• Animal Bioscience
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• 제37권4호
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• pp.576-590
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• 2024

Objective: The objective of this study was to identify genes associated with 305-day milk yield (MY) and fat yield (FY) that also influence the adaptability of the Thai multibreed dairy cattle population to tropical conditions. Methods: A total of 75,776 imputed and actual single nucleotide polymorphisms (SNPs) from 2,661 animals were used to identify genomic regions associated with MY and FY using the single-step genomic best linear unbiased predictions. Fixed effects included herd-year-season, breed regression, heterosis regression and calving age regression effects. Random effects were animal additive genetic and residual. Individual SNPs with a p-value smaller than 0.05 were selected for gene mapping, function analysis, and quantitative trait loci (QTL) annotation analysis. Results: A substantial number of QTLs associated with MY (9,334) and FY (8,977) were identified by integrating SNP genotypes and QTL annotations. Notably, we discovered 17 annotated QTLs within the health and exterior QTL classes, corresponding to nine unique genes. Among these genes, Rho GTPase activating protein 15 (ARHGAP15) and catenin alpha 2 (CTNNA2) have previously been linked to physiological traits associated with tropical adaptation in various cattle breeds. Interestingly, these two genes also showed signs of positive selection, indicating their potential role in conferring tolerance to trypanosomiasis, a prevalent tropical disease. Conclusion: Our findings provide valuable insights into the genetic basis of MY and FY in the Thai multibreed dairy cattle population, shedding light on the underlying mechanisms of tropical adaptation. The identified genes represent promising targets for future breeding strategies aimed at improving milk and fat production while ensuring resilience to tropical challenges. This study significantly contributes to our understanding of the genetic factors influencing milk production and adaptability in dairy cattle, facilitating the development of sustainable genetic selection strategies and breeding programs in tropical environments.

• Molecules and Cells
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• 제38권5호
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• pp.466-473
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• 2015

Over the last 30 years, Hanwoo has been selectively bred to improve economically important traits. Hanwoo is currently the representative Korean native beef cattle breed, and it is believed that it shared an ancestor with a Chinese breed, Yanbian cattle, until the last century. However, these two breeds have experienced different selection pressures during recent decades. Here, we whole-genome sequenced 10 animals each of Hanwoo and Yanbian cattle (20 total) using the Illumina HiSeq 2000 sequencer. A total of approximately 3.12 and 3.07 billion sequence reads were mapped to the bovine reference sequence assembly (UMD 3.1) at an average of approximately 10.71- and 10.53-fold coverage for Hanwoo and Yanbian cattle, respectively. A total of 17,936,399 single nucleotide polymorphisms (SNPs) were yielded, of which 22.3% were found to be novel. By annotating the SNPs, we further retrieved numerous nonsynonymous SNPs that may be associated with traits of interest in cattle. Furthermore, we performed whole-genome screening to detect signatures of selection throughout the genome. We located several promising selective sweeps that are potentially responsible for economically important traits in cattle; the PPP1R12A gene is an example of a gene that potentially affects intramuscular fat content. These discoveries provide valuable genomic information regarding potential genomic markers that could predict traits of interest for breeding programs of these cattle breeds.

• 한국육종학회지
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• 제49권3호
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• pp.170-179
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• 2017

분자농업은 식물을 일종의 공장개념으로 확대 적용하여 산업적으로 가치가 높은 유용물질들을 대량생산하는 분야로 최근 많은 각광을 받고 있다. 그 중에서 벼 캘러스를 이용한 단백질 발현 시스템은 대량 배양이 가능하고 목적 단백질의 높은 발현율로 인한 산업화가 가능한 기술이다. 본 연구는 이러한 벼(Oryza sativa L.) 캘러스의 활용도를 높이기 위한 효율적인 형질전환 시스템을 구축하기 위해 수행되었다. 형질전환에 이용된 종자의 종피 제거 시 손을 이용함으로써 캘러스 유도율을 높여주었고, 6년 정도의 오래된 종자에서도 원활한 캘러스 유도가 가능하였다. 목적 유전자가 도입된 캘러스의 선발은 최소한 3주 이상의 배양기간을 필요로 하였고 가장 효율적인 것은 한번의 계대를 포함한 6주 배양 후 선발하는 것이었다. 이러한 선발은 유전자가 식물세포의 genomic DNA 안에 안정적으로 삽입되어 이루어졌음을 서던 블롯 분석 및 후대검정 등을 통하여 확인할 수 있었다. 이러한 장기적이고 대량의 배양이 가능한 벼 캘러스의 효율적인 선발 시스템은 벼를 이용한 유용 재조합 단백질의 산업화에 실속있는 기술로 기여할 수 있을 것이다.

