• Asian-Australasian Journal of Animal Sciences
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• 제23권1호
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• pp.7-12
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• 2010

The full-length cDNA of the porcine peroxisomal ${\Delta}^3$,${\Delta}^2$-enoyl-CoA isomerase (PECI) gene encodes a monofunctional peroxisomal ${\Delta}^3$,${\Delta}^2$-enoyl-CoA isomerase. Cloning and sequencing of the porcine PECI cDNA revealed the presence of an 1185-base pair open reading frame predicted to encode a 394-amino acid protein by the 5'rapid amplification of cDNA ends (5'RACE) and EST sequences. The porcine PECI gene was expressed in seven tissues (heart, liver, spleen, lung, kidney, skeletal muscle, fat) which was revealed by reverse transcriptase-polymerase chain reaction (RT-PCR). The porcine PECI was mapped to SSC71/2 p11-13 using the somatic cell hybrid panel (SCHP) and the radiation hybrid panel (RH) (LOD score 12.84). The data showed that PECI was closely linked to marker S0383. A C/T single nucleotide polymorphism in PECI exon 10 (3'UTR) was detected as a PvuII PCR-RFLP. Association analysis in our experimental pig population showed that different genotypes of PECI gene were significantly associated with the Average Backfat thickness (ABF) (p<0.05) and Buttock backfat thickness (p<0.01).

• BMB Reports
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• 제40권4호
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• pp.577-587
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• 2007

Single-copy chloroplast loci are used widely to infer phylogenetic relationship at different taxonomic levels among various groups of plants. To test the utility of chloroplast loci and to provide additional data applicable to hybrid evolution in Musa, we sequenced two introns, rpl16 and ndhA, and two intergenic spacers, psaA-ycf3 and petA-psbJ-psbL-psbF and combined these data. Using these four regions, Musa acuminata Cola(A)- and M. balbisiana Colla (B)-containing genomes were clearly distinguished. Some triploid interspecific hybrids contain A-type chloroplasts (the AAB/ABB) while others contain B-type chloroplasts (the BBA/BBB). The chloroplasts of all cultivars in 'Namwa' (BBA) group came from the same wild maternal origin, but the specific parents are still unrevealed. Though, average sequence divergences in each region were little (less than 2%), we propose that petA-psbJ intergenic spacer could be developed for diversity assessment within each genome. This segment contains three single nucleotide polymorphisms (SNPs) and two indels which could distinguish diversity within A genome whereas this same region also contains one SNP and an indel which could categorize B genome. However, an inverted repeat region which could form hairpin structure was detected in this spacer and thus was omitted from the analyses due to their incongruence to other regions. Until thoroughly identified in other members of Musaceae and Zingiberales clade, utility of this inverted repeat as phylogenetic marker in these taxa are cautioned.

• Journal of Crop Science and Biotechnology
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• 제11권2호
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• pp.91-100
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• 2008

Melting curve analysis of fluorescently labeled DNA fragments is used extensively for genotyping single nucleotide polymorphism(SNP). Here, we evaluated a SNP genotyping method by melting curve analysis with the two probe chemistries in a 384-well plate format on a Roche LightCycler 480. The HybProbe chemistry is based on the fluorescence resonance energy transfer(FRET) and the SimpleProbe chemistry uses a terminal self-quenching fluorophore. We evaluated FRET HybProbes and SimpleProbes for two SNP sites closely linked to two quantitative trait loci(QTL) for southern root-knot nematode resistance. These probes were used to genotype the two parents and 94 $F_2$ plants from the cross of PI 96354$\times$Bossier. The SNP genotypes of all samples determined by the LightCycler software agreed with previously determined SSR genotypes and the SNP genotypes determined on a Luminex 100 flow cytometry instrument. Multiplexed HybProbes for the two SNPs showed a 98.4% success rate and 100% concordance between repeats two of the same 96 DNA samples. Also, we developed a HybProbe assay for the Rcs3 gene conditioning broad resistance to the frogeye leaf spot(FLS) disease. The LightCycler 480 provides rapid PCR on 384-well plate and allows simultaneous amplification and analysis in approximately 2 hours without any additional steps after amplification. This allowed for a reduction of the potential contamination of PCR products, simplicity, and enablement of a streamlined workflow. The melting curve analysis on the LightCycler 480 provided high-throughput and rapid SNP genotyping and appears highly effective for marker-assisted selection in soybean.

