging had a significant influence on all traits but height at withers and body conformation. Heritability estimates were from 0.53 to 0.78 for body measures and 0.10 to 0.19 for scored traits. Genetic correlations between body measures were highly positive, from 0.75 to 0.98, whilst genetic correlations between scored traits varied between − 0.20 and 0.51. Genetic correlations between body measures and scored traits were mainly negative, from − 0.38 to 0.09. Our results indicate that additive genetic effects are relevant determinants for body measures of Finnhorse trotters. The scored traits were of low to moderate heritability and were relevantly influenced by environmental effects.     

Cluster and meta‐analyses of genetic parameters for feed intake traits in growing beef cattle

A data set based on 50 studies including feed intake and utilization traits was used to perform a meta‐analysis to obtain pooled estimates using the variance between studies of genetic parameters for average daily gain (ADG); residual feed intake (RFI); metabolic body weight (MBW); feed conversion ratio (FCR); and daily dry matter intake (DMI) in beef cattle. The total data set included 128 heritability and 122 genetic correlation estimates published in the literature from 1961 to 2012. The meta‐analysis was performed using a random effects model where the restricted maximum likelihood estimator was used to evaluate variances among clusters. Also, a meta‐analysis using the method of cluster analysis was used to group the heritability estimates. Two clusters were obtained for each trait by different variables. It was observed, for all traits, that the heterogeneity of variance was significant between clusters and studies for genetic correlation estimates. The pooled estimates, adding the variance between clusters, for direct heritability estimates for ADG, DMI, RFI, MBW and FCR were 0.32 ± 0.04, 0.39 ± 0.03, 0.31 ± 0.02, 0.31 ± 0.03 and 0.26 ± 0.03, respectively. Pooled genetic correlation estimates ranged from ?0.15 to 0.67 among ADG, DMI, RFI, MBW and FCR. These pooled estimates of genetic parameters could be used to solve genetic prediction equations in populations where data is insufficient for variance component estimation. Cluster analysis is recommended as a statistical procedure to combine results from different studies to account for heterogeneity.     

Genetic analysis of clinical findings at health examinations of young Swedish warmblood riding horses

Background

Soundness is important for welfare and utility of the riding horse. Musculoskeletal disorders are the most common causes of interruption in training and of culling. Despite great importance, heritability of a majority of health traits in horses has previously not been estimated. The objective was to perform genetic analyses of medical and orthopaedic health traits in young riding horses, including estimates of heritability and genetic correlations between health traits, and to reveal possibilities for genetic evaluation of stallions for progeny health.

Results

The heritability of health traits was estimated using records from 8,238 Swedish warmblood riding horses examined as 4–5 year olds at the Riding Horse Quality Test in 1983–2005. The analyses were performed using multi-trait linear mixed animal models. The heritabilities of palpatory orthopaedic health (PALP), including effusion, swelling, heat, soreness and stiffness/atrophy, and hoof examination results (HOOF), of hoof shape and hoof wall quality, were 0.12 and 0.10, respectively. The genetic variation in these traits resulted in distinct health differences between progeny groups of stallions. The highest heritability among clinical signs of PALP was found for synovial effusions at 0.14. For systemic locations, joint related findings had the highest heritability; 0.13. The heritabilities of medical health and locomotion examination results were low, 0.02 and 0.04, respectively. A genetic improvement of health status has occurred over time but accounts only partly for the decrease in clinical findings of health during the studied period.

Conclusions

The genetic variation found in PALP and HOOF implies distinct differences between progeny groups. Thus, there are possibilities for improvement of these traits in the population through selection. The weak and non-significant correlation between PALP and HOOF suggests that both traits need to be selected for in practical breeding to improve both traits. Some genetic improvements over time have already been achieved, possibly due to regular stallion health inspections and an indirect selection for lifetime performance. For further improvements stallion breeding values for health may be introduced, based on RHQT examinations, complementary to present breeding values for performance.     

Genetic correlations between competition traits and traits scored at breeding field-tests in Icelandic horses

Relationships between breeding field-test traits and competition traits were studied to investigate whether the latter could be usefully included in the genetic evaluation of Icelandic horses. The current method of genetic evaluation is based on records from breeding field-tests only. The breeding field-test data included 16 401 individual records of Icelandic horses evaluated in 11 countries during 1990–2005. Competition results included 18 982 records of 3790 horses competing in sport and gæðinga competitions in Iceland and Sweden during 1998–2004. In the breeding field-tests, eight conformation traits and eight riding ability traits were scored; height of withers was also recorded. These traits were analysed together with the competition traits tölt(comp), 4-gait, 5-gait and pace test, in bivariate analyses. Animal models were used; the fixed effects for breeding field-test traits included sex by age interaction and country by year interaction. For the competition traits the model included fixed effects of sex, age and event, and a random permanent environmental effect. Estimated heritabilities and genetic correlations for breeding field-test traits were consistent with earlier results; heritabilities ranged from 0.20 to 0.67, and moderate to high genetic correlations were estimated between many of the riding ability traits, and between riding ability traits and some conformation traits. The estimated heritabilities for competition traits were about 0.20, and genetic correlations between competition traits varied from − 0.12 to 1.00. In general, high genetic correlations were estimated between breeding field-test riding ability traits and competition traits. Moderately positive genetic correlations were found between some breeding field-test conformation traits and competition traits. Competition traits add information relating to the breeding goal of the Icelandic horse; they should therefore be added to genetic evaluation in future.     

Genetic parameters for maternal behaviour traits in sows

Data from 32 nucleus and multiplier herds in Germany was used to estimate variance components and breeding values for five maternal behaviour traits in sows. The estimation was performed univariately using an animal threshold model. About 31,000 farrowings recorded from December 2003 until July 2005 were included. The heritability coefficients were 0.07 (0.06) for group behaviour, 0.06 (0.03) for attitude to people, 0.05 (0.01) for maternal ability, 0.03 (0.01) for crushing of piglets and 0.02 (0.02) for savaging of piglets. Additionally, genetic correlations between the behaviour traits and between the behaviour traits and litter size, respectively, were estimated multivariately by REML with a linear model. Low heritability and weak genetic correlation to litter size at birth indicate that it may be difficult to genetically improve the maternal behaviour, and that selection for better mothering ability is not necessarily accompanied by reduced litter size at birth.     

Genetic parameters of milk production traits and fatty acid contents in milk for Holstein cows in parity 1 – 3

The objective of this study was to estimate genetic parameters of milk, fat, and protein yields, fat and protein contents, somatic cell count, and 17 groups and individual milk fatty acid (FA) contents predicted by mid‐infrared spectrometry for first‐, second‐ and third‐parity Holstein cows. Edited data included records collected in the Walloon region of Belgium from 37 768 cows in parity 1, 22 566 cows in parity 2 and 8221 in parity 3. A total of 69 (23 traits for three parities) single‐trait random regression animal test‐day models were run. Approximate genetic correlations among traits were inferred from pairwise regressions among estimated breeding values of cow having observations. Heritability and genetic correlation estimates from this study reflected the origins of FA: de novo synthetized or originating from the diet and the body fat mobilization. Averaged daily heritabilities of FA contents in milk ranged between 0.18 and 0.47. Average daily genetic correlations (averaged across days in milk and parities) among groups and individual FA contents in milk ranged between 0.31 and 0.99. The genetic variability of FAs in combination with the moderate to high heritabilities indicated that FA contents in milk could be changed by genetic selection; however, desirable direction of change in these traits remains unclear and should be defined with respect to all issues of importance related to milk FA.