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Gmel AI, Mikko S, Ricard A, Velie BD, Gerber V, Hamilton NA, Neuditschko M. Using high-density SNP data to unravel the origin of the Franches-Montagnes horse breed. Genet Sel Evol 2024; 56:53. [PMID: 38987703 PMCID: PMC11238448 DOI: 10.1186/s12711-024-00922-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 07/03/2024] [Indexed: 07/12/2024] Open
Abstract
BACKGROUND The Franches-Montagnes (FM) is the last native horse breed of Switzerland, established at the end of the 19th century by cross-breeding local mares with Anglo-Norman stallions. We collected high-density SNP genotype data (Axiom™ 670 K Equine genotyping array) from 522 FM horses, including 44 old-type horses (OF), 514 European Warmblood horses (WB) from Sweden and Switzerland (including a stallion used for cross-breeding in 1990), 136 purebred Arabians (AR), 32 Shagya Arabians (SA), and 64 Thoroughbred (TB) horses, as introgressed WB stallions showed TB origin in their pedigrees. The aim of the study was to ascertain fine-scale population structures of the FM breed, including estimation of individual admixture levels and genomic inbreeding (FROH) by means of Runs of Homozygosity. RESULTS To assess fine-scale population structures within the FM breed, we applied a three-step approach, which combined admixture, genetic contribution, and FROH of individuals into a high-resolution network visualization. Based on this approach, we were able to demonstrate that population substructures, as detected by model-based clustering, can be either associated with a different genetic origin or with the progeny of most influential sires. Within the FM breed, admixed horses explained most of the genetic variance of the current breeding population, while OF horses only accounted for a small proportion of the variance. Furthermore, we illustrated that FM horses showed high TB admixture levels and we identified inconsistencies in the origin of FM horses descending from the Arabian stallion Doktryner. With the exception of WB, FM horses were less inbred compared to the other breeds. However, the relatively few but long ROH segments suggested diversity loss in both FM subpopulations. Genes located in FM- and OF-specific ROH islands had known functions involved in conformation and behaviour, two traits that are highly valued by breeders. CONCLUSIONS The FM remains the last native Swiss breed, clearly distinguishable from other historically introgressed breeds, but it suffered bottlenecks due to intensive selection of stallions, restrictive mating choices based on arbitrary definitions of pure breeding, and selection of rare coat colours. To preserve the genetic diversity of FM horses, future conservation managements strategies should involve a well-balanced selection of stallions (e.g., by integrating OF stallions in the FM breeding population) and avoid selection for rare coat colours.
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Affiliation(s)
- Annik Imogen Gmel
- Animal GenoPhenomics, Agroscope, Route de la Tioleyre 4, 1725, Posieux, Switzerland
- Equine Department, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8053, Zurich, Switzerland
| | - Sofia Mikko
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07, Uppsala, Sweden
| | - Anne Ricard
- Institut National de la Recherche Agronomique, Domaine de Vilvert, 78350, Jouy-en-Josas, France
| | - Brandon D Velie
- Equine Genetics and Genomics Group, School of Life and Environmental Sciences, University of Sydney, RMC Gunn B19-603, Sydney, NSW, 2006, Australia
| | - Vinzenz Gerber
- Institut Suisse de Médecine Equine ISME, Vetsuisse Faculty, University of Bern, Länggassstrasse 124, 3012, Bern, Switzerland
| | - Natasha Anne Hamilton
- Sydney School of Veterinary Science, University of Sydney, Sydney, NSW, 2006, Australia
| | - Markus Neuditschko
- Animal GenoPhenomics, Agroscope, Route de la Tioleyre 4, 1725, Posieux, Switzerland.
