Phylogenetic relationships of Turkish indigenous donkey populations determined by mitochondrial DNA D-loop region

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dc.authorscopusid8431541400
dc.authorscopusid26028615800
dc.authorscopusid56949758800
dc.authorscopusid36106722600
dc.authorscopusid55913211900
dc.authorscopusid6603553213
dc.authorscopusid6701528877
dc.contributor.authorÖzkan Ünal, Emel
dc.contributor.authorÖzdil, Fulya
dc.contributor.authorKaplan, Selçuk
dc.contributor.authorGürcan, Eser Kemal
dc.contributor.authorGenç, Serdar
dc.contributor.authorArat, Sezen
dc.contributor.authorSoysal, Mehmet İhsan
dc.date.accessioned2022-05-11T14:02:55Z
dc.date.available2022-05-11T14:02:55Z
dc.date.issued2020
dc.departmentFakülteler, Ziraat Fakültesi, Zootekni Bölümü
dc.departmentFakülteler, Ziraat Fakültesi, Tarımsal Biyoteknoloji Bölümü
dc.description.abstractIn 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 (?D ), 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. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.
dc.description.sponsorshipTürkiye Bilimsel ve Teknolojik Araştirma Kurumu, TÜBITAK: 215O555
dc.description.sponsorshipThis research was funded by TUBITAK (The Scientific and Technological Research Council of Turkey), grant number 215O555, project leader Fulya ?zdil. The authors would like to kindly thank to Selen Yatkin who provide help during the sample collection. We are also grateful to all farmers and pastoralists for allowing us to use their animal to collect blood samples for free. Many thanks to our lab team ?eref M?cahit Topalo?lu and Ayla Fidan for helping laboratory experiment. The authors want to thank four anonymous reviewers for comments on this work.
dc.identifier.doi10.3390/ani10111970
dc.identifier.endpage21
dc.identifier.issn2076-2615
dc.identifier.issue11en_US
dc.identifier.scopus2-s2.0-85094218247
dc.identifier.scopusqualityQ1
dc.identifier.startpage1
dc.identifier.urihttps://doi.org/10.3390/ani10111970
dc.identifier.urihttps://hdl.handle.net/20.500.11776/4538
dc.identifier.volume10
dc.identifier.wosWOS:000592832400001
dc.identifier.wosqualityQ1
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.institutionauthorÖzkan Ünal, Emel
dc.institutionauthorÖzdil, Fulya
dc.institutionauthorKaplan, Selçuk
dc.institutionauthorGürcan, Eser Kemal
dc.institutionauthorArat, Sezen
dc.institutionauthorSoysal, Mehmet İhsan
dc.language.isoen
dc.publisherMDPI AG
dc.relation.ispartofAnimals
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccess
dc.subjectD-loop
dc.subjectGenetic diversity
dc.subjectHaplotype
dc.subjectMaternal origin
dc.subjectMtDNA
dc.subjectTurkish donkeys
dc.subjectcytochrome c oxidase
dc.subjectgenomic DNA
dc.subjectmitochondrial DNA
dc.subjectnucleotide
dc.subjectanimal experiment
dc.subjectArticle
dc.subjectbreed
dc.subjectcladistics
dc.subjectDNA extraction
dc.subjectDNA isolation
dc.subjectDNA sequence
dc.subjectdomestication
dc.subjectdonkey
dc.subjectgene frequency
dc.subjectgene mutation
dc.subjectgene structure
dc.subjectgenetic polymorphism
dc.subjectgenetic similarity
dc.subjectgenetic variability
dc.subjectgeographic distribution
dc.subjecthaplogroup
dc.subjecthaplotype
dc.subjectmicrobial diversity
dc.subjectnonhuman
dc.subjectphylogenetic tree
dc.subjectphylogeny
dc.subjectpolymerase chain reaction
dc.subjectpopulation structure
dc.subjectTajikistan
dc.subjectTurkey (republic)
dc.titlePhylogenetic relationships of Turkish indigenous donkey populations determined by mitochondrial DNA D-loop region
dc.typeArticle

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