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Novel Insights in Horse Breeding and Genetics

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A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Equids".

Deadline for manuscript submissions: closed (28 February 2023) | Viewed by 29120

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Special Issue Editors

Dr. Isabel Cervantes

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Guest Editor

Departamento de Producción Animal, Universidad Complutense de Madrid, Avda. Puerta de Hierro s/n, E-28040 Madrid, Spain
Interests: conservation and breeding programs; breeding value prediction; population genetic structure; genetic robustness; horse breeding and selection

Dr. María Dolores Gómez Ortiz

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Guest Editor

E.T.S. de Ingeniería Agronómica, Universidad de Sevilla, Ctra. de Utrera, 41013 Sevilla, Spain
Interests: conservation and breeding programs; breeding values prediction; population genetic structure; horse breeding and selection

Special Issue Information

Dear Colleagues,

The aim of horse breeding programs is to attain genetic improvement of the breeding stock, but its application is challenging because of some equine particularities, such as long generation interval, difficulties for the early prediction of breeding values, low heritability traits, and consequent low selection intensity. The selection objectives included in these programs, as in other species, have evolved together with traditional sport performance and conformation to other characters related to fertility, health, longevity, and behavior.

Modeling horse performance using genetic–statistical approaches to design the best model to carry out the genetic assessment is difficult because of the inclusion of specific environmental factors (e.g., the rider–horse interaction), the existence of crossbreeds (non-additive effects) or the nature of the traits. Optimized selection strategies with appropriate methodology that may combine genealogical and genomic information in a selection or conservation scenario could help to address the specific issues of this species.

In this context, and to promote the application of novel research in this species, original manuscripts that address recent research and novel insights into horse breeding and genetics are invited for this Special Issue.

Dr. Isabel Cervantes
Dr. María Dolores Gómez Ortiz
Guest Editors

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Keywords

selection
multiple-traits models
equids
performance
genomic
genetic parameters
genetic response
genetic–statistical models
robustness
genetic conservation
genetic diseases

Published Papers (12 papers)

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Research

13 pages, 880 KiB

Open AccessArticle

Racing Performance of the Quarter Horse: Genetic Parameters, Trends and Correlation for Earnings, Best Time and Time Class

by Ricardo Faria, António Vicente and Josineudson Silva

Animals 2023, 13(12), 2019; https://doi.org/10.3390/ani13122019 - 17 Jun 2023

Viewed by 1677

Abstract

The aim of this study was to evaluate the sprint racing performance of Quarter Horses in Brazil. Estimating genetic parameters, trends and correlations were obtained by single- and two-trait analyses using Bayesian inference (earnings to 2 years of equestrian age, best time and time class at distances of 301 m and 402 m). The data comprised a period of 38 equestrian years (1978 to 2015) with 23,482 sprint race records from 5861 animals. The heritability estimates were of low to moderate magnitude, ranging from 0.10 to 0.37 (single-trait) and from 0.15 to 0.41 (two-traits), and the repeatability was 0.31 to 0.46. The additive, residual and phenotypic correlations between earnings to 2 years of equestrian age and the other traits (best time and time class in distances 301 m and 402 m) were high (−0.95, −0.96, 0.69 and 0.92), low (−0.29, −0.37, 0.26 and 0.27) and moderate (−0.41, −0.47, 0.37 and 0.47), respectively. There is a positive genetic trend for all traits considered. However, evaluation of the last 10 equestrian years (2006 to 2015) showed negative trends (genetic loss) and trends close to zero (genetic stagnation). The design of breeding programs using the earnings trait in conjunction with other racing performance traits can enhance changes in the genetic gains as a whole in speed-racing Quarter Horses. These findings suggest that the traits studied should be included in breeding selection programs for racing Quarter Horses. Full article

(This article belongs to the Special Issue Novel Insights in Horse Breeding and Genetics)