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Atroshchenko M, Dementieva N, Shcherbakov Y, Nikolaeva O, Azovtseva A, Ryabova A, Nikitkina E, Makhmutova O, Datsyshin A, Zakharov V, Zaitsev A. The Genetic Diversity of Horse Native Breeds in Russia. Genes (Basel) 2023; 14:2148. [PMID: 38136970 PMCID: PMC10743158 DOI: 10.3390/genes14122148] [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: 11/03/2023] [Revised: 11/24/2023] [Accepted: 11/26/2023] [Indexed: 12/24/2023] Open
Abstract
Horses were domesticated later than other farm animals. Horse breeds have been selectively developed by humans to satisfy different needs and purposes. The factory and indigenous breeds are of particular interest, having been bred in purity for many centuries without the addition of foreign blood. Data from 31 stud farms, as well as ranches, located in fifteen regions of the Russian Federation were used in this work. DNA was sampled from 102 stallions of 11 breeds: Arabian, Akhal-Teke, Don, Orlov Trotter, Vladimir Heavy Draft, Russian Heavy Draft, Soviet Heavy Draft, Kabardin, Yakut, Tuva, and Vyatka. Data on the origin of each animal from which the material was collected were taken into account. DNA genotyping was carried out using GGP Equine 70 k ® array chips (Thermo Fisher Scientific, USA). Genetic diversity of horse breeds was estimated using Admixture 1.3. and PLINK 1.9 software. FROH inbreeding was computed via the R detectRUNS package. The minimum length for ROH was set at 1 Mb to reduce the occurrence of false positives. We conducted PCA analysis using PLINK 1.9, and used the ggplot2 library in R for visualizing the results. Indigenous equine breeds, such as Vyatka, Tuva, and Yakut, are very hardy, and well adapted to local environmental and climatic conditions. They are employed as draft power, as well as for milk and meat. Both the Akhal-Teke breed and the Arabian breed have retained a minimum effective population size over many generations. We note significant accumulations of homozygosity in these breeds. In equestrian sports, performance is a top priority. ADMIXTURE and PCA analyses showed similarities between Don equine breeds and Kabardin, as well as some Arabian breed animals. Earlier research indicated the presence of thoroughbred traits in Don stallions. The Orlov Trotter breed stands out as a separate cluster in the structural and PCA analyses. Considering the small population size of this breed, our study found high FROH in all tested animals. The general reduction in the diversity of the horse breed gene pool, due to numerous crosses for breed improvement with thoroughbreds, has lead to a decline in the differences between the top sporting breeds. Our study presents new opportunities for exploring the genetic factors that influence the formation of adaptive traits in indigenous breeds, and for finding ways to preserve genetic diversity for effective population reproduction.
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Affiliation(s)
- Mikhail Atroshchenko
- All-Russian Research Institute of Horse Breeding (ARRIH), Ryazan Region, Rybnovskij District, Divovo 391105, Russia; (M.A.); (O.M.); (A.D.); (V.Z.); (A.Z.)
| | - Natalia Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, St. Petersburg, Pushkin 196625, Russia; (Y.S.); (O.N.); (A.A.); (A.R.); (E.N.)
| | - Yuri Shcherbakov
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, St. Petersburg, Pushkin 196625, Russia; (Y.S.); (O.N.); (A.A.); (A.R.); (E.N.)
| | - Olga Nikolaeva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, St. Petersburg, Pushkin 196625, Russia; (Y.S.); (O.N.); (A.A.); (A.R.); (E.N.)
| | - Anastasiia Azovtseva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, St. Petersburg, Pushkin 196625, Russia; (Y.S.); (O.N.); (A.A.); (A.R.); (E.N.)
| | - Anna Ryabova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, St. Petersburg, Pushkin 196625, Russia; (Y.S.); (O.N.); (A.A.); (A.R.); (E.N.)
| | - Elena Nikitkina
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, St. Petersburg, Pushkin 196625, Russia; (Y.S.); (O.N.); (A.A.); (A.R.); (E.N.)
| | - Oksana Makhmutova
- All-Russian Research Institute of Horse Breeding (ARRIH), Ryazan Region, Rybnovskij District, Divovo 391105, Russia; (M.A.); (O.M.); (A.D.); (V.Z.); (A.Z.)
| | - Andrey Datsyshin
- All-Russian Research Institute of Horse Breeding (ARRIH), Ryazan Region, Rybnovskij District, Divovo 391105, Russia; (M.A.); (O.M.); (A.D.); (V.Z.); (A.Z.)
| | - Viktor Zakharov
- All-Russian Research Institute of Horse Breeding (ARRIH), Ryazan Region, Rybnovskij District, Divovo 391105, Russia; (M.A.); (O.M.); (A.D.); (V.Z.); (A.Z.)
| | - Alexander Zaitsev
- All-Russian Research Institute of Horse Breeding (ARRIH), Ryazan Region, Rybnovskij District, Divovo 391105, Russia; (M.A.); (O.M.); (A.D.); (V.Z.); (A.Z.)
