• Horticultural Science & Technology
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• v.30 no.1
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• pp.64-72
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• 2012

Phytophthora root rot has been causing a serious yield loss in pepper production. Since 2004, the year in which commercial cultivars resistant to the disease were firstly commercialized, it has been necessary to introduce the resistance into domestic pepper cultivars for dried red pepper. Therefore, developing molecular markers linked to the resistance is required for an accurate selection of resistant plants and increasing breeding efficiency. Until now, several markers associated with the major dominant gene resistant to Phytophthora root rot have been reported but they have some serious limitations for their usage. In this study, we aimed to develop molecular markers linked to the major dominant gene that can be used for almost of all genetic resources resistant to Phytophthora root rot. Two segregating $F_2$ populations derived from a 'Subicho' ${\times}$ 'CM334' combination and a commercial cultivar 'Dokyacheongcheong' were used to develop molecular markers associated with the resistance. After screening 1,024 AFLP primer combinations with bulked segregant analysis, three AFLP (AFLP1, AFLP2, and AFLP3) markers were identified and converted into three CAPS markers (M1-CAPS, M2-CAPS, and M3-CAPS), respectively. Among them, M3-CAPS marker was further studied in ten resistants, fourteen susceptibles, five hybrids and 53 commercial cultivars. As a result, M3-CAPS marker was more fitted to identify Phytophthora resistance than previously reported P5-SNAP and Phyto5.2-SCAR markers. The result indicated that the M3-CAPS marker will be useful for resistance breeding to Phytophthora root rot in chili pepper.

• Horticultural Science & Technology
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• v.31 no.2
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• pp.219-223
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• 2013

DNA markers can determine the genotype of many species. Single nucleotide polymorphism (SNP) detection is difficult without sequencing but it becomes easier with sdCAPS method. Here an experiment was performed for developing molecular markers using two SNPs, CSatpB-SNP and CSycf1-SNP, of chloroplast in cucumber plants. Properly designed primers with nucleotide sequences for restriction enzymes proved success of PCR and efficacy of digestion by the restriction enzymes. Then these markers were used to study the genotyping of cucumber breeding lines and cultivars obtained from various sources in respect of their chilling stress response. We confirmed that a U.S. cucumber line, 'NC76' known to possess a nuclear factor for the chilling tolerance showed the chloroplast genotypes related to chilling tolerance. However all Korean cucumber cultivars tested in this study showed the chloroplast genotypes related to chilling susceptibility. In conclusion, to develop chilling tolerant cucumber, both maternal and a nuclear factors related to chilling tolerance should be transferred from 'NC76' when 'NC76' is used as a female source and other elite lines as recurrent parents.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.10a
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• pp.220-220
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• 2017

• Proceedings of the Korean Society of Crop Science Conference
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• 2020.06a
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• pp.133-133
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• 2020

• Horticultural Science & Technology
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• v.30 no.3
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• pp.286-293
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• 2012

The resistance to Tobamovirus in Capsicum spp. has been known to be controlled by five different alleles ($L^0$, $L^1$, $L^2$, $L^3$, and $L^4$) of L locus on the telomere of long arm of pepper chromosome 11. To develop a set of molecular markers differentiating all the alleles of L locus, we used five pepper differential hosts including Capsicum annuum Early California Wonder (ECW, $L^0L^0$), C. annuum Tisana ($L^1L^1$), C. annuum Criollo de Morelos 334 (CM334, $L^2L^2$), Capsicum chinense PI 159236 ($L^3L^3$), and Capsicum chacoense PI 260429 ($L^4L^4$). Developing a series of CAPS or SCAR markers specifically linked to the alleles was allowed by the sequence comparison of PCR amplicons of the $L^3$-linked markers (189D23M, A339, and 253A1R) and BAC sequences (FJ597539 and FJ597541) in the pepper differentials. Genotypes deduced by these markers in 48 out of 53 $F_1$ hybrids of commercial pepper varieties were consistent with their phenotypes by bioassay using Tobamovirus pathotypes ($P_0$, $P_1$, and $P_{1,2$). Consequently, these markers can be useful to differentiate L alleles and for breeding Tobamovirus resistance in pepper with marker-assisted selection.

• Horticultural Science & Technology
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• v.35 no.1
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• pp.108-120
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• 2017

Modern watermelon cultivars (Citrullus lanatus [Thunb.] Matsum.& Nakai var. lanatus) have fruits with diverse phenotypes, including fruit shape, rind patterns, and flesh color. Molecular markers enable efficient selection of plants harboring desirable phenotypes. In the present study, publicly available DNA markers tightly linked to fruit shape, rind stripe pattern, and flesh color were evaluated using 85 watermelon accessions with diverse fruit phenotypes. For fruit shape, the dCAPS SUN - Cla011257 marker revealed an 81% of marker - trait match for accessions with elongated or round fruits. For rind stripe pattern, the SCAR wsb6-11marker was effective for selecting Jubilee-type rind pattern from other rind patterns. For flesh color, the Clcyb.600 and Lcyb markers derived from a mutation in the Lycopene ${\beta}$ - cyclase (Lcyb) gene, were effective at selecting red or yellow flesh. Forty-eight accessions possessing diverse fruit - related traits were selected as a reference array and their genetic relationships assessed using 16 SSR markers. At a coefficient of 0.11, the 48 accessions grouped into two major clades: Clade I and Clade II. Clade I subdivided further into subclades I - 1 and I - 2 at a coefficient of 0.39. All accessions with colored flesh were classified into Clade I, whereas those with white - flesh were classified into Clade II. Differences in fruit traits between subclades I - 1 and I - 2 were observed for rind pattern and fruit color; a majority of the accessions with Crimson-type striped or non-striped rind were grouped together in subclade I - 1, while most accessions in subclade I - 2 had a Jubilee - type rind stripe pattern. These results imply that reference array watermelon accessions possess distinguishable genetic structure based on rind stripe pattern. However, no significant grouping pattern was observed based on other fruit-related traits.

