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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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Susana Lopes M, Azevedo AR, Mendonça D, Rojer H, Cabral V, Ceraolo F, Canto Brum C, Mendes B, da Câmara Machado A. Morphological and genetic characterization of the Graciosa donkey breed. JOURNAL OF APPLIED ANIMAL RESEARCH 2023. [DOI: 10.1080/09712119.2023.2171421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Affiliation(s)
- Maria Susana Lopes
- Centro de Biotecnologia dos Açores, Universidade dos Açores, Angra do Heroísmo, Açores, Portugal
| | - Ana Rita Azevedo
- Centro de Biotecnologia dos Açores, Universidade dos Açores, Angra do Heroísmo, Açores, Portugal
| | - Duarte Mendonça
- Centro de Biotecnologia dos Açores, Universidade dos Açores, Angra do Heroísmo, Açores, Portugal
| | - Horst Rojer
- Centro de Biotecnologia dos Açores, Universidade dos Açores, Angra do Heroísmo, Açores, Portugal
| | - Verónica Cabral
- Centro de Biotecnologia dos Açores, Universidade dos Açores, Angra do Heroísmo, Açores, Portugal
| | - Franco Ceraolo
- Associação de Criadores e Amigos do Burro Anão da Ilha Graciosa, Açores, Portugal
| | - Carlos Canto Brum
- Associação de Criadores e Amigos do Burro Anão da Ilha Graciosa, Açores, Portugal
| | - Bruno Mendes
- CRL, Unicol-Cooperativa Agrícola, Açores, Portugal
| | - Artur da Câmara Machado
- Centro de Biotecnologia dos Açores, Universidade dos Açores, Angra do Heroísmo, Açores, Portugal
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Wang T, Liu Z, Shi X, Zhang Z, Li Y, Huang B, Ren W, Wang X, Wang C, Chai W. An investigation of genetic diversity in three Dezhou donkey original breeding farms. Sci Rep 2023; 13:11203. [PMID: 37433834 DOI: 10.1038/s41598-023-38219-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/05/2023] [Indexed: 07/13/2023] Open
Abstract
Dezhou donkey is one of the excellent large donkey breeds in China. In our study, eight microsatellite markers were used to genotype from each of three populations of Chinese Dezhou donkeys: 67 individuals in Liaocheng (pop1), 103 individuals in Binzhou 1 (pop2), and 102 individuals in Binzhou 2 (pop3), in order to study the genetic diversity of these populations. A total of 213 alleles were detected, and the PIC results showed that eight loci were all highly polymorphic. The means of Ho and He of pop2 were the highest, which were 0.646 and 0.717, respectively. The PCoA analysis demonstrated that the samples from three conservation farms were mixed together. The phylogenetic tree showed that pop 2 and pop 3 were closely related. The phylogenetic tree results clustered that 272 donkeys were divided into six groups. AMOVA analysis showed that the genetic variation was mainly concentrated within the population and the genetic differentiation among the populations was low. Fst values between populations also indicated that genetic differentiation between populations was too small to be considered. This indicated a low probability of inbreeding within the population. And this also showed that the conservation and breeding of Dezhou donkeys in recent years have achieved excellent results. The investigation of genetic diversity in three Dezhou donkey original breeding farms can provide reference data for the selection and breeding of excellent breeds of Dezhou donkey.
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Affiliation(s)
- Tianqi Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China
| | - Ziwen Liu
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China
| | - Xiaoyuan Shi
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China
| | - Zhenwei Zhang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China
| | - Yuhua Li
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China
| | - Bingjian Huang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China
| | - Wei Ren
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China
| | - Xinrui Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China
| | - Changfa Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China.
| | - Wenqiong Chai
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China.