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Santos WB, Pereira CB, Maiorano AM, Arce CDS, Baldassini WA, Pereira GL, Chardulo LAL, Neto ORM, Oliveira HN, Curi RA. Genomic inbreeding estimation, runs of homozygosity, and heterozygosity-enriched regions uncover signals of selection in the Quarter Horse racing line. J Anim Breed Genet 2023; 140:583-595. [PMID: 37282810 DOI: 10.1111/jbg.12812] [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: 10/03/2022] [Revised: 03/30/2023] [Accepted: 05/28/2023] [Indexed: 06/08/2023]
Abstract
With the advent of genomics, significant progress has been made in the genetic improvement of livestock species, particularly through increased accuracy in predicting breeding values for selecting superior animals and the possibility of performing a high-resolution genetic scan throughout the genome of an individual. The main objectives of this study were to estimate the individual genomic inbreeding coefficient based on runs of homozygosity (FROH ), to identify and characterize runs of homozygosity and heterozygosity (ROH and ROHet, respectively; length and distribution) throughout the genome, and to map selection signatures in relevant chromosomal regions in the Quarter Horse racing line. A total of 336 animals registered with the Brazilian Association of Quarter Horse Breeders (ABQM) were genotyped. One hundred and twelve animals were genotyped using the Equine SNP50 BeadChip (Illumina, USA), with 54,602 single nucleotide polymorphisms (SNPs; 54K). The remaining 224 samples were genotyped using the Equine SNP70 BeadChip (Illumina, USA) with 65,157 SNPs (65K). To ensure data quality, we excluded animals with a call rate below 0.9. We also excluded SNPs located on non-autosomal chromosomes, as well as those with a call rate below 0.9 or a p-value below 1 × 10-5 for Hardy-Weinberg equilibrium. The results indicate moderate to high genomic inbreeding, with 46,594 ROH and 16,101 ROHet detected. In total, 30 and 14 candidate genes overlap with ROH and ROHet regions, respectively. The ROH islands showed genes linked to crucial biological processes, such as cell differentiation (CTBP1, WNT5B, and TMEM120B), regulation of glucose metabolic process (MAEA and NKX1-1), heme transport (PGRMC2), and negative regulation of calcium ion import (VDAC1). In ROHet, the islands showed genes related to respiratory capacity (OR7D19, OR7D4G, OR7D4E, and OR7D4J) and muscle repair (EGFR and BCL9). These findings could aid in selecting animals with greater regenerative capacity and developing treatments for muscle disorders in the QH breed. This study serves as a foundation for future research on equine breeds. It can contribute to developing reproductive strategies in animal breeding programs to improve and preserve the Quarter Horse breed.
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Affiliation(s)
- Wellington B Santos
- Department of Animal Science, São Paulo State University, Jaboticabal, Brazil
| | - Camila B Pereira
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
| | - Amanda M Maiorano
- Department of Animal Science, Federal University of Uberlândia, Uberlândia, Brazil
| | | | - Welder A Baldassini
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
| | - Guilherme L Pereira
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
| | - Luis Artur L Chardulo
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
| | - Otávio R M Neto
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
| | - Henrique N Oliveira
- Department of Animal Science, São Paulo State University, Jaboticabal, Brazil
| | - Rogério A Curi
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
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Lindsay-McGee V, Sanchez-Molano E, Banos G, Clark EL, Piercy RJ, Psifidi A. Genetic characterisation of the Connemara pony and the Warmblood horse using a within-breed clustering approach. Genet Sel Evol 2023; 55:60. [PMID: 37592264 PMCID: PMC10436415 DOI: 10.1186/s12711-023-00827-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 07/07/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND The Connemara pony (CP) is an Irish breed that has experienced varied selection by breeders over the last fifty years, with objectives ranging from the traditional hardy pony to an agile athlete. We compared these ponies with well-studied Warmblood (WB) horses, which are also selectively bred for athletic performance but with a much larger census population. Using genome-wide