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Domínguez-Viveros J, Molina-Villalobos JR, Camacho-Sandoval J, Cruz-Méndez A, Martínez-Rocha R, Jahuey-Martínez F. Structure and genetic variability of the Costa Rican Paso horse. J Equine Vet Sci 2024; 132:104985. [PMID: 38096926 DOI: 10.1016/j.jevs.2023.104985] [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: 08/11/2023] [Revised: 10/24/2023] [Accepted: 12/11/2023] [Indexed: 12/18/2023]
Abstract
The Costa Rican Paso Horse (CPC) is a breed developed in Costa Rica. The objectives were to estimate the genetic structure and evaluate the levels of genetic variability of the population. The genotypes of 14 microsatellites in 3654 records (2052 females and 1602 males) were analyzed. Expected (He) and observed (Ho) heterozygosity, polymorphic information content (CIP), fixation index (FIS), Shannon index, as well as Hardy-Weinberg disequilibrium (DHW) were evaluated. Kinship relationships (Rij) were estimated throughout the entire population. The effective population size (Ne) was calculated, alternating allele frequencies less than 0.05, 0.02 and 0.01. The Bayesian clustering study was carried out to infer how many lines are appropriate from the analysis of genotypes using multiple loci. The number of alleles per locus ranged from 7 to 17, with an average value of 9.6; nine loci presented DHW (P < 0.05); two loci presented negative FIS values, the same as Ho > He; the average of CIP, Ho and He was 0.254, 0.756 and 0.785, respectively. At the 12 loci where He > Ho, the differences ranged from 0.002 to 0.341 (0.036 on average). For Ne, the estimates were 201.9, 230.1, and 241.5. In the Rij, 54.86% of the estimates were in the interval of 0.01 to 77.7%. The number of lines that define the population corresponds to three, with an approximate composition of 33.1%, 32.4% and 34.5%, respectively. The CPC, as a subdivided population with DHW and a reduction in heterozygotes may be associated with possible Wahlund effects. Keywords: Wahlund effect, equines, genetic markers, synthetic breed, Hardy Weinberg.
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Affiliation(s)
| | | | | | - Argerie Cruz-Méndez
- Instituto Nacional de Innovación y Transferencia en Tecnología Agropecuaria, San José, Costa Rica
| | - Ricardo Martínez-Rocha
- Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Ciudad de México, México
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Sohail Ashraf M, Basheer A, Iqbal F, Zahoor I. Unravelling of the genetic diversity, population structure, and phylogenetic relationships of the indigenous horse breeds of Pakistan. Gene 2023; 889:147736. [PMID: 37714277 DOI: 10.1016/j.gene.2023.147736] [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: 03/29/2023] [Revised: 07/21/2023] [Accepted: 08/22/2023] [Indexed: 09/17/2023]
Abstract
The current study aimed to evaluate the genetic diversity, level of admixture, and phylogenetic relationship, of the Pakistani horse breeds, along with their morphological characterization. Data for the body measurements showed that Morna horses had the highest values of body height, body length, chest girth, leg length, and head length, whereas the Baluchi horses had the lowest values for these traits. For the genetic diversity 64 animals, 15/breed except for Baluchi(14) and Topras(05), were genotyped by using the 17-plex equine genotyping kit. The AMOVA results showed that 13% of genetic diversity was explained by breed differences, whereas 27% and 60% came from among and within individuals respectively. The highest values of genetic diversity parameters including Na(7.29±0.29), Ne(5.73±0.28), Ho(0.74±0.05) and He(0.82±0.01) were observed for Morna, whereas their lowest values were found for Topras. However, the highest value of inbreeding coefficient (Fis) was found for Baluchi and the lowest for KB horses. Among the markers, CA425 was found as the most polymorphic and ASB23 as the least polymorphic and highly fixed marker. Results of structure analysis revealed that, except Topras, each local horse breed had very admixed genetic structure perhaps due to their continuous crossing with other breeds in the past. Moreover, the structure analysis also showed that Morna and Shiean breeds had mixing of each other which was also confirmed by the lowest value of their pairwise Fst values and likewise the phylogenetic analysis also showed their close genetic relationship with each other. The phylogenetic analysis also revealed that Shiean breed had close genetic relationship with Arabian horses. Collectively, our data showed that Morna is the largest and genetically most diverse horse breed of Pakistan, whereas Baluchi horses are the smallest in size and have the highest values of inbreeding coefficient. And the phylogeny analysis showed that Shiean breed had close genetic relationship with the Arabian.
