• Korean Journal of Breeding Science
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• v.40 no.4
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• pp.408-413
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• 2008

Rice blast resistance is considered one of the most important traits in rice breeding and the disease, caused by Magnaporthe grisea Barr, has brought significant crop losses annually. Moreover, breakdown of resistance normally occurs in two to five years after cultivar release, thus a more durable resistance is needed for better control of this disease. We developed a new variety, Keumo3, which showed strong resistance to leaf blast. It was tested in 2003 to 2007 at fourteen blast nursery sites covering entire rice-growing regions of South Korea. It showed resistance reactions in 12 regions and moderate in 2 regions without showing susceptible reactions. Durability test by sequential planting method indicated that this variety had better resistance. Results showed that Keumo3 was incompatible against 19 blast isolates with the exception of KI101 by artificial inoculation. To understand the genetic control of blast resistance in rice cultivar Keumo3 and facilitate its utilization, recombinant inbred lines (RIL) consisting of 290 F5 lines derived from Akidagomachi/Keumo3 were analyzed and genotyped with Pizt InDel marker zt56591. The recombination value between the marker allele of zt56591 and bioassay data of blast nursery test was 1.1%. These results indicated that MAS can be applied in selecting breeding populations for blast resistance using zt56591 as DNA marker.

• Journal of Life Science
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• v.25 no.9
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• pp.1059-1071
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• 2015

Watermelon and melon are economically important Cucurbitaceae crops. Recently, the development of molecular markers based on the construction of genetic linkage maps and detection of DNA sequence variants through next generation sequencing are essential as molecular breeding strategies for crop improvement that uses marker-assisted selection and backcrossing. In this paper, we intended to provide useful information for molecular breeding of watermelon and melon by analyzing the current status of international and domestic research efforts on genomics and molecular markers. Due to diverse genetic maps constructed and the reference genome sequencing completed in the past, DNA markers that are useful for selecting important traits including yield, fruit quality, and disease resistances have been reported and publicly available. To date, more than 16 genetic maps and loci and linked markers for more than 40 traits have reported for each watermelon and melon. Furthermore, the functional genes that are responsible for those traits are being continuously discovered by high-density genetic map and map-based cloning. In addition, whole genome resequencing of various germplasm is under progress based on the reference genome. Not only by the efforts for developing novel molecular markers, but application of public marker information currently available will greatly facilitate breeding process through genomics-assisted breeding.

• Proceedings of the KSAR Conference
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• 2001.03a
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• pp.38-38
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• 2001

Spermatogonial stem cells은 sperrnatogenesis에서 중요한 역할을 하며, 곡세정관의 기저막에 위치하고 있는 것으로 알려져 있다. 그러나, 그 동안 이 세포에 특이하게 발현되는 marker가 거의 알려져 있지 않아 spermatogonial stem cell의 연구에 많은 어려움을 가져왔다. 최근 일반적인 stem cell이 갖는 특성 중, 기저막과 상호작용을 하는 surface protein으로 integrin이 존재한다는 사실을 이용하여, anti-$\alpha$$_{6}$/ 또는 anti-$\beta$$_1$ integrin항체로 germ cell을 선발하여 정소에 이식한 결과, 높은 효율로 이식세포유래의 정자발생이 가능하다는 결과가 보고되었다 (Shinohara et al., 1999). 한편, 항암제의 일종인 busulfan을 마우스에 투여(40mg/kg)한 후 4-5주가 경과하면 세정관의 기저막에 위치하는 spermatogonia를 제외하고 대부분의 생식세포는 소멸한다 본 실험의 목적은 이러한 사실들을 이용하여 spermatogonial stem cell의 특성을 밝히고, 이 생식세포를 보다 간편하고 손쉽게 선발할 수 있는 시스템을 확립하는데 있다. Busulfan처리 후 5주가 경과된 마우스와 정상적인 13주령의 마우스 testis로부터 세포를 분리한 후 FITC-conjugated anti-IgG를 이용한 면역형광법으로 측정.분석한 결과, 형광표식된 세포비율이 대조군과 비교하여 busulfan을 처리한 경우에서 유의적인 증가를 보였다.(17$\pm$3.8%. 0.7$\pm$0.3% busulfan vs control). 또한, IgG와 결합한 단백질이 존재하는 이들 세포들은 곡세정관의 기저막을 따라 위치하며, 단백질과 복합체를 형성한 IgG는 anti-Ig $G_{2a}$와 반응하지 않는다는 사실을 관찰했다. 이러한 IgG 복합체를 형성한 세포들의 특성을 이용하여, IgG와 반응을 하지 않는 것으로 확인된 이차 항체인 an1i-Ig $G_{2}$와 일차 항체인 anti-$\alpha$$_{6}$ 또는 anti-$\beta$$_1$ integrin항체를 이용하여 측정.분석하였다. Busulfan을 처리한 마우스 정소에서 분리한 세포를 다시 laminin으로 코팅된 dish에서 선발.회수해서, anti-lgG, anti-$\alpha$$_{6}$ 또는 anti-$\beta$$_1$ integrin항체로 각각 표식된 세포비율을 비교하였다. Laminin으로부터 선발.회수한 세포에서는 IgG복합체가 $\alpha$$_{6}$ 또 는 $\beta$$_1$integrin과 거의 같은 수준에서 높은 비율로 표식되었다. 결론적으로, busulfan에 의해 유도된 IgG와 결합가능한 단백질은 $\alpha$$_{6}$나 $\beta$$_1$ integrin과 마찬가지로 immunoglobulin G를 이용하여 spermatogonial stem cell의 선발을 가능하게 했다. 따라서, busulfan처리시 IgG는 미분화된 정조세포의 선발을 위한 하나의 marker로서 사용가능함을 시사한다.다.

