• Journal of Life Science
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• v.14 no.3
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• pp.521-524
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• 2004

This experiment was carried out to analyze genetic characteristics and to develop the breed specific DNA marker for Cheju-native horse. If this marker contains high repetitive sequences, it is possible to convert a RAPD marker of interest into a single-locus PCR marker called a sequence characterized amplified region(SCAR). Twenty six Cheju-native horse and Fifty thoroughbred genomic DNA were pooled and PCR. were accomplished using 800 random primers. Comparing the pooled DNA from Cheju-native horse and thoroughbred, we found 9 primers which identified markers present in the pooled DNA from breed but absent in the other breed. Among 9 random primers, 6 primers were thoroughbred specific and 3 primers were Cheju-native horse specific. Testing individual horse revealed that 5 marker showed the similar band pattern between Cheju-native horse and Thoroughbred. However, 4 marker were wholly absent in breed while present in the other breed. UBC $126_{3500bp}$, UBC $162_{500bp}$, and UBC $244_{1200bp}$ was detected only Thoroughbred and UBC $562_{560bp}$was detected Cheju-native horse, respectively. After determining of the cloned breed-specific fragment sequence, we designed the SCAR-primers and carried out PCR. Compared to random primer, RAPD-SCAR primer didn't show significantly higher specific band. However, RAPD analysis is useful for genetic characterization of Cheju-native horse.

• 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.

• 한국약용작물학회:학술대회논문집
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• 2008.05a
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• pp.296-297
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• 2008

• BMB Reports
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• v.39 no.1
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• pp.37-45
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• 2006

Bulked segregant analysis (BSA) and AFLP were used for isolation of genomic sex determination markers in Penaeus monodon. A total of 256 primer combinations were tested against 6-10 bulked genomic DNA of P. monodon. Five and one candidate female- and male-specific AFLP fragments were identified. Female-specific fragments were cloned and further characterized. SCAR markers derived from FE10M9520, FE10M10725.1, FE10M10725.2 and FE14M16340 provided the positive amplification product in both male and female P. monodon. Further analysis of these markers using SSCP and genome walk analysis indicated that they were not sex-linked. In addition, sex-specific (or differential) expression markers in ovaries and testes of P. monodon were analyzed by RAP-PCR (150 primer combinations). Twenty-one and fourteen RAP-PCR fragments specifically/differentially expressed in ovaries and testes of P. monodon were successfully cloned and sequenced. Expression patterns of 25 transcripts were tested against the first stranded cDNA of ovaries and testes of 3-month-old and broodstock-sized P. monodon (N = 5 and N = 7 - 10 for females and N = 4 and N = 5 - 7 for males, respectively). Five (FI-4, FI-44, FIII-4, FIII-39 and FIII-58) and two (M457-A01 and MII-51) derived RAP-PCR markers revealed female- and male-specific expression patterns in P. monodon. Surprisingly, MII-5 originally found in testes showed a higher expression level in ovaries than did testes of juvenile shrimps but a temporal female-specific pattern in P. monodon adults.

• Proceedings of the Korean Society of Crop Science Conference
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• 2007.11a
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• pp.229.2-229.2
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• 2007

• Journal of Life Science
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• v.21 no.12
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• pp.1659-1665
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• 2011

In Citrus, an $F_1$ segregation population of 150 plants was constructed from a cross between 'Kiyomi' (C. unshiu ${\times}$ C. sinensis) carrying the male sterility trait and 'Jinkyool' (C. sunki). Sequence-related amplification polymorphism (SRAP) combined with bulked segregant analysis was used to develop markers linked to male fertility. In the $F_1$ population, 66 out of 150 seedlings had aborted anthers and the ratio of male sterile plants to fertile plants in the progenies matched the expected Mendelian segregation ratio of 1:1 ($x^2$ =2.16 at p=0.05). From the profiling of the 197 SRAP primer sets, three SRAP primer sets (F4/R27, F39/R60, and F15/R37) that were closely linked to the target trait were identified and successfully converted into a sequence characterized amplified region (SCAR) marker for selection of male fertility in citrus. The SCAR marker, using the pMS 33U/pMS 1462L primer set specifically, produced a single 1.4-Kb fragment that was linked to male fertility. Our results suggested that this SCAR marker can be useful for marker-assisted selection of male sterile individuals in breeding $F_1$ progenies in Citrus.

