基于高密度SNP芯片对苏丹和中国绵羊群体的全基因组种质特性研究
发布时间：2021-08-11 00:36
全基因组变异分析可为群体遗传多样性、群体结构及种群内和种群间分化提供重要信息;同时也可鉴定包括绵羊等各种家畜有关生产性能、繁殖性能和适应性等性状相关的潜在基因或基因组区域选择信号。绵羊（Ovis aries）通过长期的自然和人工选择已适应各种生态环境并表现出多种表型特征。遗传多样性特征鉴定和选择信号分析对遗传改良、环境适应的理解以及绵羊遗传资源的利用保护至关重要。高密度SNP芯片和全基因组重测序等高通量基因分型技术的快速发展,使我们能够快速检测绵羊个体基因组中的上百万个SNP,并鉴定绵羊种群中全基因组的遗传变异。然而,由于对苏丹绵羊和中国绵羊群体遗传多样性选择信号研究研究仍然有限,因此本研究使用600K芯片对苏丹地方绵羊和中国地方绵羊品种进行基因多样性、群体结构和选择信号分析。我们采集了5个苏丹沙漠羊群体,其中AL-Ahamda25只、Buzee23只、Hammri 24只、Kabashi 25只和Shanbali 24只;以及4个中国羊品种包括黑藏羊15只、欧拉羊（QOL=15）、滩羊（TS=18）和泽库羊15只,共280个样本个体。此外,我们还对来自干旱环境的和田羊、雅布依羊和卡拉...
【文章来源】：中国农业科学院北京市
【文章页数】：124 页
【学位级别】：博士
【文章目录】：
摘要
abstract
CHAPTER ONE INTRODUCTION
1.1 GENERAL INTRODUCTIONS
1.1.1 General objective
1.1.2 SPECIFIC OBJECTIVES
CHAPTER TWO LITERATURE REVIEW
2.1 SHEEP ORIGIN AND DOMESTICATIONS
2.2 SHEEP GENETIC RESOURCES IN AFRICA AND ASIA
2.3 SUDANESE INDIGENOUS SHEEP RESOURCES
2.4 METHODS OF MOLECULAR GENETICS CHARACTERIZATION TECHNIQUES IN ANIMAL
2.4.1 Whole genome sequence approaches
2.4.2 Single nucleotide polymorphisms genotyping
2.5 GENETIC DIVERSITY AND POPULATION STRUCTURES IN SHEEP POPULATIONS
2.5.1 Estimation genetic diversity within breed
2.5.2 Level of inbreeding
2.5.3 Analysis of molecular variance and population differentiations
2.5.4 Linkage disequilibrium(LD)and effective population size(Ne)
2.5.5.Detection of selection signature analysis using genomic information
2.5.6 Genes associated with importance traits and adaptation in sheep:
CHAPTER THREE ASSESSING THE GENOME ARCHITECTURE ANDSELECTION SIGNATURES OF THE SUDANESE THIN-TAILED DESERT SHEEP
3.1 INTRODUCTION
3.2 MATERIALS AND METHODS
3.2.1 Sample collection and DNA extraction
3.2.2 DNA quantification
3.2.3 Agarose gel electrophoresis
3.2.4 Data quality control and screening
3.2.5 Genetic diversity and structure
3.2.6 Genome-wide scans for signatures of selection
3.2.7 Determination of genes under selection and functional annotation
3.3 RESULTS
3.3.1 Genetic diversity and differentiation
3.3.2 AMOVA and genetic relationships
3.3.3 Population structure of Sudan thin-tailed Desert sheep ecotypes
3.3.4 Genetic diversity of Sudanese thin-tailed Desert sheep and their relationship withChinese sheep breeds
3.3.5 Phylogenetic analysis of Sudanese thin-tailed Desert and Chinese sheep breeds
3.3.6 Population structure of Sudanese Desert sheep and Chinese sheep breeds
3.3.7 Genome-wide selection signature analysis
3.3.8 Functional annotation of candidate regions and genes
3.4 DISCUSSION
3.4.1 Candidate genes related to adaptive immune response and disease resistance
3.4.2 Candidate genes associated with metabolic pathways
3.4.3 Candidate genes associated with body weight,growth,fat deposition and sheepconservation
3.4.4 Candidate genes associated with production and reproduction traits
CHAPTER FOUR GENOMIC DIVERSITY,POPULATION STRUCTURE ANDSIGNATURES OF SELECTION OF FIVE CHINESE NATIVE SHEEP BREEDSADAPTED TO EXTREM ENVIRONMENTS
