• Communications for Statistical Applications and Methods
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• 제16권1호
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• pp.67-74
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• 2009

고품질 한우를 만들기 위해 여러 경제형질에 영향을 주는 유전자 즉 single nucleotide polymorphisms(SNPs)를 규명하려고 한다. 이미 Lee 등 (2008a)에 의해 SNP(19_1)$^*$SNP(28_2)가 등심단면적 (LMA: longissimus muscle dorsi area)에 주요한 유전자로 규명되었다. 여기에 추가로 도체중 (CWT: carcass cold weight)과 일당증체량 (ADG: average daily gain)을 선형 모형에 적용하였으며 또한 상호작용에 더 유리하고 연속형 데이터에도 사용할 수 있는 expanded multifactor dimensionality reduction (expanded MDR)을 이용하여 주요한 SNP를 파악하였다. Expanded MDR 적용결과 등심단면적과 같은 결과인 SNP(19_1)과 SNP(19_1)$^*$SNP(28_2)의 상호작용 형태가 가장 좋은 SNP로 선정되었으며, 최종적으로 SNP(19_1)*SNP(28_2) 마커가 한우의 여러 경제형질에 우수 유전자임을 규명하였다.

• Asian-Australasian Journal of Animal Sciences
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• 제18권8호
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• pp.1061-1065
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• 2005

Growth rate is one of the economically important quantitative traits that affect carcass quantity in beef cattle. Two genes, bovine insulin-like growth factor I (IGF-I) and myogenic factor 5 (MYF5), were chosen as candidate genes for growth traits due to their important role in growth and development of mammals. The objectives of this study were to determine gene-specific single nucleotide polymorphism (SNP) markers of the IGF-I and MYF5 positional candidate genes and to investigate their associations with growth traits in Korean cattle. Genotyping of the SNP markers in these candidate genes was carried out using the single strand conformation polymorphism (SSCP) analysis. The frequencies of A and B alleles were 0.72 and 0.28 for IGF-I gene and 0.39 and 0.61 for MYF5 gene, respectively, in Korean cattle population examined. The gene-specific SNP marker association analysis indicated that the SNP genotype in IGF-I gene showed a significant association (p<0.05) with weight at 3 months (W3), and cows with AB genotype had higher W3 than BB genotype cows. The SNP genotype of MYF5 gene was found to have a significant effect (p<0.05) on the weight at 12 months (W12) and average daily gain (ADG), and cows with BB and AB genotypes had higher W12 and ADG compared with cows with AA genotype, respectively. However, no significant association between the SNP genotypes and any other growth traits was detected. The gene-specific SNP markers in the IGF-I and MYF5 candidate genes may be useful for selection on growth traits in Korean cattle.

• 한국균학회지
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• 제50권3호
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• pp.225-233
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• 2022

Pyogo (Shiitake, Lentinula edodes) is one of the most important edible mushrooms because of its outstanding nutritive and medicinal value. In the registration and protection procedure for newly developed mushroom cultivars, the application of molecular markers that can supplement the morphological characteristic-based distinction has been strongly requested. Sanjo 701 and Chamaram, newly developed at the Federation Forest Mushroom Research Center of Korea, have been characterized as innovative cultivars suitable for customer demands because of their high yields and cultivation rates. However, no technical tools can protect the rights to these important cultivars. In this study, using comparative genomic information from 23 commercially available pyogo cultivars, we identified single nucleotide polymorphisms (SNPs) that accurately differentiated Sanjo701 and Chamaram from the other cultivars. We also developed high-resolution melting analysis (HRM)-based SNP markers that discriminate among the tested 23 pyogo cultivars. The developed SNP markers can be utilized for rapid, accurate identification of pyogo cultivars with low genetic diversity and to prevent cultivar contamination caused by illegally distributed inocula. In addition, these markers can serve as a crucial scientific basis for securing the right to conserve new cultivars in international markets.

