• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.188-188
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• 2017

Rice (Oryza sativa L.) is one of the major crops that is seriously impacted by global soil salinization. Rice is among those crops where most of the high-yielding cultivars are highly sensitive to salinity. The key to a plant survival under NaCl salt stress is by maintaining a high $K^+/Na^+$ ratio in its cells. Selection for salinity tolerance genotypes of rice based on phenotypic performance alone is less reliable and will delay in progress in breeding. Recent advent of molecular markers, microsatellites or simple sequence repeats (SSRs) were used to find out salt tolerant rice genotypes. In the current experiment phenotyping and genotyping studies were correlated to differentiate different rice accessions for salinity tolerance. Eight rice accessions along with check plant Dongjin were screened by physiological studies using Yoshida solution with 50mM NaCl stress condition. The physiology studies identified four tolerant and four susceptible accessions based on their potassium concentration, sodium concentration, $K^+/Na^+$ ratio and biomass. 17 SSR markers were used to evaluate these rice accessions for salt tolerance out of which five molecular markers were able to discriminate tolerant accessions from the susceptible accessions. Banding pattern of the accessions was scored comparing to the banding pattern of Dongjin. The study identifies accessions based on their association of $K^+/Na^+$ ratio with molecular markers which is very reliable. These markers identified can play a significant role in screening large set of rice accessions for salt tolerance; these markers can be utilized to improve salt tolerance of commercial rice varieties with marker-assisted selection (MAS) approach.

• 한국발생생물학회지:발생과생식
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• 제18권4호
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• pp.275-286
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• 2014

To successful molecular breeding, identification and functional characterization of breeding related genes and development of molecular breeding techniques using DNA markers are essential. Although the development of a useful marker is difficult in the aspect of time, cost and effort, many markers are being developed to be used in molecular breeding and developed markers have been used in many fields. Single nucleotide polymorphisms (SNPs) markers were widely used for genomic research and breeding, but has hardly been validated for screening functional genes in olive flounder. We identified single nucleotide polymorphisms (SNPs) from expressed sequence tag (EST) database in olive flounder; out of a total 4,327 ESTs, 693 contigs and 514 SNPs were detected in total EST, and these substitutions include 297 transitions and 217 transversions. As a result, 144 SNP markers were developed on the basis of 514 SNP to selection of useful gene region, and then applied to each of eight wild and culture olive flounder (total 16 samples). In our experimental result, only 32 markers had detected polymorphism in sample, also identified 21 transitions and 11 transversions, whereas indel was not detected in polymorphic SNPs. Heterozygosity of wild and cultured olive flounder using the 32 SNP markers is 0.34 and 0.29, respectively. In conclusion, we identified SNP and polymorphism in olive flounder using newly designed marker, it supports that developed markers are suitable for SNP detection and diversity analysis in olive flounder. The outcome of this study can be basic data for researches for immunity gene and characteristic with SNP.

• Genomics & Informatics
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• 제3권2호
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• pp.77-80
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• 2005

Targeting of complex system such as human cells rather than biochemically pure molecules will be a useful approach to massively identify ligands specific for the markers associated with human disease such as cancer and simultaneously discover the specific molecular markers. In this study, we developed in vitro selection method to identify nuclease-resistant nucleic acid ligands called RNA aptamers that are specific for human cancer cells. This method is based on the combination of the cell-based selection and subtractive systematic evolution of ligands by exponential enrichment (SELEX) method. These aptamers will be useful for cancer-specific ligands for proteomic research to identify cancer-specific molecular markers as well as tumor diagnosis and therapy.

• The Plant Pathology Journal
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• 제34권6호
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• pp.506-513
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• 2018

