보고서 정보
주관연구기관 |
상지대학교 SangJi University |
보고서유형 | 최종보고서 |
발행국가 | 대한민국 |
언어 |
한국어
|
발행년월 | 2014-02 |
과제시작연도 |
2011 |
주관부처 |
농촌진흥청 Rural Development Administration(RDA) |
등록번호 |
TRKO201400011060 |
과제고유번호 |
1395021913 |
사업명 |
차세대바이오그린21 |
DB 구축일자 |
2014-07-05
|
DOI |
https://doi.org/10.23000/TRKO201400011060 |
초록
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Ⅳ. 주요 연구개발결과
○ NGS whole exome sequencing 분석을 통해 검출된 각 한우 개체별 SNPs 가운데 high 및 low marbling 그룹 간 총 840개의 SNPs를 검출하였음. Coding exons 영역 내에 존재하는 SNPs는 총 258개가 검출되었으며, 특히 이 가운데 non-synonymous SNPs는 117개, synonymous SNPs는 136개가 검출하였음.
○ 최종적으로 선발한 농가현장 검증용 한우 육질표현형 연관 후보 SNPs는 총 24개로서 엑손 영역에 존재하는 non
Ⅳ. 주요 연구개발결과
○ NGS whole exome sequencing 분석을 통해 검출된 각 한우 개체별 SNPs 가운데 high 및 low marbling 그룹 간 총 840개의 SNPs를 검출하였음. Coding exons 영역 내에 존재하는 SNPs는 총 258개가 검출되었으며, 특히 이 가운데 non-synonymous SNPs는 117개, synonymous SNPs는 136개가 검출하였음.
○ 최종적으로 선발한 농가현장 검증용 한우 육질표현형 연관 후보 SNPs는 총 24개로서 엑손 영역에 존재하는 nonsynonymous SNPs 가운데 marbling QTL에 포함된 SNPs는 11개, high 및 low marbling 그룹 간 specific SNPs는 총 6개, 그리고 선발신호 영역에 포함되어 있는 SNPs 총 7개를 선발하였음.
○ 한우와 홀스타인의 서열변이유전자위들의 MAF 추정치를 이용한 CLL 방법을 도입하여 유전체에서 213개의 선발신호를 발견하고, 이에 해당하는 유전자위를 독립된 한우 집단에서 육질관련 형질과 연관성 연구를 통하여 4개의 유의한 유전자위(SCAFFOLD65605_11456, SCAFFOLD145184_7453, BTA-136127, rs29013464)를 규명하였음 (P<1.0×10-3).
○ 한우와 앵거스의 서열변이유전자위들의 MAF 추정치를 이용한 CLL 방법을 도입하여 유전체에서 147개의 선발신호를 발견하고, 이에 해당하는 유전자위를 독립된 한우 집단에서 육질관련 형질과 연관성 연구를 통하여 4개의 유의한 유전자위 (FAM19A1, CTNNA3, MPP5, ADAM12)를 규명하였음 (P<1.0×10-3).
○ 개체 혈통정보 및 도체성적 기록이 확보된 참품한우 브랜드 집단을 대상으로 8개의 ms marker를 활용한 친자확인을 통해 25두 종모우에서 태어난 1,039두 농가검증 집단 구성
○ 총 615두의 농가현장 검증 집단을 대상으로 총 27개 후보 SNPs에 대한 SNP genotyping을 수행하고, 한우 육질형질과의 연관성을 분석한 결과 PLCB1 c.459 T>C, C/EBPα c.271A>C, TDRKH g.17257A>G, ADAM15 g.3060 G>A 및 3229 C>T등 총 5개 SNPs와 한우 육질형질과의 연관성이 입증되었음.
○ 특히 c.459 T>C와 g.3060 G>A의 TTGG, CTGA, TTGA, CCAA, TTAA유전자형을 이용할 경우 선발의 정확도가 매우 높아지는 것으로 분석되었음.
Abstract
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Hanwoo is a cattle breed native to Korea, and is known not only for its economic importance but also for its ties to country's agricultural heritage. Hanwoo are known to have an inferior ability to produce meat because of a low milk producing capacity and slow growth rate, while having a relatively
Hanwoo is a cattle breed native to Korea, and is known not only for its economic importance but also for its ties to country's agricultural heritage. Hanwoo are known to have an inferior ability to produce meat because of a low milk producing capacity and slow growth rate, while having a relatively favorable meat quality [1]. Thus, meat quality is of great importance to the beef industry where the consumer is willing to pay more for superior products [2, 3, 4]. Thus, selection of genetic markers had been carried out in order to evidence of meat quality by methods such as SNP array. Among those methods, high throughput exome (coding sequences) sequencing has become effective application in order to detection of various genetic mutations within protein coding sequences of animal population [5]. Recently, exome capture technical methods had been developed for exome capture of variety target organisms comprising a mere 2% of eukaryotic genome. Those exome captures has been tested in most model species [5, 6]. With few fully sequenced eukaryotic genome sequences available (40 complete genome, 425 draft whole genome sequences are found at NCBI database), it would appear to be useful only fully sequenced eukaryotic species. To date, cattle genome sequencing (Btau 3.1, and Btau 4.0) are performed with whole genome shotgun sequencing method similar to the sea urchin genome sequencing. At least 22,000 protein coding genes are estimated by cattle genome [7]. In the previous study, exome-wide capture has been successfully performed using probes for 16,131 exons among the 2,570 genes including 203 functional known genes in three individuals (B.taurus, B.indicus, and wild bison) [8]. However, until recent, whole exome sequencing was not perform in Hanwoo. Therefore, we are performed whole exome sequencing of ‘Korean beef cows, Hanwoo (Bostauruscoreanae)’using 64Mb designed probes (AgilentSureSelectXTBovineAllExon®)based on Bos taurus (Btau 3.1) sequences. In this study, firstly, we are analyzed genetic diversity of meat quality in Korean cattles using advanced bovine whole exome sequencing.
