• Asian-Australasian Journal of Animal Sciences
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• v.31 no.4
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• pp.473-479
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• 2018

Objective: The study was designed to perform a genome-wide association (GWA) and partitioning of genome using Illumina's PorcineSNP60 Beadchip in order to identify variants and determine the explained heritability for the total number of teats in Yorkshire pig. Methods: After screening with the following criteria: minor allele frequency, $MAF{\leq}0.01$; Hardy-Weinberg equilibrium, $HWE{\leq}0.000001$, a pair-wise genomic relationship matrix was produced using 42,953 single nucleotide polymorphisms (SNPs). A genome-wide mixed linear model-based association analysis (MLMA) was conducted. And for estimating the explained heritability with genome- or chromosome-wide SNPs the genetic relatedness estimation through maximum likelihood approach was used in our study. Results: The MLMA analysis and false discovery rate p-values identified three significant SNPs on two different chromosomes (rs81476910 and rs81405825 on SSC8; rs81332615 on SSC13) for total number of teats. Besides, we estimated that 30% of variance could be explained by all of the common SNPs on the autosomal chromosomes for the trait. The maximum amount of heritability obtained by partitioning the genome were $0.22{\pm}0.05$, $0.16{\pm}0.05$, $0.10{\pm}0.03$ and $0.08{\pm}0.03$ on SSC7, SSC13, SSC1, and SSC8, respectively. Of them, SSC7 explained the amount of estimated heritability along with a SNP (rs80805264) identified by genome-wide association studies at the empirical p value significance level of 2.35E-05 in our study. Interestingly, rs80805264 was found in a nearby quantitative trait loci (QTL) on SSC7 for the teat number trait as identified in a recent study. Moreover, all other significant SNPs were found within and/or close to some QTLs related to ovary weight, total number of born alive and age at puberty in pigs. Conclusion: The SNPs we identified unquestionably represent some of the important QTL regions as well as genes of interest in the genome for various physiological functions responsible for reproduction in pigs.

• Molecules and Cells
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• v.27 no.3
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• pp.329-336
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• 2009

To evaluate the involvement of translation initiation factors eIF4E and eIFiso4E in Chilli veinal mottle virus (ChiVMV) infection in pepper, we conducted a genetic analysis using a segregating population derived from a cross between Capsicum annuum 'Dempsey' containing an elF4E mutation ($pvr1^2$) and C. annuum 'Perennial' containing an elFiso4E mutation (pvr6). C. annuum 'Dempsey' was susceptible and C. annuum 'Perennial' was resistant to ChiVMV. All $F_1$ plants showed resistance, and $F_2$ individuals segregated in a resistant-susceptible ratio of 166:21, indicating that many resistance loci were involved. Seventy-five $F_2$ and 329 $F_3$ plants of 17 families were genotyped with $pvr1^2$ and pvr6 allele-specific markers, and the genotype data were compared with observed resistance to viral infection. All plants containing homozygous genotypes of both $pvr1^2$ and pvr6 were resistant to ChiVMV, demonstrating that simultaneous mutations in elF4E and eIFiso4E confer resistance to ChiVMV in pepper. Genotype analysis of $F_2$ plants revealed that all plants containing homozygous genotypes of both $pvr1^2$ and pvr6 showed resistance to ChiVMV. In protein-protein interaction experiments, ChiVMV viral genome-linked protein (VPg) interacted with both eIF4E and eIFiso4E. Silencing of elF4E and eIFiso4E in the VIGS experiment showed reduction in ChiVMV accumulation. These results demonstrated that ChiVMV can use both eIF4E and eIFiso4E for replication, making simultaneous mutations in eIF4E and eIFiso4E necessary to prevent ChiVMV infection in pepper.