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Affiliation(s)
- Muhammad Sohail Ashraf
- Genetics and Genomics Laboratory, Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Pattoki, Pakistan
| | - Atia Basheer
- Genetics and Genomics Laboratory, Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Pattoki, Pakistan
| | - Farheena Iqbal
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Imran Zahoor
- Genetics and Genomics Laboratory, Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Pattoki, Pakistan.
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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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Criscione A, Mastrangelo S, D'Alessandro E, Tumino S, Di Gerlando R, Zumbo A, Marletta D, Bordonaro S. Genome-wide survey on three local horse populations with a focus on runs of homozygosity pattern. J Anim Breed Genet 2022; 139:540-555. [PMID: 35445758 PMCID: PMC9541879 DOI: 10.1111/jbg.12680] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 02/04/2022] [Accepted: 04/04/2022] [Indexed: 11/26/2022]
Abstract
Purosangue Orientale Siciliano, Sanfratellano and Siciliano represent the Sicilian equine genetic resource. This study aimed to investigate the genetic diversity, population structure and the pattern of autozygosity of Sicilian horse populations using genome‐wide single‐nucleotide polymorphism (SNP) data generated with the Illumina Equine SNP70 array. The genotyping data of 17 European and Middle East populations were also included in the study. The patterns of genetic differentiation, model‐based clustering and Neighbour‐Net showed the expected positioning of Sicilian populations within the wide analysed framework and the close connections between the Purosangue Orientale Siciliano and the Arab as well as between Sanfratellano, Siciliano and Maremmano. The highest expected heterozygosity (He) and contemporary effective population size (cNe) were reported in Siciliano (He = 0.323, cNe = 397), and the lowest were reported in Purosangue Orientale Siciliano (He = 0.277, cNe = 10). The analysis of the runs of homozygosity and the relative derived inbreeding revealed high internal homogeneity in Purosangue Orientale Siciliano and Arab horses, intermediate values in Maremmano and Sanfratellano and high heterogeneity in the Siciliano population. The genome‐wide SNP analysis showed the selective pressure on Purosangue Orientale Siciliano towards traits related to endurance performance. Our results underline the importance of planning adequate conservation and exploitation programmes to reduce the level of inbreeding and, therefore, the loss of genetic diversity.
