Impact of reproductive biotechnologies on genetic variability of Argentine Polo horses

Reproductive traits in Pura Raza Española mares manifest inbreeding depression from low levels of homozygosity

Inbreeding depression is a genetic phenomenon associated with the loss of fitness and mean phenotypic performance due to mating between relatives. Historically, inbreeding coefficients have been estimated from pedigree information. However, the onset of genomic selection programs provides large datasets of individuals genotyped using SNP arrays, enabling more precise assessment of an individual's genomic-level inbreeding using genomic data. One of the traits most sensitive to issues stemming from increased inbreeding is reproduction. This is particularly important in equine, in which fertility is only moderate compared to other livestock species. To explore this further, we evaluated the effect of inbreeding on five reproductive traits (age at first foaling (AFF), average interval between foalings (AIF), total number of foalings (NF), productive life (PL) and reproductive efficiency (RE)) in Pura Raza Español mares using genomic data. Residual predicted phenotypes were obtained by purging these traits through the REML (wgResidual) and ssGREML (gResidual) approaches in reproductive data of 29,847 PRE mares using the BLUPF90+ program. Next, we used pedigree-based (Fped) and ROH-based genomic (FROH) inbreeding coefficients derived from 1018 animals genotyped with 61,271 SNPs to estimate the inbreeding depression (linear regression). Our results indicated significant levels of inbreeding depression for all reproductive traits, with the exception of the AIF trait when Fped was used. However, all traits were negatively affected by the increase in genomic inbreeding, and FROH was found to capture more inbreeding depression than Fped. Likewise, REML models (ssGREML) using genomic data for estimated predicted residual phenotypes resulted in higher variance explained by the model compared with the models not using genomics (REML). Finally, a segmented regression analysis was conducted to evaluate the effect of inbreeding depression, revealing that the levels of genealogical and genomic homozygosity do not manifest uniformly in reproductive traits. In contrast, the levels of inbreeding depression ranged from low to high as homozygosity increased. This analysis also showed that reproductive traits are very sensitive to inbreeding depression, even with relatively low levels of homozygosity.

Factors affecting the efficiency of equine embryo transfer (EET) in polo mares under subtropical conditions of Pakistan

Equine embryo transfer (EET) is a prominent technology in the equine breeding industry, and its efficacy is affected by a number of factors. The current study aimed to determine the effects of the breed of donor/recipient mares, estrus/ovulation induction treatment, cooled transportation of embryos, and synchrony between donor and recipient mares on the efficiency of the EET under subtropical conditions of Pakistan. A total of eighty-four (n = 84) Polo-playing donor mares (Argentino-polo = 41 and Anglo-Arab = 43) and seventy (n = 70) recipient mares (light breed = 26 and heavy breed = 44) were used for EET. The donor mares exhibiting natural estrus (n = 28) were detected by teaser a stallion, and corpus luteum (CL) having mares (n = 56) were treated with prostaglandin (150 μg of Cloprostenol) for estrus induction. The mares' follicular growth was monitored through ultrasonography until the dominant follicle's size reached 35 mm or more with a moderate to obvious uterine edema score. Afterward, the mares were treated either with GnRH, i.e., 50 μg of Lecirelin acetate (n = 41) or Ovusyn, i.e., 1500 IU hCG (n = 43). Insemination with chilled semen was performed 24 hours later. The embryos were collected non-surgically, 7 or 8 days after ovulation, from the donor mares. The collected embryos were transferred into the well-synchronized recipient mares as fresh (n = 44) or chilled (n = 26) embryos. The pregnancy after ET was checked through ultrasonography. Statistical analysis revealed that the embryo recovery rate (ERR) remained significantly higher (P<0.05) for the Prostaglandin (PG) treated group of donors as compared to the natural heat group of donors. The breed of donor mares, type of ovulatory treatment given, and day of embryo collection did not significantly (P>0.05) affect the ERR. There was no significant effect of the type (fresh vs chilled), classification, and stage of development of embryo on pregnancy outcomes (P>0.05). ET pregnancy rate was significantly affected by the breed of recipient mares and ovulation synchrony between donor and recipient mares (P<0.05). In conclusion, under the subtropical conditions of Pakistan, PG-based estrus induction of donor mares, breed of recipient mares, and ovulation synchrony between the donor and recipient mares had a substantial effect on the efficiency of EET.