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Wang Y, Hua X, Shi X, Wang C. Origin, Evolution, and Research Development of Donkeys. Genes (Basel) 2022; 13:1945. [PMID: 36360182 PMCID: PMC9689456 DOI: 10.3390/genes13111945] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 08/11/2023] Open
Abstract
Lack of archaeological and whole-genome diversity data has restricted current knowledge of the evolutionary history of donkeys. With the advancement of science and technology, the discovery of archaeological evidence, the development of molecular genetics, and the improvement of whole-genome sequencing technology, the in-depth understanding of the origin and domestication of donkeys has been enhanced, however. Given the lack of systematic research, the present study carefully screened and collected multiple academic papers and books, journals, and literature on donkeys over the past 15 years. The origin and domestication of donkeys are reviewed in this paper from the aspects of basic information, cultural origin, bioarcheology, mitochondrial and chromosomal microsatellite sequences, and whole-genome sequence comparison. It also highlights and reviews genome assembly technology, by assembling the genome of an individual organism and comparing it with related sample genomes, which can be used to produce more accurate results through big data statistics, analysis, and computational correlation models. Background: The donkey industry in the world and especially in China is developing rapidly, and donkey farming is transforming gradually from the family farming model to large-scale, intensive, and integrated industrial operations, which could ensure the stability of product quality and quantity. However, theoretical research on donkey breeding and its technical development lags far behind that of other livestock, thereby limiting its industrial development. This review provides holistic information for the donkey industry and researchers, that could promote theoretical research, genomic selection (GS), and reproductive management of the donkey population.
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Mira F, Canuti M, Di Bella S, Puleio R, Lavazza A, Lelli D, Vicari D, Purpari G, Cannella V, Chiaramonte G, Schirò G, Castronovo C, Guercio A. Detection and Molecular Characterization of Two Gammaherpesviruses from Pantesco Breed Donkeys during an Outbreak of Mild Respiratory Disease. Viruses 2021; 13:v13081527. [PMID: 34452391 PMCID: PMC8402663 DOI: 10.3390/v13081527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 11/30/2022] Open
Abstract
Equid and asinine gammaherpesviruses (GHVs; genus Percavirus) are members of the Herpesviridae family. Though GHVs have been reported in horse populations, less studies are available on gammaherpesviral infections in donkeys. This study reports the co-infection with two GHVs in Pantesco breed donkeys, an endangered Italian donkey breed. Samples (n = 124) were collected on a breeding farm in Southern Italy from 40 donkeys, some of which were healthy or presented erosive tongue lesions and/or mild respiratory signs. Samples were analysed by using a set of nested PCRs targeting the DNA polymerase, glycoprotein B, and DNA-packaging protein genes, and sequence and phylogenetic analyses were performed. Twenty-nine donkeys (72.5%) tested positive, and the presence of Equid gammaherpesvirus 7 and asinine herpesvirus 5 was evidenced. In 11 animals, we found evidence for co-infection with viruses from the two species. Virions with herpesvirus-like morphology were observed by electron microscopic examination, and viruses were successfully isolated in RK-13-KY cell monolayers. The histological evaluation of tongue lesions revealed moderate lympho-granulocytic infiltrates and rare eosinophilic inclusions. The detection of GHVs in this endangered asinine breed suggests the need long-life monitoring within conservation programs and reinforces the need for further investigations of GHV’s pathogenetic role in asinine species.
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Affiliation(s)
- Francesco Mira
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (R.P.); (D.V.); (G.P.); (V.C.); (G.C.); (G.S.); (C.C.); (A.G.)
- Correspondence: (F.M.); (S.D.B.)
| | - Marta Canuti
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John’s, NL A1B 3X9, Canada;
| | - Santina Di Bella
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (R.P.); (D.V.); (G.P.); (V.C.); (G.C.); (G.S.); (C.C.); (A.G.)
- Correspondence: (F.M.); (S.D.B.)
| | - Roberto Puleio
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (R.P.); (D.V.); (G.P.); (V.C.); (G.C.); (G.S.); (C.C.); (A.G.)
| | - Antonio Lavazza
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna “Bruno Ubertini”, Via Bianchi n. 9, 25124 Brescia, Italy; (A.L.); (D.L.)
| | - Davide Lelli
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna “Bruno Ubertini”, Via Bianchi n. 9, 25124 Brescia, Italy; (A.L.); (D.L.)
| | - Domenico Vicari
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (R.P.); (D.V.); (G.P.); (V.C.); (G.C.); (G.S.); (C.C.); (A.G.)
| | - Giuseppa Purpari
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (R.P.); (D.V.); (G.P.); (V.C.); (G.C.); (G.S.); (C.C.); (A.G.)
| | - Vincenza Cannella
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (R.P.); (D.V.); (G.P.); (V.C.); (G.C.); (G.S.); (C.C.); (A.G.)
| | - Gabriele Chiaramonte
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (R.P.); (D.V.); (G.P.); (V.C.); (G.C.); (G.S.); (C.C.); (A.G.)
| | - Giorgia Schirò
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (R.P.); (D.V.); (G.P.); (V.C.); (G.C.); (G.S.); (C.C.); (A.G.)
| | - Calogero Castronovo
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (R.P.); (D.V.); (G.P.); (V.C.); (G.C.); (G.S.); (C.C.); (A.G.)
| | - Annalisa Guercio
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (R.P.); (D.V.); (G.P.); (V.C.); (G.C.); (G.S.); (C.C.); (A.G.)
