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Sigurðardóttir H, Ablondi M, Kristjansson T, Lindgren G, Eriksson S. Genetic diversity and signatures of selection in Icelandic horses and Exmoor ponies. BMC Genomics 2024; 25:772. [PMID: 39118059 PMCID: PMC11308356 DOI: 10.1186/s12864-024-10682-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 08/01/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND The Icelandic horse and Exmoor pony are ancient, native breeds, adapted to harsh environmental conditions and they have both undergone severe historic bottlenecks. However, in modern days, the selection pressures on these breeds differ substantially. The aim of this study was to assess genetic diversity in both breeds through expected (HE) and observed heterozygosity (HO) and effective population size (Ne). Furthermore, we aimed to identify runs of homozygosity (ROH) to estimate and compare genomic inbreeding and signatures of selection in the breeds. RESULTS HO was estimated at 0.34 and 0.33 in the Icelandic horse and Exmoor pony, respectively, aligning closely with HE of 0.34 for both breeds. Based on genomic data, the Ne for the last generation was calculated to be 125 individuals for Icelandic horses and 42 for Exmoor ponies. Genomic inbreeding coefficient (FROH) ranged from 0.08 to 0.20 for the Icelandic horse and 0.12 to 0.27 for the Exmoor pony, with the majority of inbreeding attributed to short ROHs in both breeds. Several ROH islands associated with performance were identified in the Icelandic horse, featuring target genes such as DMRT3, DOCK8, EDNRB, SLAIN1, and NEURL1. Shared ROH islands between both breeds were linked to metabolic processes (FOXO1), body size, and the immune system (CYRIB), while private ROH islands in Exmoor ponies were associated with coat colours (ASIP, TBX3, OCA2), immune system (LYG1, LYG2), and fertility (TEX14, SPO11, ADAM20). CONCLUSIONS Evaluations of genetic diversity and inbreeding reveal insights into the evolutionary trajectories of both breeds, highlighting the consequences of population bottlenecks. While the genetic diversity in the Icelandic horse is acceptable, a critically low genetic diversity was estimated for the Exmoor pony, which requires further validation. Identified signatures of selection highlight the differences in the use of the two breeds as well as their adaptive trait similarities. The results provide insight into genomic regions under selection pressure in a gaited performance horse breed and various adaptive traits in small-sized native horse breeds. This understanding contributes to preserving genetic diversity and population health in these equine populations.
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Affiliation(s)
- Heiðrún Sigurðardóttir
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, P.O. Box 7023, Uppsala, 75007, Sweden.
- Faculty of Agricultural Sciences, Agricultural University of Iceland, Hvanneyri, Borgarbyggð, 311, Iceland.
| | - Michela Ablondi
- Department of Veterinary Science, University of Parma, Parma, 43126, Italy
| | - Thorvaldur Kristjansson
- Faculty of Agricultural Sciences, Agricultural University of Iceland, Hvanneyri, Borgarbyggð, 311, Iceland
| | - Gabriella Lindgren
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, P.O. Box 7023, Uppsala, 75007, Sweden
- Center for Animal Breeding and Genetics, Department of Biosystems, KU Leuven, Leuven, 3001, Belgium
| | - Susanne Eriksson
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, P.O. Box 7023, Uppsala, 75007, Sweden
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Herman M, Caceres AM, Albuquerque ALH, Leite RO, Araújo CET, Delfiol DJZ, Curi RA, Borges AS, Oliveira-Filho JP. DMRT3 Allele Frequencies in Batida- and Picada-Gaited Donkeys and Mules in Brazil. Animals (Basel) 2023; 13:3829. [PMID: 38136866 PMCID: PMC10741076 DOI: 10.3390/ani13243829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023] Open
Abstract
In Brazil, the production of mules with a comfortable gait primarily involves the breeding of marching saddle mules. This is achieved by crossing gaited Pêga donkeys with horses from the Mangalarga Marchador and Campolina breeds. The DMRT3:g.22999655C>A SNP is implicated in regulating gait phenotypes observed in various horse breeds, including the batida (CC) and picada (CA) gaits found in these horse breeds. We aimed to determine if genotypes influenced gait type in 159 mules and 203 donkeys genotyped for the DMRT3 SNP by PCR-RFLP analysis. About 47% of mules had the CC-genotype, while 53% had the CA-genotype. Donkeys predominantly had the CC-genotype (97%), and none had AA. Both CC- and CA-genotypes were evenly distributed among mules with the batida or picada gaits. In donkeys, the CC-genotype frequencies were consistent regardless of gait type. However, the CA-genotype was more common in picada-gaited donkeys than in batida-gaited donkeys. The prevalence of CA mules and the rare presence of the non-reference allele in donkeys align with previous findings in Mangalarga Marchador and Campolina horses. This suggests that the non-reference allele likely originated from the mares involved in donkey crosses. Our results also imply that factors beyond this variant, such as other genes and polymorphisms, influence gait traits in equids.
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Affiliation(s)
- Mariana Herman
- Department of Veterinary Clinical Science, School of Veterinary Medicine and Animal Science, São Paulo State University (Unesp), Botucatu 18618-681, Brazil; (M.H.); (A.M.C.); (A.L.H.A.); (R.O.L.); (A.S.B.)
| | - Amanda Manara Caceres
- Department of Veterinary Clinical Science, School of Veterinary Medicine and Animal Science, São Paulo State University (Unesp), Botucatu 18618-681, Brazil; (M.H.); (A.M.C.); (A.L.H.A.); (R.O.L.); (A.S.B.)
| | - Ana Luísa H. Albuquerque
- Department of Veterinary Clinical Science, School of Veterinary Medicine and Animal Science, São Paulo State University (Unesp), Botucatu 18618-681, Brazil; (M.H.); (A.M.C.); (A.L.H.A.); (R.O.L.); (A.S.B.)
| | - Raíssa O. Leite
- Department of Veterinary Clinical Science, School of Veterinary Medicine and Animal Science, São Paulo State University (Unesp), Botucatu 18618-681, Brazil; (M.H.); (A.M.C.); (A.L.H.A.); (R.O.L.); (A.S.B.)
| | - César Erineudo T. Araújo
- School of Veterinary Medicine, Centro Universitário Doutor Leão Sampaio (Unileão), Juazeiro do Norte 63041-140, Brazil;
| | - Diego José Z. Delfiol
- School of Veterinary Medicine, Federal University of Uberlandia, Uberlandia 38405-314, Brazil;
| | - Rogério A. Curi
- Department of Breeding and Animal Nutrition, School of Veterinary Medicine and Animal Science, São Paulo State University (Unesp), Botucatu 18618-681, Brazil;
| | - Alexandre S. Borges
- Department of Veterinary Clinical Science, School of Veterinary Medicine and Animal Science, São Paulo State University (Unesp), Botucatu 18618-681, Brazil; (M.H.); (A.M.C.); (A.L.H.A.); (R.O.L.); (A.S.B.)
| | - José P. Oliveira-Filho
- Department of Veterinary Clinical Science, School of Veterinary Medicine and Animal Science, São Paulo State University (Unesp), Botucatu 18618-681, Brazil; (M.H.); (A.M.C.); (A.L.H.A.); (R.O.L.); (A.S.B.)
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Sigurðardóttir H, Boije H, Albertsdóttir E, Kristjansson T, Rhodin M, Lindgren G, Eriksson S. The genetics of gaits in Icelandic horses goes beyond DMRT3, with RELN and STAU2 identified as two new candidate genes. Genet Sel Evol 2023; 55:89. [PMID: 38082412 PMCID: PMC10712087 DOI: 10.1186/s12711-023-00863-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND In domesticated animals, many important traits are complex and regulated by a large number of genes, genetic interactions, and environmental influences. The ability of Icelandic horses to perform the gait 'pace' is largely influenced by a single mutation in the DMRT3 gene, but genetic modifiers likely exist. The aim of this study was to identify novel genetic factors that influence pacing ability and quality of the gait through a genome-wide association study (GWAS) and correlate new findings to previously identified quantitative trait loci (QTL) and mutations. RESULTS Three hundred and seventy-two Icelandic horses were genotyped with the 670 K+ Axiom Equine Genotyping Array, of which 362 had gait scores from breeding field tests. A GWAS revealed several SNPs on Equus caballus chromosomes (ECA) 4, 9, and 20 that were associated (p < 1.0 × 10-5) with the breeding field test score for pace. The two novel QTL on ECA4 and 9 were located within the RELN and STAU2 genes, respectively, which have previously been associated with locomotor behavior in mice. Haplotypes were identified and the most frequent one for each of these two QTL had a large favorable effect on pace score. The second most frequent haplotype for the RELN gene was positively correlated with scores for tölt, trot, gallop, and canter. Similarly, the second most frequent haplotype for the STAU2 gene had favorable effects on scores for trot and gallop. Different genotype ratios of the haplotypes in the RELN and STAU2 genes were also observed in groups of horses with different levels of pacing ability. Furthermore, interactions (p < 0.05) were detected for the QTL in the RELN and STAU2 genes with the DMRT3 gene. The novel QTL on ECA4, 9, and 20, along with the effects of the DMRT3 variant, were estimated to account jointly for 27.4% of the phenotypic variance of the gait pace. CONCLUSIONS Our findings provide valuable information about the genetic architecture of pace beyond the contribution of the DMRT3 gene and indicate genetic interactions that contribute to the complexity of this trait. Further investigation is needed to fully understand the underlying genetic factors and interactions.