Designing an early selection morphological traits index for reproductive efficiency in Pura Raza Española mares

The low rate of reproductive efficiency in horses may be linked to the equine industry's practice of maintaining breeding stock that stands out for its athletic or morphological performance but exhibits poor reproductive efficiency. In this study, the age at first foaling, age at last foaling, interval between first and second foaling, average interval between foaling, foaling number and reproductive efficiency, and their relationship with the morphological records in 19,758 Pura Raza Española (PRE) mares were analyzed. After a partial least squares analysis height at withers, lateral hock angle, dorsal-sternal diameter, perimeter of anterior cannon bone, angle of shoulder, thoracic perimeter, hip-stifle distance, and angle of croup were the most important traits related with reproductive traits in PRE mares. A multivariate animal model with both morphological and reproductive traits was applied, including age, geographical area, coat color, and average stud size in the decade of the mare's first foaling. The results indicate that reproductive selection is feasible, and is enhanced by the use of morphological traits, given the moderate to high magnitudes of heritability values in both types of traits, which oscillated between 0.1 (interval between first and second foaling) and 0.95 (height at withers). The resulting genetic parameters were used to develop a series of selection indexes based on morphological or morphological and reproductive combination traits to improve reproductive efficiency traits in PRE mares and thus compute the expected genetic response (EGR) for the different strategies. The increase in EGR, when comparing EGR using only reproductive traits as selection criteria vs. using a combined index of both morphological and reproductive traits, oscillated between 4.0% for the age at first foaling to 46.8% for the interval between first and second foaling. In addition, two precocity indexes showed positive EGR when the age at last foaling and the interval between first and second foaling, both with and without morphological traits, were used as selection criteria. Therefore, this analysis reveals that the preselection of reproductive traits based on morphological traits is possible in PRE mares. Ultimately, this knowledge will help breeders achieve genetic progress in reproductive traits, leading to healthier and more successful breeding outcomes in horses.

Effects of Selection on Breed Contribution in the Caballo de Deporte Español

The equine breeding industry for sport’s performance has evolved into a fairly profitable economic activity. In particular, the Caballo de Deporte Español (CDE) is bred for different disciplines with a special focus on Show Jumping. The main aim of this study was to determine the effects of 15 years of selection and to find out whether it has been effective and adequate regarding the CDE main breeding objectives. The whole pedigree of 19,045 horses registered as CDE was used, comprising 47,884 animals (18,799 males and 29,085 females). An analysis performed to check for the pedigree completeness level yielded a number of equivalent complete generations (t) equal to 1.95, an average generation interval (GI) of 10.87 years, mean inbreeding coefficient (F) of 0.32%, an average relatedness coefficient (AR) of 0.09% and an effective population size (Ne) of 204. For the analyses, animals were divided into fourteen breed groups. Additionally, in order to study the evolution of these breeds over time and their influence on CDE pedigree, five different periods were considered according to the year of birth of the animals. Performance data used in the analyses were the estimated breeding values (EBV) of the Show Jumping sport discipline of 12,197 horses in the CDE pedigree, available from the 2020 routine genetic evaluations of the CDE breeding program (starting in 2004). Dressage and Eventing EBV values were also assessed. Results showed values of F higher than expected under random mating; this pointed to some degree of inbred matings. With regard to the evolution of breeding values, we found that, in general, EBVs of offspring were higher than the EBVs of parents. Notwithstanding, there is still a need for improvement in population management and the coordination of the breeders to get higher responses but controlling the loss of genetic diversity in the CDE breed.

Fine-Scale Analysis of Runs of Homozygosity Islands Affecting Fertility in Mares

The loss of genetic variability in livestock populations bred under strict selection processes is a growing concern, as it may lead to increased inbreeding values and lower fertility, as a consequence of the “inbreeding depression” effect. This is particularly important in horses, where inbreeding levels tend to rise as individuals become more and more closely related. In this study, we evaluated the effect of increased inbreeding levels on mare fertility by combining an SNP-based genomic approach using runs of homozygosity and the estimation of genetic breeding values for reproductive traits in a large population of Pura Raza Española mares. Our results showed a negative correlation between whole-genome homozygosity and fertility estimated breeding values (EBVs) at the genome level (ρ = −0.144). However, the analysis at chromosome level revealed a wide variability, with some chromosomes showing higher correlations than others. Interestingly, the correlation was stronger (−0.241) when we repeated the analysis in a reduced dataset including the 10% most and least fertile individuals, where the latter showed an increase in average inbreeding values (F_ROH) of around 30%. We also found 41 genomic regions (ROHi, runs of homozygosity islands) where homozygosity increased 100-fold, 13 of which were significantly associated with fertility after cross-validation. These regions encompassed 17 candidate genes previously related to oocyte and embryo development in several species. Overall, we demonstrated the relationship between increased homozygosis at the genomic level and fertility in mares. Our findings may help to deal with the occurrence of inbreeding depression, as well as further our understanding of the mechanisms underlying fertility in mares.

