Horse Breeding and Genetics

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

Deadline for manuscript submissions: closed (15 May 2020) | Viewed by 84129

Special Issue Editors


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Guest Editor
Department of Agronomy, Food, Natural Resources, Animals & Environment, Università di Padova, Legnaro, PD, Italy
Interests: animal breeding; quantitative genetics; selection response; evolutionary biology; animal behaviour; functional traits; genetic diversity; horse; cattle; small populations
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell’Università 16, 35020 Legnaro, Padova, Italy
Interests: animal breeding; quantitative genetics; horse genomics, horse breeding management, small horse populations; cattle breeding management; small cattle populations

Special Issue Information

Dear Colleagues,

Studies on horse breeding and genetics are often dispersed in many scientific journals, and little attention is generally paid to topics such as horse genetic improvement and horse genomics, despite horses have been selected over time for a number of traits like speed, gaits, jumping performances, strength, or for more conventional traits like morphology or temperament. Worldwide, many horse breeds have been selected for preserving and improving traits of interest for sport performances or work. In addition, most horse breeds are small close populations with high levels of inbreeding and homozygosis, requiring appropriate breeding management. Novel traits such as fertility, longevity, and health have been recently included or should be included in breeding decisions. Furthermore, in spite of the current lack of genomic data, an implementation of genomic selection in equine management could provide substantial benefits, because of the long generation interval typical of horses. Additionally, new genomic features have increased interest in analyzing genetic diversity among horse breeds, and in attaining deep knowledge on the functionality of single or groups of genes involved in the expression of economical important traits. Gene networking or studies on other “omics-science” are also hot topics in horse breeding and genetics. We hereby are glad to invite authors to submit original manuscripts that address any aspect related to horse breeding and genetics. Topics of interest include the genetic improvement of novel and traditional traits, genetic correlations, and the response to selection; genome-wide association studies, genomic selection, and pathway analyses of traits; and genetic diversity, optimal contribution selection, characterization of horse genome variation, and studies on gene functionality.

Dr. Cristina Sartori
Prof. Roberto Mantovani
Guest Editors

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Keywords

  • Animal breeding
  • Genetic parameters
  • Heritability
  • Selection
  • Genomics
  • Genetic diversity
  • Inbreeding
  • Animal genetic resources
  • Horse
  • New traits
  • Conformation
  • Tenmperament
  • Sport horses
  • Racing horses
  • Riding horses
  • Draught horses

Published Papers (25 papers)

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Research

21 pages, 2754 KiB  
Article
Phylogenetic Relationships of Turkish Indigenous Donkey Populations Determined by Mitochondrial DNA D-loop Region
by Emel Özkan Ünal, Fulya Özdil, Selçuk Kaplan, Eser Kemal Gürcan, Serdar Genç, Sezen Arat and Mehmet İhsan Soysal
Animals 2020, 10(11), 1970; https://doi.org/10.3390/ani10111970 - 27 Oct 2020
Cited by 5 | Viewed by 3544
Abstract
In this study, to analyze the mtDNA D-loop region and the origin of the maternal lineages of 16 different donkey populations, and to assess the domestication of Turkish indigenous donkeys in seven geographical regions, we investigated the DNA sequences of the D-loop region [...] Read more.
In this study, to analyze the mtDNA D-loop region and the origin of the maternal lineages of 16 different donkey populations, and to assess the domestication of Turkish indigenous donkeys in seven geographical regions, we investigated the DNA sequences of the D-loop region of 315 indigenous donkeys from Turkey. A total of 54 haplotypes, resulting from 35 polymorphic regions (27 parsimoniously informative and 6 singleton sites), were defined. Twenty-eight of these haplotypes are unique (51.85%), and 26 are shared among different Turkish indigenous donkey populations. The most frequent haplotype was Hap 1 (45.71%), followed by two haplotypes (Hap 4, 15.55% and Hap 7, 5.39%). The breed genetic diversity, evaluated by the haplotype diversity (HD) and nucleotide diversity (πD), for the Turkish donkey populations ranged from 0.533 ± 0.180 (Tekirdağ–Malkara, MAL) to 0.933 ± 0.122 (Aydin, AYD), and from 0.01196 ± 0.0026 (Antalya, ANT) to 0.02101 ± 0.0041 (Aydin, AYD), respectively. We observed moderate-to-high levels of haplotype diversity and moderate nucleotide diversity, indicating plentiful genetic diversity in all of the Turkish indigenous donkey populations. Phylogenetic analysis (NJT) and median-joining network analysis established that all haplotypes were distinctly grouped into two major haplogroups. The results of AMOVA analyses, based on geographic structuring of Turkish native donkey populations, highlighted that the majority of the observed variance is due to differences among samples within populations. The observed differences between groups were found to be statistically significant. Comparison among Turkish indigenous donkey mtDNA D-loop regions and haplotypes, and different countries’ donkey breeds and wild asses, identified two clades and which is named Somali (Clade IV) and Nubian (Clade V) lineages. The results can be used to understand the origin of Turkish donkey populations clearly, and to resolve the phylogenetic relationship among all of the different regions. Full article
(This article belongs to the Special Issue Horse Breeding and Genetics)
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13 pages, 621 KiB  
Article
Survey of Risk Factors and Genetic Characterization of Ewe Neck in a World Population of Pura Raza Español Horses
by María Ripolles, María J. Sánchez-Guerrero, Davinia I. Perdomo-González, Pedro Azor and Mercedes Valera
Animals 2020, 10(10), 1789; https://doi.org/10.3390/ani10101789 - 1 Oct 2020
Cited by 7 | Viewed by 3265
Abstract
Ewe Neck is a relatively common morphological defect in Pura Raza Español (PRE) horses and other Baroque type horse breeds, which adversely affects the breeding industry; (1) objectives: to establish the within-breed prevalence, possible associated factors, and heritability of Ewe Neck in PRE [...] Read more.