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Affiliation(s)
- Heiðrún Sigurðardóttir
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 75007, Uppsala, Sweden.
- Faculty of Agricultural Sciences, Agricultural University of Iceland, Borgarbyggð, 311, Hvanneyri, Iceland.
| | - Henrik Boije
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Elsa Albertsdóttir
- The Icelandic Agricultural Advisory Centre, Hagatorgi 1, 107, Reykjavik, Iceland
| | - Thorvaldur Kristjansson
- Faculty of Agricultural Sciences, Agricultural University of Iceland, Borgarbyggð, 311, Hvanneyri, Iceland
| | - Marie Rhodin
- Department of Anatomy, Physiology, and Biochemistry, Swedish University of Agricultural Sciences, P.O. Box 7011, 75007, Uppsala, Sweden
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 75007, Uppsala, Sweden
- Department of Biosystems, Center for Animal Breeding and Genetics, KU Leuven, Kasteelpark Arenberg 30, 3001, Leuven, Belgium
| | - Susanne Eriksson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 75007, Uppsala, Sweden
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Vincelette A. The Characteristics, Distribution, Function, and Origin of Alternative Lateral Horse Gaits. Animals (Basel) 2023; 13:2557. [PMID: 37627349 PMCID: PMC10451235 DOI: 10.3390/ani13162557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
This article traces the characteristics, origin, distribution, and function of alternative lateral horse gaits, i.e., intermediate speed lateral-sequence gaits. Such alternative lateral gaits (running walk, rack, broken pace, hard pace, and broken trot) are prized by equestrians today for their comfort and have been found in select horse breeds for hundreds of years and even exhibited in fossil equid trackways. After exploring the evolution and development of alternative lateral gaits via fossil equid trackways, human art, and historical writings, the functional and genetic factors that led to the genesis of these gaits are discussed. Such gaited breeds were particularly favored and spread by the Scythians, Celts, Turks, and Spaniards. Fast and low-swinging hard pacing gaits are common in several horse breeds of mountainous areas of East and North Asia; high-stepping rack and running walk gaits are often displayed in European and North and South American breeds; the broken pace is found in breeds of Central Asia, Southeast Asia, West Asia, Western North America, and Brazil in South America; and the broken trot occurs in breeds of North Asia, South Asia, the Southern United States, and Brazil in South America, inhabiting desert or marshy areas.
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Affiliation(s)
- Alan Vincelette
- Department of Pretheology, St. John's Seminary, 5012 Seminary Road, Camarillo, CA 93021, USA
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Rhodin M, Smit IH, Persson-Sjodin E, Pfau T, Gunnarsson V, Björnsdóttir S, Zetterberg E, Clayton HM, Hobbs SJ, Serra Bragança F, Hernlund E. Timing of Vertical Head, Withers and Pelvis Movements Relative to the Footfalls in Different Equine Gaits and Breeds. Animals (Basel) 2022; 12:ani12213053. [PMID: 36359178 PMCID: PMC9657284 DOI: 10.3390/ani12213053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/31/2022] [Accepted: 10/31/2022] [Indexed: 11/09/2022] Open
Abstract
Simple Summary Movement symmetry of the head and pelvis are used to measure lameness in horses in trot. Although head, pelvis and limb movements have been described, less is known about the temporal relationships between them. This information is needed to understand how the movements change with lameness. This is particularly relevant in gaited horses, such as the Icelandic horse that perform gaits such as tölt and pace, which are challenging to evaluate. This study used inertial measurement units to investigate head, withers and pelvis motion relative to limb movements in Icelandic, Warmblood and Iberian horses. Limb movements, together with vertical movements and lowest/highest positions of the head, withers and pelvis were calculated, and the relative timing of the events was compared across breeds. Additionally, data for tölt and pace were collected and evaluated in ridden Icelandic horses. For all gaits except walk and pace, the lowest/highest positions of the head/withers/pelvis were closely temporally related to midstance and hoof-off, respectively. Pelvic and withers total range of motion differed between all breeds. The Icelandic horses showed shorter stride duration and smaller movements of the upper body than the other breeds at trot, which may explain why lameness evaluation in this breed is challenging. Abstract Knowledge of vertical motion patterns of the axial body segments is a prerequisite for the development of algorithms used in automated detection of lameness. To date, the focus has been on the trot. This study investigates the temporal synchronization between vertical motion of the axial body segments with limb kinematic events in walk and trot across three popular types of sport horses (19 Warmbloods, 23 Iberians, 26 Icelandics) that are known to have different stride kinematics, and it presents novel data describing vertical motion of the axial body segments in tölting and pacing Icelandic horses. Inertial measurement unit sensors recorded limb kinematics, vertical motion of the axial body at all symmetrical gaits that the horse could perform (walk, trot, tölt, pace). Limb kinematics, vertical range of motion and lowest/highest positions of the head, withers and pelvis were calculated. For all gaits except walk and pace, lowest/highest positions of the pelvis and withers were found to be closely related temporally to midstance and start of suspension of the hind/fore quarter, respectively. There were differences in pelvic/withers range of motion between all breeds where the Icelandic horses showed the smallest motion, which may explain why lameness evaluation in this breed is challenging.
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Affiliation(s)
- Marie Rhodin
- Department of Anatomy Physiology and Biochemistry, Swedish University of Agricultural Sciences, S-750 07 Uppsala, Sweden
- Correspondence: ; Tel.: +461-867-2194
| | - Ineke H. Smit
- Department of Equine Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 112-114, NL-3584 CM Utrecht, The Netherlands
| | - Emma Persson-Sjodin
- Department of Anatomy Physiology and Biochemistry, Swedish University of Agricultural Sciences, S-750 07 Uppsala, Sweden
| | - Thilo Pfau
- Faculty of Kinesiology, University of Calgary, Calgary, AB T2N 1N4, Canada
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | | | - Sigridur Björnsdóttir
- Faculty of Agricultural Sciences, Agricultural University of Iceland, 311 Hvanneyri, Iceland
| | - Ebba Zetterberg
- Department of Anatomy Physiology and Biochemistry, Swedish University of Agricultural Sciences, S-750 07 Uppsala, Sweden
| | | | - Sarah J. Hobbs
- Research Centre for Applied Sport, Physical Activity and Performance, University of Central Lancashire, Preston PR1 2HE, UK
| | - Filipe Serra Bragança
- Department of Equine Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 112-114, NL-3584 CM Utrecht, The Netherlands
| | - Elin Hernlund
- Department of Anatomy Physiology and Biochemistry, Swedish University of Agricultural Sciences, S-750 07 Uppsala, Sweden
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Colpitts J, McLoughlin PD, Poissant J. Runs of homozygosity in Sable Island feral horses reveal the genomic consequences of inbreeding and divergence from domestic breeds. BMC Genomics 2022; 23:501. [PMID: 35820826 PMCID: PMC9275264 DOI: 10.1186/s12864-022-08729-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Understanding inbreeding and its impact on fitness and evolutionary potential is fundamental to species conservation and agriculture. Long stretches of homozygous genotypes, known as runs of homozygosity (ROH), result from inbreeding and their number and length can provide useful population-level information on inbreeding characteristics and locations of signatures of selection. However, the utility of ROH for conservation is limited for natural populations where baseline data and genomic tools are lacking. Comparing ROH metrics in recently feral vs. domestic populations of well understood species like the horse could provide information on the genetic health of those populations and offer insight into how such metrics compare between managed and unmanaged populations. Here we characterized ROH, inbreeding coefficients, and ROH islands in a feral horse population from Sable Island, Canada, using ~41 000 SNPs and contrasted results with those from 33 domestic breeds to assess the impacts of isolation on ROH abundance, length, distribution, and ROH islands. RESULTS ROH number, length, and ROH-based inbreeding coefficients (FROH) in Sable Island horses were generally greater than in domestic breeds. Short runs, which typically coalesce many generations prior, were more abundant than long runs in all populations, but run length distributions indicated more recent population bottlenecks in Sable Island horses. Nine ROH islands were detected in Sable Island horses, exhibiting very little overlap with those found in domestic breeds. Gene ontology (GO) enrichment analysis for Sable Island ROH islands revealed enrichment for genes associated with 3 clusters of biological pathways largely associated with metabolism and immune function. CONCLUSIONS This study indicates that Sable Island horses tend to be more inbred than their domestic counterparts and that most of this inbreeding is due to historical bottlenecks and founder effects rather than recent mating between close relatives. Unique ROH islands in the Sable Island population suggest adaptation to local selective pressures and/or strong genetic drift and highlight the value of this population as a reservoir of equine genetic variation. This research illustrates how ROH analyses can be applied to gain insights into the population history, genetic health, and divergence of wild or feral populations of conservation concern.