4.1 INTRODUCTION
4.2 MATERIALS AND METHODS
4.2.1 Samples collection and DNA extraction
4.2.2 Animal's genotyping and quality control
4.2.3 Genetic diversity and population structure analyses
4.2.4 Genome-wide selection signatures
4.2.5 Annotation of highly significant regions
4.2.6 Functional Enrichments analysis of candidate genes
4.3 RESULTS
4.3.1 Genetics diversity analysis
4.3.2 Population structure Analyses
4.3.3 Detection of selection signature
4.4 DISCUSSION
4.4.1 Genetic diversity within population
4.4.2 Population structure of Chinese sheep breeds from dry and humid environments
4.4.3 Selection signatures of candidate genes
CHAPTER FIVE ESTIMATES OF AUTOZYGOSITY AND EXTENT OF EFFECTIVEPOPULATION SIZES IN FIVE NATIVE CHINESE SHEEP BREEDS ADAPTED TOEXTREME ENVIRONMENTS
5.1 BACKGROUND
5.2 MATERIALS AND METHODS
5.2.1 Samples collection and DNA extraction
5.2.2 ANIMAL'S GENOTYPING AND QUALITY CONTROL
5.2.3 Run of homozygosity analyses
5.2.4 Detection of common autozygosity islands
5.2.5 Effective population size(Ne)
5.3 RESULTS
5.3.1 SNPs filtration,miner Allele frequency and Linkage disequilibrium
5.3.2 Runs of homozygosity(ROH)Patterns
5.3.3 Genomic regions with a high ROH frequency
5.3.4 Effective population sizes(Ne)
5.4 DISCUSSION
5.4.1 Effective Population Size
5.4.2 ROHs
5.4.3 ROH candidate genes
5.4.4 Adaptive and innate immunity response genes related
5.4.5 Genes associated with disease resistant
5.4.6 Genes associated with body weight and digestive metabolism traits
CHAPTER SIX CONCLUSIONS AND RECOMMENDATIONS
6.1 CONCLUSIONS
6.2 RECOMMENDATIONS
APPENDIXES A
7.1 APPENDIX TABLES
7.2 APPENDIX FIGURES
REFERENCES
ACKNOWLEDGMENTS
AUTHOR RESUME
本文编号：3335084
【文章来源】：中国农业科学院北京市
【文章页数】：124 页
【学位级别】：博士
【文章目录】：
摘要
abstract
CHAPTER ONE INTRODUCTION
1.1 GENERAL INTRODUCTIONS
1.1.1 General objective
1.1.2 SPECIFIC OBJECTIVES
CHAPTER TWO LITERATURE REVIEW
2.1 SHEEP ORIGIN AND DOMESTICATIONS
2.2 SHEEP GENETIC RESOURCES IN AFRICA AND ASIA
2.3 SUDANESE INDIGENOUS SHEEP RESOURCES
2.4 METHODS OF MOLECULAR GENETICS CHARACTERIZATION TECHNIQUES IN ANIMAL
2.4.1 Whole genome sequence approaches
2.4.2 Single nucleotide polymorphisms genotyping
2.5 GENETIC DIVERSITY AND POPULATION STRUCTURES IN SHEEP POPULATIONS
2.5.1 Estimation genetic diversity within breed
2.5.2 Level of inbreeding
2.5.3 Analysis of molecular variance and population differentiations
2.5.4 Linkage disequilibrium(LD)and effective population size(Ne)
2.5.5.Detection of selection signature analysis using genomic information
2.5.6 Genes associated with importance traits and adaptation in sheep:
CHAPTER THREE ASSESSING THE GENOME ARCHITECTURE ANDSELECTION SIGNATURES OF THE SUDANESE THIN-TAILED DESERT SHEEP
3.1 INTRODUCTION
3.2 MATERIALS AND METHODS
3.2.1 Sample collection and DNA extraction
3.2.2 DNA quantification
3.2.3 Agarose gel electrophoresis
3.2.4 Data quality control and screening
