咖啡是世界性的重要飲料作物之一并對肯尼亞經(jīng)濟產(chǎn)生了深遠(yuǎn)影響。由于咖啡的馴化歷史短、栽培品種基因交流低而導(dǎo)致咖啡的基因多樣性十分低�；蚪M分析有利于育種家改良并創(chuàng)制咖啡新品種�；诖�,本研究分析了來源于肯尼亞和中國的咖啡品種基因多樣性以及關(guān)鍵性狀的群體結(jié)構(gòu)。本研究還調(diào)查分析了 710Mbp卡尼弗拉咖啡(Coffea canephora)基因組組裝序列中微衛(wèi)星的分布及其出現(xiàn)頻率,總共159,041個SSR得以鑒定。此外,11條染色體和未錨定序列上SSR的分布頻率為308 SSRs/Mbp。SSR中四核苷酸重復(fù)序列(TtNRs)出現(xiàn)頻率最高,占比達32%,而二核苷酸重復(fù)序列(DNR)、三核苷酸重復(fù)序列(TNRs)、五核苷酸重復(fù)序列(PNRs)和六核苷酸重復(fù)序列(HNRs)所占比例分別為29.2%、21.4%、11.3%和6.1%。我們還觀察到SSR數(shù)量減少伴隨著重復(fù)基序數(shù)量的增加。99.3%SSR的長度通常短于30bp,因而二核苷酸重復(fù)序列(DNR)、三核苷酸重復(fù)序列(TNRs)、四核苷酸重復(fù)序列(TtNRs)、五核苷酸重復(fù)序列(PNRs)和六核苷酸重復(fù)序列(HNRs)的重復(fù)單位數(shù)目分別為6...

【文章頁數(shù)】：120 頁

【學(xué)位級別】：博士

【文章目錄】：
摘要
Abstract
Abbreviations
Chapter 1 Introduction
    1.1 Background
    1.2 Molecular markers
    1.3 Hybridization based markers
        1.3.1 Restriction Fragment Length Polymorphism
    1.4 PCR Based Markers
        1.4.1 Random Amplified Polymorphic DNA Markers
        1.4.2 Amplified Fragment Length Polymorphism (AFLP)
        1.4.3 Single Nucleotide Polymorphism (SNP)
        1.4.4 Inter Simple Sequence Repeats (ISSR)
        1.4.5 Simple Sequence Repeats (SSR)
    1.5 Genome-wide Microsatellite Characterization in C. canephora
    1.6 Research question
        1.6.1 Hypotheses
        1.6.2 Objectives
    1.7 Materials and methods
        1.7.1 Sample collection
        1.7.2 Genome-wide SSRs Characterization
        1.7.3 DNA extraction and Marker validation
        1.7.4 Polyacrylamide Gel Electrophoresis (PAGE) analysis
        1.7.5 Data scoring and statistical analysis of genetic diversity
        1.7.6 Population structure analysis
    1.8 Results
        1.8.1 Genome-wide SSRs Characterization
        1.8.2 Distribution of genome-wide Dinucleotide repeats (DNRs)
        1.8.3 Distribution of Trinucleotide repeats (TNRs)
        1.8.4 Distribution of Tetra nucleotide repeats (TtNRs)
        1.8.5 Distribution of Penta- and Hexa- nucleotide repeats
        1.8.6 Polymorphism assessment and validation of SSR markers in coffee
        1.8.7 Genetic relationship of cultivated and wild coffee from Mt. Marsabit
        1.8.8 Population structure analysis
    1.9 Discussion
Chapter 2 Genetic structure analysis using ISSRs
    2.1 Background
    2.2 Materials and Methods
        2.2.1 Plant material
        2.2.2 DNA extraction and ISSR-PCR genotyping
        2.2.3 Population structure analysis
        2.2.4 Population genetic analysis and selection test
    2.3 Results
        2.3.1 Screening of the coffee collection using ISSR primers
        2.3.2 Analysis of Bayesian clustering in STRUCTURE
        2.3.3 Pairwise genetic distance (GD) and differentiation (F_ST) analysis
        2.3.4 Identification of putative loci under selection
    2.4 Discussion
Chapter 3 Conclusion
Chapter 4 Reference
Appendix A
Appendix B
Appendix C
Acknowledgement
Student profile and publications



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