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.

Sperm morphometry is affected by increased inbreeding in the Retinta cattle breed: A molecular approach

The effect of inbreeding depression on sperm motility is well documented, but its influence on sperm morphometry has been scarcely examined to date. Here, we combined the use of computer-assisted sperm morphometry analysis (CASMA) with a SNP-based genomic approach to determine and characterize the effect of inbreeding on the sperm shape of a highly inbred cattle population. We determined seven morphometric parameters on frozen-thawed sperm samples of 57 Retinta bulls: length (L, µm), width (W, µm), area (A, µm² ), perimeter (P, µm), ellipticity (ELI; L/W), elongation (L-W)/(L + W) and perimeter-to-area shape factor (p2a; P² /4 × π × A). The comparison of highly inbred (HI) and lowly inbreed (LI) individuals based on runs of homozygosity (ROH) inbreeding values (F _ROH ) showed no differences between groups. An additional two-step unsupervised sperm subpopulation analysis based on morphometric parameters showed significant differences in the abundance of different sperm subpopulations between groups (p < 0.05). This analysis revealed that HI bulls harbored a higher percentage of narrow-head sperm as opposed to the higher percentage of large- and round-headed sperm detected in LI. A further genomic characterization revealed 23 regions differentially affected by inbreeding in both groups, detecting six genes (SPAG6, ARMC3, PARK7, VAMP3, DYNLRB2, and PHF7) previously related to different spermatogenesis-associated processes.

Impaired Reproductive Function in Equines: From Genetics to Genomics

Fertility is one of the key factors in the economic and productive success of the equine industry. Despite this, studies on the genetic causes affecting reproductive performance are scarce, especially in mares, where the genetic architecture of the reproductive traits is extremely complex. Today, with the increasing availability of new genomic methodologies for this species, we are presented with an interesting opportunity to understand the genetic basis of equine reproductive disorders. These include, among others, novel techniques for detecting chromosomal abnormalities, whose association with infertility in horses was established over 50 years ago; new sequencing technologies permitting an accurate detection of point mutations influencing fertility, as well as the study of inbreeding and molecular homozygosity, which has been widely suggested as one of the main causes of low reproductive performance in horses. Finally, over the last few years, reproductive performance has also been associated with copy number variants and candidate genes detected by genome-wide association studies on fertility traits. However, such studies are still scarce, probably because they depend on the existence of large and accurate phenotypic datasets of reproductive and/or fertility traits, which are still difficult to obtain in equines.

Analysis of Genetic Variability in the Argentine Polo Horse With a Panel of Microsatellite Markers

Argentine Polo (AP) is a young horse breed with a fast expansion because of an open registry policy and the application of assisted reproduction technologies. In the last years, AP showed a remarkable progress associated with the use of embryo transfer technology and intensive selection based on sport performance. However, these practices could have affected the genetic variability of the breed. To monitor these potential changes, a parentage panel of 11-15 microsatellites was investigated for changes in allele frequencies, heterozygosity, and exclusion probability over a 16 year period. Frequency of 36 alleles in 13 markers showed significant departures from expected changes because of random genetic drift. Six markers showed both allelic frequency increase and expected heterozygosity (He) reduction, suggesting the influence of selective breeding or hitchhiking effects. The average He decreased significantly although was lower than the observed heterozygosity, indicating a still low inbreeding level. Although the exclusion probability of the panel showed a trend to decrease, it is over 0.9995, the recommended value for equine parentage exclusion.

Genetic Structure Analysis of the Pura Raza Español Horse Population through Partial Inbreeding Coefficient Estimation

The aim of this work was to analyze genetic parameters such as the inbreeding coefficient (F), relatedness coefficient (AR) and partial inbreeding coefficient (Fij) of the whole PRE population, and the ancestors which account for 50% of the total genetic variability of the current population, from genealogical information. The average F of the whole PRE population (328,706 animals) has decreased from 8.45% to 7.51% in the least 20 years. The Fij was estimated for the whole PRE population, resulting in a database of 58,772,533 records containing one record for each Fij that each animal receives from a certain common ancestor (CA). A total of 10,244 CAs contributed to the Fij with an average of 5370 descendants, with each descendant having an average of 170 CAs. Over the generations, the number of CAs has increased, while the proportion of Fij by each one has decreased. In addition, the contributions of the more influential ancestors have changed. The increased census, the limited use of artificial insemination and our increased knowledge about inbreeding depression and the animals' breeding values allow breeders to select horses more for their functionality and conformation than for their pedigree reputation, which is the cause of all these changes.