Ewe Neck is a relatively common morphological defect in Pura Raza Español (PRE) horses and other Baroque type horse breeds, which adversely affects the breeding industry; (1) objectives: to establish the within-breed prevalence, possible associated factors, and heritability of Ewe Neck in PRE horses; (2) methods: the database included evaluations of 35,267 PRE horses. The Ewe Neck defect, 16 morphological traits, and 4 body indices were recorded. A Bayesian genetic animal model included the following systematic effects: sex, age, coat color, geographical area of the stud, and birth stud size were used; (3) results: in this PRE population, a total of 27.12% was affected. All the risk factors studied were significantly associated with the Ewe Neck score. The heritability coefficient for Ewe Neck score ranged from 0.23 to 0.34. Morphological traits (height at chest, length of back, head-neck junction, and bottom neck-body junction) and the indices (head and thoracic index) were those most closely related with the appearance of Ewe Neck; (4) conclusions: Ewe Neck is a relatively frequent defect in PRE horses, associated with risk factors and other morphological traits, with a moderate level of heritability. Breeding to select against this condition may therefore be beneficial in this breed. Full article
(This article belongs to the Special Issue Horse Breeding and Genetics)
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11 pages, 1537 KiB  
Article
Genetic Diversity and Population Structure of Polish Konik Horse Based on Individuals from All the Male Founder Lines and Microsatellite Markers
by Agnieszka Fornal, Katarzyna Kowalska, Tomasz Zabek, Agata Piestrzynska-Kajtoch, Adrianna D. Musiał and Katarzyna Ropka-Molik
Animals 2020, 10(9), 1569; https://doi.org/10.3390/ani10091569 - 3 Sep 2020
Cited by 10 | Viewed by 3116
Abstract
The Polish Konik horse is a primitive native breed included in the genetic resource conservation program in Poland. After World War II, intensive breeding work began, aimed at rebuilding this breed. Now, the whole Polish Konik population is represented by six male founder [...] Read more.
The Polish Konik horse is a primitive native breed included in the genetic resource conservation program in Poland. After World War II, intensive breeding work began, aimed at rebuilding this breed. Now, the whole Polish Konik population is represented by six male founder lines (Wicek, Myszak, Glejt I, Goraj, Chochlik and Liliput). Individuals representing all six paternal lineages were selected based on their breeding documentation. We performed a fragment analysis with 17 microsatellite markers (STRs) recommended by the International Society for Animal Genetics (ISAG). The genetic diversity and structure within the paternal lineages and the whole of the studied group were investigated. The average allelic richness was 6.497 for the whole studied group. The fixation index (FST; measure of population differentiation) was low (about 3%), the mean inbreeding coefficient (FIT) was low and close to 0, and the mean inbreeding index value (FIS) was negative. The mean expected heterozygosity was established at 0.7046 and was lower than the observed heterozygosity. The power of discrimination and power of exclusion were 99.9999%. The cumulative parentage exclusion probability equaled 99.9269% when one parental genotype was known and 99.9996% with both parents’ genotypic information was available. About 3% of the genetic variation was caused by differences in the breed origin and about 97% was attributed to differences among individuals. Our analysis revealed that there has been no inbreeding in the Polish Konik breed for the studied population. The genetic diversity was high, and its parameters were similar to those calculated for native breeds from other countries reported in the literature. However, due to the small number of breed founders and paternal lineages with unknown representation, the population’s genetic diversity and structure should be monitored regularly. Full article
(This article belongs to the Special Issue Horse Breeding and Genetics)
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13 pages, 827 KiB  
Article
Genetic Structure Analysis of the Pura Raza Español Horse Population through Partial Inbreeding Coefficient Estimation
by Davinia I. Perdomo-González, María J. Sánchez-Guerrero, Antonio Molina and Mercedes Valera
Animals 2020, 10(8), 1360; https://doi.org/10.3390/ani10081360 - 6 Aug 2020
Cited by 17 | Viewed by 3549
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Horse Breeding and Genetics)
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19 pages, 2138 KiB  
Article
Genetic Variability in the Italian Heavy Draught Horse from Pedigree Data and Genomic Information
by Enrico Mancin, Michela Ablondi, Roberto Mantovani, Giuseppe Pigozzi, Alberto Sabbioni and Cristina Sartori
Animals 2020, 10(8), 1310; https://doi.org/10.3390/ani10081310 - 30 Jul 2020
Cited by 14 | Viewed by 3242
Abstract
This study aimed to investigate the genetic diversity in the Italian Heavy Horse Breed from pedigree and genomic data. Pedigree information for 64,917 individuals were used to assess inbreeding level, effective population size (Ne), and effective numbers of founders and ancestors (f [...] Read more.
This study aimed to investigate the genetic diversity in the Italian Heavy Horse Breed from pedigree and genomic data. Pedigree information for 64,917 individuals were used to assess inbreeding level, effective population size (Ne), and effective numbers of founders and ancestors (fa/fe). Genotypic information from SNP markers were available for 267 individuals of both sexes, and it allowed estimating genomic inbreeding in two methods (observed versus expected homozygosity and from ROH) to study the breed genomic structure and possible selection signatures. Pedigree and genomic inbreeding were greatly correlated (0.65 on average). The inbreeding trend increased over time, apart from periods in which the base population enlarged, when Ne increased also. Recent bottlenecks did not occur in the genome, as fa/fe have shown. The observed homozygosity results were on average lower than expected, which was probably due to the use of French Breton stallions to support the breed genetic variability. High homozygous regions suggested that inbreeding increased in different periods. Two subpopulations were distinguished, which was probably due to the different inclusion of French animals by breeders. Few selection signatures were found at the population level, with possible associations to disease resistance. The almost low inbreeding rate suggested that despite the small breed size, conservation actions are not yet required. Full article
(This article belongs to the Special Issue Horse Breeding and Genetics)
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11 pages, 1346 KiB  
Article
Historical Changes and Description of the Current Hungarian Hucul Horse Population
by János Posta, Enikő Somogyvári and Sándor Mihók
Animals 2020, 10(7), 1242; https://doi.org/10.3390/ani10071242 - 21 Jul 2020
Cited by 7 | Viewed by 2576
Abstract
Gene conservation and management of small populations requires proper knowledge of the background and history of the breed. The aim of the study was the evaluation of population structure and changes of the Hungarian Hucul horse population. Population changes were described for the [...] Read more.
