全基因組關(guān)聯(lián)研究(GWAS)通常用于發(fā)現(xiàn)控制畜禽重要經(jīng)濟性狀的候選基因。本研究的目的是發(fā)掘與牛后軀體尺和凈肉重性狀有關(guān)的潛在候選基因。二代測序(NGS)填充得到的數(shù)據(jù)集包含1200萬個單核苷酸多態(tài)性(SNP)(來自1252個中國肉用西門塔爾肉牛),使用線性混合模型分析配合單倍型和LD座方法研究影響后肢性狀的基因位點。基于嚴格的統(tǒng)計閾值(P=0.05/SNP的有效數(shù)量),我們在BTA4區(qū)域中發(fā)現(xiàn)了202個與后腿寬度相關(guān)的SNP。檢索這些SNP周圍的區(qū)域后,我們發(fā)現(xiàn)了相關(guān)的候選基因。更重要的是,我們在BTA4上確定了一個大約280 kb的區(qū)域,該區(qū)域包含有幾個肌肉發(fā)育的潛在基因。但是,我們還在BTA4上發(fā)現(xiàn)了與骨骼疾病(例如軟骨發(fā)育不良)相關(guān)的候選基因SLC13A1。在凈肉重中,我們在BTA4中鑒定出一個SNP(chr4:100670823)超過了我們的嚴格閾值(p=8.58×10-8),因此,該SNP被列為與凈肉重有關(guān)的候選QTL。我們在西門塔爾牛中進一步鑒定了與該標記相關(guān)的候選基因MTPN。在GWAS之后,需要進行基本驗證,不僅要對基因功能進行嚴格分析,而且還要驗證所檢測基因的生物學(xué)意...

【文章頁數(shù)】：98 頁

【學(xué)位級別】：博士

【文章目錄】：
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



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