• Journal of Crop Science and Biotechnology
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• v.11 no.2
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• pp.83-90
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• 2008

Two hundred and sixty Korean soybean landrace accessions were analyzed for polymorphism at 92 simple sequence repeat(SSR) loci. The 995 identified alleles served as raw data for estimating genetic diversity and population structure. The number of alleles at a locus ranged from three to 27 with a mean of 10.4 alleles per locus. $F_{ST}$ values estimated by analysis of molecular variance(AMOVA) using SSR data set were 0.018, 0.027, and 0.016 for usage, collection site and maturity groups, respectively, indicating little genetic differentiation. The model-based clustering analysis placed the accessions into three clusters(K=3) with 0.0503 of $F_{ST}$, indicating moderate genetic differentiation. Duncan's Multiple Range Test at K = 3 on the basis of 18 quantitative traits revealed that one cluster was mainly differentiated from the other two clusters by seed related traits and the other two clusters were differentiated from each other by biochemical traits. Genetic structure of Korean soybean landraces was differentiated by model-based clustering and supported by their phenotypic traits in part. This preliminary study could be the first step towards more efficient germplasm management and utilization of soybean landraces and helpful in association studies between genotypic and phenotypic traits in Korean soybean landraces.

• Proceedings of the Korea Society of Poultry Science Conference
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• 2005.11a
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• pp.68-69
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• 2005

To identify germline chimeric chicken using germ cell transplantation method, the testcross, spends much time, labor and cost to perform, is the only way for distinguishing germline chimeric chicken from normal one And to enhance the method, development of breed-specific molecular markers have been needed. We have just identified breed-specific sequence polymorphisms among Barred Plymouth rock, Korean Ogol Chicken and White Leghorn in PMEL17 and MC1R gene the loci of which are identical to dominant white and extended black loci. These sequence polymorphism will be very useful for screening germline chimera.

• Korean Journal of Plant Resources
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• v.24 no.3
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• pp.272-279
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• 2011

It is very crucial to evaluate the genetic diversity of peanut genetic resources for identification of peanut germplasm accessions and variety improvement. Cultivated peanut generally has two subspecies, hypogaea and fastigiata. In this study, we identified peanut into three plant types, virginia (var. hypogaea), spanish (var. vulgaris), and valencia (var. fastigiata). Former one belongs to ssp. hypogaea and latter two are involved in ssp. fastigiata. Twenty SSR markers were used to assess the genetic variation of three sets, hypogaea, vulgaris, and fastigiata, respectively. Out of variety-specific SSR primers tried in this study, ten pairs of SSR primers showed polymorphisms. Each accession could be identified by a specific set of polymorphic SSR primers, and allele number was evaluated among accessions, with an average of 6.7 in var. hypogaea and 5.4 in var. vulgaris and fastigiata. For evaluation of genetic diversity, gene diversity ranged from 0.336 to 0.844 and PIC (polymorphism information contents) ranged from 0.324 to 0.827 were investigated. Dendrograms based on genetic distances were constructed, which showed the existence of three different clusters. And these three different clusters might be associated with the genes involved in three plant types. The results also suggested that there were plentiful SSR polymorphisms among peanut germplasm accessions in RDA (Rural Development Administration, Korea) Genebank and SSRs might play an important role in evaluating peanut accessions and cultivar improvement.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.106-106
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• 2017

The soybean [Glycine max (L.) Merr.] is one of the most important crop resources worldwide as food and forage. It is also important and valuable that to hold crop resources to have high genetic diversities. Recently, a core collection has been constructed in many plants to preserve the genetic resources of various plants. A core collection is small population to represent the genetic diversity of the total collection, and is of strategic importance as they allow the use of a small part of a germplasm collection that is representative of the total collection. Here, we developed the core collection consisting of 816 accessions by using approximately 180,000 (180K) single nucleotide polymorphisms (SNPs) developed in previous study. In addition, we performed genetic diversity and population structure analysis to construct the core collection from entire 4,392 collections. there were excluded sample call rates less than 93% and duplicated samples more than 99.9% according to genotype analysis using 180K SNPs from entire collections. Furthermore, we were also excluded natural hybrid resources which Glycine max and Glycine soja are mixed in half through population structure analysis. As a result, we are constructed the core collection of genetic diversity that reflects 99% of the entire collections, including 430 cultivated soybeans (Glycine max) and 386 wild soybeans (Glycine soja). The core collection developed in this study should be to provide useful materials for both soybean breeding programs and genome-wide association studies.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.4
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• pp.564-570
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• 2016

