Title Page
ABSTRACT
국문 초록
PREFACE
Contents
LIST OF ABBREVIATION 25
CHAPTER 1. GENERAL INTRODUCTION 28
1.1. Background 29
1.2. The characteristics of Samgyeopsal 34
1.2.1. The structure of the Samgyeopsal 34
1.2.2. The measurement of the Samgyeopsal traits 37
1.3. Consumer preference of the Samgyeopsal 40
1.4. The determining factors for the Samgyeopsal in the growth stage 42
1.4.1. Phenotype correlation with lean meat production ability 44
1.4.2. Phenotype correlation with meat quality 45
1.5. The genetic potential for improving Samgyeopsal traits 47
1.5.1. The genetic factors 47
1.5.2. The candidate genes for Samgyeopsal 48
1.5.3. The fat deposition-associated genes in the other species 50
CHAPTER 2. ESTIMATION OF GENETIC PARAMETERS FOR SAMGYEOPSAL TRAITS 54
2.1. Abstract 55
2.2. Introduction 56
2.3. Materials and methods 58
2.3.1. Animals and muscle samples 58
2.3.2. Carcass trait measurements 58
2.3.3. The measurement of the Samgyeopsal characteristics 58
2.3.4. The measurement of the Samgyeopsal components in Section 7 60
2.3.5. The measurement of the meat quality 62
2.3.6. Genotypes 62
2.3.7. Statistical analysis 63
2.4. Results 66
2.4.1. Descriptive Statistics 66
2.4.2. Heritability 69
2.4.3. Phenotypic correlations 71
2.3.4. Genetic correlations 73
2.5. Discussion 78
2.6. Conclusion 86
CHAPTER 3. IDENTIFICATION OF KEY ADIPOGENIC TRANSCRIPTION FACTORS FOR THE SAMGYEOPSAL PARAMETERS VIA THE ASSOCIATION WEIGHT MATRIX 87
3.1. Abstract 88
3.2. Introduction 89
3.3. Materials and methods 91
3.3.1. Animals 91
3.3.2. Phenotypic Evaluation 91
3.3.3. Genotypic evaluation and genome-wide association analysis 93
3.3.4. Co-association network analysis 95
3.4. Results 97
3.5. Discussion 106
3.6. Conclusion 117
CHAPTER 4. GENOMIC CHARACTERIZATION OF THE PORCINE CRTC3 AND THE EFFECTS OF A NON-SYNONYMOUS MUTATION P.V515F ON LEAN MEAT PRODUCTION AND SAMGYEOPSAL FAT 118
4.1. Abstract 119
4.2. Introduction 120
4.3. Materials and methods 123
4.3.1. Animals and trait measurements 123
4.3.2. Identification of genomic sequence variations 126
4.3.3. Genotyping of p.V515F 126
4.3.4. Quantitative real-time PCR (qPCR) analysis 131
4.3.5. Statistical analysis 133
4.4. Results and Discussion 134
4.4.1. mRNA expression of porcine CRTC3 in muscle and fat tissues 134
4.4.2. Identification of non-synonymous mutations in CRTC3 in pig populations 136
4.4.3. Associations with measured traits and additive and dominance effects 140
4.5. Conclusion 144
CHAPTER 5. GENOME-TO-PHENOME ASSOCIATION REVEALS TWO-DIMENSIONAL LANDSCAPE FOR SAMGYEOPSAL PARAMETERS AND MUSCLE FORMATION CHARACTERISTICS 145
5.1. Abstract 146
5.2. Introduction 147
5.3. Materials and methods 150
5.3.1. Animals 150
5.3.2. Phenotypic Evaluation 150
5.3.3. Statistical analysis 153
5.3.4. Genotypic evaluation and genome to phenome analysis 153
5.3.5. Functional enrichment analysis 155
5.4. Results 156
5.4.1. Descriptive Statistics 156
5.4.2. Phenotypic correlation 165
5.4.3. Genome-to-Phenome study 168
5.4.4. Comparing the significance of SNP effects via standardizing treatment 196
5.4.5. Functional enrichment of the significant genes 203
5.5. Discussion 206
5.6. Conclusion 212
CHAPTER 6. GENERAL DISCUSSION 213
REFERENCES 217
APPENDICES 237
Table 1.1. Automated measurement method for carcass traits 39
Table 1.2. Associated genes with fat deposition and Samgyeopsal 52