Gene conservation and management of small populations requires proper knowledge of the background and history of the breed. The aim of the study was the evaluation of population structure and changes of the Hungarian Hucul horse population. Population changes were described for the actual breeding stock as well as for groups of 10-year epochs reflecting major periods of change in the breed. Pedigree data of the registered population were analyzed using Endog and GRain software. The average value of equivalent complete generations was above nine for the actual breeding population. The longest generation interval was the sire-to-daughter pathway. The fe/f ratio had smaller changes than fa/fe ratio across the population history. Inbreeding and average relatedness as well as ancestral coefficients had increased during history. Kalinowski’s decomposition of inbreeding showed that present inbreeding is smaller than it was done earlier during the last 20 years. Due to the continuous imports from other breeder countries, the genetic variability increased during the evaluated time periods. Full article
(This article belongs to the Special Issue Horse Breeding and Genetics)
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10 pages, 673 KiB  
Article
Dynamics of the Inbreeding Coefficient and Homozygosity in Thoroughbred Horses in Russia
by Valery Kalashnikov, Lyudmila Khrabrova, Nina Blohina, Alexander Zaitcev and Tatyana Kalashnikova
Animals 2020, 10(7), 1217; https://doi.org/10.3390/ani10071217 - 17 Jul 2020
Cited by 6 | Viewed by 2919
Abstract
The Thoroughbred (TB) horse has hugely impacted the development of horse breeding around the world. This breed has unique genetic qualities due to having had a closed studbook for approximately 300 years. In Russia, TBs have been bred since the second half of [...] Read more.
The Thoroughbred (TB) horse has hugely impacted the development of horse breeding around the world. This breed has unique genetic qualities due to having had a closed studbook for approximately 300 years. In Russia, TBs have been bred since the second half of the 18th century. Here, we analyzed the genetic diversity and the inbreeding level in TB horses (n = 9680) for the period from 1990 to 2018 using polymorphisms of 17 microsatellite loci. We found that the genetic structure of the TB breed in Russia is represented by 100 alleles of panel STR (short tandem repeat) loci and has been stable for the past three decades. The conducted monitoring revealed a slight increase in the Wright’s inbreeding coefficient in all age and sex groups of TB horses (stallions, broodmares, and foals) from 0.68% to 0.90%, which was followed by a decrease in the degree of heterozygosity, Ho, from 68.5% to 67.6%. The Spearman’s rank correlation coefficient between the level of inbreeding and the degree of homozygosity was estimated (r = 0.022; p > 0.05). The obtained data on the DNA genotypes of horses of different breeds provide a unique base for the evaluation of genetic variability and the control of genetic variability of horses in selection programs. Full article
(This article belongs to the Special Issue Horse Breeding and Genetics)
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20 pages, 1823 KiB  
Article
Identification and Functional Annotation of Genes Related to Horses’ Performance: From GWAS to Post-GWAS
by Thayssa O. Littiere, Gustavo H. F. Castro, Maria del Pilar R. Rodriguez, Cristina M. Bonafé, Ana F. B. Magalhães, Rafael R. Faleiros, João I. G. Vieira, Cassiane G. Santos and Lucas L. Verardo
Animals 2020, 10(7), 1173; https://doi.org/10.3390/ani10071173 - 10 Jul 2020
Cited by 9 | Viewed by 4405
Abstract
Integration of genomic data with gene network analysis can be a relevant strategy for unraveling genetic mechanisms. It can be used to explore shared biological processes between genes, as well as highlighting transcription factors (TFs) related to phenotypes of interest. Unlike other species, [...] Read more.
Integration of genomic data with gene network analysis can be a relevant strategy for unraveling genetic mechanisms. It can be used to explore shared biological processes between genes, as well as highlighting transcription factors (TFs) related to phenotypes of interest. Unlike other species, gene–TF network analyses have not yet been well applied to horse traits. We aimed to (1) identify candidate genes associated with horse performance via systematic review, and (2) build biological processes and gene–TF networks from the identified genes aiming to highlight the most candidate genes for horse performance. Our systematic review considered peer-reviewed articles using 20 combinations of keywords. Nine articles were selected and placed into groups for functional analysis via gene networks. A total of 669 candidate genes were identified. From that, gene networks of biological processes from each group were constructed, highlighting processes associated with horse performance (e.g., regulation of systemic arterial blood pressure by vasopressin and regulation of actin polymerization and depolymerization). Transcription factors associated with candidate genes were also identified. Based on their biological processes and evidence from the literature, we identified the main TFs related to horse performance traits, which allowed us to construct a gene–TF network highlighting TFs and the most candidate genes for horse performance. Full article
(This article belongs to the Special Issue Horse Breeding and Genetics)
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13 pages, 3251 KiB  
Article
Simulation Study on the Integration of Health Traits in Horse Breeding Programs
by Lisa Büttgen, Johannes Geibel, Henner Simianer and Torsten Pook
Animals 2020, 10(7), 1153; https://doi.org/10.3390/ani10071153 - 7 Jul 2020
Cited by 6 | Viewed by 3316
Abstract
Osteochondrosis dissecans (OCD) is a degenerative disease of the cartilage leading to osseous fragments in the joints. It is important in horse breeding both from an animal welfare and an economic perspective. To study adequate breeding strategies to reduce OCD prevalence, a lifelike [...] Read more.
