声明
CHAPTER 1 INTRODUCTION AND REVIEW OF LITERATURE
1.1 BACKGROUND
1.2ORIGIN,DOMESTICATION AND DISTRIBUTION OF GOATS
1.3GOAT GENETIC RESOURCES IN ASIA
1.4GENETIC DIVERSITY
1.5CLIMATE CHANGE AND GENETIC DIVERSITY
1.6CONSERVATION OF ANIMAL GENETIC RESOURCES
1.7IMPLICATION OF MOLECULAR MARKER FORGENETIC STUDIES
1.8GENOMIC TOOLS FOR EFFECTIVE CONSERVATION OF LIVESTOCK BREED DIVERSITY
1.8.1 Runs of homozygosity (ROH)
1.8.2 Homozygosity by decent (HBD)
1.8.3 Effective population Size (Ne)
1.9DETECTION OF SELECTION SIGNATURE
1.10 GENOME WIDE ASSOCIATION STUDIES (GWAS)
1.11LITTER SIZE TRAIT
1.12 JUSTIFICATION
1.13GENERAL OBJECTIVE
1.14SPECIFIC OBJECTIVES
CHAPTER 2 Genetic Diversity and Genomic Detection of Positive Selection Signatures in Six Chinese Goat Breeds
2.1 INTRODUCTION
2.2MATERIALS AND METHODS
2.2.1 Sampling and Genotyping
2.2.2 Data Quality Control
2.2.3 Genetic diversity analysis
2.2.4 Distribution of ROH
2.2.5 Inbreeding Coefficient
2.2.6 Detection of Common ROHs
2.2.7 Homozygosity by Descent (HBD)
2.2.8 Effective Population Size (Ne)
2.2.9 Population Differentiations, Analysis of Molecular Variance, and Structure
2.2.10 Selective Sweep Analyses
2.3 RESULTS
2.3.1 Sample and SNP Filtration
2.3.2 Genetic diversity analysis
2.3.3 ROH Patterns
2.3.4 Inbreeding Coefficient of Runs of Homozygosity (FROH)
2.3.5 Genomic Regions with a High ROH Frequency
2.3.6 Homozygosity by Descent (HBD) Classes
2.3.7 Effective Population Size (Ne)
2.3.8 Population Differentiation, AMOVA, and Structure
2.3.9 Distinct Population Structure Pattern
2.3.10Genome-Wide Selective Sweep Analysis
2.3.11 GO Annotation and KEGG Pathway of the Target Genes
2.4 DISCUSSION
CHAPTER 3 A genome-wide perspective about runs of homozygosity, population structure and effective population size in nine Pakistani goatbreeds
3.1 INTRODUCTION
3.2MATERIALS AND METHODS
3.2.1 Sampling and Genotyping
3.2.2 Data Quality Control
3.2.3 Distribution of ROH
3.2.4 Inbreeding Coefficient
3.2.5 Detection of Common ROHs
3.2.6 Gene Annotation and Functional Enrichment Analysis
3.2.7Homozygosity by decent (HBD)
3.2.8 Effective Population Size (Ne)
3.2.9 Population Differentiations, Analysis of Molecular Variance, and Structure
3.3 RESULTS
3.3.1 Sample and SNP Filtration
3.3.2 Distribution of ROH
3.3.3 Inbreeding Coefficients of Runs of Homozygosity (FROH)
3.3.4 Genomic Regions with a High ROH Frequency
3.3.5 Gene Ontology (GO) and KEGG pathways analysis
3.3.6 Homozygosity by decent (HBD)
3.3.7 Effective Population Size (Ne)
3.3.8 Population Differentiations, AMOVA, and Structure
3.4 DISCUSSION
CHAPTER 4Conservation assessment of the state goat farms by using SNP genotyping data
4.1 INTRODUCTION
4.2MATERIALS ANDMETHODS
4.2.1 Sampling, Genotyping and Quality Control
4.2.2 Genomic Relationships Analysis and population structure
4.2.3 Runs of homozygosity calling option and estimation of Inbreeding
4.2.4 Effective Population Size (Ne)
4.3 RESULTS
4.3.1 Sample and SNP Filtration
4.3.2 Genomic Relationships Analysis and population structure
4.3.3Genetic diversity and Inbreeding coefficient
4.3.4 Effective Population Size
4.4 DISCUSSION
CHAPTER 5 Genome-wide association analysis reveals the genetic locus forlitter sizetrait in Chinese Arbas Cashmere goat
5.1 INTRODUCTION
5.2MATERIALS AND METHODS
5.2.1 Sampling and genotyping
5.2.2 Quality control of data
5.2.3 Genome-Wide Association studies
5.2.4 Gene Ontology and KEGG analysis
5.3 RESULTS
5.3.1 Genome-Wide Association studies
5.3.2 Gene Ontology and KEGG analysis
5.4 DISCUSSION
SUMMARY OF FINDINGS AND FUTURE PERSPECTIVES
参考文献
APPENDIX A
致谢
RESUME
中国农业科学院;