single nucleotide polymorphism (SNP) and whole-genome sequencing data from 116 WB (94 UK WB and 22 European WB) and 36 CP (33 UK CP and 3 US CP), we studied the genomic diversity, inbreeding and population structure of these breeds. RESULTS The k-means clustering approach divided both the CP and WB populations into four genetic groups, among which the CP genetic group 1 (C1) associated with non-registered CP, C4 with US CP, WB genetic group 1 (W1) with Holsteiners, and W3 with Anglo European and British WB. Maximum and mean linkage disequilibrium (LD) varied significantly between the two breeds (mean from 0.077 to 0.130 for CP and from 0.016 to 0.370 for WB), but the rate of LD decay was generally slower in CP than WB. The LD block size distribution peaked at 225 kb for all genetic groups, with most of the LD blocks not exceeding 1 Mb. The top 0.5% harmonic mean pairwise fixation index (FST) values identified ontology terms related to cancer risk when the four CP genetic groups were compared. The four CP genetic groups were less inbred than the WB genetic groups, but C2, C3 and C4 had a lower proportion of shorter runs of homozygosity (ROH) (74 to 76% < 4 Mb) than the four WB genetic groups (80 to 85% < 4 Mb), indicating more recent inbreeding. The CP and WB genetic groups had a similar ratio of effective number of breeders (Neb) to effective population size (Ne). CONCLUSIONS Distinct genetic groups of individuals were revealed within each breed, and in WB these genetic groups reflected population substructure better than studbook or country of origin. Ontology terms associated with immune and inflammatory responses were identified from the signatures of selection between CP genetic groups, and while CP were less inbred than WB, the evidence pointed to a greater degree of recent inbreeding. The ratio of Neb to Ne was similar in CP and WB, indicating the influence of popular sires is similar in CP and WB.
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Affiliation(s)
- Victoria Lindsay-McGee
- Royal Veterinary College, London, UK
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | | | | | - Emily L Clark
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
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Capomaccio S, Ablondi M, Colombi D, Sartori C, Giontella A, Cappelli K, Mancin E, Asti V, Mantovani R, Sabbioni A, Silvestrelli M. Exploring the Italian equine gene pool via high-throughput genotyping. Front Genet 2023; 14:1099896. [PMID: 36755577 PMCID: PMC9900106 DOI: 10.3389/fgene.2023.1099896] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 01/10/2023] [Indexed: 01/24/2023] Open
Abstract
Introduction: The Italian peninsula is in the center of the Mediterranean area, and historically it has been a hub for numerous human populations, cultures, and also animal species that enriched the hosted biodiversity. Horses are no exception to this phenomenon, with the peculiarity that the gene pool has been impacted by warfare and subsequent "colonization". In this study, using a comprehensive dataset for almost the entire Italian equine population, in addition to the most influential cosmopolitan breeds, we describe the current status of the modern Italian gene pool. Materials and Methods: The Italian dataset comprised 1,308 individuals and 22 breeds genotyped at a 70 k density that was merged with publicly available data to facilitate comparison with the global equine diversity. After quality control and supervised subsampling to ensure consistency among breeds, the merged dataset with the global equine diversity contained data for 1,333 individuals from 54 populations. Multidimensional scaling, admixture, gene flow, and effective population size were analyzed. Results and Discussion: The results show that some of the native Italian breeds preserve distinct gene pools, potentially because of adaptation to the different geographical contexts of the peninsula. Nevertheless, the comparison with international breeds highlights the presence of strong gene flow from renowned breeds into several Italian breeds, probably due to historical introgression. Coldblood breeds with stronger genetic identity were indeed well differentiated from warmblood breeds, which are highly admixed. Other breeds showed further peculiarities due to their breeding history. Finally, we observed some breeds that exist more on cultural, traditional, and geographical point of view than due to actual genetic distinctiveness.