Osteochondrosis dissecans (OCD) is a degenerative disease of the cartilage leading to osseous fragments in the joints. It is important in horse breeding both from an animal welfare and an economic perspective. To study adequate breeding strategies to reduce OCD prevalence, a lifelike simulation of the breeding program of German Warmblood horses was performed with the R package MoBPS. We simulated complex breeding schemes of riding horses with different selection steps and realistic age structure, mimicking the German situation. As an example, osseous fragments in fetlock and hock joints were considered. Different scenarios, either using threshold selection, index selection or genomic index selection, respectively, were compared regarding their impact on health and performance traits. A rigorous threshold selection as well as the integration of OCD in a selection index at the stage of stallion licensing and chosen frequency of use in breeding cases on a selection index that includes breeding values for OCD traits performed best on a comparable level. Simply integrating OCD in this breeding value was less effective in terms of OCD reduction. Scenarios with a higher reduction of OCD also showed a slightly reduced improvement in the riding horse performance traits. Full article
(This article belongs to the Special Issue Horse Breeding and Genetics)
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9 pages, 247 KiB  
Article
Elo Method and Race Traits: A New Integrated System for Sport Horse Genetic Evaluation
by Andrea Giontella, Francesca Maria Sarti, Giovanni Paolo Biggio, Samira Giovannini, Raffaele Cherchi, Maurizio Silvestrelli and Camillo Pieramati
Animals 2020, 10(7), 1145; https://doi.org/10.3390/ani10071145 - 6 Jul 2020
Cited by 7 | Viewed by 2244
Abstract
This first survey on Sardinian Anglo-Arab horse (SAA) race traits highlights important aspects for the breeding purpose of this population. The heritability of the race traits were estimated through a trivariate model; the estimates were 0.39, 0.33, and 0.30 for the number of [...] Read more.
This first survey on Sardinian Anglo-Arab horse (SAA) race traits highlights important aspects for the breeding purpose of this population. The heritability of the race traits were estimated through a trivariate model; the estimates were 0.39, 0.33, and 0.30 for the number of placings, total earnings and Elo rating, respectively. The genetic progress could be improved by using an MT genetic evaluation of stallions and mares, combining information from competition traits. Full article
(This article belongs to the Special Issue Horse Breeding and Genetics)
17 pages, 2442 KiB  
Article
Genetic Parameters of Linear Type Traits Scored at 30 Months in Italian Heavy Draught Horse
by Fabio Folla, Cristina Sartori, Enrico Mancin, Giuseppe Pigozzi and Roberto Mantovani
Animals 2020, 10(6), 1099; https://doi.org/10.3390/ani10061099 - 25 Jun 2020
Cited by 8 | Viewed by 2766
Abstract
The Italian Heavy Draught Horse (IHDH) breed is selected based on linear type traits (LTT) evaluated at young age on six-month-old foals. However, animals retained for reproduction are scored also at adults age (about 30 months), and the evaluation is mandatory for the [...] Read more.
The Italian Heavy Draught Horse (IHDH) breed is selected based on linear type traits (LTT) evaluated at young age on six-month-old foals. However, animals retained for reproduction are scored also at adults age (about 30 months), and the evaluation is mandatory for the final official admission to the stud book of candidate mares and stallions. This study aimed to estimate genetic parameters of LTT scored at 30 months to consider if they are feasible for selection instead of using foal data and to reduce costs of selection plan. Data included 19 years of evaluation for 14 LTT and an overall score. Analyses were performed on 5835 females and 856 males via animal model. The heritability ranged from 0.03 (upper line length) to 0.40 (frame size). Traits of selection interest (head size and expression; temperament/movement; fleshiness; fore diameter; rear diameter) reported heritability between 0.21 and 0.31. High genetic correlations were obtained among traits related to muscular development, 0.73 on average. Positive genetic trends were found in traits of selection interest, already selected from foal type trait data. Accounting for genetic parameters estimated in adult animals instead in foals is feasible in IHDH selection. Full article
(This article belongs to the Special Issue Horse Breeding and Genetics)
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19 pages, 1374 KiB  
Article
Genetic Characterization of Native Donkey (Equus asinus) Populations of Turkey Using Microsatellite Markers
by Selen Yatkın, Fulya Özdil, Emel Özkan Ünal, Serdar Genç, Selçuk Kaplan, Eser Kemal Gürcan, Sezen Arat and Mehmet İhsan Soysal
Animals 2020, 10(6), 1093; https://doi.org/10.3390/ani10061093 - 24 Jun 2020
Cited by 8 | Viewed by 3155
Abstract
This study presents the first insights to the genetic diversity and structure of the Turkish donkey populations. The primary objectives were to detect the main structural features of Turkish donkeys by microsatellite markers. A panel of 17 microsatellite markers was applied for genotyping [...] Read more.
This study presents the first insights to the genetic diversity and structure of the Turkish donkey populations. The primary objectives were to detect the main structural features of Turkish donkeys by microsatellite markers. A panel of 17 microsatellite markers was applied for genotyping 314 donkeys from 16 locations of Turkey. One hundred and forty-two alleles were identified and the number of alleles per locus ranged from 4 to 12. The highest number of alleles was observed in AHT05 (12) and the lowest in ASB02 and HTG06 (4), while ASB17 was monomorphic. The mean HO in the Turkish donkey was estimated to be 0.677, while mean HE was 0.675. The polymorphic information content (PIC) was calculated for each locus and ranged from 0.36 (locus ASB02) to 0.98 (locus AHT05), which has the highest number of alleles per locus in the present study. The average PIC in our populations was 0.696. The average coefficient of gene differentiation (GST) over the 17 loci was 0.020 ± 0.037 (p < 0.01). The GST values for single loci ranged from −0.004 for LEX54 to 0.162 for COR082. Nei’s gene diversity index (Ht) for loci ranged from 0.445 (ASB02) to 0.890 (AHT05), with an average of 0.696. A Bayesian clustering method, the Structure software, was used for clustering algorithms of multi-locus genotypes to identify the population structure and the pattern of admixture within the populations. When the number of ancestral populations varied from K = 1 to 20, the largest change in the log of the likelihood function (ΔK) was when K = 2. The results for K = 2 indicate a clear separation between Clade I (KIR, CAT, KAR, MAR, SAN) and Clade II (MAL, MER, TOK, KAS, KUT, KON, ISP, ANT, MUG, AYD and KAH) populations. Full article
(This article belongs to the Special Issue Horse Breeding and Genetics)
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14 pages, 432 KiB  
Article
Genetics of Lifetime Reproductive Performance in Italian Heavy Draught Horse Mares
by Roberto Mantovani, Fabio Folla, Giuseppe Pigozzi, Shogo Tsuruta and Cristina Sartori
Animals 2020, 10(6), 1085; https://doi.org/10.3390/ani10061085 - 23 Jun 2020
Cited by 4 | Viewed by 2158
Abstract
Our aims were to find a phenotypic variable to express mares’ lifetime reproductive performance after 6 breeding seasons (BS) in Italian Heavy Draught Horse breed (IHDH), and to estimate its heritability. At first, 1487 mares in a training dataset were used to implement [...] Read more.
