INDEL是植物基因組中一類序列和長度多態(tài)性的變異類型,兼?zhèn)淞撕唵沃貜?fù)序列（SSRs）和單核苷酸多態(tài)性（SNPs）變異的特征,因此該類型變異可以被開發(fā)成遺傳學(xué)研究和作物育種中理想的分子標記。目前,在甘藍型油菜中,還沒有報道大規(guī)模的INDEL變異被報道。本研究中,我們對來自不同生態(tài)地區(qū)且擁有不同生長習(xí)性的23個甘藍型油菜自交系進行基因組重測序,共獲得了351.2Gb數(shù)據(jù);隨后,將這些短序列比對到甘藍型油菜參考基因組（AC）以及祖先種參考基因組（A+C）,鑒定到了大量的INDEL變異位點。以AC和A+C參考基因組分別分析得到的測序深度平均為12.4和9.4倍。23個甘藍型油菜自交系以AC和A+C參考基因組分析得到的成功比對率分別為61.1%-89.1%和46%-66.9%。本研究中共鑒定到538,691個序列長度為1-10bp的INDEL變異位點,其中104,190個被特異地定位到參考基因組的各個染色體上。在這些被定位的INDEL變異位點中,135,596（25.17%）個位于注釋的基因中。單個堿基長度的INDEL變異位點數(shù)目（63.6%）顯著得多余其它序列長度的變異位點數(shù)目。核苷酸A和T... 

【文章來源】：華中農(nóng)業(yè)大學(xué)湖北省 211工程院校 教育部直屬院校

【文章頁數(shù)】：129 頁

【學(xué)位級別】：博士

【文章目錄】：
Abbreviation
摘要
Abstract
1 Introduction
    1.1 Rapeseed relationship to brassica species, its origin and genome components
        1.1.1 Genus Brassica in Brassicaceae and U’s triangle
        1.1.2 Rapeseed: genetics and origin
        1.1.3 Genomic constituents of B.napus, their genetics and genomics
    1.2 B.napus genome Complexity
        1.2.1 Whole genome triplication (WGT) in brassica
        1.2.2 Genome down sizing
        1.2.3 Subgenome dominance in polyploidy B.napus
        1.2.4 Homeologous pairing and Chromosomal rearrangement in B.napus
    1.3 Role of comparative mapping to dissect genomic components of B.napus
        1.3.1 Comparative mapping between Arabidopsis and B.napus
        1.3.2 Comparative mapping between B.napus and ancestors B.rapa and B.oleracea
    1.4 Advent of molecular marker technology and application in B.napus
    1.5 INDELs variations in genomes
        1.5.1 Characteristics of INDELs
        1.5.2 Mechanism of INDELs mutation
        1.5.3 Factors effecting density and distribution of INDEL across the genomes
    1.6 Objectives
2 Materials and methods
    2.1 Plant materials
    2.2 DNA extraction and sample preparation
    2.3 Construction of whole-genome shotgun libraries and sequencing
    2.4 Procedures for INDEL discovery
    2.5 Development of single-locus INDELs markers
    2.6 Experimental validation of INDELs polymorphism
    2.7 Polyacrylamide gel electrophoresis
        2.7.1 Gel preparation
        2.7.2 PCR product separation by electrophoresis
        2.7.3 Silver staining
    2.8 INDELs genetic linkage map construction
3 Results
    3.1 Whole-genome re-sequencing of the 22 ILs
    3.2 Identification of short INDEL polymorphisms
    3.3 Genomic distribution of INDEL variations
    3.4 Distribution of INDEL relative to genes and transposable elements
    3.5 Development of INDEL markers
    3.6 Genetic mapping of INDELs
4 Discussions
    4.1 Certainty of B. napus genome sequencing
    4.2 Challenges to B.napus sequencing and polymorphism detection
    4.3 Identification of INDEL polymorphism
    4.4 Characterization of INDEL polymorphism
    4.5 Role of INDEL in genome complexity and variation
    4.6 INDEL genotyping and mapping accuracy
Summary
References
Appendix
Sequence location of INDEL markers in B.napus genome and primer sequence information
ACKNOWLEDGEMENTS


【參考文獻】：
期刊論文
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