genetic diversity of native and crossbreed sheep breeds in anatolia a thesis submitted to the ...

138 Pages·2005·1.93 MB·English

GENETIC DIVERSITY OF NATIVE AND CROSSBREED SHEEP BREEDS IN
ANATOLIA

A THESIS SUBMITTED TO
THE GRADUATE SCHOOL OF NATURAL AND APPLIED SCIENCES
OF
MIDDLE EAST TECHNICAL UNIVERSITY

BY

EVREN KOBAN

IN PARTIAL FULFILLMENT OF THE REQUIREMENTS
FOR
THE DEGREE OF DOCTOR OF PHILOSOPHY
IN
DEPARTMENT OF BIOLOGY

DECEMBER 2004
Approval of the Graduate School of Natural and Applied Sciences

________________________
Prof. Dr. Canan ÖZGEN
Director

I certify that this thesis satisfies all the requirements as a thesis for the degree of
Doctor of Philosophy.

________________________
Prof. Dr. Semra KOCABIYIK
Head of the Department

This is to certify that we have read this thesis and that in our opinion it is fully
adequate, in scope and quality, as a thesis for the degree of Doctor of Philosophy.

________________________
Prof. Dr. (cid:1)nci TOGAN
Supervisor

Examining Committee Members

Prof. Dr. Zeki KAYA (METU, BIO) _________________
Prof. Dr. (cid:1)nci TOGAN (METU, BIO) _________________
Prof. Dr. M. (cid:1)hsan SOYSAL (Trakya Ünv., TZF) _________________
Prof. Dr. Mehmet N(cid:1)ZAMLIO(cid:2)LU (Selçuk Ünv., Vet. Fak.) _________________
Prof. Dr. Okan ERTU(cid:2)RUL (Ankara Ünv., Vet. Fak.) _________________
I hereby declare that all information in this document has been obtained and
presented in accordance with academic rules and ethical conduct. I also declare that,
as required by these rules and conduct, I have fully cited and referenced all material
and results that are not original to this work.

Evren KOBAN

iii
ABSTRACT

GENETIC DIVERSITY OF NATIVE AND CROSSBREED SHEEP BREEDS IN
ANATOLIA

Koban, Evren
Ph.D., Department of Biology
Supervisor: Prof. Dr. (cid:1)nci Togan

December 2004, 125 pages

In this study the genetic diversity in Turkish native sheep breeds was
investigated based on microsatellite DNA loci. In total, 423 samples from 11 native
and crossbreed Turkish sheep breeds (Akkaraman, Morkaraman, Kıvırcık, (cid:1)vesi,
Da(cid:3)lıç, Karayaka, Hem(cid:4)in, Norduz, Kangal, Konya Merinosu, Türkgeldi) and one
Iraqi breed (Hamdani) were analyzed by sampling from breeding farms and local
breeders.

After excluding close relatives by Kinship analysis, the genetic variation
within breeds was estimated as gene diversities (H ), which ranged between 0.686
E
and 0.793. The mean number of observed alleles (MNA) ranged between 5.8 and
11.8. The allele frequency distribution across Turkey showed no gradient from east
to west expected in accordance with the Neolithic Demic Diffusion model. The
differentiation between different samples of Akkaraman, Da(cid:3)lıç and Karayaka
breeds was tested by F index. Akkaraman1 sample from the breeding farm was
ST
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significantly (P<0.001) different from the other two Akkaraman samples. Deviation
from HW expectations observed for Akkaraman1, (cid:1)vesi, Morkaraman and Hem(cid:4)in
breeds. AMOVA analysis revealed that most of the total genetic variation (~90%)
was partitioned within the individuals. In parallel to this observation, when factorial
correspondence analysis and shared alleles distances were used to analyze the
relationship between the individuals of the breeds, there was no clear discrimination
between breeds. Moreover, NJ tree constructed based on D genetic distance, and PC
A
analyses were used to analyze among breed differentiation. Delaunay Network drew
4 genetic boundaries (two of them being parallel to geographic boundaries) between
breeds. All the results indicated that Kıvırcık was the most differentiated breed.
Finally, Mantel Test and Bottleneck analysis did not reveal a significant result.