• Journal of Life Science
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• v.18 no.9
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• pp.1225-1229
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• 2008

A total of 10 polymorphic microsatellite markers on bovine chromosome 5 were used for allelic association tests with phenotypic characteristics in Hanwoo. The data analyzed in this study were collected from 326 steers. Chi-square tests were performed to compare the frequencies of individual alleles between the high and the low breeding value groups. The following breeding values were analyzed for QTL effects. The frequency of allele 239 of DIK2828 showed a significant difference between the high and the low breeding value groups in the breeding value of marbling score (MSBV). The allele 279 of BMC1009 was found to show significant differences in allelic distribution for the breeding value of cold carcass weight (CWBV) and the breeding value of backfat thickness (BFBV) and allele 285 showed significant differences in allelic distribution for CWBV, BFBV, and MSBV. The allele 200 of DIK4329 showed significant differences in allelic distributions for the breeding values of longissimus muscle area (LMABV) and BFBV. In this study, we identified the QTL for carcass traits at around 20 (DIK2828), 41 (BMC1009) and 95 (DIK4329) cM in chromosome 5. The results provided a useful reference for further positional candidate gene research and marker-assisted selection for fat metabolism and carcass traits.

• Horticultural Science & Technology
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• v.33 no.4
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• pp.566-574
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• 2015

Yellow or transparent fruit peel color is caused by the accumulation or lack of naringenin chalcone (NG, C) in fruit peel and determines the red or pink appearance of tomato fruit, respectively. NGC biosynthesis is regulated by the SlMYB12 gene of the Y locus on chromosome 1, and DNA markers derived from SlMYB12 would be useful for marker-assisted selection (MAS) of tomato fruit color. To develop a gene-based marker, 4.9 kb of the SlMYB12 gene including a potential promoter region was sequenced from the red-fruited (YY) line 'FCR' and pink-fruited (yy) line 'FCP'. Sequence alignment of these SlMYB12 alleles revealed no sequence variations between 'FCR' and 'FCP'. To identify SlMYB12-linked single nucleotide polymorphisms (SNPs), 'FCR' and 'FCP' were genotyped using a SolCAP Tomato SNP array and CAPS markers (CAPS-456, 531, 13762, and 38123) were developed from the four SNPs (solcap_snp_sl_456, 531, 13762, and 38123) most closely flanking the SlMYB12. These CAPS markers were mapped using $F_2$ plants derived from 'FCR' ${\times}$ 'FCP'. The map positions of the fruit peel color locus (Y) were CAPS-13762 (0 cM) - 456 (11.09 cM) - Y (15.71 cM) - 38123 (17.82 cM) - 531 (30.86 cM), and the DNA sequence of SlMYB12 was physically anchored in the middle of CAPS-456 and CAPS-38123, indicating that fruit peel color in domesticated tomato is controlled by SlMYB12. A total of 64 SolCAP tomato germplasms were evaluated for their fruit peel color and SNPs located between solcap_snp_sl_456 and 38123. Seven SNPs that were detected in this interval were highly conserved for pink-fruited accessions and specific to transparent fruit peel traits, as depicted by a phenetic tree of 64 accessions based on the seven SNPs.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.55 no.3
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• pp.253-258
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• 2010