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Affiliation(s)
- Stefano Capomaccio
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy,Sport Horse Research Centre (CRCS), University of Perugia, Perugia, Italy,*Correspondence: Stefano Capomaccio, ; Michela Ablondi,
| | - Michela Ablondi
- Department of Veterinary Science, University of Parma, Parma, Italy,*Correspondence: Stefano Capomaccio, ; Michela Ablondi,
| | - Daniele Colombi
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy,Department of Agricultural, Food, and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Cristina Sartori
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padua, Padua, Italy
| | - Andrea Giontella
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy,Sport Horse Research Centre (CRCS), University of Perugia, Perugia, Italy
| | - Katia Cappelli
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy,Sport Horse Research Centre (CRCS), University of Perugia, Perugia, Italy
| | - Enrico Mancin
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padua, Padua, Italy
| | - Vittoria Asti
- Department of Veterinary Science, University of Parma, Parma, Italy
| | - Roberto Mantovani
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padua, Padua, Italy
| | - Alberto Sabbioni
- Department of Veterinary Science, University of Parma, Parma, Italy
| | - Maurizio Silvestrelli
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy,Sport Horse Research Centre (CRCS), University of Perugia, Perugia, Italy
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Cardinali I, Giontella A, Tommasi A, Silvestrelli M, Lancioni H. Unlocking Horse Y Chromosome Diversity. Genes (Basel) 2022; 13:genes13122272. [PMID: 36553539 PMCID: PMC9777570 DOI: 10.3390/genes13122272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 12/11/2022] Open
Abstract
The present equine genetic variation mirrors the deep influence of intensive breeding programs during the last 200 years. Here, we provide a comprehensive current state of knowledge on the trends and prospects on the variation in the equine male-specific region of the Y chromosome (MSY), which was assembled for the first time in 2018. In comparison with the other 12 mammalian species, horses are now the most represented, with 56 documented MSY genes. However, in contrast to the high variability in mitochondrial DNA observed in many horse breeds from different geographic areas, modern horse populations demonstrate extremely low genetic Y-chromosome diversity. The selective pressures employed by breeders using pedigree data (which are not always error-free) as a predictive tool represent the main cause of this lack of variation in the Y-chromosome. Nevertheless, the detailed phylogenies obtained by recent fine-scaled Y-chromosomal genotyping in many horse breeds worldwide have contributed to addressing the genealogical, forensic, and population questions leading to the reappraisal of the Y-chromosome as a powerful genetic marker to avoid the loss of biodiversity as a result of selective breeding practices, and to better understand the historical development of horse breeds.
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Affiliation(s)
- Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
- Correspondence: (I.C.); (A.G.)
| | - Andrea Giontella
- Department of Veterinary Medicine, University of Perugia, 06126 Perugia, Italy
- Correspondence: (I.C.); (A.G.)
| | - Anna Tommasi
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | | | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
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Perdomo-González DI, Laseca N, Demyda-Peyrás S, Valera M, Cervantes I, Molina A. Fine-tuning genomic and pedigree inbreeding rates in equine population with a deep and reliable stud book: the case of the Pura Raza Española horse. J Anim Sci Biotechnol 2022; 13:127. [PMID: 36336696 PMCID: PMC9639299 DOI: 10.1186/s40104-022-00781-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Estimating inbreeding, which is omnipresent and inevitable in livestock populations, is a primary goal for management and animal breeding especially for those interested in mitigating the negative consequences of inbreeding. Inbreeding coefficients have been historically estimated by using pedigree information; however, over the last decade, genome-base inbreeding coefficients have come to the forefront in this field. The Pura Raza Española (PRE) horse is an autochthonous Spanish horse breed which has been recognised since 1912. The total PRE population (344,718 horses) was used to estimate Classical (F), Ballou's ancestral, Kalinowski's ancestral, Kalinowski's new and the ancestral history coefficient values. In addition, genotypic data from a selected population of 805 PRE individuals was used to determine the individual inbreeding coefficient using SNP-by-SNP-based techniques (methods of moments -FHOM-, the diagonal elements of the genomic -FG-, and hybrid matrixes -FH-) and ROH measures (FRZ). The analyse of both pedigree and genomic based inbreeding coefficients in a large and robust population such as the PRE horse, with proven parenteral information for the last 40 years and a high degree of completeness (over 90% for the last 70 years) will allow us to understand PRE genetic variability better and the correlations between the estimations will give the data greater reliability. RESULTS The mean values of the pedigree-based inbreeding coefficients ranged from 0.01 (F for the last 3 generations -F3-) to 0.44 (ancestral history coefficient) and the mean values of genomic-based inbreeding coefficients varied from 0.05 (FRZ for three generations, FH and FHOM) to 0.11 (FRZ for nine generations). Significant correlations were also found between pedigree and genomic inbreeding values, which ranged between 0.58 (F3 with FHOM) and 0.79 (F with FRZ). In addition, the correlations between FRZ estimated for the last 20 generations and the pedigree-based inbreeding highlight the fact that fewer generations of genomic data are required when comparing total inbreeding values, and the opposite when ancient values are calculated. CONCLUSIONS Ultimately, our results show that it is still useful to work with a deep and reliable pedigree in pedigree-based genetic studies with very large effective population sizes. Obtaining a satisfactory parameter will always be desirable, but the approximation obtained with a robust pedigree will allow us to work more efficiently and economically than with massive genotyping.