Our aims were to find a phenotypic variable to express mares’ lifetime reproductive performance after 6 breeding seasons (BS) in Italian Heavy Draught Horse breed (IHDH), and to estimate its heritability. At first, 1487 mares in a training dataset were used to implement and validate a set of predictive coefficients (LFR-C) or equations (LFR-E) to estimate a lifetime foaling rate (LFR) after 6 BS, i.e., the number of foals generated divided by the opportunities to do so. Then, 3033 mares in a dataset with at least 3 registered BS, was used to estimate LFR for mares with 3, 4, or 5 registered RS. This dataset contained actual (n = 1950) and estimated (n = 1443) LFR, obtained by LFR-C, and LFR-E; Arcsine transformation of LFR-C and LFR-E were also analyzed in single trait animal models to estimate heritability. Overall, the LFR showed a moderate but significant genetic variation, and the heritability of the trait was high (0.24) considering it is a fitness trait. The arcsine transformation of LFR did not show any improvement of heritability. The present study indicates the possible use of a linear LFR variable for breeding purposes in IHDH breed considering both complete and incomplete reproductive careers. Full article
(This article belongs to the Special Issue Horse Breeding and Genetics)
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14 pages, 885 KiB  
Article
Combining Threshold, Thurstonian and Classical Linear Models in Horse Genetic Evaluations for Endurance Competitions
by Isabel Cervantes, Juan Pablo Gutiérrez, Silvia García-Ballesteros and Luis Varona
Animals 2020, 10(6), 1075; https://doi.org/10.3390/ani10061075 - 22 Jun 2020
Cited by 4 | Viewed by 2153
Abstract
The racing time and rank at finish traits are commonly used for endurance horse breeding programs as a measure of their performance. Even so, given the nature of endurance competitions, many horses do not finish the race. However, the exclusion of non placed [...] Read more.
The racing time and rank at finish traits are commonly used for endurance horse breeding programs as a measure of their performance. Even so, given the nature of endurance competitions, many horses do not finish the race. However, the exclusion of non placed horses from the dataset could have an influence on the prediction of individual breeding values. The objective of the present paper was to develop a multitrait model including race time (T), rank (R) and placing (P), with different methodologies, to improve the genetic evaluation in endurance competitions in Spain. The database contained 6135 records from 1419 horses, with 35% of the records not placed. Horse pedigree included 10868 animals, with 52% Arab Horses. All models included gender, age and race effect as systematic effects and combined different random effects beside the animal and residual effects: rider, permanent environmental effect, and interaction horse-rider. The kilometers per race was included as a covariate for T. Heritabilities were estimated as moderately low, ranging from 0.06 to 0.14 for T, 0.09 to 0.15 for P, and 0.07 to 0.17 for R, depending on the model. T and R appeared mostly as inverse measures of the same trait due to their high genetic correlation, suggesting that T can be ignored in future genetic evaluations. P was the most independent trait from the genetic correlations. The possibility of simultaneously processing the threshold, Thurstonian and continuous traits has opened new opportunities for genetic evaluation in horse populations, and much more practical genetic evaluations can be done to help a proper genetic selection. Full article
(This article belongs to the Special Issue Horse Breeding and Genetics)
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11 pages, 1030 KiB  
Article
Genetic Variability and Population Structure in the Sardinian Anglo-Arab Horse
by Andrea Giontella, Francesca Maria Sarti, Irene Cardinali, Samira Giovannini, Raffaele Cherchi, Hovirag Lancioni, Maurizio Silvestrelli and Camillo Pieramati
Animals 2020, 10(6), 1018; https://doi.org/10.3390/ani10061018 - 11 Jun 2020
Cited by 13 | Viewed by 2343
Abstract
The Sardinian Anglo Arab (SAA) is a famous horse breed in Italy, with a significant historical background in the island of Sardinia. The aim of the study is to perform an evaluation of genetic variability in SAA using pedigree and mitochondrial data. In [...] Read more.
The Sardinian Anglo Arab (SAA) is a famous horse breed in Italy, with a significant historical background in the island of Sardinia. The aim of the study is to perform an evaluation of genetic variability in SAA using pedigree and mitochondrial data. In the current population, pedigree completeness was observed to be close to 100%, while the inbreeding coefficient and the average relatedness were lower than 3%. The ratio of effective founders/numbers of ancestors was 3.68 for the whole pedigree. The effective population size (Ne) computed by an individual increase in inbreeding (Ne_1) was 456.86, the Ne on equivalent generations (Ne_2) was 184.75, and this value slightly increased to 209.31 when computed by log-regression on equivalent generations (Ne_3). These results suggest the presence of crossbreeding and bottleneck phenomena, and they were compared with other Italian horses (reported in bibliography) to present the SAA among the Italian horse breeds scenario. Furthermore, the noteworthy mitochondrial variability reflects the use of a considerable number of founder mares; the contribution of L lineage was very important, probably because of the re-colonization from the Iberian Peninsula after the Last Glacial Maximum. Full article
(This article belongs to the Special Issue Horse Breeding and Genetics)
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15 pages, 2237 KiB  
Article
Genetic Diversity and Signatures of Selection in a Native Italian Horse Breed Based on SNP Data
by Michela Ablondi, Christos Dadousis, Matteo Vasini, Susanne Eriksson, Sofia Mikko and Alberto Sabbioni
Animals 2020, 10(6), 1005; https://doi.org/10.3390/ani10061005 - 8 Jun 2020
Cited by 24 | Viewed by 5160
Abstract
Horses are nowadays mainly used for sport and leisure activities, and several local breeds, traditionally used in agriculture, have been exposed to a dramatic loss in population size and genetic diversity. The loss of genetic diversity negatively impacts individual fitness and reduces the [...] Read more.
