Molecular effects of SNPs in the 3’UTR of PPARGC1A and muscle-specific microRNA genes on muscle traits
- 주제(키워드) miR-1 , miR-133b , miR-206 , PPARGC1A , Single nucleotide polymorphism , muscle fiber type composition , Meat quality , 3' UTR
- 발행기관 고려대학교 대학원
- 지도교수 이영식
- 발행년도 2012
- 학위수여년월 2012. 2
- 학위구분 석사
- 학과 일반대학원 생명공학과
- 세부전공 동물생명공학전공
- 원문페이지 104 p
- 비고 Effects of polymorphisms in the 3’ untranslated region of the porcine PPARGC1A gene on muscle fiber characteristics
- 실제URI http://www.dcollection.net/handler/korea/000000033138
- 본문언어 영어
- 제출원본 000045696528
초록/요약
Summary MicroRNAs (miRNAs) are small non-coding RNAs that negatively regulate gene expression post-transcriptionally. Emerging evidence demonstrated that miRNAs play critical roles in diverse biological processes including skeletal muscle development. Polymorphism in precursor miRNAs can affect the binding to their targets and the processing into mature miRNAs. In addition, polymorphisms including SNPs in the 3’ UTR of targeted mRNA can affect the recognition between a miRNA and its binding sites because the majority of miRNA binding sites lie within the 3’ UTR of the targeted mRNA. Therefore, these polymorphisms can potentially contribute to phenotypic differences in livestock. In the first part, total 14 single nucleotide polymorphisms (SNPs) in the genomic region of the porcine miR-1 locus and miR-206/133b cluster were identified. 12 (miR-206: 10 SNPs and miR-133b: 2 SNPs) and 2 of which were associated with miR-206/133b cluster and miR-1, respectively. Allele frequency determination in different pig breeds (Berkshire, n = 153; Landrace, n = 125; Yorkshire, n = 173) and association study with muscle fiber characteristics and lean meat production and meat quality traits were performed on the selected miR-1, miR-206 and miR-133b SNPs. The miR-206 SNP was positively associated with the percentage of type IIa and IIb fibers for muscle fiber area composition and meat quality traits including drip loss and lightness, but negatively with backfat thickness. In addition, miR-133b SNP was significantly associated with total muscle fiber number, loin eye area and muscle pH. Moreover, miR-1 SNPs were significantly associated with muscle pH, drip loss, and muscle fiber composition traits. Furthermore, these SNPs significantly affected the levels of mature miR-206, miR-133b, and miR-1, respectively. These data suggest that polymorphisms in the porcine miR-1 and miR-206/133b are a genetic factor affecting muscle and meat quality traits. In the second part, two single nucleotide polymorphisms (SNPs; *2690T>C and *2864T>C) and one insertion/deletion in the 3’untranslated region of porcine PPARGC1A which is involved in a variety of biological processes including muscle fiber type composition were identified. These SNPs were genotyped by direct sequencing in a total of 439 pigs representing three different pig breeds (Berkshire, n = 156; Yorkshire, n = 163; Landrace, n = 120). It was evaluated that diplotypes of individual PPARGC1A 3’untranslated region (3’UTR) SNPs have effects on muscle fiber characteristics and meat quality traits. These SNPs were significantly associated with muscle fiber number, area composition, muscle PH, drip loss, and lightness. Interestingly, each SNP affected PPARGC1A expression significantly at the protein level but not at the mRNA level, thereby accounting for phenotypic variability among genotypes. These results suggest that polymorphisms on PPARGC1A 3’untranslated region (3’UTR) can be used as genetic markers for selection toward improved meat quality. Taken together, these results indicate that polymorphisms in precursor miRNAs and the 3’UTR of the targeted mRNA can affect muscle development and meat quality.
more목차
CONTENTS
SUMMARY І
CONTENTS IV
LIST OF TABLES Ⅶ
LST OF FIGURES Ⅷ
1 CHAPTER Polymorphisms in the porcine miR-1 locus and miR-206/133b cluster are associated with muscle fiber and meat quality traits
1.1 Abstract 2
1.2 Introduction 4
1.3 Materials and methods 7
Animals and trait measurements 7
Polymorphism idenrification 8
DNA extraction and Single-nucleotide polymorphisms(SNP) genotyping 11
Association analysis of the miR-1 and miR-206/133b cluster SNPs with muscle fiver characteristics meat quality traits 15
miR-Q: Quantitative RT-PCR analysis 15
1.4 Results 18
Identification and genotyping of polymorphisms in the miR-1 locus and miR-206/133b cluster 18
miR-1 locus and miR-206/133b cluster SNPs are associated with muscle fiber characteristics and meat quality traits 25
SNPs in the miR-1 locus and miR-206/133b cluster alter miRNAs expression level 33
1.5 Discussion 39
1.6 References 40
2.CHAPTER Effects of polymorphisms in the 3’ untranslated region of the porcine PPARGC1A gene on muscle fiber characteristics and meat quality traits
2.1 Abstract 44
2.2 Introduction 46
2.3 Materials and methods 49
Animals and trait measurements 49
Polymorphism identification 50
Single-nucleotide polymorphisms (SNP) genotyping 51
Association analysis of the PPARGC1A 3’UTR SNPs with muscle fiber characteristics and meat quality traits 54
Quantitative RT-PCR analysis 54
Western blot analysis 55
2.4 Results 57
Identification and genotyping of polymorphisms in the 3’UTR Of PPARGC1A 57
PPARGC1A 3’UTR SNPs are associated with muscle fiber Characteristics and meat quality traits 63
PPARGC1A 3’UTR SNPs alter protein expression level 66
2.5 Discussion 75
2.6 References 78
ABSTRACT IN KOREAN 81
APPENDICES 84
