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Quercus Cerris L.) Populations

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Quercus Cerris L.) Populations PATTERN OF GENETIC DIVERSITY IN TURKEY OAK (QUERCUS CERRIS L.) POPULATIONS A THESIS SUBMITTED TO THE GRADUATE SCHOOL OF NATURAL AND APPLIED SCIENCES OF MIDDLE EAST TECHNICAL UNIVERSITY BY YELĠZ TÜMBĠLEN ÖZER IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN BIOLOGY JULY 2014 Approval of the Thesis PATTERN OF GENETIC DIVERSITY IN TURKEY OAK (QUERCUS CERRIS L.) POPULATIONS submitted by YELİZ TÜMBİLEN ÖZERin partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biology Department, Middle East Technical University by, Prof. Dr. Canan Özgen _______________ Dean, Graduate School of Natural and Applied Sciences Prof. Dr. Orhan Adalı _______________ Head of the Department, Biology Prof. Dr. Zeki Kaya _______________ Supervisor, Biology Dept., METU Examining Committee Members: Prof. Dr. Musa Doğan _______________ Biology Dept., METU Prof.Dr. Zeki Kaya _______________ Biology Dept., METU Prof. Dr. Hayri Duman _______________ Biology Dept., Gazi University Assoc. Prof. Dr. Sertaç Önde _______________ Biology Dept., METU Assist. Prof. Dr. AyĢegül Birand _______________ Biology Dept., METU Date: 03.07.2014 iii 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. Name, Last name : Yeliz TÜMBĠLEN ÖZER Signature: iv ABSTRACT PATTERN OF GENETIC DIVERSITY IN TURKEY OAK (QUERCUS CERRIS L.) POPULATIONS TÜMBĠLEN ÖZER, Yeliz Ph D., Department of Biology Supervisor: Prof. Dr. Zeki KAYA July 2014, 119 pages Quercus cerris L. is a native and widely distributed species in Turkey. It is an important element of Anatolian forests and with other oak species constitute 76.4% of broadleafed forests. However, there is little information on the genetic make-up of Turkish populations. In the current study, the genetic diversity of Q. cerris populations sampled within their natural range is assessed with microsatellite loci (SSRs) polymorphism. Thirteen populations were sampled from seven different locations. Four of these are rich in different oak species coexisting and possibly hybridizing. To estimate population genetic diversity parameters, twelve microsatellite primers were applied to 172 Q. cerris genotypes and 47 suspected hybrid genotypes. All genetic analysis were carried out in duplicate. Also, in order to evaluate the genetic proximity v between Q. cerris and other oaks with suspected hybrid genotypes, Principle Component Analysis (PCA) were conducted for different regions. It was found that the highest molecular diversity was detected in KahramanmaraĢ- Adıyaman region’s populations. The populations that had the least genetical diversity were from Kastamonu and Ankara. According to the UPGMA dendrogram results, two major clusters were defined. One of them was composed of Kastamonu-Ankara populations while the other cluster had the rest of the studied populations. When the most probable number of populations (K) was estimated, it was found to be two for just Q. cerris genotypes and nine for Q. cerris genotypes analyzed with 47 suspected hybrid genotypes. For nine clusters, KahramanmaraĢ-Adıyaman populations and Kastamonu-Ankara populations formed big clusters as the rest formed their individual clusters. Among suspected hybrid genotypes, except six of them, all was inferred to have certain type of populational genomic composition with a minimum 0.93 membership of coefficient for these populations. Among six, four of them had coefficients less than 0.80 and membership of two or three populations. As a result of this study, pattern of genetic diversity in Turkey oak obtained for the first time. This genetic information will be useful for establishing principles for conservation and management of genetic resources of the species since most of Turkey oak dispersion ranges are faced with a serious degradation rates. Key words: Quercus cerris L., genetic diversity, microsatellites, hybridization vi ÖZ TÜRK MEŞESİ (QUERCUS CERRIS L.) POPULASYONLARINDA GENETİK ÇEŞİTLİLİĞİN YAPILAŞMASI TÜMBĠLEN ÖZER, Yeliz Doktora, Biyoloji Bölümü Tez Yöneticisi: Prof. Dr. Zeki KAYA Temmuz 2014, 119 sayfa Quercus cerris L., Türkiye’de doğal olarak yetiĢen ve geniĢ yayılım gösteren bir türdür. Anadolu ormanlarının önemli bir bileĢenidir ve diğer meĢe türleriyle birlikte geniĢ yapraklı ormanların %76,4’ünü oluĢturmaktadır. Ancak Türk populasyonlarının genetik yapısı hakkında çok az miktarda bilgi mevcuttur. Bu çalıĢmada, doğal yayılım alanlarından örneklenmiĢ Q. cerris populasyonlarının genetik çeĢitliliği, mikrosatellit lokusları (SSRs) polimorfizmiyle değerlendirilmektedir. Yedi farklı bölgeden on üç populasyon örneklenmiĢtir. Bunlardan dört tanesi, beraberce yayılım