Horses are nowadays mainly used for sport and leisure activities, and several local breeds, traditionally used in agriculture, have been exposed to a dramatic loss in population size and genetic diversity. The loss of genetic diversity negatively impacts individual fitness and reduces the potential long-term survivability of a breed. Recent advances in molecular biology and bioinformatics have allowed researchers to explore biodiversity one step further. This study aimed to evaluate the loss of genetic variability and identify genomic regions under selection pressure in the Bardigiano breed based on GGP Equine70k SNP data. The effective population size based on Linkage Disequilibrium (Ne) was equal to 39 horses, and it showed a decline over time. The average inbreeding based on runs of homozygosity (ROH) was equal to 0.17 (SD = 0.03). The majority of the ROH were relatively short (91% were ≤2 Mbp long), highlighting the occurrence of older inbreeding, rather than a more recent occurrence. A total of eight ROH islands, shared among more than 70% of the Bardigiano horses, were found. Four of them mapped to known quantitative trait loci related to morphological traits (e.g., body size and coat color) and disease susceptibility. This study provided the first genome-wide scan of genetic diversity and selection signatures in an Italian native horse breed. Full article
(This article belongs to the Special Issue Horse Breeding and Genetics)
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8 pages, 874 KiB  
Article
GIBBSTHUR: Software for Estimating Variance Components and Predicting Breeding Values for Ranking Traits Based on a Thurstonian Model
by Luis Varona and Andrés Legarra
Animals 2020, 10(6), 1001; https://doi.org/10.3390/ani10061001 - 8 Jun 2020
Cited by 1 | Viewed by 2028
Abstract
(1) Background: Ranking traits are used commonly for breeding purposes in several equine populations; however, implementation is complex, because the position of a horse in a competition event is discontinuous and is influenced by the performance of its competitors. One approach to overcoming [...] Read more.
(1) Background: Ranking traits are used commonly for breeding purposes in several equine populations; however, implementation is complex, because the position of a horse in a competition event is discontinuous and is influenced by the performance of its competitors. One approach to overcoming these limitations is to assume an underlying Gaussian liability that represents a horse’s performance and dictates the observed classification in a competition event. That approach can be implemented using Montecarlo Markov Chain (McMC) techniques with a procedure known as the Thurstonian model. (2) Methods: We have developed software (GIBBSTHUR) that analyses ranking traits along with other continuous or threshold traits. The software implements a Gibbs Sampler scheme with a data-augmentation step for the liability of the ranking traits and provides estimates of the variance and covariance components and predictions of the breeding values and the average performance of the competitors in competition events. (3) Results: The results of a simple example are presented, in which it is shown that the procedure can recover the simulated variance and covariance components. In addition, the correlation between the simulated and predicted breeding values and between the estimates of the event effects and the average additive genetic effect of the competitors demonstrates the ability of the software to produce useful predictions for breeding purposes. (4) Conclusions: the GIBBSTHUR software provides a useful tool for the breeding evaluation of ranking traits in horses and is freely available in a public repository (https://github.com/lvaronaunizar/Gibbsthur). Full article
(This article belongs to the Special Issue Horse Breeding and Genetics)
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9 pages, 524 KiB  
Article
Mobility and Invasion Related Gene Expression Patterns in Equine Sarcoid
by Przemysław Podstawski, Wojciech Witarski, Tomasz Szmatoła, Monika Bugno-Poniewierska and Katarzyna Ropka-Molik
Animals 2020, 10(5), 880; https://doi.org/10.3390/ani10050880 - 19 May 2020
Cited by 1 | Viewed by 2336
Abstract
Sarcoids are the most common skin neoplasm in the Equidae family. Sarcoids are benign, but may cause severe damage in affected animals. Due to the high risk of post-treatment recurrence and the lack of an effective method of treatment, it is reasonable to [...] Read more.
Sarcoids are the most common skin neoplasm in the Equidae family. Sarcoids are benign, but may cause severe damage in affected animals. Due to the high risk of post-treatment recurrence and the lack of an effective method of treatment, it is reasonable to perform studies on the molecular aspects of this neoplasm. Therefore, the present studies analyzed five genes (cell cycle control binding protein alpha, coronin 1b, metalloproteinase 2, tissue inhibitor of metalloproteinases 3 and vimentin) related to cell mobility and invasion traits. Primary healthy fibroblasts and sarcoid cells were obtained from skin biopsies. Cell lines were cultured in two different medium types with different concentrations of foetal bovine serum (10% and 0.5% FBS) to study its influence on the analyzed genes. Gene expression was measured using the real-time PCR method. The results showed significant differences in two genes (coronin and vimentin) depending on culture conditions. In conclusion, the results enabled finding two new genes, related to cell motility and invasion traits, in which gene expression is deregulated. Results of the study may put new knowledge into the complexity of the genetic background of this disease and show the importance of further analysis on this subject. Full article
(This article belongs to the Special Issue Horse Breeding and Genetics)
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9 pages, 1003 KiB  
Article
Comparative Semen Microbiota Composition of a Stallion in a Taylorella equigenitalis Carrier and Non-Carrier State
by Carlota Quiñones-Pérez, Amparo Martínez, Francisco Crespo and José Luis Vega-Pla
Animals 2020, 10(5), 868; https://doi.org/10.3390/ani10050868 - 17 May 2020
Cited by 5 | Viewed by 2400
Abstract
Contagious equine metritis is receiving renewed attention due to the continuous detection of carriers in apparent agent-free farms. Interactions of Taylorella with the seminal microflora may be the plausible cause behind these spontaneous changes of the carrier state. Accordingly, the aim of this [...] Read more.
