Please use this identifier to cite or link to this item:
Analysis of genetic diversity and conservation priorities in Asian domestic chicken populations based on microsatellites
Hung, Pham Manh
Bayesian clustering analysis
effective population sizes
principal component analysis
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第5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6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。|
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 1 presents the background information, material and methods used in this thesis. Chapter 2 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. Chapter 4 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 5. 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 6 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.
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