• Genomics & Informatics
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• 제14권4호
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• pp.196-204
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• 2016

Many researchers have found that one of the most important characteristics of the structure of linkage disequilibrium is that the human genome can be divided into non-overlapping block partitions in which only a small number of haplotypes are observed. The location and distribution of haplotype blocks can be seen as a population property influenced by population genetic events such as selection, mutation, recombination and population structure. In this study, we investigate the effects of the density of markers relative to the full set of all polymorphisms in the region on the results of haplotype partitioning for five popular haplotype block partition methods: three methods in Haploview (confidence interval, four gamete test, and solid spine), MIG++ implemented in PLINK 1.9 and S-MIG++. We used several experimental datasets obtained by sampling subsets of single nucleotide polymorphism (SNP) markers of chromosome 22 region in the 1000 Genomes Project data and also the HapMap phase 3 data to compare the results of haplotype block partitions by five methods. With decreasing sampling ratio down to 20% of the original SNP markers, the total number of haplotype blocks decreases and the length of haplotype blocks increases for all algorithms. When we examined the marker-independence of the haplotype block locations constructed from the datasets of different density, the results using below 50% of the entire SNP markers were very different from the results using the entire SNP markers. We conclude that the haplotype block construction results should be used and interpreted carefully depending on the selection of markers and the purpose of the study.

• Mycobiology
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• 제43권1호
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• pp.75-80
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• 2015

We identified single nucleotide polymorphism (SNP) markers in the laccase gene to establish a line-diagnostic system for shiitake mushrooms. A total of 89 fungal isolates representing four lines, including Korean registered, Korean wild type, Chinese, and Japanese lines, were analyzed. The results suggest that SNP markers in the laccase gene can be useful for line typing in shiitake mushrooms.

• 원예과학기술지
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• 제35권4호
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• pp.465-479
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• 2017

Chili pepper (Capsicum annuum L.) is an economically important horticultural crop in Korea; however, various diseases, including Phytophthora root rot, anthracnose, powdery mildew, Cucumber mosaic virus (CMV), Pepper mild mottle virus (PMMoV), and Pepper mottle virus (PepMoV), severely affect their productivity and quality. Therefore, pepper varieties with resistance to multiple diseases are highly desired. In this study, we developed 20 SNP type assays for three pepper populations using Fluidigm nanofluidic dynamic arrays. A total of 4,608 data points can be produced with a 192.24 dynamic array consisting of 192 samples and 24 SNP markers. The assays were converted from previously developed sequence-tagged-site (STS) markers and included markers for resistance to Phytophthora root rot (M3-2 and M3-3), anthracnose (CcR9, CA09g12180, CA09g19170, CA12g17210, and CA12g19240), powdery mildew (Ltr4.1-40344, Ltr4.2-56301, and Ltr4.2-585119), bacterial spot (Bs2), CMV (Cmr1-2), PMMoV (L4), and PepMoV (pvr1 and pvr2-123457), as well as for capsaicinoids content (qcap3.1-40134, qcap6.1-299931, qcap6.1-589160, qdhc2.1-1335057, and qdhc2.2-43829). In addition, 11 assays were validated through a comparison with the corresponding data of the STS markers. Furthermore, we successfully applied the assays to commercial $F_1$ cultivars and to our breeding lines. These 20 SNP type assays will be very useful for developing new superior pepper varieties with resistance to multiple diseases and a higher content of capsaicinoids for increased pungency.

• Genomics & Informatics
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• 제10권3호
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• pp.200-205
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• 2012

Although a large number of single nucleotide polymorphisms (SNPs) have been identified from the bovine genome-sequencing project, few of these have been validated at large in Bos indicus breeds. We have genotyped 192 animals, representing 5 cattle populations of Ethiopia, with the Illumina Bovine 8K SNP BeadChip. These include 1 Sanga (Danakil), 3 zebu (Borana, Arsi and Ambo), and 1 zebu ${\times}$ Sanga intermediate (Horro) breeds. The Hanwoo (Bos taurus) was included for comparison purposes. Analysis of 7,045 SNP markers revealed that the mean minor allele frequency (MAF) was 0.23, 0.22, 0.21, 0.21, 0.23, and 0.29 for Ambo, Arsi, Borana, Danakil, Horro, and Hanwoo, respectively. Significant differences of MAF were observed between the indigenous Ethiopian cattle populations and Hanwoo breed (p < 0.001). Across the Ethiopian cattle populations, a common variant MAF (${\geq}0.10$ and ${\leq}0.5$) accounted for an overall estimated 73.79% of the 7,045 SNPs. The Hanwoo displayed a higher proportion of common variant SNPs (90%). Investigation within Ethiopian cattle populations showed that on average, 16.64% of the markers were monomorphic, but in the Hanwoo breed, only 6% of the markers were monomorphic. Across the sampled Ethiopian cattle populations, the mean observed and expected heterozygosities were 0.314 and 0.313, respectively. The level of SNP variation identified in this particular study highlights that these markers can be potentially used for genetic studies in African cattle breeds.