Contagious equine metritis is receiving renewed attention due to the continuous detection of carriers in apparent agent-free farms. Interactions of Taylorella with the seminal microflora may be the plausible cause behind these spontaneous changes of the carrier state. Accordingly, the aim of this study was to compare the differences in the seminal microbiome composition of one stallion in the contagious equine metritis carrier state and non-carrier state. Samples were cryopreserved after their extraction. Cell disruption was performed by high-speed homogenization in grinding media. Bacterial families were identified via V3 amplification of the 16S rRNA gene and Ion Torrent sequencing. Only bacterial families with relative abundance above 5% were taken into consideration. The positive sample contained a strong dominance of Corynebacteriaceae (37.75%) and Peptoniphilaceae (28.56%). In the negative sample, the Porphyromonadaceae (20.51%), Bacteroidaceae (19.25%) and Peptoniphilaceae (18.57%) families prevailed. In conclusion, the microbiome seminal composition varies when an individual carries Taylorella from when it is free of it. The wider differences were found in the Corynebacteriaceae, Porphyromonadaceae and Bacteroidaceae families. Due to the limitations of a single-case analysis, further studies are needed for a better understanding of the stallion seminal microflora interactions. Full article
(This article belongs to the Special Issue Horse Breeding and Genetics)
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11 pages, 1877 KiB  
Article
Mitochondrial DNA Survey Reveals the Lack of Accuracy in Maremmano Horse Studbook Records
by Andrea Giontella, Irene Cardinali, Hovirag Lancioni, Samira Giovannini, Camillo Pieramati, Maurizio Silvestrelli and Francesca Maria Sarti
Animals 2020, 10(5), 839; https://doi.org/10.3390/ani10050839 - 12 May 2020
Cited by 13 | Viewed by 2858
Abstract
The Maremmano horse is considered one of the most important Italian warmblood breeds which originated from an ancient population. In 1980, the National Association of Maremmano Breeders established the first Studbook that recorded 440 dams and four sire founders. In this study, we [...] Read more.
The Maremmano horse is considered one of the most important Italian warmblood breeds which originated from an ancient population. In 1980, the National Association of Maremmano Breeders established the first Studbook that recorded 440 dams and four sire founders. In this study, we selected the most significant maternal lines in terms of offspring (for a total of 74 lineages and 92 Maremmano horses) and analyzed their mitochondrial DNA control regions. We found a high variability, reflecting the importance of this local breed as a genetic resource to be preserved. Through multiple sampling, we then verified the pedigree information for 12 dam lines by matching genealogical data with mitochondrial haplotypes. A complete concordance was demonstrated in nine lineages, while for the other we highlighted a different number of haplotypes for each line (three in Fiorella, two in Nizza I, and two in Pomposina), thus suggesting that the information recorded in the Studbook could be wrong and the samples do not descend from the same maternal founder. Our combined analysis provides the opportunity to confirm the ancestry of animals and could be employed to prevent errors in pedigree data also for other breeds and species. Full article
(This article belongs to the Special Issue Horse Breeding and Genetics)
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8 pages, 979 KiB  
Article
Genetic Parameters and Inbreeding Effect of Morphological Traits in Sardinian Anglo Arab Horse
by Andrea Giontella, Francesca Maria Sarti, Giovanni Paolo Biggio, Samira Giovannini, Raffaele Cherchi, Camillo Pieramati and Maurizio Silvestrelli
Animals 2020, 10(5), 791; https://doi.org/10.3390/ani10050791 - 2 May 2020
Cited by 12 | Viewed by 4293
Abstract
The purpose of this study was to estimate the heritability and genetic correlations of four biometric measurements and an overall score (OS) in the Sardinian Anglo-Arab horse (SAA); moreover, the effect of inbreeding on these traits was investigated. A dataset with 43,624 horses [...] Read more.
The purpose of this study was to estimate the heritability and genetic correlations of four biometric measurements and an overall score (OS) in the Sardinian Anglo-Arab horse (SAA); moreover, the effect of inbreeding on these traits was investigated. A dataset with 43,624 horses (27,052 females and 16,572 males) was provided by the Agricultural Research Agency of Sardinia (AGRIS). Cannon bone circumference (BC), chest girth (CG), shoulder length (SL), and withers height (WH) were measured on 6033 SAA horses born in Sardinia between 1967 and 2005; beside the measurements, an overall score (OS) was taken comparing the morphology of each horse to an “ideal type” that is scored out of 100. The mean value is 20.5 cm for BC, 185.9 cm for CG, 67.6 cm for SL, 160.8 cm for WH, and 73.2 for the OS. The heritability estimates ranged from 0.78 to 0.23. The results allow to foresee high genetic progress through the breeding programs. The most affected trait by the inbreeding rate seems to only be the withers height. Full article
(This article belongs to the Special Issue Horse Breeding and Genetics)
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13 pages, 5030 KiB  
Article
Genetic Differentiation of the Two Types of Polish Cold-blooded Horses Included in the National Conservation Program
by Artur Gurgul, Igor Jasielczuk, Ewelina Semik-Gurgul, Klaudia Pawlina-Tyszko, Tomasz Szmatoła, Grażyna Polak and Monika Bugno-Poniewierska
Animals 2020, 10(3), 542; https://doi.org/10.3390/ani10030542 - 24 Mar 2020
Cited by 4 | Viewed by 3360
Abstract
The current role of the horse as a companion animal resulted in a decrease of interest in breeding and usage of draft horses. This meant that the population of cold-blooded horses in Poland has been dramatically reduced during the last decades. To avoid [...] Read more.