3.2.5 Genetic diversity and structure
3.2.6 Genome-wide scans for signatures of selection
3.2.7 Determination of genes under selection and functional annotation
3.3 RESULTS
3.3.1 Genetic diversity and differentiation
3.3.2 AMOVA and genetic relationships
3.3.3 Population structure of Sudan thin-tailed Desert sheep ecotypes
3.3.4 Genetic diversity of Sudanese thin-tailed Desert sheep and their relationship withChinese sheep breeds
3.3.5 Phylogenetic analysis of Sudanese thin-tailed Desert and Chinese sheep breeds
3.3.6 Population structure of Sudanese Desert sheep and Chinese sheep breeds
3.3.7 Genome-wide selection signature analysis
3.3.8 Functional annotation of candidate regions and genes
3.4 DISCUSSION
3.4.1 Candidate genes related to adaptive immune response and disease resistance
3.4.2 Candidate genes associated with metabolic pathways
3.4.3 Candidate genes associated with body weight,growth,fat deposition and sheepconservation
3.4.4 Candidate genes associated with production and reproduction traits
CHAPTER FOUR GENOMIC DIVERSITY,POPULATION STRUCTURE ANDSIGNATURES OF SELECTION OF FIVE CHINESE NATIVE SHEEP BREEDSADAPTED TO EXTREM ENVIRONMENTS
4.1 INTRODUCTION
4.2 MATERIALS AND METHODS
4.2.1 Samples collection and DNA extraction
4.2.2 Animal's genotyping and quality control
4.2.3 Genetic diversity and population structure analyses
4.2.4 Genome-wide selection signatures
4.2.5 Annotation of highly significant regions
4.2.6 Functional Enrichments analysis of candidate genes
4.3 RESULTS
4.3.1 Genetics diversity analysis
4.3.2 Population structure Analyses
4.3.3 Detection of selection signature
4.4 DISCUSSION
4.4.1 Genetic diversity within population
4.4.2 Population structure of Chinese sheep breeds from dry and humid environments
4.4.3 Selection signatures of candidate genes
CHAPTER FIVE ESTIMATES OF AUTOZYGOSITY AND EXTENT OF EFFECTIVEPOPULATION SIZES IN FIVE NATIVE CHINESE SHEEP BREEDS ADAPTED TOEXTREME ENVIRONMENTS
5.1 BACKGROUND
5.2 MATERIALS AND METHODS
5.2.1 Samples collection and DNA extraction
5.2.2 ANIMAL'S GENOTYPING AND QUALITY CONTROL
5.2.3 Run of homozygosity analyses
5.2.4 Detection of common autozygosity islands
5.2.5 Effective population size(Ne)
5.3 RESULTS
5.3.1 SNPs filtration,miner Allele frequency and Linkage disequilibrium
5.3.2 Runs of homozygosity(ROH)Patterns
5.3.3 Genomic regions with a high ROH frequency
5.3.4 Effective population sizes(Ne)
5.4 DISCUSSION
5.4.1 Effective Population Size
5.4.2 ROHs
5.4.3 ROH candidate genes
5.4.4 Adaptive and innate immunity response genes related
5.4.5 Genes associated with disease resistant
5.4.6 Genes associated with body weight and digestive metabolism traits
CHAPTER SIX CONCLUSIONS AND RECOMMENDATIONS
6.1 CONCLUSIONS
6.2 RECOMMENDATIONS
APPENDIXES A
7.1 APPENDIX TABLES
7.2 APPENDIX FIGURES
REFERENCES
ACKNOWLEDGMENTS
AUTHOR RESUME
本文编号：3335084
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