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Maternal Phylogenetic Relationships and Genetic Variation among Rare, Phenotypically Similar Donkey Breeds. Genes (Basel) 2021; 12:genes12081109. [PMID: 34440283 PMCID: PMC8392470 DOI: 10.3390/genes12081109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/02/2021] [Accepted: 07/13/2021] [Indexed: 11/17/2022] Open
Abstract
The mitochondrial DNA (mtDNA) D-loop of endangered and critically endangered breeds has been studied to identify maternal lineages, characterize genetic inheritance, reconstruct phylogenetic relations among breeds, and develop biodiversity conservation and breeding programs. The aim of the study was to determine the variability remaining and the phylogenetic relationship of Martina Franca (MF, with total population of 160 females and 36 males), Ragusano (RG, 344 females and 30 males), Pantesco (PT, 47 females and 15 males), and Catalonian (CT) donkeys by collecting genetic data from maternal lineages. Genetic material was collected from saliva, and a 350 bp fragment of D-loop mtDNA was amplified and sequenced. Sequences were aligned and evaluated using standard bioinformatics software. A total of 56 haplotypes including 33 polymorphic sites were found in 77 samples (27 MF, 22 RG, 8 PT, 19 CT, 1 crossbred). The breed nucleotide diversity value (π) for all the breeds was 0.128 (MF: 0.162, RG: 0.132, PT: 0.025, CT: 0.038). Principal components analysis grouped most of the haplogroups into two different clusters, I (including all haplotypes from PT and CT, together with haplotypes from MF and RG) and II (including haplotypes from MF and RG only). In conclusion, we found that the primeval haplotypes, haplogroup variability, and a large number of maternal lineages were preserved in MF and RG; thus, these breeds play putative pivotal roles in the phyletic relationships of donkey breeds. Maternal inheritance is indispensable genetic information required to evaluate inheritance, variability, and breeding programs.
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Abstract
The equid family contains only one single extant genus, Equus, including seven living species grouped into horses on the one hand and zebras and asses on the other. In contrast, the equine fossil record shows that an extraordinarily richer diversity existed in the past and provides multiple examples of a highly dynamic evolution punctuated by several waves of explosive radiations and extinctions, cross-continental migrations, and local adaptations. In recent years, genomic technologies have provided new analytical solutions that have enhanced our understanding of equine evolution, including the species radiation within Equus; the extinction dynamics of several lineages; and the domestication history of two individual species, the horse and the donkey. Here, we provide an overview of these recent developments and suggest areas for further research.
