• Asian-Australasian Journal of Animal Sciences
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• 제26권12호
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• pp.1665-1671
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• 2013

Real-time quantitative PCR (qRT-PCR) is one of the important methods for investigating the changes in mRNA expression levels in cells and tissues. Selection of the proper reference genes is very important when calibrating the results of real-time quantitative PCR. Studies on the selection of reference genes in goat tissues are limited, despite the economic importance of their meat and dairy products. We used real-time quantitative PCR to detect the expression levels of eight reference gene candidates (18S, TBP, HMBS, YWHAZ, ACTB, HPRT1, GAPDH and EEF1A2) in ten tissues types sourced from Boer goats. The optimal reference gene combination was selected according to the results determined by geNorm, NormFinder and Bestkeeper software packages. The analyses showed that tissue is an important variability factor in genes expression stability. When all tissues were considered, 18S, TBP and HMBS is the optimal reference combination for calibrating quantitative PCR analysis of gene expression from goat tissues. Dividing data set by tissues, ACTB was the most stable in stomach, small intestine and ovary, 18S in heart and spleen, HMBS in uterus and lung, TBP in liver, HPRT1 in kidney and GAPDH in muscle. Overall, this study provided valuable information about the goat reference genes that can be used in order to perform a proper normalisation when relative quantification by qRT-PCR studies is undertaken.

• Molecules and Cells
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• 제27권3호
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• pp.329-336
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• 2009

To evaluate the involvement of translation initiation factors eIF4E and eIFiso4E in Chilli veinal mottle virus (ChiVMV) infection in pepper, we conducted a genetic analysis using a segregating population derived from a cross between Capsicum annuum 'Dempsey' containing an elF4E mutation ($pvr1^2$) and C. annuum 'Perennial' containing an elFiso4E mutation (pvr6). C. annuum 'Dempsey' was susceptible and C. annuum 'Perennial' was resistant to ChiVMV. All $F_1$ plants showed resistance, and $F_2$ individuals segregated in a resistant-susceptible ratio of 166:21, indicating that many resistance loci were involved. Seventy-five $F_2$ and 329 $F_3$ plants of 17 families were genotyped with $pvr1^2$ and pvr6 allele-specific markers, and the genotype data were compared with observed resistance to viral infection. All plants containing homozygous genotypes of both $pvr1^2$ and pvr6 were resistant to ChiVMV, demonstrating that simultaneous mutations in elF4E and eIFiso4E confer resistance to ChiVMV in pepper. Genotype analysis of $F_2$ plants revealed that all plants containing homozygous genotypes of both $pvr1^2$ and pvr6 showed resistance to ChiVMV. In protein-protein interaction experiments, ChiVMV viral genome-linked protein (VPg) interacted with both eIF4E and eIFiso4E. Silencing of elF4E and eIFiso4E in the VIGS experiment showed reduction in ChiVMV accumulation. These results demonstrated that ChiVMV can use both eIF4E and eIFiso4E for replication, making simultaneous mutations in eIF4E and eIFiso4E necessary to prevent ChiVMV infection in pepper.

• Journal of Ginseng Research
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• 제41권1호
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• pp.60-68
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• 2017

Background: Various Panax ginseng cultivars exhibit a range of diversity for morphological and physiological traits. However, there are few studies on diversity of metabolic profiles and genetic background to understand the complex metabolic pathway in ginseng. Methods: To understand the complex metabolic pathway and related genes in ginseng, we tried to conduct integrated analysis of primary metabolite profiles and related gene expression using five ginseng cultivars showing different morphology. We investigated primary metabolite profiles via gas chromatography-mass spectrometry (GC-MS) and analyzed transcriptomes by Illumina sequencing using adventitious roots grown under the same conditions to elucidate the differences in metabolism underlying such genetic diversity. Results: GC-MS analysis revealed that primary metabolite profiling allowed us to classify the five cultivars into three independent groups and the grouping was also explained by eight major primary metabolites as biomarkers. We selected three cultivars (Chunpoong, Cheongsun, and Sunhyang) to represent each group and analyzed their transcriptomes. We inspected 100 unigenes involved in seven primary metabolite biosynthesis pathways and found that 21 unigenes encoding 15 enzymes were differentially expressed among the three cultivars. Integrated analysis of transcriptomes and metabolomes revealed that the ginseng cultivars differ in primary metabolites as well as in the putative genes involved in the complex process of primary metabolic pathways. Conclusion: Our data derived from this integrated analysis provide insights into the underlying complexity of genes and metabolites that co-regulate flux through these pathways in ginseng.