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Affiliation(s)
- Julie Colpitts
- Department of Biology, University of Saskatchewan, Saskatchewan, Canada.
| | | | - Jocelyn Poissant
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada.
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Wolfsberger WW, Ayala NM, Castro-Marquez SO, Irizarry-Negron VM, Potapchuk A, Shchubelka K, Potish L, Majeske AJ, Oliver LF, Lameiro AD, Martínez-Cruzado JC, Lindgren G, Oleksyk TK. Genetic diversity and selection in Puerto Rican horses. Sci Rep 2022; 12:515. [PMID: 35017609 PMCID: PMC8752667 DOI: 10.1038/s41598-021-04537-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/23/2021] [Indexed: 11/21/2022] Open
Abstract
Since the first Spanish settlers brought horses to America centuries ago, several local varieties and breeds have been established in the New World. These were generally a consequence of the admixture of the different breeds arriving from Europe. In some instances, local horses have been selectively bred for specific traits, such as appearance, endurance, strength, and gait. We looked at the genetics of two breeds, the Puerto Rican Non-Purebred (PRNPB) (also known as the "Criollo") horses and the Puerto Rican Paso Fino (PRPF), from the Caribbean Island of Puerto Rico. While it is reasonable to assume that there was a historic connection between the two, the genetic link between them has never been established. In our study, we started by looking at the genetic ancestry and diversity of current Puerto Rican horse populations using a 668 bp fragment of the mitochondrial DNA D-loop (HVR1) in 200 horses from 27 locations on the island. We then genotyped all 200 horses in our sample for the "gait-keeper" DMRT3 mutant allele previously associated with the paso gait especially cherished in this island breed. We also genotyped a subset of 24 samples with the Illumina Neogen Equine Community genome-wide array (65,000 SNPs). This data was further combined with the publicly available PRPF genomes from other studies. Our analysis show an undeniable genetic connection between the two varieties in Puerto Rico, consistent with the hypothesis that PRNPB horses represent the descendants of the original genetic pool, a mix of horses imported from the Iberian Peninsula and elsewhere in Europe. Some of the original founders of PRNRB population must have carried the "gait-keeper" DMRT3 allele upon arrival to the island. From this admixture, the desired traits were selected by the local people over the span of centuries. We propose that the frequency of the mutant "gait-keeper" allele originally increased in the local horses due to the selection for the smooth ride and other characters, long before the PRPF breed was established. To support this hypothesis, we demonstrate that PRNPB horses, and not the purebred PRPF, carry a signature of selection in the genomic region containing the DMRT3 locus to this day. The lack of the detectable signature of selection associated with the DMRT3 in the PRPF would be expected if this native breed was originally derived from the genetic pool of PRNPB horses established earlier and most of the founders already had the mutant allele. Consequently, selection specific to PRPF later focused on allels in other genes (including CHRM5, CYP2E1, MYH7, SRSF1, PAM, PRN and others) that have not been previously associated with the prized paso gait phenotype in Puerto Rico or anywhere else.
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Affiliation(s)
- Walter W Wolfsberger
- Department of Biological Sciences, Oakland University, Rochester, MI, USA
- Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
- Biology Department, Uzhhorod National University, Uzhhorod, Ukraine
| | - Nikole M Ayala
- Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | - Stephanie O Castro-Marquez
- Department of Biological Sciences, Oakland University, Rochester, MI, USA
- Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | | | - Antoliy Potapchuk
- Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | - Khrystyna Shchubelka
- Department of Biological Sciences, Oakland University, Rochester, MI, USA
- Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
- Biology Department, Uzhhorod National University, Uzhhorod, Ukraine
| | - Ludvig Potish
- Department of Forestry, Uzhhorod National University, Uzhhorod, Ukraine
| | - Audrey J Majeske
- Department of Biological Sciences, Oakland University, Rochester, MI, USA
- Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | - Luis Figueroa Oliver
- Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | - Alondra Diaz Lameiro
- Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | | | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Livestock Genetics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Taras K Oleksyk
- Department of Biological Sciences, Oakland University, Rochester, MI, USA.
- Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico.
- Biology Department, Uzhhorod National University, Uzhhorod, Ukraine.
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Alves AAC, Andrietta LT, Lopes RZ, Bussiman FO, Silva FFE, Carvalheiro R, Brito LF, Balieiro JCDC, Albuquerque LG, Ventura RV. Integrating Audio Signal Processing and Deep Learning Algorithms for Gait Pattern Classification in Brazilian Gaited Horses. FRONTIERS IN ANIMAL SCIENCE 2021. [DOI: 10.3389/fanim.2021.681557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This study focused on assessing the usefulness of using audio signal processing in the gaited horse industry. A total of 196 short-time audio files (4 s) were collected from video recordings of Brazilian gaited horses. These files were converted into waveform signals (196 samples by 80,000 columns) and divided into training (N = 164) and validation (N = 32) datasets. Twelve single-valued audio features were initially extracted to summarize the training data according to the gait patterns (Marcha Batida—MB and Marcha Picada—MP). After preliminary analyses, high-dimensional arrays of the Mel Frequency Cepstral Coefficients (MFCC), Onset Strength (OS), and Tempogram (TEMP) were extracted and used as input information in the classification algorithms. A principal component analysis (PCA) was performed using the 12 single-valued features set and each audio-feature dataset—AFD (MFCC, OS, and TEMP) for prior data visualization. Machine learning (random forest, RF; support vector machine, SVM) and deep learning (multilayer perceptron neural networks, MLP; convolution neural networks, CNN) algorithms were used to classify the gait types. A five-fold cross-validation scheme with 10 repetitions was employed for assessing the models' predictive performance. The classification performance across models and AFD was also validated with independent observations. The models and AFD were compared based on the classification accuracy (ACC), specificity (SPEC), sensitivity (SEN), and area under the curve (AUC). In the logistic regression analysis, five out of the 12 audio features extracted were significant (p < 0.05) between the gait types. ACC averages ranged from 0.806 to 0.932 for MFCC, from 0.758 to 0.948 for OS and, from 0.936 to 0.968 for TEMP. Overall, the TEMP dataset provided the best classification accuracies for all models. The most suitable method for audio-based horse gait pattern classification was CNN. Both cross and independent validation schemes confirmed that high values of ACC, SPEC, SEN, and AUC are expected for yet-to-be-observed labels, except for MFCC-based models, in which clear overfitting was observed. Using audio-generated data for describing gait phenotypes in Brazilian horses is a promising approach, as the two gait patterns were correctly distinguished. The highest classification performance was achieved by combining CNN and the rhythmic-descriptive AFD.
