Analysis of genetic diversity and conservation priorities in asian domestic chicken populations based on microsatellites

NATIONAL CHUNG HSING UNIVERSITY DEPARTMENT OF ANIMAL SCIENCE Doctoral Dissertation Analysis of genetic diversity and conservation priorities in Asian domestic chicken populations based on microsatellites Advisors: Yen-Pai Lee, Ph.D Chih-Feng Chen, Ph.D Graduate Student: Pham Manh Hung July, 2013 ACKNOWLEDGEMENTS It is impossible to complete my Ph.D program without the help and support from many people I owe my deep gratitude to those who made this Doctoral dissertation as much as possible Firstly, I would sincerely thank my advisors, Prof Yen-Pai Lee, Prof Chih-Feng Chen and Dr Tran Xuan Hoan, for your daily supervision and great supports during my Ph.D program I hereby would like to give my special thanks to Prof Michèle TixierBoichard, Dr Cécile Berthouly-Salazar and Dr Richard Crooijmans for your critically scientific suggestions and linguistic revisions I would like to thank the Committee members for your useful comments to this Doctoral dissertation I sincerely appreciate Poultry Breeding Lab members, teachers in Department of Animal Science, National Chung Hsing University, as well as many colleagues for your kind helps and sharing experiences, especially Mr Wen-Long Hsiao for Chinese translation of the abstract I am very grateful to the members of Department of Animal Breeding and Genetics, Institute of Agricultural Sciences for Southern Vietnam and the recent Institute of Animal Sciences of Southern Vietnam, Ministry of Agriculture and Rural Development of Vietnam for your valuable supports within my study period My special thanks are given to the colleagues of the National Institute of Animal Sciences in Hanoi and many Vietnamese private farmers for their help in collecting blood samples as well as breeding information of chicken populations The project is not successfully done without the financial support from the National Science Council, Taiwan Personally, I gratefully acknowledge a grant from Taiwan Scholarship Program I hereby would like to respect my all dear family members for your great support and encouragement I am never forgetting your kind contributions to me Finally, I wish to express my deepest love to my wife, Pham Ha Phuong, and my little daughter, Pham Phuong Ngan This Doctoral dissertation is for your endless love and patience since the summer of 2009 Cám ơn gia đình, vợ nhiều! i ABSTRACT IN CHINESE 亞洲家雞族群以微衛星基礎分析遺傳多樣性和保護優先 摘要 這項研究的目的是（i）對於亞洲雞族群基因構成的特徵及（ii）提供有關 遺傳多樣性保存的標準。 第 章介紹本篇論文中所使用到的文獻、材料和方法。第 章敘述遺傳多 樣性組成和族群的結構，在越南以 20 個微衛星（microsatellites）評估越南本地雞 （VNN，及 種中國原產（CNO）雞群和 種紅色叢林雞（RJF）群的樣本。利 用幾種方法，例如貝氏群聚（Bayesian clustering）和主成分分析，探討族群內和 族群之間的遺傳完整性和相關聯。此外，對於越南採樣的 23 個家雞族群，我們 提出保護優先的兩個標準。結果顯示整體高度遺傳多樣性，然而缺點是近親繁殖 率非常高。從某種程度上來說，雞群之間的遺傳分化被發現比預期的重要，質疑 地方品種族群的遺傳同質性及在少數情況下產生誤導保護優先。研究顯示開發中 國家的地方雞種，發現到一個非常普遍的問題（缺乏品種遺傳同質性，保護政策 裡很少被考慮到。 第 章在文中敘述台灣商業土雞生產及遺傳特性的重要角色，10 個台灣商 業土雞（TCOM）族群內和之間的，連同在台灣的兩個外來品種和一個 RJF 雞群 比較，利用 22 個微衛星。我們用傳統方法量化遺傳多樣性和貝氏群聚方法量化 混合模式，在 TCOM 表現出較高的遺傳多樣性，TCOM 品種比外來品種有較多的 被，而混合表現高產量和適合台灣傳統的烹飪風格及文化價值。這項研究結果表 示，TCOM 的基因庫是均勻分佈在不同品種間，因此有良好的潛力適應新環境或 市場。第 章目的是利用譜系和分子數據，估計遺傳風險狀況與 個台灣保種雞 （TCS）群的保護優先。利用三個策略設定優先保護，我們以譜系基礎分析 個 雞群估計不同的有效族群大小和的遺傳貢獻。用分子基礎分析，以連鎖不平衡方 法從 22 個微衛星的基因型數據計算估計當代有效的族群規模。此外，我們用了 ii 三個標準，對於 個族群提出保護優先。研究結果顯示，依譜系和分子基礎的方 法，認為大多數 TCS 族群是安全跨越。因此，TCS 族群的研究顯示不同類型的數 據如何被結合定義地方品種的風險性、多樣性或實用性，以確定保護優先考慮。 第 章中敘述利用貝氏群聚方法研究亞洲家雞族群之間的遺傳結構。VNN 族群因基因群之間的基因流動，比 CNO、TCS 和 TCOM 族群具有較高程度的混 合。觀察白色來航雞和其餘雞群間，幾乎沒有基因流動的證據，貝氏群聚方法顯 示 CNO，TCS，TCOM 族群和白色來航雞是聚集在一起，而 VNN 族群是分開。 有趣的是，台灣鬥雞和兩個紅色叢林雞族群是集聚到 VNN 族群。BAPS (Bayesian Analysis of Population Structure) 軟體比 STRUCTURE 軟體提供更精細的混合圖像。 第 章討論了整個論文的最終結果和需要加以改進的問題，把這些建議列入未來 的研究。 關鍵詞：貝氏群聚分析，有效的族群規模，遺傳變異，近親繁殖，系譜資料，主 成分分析 iii Analysis of genetic diversity and conservation priorities in Asian domestic chicken populations based on microsatellites ABSTRACT The objectives of this study were (i) to characterize the genetic makeup of Asian chicken populations and (ii) to provide criteria for the conservation of genetic diversity Chapter presents the background information, material and methods used in this thesis Chapter describes genetic diversity components and population structure of Vietnamese local chickens (VNN), together with six populations of Chinese origin (CNO) and one Red Jungle Fowl (RJF) population sampled in Vietnam assessed by 20 microsatellites Using several methods such as Bayesian clustering and principal component analyses, we investigated the genetic integrity and relationships between and within populations In addition, we used two criteria to propose conservation priorities for 23 domestic chicken populations sampled in Vietnam The results showed an overall high genetic diversity however blemished by very high inbreeding rate To some extent, genetic differentiation between flocks was found to be more important than expected, questioning the genetic homogeneity of local breed populations and in few cases misleading conservation priorities The study showed a very common issue