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Affiliation(s)
- Davinia Isabel Perdomo-González
- Departamento Agronomía, Escuela Técnica Superior de Ingeniería Agromómica, Universidad de Sevilla, Ctra Utrera Km 1, 41013, Sevilla, Spain.
| | - Nora Laseca
- Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
| | - Sebastián Demyda-Peyrás
- Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), La Plata, Argentina
| | - Mercedes Valera
- Departamento Agronomía, Escuela Técnica Superior de Ingeniería Agromómica, Universidad de Sevilla, Ctra Utrera Km 1, 41013, Sevilla, Spain
| | - Isabel Cervantes
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Antonio Molina
- Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
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Ablondi M, Sabbioni A, Stocco G, Cipolat-Gotet C, Dadousis C, van Kaam JT, Finocchiaro R, Summer A. Genetic Diversity in the Italian Holstein Dairy Cattle Based on Pedigree and SNP Data Prior and After Genomic Selection. Front Vet Sci 2022; 8:773985. [PMID: 35097040 PMCID: PMC8792952 DOI: 10.3389/fvets.2021.773985] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/30/2021] [Indexed: 01/09/2023] Open
Abstract
Genetic diversity has become an urgent matter not only in small local breeds but also in more specialized ones. While the use of genomic data in livestock breeding programs increased genetic gain, there is increasing evidence that this benefit may be counterbalanced by the potential loss of genetic variability. Thus, in this study, we aimed to investigate the genetic diversity in the Italian Holstein dairy cattle using pedigree and genomic data from cows born between 2002 and 2020. We estimated variation in inbreeding, effective population size, and generation interval and compared those aspects prior to and after the introduction of genomic selection in the breed. The dataset contained 84,443 single-nucleotide polymorphisms (SNPs), and 74,485 cows were analyzed. Pedigree depth based on complete generation equivalent was equal to 10.67. A run of homozygosity (ROH) analysis was adopted to estimate SNP-based inbreeding (FROH). The average pedigree inbreeding was 0.07, while the average FROH was more than double, being equal to 0.17. The pattern of the effective population size based on pedigree and SNP data was similar although different in scale, with a constant decrease within the last five generations. The overall inbreeding rate (ΔF) per year was equal to +0.27% and +0.44% for Fped and FROH throughout the studied period, which corresponded to about +1.35% and +2.2% per generation, respectively. A significant increase in the ΔF was found since the introduction of genomic selection in the breed. This study in the Italian Holstein dairy cattle showed the importance of controlling the loss of genetic diversity to ensure the long-term sustainability of this breed, as well as to guarantee future market demands.
