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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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Çelik Ş, Yılmaz O. Investigation of the Relationships between Coat Colour, Sex, and Morphological Characteristics in Donkeys Using Data Mining Algorithms. Animals (Basel) 2023; 13:2366. [PMID: 37508143 PMCID: PMC10376350 DOI: 10.3390/ani13142366] [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: 05/22/2023] [Revised: 07/02/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
This study was carried out in order to determine the morphological characteristics, body coat colour distribution, and body dimensions of donkeys raised in Turkey, as well as to determine the relationships between these factors. For this reason, the predictive performance of various machine learning algorithms (i.e., CHAID, Random Forest, ALM, MARS, and Bagging MARS) were compared, utilising the biometric data of donkeys. In particular, mean measurements were taken from a total of 371 donkeys (252 male and 119 female) with descriptive statistical values as follows: height at withers, 100.7 cm; rump height, 103.1 cm; body length, 103.8 cm; chest circumference, 112.8 cm; chest depth, 45.7 cm; chest width, 29.1 cm; front shin circumference, 13.5 cm; head length, 55 cm; and ear length, 22 cm. The body colour distribution of the donkeys considered in this study was calculated as 39.35% grey, 19.95% white, 21.83% black, and 18.87% brown. Model fit statistics, including the coefficient of determination (R2), mean square error, root-mean-square error (RMSE), mean absolute percentage error (MAPE), and standard deviation ratio (SD ratio), were calculated to measure the predictive ability of the fitted models. The MARS algorithm was found to be the best model for defining the body length of donkeys, with the highest R2 value (0.916) and the lowest RMSE, MAPE, and SD ratio values (2.173, 1.615, and 0.291, respectively). The experimental results indicate that the most suitable model is the MARS algorithm, which provides a good alternative to other data mining algorithms for predicting the body length of donkeys.
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Affiliation(s)
- Şenol Çelik
- Biometry and Genetic Unit, Department of Animal Science, Faculty of Agriculture, Bingol University, Bingol 12000, Turkey
| | - Orhan Yılmaz
- Plant and Animal Production Department, Posof Vocational School, Ardahan University, Ardahan 75000, Turkey
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Ahlawat S, Sharma U, Arora R, Sharma R, Chhabra P, Veer Singh K, Vijh RK. Mitogenomic phylogeny reveals the predominance of the Nubian lineage of African wild ass in Indian donkeys. Gene 2023:147627. [PMID: 37429369 DOI: 10.1016/j.gene.2023.147627] [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: 05/18/2023] [Revised: 06/27/2023] [Accepted: 07/06/2023] [Indexed: 07/12/2023]
Abstract
To contribute to the knowledge of maternal genetic diversity in domestic donkeys, this study investigated the mitochondrial DNA variations and analyzed the genetic structure in Indian donkeys based on 31 mitogenome sequences representing four breeds/populations (Agra, Halari, Kachchhi and Spiti). A total of 27 haplotypes with a haplotype diversity value of 0.989 were evident in the donkey genetic resources of India. The genetic differentiation between the investigated populations was evaluated using population pairwise FST values, which showed maximum differentiation between Kachchhi and Halari donkeys. The Neighbor-Joining (NJ) tree based on the whole mitogenome sequence and the Median-Joining (MJ) network for partial D-loop fragment showed clear demarcation of Indian donkeys into Nubian and Somali clades, substantiating African maternal origin of Indian domestic donkeys. The topology of the MJ network excluded the Asian wild asses as the possible progenitors of Indian donkeys. Halari and Agra donkeys showed conformity exclusively to the Nubian lineage of the African wild asses. However, representation of both the Nubian and Somali lineages was observed in Kachchhi and Spiti donkeys. Comprehensive analysis carried out by retrieving D-loop sequences from different countries representing Asia, Africa, Europe and South America revealed existence of shared haplotypes across geographically isolated regions of the globe. This observation is indicative of utility of donkeys as pack animals across inter-continental trading routes during development of human civilizations. Our results represent a valuable contribution to maternal genetic diversity of Indian donkeys and provide insights into the worldwide spread of the species following initial domestication in Africa.
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Affiliation(s)
- Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal.