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Affiliation(s)
- Pablo Librado
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France;
| | - Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France;
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Genetic Characterization of Native Donkey ( Equus asinus) Populations of Turkey Using Microsatellite Markers. Animals (Basel) 2020; 10:ani10061093. [PMID: 32599857 PMCID: PMC7341297 DOI: 10.3390/ani10061093] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/18/2020] [Accepted: 06/18/2020] [Indexed: 11/20/2022] Open
Abstract
Simple Summary This study was conducted to evaluate the genetic variability of Turkish native donkey (Equus asinus) populations, using polymorphism of 17 microsatellite markers. The results revealed a highly mixed genotype of all the examined donkeys, suggesting that two different group of breeds can be distinguished from each other on the basis of microsatellite markers. Abstract This study presents the first insights to the genetic diversity and structure of the Turkish donkey populations. The primary objectives were to detect the main structural features of Turkish donkeys by microsatellite markers. A panel of 17 microsatellite markers was applied for genotyping 314 donkeys from 16 locations of Turkey. One hundred and forty-two alleles were identified and the number of alleles per locus ranged from 4 to 12. The highest number of alleles was observed in AHT05 (12) and the lowest in ASB02 and HTG06 (4), while ASB17 was monomorphic. The mean HO in the Turkish donkey was estimated to be 0.677, while mean HE was 0.675. The polymorphic information content (PIC) was calculated for each locus and ranged from 0.36 (locus ASB02) to 0.98 (locus AHT05), which has the highest number of alleles per locus in the present study. The average PIC in our populations was 0.696. The average coefficient of gene differentiation (GST) over the 17 loci was 0.020 ± 0.037 (p < 0.01). The GST values for single loci ranged from −0.004 for LEX54 to 0.162 for COR082. Nei’s gene diversity index (Ht) for loci ranged from 0.445 (ASB02) to 0.890 (AHT05), with an average of 0.696. A Bayesian clustering method, the Structure software, was used for clustering algorithms of multi-locus genotypes to identify the population structure and the pattern of admixture within the populations. When the number of ancestral populations varied from K = 1 to 20, the largest change in the log of the likelihood function (ΔK) was when K = 2. The results for K = 2 indicate a clear separation between Clade I (KIR, CAT, KAR, MAR, SAN) and Clade II (MAL, MER, TOK, KAS, KUT, KON, ISP, ANT, MUG, AYD and KAH) populations.
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Stanisic L, Aleksić JM, Dimitrijevic V, Kovačević B, Stevanovic J, Stanimirovic Z. Banat donkey, a neglected donkey breed from the central Balkans (Serbia). PeerJ 2020; 8:e8598. [PMID: 32175186 PMCID: PMC7059758 DOI: 10.7717/peerj.8598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/19/2020] [Indexed: 11/20/2022] Open
Abstract
The dominant donkey breed in the Balkans is the mid-sized Balkan donkey with a grey to chocolate coat color. Local breeders from Serbia, however, still maintain a few larger individuals of a lighter coat color, named Banat donkey, and speculate that they are descendants of a Spanish donkey heard that had been transferred to the Banat region by the Hapsburg Queen Maria Theresa in the XVIII century for a specific purpose, to work in local vineyards. We have previously found a unique nuclear gene-pool and a prevalence of mitochondrial Clade 2 haplotypes in several such animals. In this study, we: (i) perform a comparative analysis of 18 morphological traits of the Banat donkey (seven individuals), Balkan donkey (53 individuals from two sub-populations of this breed) and the potential hybrids (eight individuals), and demonstrate the morphological distinctiveness of the Banat donkey, highlighting the diagnostic traits for distinguishing the breed: hip height, croup width, body length and chest depth; (ii) re-analyse published nuclear microsatellite data for these groups, and reveal that, although severely depopulated, the genetically distinct Banat donkey is not severely affected by the loss of genetic diversity and inbreeding; (iii) demonstrate that previously published Banat donkey mitochondrial haplotypes, analyzed genealogically together with those reported in ancient and modern individuals from Spain, Italy, Turkey, Cyprus and Africa, are shared with three Spanish breeds and individuals belonging to Amiata and some other Italian breeds. A unique morphological feature present in Banat and Somali wild donkeys, but also in Amiata donkeys, black stripes on legs, suggests that the origin of Clade 2 donkeys may be much more complex than previously thought. Actions to preserve the Banat donkey, a valuable but critically endangered genetic resource (<100 individuals), are urgent.
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Affiliation(s)
- Ljubodrag Stanisic
- Department of Reproduction, Fertility and Artificial Insemination, Faculty of Veterinary Medicine, University of Belgrade, Belgrade, Serbia
| | - Jelena M. Aleksić
- Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade, Belgrade, Serbia
| | - Vladimir Dimitrijevic
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine, University of Belgrade, Belgrade, Serbia
| | - Branislav Kovačević
- Institute of Lowland Forestry and Environment (ILFE), University of Novi Sad, Novi Sad, Serbia
| | - Jevrosima Stevanovic
- Department of Biology, Faculty of Veterinary Medicine, University of Belgrade, Belgrade, Serbia
| | - Zoran Stanimirovic
- Department of Biology, Faculty of Veterinary Medicine, University of Belgrade, Belgrade, Serbia
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Brosnahan MM. Genetics, Evolution, and Physiology of Donkeys and Mules. Vet Clin North Am Equine Pract 2019; 35:457-467. [PMID: 31672199 DOI: 10.1016/j.cveq.2019.08.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The genus Equus is made up of donkeys, horses, and zebras. Despite significant variation in chromosome number across these species, interspecies breeding results in healthy, although infertile, hybrid offspring. Most notable among these are the horse-donkey hybrids, the mule and hinny. Donkeys presently are used for everything from companion animals to beasts of burden. Although closely related from an evolutionary standpoint, differences in anatomy and physiology preclude the assumption that they can be treated identically to the domestic horse. Veterinarians should be aware of these differences and adjust their practice accordingly.