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10 pages, 270 KiB

Open AccessArticle

SNP-Based Heritability of Osteochondrosis Dissecans in Hanoverian Warmblood Horses

by Elisa Zimmermann and Ottmar Distl

Animals 2023, 13(9), 1462; https://doi.org/10.3390/ani13091462 - 25 Apr 2023

Cited by 1 | Viewed by 1344

Abstract

Before the genomics era, heritability estimates were performed using pedigree data. Data collection for pedigree analysis is time consuming and holds the risk of incorrect or incomplete data. With the availability of SNP-based arrays, heritability can now be estimated based on genotyping data. We used SNP array and 1.6 million imputed genotype data with different minor allele frequency restrictions to estimate heritabilities for osteochondrosis dissecans in the fetlock, hock and stifle joints of 446 Hanoverian warmblood horses. SNP-based heritabilities were estimated using a genomic restricted maximum likelihood (GREML) method and accounting for patterns of regional linkage disequilibrium in the equine genome. In addition, we employed GREML for family data to account for different degrees of relatedness in the study population. Our results indicate that we were able to capture a larger proportion of additive genetic variance compared to pedigree-based estimates in the same population of Hanoverian horses. Heritability estimates on the linear scale for fetlock-, hock- and stifle-osteochondrosis dissecans were 0.41–0.43, 0.62–0.63, and 0.23–0.25, respectively, with standard errors of 0.11–0.14. Accounting for linkage disequilibrium patterns had an upward effect on the imputed data and a downward impact on the SNP array genotype data. GREML for family data resulted in higher heritability estimates for fetlock-osteochondrosis dissecans and slightly higher estimates for hock-osteochondrosis dissecans, but had no effect on stifle-osteochondrosis dissecans. The largest and most consistent heritability estimates were obtained when we employed GREML for family data with genomic relationship matrices weighted through patterns of regional linkage disequilibrium. Estimation of SNP-based heritability should be recommended for traits that can only be phenotyped in smaller samples or are cost-effective. Full article

(This article belongs to the Special Issue Novel Insights in Horse Breeding and Genetics)

10 pages, 1296 KiB

Open AccessArticle

Cortisol Variations to Estimate the Physiological Stress Response in Horses at a Traditional Equestrian Event

by Sergi Olvera-Maneu, Annaïs Carbajal, Paula Serres-Corral and Manel López-Béjar

Animals 2023, 13(3), 396; https://doi.org/10.3390/ani13030396 - 24 Jan 2023

Cited by 3 | Viewed by 1841

Abstract

In many countries, horses remain involved in traditional equestrian events such as those celebrated in Menorca (Balearic Islands, Spain) every year since at least the 14th century. The present study aimed to evaluate the variations in salivary cortisol concentrations to estimate the physiological stress response in horses at the Menorca patronal festivals. Two different editions (years 2016 and 2018) of the festivals in honor of the Virgin of Grace in Maó (Menorca, Spain) were studied. Nineteen and seventeen Pure Breed Menorca stallions were included in the study, respectively. The stallions were aged between seven and twelve years. During celebrations, samples were collected before the start of the festivals between 8–9 a.m. and during the festivals at 8–9 p.m. On the second day of celebrations, the samples were collected at 8–9 a.m. and 3–4 p.m. Finally, on the day after the festivals, one sample was collected at 8–9 p.m. Additionally, a control group was sampled at 8–9 a.m., 3–4 p.m., and 8–9 p.m. Salivary cortisol concentrations were assessed by using a commercial enzyme immunoassay kit specially validated to quantify salivary cortisol in horses. Salivary cortisol concentrations did not show significant differences between sampling hours in the control group (p > 0.05). All the samples collected during festivals were significantly higher than samples of the control group (p < 0.05). Within the twenty-four hours after the end of the celebrations, cortisol concentrations returned to baseline levels and did not differ significantly from the control group (p > 0.05). Hence, the present study describes that the participation of the horses in these particular acts generate an acute and transitory stress response. Overall, the current work provides a reasonable basis for future research on the stress physiology and well-being of horses participating in traditional celebrations or similar events. Full article