• Horticultural Science & Technology
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• v.29 no.1
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• pp.53-60
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• 2011

Cytoplasmic male sterility (CMS) induced by mutant mitochondria genome, has been used for commercial seed production of $F_1$ hybrid cultivars in diverse crops. In pepper (Capsicum annuum L.), two sterile cytoplasm specific gene organization, atp6-2 and coxII were identified. An open reading frame, orf456 nearby coxII gene has been speculated to induce male sterility (MS) by mutagenic analysis. Moreover, molecular markers for atp6-2 and coxII of mitochondrial genotype (mitotype) were developed. However, the Cytoplasmic MS specific markers, atp6SCAR and coxIISCAR markers appeared in both N and S cytoplasms when polymerase chain reaction (PCR) cycles prolonged more than 40 cycles. Since the reported molecular markers were dominant markers, the presence of the faint sterile-specific band in normal cytoplasm may lead to the mis-classification of pepper breeding lines. To solve this problem, one common forward primer and two different reverse primers specific to normal coxII and sterile orf456 genes were designed after analyzing their gene organizations. By using these three primers, N and S coxII specific bands were co-amplified in male-sterile lines, but only normal coxII specific band was amplified in maintainer lines. Since the reverse primer for sterile coxII was specifically designed 275 bp downstream of orf456, relatively stable PCR amplification patterns were observed regardless of the number of PCR cycles. These primer sets easily identified different mitotypes among the divergent breeding lines, commercial cultivars and diverse germplasms.

• Journal of Life Science
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• v.15 no.3 s.70
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• pp.474-478
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• 2005

This study was conducted to analyze genetic characteristics and to develop the specific marker for Cheju native horse (Coo) at the level of sequence characterized amplified regions (SCARs). We collected blood samples from Cheju native horse and Thoroughbred horse (Th) and obtained genomic DNA from the blood of 50 individuals randomly selected within the breeds. Seven hundred primers were chosen randomly and were used to examin the polymorphism and 40 kinds of primers showed polymorphic RAPD band patterns between two breeds. Thirty primers of them showed horse specific bands. With the primer MG 30, amplified band of 2.0 kb showed the specificity to Cheju native horse (Cnh). Additionally MG 53 detected the thoroughbred horse (Th) specific markers at size of 2.3 kb. As the next, 2.3 kb band from MG 53 was checked with the all individuals from all the breeds of this study, and it maintained the reproducible breed specificity to thoroughbred horse (Th). With this results, 2.3 kb band was cloned into plasmid vector and sequenced bidirectionally from both ends of the cloned fragment. With the obtained sequences 10 nucleotide extended primers including the original arbitray primer were designed as a SCARs primer. Finally, the primer with extended sequence showed the reproducible breed differentiation pattern and it was possible to identify Cheju native horse (Cnh) from other breeds. The SCARs marker 2.3 kb from MG 53 could be used to identify Cheju native horse (Cnh) for not only registration but also horse breeding programe.

• 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.

• BMB Reports
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• v.37 no.2
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• pp.213-222
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• 2004

A randomly amplified polymorphic DNA (RAPD) analysis was used to identify the species- and population-specific markers of abalone; Haliotis asinina, H. ovina, and H. varia in Thai waters. Fifteen species-specific and six population-specific RAPD markers were identified. In addition, an 1650 bp band (UBC195) that was restricted to H. ovina from the Gulf of Thailand (east) was also found. All of the specific RAPD markers were cloned and sequenced. Twenty pairs of primers were designed and specificity-tested (N = 12 and 4 for target and non-target species, respectively). Seven primer pairs (CUHA1, 2, 4, 11, 12, 13, and 14) were specifically amplified by H. asinina DNA, whereas a single pair of primers showed specificity with H. ovina (CUHO3) and H. varia (CUHV1), respectively. Four primer pairs, including CUHA2, CUHA12, CUHO3, and CUHV1, were further examined against 216 individuals of abalone (N = 111, 73, and 32, respectively). Results indicated the species-specific nature of all of them, except CUHO3, with the sensitivity of detection of 100 pg and 20 pg of the target DNA template for CUHA2 and CUHA12 and CUHV1, respectively. The species-origin of the frozen, ethanol-preserved, dried, and boiled H. asinina specimens could also be successfully identified by CUHA2.