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Affiliation(s)
- Margaret M Brosnahan
- College of Veterinary Medicine, Midwestern University, 19555 North 59th Avenue, Cactus Wren Hall 336-P, Glendale, AZ 85308, USA.
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11
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Zeng L, Dang R, Dong H, Li F, Chen H, Lei C. Genetic diversity and relationships of Chinese donkeys using microsatellite markers. Arch Anim Breed 2019; 62:181-187. [PMID: 31807628 PMCID: PMC6853031 DOI: 10.5194/aab-62-181-2019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 03/05/2019] [Indexed: 12/02/2022] Open
Abstract
Donkeys are one important livestock in China because of their
nourishment and medical values. To investigate the genetic diversity and phylogenetic
relationships of Chinese donkey breeds, a panel of 25 fluorescently labeled
microsatellite markers was applied to genotype 504 animals from 12 Chinese donkey breeds.
A total of 226 alleles were detected, and the expected heterozygosity ranged from 0.6315
(Guanzhong) to 0.6999 (Jiami). The mean value of the polymorphism information content,
observed number of alleles, and expected number of alleles for all the tested Chinese
donkeys were 0.6600, 6.890, and 3.700, respectively, suggesting that Chinese indigenous
donkeys have relatively abundant genetic diversity. Although there were abundant genetic
variations found, the genetic differentiation between the Chinese donkey breeds was
relatively low, which displayed only 5.99 % of the total genetic variance among
different breeds. The principal coordinates analysis clearly splits 12 donkey breeds into
two major groups. The first group included Xiji, Xinjiang, Liangzhou, Kulun, and
Guanzhong donkey breeds. In the other group, Gunsha, Dezhou, Biyang, Taihang, Jiami,
Qingyang, and Qinghai donkeys were clustered together. This grouping pattern was further
supported by structure analysis and neighbor-joining tree analysis. Furthermore, genetic
relationships between different donkey breeds identified in this study were corresponded
to their geographic distribution and breeding history. Our results provide comprehensive
and precise baseline information for further research on preservation and utilization of
Chinese domestic donkeys.
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Affiliation(s)
- Lulan Zeng
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ruihua Dang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Hong Dong
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Fangyu Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
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12
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SHARMA REKHA, SHARMA HIMANI, AHLAWAT SONIKA, PANCHAL POONAM, PAL YASH, BEHL RAHUL, TANTIA MS. Simple sequence repeat (SSR) genotypic data reveal high genetic diversity in Rajasthan donkey of India. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2018. [DOI: 10.56093/ijans.v87i12.79860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Spiti is the only breed of donkey in the list of 160 breeds registered so far for the indigenous germplasm. It points towards the fact that Indian donkey diversity is largely unexplored, in spite of its role in support system of poorest of the poor countrymen. Rajasthan state harbours more than eighty thousand donkey. Genetic diversity underpins population resilience and persistence so a need was felt for the systematic and scientific evaluation of existing diversity in this population. The diversity status of Rajasthan donkey population was investigated by using 20 microsatellite markers. Two of the loci, HMS5 and ASB17, depicted less than 4 alleles and were thus excluded from further analyses. Rajasthan donkey was found to host considerable diversity. This conclusion is evidenced by the number of alleles observed across loci (average 8.16±0.89), and by mean observed heterozygosity (0.688±0.06). Signatures of inbreeding could not be detected by the FIS indices in the Rajasthan donkey population. The population did not suffer any bottleneck in the recent past. The study provides the first scientific assessment of the genetic diversity status of Rajasthan donkey population. This information on the genetic analysis can be used in conjunction with the information on physical and phenotypic characteristics and management practices for registration of this population as a breed.