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Patterson Rosa L, Staiger EA, Martin K, Vierra M, Foster G, Lundquist E, Brooks SA, Lafayette C. Stock-type equine disciplines Hunter, Reining and Roping are associated with the A allele at the DMRT3 locus for gait phenotypes in the horse. Anim Genet 2021; 52:773-774. [PMID: 34250625 DOI: 10.1111/age.13110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2021] [Indexed: 11/28/2022]
Affiliation(s)
| | - E Ann Staiger
- Department of Animal Sciences, Auburn University, Auburn, AL, 36849, USA
| | | | | | | | | | - Samantha A Brooks
- Department of Animal Sciences, UF Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
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Microevolution operating in domestic animals: evidence from the Colombian Paso horses. Mamm Biol 2021. [DOI: 10.1007/s42991-021-00103-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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11
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Stefánsdóttir G, Jansson A, Ragnarsson S, Gunnarsson V. Speed of gaits in Icelandic horses and relationships to sex, age, conformation measurements and subjective judges’ scores. COMPARATIVE EXERCISE PHYSIOLOGY 2021. [DOI: 10.3920/cep200039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The aim was to measure the mean and maximum speed and the range of speed in all gaits of Icelandic horses shown at a breed evaluation field test (BEFT). In addition, the effect of speed on scores for the gaits and whether speed was affected by age, sex and conformation measurements were investigated. The study was carried out in Iceland on 266 horses (180 mares and 86 stallions). Horse speed and distance ridden were recorded by global positioning system during the riding assessment in BEFT. Conformation measurements and scores for each gait were obtained from the official studbook Worldfengur. The range of speed in walk, slow tölt, tölt, trot, pace, canter and gallop was, respectively, 1.5-2.2, 3.2-5.5, 4.6-10.6, 4.5-8.6, 7.1-11.9, 5.8-9.8 and 7.9-13.5 m/s (n=149-248). Scores for all gaits were affected by speed of the gait, with speed explaining most variance in scores for pace (53%) and least in scores for slow tölt and walk (2 and 3%, respectively). Stallions were faster than mares in tölt, trot, pace and canter (P<0.05). Horses aged ≥7 years and 6-year-olds were faster in pace and canter than 4-year-olds (P<0.05). Horse conformation measurements most affected speed in pace and walk, which were elevated with increased height at withers, height at croup, body length and length of front legs (P<0.05). In conclusion, objective measurements of speed in the gaits of Icelandic horses shown in a BEFT were documented for the first time. The information can be used to formulate requirements for gaits in BEFT and in competition manuals. Objective measurements of speed should be used in future assessments of gaits in Icelandic horses in BEFT, and thus improve standardisation and genetic evaluation of breeding horses.
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Affiliation(s)
- G.J. Stefánsdóttir
- Department of Equine Science, Hólar University, 551 Sauðárkrókur, Iceland
| | - A. Jansson
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, P.O. Box 7011, 750 07 Uppsala, Sweden
| | - S. Ragnarsson
- Department of Equine Science, Hólar University, 551 Sauðárkrókur, Iceland
| | - V. Gunnarsson
- Department of Equine Science, Hólar University, 551 Sauðárkrókur, Iceland
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12
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Ricard A, Duluard A. Genomic analysis of gaits and racing performance of the French trotter. J Anim Breed Genet 2020; 138:204-222. [PMID: 33249655 PMCID: PMC7898598 DOI: 10.1111/jbg.12526] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/04/2020] [Accepted: 11/11/2020] [Indexed: 01/16/2023]
Abstract
The aim was to disentangle gait characteristics from other qualities needed for racing performances with a genomic analysis of French trotters (FT). A sample of 1,390 horses were recruited, from which 46% were genotyped with Illumina chip of 54,602 SNPs, 49% with Affymetrix chip of 670,806 SNPs and 586 had a completed questionnaire on trotting technique. Racing performances cover the period 1996 to 2018. There were 252,368 FT-born; 96,617 qualified and 83,962 which participated in a race. After quality control, 377,611 SNPs were retained and imputed. Questionnaire described trotting technique over 13 questions which were summarized, after principal component analysis in 3 traits: pacer, heavy trot/gallop and other defects. GWAS and genomic evaluation were performed using single-step approach. We found 25 QTL for racing performances and 9 for trotting technique. Only DMRT3 mutation was significant for both traits. To tend to pace avoid the defect at gallop and lead to a better early career for earnings, less percentage of disqualified races at all ages and more harness than under saddle career. This is the portrait of AA genotype at DMRT3. We found 5 other QTL, not linked to gait traits, which might improve selection of genetically independent performance traits of earnings per races and percentage of finished races. For only earnings at different ages and in under saddle or harness races, genomic evaluation remains the best way to predict performances.
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Affiliation(s)
- Anne Ricard
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.,Pole Développement Innovation Recherche, IFCE, Gouffern en Auge, France
| | - Arnaud Duluard
- Département Elevage & Santé Animale, LeTrot, Paris, France
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13
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Moazemi I, Mohammadabadi MR, Mostafavi A, Esmailizadeh AK, Babenko OI, Bushtruk MV, Tkachenko SV, Stavetska RV, Klopenko NI. Polymorphism of DMRT3 Gene and Its Association with Body Measurements in Horse Breeds. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420100087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Abstract
Genetic testing in horses began in the 1960s, when parentage testing using blood group markers became the standard. In the 1990s, parentage testing shifted from evaluating blood groups to DNA testing. The development of genetics and genomics in both human and veterinarian medicine, along with continued technological advances in the last 2 decades, has helped unravel the causal variants for many horse traits. Genetic testing is also now possible for a variety of phenotypic and disease traits and is used to assist in breeding and clinical management decisions. This article describes the genetic tests that are currently available for horses.
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Affiliation(s)
- Rebecca R Bellone
- Department of Population Health and Reproduction Davis, CA 95616, USA; Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA.
| | - Felipe Avila
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA
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15
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Ahmad HI, Ahmad MJ, Jabbir F, Ahmar S, Ahmad N, Elokil AA, Chen J. The Domestication Makeup: Evolution, Survival, and Challenges. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00103] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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16
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Kierkegaard LS, Groeneveld LF, Kettunen A, Berg P. The status and need for characterization of Nordic animal genetic resources. ACTA AGR SCAND A-AN 2020. [DOI: 10.1080/09064702.2020.1722216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
| | | | - Anne Kettunen
- Farm Animal Section, NordGen – The Nordic Genetic Resource Center, Ås, Norway
- Nofima AS, Ås, Norway
| | - Peer Berg
- Farm Animal Section, NordGen – The Nordic Genetic Resource Center, Ås, Norway
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
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17
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Ayala-Valdovinos MA, Galindo-García J, Sánchez-Chiprés D, Duifhuis-Rivera T, Anguiano-Estrella R. A novel simple genotyping assay for detection of the 'Gait keeper' mutation in DMRT3 and allele frequencies in Azteca and Costa Rican Saddle Horse breeds. Mol Cell Probes 2020; 50:101506. [PMID: 31917254 DOI: 10.1016/j.mcp.2019.101506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 12/13/2019] [Accepted: 12/29/2019] [Indexed: 11/25/2022]
Abstract
The 'Gait keeper' mutation in the DMRT3 gene alters locomotion and gait patterns in horses. This mutation (C>A) has been found in all gaited breeds of horses analyzed but is absent in most non-gaited breeds. We developed a new mutagenically separated polymerase chain reaction (MS-PCR) based method for simple detection of horse DMRT3 genotype. Our method was applied in a preliminary study to determine DMRT3 allele frequencies in 78 Azteca horses (AZ) and 53 Costa Rican Saddle Horses (CRSH). We found a wild-type C allele frequency of 100% in the AZ horses. For the CRSH, the wild-type C frequency and mutant A allele frequency were 88.7% and 11.3%, respectively.
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Affiliation(s)
- Miguel Angel Ayala-Valdovinos
- Departamento de Producción Animal, División de Ciencias Veterinarias, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, A.P. 218 Zapopan 1, C.P. 45101, Zapopan, Jalisco, Mexico.
