• 한국패류학회지
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• 제30권3호
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• pp.197-210
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• 2014

Single nucleotide polymorphisms (SNPs) are widely acknowledged as the marker of choice for many genetic and genomic applications because they show co-dominant inheritance, are highly abundant across genomes and are suitable for high-throughput genotyping. Here we evaluated the applicability of SNP markers developed from Crassostrea gigas and C. virginica expressed sequence tags (ESTs) in closely related Crassostrea and Ostrea species. A total of 213 putative interspecific level SNPs were identified from re-sequencing data in six amplicons, yielding on average of one interspecific level SNP per seven bp. High polymorphism levels were observed and the high success rate of transferability show that genic EST-derived SNP markers provide an efficient method for rapid marker development and SNP discovery in closely related oyster species. The six EST-SNP markers identified here will provide useful molecular tools for addressing questions in molecular ecology and evolution studies including for stock analysis (pedigree monitoring) in related oyster taxa.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2018년도 추계학술대회
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• pp.74-74
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• 2018

Little millet (Panicum sumatrense) is well known for its salt and drought stress tolerance and high nutritional value, but very limited knowledge of genetic variation and genomic information is available. This study was to develop highly polymorphic EST-SSR markers based on cross-species transferability of derived SSRs from switchgrass EST databases and characterize newly developed EST - SSRs to better understand the genetic diversity of collected 37 germplasm accessions of little millet. A total of 779 primer pairs were designed from the 22,961 EST sequences of switchgrass (Pancium virgatum), of which 48 EST - SSR markers were developed based on the trials of transferability of these primers in little millet. The EST - SSR amplicons showed reproducible single band polymorphism and produced a total of 160 alleles with an average of 3.3 alleles per locus in 37 accessions of little millet. T he average values of expected and observed heterozygosities were 0.266 and 0.123, respectively. T he polymorphic information content (PIC) values were observed in range of 0.026 to 0.549 with an average of 0.240. The genetic relatedness among the little millet accessions was evaluated by neighbor-joining dendrogram, which grouped all accessions into two distinct groups. The validation thus demonstrated the utility of the switchgrass EST - SSR markers in assessing genomic relationships in little millet. T he findings from this study could be useful for designing strategies for the identification of diverse germplasm for conservation and future molecular breeding programs for little millet.

• The Plant Pathology Journal
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• 제27권2호
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• pp.110-115
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• 2011

Aggressiveness was studied in seven Plasmopara halstedii (sunflower downy mildew) pathotypes: 100, 300, 304, 314, 704, 710 and 714. Aggressiveness criteria including percentage infection, latent period, sporulation density and reduction of hypocotyl length (dwarfing) were analysed in one sunflower inbred line showing a high level of quantitative resistance. Genetic relationships were detected between the seven pathotypes using 12 EST-derived markers. Pathotypes 100, 300, 304 and 314 were characterized with shorter latent period and higher sporulation density than pathotypes 710, 704 and 714. All pathotypes showed high percentage infection values and caused a large reduction in seedling size except for pathotype 314 involved in dwarfing. Pathotypes 714, 704 and 314 had an intermediary genetic position between the pathotypes 100 and 710. No correlation was detected between aggressiveness traits and EST genotypes.

• Journal of Plant Biotechnology
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• 제46권3호
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• pp.158-164
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• 2019

Molecular characterization of different genotypes reveals accurate information about the degree of genetic diversity that helps to develop a proper breeding program. In this study, a total of 30 EST-based simple sequence repeat (EST-SSR) markers derived from trumpet lily (Lilium longiflorum) were used across 11 native lily species for their genetic relationship. Among these 30 markers, 24 SSR markers that showed polymorphism were used for evaluation of diversity spectrum. The allelic number at per locus ranged from 1 at SSR2 locus to 34 alleles at SSR15 locus, with an average of 11.25 alleles across 24 loci observed. The polymorphic information content, PIC, values ranged from 0.0523 for SSR9 to 0.9919 for SSR2 in all 24 loci with an average of 0.3827. The allelic frequency at every locus ranged from 0.81% at SSR2 locus to 99.6% at SSR14 locus. The pairwise genetic dissimilarity coefficient revealed the highest genetic distance with a value of 81.7% was in between L. dauricum and L. amabile. A relatively closer genetic distance was found between L. lancifolium and L. dauricum, L. maximowiczii and L. concolor, L. maximowiczii and L. distichum (Jeju), L. tsingtauense and L. callosum, L. cernuum and L. distichum (Jeju ecotype), of which dissimilarity coefficient was 50.0%. The molecular fingerprinting based on microsatellite marker could serve boldly to recognize genetically distant accessions and to sort morphologically close as well as duplicate accessions.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2020년도 춘계학술대회
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• pp.45-45
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• 2020

