全基因組變異分析可為群體遺傳多樣性、群體結(jié)構(gòu)及種群內(nèi)和種群間分化提供重要信息;同時也可鑒定包括綿羊等各種家畜有關(guān)生產(chǎn)性能、繁殖性能和適應(yīng)性等性狀相關(guān)的潛在基因或基因組區(qū)域選擇信號。綿羊（Ovis aries）通過長期的自然和人工選擇已適應(yīng)各種生態(tài)環(huán)境并表現(xiàn)出多種表型特征。遺傳多樣性特征鑒定和選擇信號分析對遺傳改良、環(huán)境適應(yīng)的理解以及綿羊遺傳資源的利用保護至關(guān)重要。高密度SNP芯片和全基因組重測序等高通量基因分型技術(shù)的快速發(fā)展,使我們能夠快速檢測綿羊個體基因組中的上百萬個SNP,并鑒定綿羊種群中全基因組的遺傳變異。然而,由于對蘇丹綿羊和中國綿羊群體遺傳多樣性選擇信號研究研究仍然有限,因此本研究使用600K芯片對蘇丹地方綿羊和中國地方綿羊品種進行基因多樣性、群體結(jié)構(gòu)和選擇信號分析。我們采集了5個蘇丹沙漠羊群體,其中AL-Ahamda25只、Buzee23只、Hammri 24只、Kabashi 25只和Shanbali 24只;以及4個中國羊品種包括黑藏羊15只、歐拉羊（QOL=15）、灘羊（TS=18）和澤庫羊15只,共280個樣本個體。此外,我們還對來自干旱環(huán)境的和田羊、雅布依羊和卡拉... 

【文章來源】：中國農(nóng)業(yè)科學院北京市

【文章頁數(shù)】：124 頁

【學位級別】：博士

【文章目錄】：
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



本文編號：3335084