| | - Jorge Galindo-García
- Departamento de Producción Animal, División de Ciencias Veterinarias, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, A.P. 218 Zapopan 1, C.P. 45101, Zapopan, Jalisco, Mexico
| | - David Sánchez-Chiprés
- Departamento de Producción Animal, División de Ciencias Veterinarias, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, A.P. 218 Zapopan 1, C.P. 45101, Zapopan, Jalisco, Mexico
| | - Theodor Duifhuis-Rivera
- Departamento de Producción Animal, División de Ciencias Veterinarias, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, A.P. 218 Zapopan 1, C.P. 45101, Zapopan, Jalisco, Mexico
| | - Rubén Anguiano-Estrella
- Departamento de Producción Animal, División de Ciencias Veterinarias, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, A.P. 218 Zapopan 1, C.P. 45101, Zapopan, Jalisco, Mexico
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18
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Clayton HM, Hobbs SJ. A Review of Biomechanical Gait Classification with Reference to Collected Trot, Passage and Piaffe in Dressage Horses. Animals (Basel) 2019; 9:ani9100763. [PMID: 31623360 PMCID: PMC6826507 DOI: 10.3390/ani9100763] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 09/30/2019] [Accepted: 10/02/2019] [Indexed: 01/08/2023] Open
Abstract
Simple Summary This paper reviews the biomechanical classification of diagonally coordinated gaits of dressage horses, specifically, collected trot, passage and piaffe. Each gait was classified as a walking gait or a running gait based on three criteria: limb kinematics, ground reaction forces and center of mass mechanics. The data for trot and passage were quite similar and both were classified as running gaits according to all three criteria. In piaffe, the limbs have relatively long stance durations and there are no aerial phases, so kinematically it was classified as a walking gait. However, the shape of the vertical ground reaction force curve and the strategies used to control movements of the center of mass were more similar to those of a running gait. The hind limbs act as springs with limb compression increasing progressively from collected trot to passage to piaffe, whereas the forelimbs show less compression in passage and piaffe and behave more like struts. Abstract Gaits are typically classified as walking or running based on kinematics, the shape of the vertical ground reaction force (GRF) curve, and the use of inverted pendulum or spring-mass mechanics during the stance phase. The objectives of this review were to describe the biomechanical characteristics that differentiate walking and running gaits, then apply these criteria to classify and compare the enhanced natural gait of collected trot with the artificial gaits of passage and piaffe as performed by highly trained dressage horses. Limb contact and lift off times were used to determine contact sequence, limb phase, duty factor, and aerial phase duration. Ground reaction force data were plotted to assess fore and hind limb loading patterns. The center of mass (COM) trajectory was evaluated in relation to changes in potential and kinetic energy to assess the use of inverted pendulum and spring-mass mechanics. Collected trot and passage were classified as running gaits according to all three criteria whereas piaffe appears to be a hybrid gait combining walking kinematics with running GRFs and COM mechanics. The hind limbs act as springs and show greater limb compression in passage and piaffe compared with trot, whereas the forelimbs behave more like struts showing less compression in passage and piaffe than in trot.
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Affiliation(s)
- Hilary M Clayton
- Sport Horse Science, 3145 Sandhill Road, Mason, MI 48854, USA.
- College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA.
| | - Sarah Jane Hobbs
- Centre for Applied Sport and Exercise Sciences, University of Central Lancashire, Preston PR1 2HE, UK.
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19
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Fages A, Hanghøj K, Khan N, Gaunitz C, Seguin-Orlando A, Leonardi M, McCrory Constantz C, Gamba C, Al-Rasheid KAS, Albizuri S, Alfarhan AH, Allentoft M, Alquraishi S, Anthony D, Baimukhanov N, Barrett JH, Bayarsaikhan J, Benecke N, Bernáldez-Sánchez E, Berrocal-Rangel L, Biglari F, Boessenkool S, Boldgiv B, Brem G, Brown D, Burger J, Crubézy E, Daugnora L, Davoudi H, de Barros Damgaard P, de Los Ángeles de Chorro Y de Villa-Ceballos M, Deschler-Erb S, Detry C, Dill N, do Mar Oom M, Dohr A, Ellingvåg S, Erdenebaatar D, Fathi H, Felkel S, Fernández-Rodríguez C, García-Viñas E, Germonpré M, Granado JD, Hallsson JH, Hemmer H, Hofreiter M, Kasparov A, Khasanov M, Khazaeli R, Kosintsev P, Kristiansen K, Kubatbek T, Kuderna L, Kuznetsov P, Laleh H, Leonard JA, Lhuillier J, Liesau von Lettow-Vorbeck C, Logvin A, Lõugas L, Ludwig A, Luis C, Arruda AM, Marques-Bonet T, Matoso Silva R, Merz V, Mijiddorj E, Miller BK, Monchalov O, Mohaseb FA, Morales A, Nieto-Espinet A, Nistelberger H, Onar V, Pálsdóttir AH, Pitulko V, Pitskhelauri K, Pruvost M, Rajic Sikanjic P, Rapan Papeša A, Roslyakova N, Sardari A, Sauer E, Schafberg R, Scheu A, Schibler J, Schlumbaum A, Serrand N, Serres-Armero A, Shapiro B, Sheikhi Seno S, Shevnina I, Shidrang S, Southon J, Star B, Sykes N, Taheri K, Taylor W, Teegen WR, Trbojević Vukičević T, Trixl S, Tumen D, Undrakhbold S, Usmanova E, Vahdati A, Valenzuela-Lamas S, Viegas C, Wallner B, Weinstock J, Zaibert V, Clavel B, Lepetz S, Mashkour M, Helgason A, Stefánsson K, Barrey E, Willerslev E, Outram AK, Librado P, Orlando L. Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series. Cell 2019; 177:1419-1435.e31. [PMID: 31056281 PMCID: PMC6547883 DOI: 10.1016/j.cell.2019.03.049] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 02/14/2019] [Accepted: 03/27/2019] [Indexed: 11/30/2022]
Abstract
Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (≥1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modern legacy of past equestrian civilizations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN "speed gene," only rose in popularity within the last millennium. Finally, the development of modern breeding impacted genetic diversity more dramatically than the previous millennia of human management.
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Affiliation(s)
- Antoine Fages
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France; Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Kristian Hanghøj
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France; Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Naveed Khan
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark; Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan
| | - Charleen Gaunitz
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Andaine Seguin-Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France; Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Michela Leonardi
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark; Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Christian McCrory Constantz
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark; Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Cristina Gamba
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Khaled A S Al-Rasheid
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Silvia Albizuri
- Seminari d'Estudis i Recerques Prehistoriques, HAR2017-87695-P, Universitat de Barcelona, Barcelona, Spain
| | - Ahmed H Alfarhan
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Morten Allentoft
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Saleh Alquraishi
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - David Anthony
- Anthropology Department, Hartwick College 1, Oneonta, NY 13820, USA
| | | | - James H Barrett
- McDonald Institute for Archaeological Research, Department of Archaeology, University of Cambridge, Cambridge CB2 3ER, UK
| | | | - Norbert Benecke
- Deutsches Archäologisches Institut (DAI), 14195 Berlin, Germany
| | - Eloísa Bernáldez-Sánchez
- Laboratorio de Paleontologia y Paleobiologia, Instituto Andaluz del Patrimonio Historico, Sevilla, Spain
| | - Luis Berrocal-Rangel
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Fereidoun Biglari
- Department of Paleolithic, National Museum of Iran, 1136918111, Tehran, Iran
| | - Sanne Boessenkool
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Postbox 1066, Blindern, 0316 Oslo, Norway
| | - Bazartseren Boldgiv
- Ecology Group, Department of Biology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar 14201, Mongolia
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, Veterinary University of Vienna, 1210 Vienna, Austria
| | - Dorcas Brown
- Anthropology Department, Hartwick College 1, Oneonta, NY 13820, USA
| | - Joachim Burger
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg-University Mainz, 55099 Mainz, Germany
| | - Eric Crubézy
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
| | - Linas Daugnora
- Osteological material research laboratory, Klaipėda university, Klaipėda 92294, Lithuania
| | - Hossein Davoudi
- Department of Osteology, National Museum of Iran, 1136918111, Tehran, Iran; Department of Archaeology, Faculty of Humanities, Tarbiat Modares University, Tehran, Iran
| | | | | | - Sabine Deschler-Erb
- Integrative prähistorische und naturwissenschaftliche Archäologie (IPNA), 4055 Basel, Switzerland
| | - Cleia Detry
- Uniarq, Centro de Arqueologia da Universidade de Lisboa, Faculdade de Letras da Universidade de Lisboa, 1600-214 Lisboa, Portugal
| | - Nadine Dill
- Integrative prähistorische und naturwissenschaftliche Archäologie (IPNA), 4055 Basel, Switzerland
| | - Maria do Mar Oom
- CE3C-Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Anna Dohr
- Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig-Maximilians-University Munich, 80539 München, Germany; ArchaeoBioCenter, Ludwig-Maximilians-University Munich, 80539 München, Germany; Institute of Palaeoanatomy, Domestication Research and History of Veterinary Medicine, Ludwig-Maximilians-University Munich, 80539 München, Germany
