Abstract ▼

The swine industry focuses on improving meat quality since it is one of the most important traits for consumers’ preference and profitability of the industry. The meat quality is commonly determined by measuring pH, water-binding capacity (drip loss), color, and amino acids and fatty acids compositi

The swine industry focuses on improving meat quality since it is one of the most important traits for consumers’ preference and profitability of the industry. The meat quality is commonly determined by measuring pH, water-binding capacity (drip loss), color, and amino acids and fatty acids compositions in loin muscle tissue (longissimus dorsi, LDM). These traits are related with metabolism of the tissue resulting from expression of multiple genes. Thus, there has been a strong rationale for understanding underlying regulatory mechanism of expression of genes in the LDM. DNA methylation plays a major role in regulating expression of genes, and it has also been suggested to be related with economic traits (e.g. daily gain) in livestock animals. However, to the best our knowledge, a comprehensive and genome-wide DNA methylation profile of the LDM tissue and its functional inferences have not been investigated. The objective of this study, thus, were to identify and characterize genome-wide DNA methylation profile of the LDM and to identify differentially metylated regions of LDM tissue in swine. A total of 7.06 Gb methylated DNA immunoprecipitation sequencing (MeDIP-seq) data were aligned on the reference genome. The methylated regions overlapped between at least two samples were regarded as putative methylated regions (PMR). A total of 33,506 PMR were identified in the LDM in swine. Among them only 3.1% were commonly observed in all eight samples we tested. The highest density of PMR was observed in the chromosome 10. A major portion of PMR were presented in the repeat regions (47.7%) followed by intron (21.5%). Within the repeat regions, we observed relatively high levels of methylation in the LINE (55.4%) and SINE (27.6%) elements. Among functional genomic regions, CpG islands showed the highest percentage (12.1%) of PMR that were commonly observed in all eight samples. Clustering analysis indicated large individual variation in the distribution of PMR. This project is focused on finding genomic regions responsible for the meat quality trait in korean paternal line of breeding pig. It used some analytical methods such as selective sweep and genome-wide association study (GWAS). Positive selection in duroc samples based on single nucleotide polymorphsim (SNP) revealed some genomic regions associated with higher meat quality score in pig. Using GRAMMAR software, this project found out SNPs that could possibly alter the level of meat quality. GRAMMAR method was more advantageous in inbred populations such as our duroc samples. The potential genes are: ANK1, BMP6, SHH, PIP4K2A, and FOXN2.
Based on these findings, the project also discovered the clusters of candidate genes through gene ontology KEGG pathway and animal QTL database analyses. This functional analysis enabled to focus on a cluster of genes rather than individual genes. Economic traits such as meat quality is polygenic; this functional analysis would contribute to this society.
The aim of this project was to determine the novel miRNAs which related to economic performance in pig. In particular, we focused on the miRNA transcriptome associated with meat quality traits in Duroc. Firstly, we determined the role of miR-143 which was known to be increased during adipocyte differentiation. After the induction of adipocyte differentiation the level of miR-143 was increased, whereas the expression of pref-1 mRNA as an adipogenesis inhibitor was decreased.
The pref-1 protein level was also down-regulated in preadipocytes ectopically expressing miR-143, and recovered by miR-143 inhibitor. The binding region for miR-143 was predicted to be located between positions 247 and 252 in the 3’-UTR of pref-1. The luciferase activity of the vector containing the wild-type 3’-UTR of pref-1 was decreased by 65% in cells transfected with miR-143 mimic compared to that of the corresponding control. The ectopic expression of miR-143 mimic suppressed the phosphorylation of ERK1/2 induced by pref-1 in 3T3-L1 cells. Taken together, these data suggest that miR-143 promotes adipogenesis by directly modulating the pref-1 expression in adipocytes. In addition, we constructed the profiling of microRNAs in serum of Duroc by using next generation sequencing.
As results, we profiled several different microRNAs related to meat quality traits and confirmed their expressions by real-time PCR. Finally, we studied candidate microRNAs as target genes against meat quality traits-related genes SCD1 and CtsD. By using miRanda, Targetscan program, we selected miR-429 and miR-145, and confirmed that these miRNAs downregulated the level of SCD1 and CtsD expression, respectively. In conclusion, our study will contribute to investigate the molecular mechanims of meat quality traits-associated genes and it could be useful for biomarker assisted selection in pig. This analysis reveals that Duroc was not admixed with other breeds, leading to the fact that Duroc can be compared with other breeds to look for evolutionary hot spots, and this might lead to some interesting genes that confer duroc specific characteristics, higher meat-quality traits. Obtain the overall information of the protein that is expressed in cells from control group of muscle tissue and normal pig. Get information of activated protein to separate the proteomics associated with cell viability (glycoproteins, phosphorylated proteins). Get information meat quality-associated cell membrane receptor protein through the membrane proteom analysis method in the muscle tissue of the comparative group and pigs on to discover maker protein that can be applied and investigate the pathway between related proteomics and expression proteomics group using bioinformatics. Establishing a primary cell culture method between objects, separated/analyzed related protein investigation and analysis through functionalanalysis of proteins. Confirmed the expression of the desired protein by processing the meat quality improvement or suppression material involved and excavation of new marker factor using the receptor proteome analysis information of tissue cells.
Get information of activated protein (glycoprotein, phosphoprotein) for separating proteomics. The discovery of meat quality-related candidates difference can be seen in the comparison group and the control group. Detection and identification of alteration in cell membrane proteins body through receptor proteome analysis. Via receptor proteome analysis sort and detection of changes in cell membrane proteins. After obtaining the genetic information for the sorted protein , amplification of the gene of interest using the E.coli system. Establishes a primary cell culture methods of each population. Related protein investigation and analysis through the functional analysis of protein. Confirm the expression of the protein. Excavation of novel marker factor using the receptor proteome analysis information of tissue cells. Direction presentation of improvement of Korea type pig for the development of excellent Korea breeding pig. Shortening of the generation interval in the early selection based on the estimated breeders of genomic selection approach. Contribute to the creation of training and human resources of related industries through the industrialization of research results. Improvement of competitiveness of pig farmers with import open to the development of Korea type paternal breeding pigs owns differentiated meat quality.