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Affiliation(s)
- Andrea Criscione
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | | | - Serena Tumino
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
| | - Rosalia Di Gerlando
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | - Alessandro Zumbo
- Dipartimento di Scienze Veterinarie, Università di Messina, Messina, Italy
| | - Donata Marletta
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
| | - Salvatore Bordonaro
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
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Yun J, Oyungerel B, Kong HS. Genetic diversity and population structure of Mongolian regional horses with 14 Microsatellite markers. Anim Biosci 2022; 35:1121-1128. [PMID: 35240022 PMCID: PMC9262727 DOI: 10.5713/ab.21.0497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/16/2022] [Indexed: 11/27/2022] Open
Abstract
Objective This study aimed to identify the genetic diversity and population structure of Mongolian horse populations according to the province of residence (Khentii, KTP; Uvs, USP; Omnogovi and Dundgovi, GOP; Khovsgol, KGP) using 14 microsatellite (MS) markers. Methods A total of 269 whole blood samples were obtained from the four populations (KTP, USP, GOP, KGP) geographically distinct provinces. Multiplex polymerase chain reaction (PCR) was conducted using 14 MS markers (AHT4, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG6, HTG7, and VHL20), as recommended by the International Society for Animal Genetics. Capillary electrophoresis was conducted using the amplified PCR products, alleles were determined. Alleles were used for statistical analysis of genetic variability, Nei’s DA genetic distance, principal coordinate analysis (PCoA), factorial corresponding analysis (FCA), and population structure. Results On average, the number of alleles, expected heterozygosity (HExp), observed heterozygosity (HObs), and polymorphic information content among all populations were 11.43, 0.772, 0.757, and 0.737, respectively. In the PCoA and FCA, GOP, and KGP were genetically distinct from other populations, and the KTP and USP showed a close relationship. The two clusters identified using Nei’s DA genetic distance analysis and population structure highlighted the presence of structurally clear genetic separation. Conclusion Overall, the results of this study suggest that genetic diversity between KTP and USP was low, and that between GOP and KGP was high. It is thought that these results will help in the effective preservation and improvement of Mongolian horses through genetic diversity analysis and phylogenetic relationships.
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Genetic Variability Trend of Lusitano Horse Breed Reared in Italy. Animals (Basel) 2022; 12:ani12010098. [PMID: 35011204 PMCID: PMC8749805 DOI: 10.3390/ani12010098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 12/20/2021] [Accepted: 12/29/2021] [Indexed: 11/17/2022] Open
Abstract
The Lusitano Horse (LH) originates from Portugal, but is reared worldwide. Since 1994, the University of Milan has routinely tested the LHs bred in Italy for parentage control. This study aims to assess the genetic variability of the LH reared in Italy using 16 microsatellites markers. Moreover, the genetic variability changes over the years in the total population (n.384) and in unrelated horses (n.47) were evaluated. Horses were grouped according to their date of birth (1975–1990, 1991–2000, 2001–2010, 2010–2019). Standard genetic diversity parameters, including observed (Ho) and expected (He) heterozygosity, Hardy-Weinberg equilibrium (HWE; P-Val), allelic richness, and inbreeding coefficient (Fis) were estimated. In the whole period, the total population showed Ho as high as 0.69, low Fis (0.057), and imbalance for HWE. When considering the unrelated horses, Ho was seen to increase over time (from 0.594 in 1975–1990 to 0.68 in 2010–2019) and frequencies were in HWE, again having low and decreasing values of Fis (from 0.208 in 1975–1990 to 0.019 in 2010–2019). Bottleneck analysis excluded a recent population decline. Principal Coordinate Analysis at the individual level defined two clusters, the major cluster including all the most recent horses. An increasing number of dams (156% more from 2001–2010 to 2011–2019) supports the good variability recorded in the population so far. However, the high number of foals (77.2%) sired by only four stallions in recent years suggests caution in the choice of the sires for the future.
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Assessment of genetic diversity and population structure of Colombian Creole cattle using microsatellites. Trop Anim Health Prod 2021; 53:122. [PMID: 33443652 DOI: 10.1007/s11250-021-02563-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 01/05/2021] [Indexed: 10/22/2022]
Abstract
To establish the diversity, structure, and phylogenetic relationships among Colombian Creole cattle, six native breeds and one introduced breed were genotyped for 20 microsatellite loci. The average number of alleles per breed ranged from 7050 (Romosinuano) to 10,100 (Casanareño), and the expected heterozygosity ranged from 0.691 (San martinero) to 0.785 (Casanareño). The deviation from the Hardy-Weinberg equilibrium (HWE) was statistically significant (p < 0.05) in 59 out of 120 tests carried out in the six breeds for the 20 microsatellite loci analyzed. Colombian Creole bovine breeds have maintained a high level of genetic differentiation within the same populations (93%), and the rest is explained by differences between breeds (7%). The differentiation pattern and the genetic relationships between the Colombian Creole bovine breeds showed high consistency with the evolutionary history of each. Both the Bayesian grouping analysis and the neighbor-joining tree exhibited a reliable grouping pattern, which revealed two main groups: one comprised by the breeds Blanco Orejinegro, Hartón del Valle, Costeño Con Cuernos, Romosinuano, and San Martinero, and the other one by the Creole breed Casanareño and Zebu. These were probably caused by different historical, reproductive, and geographic isolation precedents, as well as by different levels of inbreeding. This study will help understand the genetic characteristics of Colombian Creole cattle and will benefit future conservation programs.