The Sal-like 1 gene (Sall1) is essential for kidney development, and mutations in this gene result in abnormalities in the kidneys. Mice lacking Sall1 show agenesis or severe dysgenesis of the kidneys. In a recent study, blastocyst complementation was used to develop mice and pigs with exogenic organs. In the present study, transcription activator-like effector nuclease (TALEN)-mediated homologous recombination was used to produce Sall1-knockout porcine fibroblasts for developing knockout pigs. The vector targeting the Sall1 locus included a 5.5-kb 5' arm, 1.8-kb 3' arm, and a neomycin resistance gene as a positive selection marker. The knockout vector and TALEN were introduced into porcine fibroblasts by electroporation. Antibiotic selection was performed over 11 days by using $300{\mu}g/mL$ G418. DNA of cells from G418-resistant colonies was amplified using polymerase chain reaction (PCR) to confirm the presence of fragments corresponding to the 3' and 5' arms of Sall1. Further, mono- and bi-allelic knockout cells were isolated and analyzed using PCR-restriction fragment length polymorphism. The results of our study indicated that TALEN-mediated homologous recombination induced bi-allelic knockout of the endogenous gene.

• Korean Journal of Breeding Science
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• v.43 no.4
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• pp.322-329
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• 2011

Microsatellite markers were utilized to investigate genetic diversity among 70 Korean barley varieties (Hordeum vulgare). Ninety nine microsatellite primer pairs were screened for 9 varieties. Twenty primer pairs showed highly polymorphic. The relationship between markers genotypes and 70 varieties was analyzed. A total of 124 polymorphic amplified fragments were obtained by using 20 microsatellite markers. Two to nine SSR alleles were detected for each locus with an average of 6.2 alleles per locus. Average polymorphism information content (PIC) was 0.734, ranging from 0.498 to 0.882. A total of 124 marker loci were used to calculate Jaccard's distance coefficients for cluster analysis using UPGMA. Clustering group was divided 2 groups corresponding to 2-rowed and 6-rowed barley varieties. The phenogram was discriminated all varieties by markers genotypes. These markers may be used wide range of practical application in variety identification and genetic purity assessment of barley.

• Animal Bioscience
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• v.34 no.8
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• pp.1283-1289
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• 2021

Objective: The progestogen-associated endometrial protein (PAEP) gene encodes the main whey protein in milk, β-lactoglobulin. The aim of the study was to investigate polymorphism in the PAEP gene and its association with milk yield, composition, and quality. Methods: Test-day records for 782 dairy cows were analysed. A total of 10 single nucleotide polymorphisms (SNP) within the PAEP gene were investigated. The following parameters were recorded: milk yield (MY, kg/d), percent milk fat (%), protein (PP, %), dry matter (DMP, %) and lactose (LP, %), urea content (UC, mg/L) as well as natural logarithm for somatic cell count (LnSCC, ln). Effect on genomic estimated breeding values accuracy was evaluated with pedigree and single step model. Results: Results show that only three SNPs were polymorphic, creating 5 composite genotypes: P1 to P5. Differences in MY between composite genotypes were noted in the two tested herds. Cows with P5 composite genotypes were characterised by the highest PP and LnSCC and the lowest LP and UC (p<0.05). P4 was linked to an increased DMP and UC, while P3 to an increase in LP and decrease in PP and LnSCC. Both factors are important markers in herd management and have high influences on the herds economics. For 5 out of 7 traits the accuracy of prediction was improved by including the haplotype as a fixed effect. Conclusion: Presented results may suggest a new way to optimise breeding programmes and demonstrate the impact of using genomic data during that process.

• Childhood Kidney Diseases
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• v.9 no.2
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• pp.175-182
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• 2005