Kıvırcık breed, among all native Turkish breeds, was found to be the
genetically closest to the European breeds based on the loci analyzed. The genetic
variation in Turkish breeds was not much higher than that of European breeds, which
might be a consequence of the recent sharp decrease in sheep number.

Keywords: Genetic variation, microsatellite, sheep, Turkish breeds.
v
ÖZ

ANADOLU YERL(cid:1) VE MELEZ KOYUN IRKLARININ GENET(cid:1)K ÇE(cid:5)(cid:1)TL(cid:1)L(cid:1)(cid:2)(cid:1)

Koban, Evren
Doktora, Biyoloji Bölümü
Tez Yöneticisi: Prof. Dr. (cid:1)nci Togan

Aralık 2004, 125 sayfa

Bu çalı(cid:4)mada, Türk koyun ırklarında mevcut genetic çe(cid:4)itlilik Mikrosatelit
DNA lokusları kullanılarak incelenmi(cid:4)tir. Devlet üretim çiftlikleri, üniversite üretim
çiftlikleri ve yerel yeti(cid:4)tiricilerin elinde bulunan sürülerden yerli ve melez onbir Türk
ırkı (Akkaraman, Morkaraman, Kıvırcık, (cid:1)vesi, Da(cid:3)lıç, Karayaka, Hem(cid:4)in, Narduz,
Kangal, Konya Merinosu, Türkgeldi) ile bireyleri Irak'tan getirilmi(cid:4) yabancı bir ırkı
(Hamdani) temsil eden toplam 423 örnek bu çalı(cid:4)mada kullanılmı(cid:4)tır.

Öncelikle üretim çiftliklerinden toplanan populasyonlardan akrabalık derecesi
yüksek bireylere ait veriler yakınlık (kinship) analizinin sonuçları do(cid:3)rultusunda
çıkartılmı(cid:4)tır. Genetik varyasyonun ölçütlerinden beklenen heterozigotluk (H ) 0.686
E
ile 0.793 arasında, ortalama gözlenen alel sayıları (OAS) ise 5.8 ile 11.8 arasında
de(cid:3)i(cid:4)mi(cid:4)tir. Türkiye üzerinde alel frekans da(cid:3)ılımları Neolitik Gruplarca Yayılma
Modeli'nin bekledi(cid:3)i gibi bir de(cid:3)i(cid:4)im göstermemi(cid:4)tir. F indeksi Akkaraman,
ST
Karayaka ve Da(cid:3)lıç'ta aynı ırkın farklı populasyonlarındaki farklıla(cid:4)mayı ölçmek
için kullanılmı(cid:4)tır ve yeti(cid:4)tirme çiftli(cid:3)inden alınan Akkarman1'in di(cid:3)er iki
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Akkaraman populasyonundan istatistiki önemle (P<0.001) farklı oldu(cid:3)u
bulunmu(cid:4)tur. F indeksi ile ırklar Hardy-Weinberg dengesi açısından test edilmi(cid:4),
IS
Akkaraman1, (cid:1)vesi, Morkaraman ve Hem(cid:4)in'de H-W'den sapma tespit edilmi(cid:4)tir.
AMOVA analizi toplam genetik varyasyonun büyük bir kısmının (~%90) bireyler
içinde ayrı(cid:4)arak payla(cid:4)ıldı(cid:3)ını göstermi(cid:4)tir. Paralel sonuçlar bireyler arası genetik
ili(cid:4)kinin incelendi(cid:3)i faktöryel benzerlik analizi ve alel payla(cid:4)ım uzaklı(cid:3)ı ile de elde
edilmi(cid:4) ve ırklar arası belirgin bir fark görülmemi(cid:4)tir. D genetik uzaklı(cid:3)ı ile çizilen
A
NJ a(cid:3)acı ve temel ögeler analizi ise populasyonlar arası farklıla(cid:4)mayı incelemek için
kullanılmı(cid:4)tır. Delaunay örgüsü ırklar arasında 4 adet (ikisi co(cid:3)rafi bariyer ile
paralel) genetik sınır belirlemi(cid:4)tir. Sonuçların hepsi Kıvırcık'ın di(cid:3)erlerinden çok
farklı oldu(cid:3)u yönündedir. Mantel testi ve Bottleneck testi istatistiksel olarak anlamlı
bir sonuç ortaya koymamı(cid:4)tır.