(This article belongs to the Special Issue Novel Insights in Horse Breeding and Genetics)

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15 pages, 2279 KiB

Open AccessArticle

Reconstruction of the Major Maternal and Paternal Lineages in the Feral New Zealand Kaimanawa Horses

by Muhammad Bilal Sharif, Robert Rodgers Fitak, Barbara Wallner, Pablo Orozco-terWengel, Simone Frewin, Michelle Fremaux and Elmira Mohandesan

Animals 2022, 12(24), 3508; https://doi.org/10.3390/ani12243508 - 12 Dec 2022

Cited by 1 | Viewed by 2084

Abstract

New Zealand has the fourth largest feral horse population in the world. The Kaimanawas (KHs) are feral horses descended from various domestic horse breeds released into the Kaimanawa ranges in the 19th and 20th centuries. Over time, the population size has fluctuated dramatically due to hunting, large-scale farming and forestry. Currently, the herd is managed by an annual round-up, limiting the number to 300 individuals to protect the native ecosystem. Here, we genotyped 96 KHs for uniparental markers (mitochondrial DNA, Y-chromosome) and assessed their genetic similarity with respect to other domestic horses. We show that at least six maternal and six paternal lineages contributed unequally to the KH gene pool, and today’s KH population possibly represents two sub-populations. Our results indicate that three horse breeds, namely Welsh ponies, Thoroughbreds and Arabian horses had a major influence in the genetic-makeup of the extant KH population. We show that mitochondrial genetic diversity in KHs (π = 0.00687 ± 0.00355) is closer to that of the Sable Island horses (π = 0.0034 ± 0.00301), and less than other feral horse populations around the world. Our current findings, combined with ongoing genomic research, will provide insight into the population-specific genetic variation and inbreeding among KHs. This will largely advance equine research and improve the management of future breeding programs of these treasured New Zealand horse. Full article

(This article belongs to the Special Issue Novel Insights in Horse Breeding and Genetics)

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14 pages, 1303 KiB

Open AccessArticle

Identification of Copy Number Variations in Four Horse Breed Populations in South Korea

by Yong-Min Kim, Seok-Joo Ha, Ha-Seung Seong, Jae-Young Choi, Hee-Jung Baek, Byoung-Chul Yang, Jung-Woo Choi and Nam-Young Kim

Animals 2022, 12(24), 3501; https://doi.org/10.3390/ani12243501 - 12 Dec 2022

Cited by 3 | Viewed by 1215

Abstract

In this study, genome-wide CNVs were identified using a total of 469 horses from four horse populations (Jeju horses, Thoroughbreds, Jeju riding horses, and Hanla horses). We detected a total of 843 CNVRs throughout all autosomes: 281, 30, 301, and 310 CNVRs for Jeju horses, Thoroughbreds, Jeju riding horses, and Hanla horses, respectively. Of the total CNVRs, copy number losses were found to be the most abundant (48.99%), while gains and mixed CNVRs accounted for 41.04% and 9.96% of the total CNVRs, respectively. The length of the CNVRs ranged from 0.39 kb to 2.8 Mb, while approximately 7.2% of the reference horse genome assembly was covered by the total CNVRs. By comparing the CNVRs among the populations, we found a significant portion of the CNVRs (30.13%) overlapped; the highest number of shared CNVRs was between Hanla horses and Jeju riding horses. When compared with the horse CNVRs of previous studies, 26.8% of CNVRs were found to be uniquely detected in this study. The CNVRs were not randomly distributed throughout the genome; in particular, the Equus caballus autosome (ECA) 7 comprised the largest proportion of its genome (16.3%), while ECA 24 comprised the smallest (0.7%). Furthermore, functional analysis was applied to CNVRs that overlapped with genes (genic-CNVRs); these overlapping areas may be potentially associated with the olfactory pathway and nervous system. A racing performance QTL was detected in a CNVR of Thoroughbreds, Jeju riding horses, and Hanla horses, and the CNVR value was mixed for three breeds. Full article