In this study, a total of 25 lines consisting of five native ginseng collections from Poonggi area, five lines from Geumsam area and 15 varieties were analyzed and clustered for the selection of Poonggi native ginseng in Korea using DNA markers. The results indicated that the long cluster distance were observed between the collections of 331002, 331004, 331005, 331007 and 331026 from Poonggi area, and the collections of 332009, 332021, 332046, 332050 and 332066 from Geumsan area because of the sensible differences on the number of leaves per stem, stem color and petiole color. Thus, the collections from Poonggi area with specific characters consisting of one stem per plant, five leaves per stem and broad elliptic leaflet shape were finely classified using nine primers including OPD05, OPD20, OPG17, OPH05 and so on. In this study, the collection of 331007 from Poonggi area was considered as the respective collection with above characters. Thus, the nine primers such as OPD05 and so on, will be used to select the Poonggi ginseng in the future studies.

• Journal of Life Science
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• v.15 no.6 s.73
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• pp.968-971
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• 2005

The Melanocortin-4 receptor gene (MC4R) regulates the energy balance and the genetic basis of obesity. A polymorphism in the porcine melanocortin-4 receptor has previously shown to be associated with growth, fat deposition and feed intake. In this study, the polymorphism of the gene was studied in several pig breeds of Duroc, Landrace, Berkshire, and Yorkshire. The results showed that the frequencies of MC4R genotype varied among those breeds. Association analyses were also performed between the MC4R polymorphism and average daily gain, feed conversion ratio, backfat thickness and lean percentage phenotypes. The results strongly support that the MC4R polymorphism can be used DNA marker selection indicator for economically important traits for pig breeding program in Korea.

• Korean Journal of Plant Resources
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• v.32 no.4
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• pp.303-311
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• 2019

Various colors of fruit skin and flesh are the most popular commercial criteria for peach classification. In order to breed new red-fleshed peach cultivar, many cross seedlings and generations should be maintained. Therefore it is necessary to develop early selection markers to screen seedlings with target traits to increase breeding efficiency. For the comparison of transcription profiles in peach cultivars differing in flesh color expression, two cDNA libraries were constructed. Differences in gene expression between red-fleshed peach cultivar, 'Josanghyeoldo' and white-fleshed peach cultivar, 'Mibaekdo' were analyzed by next-generation sequencing (NGS). Expressed sequence tag (EST) of clones from the two cultivars were selected for nucleotide sequence determination and homology searches. Putative single nucleotide polymorphisms (SNP) were screened from peach EST contigs by high resolution melting (HRM) analysis displayed specific difference between 8 red-fleshed peach cultivars and 24 white-fleshed peach cultivars. All 72 pairs of SNPs were discriminated and the HRM profiles of amplicons were established. In the study reported here, the development of SNP markers for distinguishing between red and white fleshed peach cultivars by HRM analysis offers the opportunity to use DNA markers. This SNP marker could be useful for peach marker assisted breeding and provide a good reference for relevant research on molecular mechanisms of color variation in peach cultivars.

• Korean Journal of Breeding Science
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• v.41 no.4
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• pp.474-481
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• 2009

The purpose of this study was to identify the quantitative trait loci (QTL) associated with gel consistency (GC), and to evaluate the relationships between GC and physico-chemical properties related to eating quality in rice. A total of 120 doubled haploid (DH) lines derived from a cross between 'Samgang' and 'Nagdong' and 26 varieties were used for this study. The 120 DH lines were divided into four groups, soft (61~100 mm), medium (41~60 mm), hard (26~40 mm) and whole population, according to the gel length. A negative correlation between GC and amylose content was observed only in the soft group. The GC negatively correlated with lipid content in the medium, and the whole population, but positively correlated with lipid content in the soft group. The positive correlation between GC and protein content was observed in the soft group, while negative correlations were observed in the medium group and the whole population. Two significant QTLs regarding GC were detected on chromosomes 4 and 11. They collectively explained 23% of phenotypic variation with LOD score of 3.1 and 2.9, respectively. The DNA markers of S4026 and RM287 were tightly linked to GC in the DH population and 26 varieties, respectively.

• Plant Breeding and Biotechnology
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• v.6 no.4
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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.