Clubroot is one of the most economically important diseases of the Brassicaceae family. Clubroot disease is caused by the obligate parasite Plasmodiophora brassicae, which is difficult to study because it is nonculturable in the laboratory and its races are genetically variable worldwide. In Korea, there are at least five races that belongs to four pathotype groups. A recent study conducted in Korea attempted to develop molecular markers based on ribosomal DNA polymorphism to detect P. brassicae isolates, but none of those markers was either race-specific or pathotype-specific. Our current study aimed to develop race- and isolate-specific markers by exploiting genomic sequence variations. A total of 119 markers were developed based on unique variation exists in genomic sequences of each of the races. Only 12 markers were able to detect P. brassicae strains of each isolate or race. Ycheon14 markers was specific to isolates of race 2, Yeoncheon and Hoengseong. Ycheon9 and Ycheon10 markers were specific to Yeoncheon isolate (race 2, pathotype 3), ZJ1-3, ZJ1-4 and ZJ1-5 markers were specific to Haenam2 (race 4) isolate, ZJ1-35, ZJ1-40, ZJ1-41 and ZJ1-49 markers were specific to Hoengseong isolate and ZJ1-56 and ZJ1-64 markers were specific to Pyeongchang isolate (race 4, pathotype 3). The PCR-based sequence characterized amplified region (SCAR) markers developed in this study are able to detect five Korean isolates of P. brassicae. These markers can be utilized in identifying four Korean P. brassicae isolates from different regions. Additional effort is required to develop race- and isolate-specific markers for the remaining Korean isolates.

• Molecules and Cells
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• 제19권2호
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• pp.262-267
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• 2005

The capsaicinoid synthetase (CS) gene cosegregated perfectly with the C locus, which controls the presence of pungency, in 121 $F_2$ individuals from a cross between 'ECW123R' and 'CM334', both of Capsicum annuum. We concluded that CS and C are tightly linked. Sequence analysis of the genes of four pungent and four non-pungent pepper lines showed that the non-pungent peppers had a 2,529 bp-deletion in the 5' upstream region of CS. We have developed molecular markers of the C locus to detect pungency at the seedling stage. Based on the deleted sequence, we developed five SCAR markers, two of them being codominant. These SCAR markers will be useful for easy, accurate, and early detection of non-pungent individuals in breeding programs.

• Journal of Plant Biotechnology
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• 제33권2호
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• pp.139-145
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• 2006

The present study is the first report of molecular variations in different accessions of Rauvolfia tetraphylla L.f, a medicinally important plant collected from seven locations of Andhra Pradesh, India. Molecular analysis was carried out using RAPD markers. Out of the 40 primers screened from OPA and OPC Kts, a total of 205 scorable polymorphic markers out of 397 total markers were generated. Polymorphism of 51.6% was found with 3 unique markers. Levels of genetic diversity within accessions i.e., the genetic distance ranged from 0.816-0.932. Cluster analysis based on Dice coefficient showed two major groups indicating that mostly in cross-pollinated plants, high levels of differentiation among accessions exists independent of geographical distance. Hence the results of the present study can be seen as a starting point for future researches on the population and evolutionary genetics of this species. Understanding such variation would also facilitate their use in various conservational management practices, rootstock breeding and hybridisation programmes.

• 한국작물학회지
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• 제48권4호
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• pp.297-302
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• 2003

Genetic linkage maps serve the plant geneticist in a number of ways, from marker assisted selection in plant improvement to map-based cloning in molecular genetic research. Genetic map based upon DNA polymorphism is a powerful tool for the study of qualitative and quantitative traits in crops. The objective of this study was to develop genetic linkage map of soybean using the population derived from the cross of Korean soybean cultivar 'Kwangkyo, and wild accession 'IT182305'. Total 1,000 Operon random primers for RAPD marker, 49 combinations of primer for AFLP marker, and 100 Satt primers for SSR marker were used to screen parental polymorphism. Total 341 markers (242 RAPD, 83 AFLP, and 16 SSR markers) was segregated in 85 $\textrm{F}_2$ population. Forty two markers that shown significantly distorted segregation ratio (1:2:1 for codominant or 3:1 for domimant marker) were not used in mapping procedure. A linkage map was constructed by applying the computer program MAPMAKER/EXP 3.0 to the 299 marker data with LOD 4.0 and maximum distance 50 cM. 176 markers were found to be genetically linked and formed 25 linkage groups. Linkage map spanned 2,292.7 cM across all 25 linkage groups. The average linkage distance between pair of markers among all linkage groups was 13.0 cM. The number of markers per linkage group ranged from 2 to 55. The longest linkage group 3 spanned 967.4 cM with 55 makers. This map requires further saturation with more markers and agronomically important traits will be joined over it.