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Koseman A, Ozsensoy Y, Erdogan M, Yarali C, Toprak B, Zengin K, Seker I. Investigation of Genetic Variations using Microsatellite Markers in Colored Horses in Turkey. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420050075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Vázquez-Armijo JF, Parra-Bracamonte GM, Velazquez MA, Sifuentes-Rincón AM, Tinoco-Jaramillo JL, Ambriz-Morales P, Arellano-Vera W, Moreno-Medina VR. Diversity and effective population size of four horse breeds from microsatellite DNA markers in South-Central Mexico. Arch Anim Breed 2017. [DOI: 10.5194/aab-60-137-2017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. The South-Central region of Mexico has experienced a sizeable introduction of purebred horses for recreational aims. A study was designed to assess effective population sizes and genetic diversity and to verify the genetic integrity of four horse breeds. Using a 12-microsatellite panel, Quarter Horse, Azteca, Thoroughbred and Creole (CRL) horses were sampled and analysed for diversity and genetic structure. Genetic diversity parameters showed high numbers of heterozygous horses but small effective population sizes in all breeds. Population structure results suggested some degree of admixture of CRL with the other reference breeds. The highly informative microsatellite panel allowed the verification of diversity in introduced horse populations and the confirmation of small effective population sizes, which suggests a risk for future breed integrity.
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Criscione A, Bordonaro S, Moltisanti V, Marletta D. Differentiation of South Italian goat breeds in the focus of biodiversity conservation. Small Rumin Res 2016. [DOI: 10.1016/j.smallrumres.2016.09.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Pablo Gómez M, Landi V, Martínez AM, Gómez Carpio M, Nogales Baena S, Delgado Bermejo JV, Oom MDM, Luis C, Ouragh L, Vega-Pla JL. Genetic diversity of the semi-feral Marismeño horse breed assessed with microsatellites. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.1080/1828051x.2016.1241132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
| | - Vincenzo Landi
- Departamento de Genética, University of Cordoba, Córdoba, Spain
| | | | | | | | | | - María do Mar Oom
- Centro de Biologia Ambiental, University of Lisboa, Lisboa, Portugal
| | - Cristina Luis
- Centro Interuniversitário de História das Ciências e da Tecnologia, University of Lisboa, Lisboa, Portugal
- Museu Nacional de História Natural e da Ciência, University of Lisboa, Lisboa, Portugal
| | | | - José Luis Vega-Pla
- Laboratorio de Investigación Aplicada, Ministerio de Defensa, Cordoba, Spain
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Zuccaro A, Bordonaro S, Longeri M, Cristina Cozzi M, Guastella AM, D’Urso G, Marletta D. Mitochondrial DNA control region variation in Sanfratellano horse and two other Sicilian autochthonous breeds. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2009.s2.180] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Antonio Zuccaro
- DACPA, Sezione di Scienze delle Produzioni Animali, Università di Catania, Italy
| | - Salvatore Bordonaro
- DACPA, Sezione di Scienze delle Produzioni Animali, Università di Catania, Italy
| | - Maria Longeri
- Dipartimento di Scienze Animali, Università di Milano, Italy
| | | | - Anna Maria Guastella
- DACPA, Sezione di Scienze delle Produzioni Animali, Università di Catania, Italy
| | - Giuseppe D’Urso
- DACPA, Sezione di Scienze delle Produzioni Animali, Università di Catania, Italy
| | - Donata Marletta