| | | | | | - Homa Fathi
- Department of Osteology, National Museum of Iran, 1136918111, Tehran, Iran; Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran
| | - Sabine Felkel
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, Veterinary University of Vienna, 1210 Vienna, Austria
| | | | - Esteban García-Viñas
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Mietje Germonpré
- Operational Direction, Earth and History of Life, Royal Belgian Institute of Natural Sciences, 1000, Brussels, Belgium
| | - José D Granado
- Integrative prähistorische und naturwissenschaftliche Archäologie (IPNA), 4055 Basel, Switzerland
| | - Jón H Hallsson
- Faculty of Agricultural and Environmental Sciences, The Agricultural University of Iceland, Keldnaholti - Árleyni 22, 112 Reykjavík, Iceland
| | - Helmut Hemmer
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg-University Mainz, 55099 Mainz, Germany
| | - Michael Hofreiter
- University of Potsdam, Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, 14476 Potsdam, Germany
| | - Aleksei Kasparov
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg 191186, Russia
| | | | - Roya Khazaeli
- Department of Osteology, National Museum of Iran, 1136918111, Tehran, Iran; Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran
| | - Pavel Kosintsev
- Institute of Plant and Animal Ecology, Urals Branch of the Russian Academy of Sciences, Ekaterinburg 620144, Russia
| | | | - Tabaldiev Kubatbek
- Department of History, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan
| | - Lukas Kuderna
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Catalonia 08003, Spain
| | - Pavel Kuznetsov
- Samara State University of Social Science and Education, Samara, Russia
| | - Haeedeh Laleh
- Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran; Department of Archaeology, Faculty of Humanities, University of Tehran, Iran
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), 41092 Sevilla, Spain
| | - Johanna Lhuillier
- Laboratoire Archéorient, UMR 5133, Maison de l'Orient et de la Méditerranée, 69365 Lyon Cedex 7, France
| | | | - Andrey Logvin
- Laboratory for Archaeological Research, Faculty of History and Law, Kostanay State University, Kostanay, Kazakhstan
| | - Lembi Lõugas
- Archaeological Research Collection, Tallinn University, 10130 Tallinn, Estonia
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany; Faculty of Life Sciences, Albrecht Daniel Thaer-Institute, Humboldt University Berlin, 10115 Berlin, Germany
| | - Cristina Luis
- Museu Nacional de História Natural e da Ciência, Universidade de Lisboa, Lisboa, Portugal; Centro Interuniversitário de História das Ciências e da Tecnologia (CIUHCT), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal; Instituto Universitário de Lisboa (ISCTE-IUL), CIES-IUL, Lisboa, Portugal
| | - Ana Margarida Arruda
- Uniarq, Centro de Arqueologia da Universidade de Lisboa, Faculdade de Letras da Universidade de Lisboa, 1600-214 Lisboa, Portugal
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Catalonia 08003, Spain; Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193, Cerdanyola del Vallès, Barcelona, Spain
| | | | - Victor Merz
- S.Toraighyrov Pavlodar State University, Joint Research Center for Archeological Studies, 637000 Pavlodar, Kazakhstan
| | - Enkhbayar Mijiddorj
- Department of Archaeology, Ulaanbaatar State University, Ulaanbaatar 51, Mongolia
| | - Bryan K Miller
- University of Oxford, Faculty of History, George Street, Oxford, OX1 2RL, UK
| | - Oleg Monchalov
- Samara State University of Social Science and Education, Samara, Russia
| | - Fatemeh A Mohaseb
- Department of Osteology, National Museum of Iran, 1136918111, Tehran, Iran; Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran; Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 75005 Paris, France
| | - Arturo Morales
- Laboratory of Archaeozoology, Department Biología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ariadna Nieto-Espinet
- Archaeology of Social Dynamics Group (ADS), Institució Milà i Fontanals-Consejo Superior de Investigaciones Científicas (IMF-CSIC), 08001 Barcelona, Spain; Grup d'Investigació Prehistòrica, HAR2016-78277-R, Universitat de Lleida, 25003 Lleida, Spain
| | - Heidi Nistelberger
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Postbox 1066, Blindern, 0316 Oslo, Norway
| | - Vedat Onar
- Osteoarchaeology Practice and Research Center and Department of Anatomy, Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, 34320, Avcılar, Istanbul, Turkey
| | - Albína H Pálsdóttir
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Postbox 1066, Blindern, 0316 Oslo, Norway; Faculty of Agricultural and Environmental Sciences, The Agricultural University of Iceland, Keldnaholti - Árleyni 22, 112 Reykjavík, Iceland
| | - Vladimir Pitulko
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg 191186, Russia
| | | | - Mélanie Pruvost
- Université de Bordeaux, CNRS, UMR 5199-PACEA, 33615 Pessac Cedex, France
| | | | | | | | - Alireza Sardari
- Iranian Center for Archaeological Research (ICAR), Iranian Cultural Heritage, Handicrafts, and Tourism Organization (ICHHTO), 1136918111, Tehran, Iran
| | - Eberhard Sauer
- School of History, Classics and Archaeology, The University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Renate Schafberg
- Central Natural Science Collections (ZNS), Martin Luther University Halle-Wittenberg, Domplatz 4, 06108 Halle (Saale), Germany
| | - Amelie Scheu
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg-University Mainz, 55099 Mainz, Germany
| | - Jörg Schibler
- Integrative prähistorische und naturwissenschaftliche Archäologie (IPNA), 4055 Basel, Switzerland
| | - Angela Schlumbaum
- Integrative prähistorische und naturwissenschaftliche Archäologie (IPNA), 4055 Basel, Switzerland
| | - Nathalie Serrand
- Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 75005 Paris, France; INRAP Guadeloupe, Centre de recherches archéologiques, UMR 7209 CNRS/MNHN, 97113 Gourbeyre, Guadeloupe
| | - Aitor Serres-Armero
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Catalonia 08003, Spain
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology and Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Shiva Sheikhi Seno
- Department of Osteology, National Museum of Iran, 1136918111, Tehran, Iran; Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran; Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 75005 Paris, France
| | - Irina Shevnina
- Laboratory for Archaeological Research, Faculty of History and Law, Kostanay State University, Kostanay, Kazakhstan
| | - Sonia Shidrang
- Saeedi Institute for Advanced Studies, University of Kashan, Kashan 87317-51167, Iran
| | - John Southon
- Department Earth System Science, University of California, Irvine, Irvine, CA 92697, USA
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Postbox 1066, Blindern, 0316 Oslo, Norway
| | - Naomi Sykes
- Department of Archaeology, University of Nottingham, Nottingham, NG7 2RD, UK; Department of Archaeology, University of Exeter, Exeter, EX4 4QE, UK
| | - Kamal Taheri
- Kermanshah Regional Water Authority, Kermanshah 67145-1466, Iran
| | - William Taylor
- Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Wolf-Rüdiger Teegen
- Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig-Maximilians-University Munich, 80539 München, Germany; ArchaeoBioCenter, Ludwig-Maximilians-University Munich, 80539 München, Germany
| | - Tajana Trbojević Vukičević
- Department of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, University of Zagreb, 10 000 Zagreb, Croatia
| | - Simon Trixl
- Institute of Palaeoanatomy, Domestication Research and History of Veterinary Medicine, Ludwig-Maximilians-University Munich, 80539 München, Germany
| | - Dashzeveg Tumen
- Department of Anthropology and Archaeology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar 14201, Mongolia
| | - Sainbileg Undrakhbold
- Ecology Group, Department of Biology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar 14201, Mongolia
| | - Emma Usmanova
- Saryarka Archaeological Institute of Buketov Karaganda State University, Karaganda 100074, Kazakhstan
| | - Ali Vahdati
- Iranian Center for Archaeological Research (ICAR), Iranian Cultural Heritage, Handicrafts, and Tourism Organization (ICHHTO), 1136918111, Tehran, Iran
| | - Silvia Valenzuela-Lamas
- Archaeology of Social Dynamics Group (ADS), Institució Milà i Fontanals-Consejo Superior de Investigaciones Científicas (IMF-CSIC), 08001 Barcelona, Spain
| | - Catarina Viegas
- Uniarq, Centro de Arqueologia da Universidade de Lisboa, Faculdade de Letras da Universidade de Lisboa, 1600-214 Lisboa, Portugal
| | - Barbara Wallner
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, Veterinary University of Vienna, 1210 Vienna, Austria
| | - Jaco Weinstock
- Faculty of Humanities (Archaeology), University of Southampton, Avenue Campus, Highfield, Southampton SO17 1BF, UK
| | - Victor Zaibert
- Scientific Research Institute of Archaeology and Steppe Civilizations, Al Farabi Kazakh National University, 050040 Almaty, Kazakhstan
| | - Benoit Clavel
- Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 75005 Paris, France
| | - Sébastien Lepetz
- Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 75005 Paris, France
| | - Marjan Mashkour
- Department of Osteology, National Museum of Iran, 1136918111, Tehran, Iran; Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran; Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 75005 Paris, France
| | | | | | - Eric Barrey
- GABI UMR1313, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Alan K Outram
- Department of Archaeology, University of Exeter, Exeter, EX4 4QE, UK
| | - Pablo Librado
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France; Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France; Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark.