• 생태와환경
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• 제52권4호
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• pp.385-393
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• 2019

Chironomid communities are indicators of water pollution because of their ability to thrive under freshwater conditions. However, it is difficult to distinguish between chironomid larvae based on morphology. DNA barcoding, based on nucleotide sequences of marker genes, can be used to identify chironomid larvae. Samples of chironomid larvae were collected from Gwangju Stream and Pungyeongjeong Stream, tributaries of the Yeongsan River in South Korea. We identified 3 subfamilies, 13 genera, 16 species, and 1 cryptic species. There were 7 genera and 10 species from the subfamily Chironominae, 5 genera and 5 species from subfamily Orthocladiinae, 1 genus and 1 species from subfamily Tanipodinae, and the cryptic chironomid species of the family Chironomidae. There were 21 individuals from, 7 species and 1 cryptic species from the Gwangju Stream and 24 individuals, belonging to 10 species from the Pungyeongjeong Stream. The only species detected in both streams was Cricotopus bicinctus. The relationship between water quality and the species detected was difficult to explain, but the number of species showed a tendency to increase at sites where water quality was poor. Additional investigations and studies are needed to understand the relationship between water quality and the chironomid species occurring in these two streams.

• Parasites, Hosts and Diseases
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• 제55권1호
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• pp.95-98
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• 2017

Fasciola hepatica is a trematode that causes zoonosis, mainly in cattle and sheep, and occasionally in humans. Few recent studies have determined the infection status of this fluke in Korea. In August 2015, we collected 402 samples of freshwater snails at Hoenggye-ri (upper stream) and Suha-ri (lower stream) of Song-cheon (stream) in Daegwalnyeong-myeon, Pyeongchang-gun in Gangwon-do (Province) near many large cattle or sheep farms. F. hepatica infection was determined using PCR on the nuclear ribosomal internal transcribed spacer 2 (ITS-2). Among the 402 samples, F. hepatica 1TS-2 marker was detected in 6 freshwater snails; thus, the overall prevalence in freshwater snails was 1.5%. The prevalence varied between collection areas, ranging from 0.0% at Hoenggye-ri to 2.9% at Suha-ri. However, F. gigantica ITS-2 was not detected in the 6 F. hepatica-positive samples by PCR. The nucleotide sequences of the 6 F. hepatica ITS-2 PCR-positive samples were 99.4% identical to the F. hepatica ITS-2 sequences in GenBank, whereas they were 98.4% similar to F. gigantica ITS-2 sequences. These results indicated that the prevalence of F. hepatica in snail intermediate hosts was 1.5% in Gangwon-do, Korea; however the prevalence varied between collection areas. These results may help us to understand F. hepatica infection status in natural environments.

• Ocean and Polar Research
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• 제26권4호
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• pp.551-557
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• 2004

Polymorphism of the lipoprotein lipase (LPL) gene which plays an important role in regulation of lipid deposition was analysed in two red seabream (pagrus major) populations (KF4, cultured KORDI line, n=100 : JPN, imported from Japan, n=100). We amplified a DNA fragment (1,091 bp) including the exon 2 region of the LPL gene, and conducted PCR-RFLP analysis using MspI and AluI. The PCR products were also sequenced. Two alleles (A and B) were found in MspI digestion and Sve alleles (A, B, C, D and E) in AluI digestion. The sequenced data revealed four nucleotide substitutions including one transversion at the MspI recognition site (nt 2,235, $C{\rightarrow}10$) and three transitions at the AluI recognition sites (nt 1,721, $A{\rightarrow}G;$ nt 2,319, $C{\rightarrow}T;$ nt 2,319, $T{\rightarrow}C$). Among them, substitutions at the nt 2,235 and 2,319 sites which are located in the exon 2 were proved to be silent point mutations. MspI polymorphism resulted in 3 genotypes, and the allele frequency was significantly different between the two fish populations, KF4 and JPN. In the case of AluI polymorphism, the 5 alleles (A, B, C, D, E) comprised 12 genotypes of the 5 alleles. KF4 population, alleles D and I were specific to the LPL gene Polymorphisms would be useful DNA markers for red seabream population.

• Asian-Australasian Journal of Animal Sciences
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• 제27권9호
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• pp.1328-1335
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• 2014

Significant SNPs associated with Warner-Bratzler (WB) shear force and sensory traits were confirmed for Hanwoo beef (Korean cattle). A Bonferroni-corrected genome-wide significant association (p< $1.3{\times}10^{-6}$) was detected with only one single nucleotide polymorphism (SNP) on chromosome 5 for WB shear force. A slightly higher number of SNPs was significantly (p<0.001) associated with WB shear force than with other sensory traits. Further, 50, 25, 29, and 34 SNPs were significantly associated with WB shear force, tenderness, juiciness, and flavor likeness, respectively. The SNPs between p = 0.001 and p = 0.0001 thresholds explained 3% to 9% of the phenotypic variance, while the most significant SNPs accounted for 7% to 12% of the phenotypic variance. In conclusion, because WB shear force and sensory evaluation were moderately affected by a few loci and minimally affected by other loci, further studies are required by using a large sample size and high marker density.

