基于填充测序的肉用西门塔尔牛肌肉特异性候选基因的鉴定和验证
发布时间：2024-03-20 04:25
全基因组关联研究(GWAS)通常用于发现控制畜禽重要经济性状的候选基因。本研究的目的是发掘与牛后躯体尺和净肉重性状有关的潜在候选基因。二代测序(NGS)填充得到的数据集包含1200万个单核苷酸多态性(SNP)(来自1252个中国肉用西门塔尔肉牛),使用线性混合模型分析配合单倍型和LD座方法研究影响后肢性状的基因位点。基于严格的统计阈值(P=0.05/SNP的有效数量),我们在BTA4区域中发现了202个与后腿宽度相关的SNP。检索这些SNP周围的区域后,我们发现了相关的候选基因。更重要的是,我们在BTA4上确定了一个大约280 kb的区域,该区域包含有几个肌肉发育的潜在基因。但是,我们还在BTA4上发现了与骨骼疾病(例如软骨发育不良)相关的候选基因SLC13A1。在净肉重中,我们在BTA4中鉴定出一个SNP(chr4:100670823)超过了我们的严格阈值(p=8.58×10-8),因此,该SNP被列为与净肉重有关的候选QTL。我们在西门塔尔牛中进一步鉴定了与该标记相关的候选基因MTPN。在GWAS之后,需要进行基本验证,不仅要对基因功能进行严格分析,而且还要验证所检测基因的生物学意...
【文章页数】：98 页
【学位级别】：博士
【文章目录】：
摘要
abstract
CHAPTER1.INTRODUCTION
1.1.General Introductions
1.1.1.General objective
1.1.2.Specific objectives
CHAPTER2.LITERATURE REVIEW
2.1.How quantitative traits are controlled
2.2.Genome wide association studies
2.3.Benefits of GWAS
2.3.1.GWAS can lead to the discovery of novel biological mechanisms
2.3.2.GWAS are relevant to the study of low-frequency and rare variants
2.3.3 GWAS data are used for multiple applications beyond gene identification
2.4.Benefits specific to SNP array-based GWAS
2.5.GWAS based on SNP arrays are cost-effective for identifying risk loci
2.6.Limitations of GWAS
2.6.1.GWAS do not necessarily pinpoint causal variants and genes
CHAPTER3.IDENTIFICATION OF MUSCLE-SPECIFIC CANDIDATE GENES IN SIMMENTAL BEEF CATTLE USING IMPUTED NEXT GENERATION SEQUENCING
3.1.Introduction
3.2.Materials and methods
3.2.1.Ethics statement
3.2.2.Animal resources and phenotype data
3.2.3.Genotype data and quality control of SNP array
3.2.4.Resequencing
3.2.5.Imputation of sequence variants
3.2.6.Statistical analysis
3.2.7. SNP distribution
3.3.Results
3.3.1.Association analysis
3.4.Discussion
CHAPTER4.IDENTIFICATION AND VALIDATION OF CANDIDATE GENES REGULATING NET MEAT WEIGHT IN SIMMENTAL BEEF CATTLE BASED ON IMPUTED NEXT-GENERATION SEQUENCING
4.1.Introduction
4.2.Material and methods
4.2.1 Ethic statement
4.2.2.Animal resources and phenotype data
4.2.3.Genotype analyses and quality control
4.2.4.Resequencing
4.2.5.Imputation of SNP
4.2.6.Statistical model
4.2.7.SNP propagation
4.2.8. Primary Cell Isolation, Cell Culture and MTPN treatments for differentiation and hypertrophy
4.2.9.Myotrophin
4.2.10.RNA isolation,Reverse transcription-and Quantitative PCR(q PCR)
4.2.11.The number of nuclei,fusion index and the diameter of myotube
4.2.12.Proliferation CCK assay
4.2.13.Flow Cytometry
4.2.14.Statistical analysis
4.3.Results
4.3.1.Association analysis
4.3.2.Effect of myotrophin on expression of six muscle-related markers regulating differentiation and hypertrophy
4.3.3.Myotrophin promotes differentiation of myoblast into myotubes
4.3.4.Myotrophin attenuates proliferation of skeletal muscle cells