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20
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MHC haplotype diversity in Icelandic horses determined by polymorphic microsatellites. Genes Immun 2019; 20:660-670. [PMID: 31068686 DOI: 10.1038/s41435-019-0075-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/07/2019] [Accepted: 03/18/2019] [Indexed: 01/31/2023]
Abstract
The Icelandic horse has been maintained as a closed population in its eponymous homeland for many generations, with no recorded introductions of new horses of any breed since the year 1000 CE. Here we determined the diversity of major histocompatibility complex (MHC) haplotypes in 156 Icelandic horses from two groups, based on a panel of 12 polymorphic intra-MHC microsatellites tested in families of various composition. We identified a total of 79 MHC haplotypes in these two groups, including one documented intra-MHC recombination event from a total of 147 observed meioses. None of these MHC haplotypes have been previously described in any other horse breed. Only one MHC homozygote was found in the entire population studied. These results indicate a very high level of MHC heterozygosity and haplotype diversity in the Icelandic horse. The environment in Iceland is remarkable for its lack of common agents of equine infectious disease, including equine herpesvirus type 1, influenza virus, and streptococcus equi. The driving forces for maintenance of MHC heterozygosity in Icelandic horses must thus be sought outside of these major horse pathogens. Based on our results, we propose that intra-MHC recombination may play a major role in the generation of novel haplotypes.
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21
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Giantsis IA, Diakakis NE, Avdi M. Genetic Composition and Evaluation of the Status of a Non-descript Indigenous Horse Population From Greece, the Macedonian Pacer. J Equine Vet Sci 2018. [DOI: 10.1016/j.jevs.2018.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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22
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Novoa-Bravo M, Jäderkvist Fegraeus K, Rhodin M, Strand E, García LF, Lindgren G. Selection on the Colombian paso horse's gaits has produced kinematic differences partly explained by the DMRT3 gene. PLoS One 2018; 13:e0202584. [PMID: 30118522 PMCID: PMC6097835 DOI: 10.1371/journal.pone.0202584] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 08/06/2018] [Indexed: 11/18/2022] Open
Abstract
The Colombian paso horse, the most important horse breed in Colombia, performs specific and particular gaits (paso fino, trocha, and Colombian trot), which display different footfall patterns and stride frequencies. The breed has been selected for gait and conformation for more than 50 years and we hypothesize that this selection has led to kinematic differences of the gaits that can be explained by different genetic variants. Hence, the aims of the study were: 1. To identify if there are any differences in the kinematic and genetic variants between the Colombian paso horse’s gaits. 2. To evaluate if and how much the gait differences were explained by the nonsense mutation in the DMRT3 gene and 3. To evaluate these results for selecting and controlling the horses gait performance. To test our hypotheses, kinematic data, microsatellites and DMRT3 genotypes for 187 Colombian paso horses were analyzed. The results indicated that there are significant kinematic and DMRT3 differences between the Colombian paso horse’s gaits, and those parameters can be used partially to select and control the horses gait performance. However, the DMRT3 gene does not play a major role in controlling the trocha and the Colombian trot gaits. Therefore, modifying genes likely influence these gaits. This study may serve as a foundation for implementing a genetic selection program in the Colombian paso horse and future gene discovery studies for locomotion pattern in horses.
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Affiliation(s)
- Miguel Novoa-Bravo
- Genética Animal de Colombia Ltda. Bogotá, Colombia
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Uppsala, Sweden
- Department of Biology, National University of Colombia, Bogotá, Cundinamarca, Colombia
- * E-mail:
| | - Kim Jäderkvist Fegraeus
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Uppsala, Sweden
| | - Marie Rhodin
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Uppsala, Sweden
| | - Eric Strand
- Department of Companion Animal Clinical Sciences, Norwegian University of Life Sciences, Oslo, Norway
| | - Luis Fernando García
- Department of Biology, National University of Colombia, Bogotá, Cundinamarca, Colombia
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Uppsala, Sweden
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23
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Jäderkvist Fegraeus K, Hirschberg I, Árnason T, Andersson L, Velie BD, Andersson LS, Lindgren G. To pace or not to pace: a pilot study of four- and five-gaited Icelandic horses homozygous for the DMRT3 'Gait Keeper' mutation. Anim Genet 2017; 48:694-697. [PMID: 29023800 DOI: 10.1111/age.12610] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2017] [Indexed: 01/26/2023]
Abstract
The Icelandic horse is a breed known mainly for its ability to perform the ambling four-beat gait 'tölt' and the lateral two-beat gait pace. The natural ability of the breed to perform these alternative gaits is highly desired by breeders. Therefore, the discovery that a nonsense mutation (C>A) in the DMRT3 gene was the main genetic factor for horses' ability to perform gaits in addition to walk, trot and canter was of great interest. Although several studies have demonstrated that homozygosity for the DMRT3 mutation is important for the ability to pace, only about 70% of the homozygous mutant (AA) Icelandic horses are reported to pace. The aim of the study was to genetically compare four- and five-gaited (i.e. horses with and without the ability to pace) AA Icelandic horses by performing a genome-wide association (GWA) analysis. All horses (n = 55) were genotyped on the 670K Axiom Equine Genotyping Array, and a GWA analysis was performed using the genabel package in r. No SNP demonstrated genome-wide significance, implying that the ability to pace goes beyond the presence of a single gene variant. Despite its limitations, the current study provides additional information regarding the genetic complexity of pacing ability in horses. However, to fully understand the genetic differences between four- and five-gaited AA horses, additional studies with larger sample materials and consistent phenotyping are needed.
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Affiliation(s)
- K Jäderkvist Fegraeus
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - I Hirschberg
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - T Árnason
- IHBC AB, Knubbo, 74494, Morgongåva, Sweden
| | - L Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden.,Department of Medical Biochemistry and Microbiology, Uppsala University, 75123, Uppsala, Sweden.,Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA
| | - B D Velie
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | | | - G Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
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24
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Staiger EA, Almén MS, Promerová M, Brooks S, Cothran EG, Imsland F, Jäderkvist Fegraeus K, Lindgren G, Mehrabani Yeganeh H, Mikko S, Vega-Pla JL, Tozaki T, Rubin CJ, Andersson L. The evolutionary history of theDMRT3‘Gait keeper’ haplotype. Anim Genet 2017; 48:551-559. [DOI: 10.1111/age.12580] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2017] [Indexed: 01/25/2023]
Affiliation(s)
- E. A. Staiger
- Department of Medical Biochemistry and Microbiology; Uppsala University; SE-75123 Uppsala Sweden
| | - M. S. Almén
- Department of Medical Biochemistry and Microbiology; Uppsala University; SE-75123 Uppsala Sweden
| | - M. Promerová
- Department of Medical Biochemistry and Microbiology; Uppsala University; SE-75123 Uppsala Sweden
| | - S. Brooks
- Department of Animal Science; University of Florida; Gainesville FL 32611-0910 USA
| | - E. G. Cothran
- Department of Veterinary Integrative Biosciences; College of Veterinary Medicine and Biomedical Sciences; Texas A&M University; College Station TX 77843-4458 USA
| | - F. Imsland
- Department of Medical Biochemistry and Microbiology; Uppsala University; SE-75123 Uppsala Sweden
| | - K. Jäderkvist Fegraeus
- Department of Animal Breeding and Genetics; Swedish University of Agricultural Sciences; SE-75007 Uppsala Sweden
| | - G. Lindgren
- Department of Animal Breeding and Genetics; Swedish University of Agricultural Sciences; SE-75007 Uppsala Sweden
| | | | - S. Mikko
- Department of Animal Breeding and Genetics; Swedish University of Agricultural Sciences; SE-75007 Uppsala Sweden
| | - J. L. Vega-Pla
- Laboratorio de Investigación Aplicada; Cría Caballar de las Fuerzas Armadas; 14080 Cordoba Spain
| | - T. Tozaki
- Genetic Analysis Department; Laboratory of Racing Chemistry; Tochigi 320-0851 Utsunomiya Japan
| | - C. J. Rubin
- Department of Medical Biochemistry and Microbiology; Uppsala University; SE-75123 Uppsala Sweden
| | - L. Andersson
- Department of Medical Biochemistry and Microbiology; Uppsala University; SE-75123 Uppsala Sweden
- Department of Veterinary Integrative Biosciences; College of Veterinary Medicine and Biomedical Sciences; Texas A&M University; College Station TX 77843-4458 USA
- Department of Animal Breeding and Genetics; Swedish University of Agricultural Sciences; SE-75007 Uppsala Sweden
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25
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The Evolutionary Origin and Genetic Makeup of Domestic Horses. Genetics 2017; 204:423-434. [PMID: 27729493 DOI: 10.1534/genetics.116.194860] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 08/17/2016] [Indexed: 12/21/2022] Open
Abstract
The horse was domesticated only 5.5 KYA, thousands of years after dogs, cattle, pigs, sheep, and goats. The horse nonetheless represents the domestic animal that most impacted human history; providing us with rapid transportation, which has considerably changed the speed and magnitude of the circulation of goods and people, as well as their cultures and diseases. By revolutionizing warfare and agriculture, horses also deeply influenced the politico-economic trajectory of human societies. Reciprocally, human activities have circled back on the recent evolution of the horse, by creating hundreds of domestic breeds through selective programs, while leading all wild populations to near extinction. Despite being tightly associated with humans, several aspects in the evolution of the domestic horse remain controversial. Here, we review recent advances in comparative genomics and paleogenomics that helped advance our understanding of the genetic foundation of domestic horses.