A large number of expressed sequence tags (ESTs) in public databases have provided an opportunity for the systematic development of simple sequence repeat (SSR) markers. EST-SSRs derived from conserved coding sequences show considerable cross-species transferability in related species. In the present study, we assessed the utility of foxtail millet EST-SSRs in barnyard millet. A total of 312 EST-SSRs of foxtail millet were tested using 84 Echinochloa crus-galli germplasm accessions; a high rate of transferability (62%) and 46 primer sets (13%) were shown the polymorphism in barnyard millet. The 13% of functional EST-SSRs) was demonstrated between cereals and barnyard millet. SSR marker profile data were scored for the computation of pairwise distances as well as a Neighbor Joining (NJ) tree of all the genotypes. The averaged values of gene diversity (H_E) and polymorphism information content (PIC) were 0.213 and 0.179 within populations, respectively. The 84 barnyard millet germplasm accessions were divided into five different groups, which agreed well with their geographical origins. The exotic 12 accessions of India type barnyard millet (E. frumentacea) were all separated form Korean local collection genotype. The present results provide evidence of divergence between cultured and wild type barnyard, as a millet and grass. The polymorphic SSR markers indicated in this study were of great value in analysis of genetic diversity that can be further used for crop improvement through breeding.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2010년도 정기총회 및 추계학술발표회
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• pp.11-11
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• 2010

The Korean ginseng, Panax ginseng C. A. Meyer is a popular medicinal herb in Araliaceae. Genetic map in crops provides valuable information for breeding, genetic and genomic researches. However, little information is available for construction of genetic map in ginseng. Up to now, we have produced large amounts of expressed sequence tags (ESTs) from four ginseng cultivars (37Mb, 49Mb, 39Mb, 47Mb from Gopoong, Gumpoong, Chunpoong and Yunpoong respectively using pyrosequencing technique and 5Mb from normalized full-length cDNA library of Chunpoong) to obtain comprehensive information of gene expression, and constructed EST database including ESTs from public database. Till now, we designed 261 SSR primer sets using EST sequences and identified 106 intergenic polymorphic markers. And 44 of the 106 showed polymorphisms among panax ginseng cultivars. Among 44 markers, 27 SSR polymorphic markers were inspected to 51 $F_2$ population from Yunpoong x Chunpoong, which showed good at the fitness of Mendellian segregation ratio 1:2:1. To enrich the number of markers, and thus construct high resolution genetic map which can be used as frame map for further genome sequencing. we are planning to develop large scale EST-derived SNP markers which are available in the F2 population. This study provides genetic information as well as foundation for ginseng researches such as genetics, genomics, breeding, and the final goal for whole genome sequencing. This study was supported by Technology Development Program for Agriculture and Forestry, Ministry for Food, Agriculture, Forestry and Fisheries, Republic of Korea (Grant No. 609001-051SB210).

• 식물분류학회지
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• 제48권3호
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• pp.195-200
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• 2018

Genetic assessments of rare and endangered species are among the first steps necessary to establish the proper management of natural populations. Transcriptome-derived single-sequence repeat markers were developed for the Korean endangered species Astilboides tabularis (Saxifragaceae) to assess its genetic diversity. A total of 96 candidate microsatellite loci were isolated based on transcriptome data using Illumina pair end sequencing. Of these, 26 were polymorphic, with one to five alleles per locus in 60 individuals from three populations of A. tabularis. The observed and expected heterozygosity per locus ranged from 0.000 to 0.950 and from 0.000 to 0.741, respectively. These polymorphic transcriptome-derived simple sequence repeat markers would be invaluable for future studies of population genetics and for ecological conservation of the endangered species A. tabularis.