| | - Upasna Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal
| | - Pooja Chhabra
- ICAR-National Bureau of Animal Genetic Resources, Karnal
| | | | - R K Vijh
- ICAR-National Bureau of Animal Genetic Resources, Karnal
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Alaqeely R, Alhajeri BH, Almathen F, Alhaddad H. Mitochondrial Sequence Variation, Haplotype Diversity, and Relationships Among Dromedary Camel-Types. Front Genet 2021; 12:723964. [PMID: 34527024 PMCID: PMC8435798 DOI: 10.3389/fgene.2021.723964] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/12/2021] [Indexed: 11/22/2022] Open
Abstract
Dromedary camels are outstanding livestock that developed efficient abilities to tolerate desert conditions. Many dromedary camel-types (i.e., named populations) exist but lack defined specific breed standards, registries, and breeders’ governing organizations. The breed status of dromedary camel-types can partly be assessed by exploring mitochondrial DNA (mtDNA) variation. Accordingly, this study aimed to examine the breed status and the inter-population relationships of dromedary camel-types by analyzing sequence variation in the mtDNA control region and in three coding genes [cytochrome b, threonine, and proline tRNA, and part of the displacement loop (D-loop)] (867 bp region). Tail hair samples (n = 119) that represent six camel-types from Kuwait were collected, extracted, sequenced, and compared to other publicly available sequences (n = 853). Within the sequenced mitochondrial region, 48 polymorphic sites were identified that contributed to 82 unique haplotypes across 37 camel-types. Haplotype names and identities were updated to avoid previous discrepancies. When all sequences were combined (n = 972), a nucleotide diversity of 0.0026 and a haplotype diversity of 0.725 was observed across the dromedary-types. Two major haplogroups (A and B) were identified and the B1 haplotype was predominant and found in almost all dromedary-types whereas the A haplotypes were more abundant in African regions. Non-metric multidimensional scaling revealed an increased similarity among Arabian Peninsula “Mezayen” camel-types, despite their defining coat colors. The relationships among dromedary camel-types can partly be explained by mtDNA. Future work aimed at a deeper understanding of camel-type breed status should focus on a high number of nuclear markers.
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Affiliation(s)
- Randa Alaqeely
- Department of Biological Sciences, Kuwait University, Kuwait City, Kuwait
| | - Bader H Alhajeri
- Department of Biological Sciences, Kuwait University, Kuwait City, Kuwait
| | - Faisal Almathen
- Department of Veterinary Public Health, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia.,The Camel Research Center, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Hasan Alhaddad
- Department of Biological Sciences, Kuwait University, Kuwait City, Kuwait
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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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Phylogenetic Relationships of Turkish Indigenous Donkey Populations Determined by Mitochondrial DNA D-loop Region. Animals (Basel) 2020; 10:ani10111970. [PMID: 33120938 PMCID: PMC7692571 DOI: 10.3390/ani10111970] [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: 09/25/2020] [Revised: 10/18/2020] [Accepted: 10/22/2020] [Indexed: 11/17/2022] Open
Abstract
Simple Summary This paper represents the first fundamental report of mtDNA diversity in Turkish indigenous donkey breeds and presents findings for the origin and genetic characterization of donkey populations dispersed in seven geographical regions in Turkey, and thus reveals insights into their genetic history. The median-joining network and phylogenetic tree exhibit two different maternal lineages of the 16 Turkish indigenous donkey populations. Abstract In this study, to analyze the mtDNA D-loop region and the origin of the maternal lineages of 16 different donkey populations, and to assess the domestication of Turkish indigenous donkeys in seven geographical regions, we investigated the DNA sequences of the D-loop region of 315 indigenous donkeys from Turkey. A total of 54 haplotypes, resulting from 35 polymorphic regions (27 parsimoniously informative and 6 singleton sites), were defined. Twenty-eight of these haplotypes are unique (51.85%), and 26 are shared among different Turkish indigenous donkey populations. The most frequent haplotype was Hap 1 (45.71%), followed by two haplotypes (Hap 4, 15.55% and Hap 7, 5.39%). The breed genetic diversity, evaluated by the haplotype diversity (HD) and nucleotide diversity (πD), for the Turkish donkey populations ranged from 0.533 ± 0.180 (Tekirdağ–Malkara, MAL) to 0.933 ± 0.122 (Aydin, AYD), and from 0.01196 ± 0.0026 (Antalya, ANT) to 0.02101 ± 0.0041 (Aydin, AYD), respectively. We observed moderate-to-high levels of haplotype diversity and moderate nucleotide diversity, indicating plentiful genetic diversity in all of the Turkish indigenous donkey populations. Phylogenetic analysis (NJT) and median-joining network analysis established that all haplotypes were distinctly grouped into two major haplogroups. The results of AMOVA analyses, based on geographic structuring of Turkish native donkey populations, highlighted that the majority of the observed variance is due to differences among samples within populations. The observed differences between groups were found to be statistically significant. Comparison among Turkish indigenous donkey mtDNA D-loop regions and haplotypes, and different countries’ donkey breeds and wild asses, identified two clades and which is named Somali (Clade IV) and Nubian (Clade V) lineages. The results can be used to understand the origin of Turkish donkey populations clearly, and to resolve the phylogenetic relationship among all of the different regions.
