中国陆地棉遗传分化与适应性进化的基因组学研究

发布时间：2023-08-16 17:05

　　陆地棉是当今世界上最重要的纤维作物。通过人类的驯化选择、现代陆地棉品种已经拥有更高的产量和更好的品质。遗传多样性是品种改良的关键、但是在人工选择和当地环境的综合压力下、陆地棉遗传多样性损失巨大。野生种和废弃老品种是加强遗传基础和累积有利性状的优良基因源。我们重新评估了一个在中国南方广泛分布陆地棉半野生种系—蓬蓬棉(G.purpurascens)。本研究主要分析蓬蓬棉的群体结构特征、变异情况以及其对陆地棉适应性和育种的改良潜力、为揭示陆地棉驯化过程中基因组演化提供新的见解。本研究发现了蓬蓬棉与现代品种、废弃老品种、中国南方搜集材料和中美洲地理种系之间存在广泛的分化。此外、通过筛选蓬蓬棉和现代品种之间多样性减少值的前1%、共鉴定到199个选择性清除区间。这些区间与一些前人发表的性状相关QTL区间重叠。基于全基因组重测序、本研究同时对陆地棉地理种系、废弃老品种和现代品种基因型进行了综合评估。共鉴定到93个差异区间和311个选择性清除区间与驯化和改良相关。同时我们通过全基因组关联分析(GWAS)鉴定了与性状相关的差异区间和选择性清除区间、这些QTL/基因主要与开花期、纤维品质和其他一些形态性状...

【文章页数】：195 页

【学位级别】：博士

【文章目录】：
摘要
Abstract
List of Abbreviations
Chapter 1 INTRODUCTION
    1.1 History of cotton crop
    1.2 Crop domestication and selection
    1.3 History upland cotton in China
    1.4 Genetic diversity
    1.5 Gossypium hirsutum purpurascens
    1.6 Genome wide association studies(GWAS)
    1.7 Justifications and objectives of this research
Chapter 2 MATERIALS AND METHODS
    2.1 Revisiting Gossypium hirsutum purpurascens
        2.1.1 Plant material and field experiments
        2.1.2 Yield and yield component evaluation
        2.1.3 DNA extraction,sequencing,alignment,and SNP detection
        2.1.4 Sequence quality checking and filtering
        2.1.5 Sequence alignment
        2.1.6 Annotation of genetic variants
        2.1.7 Population stratification
        2.1.8 Population genomics analyses
        2.1.9 GWAS Analysis
        2.1.10 Statistical analyses
        2.1.11 Quantitative real-time PCR(q RT-PCR)analysis
    2.2 Domestication and selection history of Chinese Upland cotton
        2.2.1 Plant Material
        2.2.2 DNA Extraction,Sequencing,Alignment and SNP Detection
        2.2.3 Population Genetic Analyses
        2.2.4 Identification of Selection/Improvement Signals
        2.2.5 GWAS Analysis
Chapter 3 Results
    3.1 Revisiting Gossypium hirsutum purpurascens
        3.1.1 Population stratification of Gossypium hirsutum purpurascens
        3.1.2 Genetic differentiation between G.purpurascens and cultivated genotypes
        3.1.3 Genetic differentiation between G.purpurascens and G.hirsutum landraces(Central American)
    3.2 Domestication and selection history of upland cotton in China
        3.2.1 Population classification and structure variations
        3.2.2 Differentiation and Selection signals between MCl and OCl group
        3.2.3 Differentiation and domestication between G.hirsutum landraces and cultivar groups
    3.3 Genome Wide Association Studies(GWAS)
        3.3.1 GWAS for flowering time and fiber quality
        3.3.2 GWAS for fiber quality
        3.3.3 GWAS for anther color
Chapter 4 Discussion
    4.1 G.purpurascens,a primitive landrace
    4.2 Genetic differentiation and selection history in upland cotton
Chapter 5 Conclusions and Future perspectives
References
Appendices
Curriculum Vitae



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