• Journal of Ginseng Research
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• v.44 no.4
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• pp.637-643
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• 2020

Background: Ginseng (Panax ginseng Meyer) is one of the world's most valuable medicinal plants with numerous pharmacological effects. Ginseng has been cultivated from wild mountain ginseng collections for a few hundred years. However, the genetic diversity of cultivated and wild ginseng populations is not fully understood. Methods: We developed 92 polymorphic microsatellite markers based on whole-genome sequence data. We selected five markers that represent clear allele diversity for each of their corresponding loci to elucidate genetic diversity. These markers were applied to 147 individual plants, including cultivars, breeding lines, and wild populations in Korea and neighboring countries. Results: Most of the 92 markers displayed multiple-band patterns, resulting from genome duplication, which causes confusion in interpretation of their target locus. The five high-resolution markers revealed 3 to 8 alleles from each single locus. The proportion of heterozygosity (H_e) ranged from 0.027 to 0.190, with an average of 0.132, which is notably lower than that of previous studies. Polymorphism information content of the markers ranged from 0.199 to 0.701, with an average of 0.454. There was no statistically significant difference in genetic diversity between cultivated and wild ginseng groups, and they showed intermingled positioning in the phylogenetic relationship. Conclusion: Ginseng has a relatively high level of genetic diversity, and cultivated and wild groups have similar levels of genetic diversity. Collectively, our data demonstrate that current breeding populations have abundant genetic diversity for breeding of elite ginseng cultivars.

• Korean Journal of Ichthyology
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• v.20 no.4
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• pp.248-254
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• 2008

Olive flounder (Paralichthys olivaceus) is one of the most popular farmed fish in Korea. Genetic variability of the fish was investigated by means of microsatellite DNA markers. All of the 8 microsatellite loci were analyzed in this study. For the confirmation of genetic variation during a shift in generation, microsatellite variability was compared within the same hatchery strains but produced in different spawning years. When genetic variability of farmed flounders produced in 2006 and 2007 was compared with that of 2003, a marked reduction of genetic variability was observed in the 2006 and 2007 populations. Mean number of alleles per locus and expected mean heterozygosity decreased from 9.75 and 0.796 (in 2003 population) to 7.78 and 0.785 (in 2006 population), respectively. Moreover, we have observed the distortion of allele frequency. These results show that reduced genetic variability of farmed olive flounder in processed generation has lower numbers of alleles and genetic variability than these of wild fish. Our results suggest that to have a sustainable aquaculture of this species, there is need for scientific broodstock management based on genetic variation and more intensive breeding practices to improve genetic diversity and to avoid detrimental inbreeding effects.

• Journal of the Korean Academy of Child and Adolescent Psychiatry
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• v.22 no.4
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• pp.287-293
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• 2011

Objectives : The region of chromosome 5p14 is known to be associated with autism spectrum disorder (ASD). The cadherin9 (CDH9) and cadherin10 (CDH10) genes are located in the region of chromosome 5p14 and reported to be associated with ASD in the Caucasian population. We performed an association study to identify if single nucleotide polymorphisms (SNPs) located on the CDH9 and CDH10 genes are associated in the Korean population. Methods : Genomic DNA was extracted from the blood of 214 patients with ASD and 258 controls. SNPs selected from two genes were genotyped using an Illumina Golden-Gate Genotyping assay with VeraCode technology. Statistical analysis was performed using SAS and Plink software. Results : All controls and ASD patients were in Hardy-Weinberg equilibrium. In the results of logistic regression analyses for the genotype model and the chi-square test for the allele model, we found that SNPs on the CDH9 and CDH10 genes were not associated with ASD. Conclusion : Our data suggests that the CDH9 and CDH10 genes are not associated with ASD in the Korean population.

• Molecules and Cells
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• v.27 no.2
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• pp.175-181
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• 2009

