基于核桃全基因组NAC转录因子分析和群体遗传进化研究
发布时间：2023-02-01 13:59
普通核桃（Juglans regia L.）隶属胡桃科胡桃属,是一种重要的经济型阔叶树种。该物种主要分布在北半球的亚热带和温带地区,可生产食用价值高的坚果和优质木材。除了自然地貌和气候对核桃群体遗传结构的影响外,人为因素影响更大。普遍认为,核桃经历了末次盛冰期后,生长于亚洲整个的密闭林之中。古时候人们通过贸易活动将核桃带到了世界各地。自2012年以来,世界核桃总产量超过了300万吨,主要产自于中国、美国和伊朗。尽管核桃非常古老,但关于核桃的育种历史在20世纪才开始发展。在最近30年来,从分子标记如简单重复序列（SSRs）到基因组分析,人们已经使用了多种方法对核桃进行了多项群体遗传学方面的研究,这其中包括了多样性、系统发育关系、起源进化和遗传图谱构建等分析。NAC是植物特有的转录因子,参与植物多种发育过程,例如开花、植物生长调节与发育。但是尚未有关于NAC转录因子基因家族在核桃物种中的研究报道。本研究中,建立在核桃全基因组发布的基础上,我们对核桃NAC转录因子基因家族进行了鉴定分析研究。另外,基于14对多态性高的微卫星遗传标记,我们对欧亚大陆范围分布的150个同群体2929核桃个体进行了...
【文章页数】：113 页
【学位级别】：博士
【文章目录】：
摘要
ABSTRACT
Chapter 1 General Introduction
1.1 General introduction of common walnut (Juglans regia)
1.2 Geography distribution of Juglans regia
1.3 Origin and history of walnut
1.4 Transcription factors in plants
1.4.1 Structure of NAC transcription factor
1.4.2 The function of NAC transcription factors in common walnut
1.4.3 Whole-genome duplication
1.4.4 Gene Ontology (GO)
1.5 Genetic diversity in Juglans regia
1.5.1 Landscape genetics and gene flow
1.5.2 Refugia
1.5.3 Simple sequence repeats (SSRs)
1.6 Aims and objectives
Chapter 2 Genome-wide analysis of NAC transcription factor family in walnut:evolution and expression profiles during development
2.1 Materials and Methods
2.1.1 Identification of NAC transcription factors in J. regia
2.1.2 Phylogenetic relationship
2.1.3 Chromosome location
2.1.4 Motifs and Conserved Domain detection analysis
2.1.5 Gene structure analysis
2.1.6 Synteny analysis
2.1.7 Calculating K_a/K_s values of duplicated gene pairs
2.1.8 Cis-elements analysis and GO annotation
2.1.9 Interaction network of Jr NAC proteins
2.1.10 Plant materials,treatments,and collections
2.1.11 Quantitative real-time PCR(qRT-PCR)
2.2 Results
2.2.1 Identification and phylogenetic relationship of NAC transcription factor family in J.regia
2.2.2 The chromosome location of NAC transcription factor family
2.2.3 Conserved motifs analysis and gene structure
2.2.4 Paralogous NACs genes
2.2.5 Gene duplication
2.2.6 Synteny analysis of JrNAC genes
2.2.7 Promoter region analysis and conserved domains of JrNAC genes
2.2.8 Expression profiles and qRT-PCR analysis of JrNACs among different tissues and flowering development stages
2.2.9 The interaction network among flowering genes
Summary
Chapter 3 Evolutionary history and genetic diversity of different Juglans regia of the world
3.1 Materials and methods
3.1.1 Sample collection and DNA extraction
3.1.2 Analysis of FST outlier loci
3.1.3 Genetic diversity analysis
3.1.4 Phylogenetic relationship and population differentiation analysis
3.1.5 Genetic structure
3.1.6 Genetic barrier and gene flow analysis
3.1.7 Species distribution modeling
3.2 Results
3.2.1 Genetic diversity of J. regia based on SSR
3.2.2 Reconstruction of the past distribution shifts of J. regia
3.2.3 Spatial genetic structure of J. regia
3.2.4 Comparative landscape genetics
Chapter 4 Discussion
4.1 The JrNACs transcription factors
4.1.1 The Phylogenetic relationship
4.1.2 Expansion and evolution of the JrNACs transcription factors
4.1.3 Predicting the potential functions of JrNAC transcription factors
4.1.4 Gene structure
4.1.5 Cis-acting regulatory elements
4.1.6 Protein-protein interaction
4.2 Genetic diversity and populations structure based on molecular data
4.2.1 Genetic diversity of Juglans regia
4.2.2 The analysis of molecular variance (AMOVA)
4.2.3 The principal coordinate analysis (PCoA)