found in local breeds from developing countries (i.e absence of breed genetic homogeneity), which is seldom considered in conservation policies In Chapter 3, the paper describes the important role of Taiwan commercial native chicken production and the genetic characterization within and between 10 Taiwan commercial native chicken (TCOM) populations, together with two exotic breeds and one RJF population sampled in Taiwan for comparison, using 22 microsatellites We used traditional methods to quantify the genetic diversity and the Bayesian clustering approach to quantify the admixture pattern Consequently, the TCOM exhibited the high genetic diversity within populations The TCOM breeds were more admixed than exotic breeds but they showed high production and suited to Taiwanese traditional cooking style and cultural values The results of this study suggest that the genetic pool of TCOM is well distributed among breeds and therefore there is a good potential for adaptation to new environmental conditions or markets iv Chapter aims at estimating genetic risk status and conservation priorities of eight Taiwan conserved chicken (TCS) populations using pedigree and molecular data Using three strategies for setting priorities in conservation, we estimated different effective population sizes and genetic contributions for eight chicken populations by pedigree-based analysis For molecular-based analysis, estimates of contemporary effective population size were computed from genotypic data of 22 microsatellites by linkage disequilibrium method In addition, we used three criteria to propose conservation priorities for eight populations The results showed that most TCS populations are considered to be in safe across pedigree- and molecular-based approaches Thus, this study of TCS populations shows how different types of data can be combined to define conservation priorities considering risk, diversity, or utility of local breeds The genetic structure among 32 Asian domestic chicken populations and Red Jungle Fowls using Bayesian clustering approaches is described in Chapter VNN populations genetically exhibited higher degree of admixture than that of CNO, TCS, and TCOM populations due to gene flow among populations Little evidence of gene flow was observed between White Leghorn and remaining populations Bayesian clustering approaches revealed that CNO, TCS, TCOM populations and White Leghorn clustered together, which separated from VNN populations Interestingly, Taiwan Game bird and two Red Jungle Fowl populations were clustered to VNN populations BAPS (Bayesian Analysis of Population Structure) program provided a finer picture of admixture than STRUCTURE did Chapter discusses the final results of the whole thesis and the remaining issues that need to be improved Several suggestions are included for the future research Key words: Bayesian clustering analysis, effective population sizes, genetic variation, inbreeding, pedigree information, principal component analysis v TABLE OF CONTENTS Page ACKNOWLEDGEMENTS i ABSTRACT IN CHINESE ii ABSTRACT iv TABLE OF CONTENTS vi LIST OF TABLES viii LIST OF FIGURES ix CHAPTER General introduction 1.1 Introduction 1.1.1 Chicken domestication 1.1.2 The threats and opportunities to maintain local chickens 1.1.3 Conservation of chicken genetic resources 1.1.4 The strategies for setting priorities in conservation 1.2 Material and methods 10 1.2.1 Description of phenotypic characteristics and performance traits of chicken breeds from this study 10 1.2.2 Populations and study sites 19 1.2.3 Molecular-based analysis for monitoring genetic diversity 22 1.2.4 Pedigree-based analysis for monitoring genetic diversity 31 1.3 Scope of the thesis 35 CHAPTER 36 Genetic diversity of Vietnamese domestic chicken populations as decision-making support for conservation strategies 36 2.1 Abstract 37 2.2 Introduction 38 2.3 Material and methods 39 2.4 Results 45 2.5 Discussion 53 CHAPTER 69 vi Genetic characterization of Taiwan commercial native chickens ascertained by microsatellite markers 69 3.1 Abstract 70 3.2 Introduction 71 3.3 Material and methods 72 3.4 Results and discussion 74 CHAPTER 84 Monitoring of genetic diversity in Taiwan conserved chickens assessed by pedigree and molecular data 84 4.1 Abstract 85 4.2 Introduction 86 4.3 Material and methods 87 4.4 Results and discussion 89 CHAPTER 98 Genetic structure of 32 Asian domestic chicken populations and Red Jungle Fowls 98 5.1 Abstract 99 5.2 Introduction 100 5.3 Material and methods 101 5.4 Results and discussion 103 CHAPTER 116 General discussion, conclusions and prospective 116 6.1 General discussion 117 6.2 General conclusions 119 6.3 Prospective for further studies 119 REFERENCES 122 ANNEX 139 vii Evanno, G., S Regnaut, and J Goudet 2005 Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study Mol Ecol 14: 2611–2620 Excoffier, L., and H E L Lischer 2010 ARLEQUIN suite version 3.5: a new series of programs to perform population genetics analyses 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