- DACPA, Sezione di Scienze delle Produzioni Animali, Università di Catania, Italy
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Ivanković A, Ramljak J, Dovč P, Kelava N, Konjačić M. Genetic structure of three Croatian horse breeds: implications for their conservation strategy. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2009.677] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Rahimi-Mianji G, Nejati-Javaremi A, Farhadi A. Genetic diversity, parentage verification, and genetic bottlenecks evaluation in iranian turkmen horse1. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415090082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Felicetti M, Lopes MS, Verini-Supplizi A, Machado ADC, Silvestrelli M, Mendonça D, Distl O. Genetic diversity in the Maremmano horse and its relationship with other European horse breeds. Anim Genet 2015; 41 Suppl 2:53-5. [PMID: 21070276 DOI: 10.1111/j.1365-2052.2010.02102.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Maremmano is an Italian warmblood horse breed from central Italy. We characterized the genetic diversity and the degree of admixture in Maremmano in comparison to 14 other European horse breeds using 30 microsatellites. Between-breed diversity explained about 9 per cent of the total genetic diversity. Cluster analysis, genetic distances and genetic differentiation coefficients showed a close relationship of Maremmano with Hanoverian and Lusitano in accordance with breed history.
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Affiliation(s)
- M Felicetti
- Department of Pathology, Diagnostic and Veterinary Clinic, University of Perugia, Via San Costanzo 4, 06126 Perugia, Italy
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Coizet B, Nicoloso L, Marletta D, Tamiozzo-Calligarich A, Pagnacco G, Crepaldi P. Variation in Salivary and Pancreatic Alpha-Amylase Genes in Italian Horse Breeds. J Hered 2014; 105:429-35. [DOI: 10.1093/jhered/esu005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Bordonaro S, Guastella AM, Criscione A, Zuccaro A, Marletta D. Genetic diversity and variability in endangered Pantesco and two other Sicilian donkey breeds assessed by microsatellite markers. ScientificWorldJournal 2012; 2012:648427. [PMID: 22649301 PMCID: PMC3353311 DOI: 10.1100/2012/648427] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2011] [Accepted: 11/22/2011] [Indexed: 11/22/2022] Open
Abstract
The genetic variability of Pantesco and other two Sicilian autochthonous donkey breeds (Ragusano and Grigio Siciliano) was assessed using a set of 14 microsatellites. The main goals were to describe the current differentiation among the breeds and to provide genetic information useful to safeguard the Pantesco breed as well as to manage Ragusano and Grigio Siciliano. In the whole sample, that included 108 donkeys representative of the three populations, a total of 85 alleles were detected. The mean number of alleles was lower in Pantesco (3.7), than in Grigio Siciliano and Ragusano (4.4 and 5.9, resp.). The three breeds showed a quite low level of gene diversity (He) ranging from 0.471 in Pantesco to 0.589 in Grigio. The overall genetic differentiation index (Fst) was quite high; more than 10% of the diversity was found among breeds. Reynolds' (DR) genetic distances, correspondence, and population structure analysis reproduced the same picture, revealing that, (a) Pantesco breed is the most differentiated in the context of the Sicilian indigenous breeds, (b) within Ragusano breed, two well-defined subgroups were observed. This information is worth of further investigation in order to provide suitable data for conservation strategies.