The current role of the horse as a companion animal resulted in a decrease of interest in breeding and usage of draft horses. This meant that the population of cold-blooded horses in Poland has been dramatically reduced during the last decades. To avoid impoverishment of the gene pool of the local horse population, a conservation program was established which involves draft horses and other local horse breeds. The draft horses bred in Poland can be subdivided in a few horse types of which the most widespread and consolidated are Sztumski and Sokólski horses. These two subpopulations are phenotypically diversified, however, the overall level of their genetic differentiation seems to be relatively low and not precisely determined, especially with the use of molecular markers. In reference to this, in this study we used Illumina genotyping arrays to describe in detail the genetic differentiation of these two cold-blooded horse populations. We describe the genetic distance between them, as well as within-population variation, admixture patterns, and level of relatedness within populations. We also made an attempt to detect genome regions divergently selected between those horses by the detection of diversifying selection signals. The results of this study provide initial evidence supporting breeding decisions that were made during conservation breeding program design and answer questions raised by the breeders of Sokólski and Sztumski horses concerning the level of their genetic variation and differentiation. Full article
(This article belongs to the Special Issue Horse Breeding and Genetics)
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15 pages, 1558 KiB  
Article
Identification of Novel lncRNAs Differentially Expressed in Placentas of Chinese Ningqiang Pony and Yili Horse Breeds
by Yabin Pu, Yanli Zhang, Tian Zhang, Jianlin Han, Yuehui Ma and Xuexue Liu
Animals 2020, 10(1), 119; https://doi.org/10.3390/ani10010119 - 11 Jan 2020
Cited by 7 | Viewed by 3128
Abstract
As a nutrient sensor, the placenta plays a key role in regulating fetus growth and development. Long non-coding RNAs (lncRNAs) have been shown to regulate growth-related traits. However, the biological function of lncRNAs in horse placentas remains unclear. To compare the expression patterns [...] Read more.
As a nutrient sensor, the placenta plays a key role in regulating fetus growth and development. Long non-coding RNAs (lncRNAs) have been shown to regulate growth-related traits. However, the biological function of lncRNAs in horse placentas remains unclear. To compare the expression patterns of lncRNAs in the placentas of the Chinese Ningqiang (NQ) and Yili (YL) breeds, we performed a transcriptome analysis using RNA sequencing (RNA-seq) technology. NQ is a pony breed with an average adult height at the withers of less than 106 cm, whereas that of YL is around 148 cm. Based on 813 million high-quality reads and stringent quality control procedures, 3011 transcripts coding for 1464 placental lncRNAs were identified and mapped to the horse reference genome. We found 107 differentially expressed lncRNAs (DELs) between NQ and YL, including 68 up-regulated and 39 down-regulated DELs in YL. Six (TBX3, CACNA1F, EDN3, KAT5, ZNF281, TMED2, and TGFB1) out of the 233 genes targeted by DELs were identified as being involved in limb development, skeletal myoblast differentiation, and embryo development. Two DELs were predicted to target the TBX3 gene, which was found to be under strong selection and associated with small body size in the Chinese Debao pony breed. This finding suggests the potential functional significance of placental lncRNAs in regulating horse body size. Full article
(This article belongs to the Special Issue Horse Breeding and Genetics)
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13 pages, 2506 KiB  
Article
Transcriptomic Analysis of Testicular Gene Expression in Normal and Cryptorchid Horses
by Haoyuan Han, Hong Dong, Qiuming Chen, Yuan Gao, Jun Li, Wantao Li, Ruihua Dang and Chuzhao Lei
Animals 2020, 10(1), 102; https://doi.org/10.3390/ani10010102 - 8 Jan 2020
Cited by 5 | Viewed by 3243
Abstract
Testes produce sperm, and investigations into gene expression in the testes will enhance the understanding of the roles of testicular genes in male reproduction. Cryptorchidism, the failure of one or both testes to descend into the scrotal sac, is a common congenital malformation [...] Read more.
Testes produce sperm, and investigations into gene expression in the testes will enhance the understanding of the roles of testicular genes in male reproduction. Cryptorchidism, the failure of one or both testes to descend into the scrotal sac, is a common congenital malformation in horses. The major clinical consequence of this abnormality is impaired fertility. The aim of this study was to analyze the expression patterns of testicular genes and to identify the differentially expressed genes (DEGs) in testes between cryptorchid and normal horses. In this study, the gene expression patterns in equine testes and the DEGs between mature descended testes (DTs) and undescended testes (UDTs) were identified by RNA-seq and validated by real-time qPCR. Our results provide comprehensive transcriptomic data on equine testes. The transcriptomic analysis revealed 11 affected genes that were downregulated in UDTs, possibly as a result of the higher temperature in the abdomen than in the scrotal sac. These 11 genes have previously been associated with male reproduction, and their downregulation might explain the impaired fertility of cryptorchid horses. Two homozygous missense mutations detected in horses with cryptorchidism were absent in normal horses and were listed as potential pathogenic mutations; these mutations should be verified in the future. Full article
(This article belongs to the Special Issue Horse Breeding and Genetics)
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14 pages, 3957 KiB  
Article
Whole-Genome Signatures of Selection in Sport Horses Revealed Selection Footprints Related to Musculoskeletal System Development Processes
by Siavash Salek Ardestani, Mehdi Aminafshar, Mohammad Bagher Zandi Baghche Maryam, Mohammad Hossein Banabazi, Mehdi Sargolzaei and Younes Miar
Animals 2020, 10(1), 53; https://doi.org/10.3390/ani10010053 - 26 Dec 2019
Cited by 15 | Viewed by 4087
Abstract
Selective breeding has led to gradual changes at the genome level of horses. Deciphering selective pressure patterns is progressive to understand how breeding strategies have shaped the sport horse genome; although, little is known about the genomic regions under selective pressures in sport [...] Read more.
Selective breeding has led to gradual changes at the genome level of horses. Deciphering selective pressure patterns is progressive to understand how breeding strategies have shaped the sport horse genome; although, little is known about the genomic regions under selective pressures in sport horse breeds. The major goal of this study was to shed light on genomic regions and biological pathways under selective pressures in sport horses. In this study, whole-genome sequences of 16 modern sport and 35 non-sport horses were used to investigate the genomic selective signals of sport performance, by employing fixation index, nucleotide diversity, and Tajima’s D approaches. A total number of 49 shared genes were identified using these approaches. The functional enrichment analysis for candidate genes revealed novel significant biological processes related to musculoskeletal system development, such as limb development and morphogenesis, having been targeted by selection in sport breeds. Full article
(This article belongs to the Special Issue Horse Breeding and Genetics)
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