Genome-wide Characterization of Insertion/Deletion Variation

发布时间：2021-05-13 17:29

　　INDEL是植物基因组中一类序列和长度多态性的变异类型,兼备了简单重复序列（SSRs）和单核苷酸多态性（SNPs）变异的特征,因此该类型变异可以被开发成遗传学研究和作物育种中理想的分子标记。目前,在甘蓝型油菜中,还没有报道大规模的INDEL变异被报道。本研究中,我们对来自不同生态地区且拥有不同生长习性的23个甘蓝型油菜自交系进行基因组重测序,共获得了351.2Gb数据;随后,将这些短序列比对到甘蓝型油菜参考基因组（AC）以及祖先种参考基因组（A+C）,鉴定到了大量的INDEL变异位点。以AC和A+C参考基因组分别分析得到的测序深度平均为12.4和9.4倍。23个甘蓝型油菜自交系以AC和A+C参考基因组分析得到的成功比对率分别为61.1%-89.1%和46%-66.9%。本研究中共鉴定到538,691个序列长度为1-10bp的INDEL变异位点,其中104,190个被特异地定位到参考基因组的各个染色体上。在这些被定位的INDEL变异位点中,135,596（25.17%）个位于注释的基因中。单个碱基长度的INDEL变异位点数目（63.6%）显著得多余其它序列长度的变异位点数目。核苷酸A和T... 

【文章来源】：华中农业大学湖北省 211工程院校 教育部直属院校

【文章页数】：129 页

【学位级别】：博士

【文章目录】：
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


【参考文献】：
期刊论文
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