목차 Contents

• 표지 ... 1
• 제출문 ... 2
• 요 약 문 ... 3
• SUMMARY ... 8
• 목차 ... 11
• 제 1 장 서 론 ... 12
• 제 2 장 국내외 기술개발 현황 ... 19
• 제 3 장 연구개발수행 내용 및 결과 ... 27
• 제1세부과제 : SNP chip을 이용한 한국형 종돈 선발 체계 설정 연구 ... 27
• 제2세부과제 : 후성유전체 기법을 이용한 돼지 육질 개량 기술 개발 ... 38
• 제1협동과제 : 육질관련 형질의 연관연구 및 유전체 선발 ... 64
• 제2협동과제 : 육질관련 miRNA 전사체 기능 분석 연구 ... 65
• 제3협동과제 : 진화유전체 분석을 통한 가축화 유전자 발굴 ... 84
• 제4협동과제 : 돼지 Duroc 품종의 근육 특성 분석 및 육질 관련 단백체 연구 ... 87
• 제 4 장 연구개발목표 달성도 및 대외기여도 ... 95
• 1절. 세부과제별 정성적 연구목표대비 달성도 ... 95
• 2절. 정량적 목표대비 달성도 ... 98
• 제 5 장 연구개발결과의 활용계획 ... 99
• 제 6 장 연구개발과정에서 수집한 해외과학기술정보 ... 104
• 제 7 장 기타 중요 변동사항 ... 106
• 제 8 장 국가과학기술종합정보시스템에 등록한 연구장비현황 ... 107
• 제 9 장 참고문헌 ... 108
• 끝페이지 ... 116