• Molecules and Cells
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• 제27권1호
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• pp.21-37
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• 2009

Map-based cloning to find genes of interest, marker-assisted selection (MAS), and marker-assisted breeding (MAB) all require good genetic maps with high reproducible markers. For map construction as well as chromosome assignment, development of single copy PCR-based markers and map integration process are necessary. In this study, the 132 markers (57 STS from BAC-end sequences, 13 STS from RFLP, and 62 SSR) were newly developed as single copy type PCR-based markers. They were used together with 1830 markers previously developed in our lab to construct an integrated map with the Joinmap 3.0 program. This integrated map contained 169 SSR, 354 RFLP, 23 STS from BAC-end sequences, 6 STS from RFLP, 152 AFLP, 51 WRKY, and 99 rRAMP markers on 12 chromosomes. The integrated map contained four genetic maps of two interspecific (Capsicum annuum 'TF68' and C. chinense 'Habanero') and two intraspecific (C. annuum 'CM334' and C. annuum 'Chilsungcho') populations of peppers. This constructed integrated map consisted of 805 markers (map distance of 1858 cM) in interspecific populations and 745 markers (map distance of 1892 cM) in intraspecific populations. The used pepper STS were first developed from end sequences of BAC clones from Capsicum annuum 'CM334'. This integrated map will provide useful information for construction of future pepper genetic maps and for assignment of linkage groups to pepper chromosomes.

• 한국작물학회지
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• 제49권5호
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• pp.429-433
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• 2004

A single recessive gene, rxp, controls the bacterial leaf pustule (BLP) resistance in soybean and in our previous article, it has been mapped on linkage group (LG) D2 of molecular genetic map of soybean. A total of 130 recombinant inbred lines (RILs) from a cross between BLP-resistant SS2-2 and BLP-susceptible Jangyeobkong were used to identify molecular markers linked to rxp. Fifteen simple sequence repeat (SSR) markers on LG D2 were screened to construct a genetic map of rxp locus. Only four SSR markers, Satt135, Satt372, Satt448, and Satt486, showed parental polymorphisms. Using these markers, genetic scaffold map was constructed covering 26.2cM. Based on the single analysis of variance, Satt372 among these four SSR markers was the most significantly associated with the resistance to BLP. To develop new amplified fragment length polymorphism (AFLP) marker linked to the resistance gene, bulked segregant analysis (BSA) was employed. Resistance and susceptible bulks were made by pooling equal amount of genomic DNAs from ten of each in the segregating population. A total of 192 primer combinations were used to identify specific bands to the resistance, selecting three putative AFLP markers. These AFLP markers produced the fragment present in SS2-2 and the resistant bulk, and not in Jangyeobkong and the susceptible bulk. Linkage analysis revealed that McctEact97 $(P=0.0004,\;R^2=14.67\%)$ was more significant than Satt372, previously reported as the most closely linked marker.

• Molecules and Cells
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• 제21권3호
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• pp.360-366
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• 2006

Up to 35% of the rice genome consists of various kinds of transposons, and CACTA and MITE are two of the major class 2 DNA transposons in the genome. We have employed the consensus sequences of Rim2/Hipa CACTA, Stowaway MITE Pangrangja, and Tourist MITE Ditto for transposon display (TD) analysis to locate them on a genetic map, with 58 SSR markers used to anchor them. The TD analysis produced a high profile of the polymorphisms between the parental lines, Oryza sativa var. Gihobyeo/O. sativa var. Milyang, in intraspecific $F_{15}$ RIL lines, locating 368 markers of Rim2/Hipa CACTA, 78 markers of Tourist MITE Ditto, and 22 markers of Stowaway MITE Pangrangja. In the segregation analysis, non-parental segregating bands and segregation distortion bands were observed. The recombinant genetic map spans 3023.9 cM, with 5.7 cM the average distance between markers. The TD markers were distributed unequally on the chromosomes because many TD markers were located in pericentric chromosomal regions except in the cases of chromosomes 2, 3, 6 and 9. Although the number of transposon markers was not sufficient to include all rice class 2 transposons, the current map of CACTA and MITE transposons should provide new insight into the genome organization of rice since no previous DNA transposon map is available.