(This article belongs to the Special Issue Novel Insights in Horse Breeding and Genetics)

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13 pages, 3027 KiB

Open AccessArticle

Y Chromosome Haplotypes Enlighten Origin, Influence, and Breeding History of North African Barb Horses

by Lara Radovic, Viktoria Remer, Carina Krcal, Doris Rigler, Gottfried Brem, Ahmed Rayane, Khadija Driss, Malak Benamar, Mohamed Machmoum, Mohammed Piro, Diana Krischke, Ines von Butler-Wemken and Barbara Wallner

Animals 2022, 12(19), 2579; https://doi.org/10.3390/ani12192579 - 27 Sep 2022

Cited by 3 | Viewed by 4013

Abstract

In horses, demographic patterns are complex due to historical migrations and eventful breeding histories. Particularly puzzling is the ancestry of the North African horse, a founding horse breed, shaped by numerous influences throughout history. A genetic marker particularly suitable to investigate the paternal demographic history of populations is the non-recombining male-specific region of the Y chromosome (MSY). Using a recently established horse MSY haplotype (HT) topology and KASP™ genotyping, we illustrate MSY HT spectra of 119 Barb and Arab-Barb males, collected from the Maghreb region and European subpopulations. All detected HTs belonged to the Crown haplogroup, and the broad MSY spectrum reflects the wide variety of influential stallions throughout the breed’s history. Distinct HTs and regional disparities were characterized and a remarkable number of early introduced lineages were observed. The data indicate recent refinement with Thoroughbred and Arabian patrilines, while 57% of the dataset supports historical migrations between North Africa and the Iberian Peninsula. In the Barb horse, we detected the HT linked to Godolphin Arabian, one of the Thoroughbred founders. Hence, we shed new light on the question of the ancestry of one Thoroughbred patriline. We show the strength of the horse Y chromosome as a genealogical tool, enlighten recent paternal history of North African horses, and set the foundation for future studies on the breed and the formation of conservation breeding programs. Full article

(This article belongs to the Special Issue Novel Insights in Horse Breeding and Genetics)

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14 pages, 610 KiB

Open AccessArticle

Morpho-Functional Traits in Pura Raza Menorquina Horses: Genetic Parameters and Relationship with Coat Color Variables

by Davinia I. Perdomo-González, Rocío de las Aguas García de Paredes, Mercedes Valera, Ester Bartolomé and María Dolores Gómez

Animals 2022, 12(18), 2319; https://doi.org/10.3390/ani12182319 - 7 Sep 2022

Cited by 3 | Viewed by 1365

Abstract

The studbook of Pura Raza Menorquina horses only permits the use of black-coated animals with a small quantity of white marks as breeding stock. Its breeding program uses linear morpho-functional traits as selection criteria. Our aim was to estimate the genetic parameters of linear morpho-functional traits, and reveal relationship of quality of black coat color (QB) and percentage of white marks (WM) with the other morphological and functional linear traits in this breed. A total of 46 linear traits were scored by four appraisers using seven classes, with a total of 772 records from 333 animals (≥4 years old). Univariate animal models using a Bayesian approach were used, with a pedigree of 757 animals. Sex (two) and appraiser-season (13) were included as fixed effects, age as a linear covariate, and permanent environmental and additive genetic as random effect. The heritabilities of the morpho-functional traits were low to medium (0.09–0.58) and matched the range in the bibliography. Heritabilities for coat color traits were 0.36 for QB and 0.23 for WM. The highest genetic correlations were obtained between QB and upper neck line (0.816) and between WM and form of the hoof (0.638). The negative signs of most of the genetic correlations between WM and the functional traits is also remarkable, contributing to the selection of functional traits against the presence of white marks in this population. A clear genetic differentiation was observed between animals with better breeding values for QB and WM, corroborated by a study on founders. In conclusion, QB and WM could show different genetic backgrounds. Full article

