包含加性、显性、上位性及基因与环境互作效应的复杂性状遗传分析

发布时间：2021-05-11 13:08

　　全基因组关联分析（GWAS）已广泛用于解析人类,植物和动物复杂性状遗传结构。GWAS提供了一种强大的工具,可以将个体的表型差异归因于潜在的遗传差异。随着新一代测序技术发展,已经为不同的生物开展了重测序,生成了高密度单核苷酸多态性（SNP）阵列。众所周知,在数量遗传学中复杂性状由多基因,上位性及基因与环境互作效应控制。大多数GWAS分析忽略了显性、上位性和基因与环境互作效应对复杂性状产生的影响。忽视这些影响是GWAS遗传率缺失的重要原因之一。本研究中,通过使用QTXNetwork中混合线性模型方法,估计了显性、上位性和环境特异性遗传力对玉米NAM种群穗部性状的影响。对于NAM群体,全模型包括加性、显性、上位性和环境特异性遗传效应。对于MESA群体,混合线性模型包括加性、显性、上位性和种族特异性遗传效应。本研究中,解析了MESA群体的体表面积（BSA）和玉米穗性状的遗传结构,提供了新的见解。对于玉米穗部性状,显性和显性相关的上位效应对估计的遗传力有显著贡献。环境特异性遗传效应也是玉米穗的遗传变异的重要组成部分。只有少数控制玉米穗性状的多效位点被鉴定出来。通过利用关联分析结果预测了优良品系和... 

【文章来源】：浙江大学浙江省 211工程院校 985工程院校 教育部直属院校

【文章页数】：118 页

【学位级别】：博士

【文章目录】：
ACKNOWLEDGEMENT
ABSTRACT
摘要
CHAPTER 1 GENERAL INTRODUCTION
    1.1 Introduction
    1.2 Objectives of the Study
    1.3 Overview of the Study
CHAPTER 2 REVIEW OF LITERATURE
    2.1 Introduction
    2.2 Genetic architecture of complex traits in plant
    2.3 Statistical genetic models for analyzing gene-environment interaction effects
    2.4 Association analysis using QTXNetwork
    2.5 Breeding design using SNP marker
    2.6 Conditional GWAS analysis
    2.7 Gene ontology analysis of GWAS result
CHAPTER 3 GENOMIC SELECTION OF MAIZE EAR TRAITS FOR GENETIC EFFECTSOF ADDITIVE, DOMINANCE, EPISTASIS, AND G×E INTERACTIONS
    3.2 Introduction
    3.3 Materials and Methods
        3.3.1 Genotype and Phenotype Data
        3.3.2 Statistical Methods and Analysis
        3.3.3 Annotation of candidate genes of the identified QTSs
    3.4 Results
        3.4.0 Phenotypic distribution of maize ear traits
        3.4.1 Estimated Heritability for Ear Traits
        3.4.2 Highly significant identified loci with no gene x environment interaction effects
        3.4.3 Highly significant loci identified with gene x environment interaction effects
        3.4.4 Candidate Gene Annotation
        3.4.5 Pleiotropic QTSs of the Maize Ear Traits
        3.4.6 Breeding potential of predicted lines
    3.5 Discussions
CHAPTER 4 CONSEQUENCE OF IGNORING GENE x ENVIRONMENT INTERACTIONEFFECTS IN GENETIC ANALYSIS OF PLANT COMPLEX TRAITS
    4.2 Introduction
    4.3 Materials and Methods
        4.3.0 Real Data
        4.3.1 Simulated Data
        4.3.2 Statistical Methods and Analysis
        4.3.3 Annotation of candidate genes of the identified QTSs
    4.4 Results
        4.4.1 Heritability Estimation
        4.4.2 Identified loci associated with maize ear diameter using the full model
        4.4.3 Difference between analysis results of the full model and reduced model
        4.4.4 Simulation results
        4.4.5 Scope of breeding improvement
    4.5 Discussions
CHAPTER 5 LIFESTYLE INFLUENCES ON GENETIC REGULATION OF BODYSURFACE AREA IN MESA POPULATION
    5.2 Introduction
    5.3 Materials and methods
        5.3.1 Data
        5.3.2 Quality control
        5.3.3 Statistical model
        5.3.4 Analyzing genetic effects of loci across different ethnic groups
        5.3.5 Bioinformatics analysis
    5.4 Results
        5.4.1 Estimated heritability of BSA
        5.4.2 Genes identified for BSA using base and cofactor models
        5.4.3 Genes, not identified in the cofactor models
        5.4.4 Effects of genes increased or decreased in lifestyle cofactor models
        5.4.5 New genes identified only in the cofactor models
        5.4.6 Ethnic-specific genetics effects of BSA QTSs
        5.4.7 Gene ontology analysis
    5.5 Discussions
Chapter 6 General Conclusions
References
APPENDIX A. SUPPLEMENTAL INFORMATION FOR CHAPTER 3
APPENDIX B. SUPPLEMENTAL INFORMATION FOR CHAPTER 4
APPENDIX C. SUPPLEMENTAL INFORMATION FOR CHAPTER 5



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