Abbreviations
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 AND SELECTION 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 with Chinese 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 sheep conservation
3.4.4 Candidate genes associated with production and reproduction traits
CHAPTER FOUR GENOMIC DIVERSITY, POPULATION STRUCTURE AND SIGNATURES OF SELECTION OF FIVE CHINESE NATIVE SHEEP BREEDS ADAPTED 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 EFFECTIVE POPULATION SIZES IN FIVE NATIVE CHINESE SHEEP BREEDS ADAPTED TO EXTREME 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
参考文献
致谢
AUTHOR RESUME
中国农业科学院;