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Affiliation(s)
- Salvatore Bordonaro
- DISPA, Sezione di Scienze delle Produzioni Animali, Università degli studi di Catania, Via Valdisavoia 5, 95123 Catania, Italy
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Bigi D, Perrotta G. Genetic structure and differentiation of the Italian catria horse. ACTA ACUST UNITED AC 2012; 103:134-9. [PMID: 22156056 DOI: 10.1093/jhered/esr121] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Catria is 1 of the 22 native Italian horse breeds that now survive from a larger number. Thirty individuals, representative of the Catria horse, were analyzed for 11 microsatellites and compared with data of 10 breeds reared in Italy. Three different approaches, genetic distances, correspondence analysis, and clustering methods, were considered to study genetic relationships among Catria and the other horse populations. Genetic differentiation among breeds was highly significant (P < 0.01) for all loci. Average F(ST) values indicate that around 10% of the total genetic variation was explained by the between-breed differences and the 3 approaches utilized gave similar results. Italian native breeds are clearly separated from the other examined breeds. However, by the correspondence analysis, the Catria appears closer to Maremmano and Murgese. The results of Bayesian approaches give further information showing for Catria a common origin with Maremmano and Italian Heavy Draught. Genetic relationships among Catria and the other breeds are consistent with the breed's documented history. The data and information found here can be utilized in the organization of conservation programmes planned to reduce inbreeding and to minimize loss of genetic variability.
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Affiliation(s)
- Daniele Bigi
- Dipartimento di Protezione e Valorizzazione Agroalimentare(DIPROVAL)-Sezione Allevamenti Zootecnici, Faculty of Agriculture, University of Bologna, Via F.lli Rosselli 107, 42123 Reggio Emilia, Italy.
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Tolone M, Mastrangelo S, Rosa A, Portolano B. Genetic diversity and population structure of Sicilian sheep breeds using microsatellite markers. Small Rumin Res 2012. [DOI: 10.1016/j.smallrumres.2011.09.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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20
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Guastella AM, Zuccaro A, Criscione A, Marletta D, Bordonaro S. Genetic analysis of Sicilian autochthonous horse breeds using nuclear and mitochondrial DNA markers. ACTA ACUST UNITED AC 2011; 102:753-8. [PMID: 21914666 DOI: 10.1093/jhered/esr091] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Genetic diversity and relationship among 3 Sicilian horse breeds were investigated using 16 microsatellite markers and a 397-bp length mitochondrial D-loop sequence. The analysis of autosomal DNA was performed on 191 horses (80 Siciliano [SIC], 61 Sanfratellano [SAN], and 50 Sicilian Oriental Purebred [SOP]). SIC and SAN breeds were notably higher in genetic variability than the SOP. Genetic distances and cluster analysis showed a close relationship between SIC and SAN breeds, as expected according to the breeds' history. Sequencing of hypervariable mitochondrial DNA region was performed on a subset of 60 mares (20 for each breed). Overall, 20 haplotypes with 31 polymorphic sites were identified: A higher haplotype diversity was detected in SIC and SAN breeds, with 13 and 11 haplotypes respectively, whereas only one haplotype was found in SOP. These were compared with 118 sequences from GenBank. BLAST showed that 17 of the 20 haplotypes had been reported previously in other breeds. One haplotype, found in SIC, traces back to a Bronze Age archaeological site (Inner Mongolia). The 3 Sicilian breeds are now rare, and 2 of them are officially endangered. Our results represent a valuable tool for management strategies as well as for conservation purposes.