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Affiliation(s)
- Michela Ablondi
- Dipartimento di Scienze Medico-Veterinarie, University of Parma, Parma, Italy
| | - Alberto Sabbioni
- Dipartimento di Scienze Medico-Veterinarie, University of Parma, Parma, Italy
| | - Giorgia Stocco
- Dipartimento di Scienze Medico-Veterinarie, University of Parma, Parma, Italy
| | - Claudio Cipolat-Gotet
- Dipartimento di Scienze Medico-Veterinarie, University of Parma, Parma, Italy
- *Correspondence: Claudio Cipolat-Gotet
| | - Christos Dadousis
- Dipartimento di Scienze Medico-Veterinarie, University of Parma, Parma, Italy
| | - Jan-Thijs van Kaam
- Associazione Nazionale Allevatori della Razza Frisona Bruna e Jersey Italiana, Cremona, Italy
| | - Raffaella Finocchiaro
- Associazione Nazionale Allevatori della Razza Frisona Bruna e Jersey Italiana, Cremona, Italy
| | - Andrea Summer
- Dipartimento di Scienze Medico-Veterinarie, University of Parma, Parma, Italy
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9
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Poyato-Bonilla J, Laseca N, Demyda-Peyrás S, Molina A, Valera M. 500 years of breeding in the Carthusian Strain of Pura Raza Español horse: An evolutional analysis using genealogical and genomic data. J Anim Breed Genet 2021; 139:84-99. [PMID: 34363624 DOI: 10.1111/jbg.12641] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/19/2021] [Accepted: 07/25/2021] [Indexed: 01/19/2023]
Abstract
The Carthusian horse is a Pura Raza Español (PRE) strain (CS), bred as a closed population since its creation more than 500 years ago. The aim of this study was to analyse for the first time its population structure and situation of variability combining both genealogical (GEL) and genomic (GEN) data. The GEL data comprised 348,429 pedigree records (56,105 CS horses), while the GEN analysis included the high-density genotypes (670,804 SNPs) of 287 horses. Pedigree completeness demonstrated its accuracy, showing a good correlation of GEL (F) and GEN (FROH ) inbreeding coefficient in the case of PRE subpopulations partially related and non-related to Carthusian strain (0.68) but a lower value in the 100% Carthusian horses (0.42), due to the high weight of founders not detected by GEL analysis. GEN (PCA, AMOVA, and Admixture) and GEL analysis showed a good differentiation of subpopulations, but also a high level of introgression of the CS in the breed during past decades. A recent change in this trend was noteworthy, with a considerable reduction in CS variability and a genetic bottleneck (effective population sizes of 31.57 and 30.20 in GEL and GEN analysis, respectively, in last generation). The PRE has maintained its variability, and a considerable difference in estimated Ne by GEL (60.77) and GEN (188.0) data was observed. Using two sources of complementary information, it was found the existence of an ancient PRE strain with a unique genetic landmark, practically free from the influence of other equine populations.
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Affiliation(s)
- Julia Poyato-Bonilla
- Dpto. Agronomía. Escuela Técnica Superior de Ingeniería Agronómica, Universidad de Sevilla, Sevilla, Spain
| | - Nora Laseca
- Dpto. Genética. Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Sebastián Demyda-Peyrás
- Departamento de Producción Animal, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Buenos Aires, Argentina.,CONICET, CCT La Plata, La Plata, Argentina
| | - Antonio Molina
- Dpto. Genética. Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Mercedes Valera
- Dpto. Agronomía. Escuela Técnica Superior de Ingeniería Agronómica, Universidad de Sevilla, Sevilla, Spain
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10
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Faria RAS, Vicente APA, Ospina AMT, Silva JAIIV. Pedigree analysis of the racing line Quarter Horse: Genetic diversity and most influential ancestors. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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11
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Polak G, Gurgul A, Jasielczuk I, Szmatoła T, Krupiński J, Bugno-Poniewierska M. Suitability of Pedigree Information and Genomic Methods for Analyzing Inbreeding of Polish Cold-Blooded Horses Covered by Conservation Programs. Genes (Basel) 2021; 12:genes12030429. [PMID: 33802830 PMCID: PMC8002693 DOI: 10.3390/genes12030429] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/21/2021] [Accepted: 03/08/2021] [Indexed: 11/16/2022] Open
Abstract
Traditionally, pedigree-based relationship coefficients were used to manage inbreeding and control inbreeding depression that occurs within populations. The extensive incorporation of genomic data in livestock breeding creates the opportunity to develop and implement methods to manage populations at the genomic level. Consequently, the realized proportion of the genome that two individuals share can be more accurately estimated instead of using pedigree information to estimate the expected proportion of shared alleles. To make use of this improvement, in this study we evaluated the genomic inbreeding measures in the Polish conserved cold-blooded horse population and compared the data with the traditional measures of inbreeding. Additionally, an ancestry fractions/proportions from Admixture software were tested as an estimate of lineage (ancestry coefficient) used for horses qualifying for the conservation program. The highest correlation of pedigree-based (FPED) and genomic inbreeding estimates was found for FROH (runs of homozygosity-based F coefficient) and FUNI (F coefficient based on the correlation between uniting gametes). FROH correlation with FPED tended to increase as the number of generations registered as pedigree increased. While lineage and gene contributions (Q) from Admixture software correlated, they showed poor direct compliance; hence, Q-value cannot be recommended as the estimate of pedigree-based lineage. All these findings suggest that the methods of genomics should be considered as an alternative or support in the analysis of population structure in conservative breeding that can help control inbreeding in rare horse populations.
