Molecular phylogeny of Anatolian and Cypriot donkey populations based on mitochondrial DNA and Y-chromosomal STRs

Bengi Cınar Kul; Nuket Bılgen; Bilal Akyuz; Okan Ertugrul

doi:10.1501/Vetfak_0000002722

Letter to Editor

Molecular phylogeny of Anatolian and Cypriot donkey populations based on mitochondrial DNA and Y-chromosomal STRs

Year 2016, , 143 - 149, 01.06.2016

Bengi Cınar Kul Nuket Bılgen Bilal Akyuz Okan Ertugrul

https://doi.org/10.1501/Vetfak_0000002722

Cited By: 8

Abstract

Domestication centers and the lineages of the wild ass contributing to modern domestic donkey population are still unknown, except the Nubian wild ass. This study is designed to fill the gaps about Anatolian donkey domestication. A total of 68 samples of Anatolian donkeys obtained from Turkey and seven donkeys from Cyprus were analyzed for D-loop and cytochrome b gene regions. Males were also genotyped with three equine Y-chromosomal short tandem repeats (STRs) namely Eca.YM2, Eca.YP9 and Eca.YE1. While the haplotype and nucleotide diversities (h=0.756±0.0500 and π=0.1688±0.0012) obtained from D-loop sequences of Anatolian donkey population were found to be moderately high, the Cypriot donkey population were found dramatically reduced (h=0.524±0.209 and π=0.00176 ± 0.001) than those in Turkey. Only 35% of the Anatolian donkeys were clustered in Clade 1 linked with Nubian ass, while the remaining 65% and 100% of the Cypriot donkeys were clustered in Clade 2. In the present study, Clade 2 was genetically divergent from Somali lineage and from Asiatic wild asses. Thus, they were excluded from to be ancestor of Anatolian and Cypriot donkey populations. A total of 17 and 4 nucleotide differences, discriminating 15 and 6 haplotypes, were defined for D-loop and cytochrome b sequences, respectively. Analyzed Y chromosomal STRs were found to be monomorphic. The allele size of 109, 190 and 195 were identified for Eca.YM2, Eca.YP9 and Eca.YE1, respectively

