• Asian-Australasian Journal of Animal Sciences
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• v.24 no.11
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• pp.1504-1513
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• 2011

It is important to identify genetic interactions related to human diseases or animal traits. Many linear statistical models have been reported but they did not consider genetic interactions. Genotype matrix mapping (GMM) has been developed to identify genetic interactions. This study uses the GMM method to detect superior SNP combinations of the CCDC158 gene that influences average daily gain, marbling score, cold carcass weight and longissimus muscle dorsi area traits in Hanwoo. We evaluated the statistical significance of the major SNP combinations selected by implementing the permutation test of the F-measure. The effect of g.34425+102 A>T (AA), g.8778G>A (GG) and g.4102+36T>G (GT) SNP combinations produced higher performance of average daily gain, marbling score, cold carcass weight and the longissimus muscle dorsi area traits than the effect of a single SNP. GMM is a fast and reliable method for multiple SNP analysis with potential application in marker-assisted selection. GMM may prospectively be used for genetic assessment of quantitative traits after further development.

• The Korean Journal of Malacology
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• v.30 no.3
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• pp.197-210
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• 2014

Single nucleotide polymorphisms (SNPs) are widely acknowledged as the marker of choice for many genetic and genomic applications because they show co-dominant inheritance, are highly abundant across genomes and are suitable for high-throughput genotyping. Here we evaluated the applicability of SNP markers developed from Crassostrea gigas and C. virginica expressed sequence tags (ESTs) in closely related Crassostrea and Ostrea species. A total of 213 putative interspecific level SNPs were identified from re-sequencing data in six amplicons, yielding on average of one interspecific level SNP per seven bp. High polymorphism levels were observed and the high success rate of transferability show that genic EST-derived SNP markers provide an efficient method for rapid marker development and SNP discovery in closely related oyster species. The six EST-SNP markers identified here will provide useful molecular tools for addressing questions in molecular ecology and evolution studies including for stock analysis (pedigree monitoring) in related oyster taxa.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.10
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• pp.1374-1378
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• 2013

Based on a quantitative traits locus (QTL) study using a $F_2$ intercross between Landrace and Korean native pigs, a significant QTL affecting teat numbers in SSC7 was identified. The strong positional candidate gene, TBC1D21, was selected due to its biological function for epithelial mesenchymal cell development. Sequence analysis revealed six single nucleotide polymorphisms (SNPs) in the TBC1D21 gene. Among these, two SNP markers, one silent mutation (SNP01) for g.13,050A>G and one missense mutation (SNP04) for c.829A>T (S277C), were genotyped and they showed significant associations with teat number traits (p value = 6.38E-05 for SNP01 and p value = 1.06E-07 for SNP04 with total teat numbers). Further functional validation of these SNPs could give valuable information for understanding the teat number variation in pigs.

• Plant Biotechnology Reports
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• v.4 no.4
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• pp.243-251
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• 2010

Nitric oxide (NO) has been shown to be involved in diverse physiological processes in microbes, animals and plants. In this study, the involvement of NO in the development and possible roles in oxidative stress protection of Chinese cabbage (Brassica rapa subsp. pekinensis cv. Samrack-ulgari) seedlings were investigated. Exogenous application of sodium nitroprusside (SNP) retarded root elongation, while increasing lateral root formation of Chinese cabbage. Plants showed no signs of external stress due to SNP application in true leaves. Cotyledons of 3-week-old Chinese cabbage plants were found to be highly sensitive to SNP application. Treated cotyledons displayed rapid tissue collapse and associated cell death. Although SNP application reduced root growth under normal growth conditions, it also enhanced methyl viologen (MV)-mediated oxidative stress tolerance. Analysis of SNP application to Chinese cabbage leaf disks, revealed SNP-induced tolerance against oxidative stresses by MV and $H_2O_2$, and evidence includes prevention of chlorophyll loss, superoxide anion (${O_2}^-$) accumulation and lipid peroxidation. This report supports a role for nitric oxide in modulating early seedling development, programmed cell death and stress tolerance in Chinese cabbage.

• Journal of Plant Biotechnology
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• v.43 no.1
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• pp.1-11
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• 2016

Single nucleotide polymorphism (SNP) is an abundant form of genetic variation within individuals of species. DNA polymorphism can arise throughout the whole genome at different frequencies in different species. SNP may cause phenotypic diversity among individuals, such as individuals with different color of plants or fruits, fruit size, ripening, flowering time adaptation, quality of crops, grain yields, or tolerance to various abiotic and biotic factors. SNP may result in changes in amino acids in the exon of a gene (asynonymous). SNP can also be silent (present in coding region but synonymous). It may simply occur in the noncoding regions without having any effect. SNP may influence the promoter activity for gene expression and finally produce functional protein through transcription. Therefore, the identification of functional SNP in genes and analysis of their effects on phenotype may lead to better understanding of their impact on gene function for varietal improvement. In this mini-review, we focused on evidences revealing the role of functional SNPs in genes and their phenotypic effects for the purpose of crop improvements.