The myosin light chain kinase (MYLK) gene encodes both smooth muscle and nonmuscle cell isoforms. Recently, polymorphisms in MYLK have been reported to be associated with several diseases. To examine the genetic effects of polymorphisms on the risk of asthma and related phenotypes, we scrutinized MYLK by re-sequencing/genotyping and statistical analysis in Korean population (n = 1,015). Seventeen common polymorphisms located in or near exons, having pairwise $r^2$ values less than 0.25, were genotyped. Our statistical analysis did not replicate the associations with the risk of asthma and log-transformed total IgE levels observed among African descendant populations. However, two SNPs in intron 16 (+89872C> G and +92263T> C), which were in tight LD (|D'| = 0.99), revealed significant association with log-transformed blood eosinophil level even after correction multiple testing ($P=0.002/P^{corr}=0.01$ and $P=0.002/P^{corr}=0.01$, respectively). The log-transformed blood eosinophil levels were higher in individuals bearing the minor alleles for +89872C> G and +92263T> C than in those bearing other allele. In additional subgroup analysis, the genetic effects of both SNPs were much more apparent among asthmatic patients and atopic asthma patients. Among atopic asthma patients, the log-transformed blood eosinophil levels were proportionally increased by gene-dose dependent manner of in both +89872C> G and +92263T> C(P = 0.0002 and P = 0.00007, respectively). These findings suggest that MYLK polymorphisms might be among the genetic factors underlying differential increases of blood eosinophil levels among asthmatic patients. Further biological and/or functional studies are needed to confirm our results.

• Genes and Genomics
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• v.40 no.12
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• pp.1319-1329
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• 2018

SSRs were successfully isolated from the Perilla crop in our current study, and used to analyze Perilla accessions from East Asia. Analyses of the clear genetic diversity and relationship for Perilla crop still remain insufficient. In this study, 40 new simple sequence repeat (SSR) primer sets were developed from RNA sequences using transcriptome analysis. These new SSR markers were applied to analyze the diversity, relationships, and population structure among 35 accessions of the two cultivated types of Perilla crop and their weedy types. A total of 220 alleles were identified at all loci, with an average of 5.5 alleles per locus and a range between 2 and 10 alleles per locus. The MAF (major allele frequency) per locus varied from 0.229 to 0.943, with an average of 0.466. The average polymorphic information content (PIC) value was 0.603, ranging from 0.102 to 0.837. The genetic diversity (GD) ranged from 0.108 to 0.854, with an average of 0.654. Based on population structure analysis, all accessions were divided into three groups: Group I, Group II and the admixed group. This study demonstrated the utility of new SSR analysis for the study of genetic diversity and population structure among 35 Perilla accessions. The GD of each locus for accessions of cultivated var. frutescens, weedy var. frutescens, cultivated var. crispa, and weedy var. crispa were 0.415, 0.606, 0.308, and 0.480, respectively. Both weedy accessions exhibited higher GD and PIC values than their cultivated types in East Asia. The new SSR primers of Perilla species reported in this study may provide potential genetic markers for population genetics to enhance our understanding of the genetic diversity, genetic relationship and population structure of the cultivated and weedy types of P. frutescens in East Asia. In addition, new Perilla SSR primers developed from RNA-seq can be used in the future for cultivar identification, conservation of Perilla germplasm resources, genome mapping and tagging of important genes/QTLs for Perilla breeding programs.

• Journal of Nutrition and Health
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• v.57 no.2
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• pp.211-227
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• 2024

Introduction: Seaweed is a sustainable and underexplored source of bioactive compounds with potent anti-inflammatory activities. However, studies on the interaction between seaweed and genes on inflammation are limited. Purpose: We aimed to evaluate the relationships between seaweed consumption and the polygenic risk scores (PRS) and their interactions with high-sensitivity C-reactive protein (hs-CRP) levels. Methods: Information on seaweed consumption was collected using a food frequency questionnaire, which included laver, kelp, and sea mustard among the items consumed. A total of 31 hs-CRP-related single nucleotide polymorphisms (SNPs) were selected using genome-wide association studies and clumping analysis, and the individual PRS were calculated by weighting the effect size of each allele in the selected SNPs of 39,369 middle-aged (≥40 years) Koreans using the Korean Genome and Epidemiology Study (KoGES)-Health Examinees (HEXA) cohort data. To investigate the interaction between seaweed intake and the PRS on hs-CRP levels >1 mg/L, hazard ratios (HRs) and 95% confidence intervals (CIs) were assessed using multivariable Cox proportional hazards models. Results: During a mean follow-up period of 4.8 years, we recorded 436 patients with elevated hs-CRP levels. Women in the highest tertile of the PRS with the lowest quartile of seaweed intake had an increased incidence of elevated hs-CRP levels compared with women in the lowest tertile of the PRS with the lowest seaweed intake quartile (HR 2.34, 95% CI 1.23-4.45). No significant association was observed among the men. Conclusion: In conclusion, we identified a new interaction between the PRS, seaweed intake, and inflammation in Korean women, and this study suggests that the interaction between the identification of genetic predisposition and dietary seaweed intake may have an impact on determining the risk of developing hyperinflammation in the future.