• Asian-Australasian Journal of Animal Sciences
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• 제18권10호
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• pp.1375-1378
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• 2005

The objective of this study was to investigate polymorphisms of BMPRIB (bone morphogenetic protein type IB receptor) gene and its effect on litter size traits in sheep. Three populations including 101 Small Tailed Han sheep, 79 Poll Dorset and 81 hybrids (Poll Dorset${\times}$Small Tailed Han sheep) were used to detect the polymorphisms in exon 6 region of sheep BMPRIB gene. A fragment of approximately 190bp was amplified by one pair of primers, the polymorphism was revealed from the analysis of three populations by the technique of PCR -SSCP, and a mutation from A to G at 746 of the coding region was confirmed by sequencing in several individual. Statistical results indicated the distribution of allele B (with a A$\longrightarrow$G mutation) and A (without mutation) or genotype AA, AB and BB frequencies differed in three populations. BB genotype (44.55%) and B allele (66.34%) frequencies of Small Tailed Han sheep were higher than those of the others. Analysis of variance showed that the polymorphism of BMPRIB gene was associated with positive effect on litter size traits. The means of genotype BB and AB were about 1.04 and 0.74 more than genotype AA for litter size (p<0.05). Analysis of BMPRIB genotype effects on litter size in three populations indicates the existence of genotype BB or B allele increases the litter size. It suggested that the polymorphism in exon 6 (at 746 in the coding region) of sheep BMPRIB gene may be used as a marker for early selection of prolificacy in sheep.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.154-154
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• 2017

In accordance with the opening of the Korean rice market, this study was focused on establishment of database for discriminating the Korean rice varieties and imported brand rices using DNA markers. In this study, the SNP markers were developed using single nucleotide polymorphisms between the reference sequences of japonica and them of 40 brand rices which collected in Australia, China, Thailand, United States and Vietnam. The developed SNP markers were screened to a total of 360 rices including 320 Korean rice varieties and 40 imported brand rices. We selected polymorphic markers among Korean bred rive varieties and imported brand rices. The selected markers were classified into 3 grades. The markers of A grade produced DNA band in 360 rices of 30~40%, B grades produced in 40~60%, and C grades produced bands over 60% rices. First, we tried to set-up the discriminating system using the minimum SNP markers of A grade. Especially, a set of sixteen SNP markers could identify among Korean bred rice varieties and imported brand rices. Additionally, some SNP markers like NSb for Pib gene, JJ80-T for Pi5 and YL155/YL87 for Pita which linked to resistance genes to blast were used to fingerprinting system. These markers were set-up as multiplex set for enhancing the identification efficiency among rice varieties. Finally, the selected SNP markers would be used to the fluidigm assay to construct the database for elaborate discrimination of rice varieties.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.31-31
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• 2017

Understanding the mechanism(s) to overcome or prevent seed ageing deterioration during storage is of fundamental interest to seed physiologists. Vitamin E (tocols) is known as a key metabolite to efficiently scavenge lipid peroxy radicals which cause membrane breakdown resulting in seed ageing. However, in rice research this hypothesis has been tested for very few lines only without considering intraspecific variation in genomic structure. Here, we present a correlation study between tocols and seed longevity using a diverse rice panel. Seeds of 20 rice accessions held in the International Rice Genebank at the International Rice Research Institute, representing aus, indica, temperate japonica and tropical japonica subpopulations, were used for tocols analysis (quantification of ${\alpha}$-, ${\beta}$-, ${\gamma}$-, ${\delta}$-tocopherol/tocotrienol by ultra performance liquid chromatography) and storage experiments at $45^{\circ}C$ and 10.9% seed moisture content (sample taken for germination testing every 3 days up to 60 days). To examine interactions between DNA sequences and phenotype, the 700k high-density single-nucleotide polymorphism marker data-set was utilized. Both seed longevity (time for viability to fall to 50%; $p_{50}$) and tocols content varied across subpopulations due to heterogeneity in the genetic architecture. Among eight types of tocol homologues, ${\alpha}$-tocopherol and ${\gamma}$-tocotrienol were significantly correlated with $p_{50}$ (negatively and positively, respectively). While temperate japonica varieties were most abundant in ${\alpha}$-tocopherol, indica varieties recorded 1.3 to 1.7-fold higher ${\gamma}$-tocotrienol than those of other subpopulations. It was highlighted that specific ratio of tocol homologues rather than total tocols content plays an important role in the seed longevity mechanism.