• 한국연초학회지
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• 제30권2호
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• pp.85-93
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• 2008

This report describes a set of seven informative single-nucleotide polymorphisms (SNPs) and one insertion-deletion (INDEL) distributed over 24 cultivars that can be used for tobacco (Nicotiana tabacum L.) cultivar identification. We analyzed 163,000 genomic DNA sequences downloaded from Tobacco Genome Initiative database and assembled 31,370 contigs and 60,000 singletons. Using relatively long contigs, we designed primer sets for PCR amplification. We amplified 61 loci from 24 cultivars and sequenced the PCR products. We found seven significant SNPs and one INDEL among the sequences and we classified the 24 cultivars into 10 groups. SNP frequency of tobacco, 1/8,380 bp, was very low in comparison with those of other plant species, between 1/46 bp and 1/336 bp. For exact identification of tobacco cultivars, many more SNP markers should be developed. This study is the first attempt to identify tobacco cultivars using SNP markers.

• Plant Breeding and Biotechnology
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• 제6권4호
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• pp.391-403
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• 2018

Genome resequencing by next-generation sequencing technology can reveal numerous single nucleotide polymorphisms (SNPs) within a closely-related cultivar group, which would enable the development of sufficient SNP markers for mapping and the identification of useful genes present in the cultivar group. We analyzed genome sequence data from 13 Korean japonica rice varieties and discovered 740,566 SNPs. The SNPs were distributed at 100-kbp intervals throughout the rice genome, although the SNP density was uneven among the chromosomes. Of the 740,566 SNPs, 1,014 SNP sites were selected on the basis of polymorphism information content (PIC) value higher than 0.4 per 200-kbp interval, and 506 of these SNPs were converted to Kompetitive Allele-Specific PCR (KASP) markers. The 506 KASP markers were tested for genotyping with the 13 sequenced Korean japonica rice varieties, and polymorphisms were detected in 400 KASP markers (79.1%) which would be suitable for genetic analysis and molecular breeding. Additionally, a genetic map comprising 205 KASP markers was successfully constructed with 188 $F_2$ progenies derived from a cross between the varieties, Junam and Nampyeong. In a phylogenetic analysis with 81 KASP markers, 13 Korean japonica varieties showed close genetic relationships and were divided into three groups. More KASP markers are being developed and these markers will be utilized in gene mapping, quantitative trait locus (QTL) analysis, marker-assisted selection and other strategies relevant to crop improvement.

• 원예과학기술지
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• 제28권4호
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• pp.627-637
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• 2010

최근 들어 우리나라에서 토마토 소비가 급증하고 있으며 많은 토마토 품종이 시장에서 거래되고 있다. 그러나 토마토 품종 육성에 이용되는 부모 계통의 유전적 다양성이 낮아 형태적인 특성에 의한 토마토 품종의 구분은 매우 어려운 현실이다. 이에 따라 토마토의 품종을 구별해 낼 수 있는 분자표지의 개발이 필요한 실정이다. 본 연구에서는 SNP를 탐색하고 토마토 품종 구분을 위한 SNP 마커를 개발하였다. SNP분자표지는 고추 유전체 서열로부터 파생된 COS II 분자표지와 인트론 기반 분자표지를 기반으로 선발되었으며, HRM분석을 통해 다형성을 테스트 하였다. 전체 628개의 프라이머 조합 가운데 PCR을 통해 크기가 500bp 이하의 단일 밴드가 증폭된 417개의 프라이머 조합을 선발하였다. 417개의 프라이머 조합을 이용해 4개의 토마토 계통을 대상으로 HRM 분석을 실시하였으며, 다형성을 보인 70개의 프라이머 조합을 선발하였다. 70개의 프라이머 조합을 이용하여 32개의 토마토 품종을 대상으로 HRM 분석을 실시하였다. HRM분석을 통해 총 11개의 SNP 분자표지가 선발되었으며, 이 분자표지를 이용해 시판중인 32개의 토마토 품종을 모두 구분할 수 있었다.