• 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 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.

• 한국자원식물학회지
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• 제30권3호
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• pp.287-297
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• 2017

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. In this study, 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. The average values of expected and observed heterozygosities were 0.266 and 0.123, respectively. The 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. The 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.

• 원예과학기술지
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• 제33권1호
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• pp.93-105
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• 2015

본 연구는 수박의 EST-SSR 마커를 이용하여, 네 개의 주요 박과(Cucurbitaceae) 작물인 수박, 호박, 오이, 멜론의 유연 관계를 분석하고 마커의 타 박과 작물에 활용 가능성을 알아보기 위해 수행되었다. Cucurbit Genomics Initiative(ICuGI) database로부터 선발된 120 EST-SSR 프라이머 중 51(49.17%)가 PCR이 성공하였고, 49(40.8%)가 8개 박과 유전자원에서 다형성을 보였다. 총 24개 박과 유전자원을 24개 EST-SSR 프라이머로 분석한 결과 총 382개 대립유전자 특이적 PCR 밴드를 얻었으며, 이를 토대로 짝유사행렬과 계통도를 작성하였다. 짝유사행렬의 범위는 0.01-0.85였으며, 작성된 계통도에서 24개 유전자원이 두 개의 주요그룹(Clade I, II)으로 분류되었다. Clade I은 다시 수박으로 구성된 하위집단 I-1[I-1a, I-1b-2: 각 1개와 2수박 야생종(Citrullus lanatus var. citroides Mats. & Nakai)으로 구성, I-1b-1: 6개수박 재배종(Citrullus lanatus var. vulgaris Schrad.)로 구성]과 멜론과 오이로 구성된 하위집단I-2[I-2a-1: 4개 멜론 재배종(Cucumis melo var. cantalupensis Naudin.), I-2a-2: 2개 참외 재배종(Cucumis melo var. conomon Makino.), I-2b: 5개 오이 재배종(Cucumis sativus L.)]로 분류되었다. 호박으로 구성된 Clade II는 다시 Cucurbita moschata(Duch. ex Lam.) Duch. & Poir와 Cucurbita maxima Duch.로 구성된 하위집단 II-1과 Cucurbita pepo L.과 Cucurbita ficifolia Bouche로 구성된 하위집단 II-2로 나누어졌다. 이러한 결과는 기존의 종명법에 따른 분류와 일치하며, 따라서 수박 EST-SSR 마커를 이용한 타 박과 작물의 비교 유전체 등 연구분야에 적용 가능성을 확인하였다.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2018년도 춘계학술발표회
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• pp.105-105
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• 2018

Finger millet, Eleusine coracana Gaertn., is more nutritious than other cereals and millets and widely cultivate in tropical regions of the world. However, status of its genetic diversity remained concealed due to lack of research work in this species. In recent years, microsatellites have become the most used markers for studying population genetic diversity. In present study, genetic diversity and structure of different populations of finger millet from Africa and South Asia was examined at molecular level using newly developed EST-Simple Sequence Repeat (EST-SSR) markers using a total of 1,927 ESTs of Eleusine coracana available in the NCBI database. In total, 46 primers produced 292 alleles in a size range of 100-500 bp and mean Polymorphism Information Content (PIC) and Marker Index (MI) were 0.372 and 1.04, respectively. 46 primers showed polymorphism and 21 primers were identified as having a PIC value above 0.5. Principal coordinates analysis and the dendrogram constructed out of combined data of both markers showed grouping of finger millet accessions to their respective area of collection. The 156 accessions was classified into four groups, such as three groups of Africa collection and one group of Asia. Results of present study can be useful in identifying diverse accessions and management of this plant resource. Moreover, the novel SSR markers developed can be utilized for various genetic analyses in this species in future.

• 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.

• Genomics & Informatics
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• 제9권4호
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• pp.189-193
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• 2011

Simple sequence repeats (SSRs) are ubiquitous short tandem duplications found within eukaryotic genomes. Their length variability and abundance throughout the genome has led them to be widely used as molecular markers for crop-breeding programs, facilitating the use of marker-assisted selection as well as estimation of genetic population structure. Here, we report a software application, "SSR-Primer Generator " for SSR discovery, SSR-primer design, and homology-based search of in silico amplicons from a DNA sequence dataset. On submission of multiple FASTA-format DNA sequences, those analyses are batch processed in a Java runtime environment (JRE) platform, in a pipeline, and the resulting data are visualized in HTML tabular format. This application will be a useful tool for reducing the time and costs associated with the development and application of SSR markers.

• 한국작물학회지
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• 제66권4호
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• pp.443-451
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• 2021

Finger millet (Eleusine coracana) is widely cultivated in tropical regions worldwide owing to its high nutritional value. Finger millet is more tolerant against biotic and abiotic stresses such as pests, drought, and salt than other millet crops; therefore, it was proposed as a candidate crop to adapt to climate change in Korea. In 2019, we used expressed sequence tag simple sequence repeat (EST-SSR) markers to evaluate the genetic diversity and structure of 102 finger millet accessions from two geographical regions (Africa and South Asia) to identify appropriate accessions and enhance crop diversity in Korea. In total, 40 primers produced 116 alleles, ranging in size from 135 to 457 bp, with a mean polymorphism information content (PIC) of 0.18225. Polymorphism was detected among the 40 primers, and 13 primers were found to have PIC values > 0.3. Principal coordinate and phylogenetic analyses, based on the combined data of both markers, grouped the finger millet accessions according to their respective collection areas.Therefore, the 102 accessions were classified into two groups, one from Asia and the other from Africa. We have conducted an in-depth study on the finger millet landrace pedigree. By sorting out and using the molecular characteristics of each pedigree, it will be useful for the management and accession identification of the plant resource. The novel SSR markers developed in this study will aid in future genetic analyses of E. coracana.