• Horticultural Science & Technology
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• v.31 no.1
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• pp.72-79
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• 2013

Inactivation of the gene coding for dihydroflavonol 4-reductase (DFR) is responsible for the color difference between red and yellow onions (Allium cepa L.). Two inactive DFR-A alleles, DFR-$A^{PS}$ and DFR-$A^{DEL}$, were identified in our previous study. A functional marker was developed on the basis of the premature stop codon that inactivated the DFR-$A^{PS}$ allele. A derived cleaved amplified polymorphic sequences (dCAPS) primer was designed to detect the single nucleotide polymorphism, an A/T transition, which produced the premature stop codon. Digested PCR products clearly distinguished the homozygous and heterozygous red $F_2$ individuals. Meanwhile, to develop a molecular marker for detection of the DFR-$A^{DEL}$ allele in which entire DFR-A gene was deleted, genome walking was performed and approximately 3 kb 5' and 3' flanking sequences of the DFR-$A^R$ coding region were obtained. PCR amplification using multiple primers binding to the extended flanking regions showed that more of the extended region of the DFR-A gene was deleted in the DFR-$A^{DEL}$ allele. A dominant simple PCR marker was developed to identify the DFR-$A^{DEL}$ allele using the dissimilar 3' flanking sequences of the DFR-A gene and homologous DFR-B pseudogene. Distribution of the DFR-$A^{PS}$ and DFR-$A^{DEL}$ alleles in yellow onion cultivars bred in Korea and Japan was surveyed using molecular makers developed in this study. Results showed predominant existence of the DFR-$A^{PS}$ allele in yellow onion cultivars.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2018.04a
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• pp.56-56
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• 2018

토마토에서 과형은 과실의 여러 가지 형질 중에서 눈에 가장 잘 띄는 형질이며, 소비자의 토마토를 구매를 결정하는데 많은 영향을 미치는 중요한 형질이다. 토마토의 과형을 결정하는 여러 가지 유전자 중에 OVATE는 둥근 토마토 과일을 서양 배 모양(pear shape)의 과일로 전환하는데 결정적인 역할을 하는 유전자이다. OVATE 유전자에 의해서 과일의 모양이 변하는 것은 조기종결 코돈을 초래하는 열성 돌연변이에 의해서 유도되며, 단백질의 C-말단 영역이 제거됨에 따라 그 기능을 상실하여 나타나는 현상이다. OVATE 유전자는 주로 식물의 생식기관에서 발현되며, 꽃에서는 개악하기 10일전부터부터 전사체가 만들어지고 발달중인 과실에서는 개약 후 8일까지 전사체를 확인할 수 있다. 토마토 분자육종 과정에서 과형 판별을 위해서 OVATE 유전자 연관 분자표지는 보고된 바 있으나 OVATE 유전자 유래 분자표지는 보고된바가 없다. 본 연구에서 국내에서 육성된 육종 라인들의 resequencing을 통해 OVATE 유전자 염기서열간의 SNP를 발견하고 이들을 dCAPS 마커로 전환하여 분자표지를 개발했다. 이러한 분자표지는 둥근 토마토(round)와 서양 배모양(pear shape)토마토 육종 프로그램의 효율성과 정확성을 향상시키는데 활용할 수 있을 것으로 기대한다.

• Journal of Ginseng Research
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• v.44 no.1
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• pp.135-144
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• 2020

Background: Panax species are important herbal medicinal plants in the Araliaceae family. Recently, we reported the complete chloroplast genomes and 45S nuclear ribosomal DNA sequences from seven Panax species, two (P. quinquefolius and P. trifolius) from North America and five (P. ginseng, P. notoginseng, P. japonicus, P. vietnamensis, and P. stipuleanatus) from Asia. Methods: We conducted phylogenetic analysis of these chloroplast sequences with 12 other Araliaceae species and comprehensive comparative analysis among the seven Panax whole chloroplast genomes. Results: We identified 1,128 single nucleotide polymorphisms (SNP) in coding gene sequences, distributed among 72 of the 79 protein-coding genes in the chloroplast genomes of the seven Panax species. The other seven genes (including psaJ, psbN, rpl23, psbF, psbL, rps18, and rps7) were identical among the Panax species. We also discovered that 12 large chloroplast genome fragments were transferred into the mitochondrial genome based on sharing of more than 90% sequence similarity. The total size of transferred fragments was 60,331 bp, corresponding to approximately 38.6% of chloroplast genome. We developed 18 SNP markers from the chloroplast genic coding sequence regions that were not similar to regions in the mitochondrial genome. These markers included two or three species-specific markers for each species and can be used to authenticate all the seven Panax species from the others. Conclusion: The comparative analysis of chloroplast genomes from seven Panax species elucidated their genetic diversity and evolutionary relationships, and 18 species-specific markers were able to discriminate among these species, thereby furthering efforts to protect the ginseng industry from economically motivated adulteration.