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Affiliation(s)
- Grażyna Polak
- Department of Horse Breeding, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland;
- Office of the Director for Scientific Affairs, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland
- Correspondence:
| | - Artur Gurgul
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1c, 30-248 Kraków, Poland; (A.G.); (I.J.); (T.S.)
| | - Igor Jasielczuk
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1c, 30-248 Kraków, Poland; (A.G.); (I.J.); (T.S.)
| | - Tomasz Szmatoła
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1c, 30-248 Kraków, Poland; (A.G.); (I.J.); (T.S.)
| | - Jędrzej Krupiński
- Department of Horse Breeding, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland;
| | - Monika Bugno-Poniewierska
- Department of Animal Reproduction, Anatomy and Genomics, University of Agriculture in Kraków, al. Mickiewicza 24/28, 30-059 Kraków, Poland;
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12
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Marín Navas C, Delgado Bermejo JV, McLean AK, León Jurado JM, Rodriguez de la Borbolla y Ruiberriz de Torres A, Navas González FJ. Discriminant Canonical Analysis of the Contribution of Spanish and Arabian Purebred Horses to the Genetic Diversity and Population Structure of Hispano-Arabian Horses. Animals (Basel) 2021; 11:ani11020269. [PMID: 33494478 PMCID: PMC7912545 DOI: 10.3390/ani11020269] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/11/2021] [Accepted: 01/18/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary The demographic and genetic diversity structure and the contributions of Spanish (PRE) and Arabian Purebred (PRá) horses to the process of conformation of the Hispano-Arabian (Há) horse breed were evaluated. Genetic diversity parameters (inbreeding coefficient, genetic conservation index, coancestry coefficient, non-random mating degree, relatedness coefficient, maximum, complete, and equivalent generations, and number of offspring) were evaluated using a discriminant canonical analysis to determine the partial contributions of each founder breed to the development of Há horse breed. The calculation of Nei genetic distances suggests the overlapping could be estimated in 29.55% of the gene pool of the Há having a PRE origin while 70.45% of the gene pool of the breed may derive from a PRá origin. Although a progressive loss of founder representation may have occurred, breeding strategies implemented considering mating between animals with the highest genetic conservation indices (GCI) may compensate for its effects. Abstract Genetic diversity and population structure were analyzed using the historical and current pedigree information of the Arabian (PRá), Spanish Purebred (PRE), and Hispano-Arabian (Há) horse breeds. Genetic diversity parameters were computed and a canonical discriminant analysis was used to determine the contributions of ancestor breeds to the genetic diversity of the Há horse. Pedigree records were available for 207,100 animals born between 1884 and 2019. Nei’s distances and the equivalent subpopulations number indicated the existence of a highly structured, integrated population for the Há breed, which is more closely genetically related to PRá than PRE horses. An increase in the length of the generation interval might be an effective solution to reduce the increase in inbreeding found in the studied breeds (8.44%, 8.50%, and 2.89%, for PRá, PRE, and Há, respectively). Wright’s fixation statistics indicated slight interherd inbreeding. Pedigree completeness suggested genetic parameters were highly reliable. High GCI levels found for number of founders and non-founders and their relationship to the evolution of inbreeding permit controlling potential deleterious negative effects from excessively frequent mating between interrelated individuals. For instance, the use of individuals presenting high GCI may balance founders’ gene contributions and consequently preserve genetic diversity levels (current genetic diversity loss in PRá, PRE, and Há is 6%, 7%, and 4%, respectively).
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Affiliation(s)
- Carmen Marín Navas
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain; (C.M.N.); (J.V.D.B.)
| | - Juan Vicente Delgado Bermejo
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain; (C.M.N.); (J.V.D.B.)
| | - Amy Katherine McLean
- Department of Animal Science, University of California Davis, Davis, CA 95617, USA;
| | - José Manuel León Jurado
- Centro Agropecuario Provincial de Córdoba, Diputación Provincial de Córdoba, 14071 Córdoba, Spain;
| | | | - Francisco Javier Navas González
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain; (C.M.N.); (J.V.D.B.)
- Correspondence: ; Tel.: +34-957-21-87-06
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