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 n gia đình, v r t nhi u! i ABSTRACT IN CHINESE i ii 20 VNN microsatellites CNO RJF Bayesian clustering 23 10 TCOM RJF 22 TCOM TCOM TCOM TCS 22 ii TCS TCS VNN CNO TCS CNO TCS TCOM TCOM VNN VNN Analysis of Population Structure) STRUCTURE iii BAPS (Bayesian 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 under Linux and Windows Mol Ecol Resour 10: 564–567 Falconer, D 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Fowl Chicken populations of Chinese origin (labeled in dark blue) are Luong Phuong from Hanoi; Hac Phong, Man and Quy Phi from Quang Ninh Province; and Huong Ke and Te Dong Bac from Lang Son Province 1.2.2.2 Taiwan country chicken populations The history of conservation of native chickens in Taiwan started from 1982, when native chickens were collected around the Islands and conserved at National 20... gallus and G g murghi, indicating that multiple domestication had occurred independently in different places of Asia including India and showed G g murghi as the most important contribution to Indian domestic chickens Eriksson et al (2008) found that the yellowskinned gene of domestic chickens was inherited from the G sonneratii therefore indicating a past hybridization event during domestication The... amount of genetic diversity has been conserved Until recently, the use of optimal contributions in conservation studies is based upon both pedigree information and SNP markers (Engelsma et al., 2012) 1.1.4 The strategies for setting priorities in conservation 8 Basically, there are three strategies for setting priorities in conservation: the maximum-risk strategy, the maximum -diversity strategy and the... population sizes for each population obtained by the pedigree and molecular data 91 Table 15 Genetic contributions of eight Taiwan conserved chicken populations 92 Table 16 Loss or gain of genetic diversity, contributions to allelic richness and aggregate diversity for each of the eight Taiwan conserved chicken breeds 95 Table 17 Genetic diversity within 31 Asian chicken populations, two... genetic resources Conservation of chicken genetic resources is necessary The ideal conservation strategy is to maintain local breeds in their natural environment (in situ) because they perform better in the natural environment where they are evolving, while ex situ in vivo conservation is the conservation of live animal outside their normal habitat (i.e in a national park or zoo) and is recommended... Fowl population 75 Table 11 The proportion of membership of each of nine TCOM populations, two exotic breeds and one Red Jungle Fowl population (after removing Game bird population) in the 12 inferred clusters 79 Table 12 Pedigree information in the first generation of the eight 88 Table 13 Pedigree information in founders of the eight populations 90 Table 14 Estimates of effective... jabouillei) were involved in the origin of the current domestic chickens and they suggested two domesticated centers, one in Southern China together with Southeast Asia and one in Indian subcontinent According to Oka et al (2007), game birds were developed in some areas in Southeast Asia and both non-game and game birds formed Japanese native chickens Kanginakudru et al (2008) found that Indian domestic birds... Hebei Province, 5300 BC, Shandong Province, 5000 BC, and Shaanxi Province, 4300 BC (West and Zhou, 1988) This study proposed that these bones originated from domestic chickens, since Red Jungle Fowl was never reported to have inhabited North of China The second finding of domestication was identified at Mohenjo-Daro archeological site in the Indus valley about 2500 BC (West and Zhou, 1988) In Vietnam,... used in the study 13 Table 7 History of different autosomal markers in domestic animals 23 Table 8 Summary information of 22 microsatellite markers used in this thesis 23 Table 9 Genetic diversity within 23 Vietnamese domestic chicken populations and one Red Jungle Fowl population 46 Table 10 Genetic diversity within 10 Taiwan commercial native populations, two exotic breeds and one... Vietnamese domestic chicken gene pool (Figure 8; Chapter 2) One chicken population may be conserved in several isolated places Unfortunately, as in many developing countries, the lack of pedigrees and infrastructure make impossible to estimate the relatedness of chicken, sampling was therefore done randomly Figure 8 Geographical origin of Vietnamese domestic chicken populations Vietnamese local chickens