• Animal Bioscience
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• 제37권6호
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• pp.965-981
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• 2024

Objective: Milk composition varies considerably and depends on paratypical, genetic, and epigenetic factors. MiRNAs belong to the class of small non-coding RNAs; they are one of the key tools of epigenetic control because of their ability to regulate gene expression at the post-transcriptional level. We compared the relative expression levels of miR-106b, miR-191, and miR-30d in milk to demonstrate the relationship between the content of these miRNAs with protein and fat components of milk in Holstein and Ayrshire cattle. Methods: Milk fat, protein, and casein contents were determined in the obtained samples, as well as the content of the main fatty acids (g/100 g milk), including: saturated acids, such as myristic (C14:0), palmitic (C16:0), and stearic (C18:0) acids; monounsaturated acids, including oleic (C18:1) acid; as well as long-, medium- and short-chain, polyunsaturated, and trans fatty acids. Real-time stem-loop one-tube reverse transcription polymerase chain reaction with TaqMan probes was used to measure the miRNA expression levels. Results: The miRNA expression levels in milk samples were found to be decreased in the first two months in Holstein breed, and in the first four months in Ayrshire breed. Correlation analysis did not reveal any dependence between changes in the expression level of miRNA and milk fat content, but showed a multidirectional relationship with individual milk fatty acids. Positive associations between the expression levels of miR-106b and miR-30d and protein and casein content were found in the Ayrshire breed. Receiver operating characteristic curve analysis showed that miR-106b and miR-30d expression levels can cause changes in fatty acid and protein composition of milk in Ayrshire cows, whereas miR-106b expression level determines the fatty acid composition in Holsteins. Conclusion: The data obtained in this study showed that miR-106b, miR-191, and miR-30d expression levels in milk samples have peculiarities associated with breed affiliation and the lactation period.

• 한국환경생태학회지
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• 제29권3호
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• pp.333-343
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• 2015

본 연구는 국내에서 아직 미흡한 조류 번식지 예측 모형을 이용해 참매의 서식지 예측 및 대체번식지로서 이용 가능한 지역을 선정하고, 향후 참매 번식 가능지역을 대상으로 보호관리 지역을 확대할 수 있는 근거를 제시하기 위한 방안이다. 참매의 번식지는 현장조사에서 확인된 둥지(N=10)를 이용하였으며, 출현지점은 제3차자연환경조사를 통해 확인된 참매출현지점(N=23)을 활용해 분석하였다. 모형변수로는 지형인자 4가지, 자연환경인자(식생) 3가지, 거리인자 7가지, 기후변수 9가지를 활용하였다. 활용변수 중 Random sampling을 통해 확보된 비출현 좌표와 출현좌표간 비모수 검증을 통해 최종 환경변수를 선정하였다. 유의성 검증을 통해 선택된 변수는 번식지 대상 10가지, 출현지점 대상 7가지였으며, 이 변수를 활용해 최종 서식지 예측 모형(MaxEnt)을 구축하였다. 모델 구축결과 번식에 활용된 각 변수별 모형 기여도는 온도의 계절적 변동, 혼효림 과의 거리, 입목밀도, 경급의 순이었으며, 출현지점에 활용된 각 변수별 모형 기여도는 온도의 계절적 변동, 수계와의 거리, 경작지와의 거리, 경사도의 순이었다. 번식지점을 대상으로 한 모델링은 기후환경과 숲 내부에서 번식하는 참매의 특성이 반영된 것으로 판단된다. 예상서식지는 충청북도 중부 이북지역으로 예상되었으며, 그 면적은 $189.5km^2$(2.55%)였다. 충북 이남지역은 청주와 충주 등의 비교적 큰 도시가 발달되어 있는 반면 충청북도 북부지역의 경우 산림과 경작지가 고루 발달되어 있어 번식에 있어 일정한 세력권과 먹이원이 필요한 참매로서는 번식에 유리한 지역일 것으로 판단된다. 출현지점 대상으로 한 모델링은 면적이 $3,071km^2$(41.38%)으로 확인되었으며, 이는 출현지점을 대상으로 하여 단순이동 관찰 및 계절적인 변동 미고려 등의 한계가 있기 때문에 번식지점을 대상으로 한 모델링보다 광범위한 서식예상지역을 예측하였다. 결과에서 확인된 예측지점은 번식지를 대상으로 하였을 경우 정밀한 서식예측이 가능하나, 둥지의 특성상 확인되는 지점이 적고, 참매의 행동영역을 반영하지 못하는 단점이 있다. 반면 출현지점을 대상으로 하였을 경우 더 광범위한 지점에 대한 결과 도출이 가능하였으나, 단순 이동이나 지속적인 이용실태를 반영하지 못하기 때문에 정밀도에서는 다소 떨어진다고 할 수 있다. 다만 이러한 결과들을 통해 참매의 서식지를 예측할 수 있으며, 특히 정밀한 번식지역의 예측자료는 환경영향평가나 개발계획 수립시 서식지 모형 결과를 도입하여 반영할 필요성이 있다.