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Affiliation(s)
- Anna Maria Guastella
- DISPA Sezione di Scienze delle Produzioni Animali, Università degli Studi di Catania, via Valdisavoia, 5, 95123 Catania, Italy
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Zhong T, Han J, Guo J, Zhao Q, Fu B, He X, Jeon J, Guan W, Ma Y. Genetic diversity of Chinese indigenous sheep breeds inferred from microsatellite markers. Small Rumin Res 2010. [DOI: 10.1016/j.smallrumres.2010.02.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Dalvit C, De Marchi M, Zanetti E, Cassandro M. Genetic variation and population structure of Italian native sheep breeds undergoing in situ conservation. J Anim Sci 2009; 87:3837-44. [PMID: 19717776 DOI: 10.2527/jas.2008-1682] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The genetic variability and presence of population substructures in 4 native Northern Italian sheep breeds, Alpagota, Brogna, Foza, and Lamon, undergoing in situ conservation, and 1 widespread Italian breed, Bergamasca, were studied by investigating 19 microsatellite markers. The breeds showed considerable genetic variability in terms of number of alleles and heterozygosity, with the exception of Alpagota, which was the least variable (0.607). Nevertheless, a significant deficit of heterozygotes was observed in each breed due to rather increased levels of inbreeding or to the presence of population substructures, probably caused by increased genetic variation in the founder populations. The analyses evidenced clear genetic differentiation (F(ST) = 0.085), reduced levels of admixture, and presence of private alleles among the breeds, confirming their genetic uniqueness. In particular, according to Reynolds genetic distances, Alpagota was the most differentiated, perhaps because it had been bred mostly in a rather isolated area. Loss of any of the investigated breeds would result in a loss of genetic diversity ranging from 0.5 to 1.6% of the total observed gene diversity. Results supported the decision to safeguard these breeds as important reservoirs of genetic diversity and suggested breeding and mating practices to maintain variability and to overcome within-breed substructures.
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Affiliation(s)
- C Dalvit
- Dipartimento di Scienze Animali, Università degli Studi di Padova, Viale dell'Università 16, 35020 Legnaro (PD), Italy.
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Lucas ZL, McLoughlin PD, Coltman DW, Barber C. Multiscale analysis reveals restricted gene flow and a linear gradient in heterozygosity for an island population of feral horses. CAN J ZOOL 2009. [DOI: 10.1139/z09-019] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We studied the genetic (microsatellite) diversity of a feral population of horses ( Equus caballus L., 1758) on Sable Island, Nova Scotia, Canada (1983–2003), at two spatial scales: (1) for the island as a whole and (2) at the level of four equally sized subdivisions along the length of Sable Island, which is a long (42 km) and narrow (1.5 km) vegetated sand bar. At the island scale (n = 264 horses), observed heterozygosity over 10 loci was 0.647 ± 0.035 (mean ± 1 SE), while expected heterozygosity was 0.696 ± 0.029; we observed significant heterozygote deficiency with all loci considered (P < 0.0001). At the subdivision scale, observed heterozygosity ranged from 0.589 to 0.694 in a gradient from west to east. We observed a corresponding gradient in effective number of alleles and allelic richness. Pairwise values of FST were significant for most subdivision pairs, ranging as high as 0.067 from west to east. Western areas showed highest levels of inbreeding (FIS = 0.113) with outbreeding indicated in the east (FIS = –0.008). Our results suggest that for a large mammal that lives in polygynous social groups, like the feral horse, gene flow along linear habitats (corridors) may be restricted (relative to the dispersal capabilities of the species), even over short distances.
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Affiliation(s)
- Z. L. Lucas
- Sable Island Green Horse Society, P.O. Box 64, Halifax CRO, Halifax, NS B3J 2L4, Canada
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- Department of Biology, Saint Mary's University, 923 Robie Street, Halifax, NS B3H 3C3, Canada
| | - P. D. McLoughlin
- Sable Island Green Horse Society, P.O. Box 64, Halifax CRO, Halifax, NS B3J 2L4, Canada
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- Department of Biology, Saint Mary's University, 923 Robie Street, Halifax, NS B3H 3C3, Canada
| | - D. W. Coltman
- Sable Island Green Horse Society, P.O. Box 64, Halifax CRO, Halifax, NS B3J 2L4, Canada
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- Department of Biology, Saint Mary's University, 923 Robie Street, Halifax, NS B3H 3C3, Canada
| | - C. Barber
- Sable Island Green Horse Society, P.O. Box 64, Halifax CRO, Halifax, NS B3J 2L4, Canada
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- Department of Biology, Saint Mary's University, 923 Robie Street, Halifax, NS B3H 3C3, Canada
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