• 한국약용작물학회지
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• 제21권6호
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• pp.444-454
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• 2013

The development of random amplified polymorphic DNA (RAPD) and expressed sequence tag-derived simple sequence repeats (EST-SSRs) provided a useful tool for investigating Korean ginseng genetic diversity. In this study, 18 polymorphic markers (7 RAPD and 11 EST-SSR) selected to assess the genetic diversity in 31 ginseng accessions (11 Korean ginseng cultivars and 20 breeding lines). In RAPD analysis, a total of 53 unique polymorphic bands were obtained from ginseng accessions and number of amplicons ranged from 4 to 11 with a mean of 7.5 bands. Pair-wise genetic similarity coefficient (Nei) among all pairs of ginseng accessions varied from 0.01 to 0.32, with a mean of 0.11. On the basis of the resulting data, the 31 ginseng accessions were grouped into six clusters. As a result of EST-SSR analysis, 11 EST-SSR markers detected polymorphisms among the 31 ginseng accessions and revealed 49 alleles with a mean of 4.45 alleles per primer. The polymorphism information content (PIC) value ranged from 0.06 to 0.31, with an average of 0.198. The 31 ginseng accessions were classified into five groups by cluster analysis based on Nei's genetic distances. Consequently, the results of ginseng-specific RAPD and EST-SSR markers may prove useful for the evaluation of genetic diversity and discrimination of Korean ginseng cultivars and breeding lines.

• Journal of Plant Biotechnology
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• 제44권4호
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• pp.372-378
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• 2017

과육색이 다르게 발현되는 사과(Malus domestica L.) 품종의 유전자 발현을 비교하기 위해 2개의 cDNA library를 제작하였다. 붉은 색 과육 품종인 'Redfield'와 백색 과육 품종인 'Granny Smith'의 유전자 발현 차이를 보기 위해 차세대 염기서열 분석(NGS) 기술을 사용하였고 두 품종으로부터 얻은 EST의 염기서열을 결정하고 기존에 보고된 유전자와의 상동성을 분석하였다. HRM 기술은 붉은 색 과육 품종 사과와 백색 과육 품종 사과의 짧은 PCR 증폭산물에서 한 개의 서로 다른 염기서열을 구분하여 분리해낼 수 있다. 'Redfield'와 'Granny Smith'의 EST database로부터 103쌍의 단일염기다형성(SNP) 분자표지를 선발하였고, 붉은 색 과육 품종 10개와 백색 과육 품종 11개를 구분할 수 있는 SNP 분자표지를 HRM 방법으로 분석하였다. 본 연구에서는 사과 EST database를 기반으로 HRM 분석 방법을 이용하여 사과 품종의 적육계와 백육계를 구분할 수 있는 효율적인 SNP 분자표지를 개발하였다. 이러한 SNP 분자표지는 사과육종에 유용하게 사용할 수 있으며 사과 품종의 다양한 색 변화에 관한 분자 기작 연구에 좋은 참고자료가 될 수 있을 것이다.

• 원예과학기술지
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• 제33권5호
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• pp.737-750
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• 2015

국내에서 시판되고 있는 수박 102 품종에 대한 DNA 프로 파일 데이터베이스를 구축하기 위하여 genomic microsatellite(gMS)와 expressed sequence tag(EST) microsatellite(eMS) 마커의 다형성 정도의 비교와 유전적 연관성 분석을 통한 품종식별력 검정 등에 대한 일련의 연구를 수행하였다. 수박 gMS 마커를 이용하여 국내에서 시판되고 있는 수박 102 품종을 검정하였을 때 마커당 3.63개의 평균 대립유전자가 검출되었으며, 평균 PIC 값은 0.479로 나타났다. 이에 반해 eMS 마커는 평균 대립유전자의 수가 2.50개, PIC 값이 0.425로 나타나 gMS 마커보다 다형성 정도가 낮게 나타났다. gMS와 eMS 및 이들 두 종류의 마커를 병합하여 작성된 계통도는 microsatellite 마커의 다형성에 따라 수박 102개 품종을 6-8개의 그룹으로 구분하였고 대부분의 품종의 식별이 가능하였다. 3가지 마커 유형에 따라 작성된 계통도를 Mantel test에 의해 상관 정도를 분석하였을 때 높은 상관($r{\geq}0.80$)을 나타내었다. 따라서 본 연구에 활용된 microsatellite 마커는 수박 유전자원의 특성평가, 순도검정 및 품종의 지문화 작업의 수단으로 유용하게 활용될 수 있을 것이다.