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Carrillo Heredero AM, Sabbioni A, Asti V, Ablondi M, Summer A, Bertini S. Fecal microbiota characterization of an Italian local horse breed. Front Vet Sci 2024; 11:1236476. [PMID: 38425839 PMCID: PMC10902133 DOI: 10.3389/fvets.2024.1236476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 01/23/2024] [Indexed: 03/02/2024] Open
Abstract
The Bardigiano horse is a traditional native Italian breed with a rich history and peculiar characteristics. Local breeds are proven to have unique genetic traits developed over generations to adapt to defined geographical regions and/or conditions. The specific microbial communities that coexist within these animals are unraveled by studying their microbiota, which permits a further step in the characterization of local heritage. This work aimed to characterize Bardigiano horse fecal microbiota composition. The data obtained were then compared with published data of a mix of athlete breeds to evaluate potential differences among local and specialized breeds. The study involved 11 Bardigiano mares between 3 and 4 years of age, from which stool was sampled for the study. Samples were processed for 16S rRNA sequencing. Data obtained were analyzed and plotted using R, RStudio, and FastTree software. The samples analyzed were similar to what literature has reported on horses of other breeds and attitudes at higher taxonomic levels (from phylum to genera). While at lower taxonomic levels, the difference was more marked highlighting specific families found in the Bardigiano breed only. Weight, province of origin, and breeding sites significantly affected microbiota composition (p-value ≤0.02, p-value ≤0.04, and p-value ≤0.05, respectively). The comparison with athlete breed showed a significant difference confirming that animal and environmental factors are crucial in determining fecal microbiota composition (p-value <0.001). Understanding the microbiota composition in local breeds like the Bardigiano horse is crucial for preserving biodiversity, managing animal health, and promoting sustainable farming practices.
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Affiliation(s)
| | | | - Vittoria Asti
- Department of Veterinary Sciences, University of Parma, Parma, Italy
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Criscione A, Chessari G, Cesarani A, Ablondi M, Asti V, Bigi D, Bordonaro S, Ciampolini R, Cipolat-Gotet C, Congiu M, De Palo P, Landi V, Macciotta NPP, Matassino D, Portolano B, Riggio S, Sabbioni A, Sardina MT, Senczuk G, Tumino S, Vasini M, Ciani E, Mastrangelo S. Analysis of ddRAD-seq data provides new insights into the genomic structure and patterns of diversity in Italian donkey populations. J Anim Sci 2024; 102:skae165. [PMID: 38874306 PMCID: PMC11214105 DOI: 10.1093/jas/skae165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 06/13/2024] [Indexed: 06/15/2024] Open
Abstract
With more than 150 recognized breeds, donkeys assume relevant economic importance, especially in developing countries. Even if the estimated number of heads worldwide is 53M, this species received less attention than other livestock species. Italy has traditionally been considered one of the cradles of European donkey breeding, and despite a considerable loss of biodiversity, today still counts nine autochthonous populations. A total of 220 animals belonging to nine different populations were genotyped using the double-digest restriction site associated DNA (ddRAD) sequencing to investigate the pattern of diversity using a multi-technique approach. A total of 418,602,730 reads were generated and successfully demultiplexed to obtain a medium-density SNP genotypes panel with about 27K markers. The diversity indices showed moderate levels of variability. The genetic distances and relationships, largely agree with the breeding history of the donkey populations under investigation. The results highlighted the separation of populations based on their genetic origin or geographical proximity between breeding areas, showed low to moderate levels of admixture, and indicated a clear genetic difference in some cases. For some breeds, the results also validate the success of proper management conservation plans. Identified runs of homozygosity islands, mapped within genomic regions related to immune response and local adaptation, are consistent with the characteristics of the species known for its rusticity and adaptability. This study is the first exhaustive genome-wide analysis of the diversity of Italian donkey populations. The results emphasized the high informativeness of genome-wide markers retrieved through the ddRAD approach. The findings take on great significance in designing and implementing conservation strategies. Standardized genotype arrays for donkey species would make it possible to combine worldwide datasets to provide further insights into the evolution of the genomic structure and origin of this important genetic resource.
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Affiliation(s)
- Andrea Criscione
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Giorgio Chessari
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
- Department of Animal Sciences, Georg-August-University Göttingen, Göttingen, Germany
| | - Alberto Cesarani
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
- Department of Animal and Dairy Science, University of Georgia, Athens, USA
| | - Michela Ablondi
- Dipartimento di Scienze Medico-Veterinarie, University of Parma, Parma, Italy
| | - Vittoria Asti
- Dipartimento di Scienze Medico-Veterinarie, University of Parma, Parma, Italy
| | - Daniele Bigi
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, University of Bologna, Bologna, Italy
| | - Salvatore Bordonaro
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | | | | | - Michele Congiu
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
| | - Pasquale De Palo
- Dipartimento di Medicina Veterinaria, University of Bari Aldo Moro, Valenzano, Italy
| | - Vincenzo Landi
- Dipartimento di Medicina Veterinaria, University of Bari Aldo Moro, Valenzano, Italy
| | | | - Donato Matassino
- Consorzio per la Sperimentazione, Divulgazione e Applicazione di Biotecniche Innovative, Benevento, Italy
| | - Baldassare Portolano
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Silvia Riggio
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Alberto Sabbioni
- Dipartimento di Scienze Medico-Veterinarie, University of Parma, Parma, Italy
| | - Maria Teresa Sardina
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, Campobasso, Italy
| | - Serena Tumino
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Matteo Vasini
- Associazione Nazionale Allevatori delle Razze Equine ed Asinine Italiane, ANAREAI, Roma, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari Aldo Moro, Bari, Italy
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
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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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