• 한국식물생명공학회:학술대회논문집
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• 한국식물생명공학회 2002년도 추계학술대회
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• pp.19-25
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• 2002

Biotechnology in the 21st century will be driven by three emerging technologies: genomics, high-throughput biology, and bioinformatics. These technologies are complementary to one another. A large number of economically important crops are currently subjected to whole genome sequencing. Functional genomics for determining the functions of the genes comprising the given plant genome is under progress by using various means including phenotyping data from transgenic mutants, gene expression profiling data from DNA microarrays, and metabolic profiling data from LC/mass analysis. The aim of plant molecular breeding is shifting from introducing agronomic traits such as herbicide and insect resistance to introducing quality traits such as healthful oils and proteins, which will lead to improved and nutritional food and feed products. Plant molecular breeding is also expected to aim to develop crops for producing human therapeutic and industrial proteins.

• 농업과학연구
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• 제42권3호
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• pp.215-222
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• 2015

This paper sketches the strategies and designs for monitoring system of swine genetic improvement. The system should reflect every side of pig production. The system leads us to assess the efficiency of pig production and the scope of the system includes not only nucleus, multiplying and commercial herds, but also packing and processing sectors. For more accurate statistics, data for this monitoring system must be collected from all above mentioned areas, but not by random sampling. Futhermore, data analysis results including seedstocks and distribution information of genetic trend should be included in the system. The schema of knowledge database system could be employed in the system. The monitoring system in the final destination would unify the systems derived from various sources and provide any solution in swine industry including pig breeding.

• 한국식물생명공학회:학술대회논문집
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• 한국식물생명공학회 2002년도 춘계학술대회
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• pp.19-25
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• 2002

Biotechnology in the 21st century will be driven by three emerging technologies: genomics, high-throughput biology, and bioinformatics. These technologies are complementary to one another. A large number of economically important crops are currently subjected to whole genome sequencing. Functional genomics for determining the functions of the genes comprising the given plant genome is under progress by using various means including phenotyping data from transgenic mutants, gene expression profiling data from DNA microarrays, and metabolic profiling data from LC/mass analysis. The aim of plant molecular breeding is shifting from introducing agronomic traits such as herbicide and insect resistance to introducing quality traits such as healthful oils and proteins, which will lead to improved and nutritional food and feed products. Plant molecular breeding is also expected to aim to develop crops for producing human therapeutic and industrial proteins.

• Asian-Australasian Journal of Animal Sciences
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• 제27권12호
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• pp.1678-1683
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• 2014

This study considers a problem of genomic selection (GS) for adjacent genetic markers of Yorkshire pigs which are typically correlated. The GS has been widely used to efficiently estimate target variables such as molecular breeding values using markers across the entire genome. Recently, GS has been applied to animals as well as plants, especially to pigs. For efficient selection of variables with specific traits in pig breeding, it is required that any such variable selection retains some properties: i) it produces a simple model by identifying insignificant variables; ii) it improves the accuracy of the prediction of future data; and iii) it is feasible to handle high-dimensional data in which the number of variables is larger than the number of observations. In this paper, we applied several variable selection methods including least absolute shrinkage and selection operator (LASSO), fused LASSO and elastic net to data with 47K single nucleotide polymorphisms and litter size for 519 observed sows. Based on experiments, we observed that the fused LASSO outperforms other approaches.

• Journal of Plant Biotechnology
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• 제29권3호
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• pp.145-150
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• 2002

Biotechnology in the 21st century will be driven by three emerging technologies: genomics, high-throughput biology, and bioinformatics. These technologies are complementary to one another. A large number of economically important crops are currently subjected to whole genome sequencing. Functional genomics for determining the functions of the genes comprising the given plant genome is under progress by using various means including phenotyping data from transgenic mutants, gene expression profiling data from DNA microarrays, and metabolic profiling data from LC/mass analysis. The aim of plant molecular breeding is shifting from introducing agronomic traits such as herbicide and insect resistance to introducing quality traits such as healthful oils and proteins, which will lead to improved and nutritional food and feed products. Plant molecular breeding is also expected to aim to develop crops for producing human therapeutic and industrial proteins.