• Journal of Genetic Medicine
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• 제16권2호
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• pp.76-80
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• 2019

About 15% to 20% of all clinically recognized pregnancies result in spontaneous abortion or miscarriage, and chromosomal anomalies can be identified in up to 50% of first trimester miscarriages. Chromosomal microarray analysis (CMA) is currently considered first-tier testing for detecting fetal chromosomal abnormalities and is supported by the absence of cell culture failure or erroneous results due to cell contamination in pregnancy loss. Triploidy is a lethal chromosome number abnormality characterized by an extra haploid set of chromosomes. Triploidy is one of the most common chromosomal aberrations in first trimester spontaneous abortions. Here, we report two cases of triploidy abortion that were not detected using array comparative genomic hybridization-based CMA. The aim of this report was to remind clinicians of the limitations of chromosomal testing and the misdiagnosis that can result from biased test selection.

• Asian-Australasian Journal of Animal Sciences
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• 제23권7호
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• pp.833-847
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• 2010

In the past decade, there have been many advances in whole-genome sequencing in domestic animals, as well as the development of "next-generation" sequencing technologies and high-throughput genotyping platforms. Consequently, these advances have led to the creation of the high-density SNP array as a state-of-the-art tool for genetics and genomics analyses of domestic animals. The emergence and utilization of SNP arrays will have significant impacts not only on the scale, speed, and expense of SNP genotyping, but also on theoretical and applied studies of quantitative genetics, population genetics and molecular evolution. The most promising applications in agriculture could be genome-wide association studies (GWAS) and genomic selection for the improvement of economically important traits. However, some challenges still face these applications, such as incorporating linkage disequilibrium (LD) information from HapMap projects, data storage, and especially appropriate statistical analyses on the high-dimensional, structured genomics data. More efforts are still needed to make better use of the high-density SNP arrays in both academic studies and industrial applications.

• Fisheries and Aquatic Sciences
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• 제16권4호
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• pp.303-309
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• 2013

Microsatellite markers are important for gene mapping and for marker-assisted selection. Sixty-five polymorphic microsatellite markers were developed with an enriched partial genomic library from olive flounder Paralichthys olivaceus an important commercial fish species in Korea. The variability of these markers was tested in 30 individuals collected from the East Sea (Korea). The number of alleles for each locus ranged from 2 to 33 (mean, 17.1). Observed and expected heterozygosity as well as polymorphism information content varied from 0.313 to 1.000 (mean, 0.788), from 0.323 to 0.977 (mean, 0.820), and from 0.277 to 0.960 (mean, 0.787), respectively. Nine loci showed significant deviation from the Hardy-Weinberg equilibrium after sequential Bonferroni correction. Analysis with MICROCHECKER suggested the presence of null alleles at five of these loci with estimated null allele frequencies of 0.126-0.285. These new microsatellite markers from genomic libraries will be useful for constructing a P. olivaceus linkage map.

• Asian-Australasian Journal of Animal Sciences
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• 제17권10호
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• pp.1329-1333
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• 2004

To isolate the microsatellites from the chromosomal DNA of the Korean cattle (Hanwoo) and to use those for the genetic selection, four bacteriophage genomic libraries containing the chromosomal DNA of six Hanwoo steers showing the differences in meat quality and quantity were used. Screening of the genomic libraries using $^{32}P-radiolabeled 5'-({CA})_{12}-3$nucleotide as a probe, resulted in isolation of about 3,000 positive candidate bacteriophage clones that contain $(CA)_n$-type dinucleotide microsatellites. After confirming the presence of microsatellite in each positive candidate clone by Southern blot analysis, the DNA fragments that include microsatellite and flanking sequences possessing less than 2 kb in size, were subcloned into plasmid vector. Results from the analysis of microsatellite length polymorphism, using twenty-two PCR primers designed from flanking region of each microsatellite DNA, demonstrated that 208 and 210 alleles of HW-YU-MS#3 were closely related to the economic traits such as marbling score, daily gain, backfat thickness and M. longissimus dorsi area in Hanwoo. Interestingly, HW-YU-MS#3 microsatellite was localized in bovine chromosome 17 on which QTLs related to regulation of the body fat content and muscle ypertrophy locus are previously known to exist. Taken together, the results from the present study suggest the possible use of the two alleles as a DNA marker related to economic trait to select the Hanwoo in the future.

