• BMB Reports
• /
• v.41 no.1
• /
• pp.29-34
• /
• 2008

The aim of this study was to determine whether single nucleotide polymorphisms (SNP) in the beef cattle adipocyte fatty-acid binding protein 3 and 4 (FABP3 and FABP4) genes are associated with carcass weight (CW) and back fat thickness (BF) of beef cattle. By direct DNA sequencing in 24 unrelated Korean native cattle, we identified 20 SNPs in FABP3 and FABP4. Among them, 10 polymorphic sites were selected for genotyping in our beef cattle. We performed SNP, haplotype and linkage disequilibrium studies on 419 Korean native cattle with the 10 SNPs in the FABP genes. Statistical analysis revealed that 220A>G (I74V) and 348+303T>C polymorphisms in FABP4 showed putative associations with BF traits (P=0.02 and 0.01, respectively). Our findings suggest that the polymorphisms in FABP4 may play a role in determining one of the important genetic factors that influence BF in beef cattle.

• Journal of Life Science
• /
• v.32 no.12
• /
• pp.947-955
• /
• 2022

Silkworms, which have recently shown promise as functional health foods, show functional differences between varieties; therefore, the need for variety identification is emerging. In this study, we analyzed the whole silkworm genome to identify 10 unique silkworm varieties (Baekhwang, Baekok, Daebaek, Daebak, Daehwang, Goldensilk, Hansaeng, Joohwang, Kumkang, and Kumok) using single nucleotide polymorphisms (SNP) present in the genome as biomarkers. In addition, nine SNPs were selected to discriminate between varieties by selecting SNPs specific to each variety. We subsequently created a decision tree capable of cross-verifying each variety and classifying the varieties through sequential analysis. Restriction fragment length polymorphism (RFLP) was used for SNP867 and SNP9183 to differentiate between the varieties of Daehwang and Goldensilk and between Kumkang and Daebak, respectively. A tetra-primer amplification refractory (T-ARMS) mutation was used to analyze the remaining SNPs. As a result, we could isolate the same group or select an individual variety using the nine unique SNPs from SNP780 to SNP9183. Furthermore, nucleotide sequence analysis for the region confirmed that the alleles were identical. In conclusion, our results show that combining SNP analysis of the whole silkworm genome with the decision tree is of high value as a discriminative marker for classifying silkworm varieties.

• Proceedings of the Plant Resources Society of Korea Conference
• /
• 2010.05a
• /
• pp.15-15
• /
• 2010

Koran ginseng(Pnax ginseng) is one of the most important medicinal plants in Orient. Among the nine cultivars of Korea ginseng, Chunpoong commands a much greater market value and has been planted widely. A rapid and reliable method for discriminating the Chunpoong cultivar was developed by exploiting a single nucleotide polymorphism (SNP) in the mitochondrial nad7 intron 4 region of nine Korea ginseng cultivars using universal primers. A SNP was detected between Chunpoong and other cultivars and modified allele-specific primers were designed from this SNP site to effective method for the geneic identification of the Chunpoong cultivar of ginseng.

• Korean Journal of Veterinary Research
• /
• v.45 no.1
• /
• pp.25-28
• /
• 2005

The melanocortin 1 receptor (MC1R) plays an important role in regulation of melanin pigment synthesis within mammalian melanocytes. Mutations within the gene encoding MC1R have been shown to explain coat color variations within several mammalian species including cattle. To develope a rapid and accurate method for the identification of Hanwoo meat, we performed a single nucleotide polymorphism (SNP) analysis in Melanocortin 1 receptor (MC1R) gene using TaqMan$^{(R)}$ MGB probe-based real-time PCR. Two specific probes (one for Hanwoo and the other for Holstein and Black angus) were designed. At the 5' end of 2 TaqMan$^{(R)}$ MGB probes, 6-carboxyfluorescein (FAM) was labeled for Hanwoo, and VIC for Holstein and Black angus. As a result, Hanwoo samples showed FAM-positive signal only, whereas other samples showed VIC-positive. This result suggests that the TaqMan$^{(R)}$ MGB probe based real-time PCR technique would be very accurate, easy and reproducible method to discriminate between Hanwoo meat and Holstein/Black angus meat.

• Korean Journal of Plant Resources
• /
• v.28 no.6
• /
• pp.743-751
• /
• 2015

Reynoutria japonica and R. sachalinensis have been used as medicinal resources in Korea. However, it is difficult to identify and determine these medicinal herbs correctly because they are usually customized and purchased as the fragmented rhizomes types. To develop molecular markers for distinguishing two species, we analyzed and compared the chloroplast DNA sequences of seven loci (atpB, matK, ccD-psaI, atpF-H, trnL-trnF, psbK-I and rpl32-trnL). Among them, we found two effective SNPs in psbK-I region for R. japonica and atpF-H region for R. sachalinensis. Based on these SNP sites, we designed the new R. japonica- specific primer which is able to amplify 300 bp fragment in psbK-I region. A similar strategy was applied for the atpF-H region of R. sachalinensis. These molecular markers would be successfully applied to recognize R. japonica and R. sachalinensis.