(This article belongs to the Special Issue Novel Insights in Horse Breeding and Genetics)

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15 pages, 2204 KiB

Open AccessArticle

Estimates of Genetic Parameters for Shape Space Data in Franches-Montagnes Horses

by Annik Imogen Gmel, Alexander Burren and Markus Neuditschko

Animals 2022, 12(17), 2186; https://doi.org/10.3390/ani12172186 - 25 Aug 2022

Cited by 4 | Viewed by 3591

Abstract

Conformation traits such as joint angles are important selection criteria in equine breeding, but mainly consist of subjective evaluation scores given by breeding judges, showing limited variation. The horse shape space model extracts shape data from 246 landmarks (LM) and objective joint angle measurements from triplets of LM on standardized horse photographs. The heritability was estimated for 10 joint angles (seven were measured twice with different LM placements), and relative warp components of the whole shape, in 608 Franches-Montagnes (FM) horses (480 stallions, 68 mares and 60 geldings born 1940–2018, 3–25 years old). The pedigree data comprised 6986 horses. Genetic variances and covariances were estimated by restricted maximum likelihood model (REML), including the fixed effects birth year, age (linear and quadratic), height at withers (linear and quadratic), as well as postural effects (head, neck, limb position and body alignment), together with a random additive genetic animal component and the residual effect. Estimated heritability varied from 0.08 (stifle joint) to 0.37 (poll). For the shape, the type was most heritable (0.36 to 0.37) and evolved from heavy to light over time. Image-based phenotyping can improve the selection of horses for conformation traits with moderate heritability (e.g., poll, shoulder and fetlock). Full article

(This article belongs to the Special Issue Novel Insights in Horse Breeding and Genetics)

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10 pages, 2250 KiB

Open AccessArticle

A KIT Variant Associated with Increased White Spotting Epistatic to MC1R Genotype in Horses (Equus caballus)

by Laura Patterson Rosa, Katie Martin, Micaela Vierra, Erica Lundquist, Gabriel Foster, Samantha A. Brooks and Christa Lafayette

Animals 2022, 12(15), 1958; https://doi.org/10.3390/ani12151958 - 2 Aug 2022

Cited by 5 | Viewed by 3161

Abstract

Over 40 identified genetic variants contribute to white spotting in the horse. White markings and spotting are under selection for their impact on the economic value of an equine, yet many phenotypes have an unknown genetic basis. Previous studies also demonstrate an interaction between MC1R and ASIP pigmentation loci and white spotting associated with KIT and MITF. We investigated two stallions presenting with a white spotting phenotype of unknown cause. Exon sequencing of the KIT and MITF candidate genes identified a missense variant in KIT (rs1140732842, NC_009146.3:g.79566881T>C, p.T391A) predicted by SIFT and PROVEAN as not tolerated/deleterious. Three independent observers generated an Average Grade of White (AGW) phenotype score for 147 individuals based on photographs. The KIT variant demonstrates a significant QTL association to AGW (p = 3.3 × 10⁻¹²). Association with the MC1R Extension locus demonstrated that, although not in LD, MC1R e/e (chestnut) individuals had higher AGW scores than MC1R E/- individuals (p = 3.09 × 10⁻¹⁷). We also report complete linkage of the previously reported KIT W19 allele to this missense variant. We propose to term this variant W34, following the standardized nomenclature for white spotting variants within the equine KIT gene, and report its epistatic interaction with MC1R. Full article

(This article belongs to the Special Issue Novel Insights in Horse Breeding and Genetics)

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15 pages, 1854 KiB

Open AccessArticle

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

by Ester Bartolomé, Mercedes Valera, Jesús Fernández and Silvia Teresa Rodríguez-Ramilo

Animals 2022, 12(13), 1635; https://doi.org/10.3390/ani12131635 - 25 Jun 2022

Cited by 4 | Viewed by 1770

Abstract

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. Full article

(This article belongs to the Special Issue Novel Insights in Horse Breeding and Genetics)