• Mycobiology
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• 제45권2호
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• pp.105-109
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• 2017

Sixteen genomic DNA simple sequence repeat (SSR) markers of Lentinula edodes were developed from 205 SSR motifs present in 46.1-Mb long L. edodes genome sequences. The number of alleles ranged from 3-14 and the major allele frequency was distributed from 0.17-0.96. The values of observed and expected heterozygosity ranged from 0.00-0.76 and 0.07-0.90, respectively. The polymorphic information content value ranged from 0.07-0.89. A dendrogram, based on 16 SSR markers clustered by the paired hierarchical clustering' method, showed that 33 shiitake cultivars could be divided into three major groups and successfully identified. These SSR markers will contribute to the efficient breeding of this species by providing diversity in shiitake varieties. Furthermore, the genomic information covered by the markers can provide a valuable resource for genetic linkage map construction, molecular mapping, and marker-assisted selection in the shiitake mushroom.

• 식물조직배양학회지
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• 제27권6호
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• pp.435-439
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• 2000

겨울 상추 품종인 청치마 상추의 자엽조직을 ${\gamma}$-TMT유전자가 도입된 A. tumefaciens LBA 4404와 공동배양한 후, 50 mg/L kanamycin, 500 mg/L carbenicillin, 0.1 mg/L NAA, 0.5mg/L BA가 첨가된 MS재분화 배지에 옮겨 약4주 배양하여 재분화된 신초를 얻었다. 재분화된 신초를 50 mg/L kanamycin, 250mg/L carbenicillin이 포함된 MS 기본 배지에 옮겨 발근된 소식물체를 얻었다. 선발된 형질전환 식물체의 genomic DNA에 대한 PCR분석과 Southern분석을 수행하여 애기장대 ${\gamma}$-TMT유전자 특이적 DNA단편이 상추의 genomic DNA내에 삽입되었음을 확인하였다. 선발된 상추 형질전환체 잎의 $\alpha$-tocopherol/${\gamma}$-tocopherol 함량 비율이 대조 식물체에 비하여 약 4배 증가하여 도입된 ${\gamma}$-TMT유전자가 안정적으로 발현함을 나타내었다.

• Journal of Microbiology
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• 제41권1호
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• pp.46-51
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• 2003

RAD6 in yeast mediates postreplication DNA repair and is responsible for DNA-damage induced mutations. RAD6 encodes ubiquitin-conjugating enzyme that is well conserved among eukaryotic organisms. However, the molecular targets and consequences of their ubiquitination by Rad6 have remained elusive. In Aspergillus nidulans, a RAD6 homolog has been isolated and shown to be an allele of uvs). We screened a CDNA library to isolate UVSJ-interacting proteins by the yeast two-hybrid system. JIPA was identified as an interactor of UVSJ. Their interaction was confirmed in vitro by a GST-pull down assay. JIPA was also able to interact with mutant UVSJ proteins, UVSJl and the active site cysteine mutant UVSJ-C88A. The N- and the C-terminal regions of UVSJ required for the interaction with UVSH, a RAD18 homolog of yeast which physically interacts with Rad6, were not necessary for the JIPA and UVSJ interactions. About 1.4 kb jipA transcript was detected in Northern analysis and its amount was not significantly increased in response to DNA-damaging agents. A genomic DNA clone of the jipA gene was isolated from a chromosome I specific genomic library by PCR-sib selection. Sequence determination of genomic and cDNA of jipA revealed an ORF of 893 bp interrupted by 2 introns, encoding a putative polypeptide of 262 amino acids. JIPA has 33% amino acid sequence identity to TIP41 of Saccharomyces cerevisiae which negatively regulates the TOR signaling pathway.