gösteren ve muhtemelen melezleĢen farklı meĢe türleri açısından zengindir. Populasyon genetik çeĢitlilik parametrelerini hesaplamak için on iki mikrosatellit iĢaretleyicisi 172 Q. cerris genotipine ve 47 ekstra olası melez bireyine uygulanmıĢtır. Tüm genetik analizler ikiĢer kere yapılmıĢtır. Ayrıca, Q. cerris ve vii diğer meĢe türleri ile olası melez bireylerinin genetik yakınlığını değerlendirebilmek için farklı bölgeler için Temel BileĢen Analizi (PCA) yapılmıĢtır. En yüksek moleküler çeĢitlilik KahramanmaraĢ-Adıyaman bölgesinde tespit edilmiĢtir. En düĢük genetik çeĢitliliğe sahip populasyonlar ise Kastamonu ve Ankara populasyonlarıdır. UPGMA kümelendirme sonuçlarına göre iki temel küme tanımlanmıĢtır. Bunlardan biri Kastamonu-Ankara populasyonlarından oluĢurken, diğer küme, kalan tüm populasyonları içermektedir. En olası gerçek populasyon sayısı (K) tahmin edildiğinde, sadece Q. cerris genotipleri için iki, Q. cerris genotipleri ile 47 olası melez bireyleri için ise dokuz bulunmuĢtur. Dokuz küme için, KahramanmaraĢ-Adıyaman populasyonları ve Kastamonu-Ankara populasyonları büyük kümeler oluĢtururken, kalan tüm populasyonlar kendi kümelerini oluĢturmuĢtur. Olası melez bireyleri arasında, altı tanesi hariç, tümünün minimum 0.93 aitlik katsayısı ile belli bir tip genomik kompozisyona sahip olduğu sonucuna ulaĢılmıĢtır. Altısı içinden dördü de 0.80 aitlik katsayısına sahiptir ve iki ya da üç populasyona üyelikleri tespit edilmiĢtir. Bu çalıĢmanın bir sonucu olarak, Türk meĢesinin genetik çeĢitliliğinin yapılaĢması ilk kez elde edilmiĢtir. Bu genetik bilgi, özellikle Türk meĢesi yayılım alanlarının ciddi bir tahbibatla karĢı karĢıya olduğu düĢünüldüğünde, türün genetik kaynaklarının korunması ve idaresi amacıyla ilkeler oluĢturmak açısından yararlı olacaktır. Anahtar kelimeler: Quercus cerris L., genetik çeĢitlilik, mikrosatellitler, melezleĢme viii Dedicated to my parents Serpil TÜMBĠLEN and Birol TÜMBĠLEN ix ACKNOWLEDGEMENTS I want to present my thanks to my advisor Prof. Dr. Zeki KAYA for his help and all of his support to me. Special thanks to Prof. Dr. Hayri DUMAN and Sadi ġIKLAR for their great helping for sampling in field. I would like to also thank to Assoc. Prof. Dr. Sertaç ÖNDE for his concern and kindness. I am also grateful to Prof. Dr. Musa DOĞAN for all his kind and sincere support during my doctorate. I am grateful for the financial support of the TÜBĠTAK (The Scientific and Technological Research Council of Turkey) during my education of Doctor of Philosophy in Biology. This study was financed by TÜBĠTAK- Agriculture, Forestry and Veterinary Research Support Group (TOVAG) Project No: 1080723. I am also really thankfull to my friends Ayten DĠZKIRICI and Çiğdem KANSU for their support during my thesis experimental period. Thanks to my Plant Genetic Laboratory colleagues Evrim ZEYBEK, Pelin ACAR, Aslı ÖZDĠLEK, Asiye ÇĠFTÇĠ, M. Alev ATEġ, Funda ÖZDEMĠR DEĞĠRMENCĠ and Bircan TAġKIRANfor their friendness, support and kindness during my doctorate. I present my deep gratitude and love to my dear parents, Serpil TÜMBĠLEN and Birol TÜMBĠLEN, for their endless support, encouragement and love all through my life. I want to thank to my husband, Ufuk ÖZER, not only during my doctorate period but also along lifetime that we are sharing together, for his love, trust and support to me. In the memory of my dear older sister YeĢim TÜMBĠLEN, who will always be remembered and loved. x TABLE OF CONTENTS ABSTRACT ................................................................................................................ V ÖZ ............................................................................................................................. VII ACKNOWLEDGEMENTS ........................................................................................ X TABLE OF CONTENTS …………………………………………………………..XI LIST OF TABLES .................................................................................................. XIV LIST OF FIGURES ................................................................................................ XVI LIST OF ABBREVIATIONS .............................................................................. XVIII CHAPTERS 1. INTRODUCTION ................................................................................................... 1 1.1 FAGACEAE FAMILY: GENUS QUERCUS L. ........................................................... 4 1.2 TURKEY OAK (QUERCUS CERRIS L.) ................................................................... 14 1.3 MOLECULAR TECHNIQUES AND GENETIC DIVERSITY ........................................ 17 1.3.1 Simple Sequence Repeats (SSR) ..............................................................
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