Please use this identifier to cite or link to this item: http://hdl.handle.net/11455/25577
標題: 亞洲家雞族群以微衛星基礎分析遺傳多樣性和保護優先
Analysis of genetic diversity and conservation priorities in Asian domestic chicken populations based on microsatellites
作者: 范孟興
Hung, Pham Manh
關鍵字: 貝氏群聚分析
Bayesian clustering analysis
有效的族群規模
遺傳變異
近親繁殖
系譜資料
主成分分析
effective population sizes
genetic variation
inbreeding
pedigree information
principal component analysis
出版社: 動物科學系所
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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1章介紹本篇論文中所使用到的文獻、材料和方法。第2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6種中國原產(CNO)雞群和1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3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4章目的是利用譜系和分子數據,估計遺傳風險狀況與8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8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,我們用了三個標準,對於8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.
URI: http://hdl.handle.net/11455/25577
其他識別: U0005-2507201321420100
文章連結: http://www.airitilibrary.com/Publication/alDetailedMesh1?DocID=U0005-2507201321420100
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