Meat quality has been improved in Korean cattle, and this could correspondingly increase the allelic frequencies at site of the strong directional selection and cause genetic differences from other breeds. Alleles under positive selection pressures encounter a fast increase in allele frequency. The current study aimed to detect directional selection employing composite log likelihood (CLL) of the differences in allelic frequencies between the Korean cattle and the foreign breeds with genome-wide single nucleotide polymorphism (SNP) data. Analysis was conducted with the data on 11,799 SNPs in the populations of Korean cattle, 5 foreign dairy cattle breeds, and 8 foreign beef cattle breeds. The allele frequencies obtained from this study showed that genetic diversity of Korean cattle was not smaller than those of foreign beef breeds. Selection signature analysis revealed 213 selection signals between Korean cattle and dairy cattle breeds (P < 0.01). Further genetic association analysis with genetic variants located within the selection signatures revealed that 4 sequence variants (SCAFFOLD65605_11456, SCAFFOLD145184_7453, BTA-136127, rs29013464) were associated with meat quality (P < 1.0×10-3). One hundred and forty seven selection signatures were identified from comparing Korean cattle to the 8 foreign beef cattle breeds and their genetic association analysis with meat quality found 4 sequence variants (FAM19A1, CTNNA3, MPP5, ADAM12, P<1.0×10-3). The signals would be considered in application to marker assisted selection to improve meat qualtiy of Korean cattle.
Fat quality is determined by the composition of fatty acids. Genetic relationships between this composition and single nucleotide polymorphisms (SNPs) in the phospholipase A1 member A (PLA1A), phosphoinositide 3-kinase Regulatory 4 (PIK3R4), phospholipase C beta 1 (PLCB1) and CCAAT/enhancer binding protein alpha (C/EBPα) gene were examined using 612 Korean native cattle. Single and epistatic effects of 7 SNP genetic variations were investigated, and the multifactor dimensionality reduction (MDR) method was used to investigate gene interactions in terms of oleic acid (C18:1), mono-unsaturated fatty acids (MUFAs) and marbling score (MS). The g.6850+77 A>G and g.14047 C>T SNP interactions were identified as the statistically optimal combination (C18:1, MUFAs and MS permutation p-values were 0.000, 0.000 and 0.001 respectively) of two-way gene interactions. The interaction effects of g.6850+77 A>G, g.10213 T>C and g.14047 C>T reflected the highest training-balanced accuracy (63.76%, 64.70% and 61.85% respectively) and was better than the individual effects for C18:1, MUFAs and MS. In addition, the superior genotype groups were AATTCC, AGTTCC, GGTCCC, AGTCCT, GGCCCT and AGCCTT. These results suggest that the selected SNP combination of the phospholipase A1 member A (PLA1A), phosphoinositide 3-kinase Regulatory 4 (PIK3R4), phospholipase C beta 1 (PLCB1) and CCAAT/enhancer binding protein alpha (C/EBPα) gene and superior genotype groups can provide useful inferences for the improvement of the fatty acid composition in Korean native cattle.
목차 Contents
- 표지 ... 1
- 제출문 ... 2
- 요약문 ... 3
- SUMMARY ... 10
- 목차 ... 12
- 제 1 장 서 론 ... 13
- 제 1절 연구개발의 필요성 ... 13
- 제 2절 연구개발 목표 ... 17
- 제 2 장 국내외 기술개발 현황 ... 18
- 제 1절 국내 기술개발 현황 ... 18
- 제 2절 국외 기술개발 현황 ... 19
- 제 3 장 연구개발수행 내용 및 결과 ... 22
- 제 1절 주요 연구개발수행 내용 ... 22
- 제 2절 연구개발 추진체계 ... 24
- 제 3절 세부 및 협동과제별 연구개발수행 내용 및 결과 ... 25
- 제 4 장 연구개발목표 달성도 및 대외기여도 ... 123
- 제 1절 목표대비 대외달성도 ... 123
- 제 2절 정량적 성과 ... 125
- 제 5 장 연구개발결과의 활용계획 ... 126
- 제 1절 추가 연구의 필요성 ... 126
- 제 2절 현재 추진중인 추가적인 논문게재 ... 127
- 제 3절 산업재산권 출원 및 등록 현황 ... 127
- 제 6 장 연구개발과정에서 수집한 해외과학기술정보 ... 131
- 제 7 장 기타 중요 변동사항 ... 132
- 제 8 장 국가과학기술종합정보시스템에 등록한 연구장비 현황 ... 133
- 제 9 장 참고문헌 ... 134
- 별첨 자료 ... 140
- 끝페이지 ... 212
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