4.3.5.Myotrophin decreased the percentage of cell accumulation in S+ G2/M phase
4.4.Discussion
CHAPTER5.CONCLUSIONS AND RECOMMENDATIONS
5.1.Conclusions
5.2.Recommendations
6.REFERENCES
7.APPENDIX
7.1.Appendix Tables
7.2.Appendix Figures
ACKNOWLEDGEMENTS
AUTHOR RESUME
本文编号：3932956
【文章页数】：98 页
【学位级别】：博士
【文章目录】：
摘要
abstract
CHAPTER1.INTRODUCTION
1.1.General Introductions
1.1.1.General objective
1.1.2.Specific objectives
CHAPTER2.LITERATURE REVIEW
2.1.How quantitative traits are controlled
2.2.Genome wide association studies
2.3.Benefits of GWAS
2.3.1.GWAS can lead to the discovery of novel biological mechanisms
2.3.2.GWAS are relevant to the study of low-frequency and rare variants
2.3.3 GWAS data are used for multiple applications beyond gene identification
2.4.Benefits specific to SNP array-based GWAS
2.5.GWAS based on SNP arrays are cost-effective for identifying risk loci
2.6.Limitations of GWAS
2.6.1.GWAS do not necessarily pinpoint causal variants and genes
CHAPTER3.IDENTIFICATION OF MUSCLE-SPECIFIC CANDIDATE GENES IN SIMMENTAL BEEF CATTLE USING IMPUTED NEXT GENERATION SEQUENCING
3.1.Introduction
3.2.Materials and methods
3.2.1.Ethics statement
3.2.2.Animal resources and phenotype data
3.2.3.Genotype data and quality control of SNP array
3.2.4.Resequencing
3.2.5.Imputation of sequence variants
3.2.6.Statistical analysis
3.2.7. SNP distribution
3.3.Results
3.3.1.Association analysis
3.4.Discussion
CHAPTER4.IDENTIFICATION AND VALIDATION OF CANDIDATE GENES REGULATING NET MEAT WEIGHT IN SIMMENTAL BEEF CATTLE BASED ON IMPUTED NEXT-GENERATION SEQUENCING
4.1.Introduction
4.2.Material and methods
4.2.1 Ethic statement
4.2.2.Animal resources and phenotype data
4.2.3.Genotype analyses and quality control
4.2.4.Resequencing
4.2.5.Imputation of SNP
4.2.6.Statistical model
4.2.7.SNP propagation
4.2.8. Primary Cell Isolation, Cell Culture and MTPN treatments for differentiation and hypertrophy
4.2.9.Myotrophin
4.2.10.RNA isolation,Reverse transcription-and Quantitative PCR(q PCR)
4.2.11.The number of nuclei,fusion index and the diameter of myotube
4.2.12.Proliferation CCK assay
4.2.13.Flow Cytometry
4.2.14.Statistical analysis
4.3.Results
4.3.1.Association analysis
4.3.2.Effect of myotrophin on expression of six muscle-related markers regulating differentiation and hypertrophy
4.3.3.Myotrophin promotes differentiation of myoblast into myotubes
4.3.4.Myotrophin attenuates proliferation of skeletal muscle cells
4.3.5.Myotrophin decreased the percentage of cell accumulation in S+ G2/M phase
4.4.Discussion
CHAPTER5.CONCLUSIONS AND RECOMMENDATIONS
5.1.Conclusions
5.2.Recommendations
6.REFERENCES
7.APPENDIX
7.1.Appendix Tables
7.2.Appendix Figures
ACKNOWLEDGEMENTS
AUTHOR RESUME
本文编号：3932956
本文链接：https://www.wllwen.com/yixuelunwen/dongwuyixue/3932956.html