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Cozzi MC, Valiati P, Cherchi R, Gorla E, Prinsen RTMM, Longeri M, Bagnato A, Strillacci MG. Mitochondrial DNA genetic diversity in six Italian donkey breeds (Equus asinus). Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:409-418. [PMID: 28278690 DOI: 10.1080/24701394.2017.1292505] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Donkeys have played an important role in agricultural land practices and in human historical periods of recent past and, still today, are used as a working power in several world areas. The objective of this study was to identify genetic variability in six Italian donkey breeds using mtDNA D-loop. Fifteen haplotypes, grouped in three haplogroups, were identified. The genetic indices were informative and showed a high population genetic variability. The results of AMOVA analyses based on geographic structuring of Italian populations highlighted that the majority of the observed variance is due to differences among samples within breeds. Comparison among Italian haplotypes and mtDNA D-loop sequences belonging to European domestic and Ethiopian donkeys and wild asses, clearly define two clades referred to Nubian lineage. The results can be useful to complement safeguard planes for donkey breeds that are considered to extinction endangered.
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Affiliation(s)
- Maria Cristina Cozzi
- a Department of Veterinary Medicine , Università degli Studi di Milano , Milano , Italy
| | - Paolo Valiati
- a Department of Veterinary Medicine , Università degli Studi di Milano , Milano , Italy
| | - Raffaele Cherchi
- b Agenzia per la ricerca in agricoltura-AGRIS Sardegna , Sassari , Italy
| | - Erica Gorla
- a Department of Veterinary Medicine , Università degli Studi di Milano , Milano , Italy
| | | | - Maria Longeri
- a Department of Veterinary Medicine , Università degli Studi di Milano , Milano , Italy
| | - Alessandro Bagnato
- a Department of Veterinary Medicine , Università degli Studi di Milano , Milano , Italy
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14
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Kasarda R, Vostrý L, Moravčíková N, Vostrá-Vydrová H, Dovč P, Kadlečík O. Detailed insight into genetic diversity of the Old Kladruber horse substructure in comparison to the Lipizzan breed. ACTA AGR SCAND A-AN 2016. [DOI: 10.1080/09064702.2016.1249400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- R. Kasarda
- Department of Animal Genetics and Breeding Biology, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
| | - L. Vostrý
- Department of Genetics and Breeding, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - N. Moravčíková
- Department of Animal Genetics and Breeding Biology, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
| | | | - P. Dovč
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
| | - O. Kadlečík
- Department of Animal Genetics and Breeding Biology, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
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15
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Matassino D, Cecchi F, Ciani F, Incoronato C, Occidente M, Santoro L, Ciampolini R. Genetic Diversity and Variability in two Italian Autochthonous Donkey Genetic Types Assessed by Microsatellite Markers. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2014.3028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Jordana J, Ferrando A, Miró J, Goyache F, Loarca A, Martínez López OR, Canelón JL, Stemmer A, Aguirre L, Lara MAC, Álvarez LA, Llambí S, Gómez N, Gama LT, Nóvoa MF, Martínez RD, Pérez E, Sierra A, Contreras MA, Guastella AM, Marletta D, Arsenos G, Curik I, Landi V, Martínez A, Delgado JV. Genetic relationships among American donkey populations: insights into the process of colonization. J Anim Breed Genet 2015; 133:155-64. [PMID: 26364918 DOI: 10.1111/jbg.12180] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 07/06/2015] [Indexed: 11/29/2022]
Abstract
This study presents the first insights into the genetic diversity and structure of the American donkey metapopulation. The primary objectives were to detect the main structural features underlying variability among American donkey populations, identify boundaries between differentiated gene pools, and draw the main colonization pathways since the introduction of donkeys into America in the 15th century. A panel of 14 microsatellite markers was applied for genotyping 350 American donkeys from 13 countries. The genetic structure of this metapopulation was analysed using descriptive statistics and Bayesian model-based methods. These populations were then compared to a database containing information on 476 individuals from 11 European breeds to identify the most likely ancestral donor populations. Results showed the presence of two distinct genetic pools, with confluence of the two in Colombia. The southern pool showed a unique genetic signature subsequent to an older founder event, but lacked any significant influence of modern gene flow from Europe. The northern pool, conversely, may have retained more ancestral polymorphisms and/or have experienced modern gene flow from Spanish breeds. The Andalusian and, to a lesser extent, the Catalan breeds have left a more pronounced footprint in some of the American donkey populations analysed.