Keywords

Anatolian donkey, Cypriot donkey, cytochrome b, D-loop, Y-chromosomal STRs

References

1. Aranguren-Mendez J, Beja-Pereira A, Avellanet R, et al. (2004): Mitochondrial DNA variation and genetic relationships in Spanish donkey breeds (Equus asinus). JBAG, 121, 319-330.
2. Beja-Pereira A, England PR, Ferrand N, et al. (2004): African origins of the domestic donkey. Science, 304, 1781-1781.
3. Chen SY, Zhou F, Xiao H, et al. (2006): Mitochondrial DNA diversity and population structure of four Chinese donkey breeds. Anim Genet, 37, 422-431.
4. Cinar Kul B, Bilgen N, Lenstra JA, et al (2015): Ychromosomal variation of local goat breeds of Turkey close to the domestication centre. JBAG, DOI: 10.1111/jbg.12154.
5. Ferrando A, Casas M, Jordana J (2011): Analysis of Y chromosome genetic variability of six Spanish donkey breeds with three microsatellite markers. In XIV Jordanas Sobre Produccion Animal, Zaragoza,(479-481).17-18 May 2011, Espana.
6. Hall (1999): BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. In Nucleic acids symposium series, 41, pp 95- 98.
7. Hamrick RG, Pirgalioglu T, Gunduz S, et al. (2005): Feral donkey Equus asinus populations on the Karpaz peninsula, Cyprus. Eur J Wildl Res, 51, 108-116.
8. Hutchison, CA, III, Newbold JE, SS, Potter SS, et al. (1974): Maternal inheritance of mammalian mitochondrial DNA. Nature, 251, 536-538.
9. Kefena E, Dessie T, Tegegne A, et al. (2014): Genetic diversity and matrilineal genetic signature of native Ethiopian donkeys (Equus asinus) inferred from mitochondrial DNA sequence polymorphism. Livest Sci, 167, 73-79.
10. Kimura B, Marshall FB, Chen S, et al. (2011): Ancient DNA from Nubian and Somali wild ass provides insights into donkey ancestry and domestication. Proc R Soc B, 278, 50-7.
11. Kugler W, Grunenfelder HP, Broxham E (2007): Donkey breeds in Europe. Inventory, Description, Need for Action, Conservation Report-2008. St. Gallen, Switzerland.
12. Kul BC, Ertugrul O, (2011): mtDNA diversity and phylogeography of some Turkish native g oat breeds. Vet J Ankara Univ, 58, 129-134.
13. Ling Y, Ma Y, Guan W, et al (2010): Identification of Y chromosome genetic variations in Chinese indigenous horse breeds. J Hered, 101, 639-643.
14. Leigh JW, Bryant D, (2014): PopART: Full-feature software for population genetics. Available from: http://popart.otago.ac.nz (11.01.2015).
15. Librado P, Rozas J, (2009): DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451-1452.
16. Özdemir M, Dogru Ü, (2009): Determination of Phylogenetic Relationships of Turkish Native Cattle Breeds with Other Cattle Breeds Using Mitochondrial DNA D-loop Sequence Polymorphism. Asian Australas J Anim Sci, 22, 955-961.
17. Pérez-Pardal L, Grizelj J, Traoré A, et al. (2014): Lack of mitochondrial DNA structure in Balkan donkey is consistent with a quick spread of the species after domestication. Anim Genet, 45, 144-7
18. Tamura K, Stecher G, Peterson D, et al. (2013). MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol, 30, 2725-2729.
19. TurkStat (2015): Livestock statistics. Available from: http://www.turkstat.gov.tr (21.01.2015).
20. Vilà C, Leonard JA, Beja-PereiraA, (2006): Genetic documentation of horse and donkey domestication, 342- 353. In Zeder MA (Ed), Documenting domestication, University of California Press, Berkeley, CA, USA
21. Wallner B, Piumi F, Brem G, et al., (2004): Isolation of Y chromosome-specific microsatellites in the horse and cross-species amplification in the genus Equus. J Hered, 95, 158-164.
22. Yilmaz O, Trevor RJ (2013): The domestic livestock resources of Turkey: Notes on donkeys. Anim Plant Sci, 23, 651-656.
23. Zeder MA, (2006): (Ed), Documenting domestication, University of California Press, Berkeley, CA, USA.

Anadolu ve Kıbrıs eşek populasyonlarında mitokondriyal ve Y-kromozomal STR’larına dayananmoleküler filogeni

Year 2016, , 143 - 149, 01.06.2016

Bengi Cınar Kul Nuket Bılgen Bilal Akyuz Okan Ertugrul

https://doi.org/10.1501/Vetfak_0000002722

Cited By: 8

Abstract

Evciltme bölgeleri ve modern evcil eşek populasyonuna katkıda bulunan soylar, Nubian yaban eşeği hariç, hala bilinmemektedir. Bu çalışma Anadolu eşeğinin evciltmesi hakkındaki boşlukların doldurulması için tasarlanmıştır. Türkiye’den 68 Anadolu eşeği ve Kıbrıs’tan yedi eşek, D-loop ve cytochrome b gen bölgeleri açısından analiz edilmiştir. İncelenen örneklerden 30 erkek aynı zamanda ata ait Eca.YM2, Eca.YP9 ve Eca.YE1 isimli üç adet Y-kromozomal kısa ardışık tekrar dizileri (STRlar) ile genotiplendirilmiştir. Anadolu eşek populasyonu D-loop sekanslarından elde edilen haplotip ve nükleotid çeşitliliği (h=0.756±0.0500 ve π=0.1688±0.0012) orta düzeyde yüksek bulunmuşken, Kıbrıs eşek populasyonunda büyük ölçüde düşük (h=0.524±0.209 ve π=0.00176 ± 0.001) bulunmuştur. Anadolu eşeklerinin %35’i Clade 1’de Nubian yaban eşeği ile kümelenmişken, kalan %65’i ve Kıbrıs eşeklerinin %100’ü Clade 2 olarak kümelenmiştir. Sunulan çalışmada Clade 2 Somali soyundan ve Asya yaban eşeklerinden genetik olarak farklı çıkmıştır. Böylece bu soyların Anadolu ve Kıbrıs eşeğinin atası olamayacakları belirlenmiştir. D-loop ve sitokrom bölgeleri için, sırasıyla, 15 ve 6 haplotip ayrımını sağlayan 17 ve 4 nükleotid değişimi belirlenmiştir. Analiz edilen Ykromozomal STR’lar monomorfik bulunmuştur. Eca.YM2, Eca.YP9 ve Eca.YE1 için sırasıyla 109, 190 ve 195 allel büyüklükleri belirlenmiştir