Table 2.1. Descriptive unadjusted statistics for the traits 67
Table 2.2. Estimates of the genetic (σg2) and environmental (σe2) variances and heritability (h²) for the carcass, Samgyeopsal, and meat quality traits in Yorkshire pigs[이미지참조] 70
Table 2.3. Genetic (line below) and phenotypic correlation (line above) among the carcass traits, whole Samgyeopsal traits, and Samgyeopsal components in Section 7, and the meat quality traits 76
Table 3.1. The descriptive unadjusted statistics for the traits 98
Table 4.1. Mean and standard deviation (SD) for each trait 125
Table 4.2. Primers for polymorphism identification in the porcine CRTC3 gene 128
Table 4.3. Primers for real-time quantitative PCR to analyze mRNA expression levels 132
Table 4.4. Allele and genotype frequencies of p.V515F in porcine CRTC3 139
Table 4.5. Effects of the p.V515F mutation in CRTC3 on loin muscle and Samgyeopsal fat traits in 368 Yorkshire pigs 143
Table 5.1. The descriptive unadjusted statistics for the traits 158
Table 5.2. Significance SNPs against Samgyeopsal weight and volume 176
Table 5.3. Significance SNPs against Samgyeopasl main component muscles (CTM, RAM and EAM) 182
Figure 1.1. Meat consumption per person in South Korea. 31
Figure 1.2. The price by pork cuts in South Korea. 32
Figure 1.3. The amount of Samgyeopsal (pork belly) imported in South Korea. 33
Figure 1.4. The whole shape of Samgyeopsal. 36
Figure 2.1. Scheme of Samgyeopsal components in the Section 7 region. 61
Figure 2.2. Heat map showing phenotypic and genetic correlation. 77
Figure 3.1. Network extracted from the results of the genome-wide association study via the PCIT algorithm. 102
Figure 3.2. Hierarchical cluster analysis of AWM. 103
Figure 3.3. Network extracted from the results of the genome-wide association study via the association weight matrix. 104
Figure 3.4. Pathways enriched in the network of the trio of transcription factors and their associated genes. 105
Figure 3.5. Protein interaction network of the trio of transcription factors. 110
Figure 4.1. Samgyeopsal dissection and measurement regions. 124
Figure 4.2. Genotypes of the p.V515F mutation in the CRTC3 gene after PCR- restriction fragment length polymorphism (RFLP) analysis using HincII 130
Figure 4.3. Comparison of mRNA expression profiles of the porcine CRTC3 gene between longissimus thoracis and backfat. 135
Figure 4.4. Diagrammatic representation of the CRTC3 gene and identified polymorphisms. 138
Figure 5.1. Heat map showing phenotypic correlation. 167
Figure 5.2. Manhattan and Q-Q plots of the results from the genome-wide association study against whole Samgyeopsal traits. 171
Figure 5.3. Manhattan and Q-Q plots of the results from the genome-wide association study against component muscle total volume. 174
Figure 5.4. The sorted whole trait data for significant SNPs associated with Samgyeopsal traits. 199
Figure 5.5. The sorted whole trait data for significant SNPs associated with cutaneous trunci muscle (CTM) traits. 200
Figure 5.6. The sorted whole trait data for significant SNPs associated with rectus abdominis muscle (RAM) traits. 201
Figure 5.7. The sorted whole trait data for significant SNPs associated with external abdominal oblique muscle (EAM) traits. 202
Figure 5.8. The functional approach for significant genes with whole parameters. 204