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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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Chen SG, Li J, Zhang F, Xiao B, Hu JM, Cui YQ, Hofreiter M, Hou XD, Sheng GL, Lai XL, Yuan JX. Different maternal lineages revealed by ancient mitochondrial genome of Camelus bactrianus from China. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:786-793. [PMID: 31542986 DOI: 10.1080/24701394.2019.1659250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Domestic Bactrian camel (Camelus bactrianus) used to be one of the most important livestock species in Chinese history, as well as the major transport carrier on the ancient Silk Road. However, archeological studies on Chinese C. bactrianus are still limited, and molecular biology research on this species is mainly focused on modern specimens. In this study, we retrieved the complete mitochondrial genome from a C. bactrianus specimen, which was excavated from northwestern China and dated at 1290-1180 cal. years before present (yBP). Phylogenetic analyses using 18 mitochondrial genomes indicated that the C. bactrianus clade was divided into two maternal lineages. The majority of samples originating from Iran to Japan and Mongolia belong to subclade A1, while our sample together with two Mongolian individuals formed the much smaller subclade A2. Furthermore, the divergence time of these two maternal lineages was estimated as 165 Kya (95% credibility interval 117-222 Kya), this might indicate that several different evolutionary lineages were incorporated into the domestic gene pool during the initial domestication process. Bayesian skyline plot (BSP) analysis suggest a slow increase in female effective population size of C. bactrianus from 5000 years ago, which corresponds to the beginning of domestication of C. bactrianus. The present study also revealed that there were extensive exchanges of genetic information among C. bactrianus populations in regions along the Silk Road.
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Affiliation(s)
- Shun-Gang Chen
- Faculty of Materials Science and Chemistry, China University of Geosciences , Wuhan , China.,State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan , China
| | - Ji Li
- Insitute of Silk Road Studies, Northwest University , Xi'an , China
| | - Fan Zhang
- Ancient DNA Lab, School of Life Science, Jilin University , Changchun , China
| | - Bo Xiao
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan , China
| | - Jia-Ming Hu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan , China
| | - Yin-Qiu Cui
- Ancient DNA Lab, School of Life Science, Jilin University , Changchun , China
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse , Potsdam , Germany
| | - Xin-Dong Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan , China
| | - Gui-Lian Sheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan , China
| | - Xu-Long Lai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan , China
| | - Jun-Xia Yuan
- Faculty of Materials Science and Chemistry, China University of Geosciences , Wuhan , China.,State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan , China
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Cozzi MC, Strillacci MG, Valiati P, Rogliano E, Bagnato A, Longeri M. Genetic variability of Akhal-Teke horses bred in Italy. PeerJ 2018; 6:e4889. [PMID: 30202639 PMCID: PMC6129384 DOI: 10.7717/peerj.4889] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 05/14/2018] [Indexed: 12/13/2022] Open
Abstract
Background The Akhal-Teke horse (AKH) is native of the modern Turkmenistan area. It was introduced in Italy from 1991 to 2000 mainly as an endurance horse. This paper characterizes the genetic variability of the whole Italian AKH horse population and evaluates their inbreeding level by analyzing microsatellite markers and mitochondrial D-Loop sequences. Methods Seventeen microsatellite marker loci were genotyped on 95 DNA samples from almost all the AKH horses bred in Italy in the last 20 years. Standard genetic variability measures (Ho, He, FIS) were compared against the same variables published on other eight AKH populations. In addition, 397 bp of mtDNA D-loop region were sequenced on a sub-group of 22 unrelated AKH out of the 95 sampled ones, and on 11 unrelated Arab horses. The haplotypes identified in the Italian population were aligned to sequences of AKH (56), Arab (five), Caspian Pony (13), Przewalskii (two) and Barb (15) horses available in GenBank. The Median Joining Network (MJN), Principal Component Analysis (PCA) and Neighbor-joining (NJ) tree were calculated on the total 126 sequences. Results Nucleic markers showed a high degree of polymorphism (Ho = 0.642; He = 0.649) and a low inbreeding level (FIS = 0.016) in Italian horses, compared to other AKH populations (ranged from −0.103 AKH from Estonia to 0.114 AKH from Czech Republic). High variability was also recorded in the D-Loop region. 11 haplotypes were identified with haplotype diversity (hd), nucleotide diversity (π) and average number of nucleotide differences (k) of 0.938, 0.021 and 6.448, respectively. When all the 126 D-Loop sequences were compared, 51 haplotypes were found, and four were here found only in the Italian AKH horses. The 51 haplotypes were conformed to eight recognized mtDNA haplogroups (A, C, F, G, L, M, P and Q) and confirmed by MJN analysis, Italian horses being assigned to five haplogroups (A, C, G, L and M). Using a PCA approach to the same data, the total haplotypes were grouped into two clusters including A+C+M+P and G+F haplogroups, while L and Q haplogroups remained ungrouped. Finally, the NJ algorithm effectively discretizes only the L haplogroup. All the above data univocally indicate good genetic variability and accurate management of the Akhal-Teke population in Italy.
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Affiliation(s)
- Maria C Cozzi
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Maria G Strillacci
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Paolo Valiati
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Elisa Rogliano
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Alessandro Bagnato
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Maria Longeri
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
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