Keywords

Anadolu eşeği, Kıbrıs eşeği, sitokrom b, D-loop, Y-kromozomal STR

References

1. Aranguren-Mendez J, Beja-Pereira A, Avellanet R, et al. (2004): Mitochondrial DNA variation and genetic relationships in Spanish donkey breeds (Equus asinus). JBAG, 121, 319-330.
2. Beja-Pereira A, England PR, Ferrand N, et al. (2004): African origins of the domestic donkey. Science, 304, 1781-1781.
3. Chen SY, Zhou F, Xiao H, et al. (2006): Mitochondrial DNA diversity and population structure of four Chinese donkey breeds. Anim Genet, 37, 422-431.
4. Cinar Kul B, Bilgen N, Lenstra JA, et al (2015): Ychromosomal variation of local goat breeds of Turkey close to the domestication centre. JBAG, DOI: 10.1111/jbg.12154.
5. Ferrando A, Casas M, Jordana J (2011): Analysis of Y chromosome genetic variability of six Spanish donkey breeds with three microsatellite markers. In XIV Jordanas Sobre Produccion Animal, Zaragoza,(479-481).17-18 May 2011, Espana.
6. Hall (1999): BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. In Nucleic acids symposium series, 41, pp 95- 98.
7. Hamrick RG, Pirgalioglu T, Gunduz S, et al. (2005): Feral donkey Equus asinus populations on the Karpaz peninsula, Cyprus. Eur J Wildl Res, 51, 108-116.
8. Hutchison, CA, III, Newbold JE, SS, Potter SS, et al. (1974): Maternal inheritance of mammalian mitochondrial DNA. Nature, 251, 536-538.
9. Kefena E, Dessie T, Tegegne A, et al. (2014): Genetic diversity and matrilineal genetic signature of native Ethiopian donkeys (Equus asinus) inferred from mitochondrial DNA sequence polymorphism. Livest Sci, 167, 73-79.
10. Kimura B, Marshall FB, Chen S, et al. (2011): Ancient DNA from Nubian and Somali wild ass provides insights into donkey ancestry and domestication. Proc R Soc B, 278, 50-7.
11. Kugler W, Grunenfelder HP, Broxham E (2007): Donkey breeds in Europe. Inventory, Description, Need for Action, Conservation Report-2008. St. Gallen, Switzerland.
12. Kul BC, Ertugrul O, (2011): mtDNA diversity and phylogeography of some Turkish native g oat breeds. Vet J Ankara Univ, 58, 129-134.
13. Ling Y, Ma Y, Guan W, et al (2010): Identification of Y chromosome genetic variations in Chinese indigenous horse breeds. J Hered, 101, 639-643.
14. Leigh JW, Bryant D, (2014): PopART: Full-feature software for population genetics. Available from: http://popart.otago.ac.nz (11.01.2015).
15. Librado P, Rozas J, (2009): DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451-1452.
16. Özdemir M, Dogru Ü, (2009): Determination of Phylogenetic Relationships of Turkish Native Cattle Breeds with Other Cattle Breeds Using Mitochondrial DNA D-loop Sequence Polymorphism. Asian Australas J Anim Sci, 22, 955-961.
17. Pérez-Pardal L, Grizelj J, Traoré A, et al. (2014): Lack of mitochondrial DNA structure in Balkan donkey is consistent with a quick spread of the species after domestication. Anim Genet, 45, 144-7
18. Tamura K, Stecher G, Peterson D, et al. (2013). MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol, 30, 2725-2729.
19. TurkStat (2015): Livestock statistics. Available from: http://www.turkstat.gov.tr (21.01.2015).
20. Vilà C, Leonard JA, Beja-PereiraA, (2006): Genetic documentation of horse and donkey domestication, 342- 353. In Zeder MA (Ed), Documenting domestication, University of California Press, Berkeley, CA, USA
21. Wallner B, Piumi F, Brem G, et al., (2004): Isolation of Y chromosome-specific microsatellites in the horse and cross-species amplification in the genus Equus. J Hered, 95, 158-164.
22. Yilmaz O, Trevor RJ (2013): The domestic livestock resources of Turkey: Notes on donkeys. Anim Plant Sci, 23, 651-656.
23. Zeder MA, (2006): (Ed), Documenting domestication, University of California Press, Berkeley, CA, USA.

