埃塞俄比亚粮食作物苔麸（Eragrostis tef）居群基因组学及重要农艺性状全基因组关联分析

发布时间：2021-10-18 21:54

　　苔麸（Eragrostis tef）是埃塞俄比亚种植最广泛的谷类作物之一,具有重要农业价值,同时也是一种在全球广受欢迎的健康食品。埃塞俄比亚生物多样性研究中心基因库中已保存了从不同的农业生态区域中收集的大量苔麸种质资源,然而,目前对这些种质资源的基础生物学研究十分有限,其遗传变异水平及地理分布模式、农艺性状的遗传学基础等仍不十分清楚。全基因组关联研究和开发高分辨率的分子标记对于Eragrostis tef的居群遗传学研究及分子育种等至关重要。本研究对来源于埃塞俄比亚生物多样性研究中心基因库中保存的苔麸种质资源进行了农艺性状表型的统计分析;基于叶绿体基因组测序开发了分子遗传标记并进行了代表种质资源的遗传变异及其地理分布模式分析;基于基因组重测序进行了样本的亲缘关系及重要农艺性状全基因组关联分析。相关的研究结果如下:（1）对32个E.tef样品进行了叶绿体全基因组测序及组装,结果显示,其叶绿体基因组的大小从134,349-134,437 bp,GC含量约38.3%。基因组注释得到112个基因,其中包括77个蛋白质编码,31个tRNA和4个rRNA基因。叶绿体基因组比较分析表明,其种内序列变... 

【文章来源】：中国科学院大学(中国科学院武汉植物园)湖北省

【文章页数】：130 页

【学位级别】：博士

【文章目录】：
摘要
abstract
Chapter 1 Introduction and literature review
    1.1 Origin and taxonomy of tef
    1.2 Genetic diversity study and marker development in E.tef
    1.3 Phylogenetic studies in E.tef
    1.4 Association study and QTL mapping in E.tef
    1.5 Genome-wide association and its success story in crops
    1.6 Justification
    1.7 Research question
    1.8 Aim of the study
Chapter 2 Comparative analyses of32 complete plastomes of Tef
    2.1 Introduction
    2.2 Material and methods
        2.2.1 Plant sampling and DNA extraction
        2.2.2 Plastomes sequencing,assembly and annotation
        2.2.3 Screening variable regions and intraspecific comparison
        2.2.4 Phylogenetic analysis
        2.2.5 Analyses of signatures of selection
    2.3 Results
        2.3.1 Feature of sequenced E.tef plastomes
        2.3.2 Simple sequence repeats
        2.3.3 SNPs and InDels polymorphism among E.tef accessions
        2.3.4 IR region expansion and contraction
        2.3.5 Phylogenetic analysis
        2.3.6 Selection pressure
    2.4 Discussion
        2.4.1 Plastome variations in E.tef
        2.4.2 Phylogenetic analysis
    2.5 Conclusions
Chapter 3 Agro-morphological characterization and association analysis of major traits in tef[Eragrostis tef(Zucc.)Trotter]accessions
    3.1 Introduction
    3.2 Materials and methods
        3.2.1 Germplasm selection
        3.2.2 Field experiment
        3.2.3 Phenotype data analysis
    3.3 Results
        3.3.1 Cluster analysis
        3.3.2 Correlation of trait
        3.3.3 Principal component analysis(PCA)
    3.4 Discussion
    3.5 Conclusion
Chapter 4 Genome-Wide Association Study of Major Agro-morphology Traits of E.tef
    4.1 Introduction
    4.2 Material and methods
        4.2.1 GWAS Germplasm panel selection
        4.2.2 Whole-genome resequencing
        4.2.3 Variant calling
        4.2.4 GWAS analysis
    4.3 Results
        4.3.1 Whole-genome resequencing
        4.3.2 SNPs Distribution along E.tef Chromosome
        4.3.3 Genetic diversity and differentiation analysis
        4.3.4 Analysis of transitions bias
        4.3.5 Annotation of variants
        4.3.7 Genetic structure and phylogenetic analysis of accessions
        4.3.8 Genome-Wide Association Study(GWAS)
    4.4 Discussion
        4.4.1 SNPs and InDels
        4.4.2 Population structure and genetic variation assessment of E.tef
        4.4.3 GWAS
    4.5 Conclusion
Chapter 5 Conclusion
Chapter 6 References
Appendices
Acknowledgement
Student Profile and publications



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