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Affiliation(s)
- J Jordana
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - A Ferrando
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - J Miró
- Departament de Medicina i Cirurgia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - F Goyache
- Área de Genética y Reproducción Animal, SERIDA-Deva, Gijón, Spain
| | - A Loarca
- Ministerio de Agricultura, Ganadería y Alimentación, Quetzaltenango, Guatemala
| | - O R Martínez López
- Dirección General de Investigación Científica y Tecnológica, Centro Multidisciplinario de Investigaciones Tecnológicas, Universidad Nacional de Asunción, Asunción, Paraguay
| | - J L Canelón
- Departamento de Producción e Industria Animal, Decanato de Ciencias Veterinarias, Universidad Centroccidental Lisandro Alvarado, Barquisimeto, Venezuela
| | - A Stemmer
- Facultad de Ciencias Agrícolas y Pecuarias, Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - L Aguirre
- Centro Biotecnología Reproductiva Animal, Universidad Nacional de Loja, Loja, Ecuador
| | - M A C Lara
- Instituto de Zootecnia, Nova Odessa, SP, Brazil
| | - L A Álvarez
- Sede Palmira, Universidad Nacional de Colombia, Palmira, Valle del Cauca, Colombia
| | - S Llambí
- Instituto de Producción Animal, Área Genética, Facultad de Veterinaria, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - N Gómez
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Micaela Bastidas de Apurímac, Abancay, Peru
| | - L T Gama
- Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Lisboa, Portugal
| | - M F Nóvoa
- AEPGA Associação para o Estudo e Protecção do Gado Asinino, Atenor, Portugal
| | - R D Martínez
- Mejora y Conservación de Recursos Genéticos, Facultad de Ciencias Agrarias, Universidad Nacional de Lomas de Zamora, Llavallol, Argentina
| | - E Pérez
- Departamento de Salud y Explotación Animal, Universidad de Granma, Bayamo, Cuba
| | - A Sierra
- Posgrado e Investigación, Instituto Tecnológico de Conkal, Yucatán, Mexico
| | - M A Contreras
- Escuela de Medicina Veterinaria, UST Sede Santiago, Santiago, Chile
| | - A M Guastella
- Sezione di Scienze delle Produzioni Animali, Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli studi di Catania, Catania, Italy
| | - D Marletta
- Sezione di Scienze delle Produzioni Animali, Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli studi di Catania, Catania, Italy
| | - G Arsenos
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - I Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - V Landi
- Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - A Martínez
- Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - J V Delgado
- Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
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Bertolini F, Scimone C, Geraci C, Schiavo G, Utzeri VJ, Chiofalo V, Fontanesi L. Next Generation Semiconductor Based Sequencing of the Donkey (Equus asinus) Genome Provided Comparative Sequence Data against the Horse Genome and a Few Millions of Single Nucleotide Polymorphisms. PLoS One 2015; 10:e0131925. [PMID: 26151450 PMCID: PMC4495037 DOI: 10.1371/journal.pone.0131925] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/08/2015] [Indexed: 12/13/2022] Open
Abstract
Few studies investigated the donkey (Equus asinus) at the whole genome level so far. Here, we sequenced the genome of two male donkeys using a next generation semiconductor based sequencing platform (the Ion Proton sequencer) and compared obtained sequence information with the available donkey draft genome (and its Illumina reads from which it was originated) and with the EquCab2.0 assembly of the horse genome. Moreover, the Ion Torrent Personal Genome Analyzer was used to sequence reduced representation libraries (RRL) obtained from a DNA pool including donkeys of different breeds (Grigio Siciliano, Ragusano and Martina Franca). The number of next generation sequencing reads aligned with the EquCab2.0 horse genome was larger than those aligned with the draft donkey genome. This was due to the larger N50 for contigs and scaffolds of the horse genome. Nucleotide divergence between E. caballus and E. asinus was estimated to be ~ 0.52-0.57%. Regions with low nucleotide divergence were identified in several autosomal chromosomes and in the whole chromosome X. These regions might be evolutionally important in equids. Comparing Y-chromosome regions we identified variants that could be useful to track donkey paternal lineages. Moreover, about 4.8 million of single nucleotide polymorphisms (SNPs) in the donkey genome were identified and annotated combining sequencing data from Ion Proton (whole genome sequencing) and Ion Torrent (RRL) runs with Illumina reads. A higher density of SNPs was present in regions homologous to horse chromosome 12, in which several studies reported a high frequency of copy number variants. The SNPs we identified constitute a first resource useful to describe variability at the population genomic level in E. asinus and to establish monitoring systems for the conservation of donkey genetic resources.