4.2.4 Isolation and gene flow
4.2.5 Evolution history and distribution of walnut
4.2.6 Multiple refugia for common walnut
4.2.7 Dispersal of common walnut
Summary
Conclusion
References
攻读博士/硕士学位期间取得的科研成果
Acknowledgement
About the Author
本文编号：3734223
【文章页数】：113 页
【学位级别】：博士
【文章目录】：
摘要
ABSTRACT
Chapter 1 General Introduction
1.1 General introduction of common walnut (Juglans regia)
1.2 Geography distribution of Juglans regia
1.3 Origin and history of walnut
1.4 Transcription factors in plants
1.4.1 Structure of NAC transcription factor
1.4.2 The function of NAC transcription factors in common walnut
1.4.3 Whole-genome duplication
1.4.4 Gene Ontology (GO)
1.5 Genetic diversity in Juglans regia
1.5.1 Landscape genetics and gene flow
1.5.2 Refugia
1.5.3 Simple sequence repeats (SSRs)
1.6 Aims and objectives
Chapter 2 Genome-wide analysis of NAC transcription factor family in walnut:evolution and expression profiles during development
2.1 Materials and Methods
2.1.1 Identification of NAC transcription factors in J. regia
2.1.2 Phylogenetic relationship
2.1.3 Chromosome location
2.1.4 Motifs and Conserved Domain detection analysis
2.1.5 Gene structure analysis
2.1.6 Synteny analysis
2.1.7 Calculating K_a/K_s values of duplicated gene pairs
2.1.8 Cis-elements analysis and GO annotation
2.1.9 Interaction network of Jr NAC proteins
2.1.10 Plant materials,treatments,and collections
2.1.11 Quantitative real-time PCR(qRT-PCR)
2.2 Results
2.2.1 Identification and phylogenetic relationship of NAC transcription factor family in J.regia
2.2.2 The chromosome location of NAC transcription factor family
2.2.3 Conserved motifs analysis and gene structure
2.2.4 Paralogous NACs genes
2.2.5 Gene duplication
2.2.6 Synteny analysis of JrNAC genes
2.2.7 Promoter region analysis and conserved domains of JrNAC genes
2.2.8 Expression profiles and qRT-PCR analysis of JrNACs among different tissues and flowering development stages
2.2.9 The interaction network among flowering genes
Summary
Chapter 3 Evolutionary history and genetic diversity of different Juglans regia of the world
3.1 Materials and methods
3.1.1 Sample collection and DNA extraction
3.1.2 Analysis of FST outlier loci
3.1.3 Genetic diversity analysis
3.1.4 Phylogenetic relationship and population differentiation analysis
3.1.5 Genetic structure
3.1.6 Genetic barrier and gene flow analysis
3.1.7 Species distribution modeling
3.2 Results
3.2.1 Genetic diversity of J. regia based on SSR
3.2.2 Reconstruction of the past distribution shifts of J. regia
3.2.3 Spatial genetic structure of J. regia
3.2.4 Comparative landscape genetics
Chapter 4 Discussion
4.1 The JrNACs transcription factors
4.1.1 The Phylogenetic relationship
4.1.2 Expansion and evolution of the JrNACs transcription factors
4.1.3 Predicting the potential functions of JrNAC transcription factors
4.1.4 Gene structure
4.1.5 Cis-acting regulatory elements
4.1.6 Protein-protein interaction
4.2 Genetic diversity and populations structure based on molecular data
4.2.1 Genetic diversity of Juglans regia
4.2.2 The analysis of molecular variance (AMOVA)
4.2.3 The principal coordinate analysis (PCoA)
4.2.4 Isolation and gene flow
4.2.5 Evolution history and distribution of walnut
4.2.6 Multiple refugia for common walnut
4.2.7 Dispersal of common walnut
Summary
Conclusion
References
攻读博士/硕士学位期间取得的科研成果
Acknowledgement
About the Author
本文编号：3734223
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