Avrupa ırklarının ço(cid:3)una genetik olarak en yakın bulunan Kıvırcık'tır. Türk
ırklarında Avrupa ırklarından farklı ve yüksek bir genetik çe(cid:4)itlilik belirlenmemi(cid:4)tir.
Bunda son yıllarda koyun sayısında ya(cid:4)anan hızlı dü(cid:4)ü(cid:4) etkili olmu(cid:4) olabilir.

Anahtar Kelimeler: Genetik varyasyon, mikrosatelit, koyun, Türk ırkları.
vii
.
To My Grandmothers..

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ACKNOWLEDGEMENTS

I would deeply like to express my sincere appreciation to my supervisor, Prof. Dr.
(cid:1)nci Togan, for letting me be a part of this project. Moreover, I am thankful to her for
her guidance, advices and encouragements throughout this study. I learned a lot from
her during my MSc. and PhD studies, which greatly increased my skills in the
laboratory and in the field; challenged me intellectually and changed my direction. I
will always be indebted to her.

I am sincerely thankful to Prof. Mike Bruford for such a warm welcoming me to his
laboratory in Cardiff University to complete a part of the experiments of this study.
He treated me as a part of his team; he guided me whenever I needed. I will always
be grateful to him for his kindness and understanding. Moreover, I will never forget
the Christmas lunch I had with his family.

My best wishes go to all the academic and administrative staff and the technicians at
METU, Department of Biology and at Cardiff University, School of Biosciences.

I would like to thank all the jury members; Prof. Dr. M. (cid:1)hsan Soysal, Prof. Dr.
Mehmet Nizamlıo(cid:3)lu, Prof. Dr. Okan Ertu(cid:3)rul and Prof. Dr. Zeki Kaya for their
helpful comments and criticisms on the manuscript.

My sincere thanks go to Prof. Dr. (cid:1)nci Togan, Prof. (cid:1)hsan Soysal, Prof. Okan
Ertu(cid:3)rul, Doç Dr. Vahdettin Altunok, Dr. Zafer Bulut, Emel Özkan, Trinidad Perez,
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Ahmet Zehir, Ay(cid:4)e Koca and Arzu Sandıkçı for their endless help and friendship
during the sampling trips. Otherwise, it was impossible to collect all these samples.

We are all very grateful to all those people we met in the field including the
veterinarians and veterinary technicians, who helped us for the collection of the
samples. We are also grateful to all the farmers and their families for letting us take
the samples from their sheep and for their warm welcome. The best part of the
sampling trips was to meet all these kind people.

I am indebted to the members of Lab-G10 in Cardiff University for their warm
welcome and for their help when I started at G10; especially to Lounés Chikhi,
Katherine Little, Helen Wilcock, Kathryn Jeffery, Ceri Williams, Sofia Seabra and
Carlos Fernandes.

I would also like to thank to my lab mates at Lab147 (ex Lab29) in METU; Emel
Özkan, Havva Dinç, Sinan Can Açan, Ceren Caner Berkman, Çi(cid:3)dem Gökçek and
Ceran (cid:5)ekeryapan.

Without my dearest friends I would have lost my way. Bülent Zorlulular (my brother
in law), Carlos Fernandes, Demet Erkan, Emel Özkan, Emine Özak, Erika Baus,
Evrim Zorlular (my sister), Funda Tu(cid:3)ut, Sofia Seabra, Trinidad Perez, (cid:5)eyma
Seçen... thank you all for being there no matter what.

Furthermore, I am indebted to my father Halil Koban, my friends Havva Dinç and
Emel Özkan for their help in data analysis and typing the manuscript of my thesis to
speed up. Their support is so precious to me.

This study was possible by the financial support both from Turkish Scientific and
Technical Reseach Council (TBAG-2127) and the British Council Turkey.

Last, but not least I would like to thank my dear family for their endless support and
love through all my life.
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