Purpose : Interleukin 1 receptor antagonist(IL-1ra) is an endogenous antiinflammatory agent that binds to IL-1 receptor and thus competitively inhibits the binding of IL-1$\alpha$ and IL-1$\beta$. Allele 2 in association with various autoimmune diseases has been reported. In order to evaluate the influence of IL-1ra gene VNTR polymorphism on the susceptibility to HSP and its possible association with disease severity, manifested by severe renal involvement and renal sequelae, we studied the incidence of carriage rate and allele frequency of the 2 repeats of IL-1ra allele 2($IL1RN^{*}2$) of the IL-1ra gene in children with HSP with and without renal involvement. Methods : The IL-1ra gene polymorphisms were determined in children with HSP with(n=40) or without nephritis(n=34) who had been diagnosed at Busan Paik Hospital and the control groups(n=163). Gene polymorphism was identified by PCR amplification of the genomic DNA. Results : The allelic frequency and carriage rate of $IL1RN^{*}1$ were found most frequently in patients with HSP and in controls. The allelic frequency of $IL1RN^{*}2$ was higher in patients with HSP compared to that of controls($4.7\%\;vs.\;2.5\%$, P=0.794). The carriage rate of $IL1RN^{*}2$ was higher In patients with HSP compared to that of controls($8.1\%\;vs.\;6.8\%$, P=0.916). The allelic frequency of $IL1RN^{*}2$ was higher in patients with HSP nephritis compared to that of HSP($5.3\%\;vs.\;2.9\%$, P=0.356). The carriage rate of $IL1RN^{*}2$ was higher in Patients with HSP nephritis compared to that of HSP($10.0\%\;vs.\;5.9\%$, P=0.523). Among 13 patients with heavy proteinuria(>1.0 g), 11 had $IL1RN^{*}1$, 1 had $IL1RN^{*}2$ and the others had $IL1RN^{*}4$. At the time of last follow up 4 patients had sustained proteinuria and their genotype was $IL1RN^{*}1$. Conclusion : The allelic frequency and carriage rate of $IL1RN^{*}1$ were found most frequently in patients with HSP and in controls. Our study suggests that the carriage rate and allele frequency of the 2-repeats of IL-1lra allele 2($IL1RN^{*}2$) of the IL-1ra gene may not be associated with susceptibility and severity of renal involvement in children with HSP (J Korean Soc Pediatr Nephrol 2005;9:175-182)

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.11
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• pp.1542-1547
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• 2005

The Melanocortin-4 Receptor (MC4R) and Insulin-like Growth Factor 2 (IGF2) are two important candidate genes related to fat deposition and carcass traits. MC4R was found on study on human obesity and then was studied as candidate gene affecting food intake and fat deposition traits in mice and pigs. Insulin-like Growth Factor 2 (IGF2) gene plays an important role on tumor cell proliferation and muscle growth. It also affects fat traits and live weight in pigs. In this paper, MC4R and IGF2 were studied as two candidate genes associated with important economic traits such as fat deposition and carcass traits in five different pig populations. Taq I-PCR-RFLP and Bcn I-PCR-RFLP were respectively used to detect the polymorphism of genotypes of MC4R and IGF2 genes. Different MC4R genotype frequencies were observed in four populations. IGF2 genotype frequencies were also different in two populations. The results of association analysis show both MC4R and IGF2 genes were significantly associated with fat deposition and carcass traits in about 300 pigs. This work will add new evidence of MC4R and IGF2 affecting fat deposition and carcass traits in pigs and show that two genes can be used as important candidate genes for marker assistant selection (MAS) of growth and lean meat percentage in pigs.

• Horticultural Science & Technology
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• v.31 no.4
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• pp.473-482
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• 2013

Molecular markers, as an efficient selection tool, have been and is being used for practical breeding program in chili pepper (Capsicum annuum L.). Recently, a lot of researches on inheritance and genetic analysis for quantitative traits including capsaicinoids, carotenoids, and sugar content in pepper are being performed worldwide. It has been also reported that QTL mapping is a necessary tool to develop molecular markers associated with the quantitative traits. In this study, we suggested a new method to construct a pepper genetic map using SNP (HRM) markers generated from NGS resequencing of female and male parents. Plant materials were C. annuum 'NB1' (female parent), C. chinense 'Jolokia' (male parent), and their $F_2$ population consisting of 94 progenies. Sequences of 4.6 Gbp and 6.2 Gbp were obtained from NGS resequencing of 'NB1' and 'Jolokia', respectively. Totally, 4.29 million SNPs between 'NB1' and 'Jolokia' were detected and the 1.76 million SNPs were clearly identified. Among them, total 145 SNP (HRM) primer pairs covering pepper genetic map were selected, and the 116 SNP (HRM) markers of them were located on this map. Total distance of the map, which consisted of 12 linkage groups and matched with basic chromosome numbers of pepper, was 1,167.9 cM. According to the mapping result, we concluded that our mapping method was suitable to construct a pepper genetic map fast and accurately. In addition, the genetic map could be directly used for QTL analysis of traits different between both parents.