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14 pages, 848 KiB

Open AccessArticle

Copy Number Variation (CNV): A New Genomic Insight in Horses

by Nora Laseca, Antonio Molina, Mercedes Valera, Alicia Antonini and Sebastián Demyda-Peyrás

Animals 2022, 12(11), 1435; https://doi.org/10.3390/ani12111435 - 2 Jun 2022

Cited by 6 | Viewed by 2624

Abstract

Copy number variations (CNVs) are a new-fangled source of genetic variation that can explain changes in the phenotypes in complex traits and diseases. In recent years, their study has increased in many livestock populations. However, the study and characterization of CNVs in equines is still very limited. Our study aimed to investigate the distribution pattern of CNVs, characterize CNV regions (CNVRs), and identify the biological pathways affected by CNVRs in the Pura Raza Española (PRE) breed. To achieve this, we analyzed high-density SNP genotyping data (670,804 markers) from a large cohort of 654 PRE horses. In total, we identified 19,902 CNV segments and 1007 CNV regions in the whole population. The length of the CNVs ranged from 1.024 kb to 4.55 Mb, while the percentage of the genome covered by CNVs was 4.4%. Interestingly, duplications were more abundant than deletions and mixed CNVRs. In addition, the distribution of CNVs across the chromosomes was not uniform, with ECA12 being the chromosome with the largest percentage of its genome covered (19.2%), while the highest numbers of CNVs were found in ECA20, ECA12, and ECA1. Our results showed that 71.4% of CNVRs contained genes involved in olfactory transduction, olfactory receptor activity, and immune response. Finally, 39.1% of the CNVs detected in our study were unique when compared with CNVRs identified in previous studies. To the best of our knowledge, this is the first attempt to reveal and characterize the CNV landscape in PRE horses, and it contributes to our knowledge of CNVs in equines, thus facilitating the understanding of genetic and phenotypic variations in the species. However, further research is still needed to confirm if the CNVs observed in the PRE are also linked to variations in the specific phenotypical differences in the breed. Full article

(This article belongs to the Special Issue Novel Insights in Horse Breeding and Genetics)

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15 pages, 865 KiB

Open AccessArticle

Mitochondrial DNA Variation Contributes to the Aptitude for Dressage and Show Jumping Ability in the Holstein Horse Breed

by Laura Engel, Doreen Becker, Thomas Nissen, Ingolf Russ, Georg Thaller and Nina Krattenmacher

Animals 2022, 12(6), 704; https://doi.org/10.3390/ani12060704 - 11 Mar 2022

Cited by 1 | Viewed by 2234

Abstract

Maternal lineages are considered an important factor in breeding. Mitochondrial DNA (mtDNA) is maternally inherited and plays an important role in energy metabolism. It has already been associated with energy consumption and performances, e.g., stamina in humans and racehorses. For now, corresponding studies are lacking for sport performance of warmblood breeds. MtDNA sequences were available for 271 Holstein mares from 75 maternal lineages. As all mares within a lineage showed identical haplotypes regarding the non-synonymous variants, we expanded our data set by also including non-sequenced mares and assigning them to the lineage-specific haplotype. This sample consisting of 6334 to 16,447 mares was used to perform mitochondrial association analyses using breeding values (EBVs) estimated on behalf of the Fédération Équestre Nationale (FN) and on behalf of the Holstein Breeding Association (HOL). The association analyses revealed 20 mitochondrial SNPs (mtSNPs) significantly associated with FN-EBVs and partly overlapping 20 mtSNPs associated with HOL-EBVs. The results indicated that mtDNA contributes to performance differences between maternal lineages. Certain mitochondrial haplogroups were associated with special talents for dressage or show jumping. The findings encourage to set up innovative genetic evaluation models that also consider information on maternal lineages. Full article

(This article belongs to the Special Issue Novel Insights in Horse Breeding and Genetics)

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