• Journal of Genetic Medicine
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• v.5 no.1
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• pp.34-40
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• 2008

Purpose : Preeclampsia is a major cause of maternal and perinatal mortality and morbidity and is considered to be a multifactorial disorder involving a genetic predisposition and environmental factors. Endothelin-1 (ET-1) is a potent vasoconstrictor peptide, and alterations in the ET-1 system are thought to play a role in triggering the vasoconstriction seen with preeclampsia. The aim of this study was to examine the frequency of the 4 common single-nucleotide polymorphisms (SNPs) (c.1370T>G, c.137_139delinsA, c.3539+2T>C, and c.5665G>T) of the ET-1 gene in normotensive and preeclamptic pregnancies and to investigate whether these SNPs are associated with preeclampsia in pregnant Korean women. Methods : We analyzed blood samples from 206 preeclamptic and 216 normotensive pregnancies using a commercially available SNapShot kit and an ABI Prism 3100 Genetic analyzer. Results : There were no significant differences in genotype or allele frequencies of the 4 SNPs in the ET-1 gene between preeclamptic and normotensive pregnancies. The respective frequencies of the 3 haplotypes (TDTG, GDCT, and TICT; >10% haplotype frequency) were 61%, 13% and 13%, respectively, in preeclampsic pregnancies and 62%, 14% and 12%, respectively, in normotensive pregnancies. The frequencies of these haplotypes were similar for both groups. Using multiple logistic regression analysis, we did not observe an increase in the risk of preeclampsia for the 4 SNPs of the ET-1 gene under either a recessive or dominant model. Conclusion : This study suggests that the 4 SNPs of the ET-1 gene are not associated with an increased risk for preeclampsia in pregnant Korean women.

• Horticultural Science & Technology
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• v.29 no.6
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• pp.645-650
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• 2011

Pear cultivar 'Supergold' (Pyrus pyrifolia var. culta Nakai) was originated from the cross between 'Chuwhangbae' and 'Manpungbae' with the aims of improving the fruit quality of 'Chuwhangbae' cultivar at Pear Research Station of National Institute of Horticultural & Herbal Science, Rural Development Administration in 1994. 'Supergold' was preliminarily selected in 2002 and named in 2008. The tree shows a vigorous growth habit and semi-spread characters like as 'Manpungbae'. Furthermore, it has sufficient flowers and carries abundant pollen grains, so it can also be used as a pollinator. 'Supergold' is highly resistant to black leaf spot (Alternaria kikuchiana) in the field condition. The optimum harvest time is around Sep. 11th, which is ahead of 'Whangkeumbae' about 5 days in the harvest period. The fruit shape is oblate and fruit skin color is greenish-white at harvesting time. The average weight of fruit is 570 g, and the soluble solids content is $13.6\;^{\circ}Brix$. The flesh is very soft and juicy, and renders good eating quality. Shelf life is about 6 months under the cold storage condition. To determine the self-incompatibility (SI) genotype of 'Supergold' pear cultivar, it was crossed with other cultivars of which SI genotypes have already known. The result of cross-pollinations of 'Supergold' with other cultivars showed relatively high rates of fruit set from 64.5% to 91.0%, except for the cross with pollens of 'Nijisseiki' that represented only 28.8% of fruiting rate. Although sometimes the stigma of 'Supergold' crossed with 'Hayatama', 'Chojuro', and 'Nijisseiki' showed malformed pollen tube tips, 'Supergold' is generally supposed to have cross-compatibility with all other pollen donor cultivars. It is considered that the S-allele of 'Supergold' is $S_3S_4$, which is based on the result of PCR-RFLP.