全基因組關(guān)聯(lián)分析（GWAS）已廣泛用于解析人類,植物和動物復(fù)雜性狀遺傳結(jié)構(gòu)。GWAS提供了一種強大的工具,可以將個體的表型差異歸因于潛在的遺傳差異。隨著新一代測序技術(shù)發(fā)展,已經(jīng)為不同的生物開展了重測序,生成了高密度單核苷酸多態(tài)性（SNP）陣列。眾所周知,在數(shù)量遺傳學(xué)中復(fù)雜性狀由多基因,上位性及基因與環(huán)境互作效應(yīng)控制。大多數(shù)GWAS分析忽略了顯性、上位性和基因與環(huán)境互作效應(yīng)對復(fù)雜性狀產(chǎn)生的影響。忽視這些影響是GWAS遺傳率缺失的重要原因之一。本研究中,通過使用QTXNetwork中混合線性模型方法,估計了顯性、上位性和環(huán)境特異性遺傳力對玉米NAM種群穗部性狀的影響。對于NAM群體,全模型包括加性、顯性、上位性和環(huán)境特異性遺傳效應(yīng)。對于MESA群體,混合線性模型包括加性、顯性、上位性和種族特異性遺傳效應(yīng)。本研究中,解析了MESA群體的體表面積（BSA）和玉米穗性狀的遺傳結(jié)構(gòu),提供了新的見解。對于玉米穗部性狀,顯性和顯性相關(guān)的上位效應(yīng)對估計的遺傳力有顯著貢獻。環(huán)境特異性遺傳效應(yīng)也是玉米穗的遺傳變異的重要組成部分。只有少數(shù)控制玉米穗性狀的多效位點被鑒定出來。通過利用關(guān)聯(lián)分析結(jié)果預(yù)測了優(yōu)良品系和... 

【文章來源】：浙江大學(xué)浙江省 211工程院校 985工程院校 教育部直屬院校

【文章頁數(shù)】：118 頁

【學(xué)位級別】：博士

【文章目錄】：
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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