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26
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Rothschild MF. Genomics and genetics: A daily double for the horse industry. Equine Vet J 2017; 49:260-262. [DOI: 10.1111/evj.12668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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27
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Kristjansson T, Bjornsdottir S, Albertsdóttir E, Sigurdsson A, Pourcelot P, Crevier-Denoix N, Arnason T. Association of conformation and riding ability in Icelandic horses. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.05.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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28
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Regatieri IC, Eberth JE, Sarver F, Lear TL, Bailey E. Comparison of
DMRT
3
genotypes among American Saddlebred horses with reference to gait. Anim Genet 2016; 47:603-5. [DOI: 10.1111/age.12458] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2016] [Indexed: 12/01/2022]
Affiliation(s)
- I. C. Regatieri
- Faculdade de Ciências Agrárias e Veterinárias UNESP – Univ Estadual Paulista – Jaboticabal São Paulo 14884‐900 Brazil
| | - J. E. Eberth
- Department of Veterinary Science University of Kentucky – Lexington Lexington KY 40506 USA
| | - F. Sarver
- Cornerstone Farm Carlisle Lexington KY 40311 USA
| | - T. L. Lear
- Department of Veterinary Science University of Kentucky – Lexington Lexington KY 40506 USA
| | - E. Bailey
- Department of Veterinary Science University of Kentucky – Lexington Lexington KY 40506 USA
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29
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Affiliation(s)
- Kathrin F. Stock
- Vereinigte Informationssysteme Tierhaltung w.V. (vit), Heinrich-Schroeder-Weg 1, 27283 Verden, Germany
| | - Lina Jönsson
- Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg, Denmark
- Danish Warmblood Association, Vilhelmsborg Alle 1, 8320 Mårslet, Denmark
| | - Anne Ricard
- INRA, UMR 1313 Génétique Animale et Biologie Intégrative, 78352 Jouy-en-Josas, France
- IFCE, Recherche et Innovation, 61310 Exmes, France
| | - Thomas Mark
- Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg, Denmark
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30
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Jäderkvist Fegraeus K, Johansson L, Mäenpää M, Mykkänen A, Andersson LS, Velie BD, Andersson L, Árnason T, Lindgren G. Different DMRT3 Genotypes Are Best Adapted for Harness Racing and Riding in Finnhorses. J Hered 2015; 106:734-40. [PMID: 26285915 DOI: 10.1093/jhered/esv062] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 07/29/2015] [Indexed: 11/14/2022] Open
Abstract
Previous studies showed a positive effect of the DMRT3 "gait keeper" mutation on harness racing performance in Standardbreds, French-, and Nordic trotters. The mutation has also been shown to influence riding traits in multiple breeds. This study investigated the effect of the DMRT3 mutation on harness racing performance and riding traits in Finnhorses. Finnhorses used for harness racing (n = 180) and for riding (n = 59) were genotyped for the DMRT3 mutation. For the trotters the genotypes were evaluated for association with racing performance (number of starts, victories, placings, earnings, and race times). At 3-6 years of age the AA genotype was superior compared with the CA and CC genotypes. The AA horses had a significantly higher proportion of victories (P = 1.4×10(-6)) and placings (P = 4.1×10(-7)), better race times (P = 0.01), and earned more money (P = 0.009) compared with C-horses. For the Finnhorses used for riding the owners answered a questionnaire to score how well the horse performed the gaits walk, trot, and canter on a scale from 1 to 6. These scores were tested for association with the DMRT3 genotypes. Although AA horses were more successful as racehorses, the CC and CA horses appear more adapted for classical riding disciplines. The AA horses received significantly lower gait scores compared with C-horses for the majority of gaits. Except for rhythm in extended canter (P = 0.05), there were no significant differences between CA and CC horses. This study shows that there are different optimal genotypes for different disciplines and the DMRT3 mutation clearly influences gaits and performance in Finnhorses.
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Affiliation(s)
- Kim Jäderkvist Fegraeus
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden (Jäderkvist Fegraeus, Johansson, Andersson, Velie, Andersson, and Lindgren); Suomen Hippos ry, Espoo, Finland (Mäenpää); Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland (Mykkänen); Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden (Andersson); and IHBC AB, Knubbo, Morgongåva, Sweden (Árnason)
| | - Lisa Johansson
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden (Jäderkvist Fegraeus, Johansson, Andersson, Velie, Andersson, and Lindgren); Suomen Hippos ry, Espoo, Finland (Mäenpää); Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland (Mykkänen); Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden (Andersson); and IHBC AB, Knubbo, Morgongåva, Sweden (Árnason)
| | - Minna Mäenpää
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden (Jäderkvist Fegraeus, Johansson, Andersson, Velie, Andersson, and Lindgren); Suomen Hippos ry, Espoo, Finland (Mäenpää); Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland (Mykkänen); Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden (Andersson); and IHBC AB, Knubbo, Morgongåva, Sweden (Árnason)
| | - Anna Mykkänen
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden (Jäderkvist Fegraeus, Johansson, Andersson, Velie, Andersson, and Lindgren); Suomen Hippos ry, Espoo, Finland (Mäenpää); Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland (Mykkänen); Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden (Andersson); and IHBC AB, Knubbo, Morgongåva, Sweden (Árnason)
| | - Lisa S Andersson
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden (Jäderkvist Fegraeus, Johansson, Andersson, Velie, Andersson, and Lindgren); Suomen Hippos ry, Espoo, Finland (Mäenpää); Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland (Mykkänen); Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden (Andersson); and IHBC AB, Knubbo, Morgongåva, Sweden (Árnason)
| | - Brandon D Velie
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden (Jäderkvist Fegraeus, Johansson, Andersson, Velie, Andersson, and Lindgren); Suomen Hippos ry, Espoo, Finland (Mäenpää); Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland (Mykkänen); Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden (Andersson); and IHBC AB, Knubbo, Morgongåva, Sweden (Árnason)
| | - Leif Andersson
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden (Jäderkvist Fegraeus, Johansson, Andersson, Velie, Andersson, and Lindgren); Suomen Hippos ry, Espoo, Finland (Mäenpää); Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland (Mykkänen); Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden (Andersson); and IHBC AB, Knubbo, Morgongåva, Sweden (Árnason)
| | - Thorvaldur Árnason
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden (Jäderkvist Fegraeus, Johansson, Andersson, Velie, Andersson, and Lindgren); Suomen Hippos ry, Espoo, Finland (Mäenpää); Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland (Mykkänen); Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden (Andersson); and IHBC AB, Knubbo, Morgongåva, Sweden (Árnason)
| | - Gabriella Lindgren
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden (Jäderkvist Fegraeus, Johansson, Andersson, Velie, Andersson, and Lindgren); Suomen Hippos ry, Espoo, Finland (Mäenpää); Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland (Mykkänen); Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden (Andersson); and IHBC AB, Knubbo, Morgongåva, Sweden (Árnason).
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31
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Jäderkvist K, Holm N, Imsland F, Árnason T, Andersson L, Andersson LS, Lindgren G. The importance of the DMRT3 ‘Gait keeper’ mutation on riding traits and gaits in Standardbred and Icelandic horses. Livest Sci 2015. [DOI: 10.1016/j.livsci.2015.03.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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