Title Page
Contents
Abbreviations 10
Chapter 1. Associations of the polymorphisms in DHRS4, SERPING1, and APOR genes with Postmortem pH in Berkshire pigs 11
1.1. Introduction 12
1.2. Materials and methods 15
Animals 15
Measurements of meat quality traits 15
SNP detection 16
Genotyping 16
Statistical analysis 18
1.3. Results 19
Identification of SNPs in DHRS4, SERPING1, and APOR genes 19
Analysis of the association between the SNP in DHRS4 gene and meat quality 21
Analysis of the association between the SNP in SERPING1 gene and meat quality 24
Analysis of the association between the SNP in APOR gene and meat quality 27
1.4. Discussion 30
1.5. Conclusion 34
1.6. References 35
Chapter 2. DNA methylation patterns and gene expression associated with litter size in Berkshire pig placenta 40
2.1. Introduction 41
2.2. Materials and Methods 43
Ethics statement 43
Animal and placenta collection 43
Genomic DNA isolation 44
Genome-wide bisulfite sequencing 44
DMRs analysis 44
RNA isolation and sequencing 45
Analysis of DEGs positioned in DMRs between the two groups 46
Real-time quantitative PCR (RT-qPCR) for DEG verification 46
PCR-based methylation analysis 49
2.3. Results 50
DNA methylation profile of placenta 50
Analysis of DMRs and gene ontology 57
DEGs positioned in DMRs between the two groups 60
Verification by RT-qPCR 64
PCR-based methylation analysis of three genes in blood samples 67
2.4. Discussion 71
2.5. Conclusion 76
2.6. References 77
초록 85
ABSTRACT 88
Chapter 1. Associations of the polymorphisms in DHRS4, SERPING1, and APOR genes with Postmortem pH in Berkshire pigs 17
Table 1. Primer sequences used in genotyping analysis. 17
Table 2. The information of identified SNPs in the DHRS4, SERPING1 and APOR genes 20
Table 3. Association between DHRS4 SNP, c.93C〉G, and meat quality traits related to postmortem pH. 22
Table 4. Association between DHRS4 SNP, c.93C〉G, and meat quality traits. 23
Table 5. Association between SERPING1 SNP, c.1077G〉C, and meat quality traits related to postmortem pH. 25
Table 6. Association between SERPING1 SNP, c.1077G〉C, and meat quality traits. 26
Table 7. Association between APOR SNP, c.215T〉C, and meat quality traits related to postmortem pH. 28
Table 8. Association between APOR SNP, c.215T〉C, and meat quality traits. 29
Chapter 2. DNA methylation patterns and gene expression associated with litter size in Berkshire pig placenta 48
Table 1. Primer sequences used in RT-qPCR. 48
Table 2. Summary of sequencing results and reads alignment. 51
Table 3. Genome-wide methylation levels in the two groups. 52
Table 4. List of DEGs positioned in DMRs by the litter size. 61
Table 5. Methylation region of potential DEGs positioned in DMRs. 62
Chapter 1. Associations of the polymorphisms in DHRS4, SERPING1, and APOR genes with Postmortem pH in Berkshire pigs 33
Figure 1. Scheme of skeletal muscle pH regulation by SERPING1, DHRS4 and APOR... 33
Chapter 2. DNA methylation patterns and gene expression associated with litter size in Berkshire pig placenta 54
Figure 1. Relative methylation level of mCG for different genomic regions in the two... 54
Figure 2. Distribution of CpG methylation levels in CpG island, HCP, ICP, and LCP... 56
Figure 3. Distribution of DMRs for different genomic regions in LLG compared to... 58
Figure 4. Gene ontology enrichment analysis of the differentially methylated genes. 59
Figure 5. Potential DEGs significantly positively related to DMRs. 63
Figure 6. Validation of DEGs by RT-qPCR. 65
Figure 7. Validation of DEGs by RT-qPCR analysis of PRKG2, CLCA4 and PCK1... 66
Figure 8. Analysis of PRKG2 gene methylation in blood by PCR-based methylation... 68
Figure 9. Analysis of CLCA4 gene methylation in blood by PCR-based methylation... 69
Figure 10. Analysis of PCK1 gene methylation in blood by PCR-based methylation... 70
Figure 11. Scheme of litter size increasing process by PRKG2, CLCA4 and PCK1... 75