• Journal of Animal Science and Technology
• /
• v.55 no.4
• /
• pp.231-235
• /
• 2013

Carcass weight (CW) is one of the most important economic traits in pigs, directly affecting the income of farmers. In this study, a genome wide association study was performed to detect significant single nucleotide polymorphisms (SNPs) affecting CW in pigs derived from a $F_2$ intercross between Landrace and Korean native pig (KNP). Using high-density porcine SNP chips, highly significant SNPs were identified on SSC12. Two candidate genes, LOC100523510 and LOC100621652, were subsequently selected within this region and further investigated. Within these candidate genes, five SNPs were identified and genotyped using the VeraCode GoldenGate assay. The results revealed that one SNP in the LOC100621652 gene and four SNPs in the LOC100523510 gene are highly associated with CW. These SNP markers can thus have significant applications for improving CW in KNP. However, the functions of these candidate genes are not fully understood and require further study.

• Asian-Australasian Journal of Animal Sciences
• /
• v.18 no.1
• /
• pp.3-7
• /
• 2005

The insulin-like growth factors (IGFs), their receptors, and their binding proteins play key roles in regulating cell proliferation and apoptosis. Insulin-like growth factor binding protein-3 (IGFBP3, OMIM #146732) is one of the proteins that bind to the IGFs. IGFBP3 is a modulator of IGF bioactivity, and direct growth inhibitor in the extravascular tissue compartment. We identified twenty-two novel single nucleotide polymorphisms (SNPs) in IGFBP3 gene in Korean cattle (Hanwoo, Bos taurus coreanae) by direct sequencing of full gene including -1,500 bp promoter region. Among the identified SNPs, five common SNPs were screened in 650 Korean cattle; one SNP in promoter (IGFBP3 G-854C), one in 5'UTR region (IGFBP3 G-100A), two in intron 1 (IGFBP3 G+421T, IGFBP3 T+1636A), and one in intron 2 (IGFBP3 C+3863A). The frequencies of each SNP were 0.357 (IGFBP3 G-854C), 0.472 (IGFBP3 G-100A), 0.418 (IGFBP3 G+421T), 0.363 (IGFBP3 T+1636A) and 0.226 (IGFBP3 C+3863A), respectively. Haplotypes and their frequencies were estimated by EM algorithm. Six haplotypes were constructed with five SNPs and linkage disequilibrium coefficients (|D'|) between SNP pairs were also calculated. The information on SNPs and haplotypes in IGFBP3 gene could be useful for genetic studies of this gene.

• Korean Journal of Agricultural Science
• /
• v.45 no.3
• /
• pp.385-400
• /
• 2018

Marker-assisted backcrossing (MABC) is useful for selecting offspring with a highly recovered genetic background for a recurrent parent at early generation unlike rice and other field crops. Molecular marker sets applicable to practical MABC are scarce in vegetable crops including tomatoes. In this study, we used the National Center for Biotechnology Information- short read archive (NCBI-SRA) database that provided the whole genome sequences of 234 tomato accessions and selected 27,680 tag-single nucleotide polymorphisms (tag-SNPs) that can identify haplotypes in the tomato genome. From this SNP dataset, a total of 143 tag-SNPs that have a high polymorphism information content (PIC) value (> 0.3) and are physically evenly distributed on each chromosome were selected as a MABC marker set. This marker set was tested for its polymorphism in each pairwise cross combination constructed with 124 of the 234 tomato accessions, and a relatively high number of SNP markers polymorphic for the cross combination was observed. The reliability of the MABC SNP set was assessed by converting 18 SNPs into Luna probe-based high-resolution melting (HRM) markers and genotyping nine tomato accessions. The results show that the SNP information and HRM marker genotype matched in 98.6% of the experiment data points, indicating that our sequence analysis pipeline for SNP mining worked successfully. The tag-SNP set for the MABC developed in this study can be useful for not only a practical backcrossing program but also for cultivar identification and F1 seed purity test in tomatoes.

• Proceedings of the Korean Society of Crop Science Conference
• /
• 2017.06a
• /
• pp.154-154
• /
• 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.

• Korean Journal of Poultry Science
• /
• v.41 no.1
• /
• pp.29-37
• /
• 2014

The Feather Color of chicken is considered as most obvious, and the purpose of this study is to identify the genotype following the SNP of MC1R, MITF and TYRP1, which are genes related to Feather Color, and develop a SNP marker that can be classified per breed. When a haplotype is observed through the combination of markers, a Korean Native Chicken can especially be distinguished when it is a CGG type in the SNP combination of the MC1R gene. In case of the TAG, TGG and TAA types, only Araucana was identified, and for the CAA type, Leghorn could specifically be distinguished. In the SNP combination of TYRP1 gene, only Leghorn was differentiated in case of the TTTCA and CCTCA types, and only Silky Fowl was identified in case of the CTTTA type. The SNP combination of MC1R gene enabled for Korean Native Chicken, Leghorn, and Araucana to be distinguished and each of the SNP and combination of TYRP1 gene allowed for all 4 breeds to be classified. If many researches are conducted about genetic polymorphism between breeds, then it is considered that the differences between breeds will be understood from a molecular biological aspect instead of simply distinguishing the breeds through Feather Color.