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Affiliation(s)
- Francesca Bertolini
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, Italy
- Department of Veterinary Sciences, Animal Production Unit, University of Messina, Polo Universitario dell'Annunziata, Messina, Italy
| | - Concetta Scimone
- Department of Veterinary Sciences, Animal Production Unit, University of Messina, Polo Universitario dell'Annunziata, Messina, Italy
| | - Claudia Geraci
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, Italy
| | - Giuseppina Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, Italy
| | - Valerio Joe Utzeri
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, Italy
| | - Vincenzo Chiofalo
- Department of Veterinary Sciences, Animal Production Unit, University of Messina, Polo Universitario dell'Annunziata, Messina, Italy
- Meat Research Consortium, Polo Universitario dell’Annunziata, Messina, Italy
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, Italy
- * E-mail:
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18
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Abstract
Most donkey and local horse breeds are vulnerable to extinction as mechanization of agriculture progress throughout the world. The present study analyzed the pedigree and herd records of the donkey Asinina de Miranda breed (RAM), identifying genealogical and human factors that may affect the breed genetic diversity in the future and suggesting suitable strategies to breed preservation, early on the conservation program. The breeding rate was very low, with a ratio of foaling/live animals of 0.23 (178/760). The estimated number of founders and ancestors contributing to the reference population was 128 and 121. The number of founder herds in the reference population was 64, with an effective number of founder herds for the reference population of 7.6. The mean age of herd owners was 65.50 ± 0.884 years, with a negative association among the herd size and owner's age (P<0.001). In contrast, the size of the herd and the ownership of a male were both positively associated (P<0.001) with the herd number of in-born foals. Both the owners' age and the herd location (RAM home region v. dispersal region) were negatively associated with the foaling number (P<0.001). The main identified risk factors were: low breeding rates; low number of males and their unequal contribution to the genetic pool; unequal contribution of the herds to genetic pool; and advanced age of herd owners.
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19
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Bordonaro S, Dimauro C, Criscione A, Marletta D, Macciotta NPP. The mathematical modeling of the lactation curve for dairy traits of the donkey (Equus asinus). J Dairy Sci 2013; 96:4005-14. [PMID: 23587386 DOI: 10.3168/jds.2012-6180] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 03/03/2013] [Indexed: 11/19/2022]
Abstract
In recent years, an increase in the number of donkeys farmed in Italy as a consequence of the growing demand for donkey milk for direct consumption has been observed. Some research has been carried out on jenny milk composition and on its nutritional properties, whereas milk production features are scarcely described for this species. In this work, the lactation curve shape of donkeys for milk yield and composition was investigated. A total of 453 test-day records for milk yield, fat and protein percentage, and somatic cell count of 62 lactations measured on 46 multiparous jennies of the Ragusano breed were considered. Effects of herd, age, and foaling season were assessed by using a mixed model analysis. Average and individual lactation curves were fitted using the Wood incomplete gamma function, the Cappio-Borlino modified gamma, and a third-order Legendre orthogonal polynomial model. Donkeys foaling between 6- and 10-yr-old had the highest test-day milk yield (about 1.85 kg/d). Donkeys foaling in winter and autumn had a higher daily milk yield compared with those foaling in summer and spring. Less defined results were obtained for composition traits. The general pattern of the donkey lactation curve is similar to the standard shape reported for the main dairy ruminant species, with a peak yield occurring at about 5 wk from parturition. Younger jennies tended to have lower production peaks and higher lactation persistency. Similarly to what is reported for dairy cattle, a large variability in individual patterns has been observed. No differences in goodness of fit have been observed between the models in the case of average lactation curves, whereas orthogonal polynomials were more efficient in fitting individual patterns.
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Affiliation(s)
- S Bordonaro
- Dipartimento di Scienze delle Produzioni Agrarie ed Alimentari, Sezione di Produzioni Animali, via Valdisavoia, 5, 95123 Catania, Italy
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