卡尼弗拉咖啡全基因组SSR评估以及基于SSR和ISSR分子标记的咖啡物种间遗传多样性分析

发布时间：2024-04-10 23:39

　　咖啡是世界性的重要饮料作物之一并对肯尼亚经济产生了深远影响。由于咖啡的驯化历史短、栽培品种基因交流低而导致咖啡的基因多样性十分低。基因组分析有利于育种家改良并创制咖啡新品种。基于此,本研究分析了来源于肯尼亚和中国的咖啡品种基因多样性以及关键性状的群体结构。本研究还调查分析了 710Mbp卡尼弗拉咖啡(Coffea canephora)基因组组装序列中微卫星的分布及其出现频率,总共159,041个SSR得以鉴定。此外,11条染色体和未锚定序列上SSR的分布频率为308 SSRs/Mbp。SSR中四核苷酸重复序列(TtNRs)出现频率最高,占比达32%,而二核苷酸重复序列(DNR)、三核苷酸重复序列(TNRs)、五核苷酸重复序列(PNRs)和六核苷酸重复序列(HNRs)所占比例分别为29.2%、21.4%、11.3%和6.1%。我们还观察到SSR数量减少伴随着重复基序数量的增加。99.3%SSR的长度通常短于30bp,因而二核苷酸重复序列(DNR)、三核苷酸重复序列(TNRs)、四核苷酸重复序列(TtNRs)、五核苷酸重复序列(PNRs)和六核苷酸重复序列(HNRs)的重复单位数目分别为6...

【文章页数】：120 页

【学位级别】：博士

【文章目录】：
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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