• Journal of Animal Science and Technology
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• v.64 no.5
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• pp.830-841
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• 2022

Genetic analysis has great potential as a tool to differentiate between different species and breeds of livestock. In this study, the optimal combinations of single nucleotide polymorphism (SNP) markers for discriminating the Yeonsan Ogye chicken (Gallus gallus domesticus) breed were identified using high-density 600K SNP array data. In 3,904 individuals from 198 chicken breeds, SNP markers specific to the target population were discovered through a case-control genome-wide association study (GWAS) and filtered out based on the linkage disequilibrium blocks. Significant SNP markers were selected by feature selection applying two machine learning algorithms: Random Forest (RF) and AdaBoost (AB). Using a machine learning approach, the 38 (RF) and 43 (AB) optimal SNP marker combinations for the Yeonsan Ogye chicken population demonstrated 100% accuracy. Hence, the GWAS and machine learning models used in this study can be efficiently utilized to identify the optimal combination of markers for discriminating target populations using multiple SNP markers.

• Proceedings of the Korea Information Processing Society Conference
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• 2010.11a
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• pp.95-98
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• 2010

최근 차세대 시퀀싱 기술의 급속한 발전에 따라 서열 정보의 해독이 비교적 쉬워지면서 개인별 맞춤의학의 실현에 대한 기대와 관심이 높아지고 있다. 각 개인의 서열 정보 사이에는 SNP (single nucleotide polymorphism), Indel, CNV (copy number variation) 등의 다양한 유전적 구조 변이가 존재하며, 이러한 서열 정보의 부분적 차이는 각 개인의 유전적 특성 및 질병 감수성 등과 밀접한 관련을 갖는다. 본 연구에서는 차세대 시퀀싱 결과로 산출되는 수많은 짧은 DNA 서열 조각인 리드 데이터를 이용한 SNP 추출 알고리즘을 제안한다. 제안된 알고리즘에서는 레퍼런스 시퀀스의 각 위치에 대한 리드 시퀀스의 매핑 정보를 기반으로 SNP 후보 영역을 추출하며, 품질 정보 등을 활용하여 에러 발생률을 최소화한다. 또한 대규모 시퀀싱 데이터와 SNP 구조 변이 데이터의 효율적인 저장/검색을 지원하는 시각적 분석 도구를 구현하여 제안된 방식의 유용성을 검증한다.

• Journal of Animal Science and Technology
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• v.52 no.2
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• pp.91-96
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• 2010

The purpose of the study was to develop an optimum SNP marker set to be utilized for domestic pork traceability. The study tested 51 SNP markers analyzed for origin of farm to be determined from genotypes of offspring and parents in pigs. With the simulation data through random mating population (PI), half sib mating population ($PI_{half-sib}$) and full sib mating population ($PI_{sibs}$), probability of identical genotypes were analyzed as $5.63{\times}10^{-33}$, $4.35{\times}10^{-15}$ and $1.32{\times}10^{-15}$, respectively. The 51 SNP markers also had 100% accuracy for parental determination. These results suggest that if the pig breeding stock is genotyped with the 51 SNP markers, the genotype information of individual offspring can be checked for farm origins by tracing parental sow and sire. Therefore, these SNP markers will be useful to trace the pork from production to consumption in pigs.

• Genomics & Informatics
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• v.18 no.4
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• pp.38.1-38.9
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• 2020

Chronotype is an important moderator of psychiatric illnesses, which seems to be controlled in some part by genetic factors. Clock genes are the most relevant genes for chronotype. In addition to the roles of individual genes, gene-gene interactions of clock genes substantially contribute to chronotype. We investigated genetic associations and gene-gene interactions of the clock genes BHLHB2, CLOCK, CSNK1E, NR1D1, PER1, PER2, PER3, and TIMELESS for chronotype in 1,293 healthy Korean individuals. Regression analysis was conducted to find associations between single nucleotide polymorphism (SNP) and chronotype. For gene-gene interaction analyses, the quantitative multifactor dimensionality reduction (QMDR) method, a nonparametric model-free method for quantitative phenotypes, were performed. No individual SNP or haplotype showed a significant association with chronotype by both regression analysis and single-locus model of QMDR. QMDR analysis identified NR1D1 rs2314339 and TIMELESS rs4630333 as the best SNP pairs among two-locus interaction models associated with chronotype (cross-validation consistency [CVC] = 8/10, p = 0.041). For the three-locus interaction model, the SNP combination of NR1D1 rs2314339, TIMELESS rs4630333, and PER3 rs228669 showed the best results (CVC = 4/10, p < 0.001). However, because the mean differences between genotype combinations were minor, the clinical roles of clock gene interactions are unlikely to be critical.

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