There are 23 citations in total.

Details

Primary Language	English
Subjects	Veterinary Surgery
Other ID	JA65BB45GJ
Journal Section	Research Article
Authors	Bengi Cınar Kul Nuket Bılgen Bilal Akyuz Okan Ertugrul
Publication Date	June 1, 2016
Published in Issue	Year 2016

Cite

APA	Cınar Kul, B., Bılgen, N., Akyuz, B., Ertugrul, O. (2016). Molecular phylogeny of Anatolian and Cypriot donkey populations based on mitochondrial DNA and Y-chromosomal STRs. Ankara Üniversitesi Veteriner Fakültesi Dergisi, 63(2), 143-149. https://doi.org/10.1501/Vetfak_0000002722
AMA	Cınar Kul B, Bılgen N, Akyuz B, Ertugrul O. Molecular phylogeny of Anatolian and Cypriot donkey populations based on mitochondrial DNA and Y-chromosomal STRs. Ankara Univ Vet Fak Derg. June 2016;63(2):143-149. doi:10.1501/Vetfak_0000002722
Chicago	Cınar Kul, Bengi, Nuket Bılgen, Bilal Akyuz, and Okan Ertugrul. “Molecular Phylogeny of Anatolian and Cypriot Donkey Populations Based on Mitochondrial DNA and Y-Chromosomal STRs”. Ankara Üniversitesi Veteriner Fakültesi Dergisi 63, no. 2 (June 2016): 143-49. https://doi.org/10.1501/Vetfak_0000002722.
EndNote	Cınar Kul B, Bılgen N, Akyuz B, Ertugrul O (June 1, 2016) Molecular phylogeny of Anatolian and Cypriot donkey populations based on mitochondrial DNA and Y-chromosomal STRs. Ankara Üniversitesi Veteriner Fakültesi Dergisi 63 2 143–149.
IEEE	B. Cınar Kul, N. Bılgen, B. Akyuz, and O. Ertugrul, “Molecular phylogeny of Anatolian and Cypriot donkey populations based on mitochondrial DNA and Y-chromosomal STRs”, Ankara Univ Vet Fak Derg, vol. 63, no. 2, pp. 143–149, 2016, doi: 10.1501/Vetfak_0000002722.
ISNAD	Cınar Kul, Bengi et al. “Molecular Phylogeny of Anatolian and Cypriot Donkey Populations Based on Mitochondrial DNA and Y-Chromosomal STRs”. Ankara Üniversitesi Veteriner Fakültesi Dergisi 63/2 (June 2016), 143-149. https://doi.org/10.1501/Vetfak_0000002722.
JAMA	Cınar Kul B, Bılgen N, Akyuz B, Ertugrul O. Molecular phylogeny of Anatolian and Cypriot donkey populations based on mitochondrial DNA and Y-chromosomal STRs. Ankara Univ Vet Fak Derg. 2016;63:143–149.
MLA	Cınar Kul, Bengi et al. “Molecular Phylogeny of Anatolian and Cypriot Donkey Populations Based on Mitochondrial DNA and Y-Chromosomal STRs”. Ankara Üniversitesi Veteriner Fakültesi Dergisi, vol. 63, no. 2, 2016, pp. 143-9, doi:10.1501/Vetfak_0000002722.
Vancouver	Cınar Kul B, Bılgen N, Akyuz B, Ertugrul O. Molecular phylogeny of Anatolian and Cypriot donkey populations based on mitochondrial DNA and Y-chromosomal STRs. Ankara Univ Vet Fak Derg. 2016;63(2):143-9.