• Journal of Crop Science and Biotechnology
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• 제10권2호
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• pp.98-105
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• 2007

Phylogenetic relationships in Korean watermelons were evaluated by genetic similarity coefficients using 15 SSR(simple sequence repeat), 14 SCAR(sequence characterized amplified region) and 14 CAPS(sequence characterized amplified region) markers. The SSR markers were selected from previously reported melon and watermelon SSRs through testing polymorphisms within a set of commercial $F_1$ varieties. The SCAR and CAPS markers were developed from polymorphic AFLP(amplified fragment length polymorphism) markers between inbred lines 'BN4001' and 'BN4002'. From the AFLP analysis, 105 polymorphic fragments were identified between the inbred lines using 1,440 primer combinations of EcoRI+CNNN and XbaI+ANNN. Based on the sequencing data of these polymorphic fragments, we synthesized sequence specific primer pairs and detected clear and reliable polymorphisms in 27 primer pairs by indels(insertion/deletion) or RFLP(restriction fragment length polymorphism). A total of 43 sequence-based PCR markers were obtained and polymorphic information content(PIC) was analyzed to measure the informativeness of each marker in watermelon varieties. The average PIC value of SCAR markers was 0.41, which was similar to that of SSR markers. Genetic diversity was also estimated by using these markers to assess the phylogenetic relationships among commercial varieties of watermelon. These markers differentiated 26 Korean watermelon varieties into two major phylogenetic groups, but this grouping was not significantly correlated with their morphological and physiological characteristics. The mean genetic similarity was 66% within the complete set of 26 commercial varieties. In addition, these sequence-based PCR markers were reliable and useful to identify cultivars and genotypes of watermelon.

• Genomics & Informatics
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• 제19권3호
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• pp.33.1-33.10
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• 2021

Eucalyptus is one of the major plantation species with wide variety of industrial uses. Polymorphic and informative simple sequence repeats (SSRs) have broad range of applications in genetic analysis. In this study, two individuals of Eucalyptus tereticornis (ET217 and ET86), one individual each from E. camaldulensis (EC17) and E. grandis (EG9) were subjected to whole genome resequencing. Low coverage (10×) genome sequencing was used to find polymorphic SSRs between the individuals. Average number of SSR loci identified was 95,513 and the density of SSRs per Mb was from 157.39 in EG9 to 155.08 in EC17. Among all the SSRs detected, the most abundant repeat motifs were di-nucleotide (59.6%-62.5%), followed by tri- (23.7%-27.2%), tetra- (5.2%-5.6%), penta- (5.0%-5.3%), and hexa-nucleotide (2.7%-2.9%). The predominant SSR motif units were AG/CT and AAG/TTC. Computational genome analysis predicted the SSR length variations between the individuals and identified the gene functions of SSR containing sequences. Selected subset of polymorphic markers was validated in a full-sib family of eucalypts. Additionally, genome-wide characterization of single nucleotide polymorphisms, InDels and transcriptional regulators were carried out. These variations will find their utility in genome-wide association studies as well as understanding of molecular mechanisms involved in key economic traits. The genomic resources generated in this study would provide an impetus to integrate genomics in marker-trait associations and breeding of tropical eucalypts.

• The Plant Pathology Journal
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• 제36권1호
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• pp.11-28
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• 2020

Faba bean (Vicia faba L.) is one of the most important legume crops in Egypt. However, production of faba bean is affected by several diseases including fungal diseases. Fusarium wilt incited by Fusarium oxysporum Schlecht. was shown to be the most common wilt disease of faba bean in Assiut Governorate. Evaluation of 16 faba bean genotypes for the resistance to Fusarium wilt was carried out under greenhouse conditions. Three molecular marker systems (inter-simple sequence repeat [ISSR], sequence related amplified polymorphism [SRAP], and simple sequence repeat [SSR]) and a biochemical marker (protein profiles) were used to study the genetic diversity and detect molecular and biochemical markers associated with Fusarium wilt resistance in the tested genotypes. The results showed that certain genotypes of faba bean were resistant to Fusarium wilt, while most of the genotypes were highly susceptible. The percentage of disease severity ranged from 32.83% in Assiut-215 to 64.17% in Misr-3. The genotypes Assiut-215, Roomy-3, Marut-2, and Giza2 were the most resistant, and the genotypes Misr-3, Misr-1, Assiut-143, Giza-40, and Roomy-80 performed as highly susceptible. The genotypes Assiut-215 and Roomy-3 were considered as promising sources of the resistance to Fusarium wilt. SRAP markers showed higher polymorphism (82.53%) compared with SSR (76.85%), ISSR markers (62.24%), and protein profile (31.82%). Specific molecular and biochemical markers associated with Fusarium wilt resistance were identified. The dendrogram based on combined data of molecular and biochemical markers grouped the 16 faba bean genotypes into three clusters. Cluster I included resistant genotypes, cluster II comprised all moderate genotypes and cluster III contained highly susceptible genotypes.

• 한국약용작물학회지
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• 제25권6호
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• pp.361-366
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• 2017

Background: In the herbal medicinal industry, Angelica gigas Nakai, Angelica sinensis (Oliv.) Diels. and Angelica acutiloba (Siebold & Zucc.) Kitag. are often confused, because the roots of the three species can not be distinguished by their appearance. This confusion can cause serious side effects. In this study, we determined the origins of Angelica roots distributed in the Korean market using the simple sequence repeat (SSR) markers developed based on the A. gigas chloroplast DNA sequence. Methods and Results: We collected twenty seven A. gigas and three A. acutiloba samples from the Seoul, Daegu, and Cheongju herbal medicinal markets. Fifty sections of one collection were mixed and ground to make a powder, which was used for DNA extraction using the cetyl trimethylammonium bromide (CTAB) method. Chloroplast based SSR markers were applied to the DNA for the determination of the species. In addition, polymorphism was found in eight samples. The phylogenetic analysis showed that the A. gigas roots collected from herbal medicinal markets were clearly discriminated from A. sinensis and A. acutiloba even though they were grouped into four clusters. Conclusions: This study showed that chloroplast based SSR markers would help the discrimination of Angelica roots in the Korean herbal medicinal industry and the markers are useful to prevent confusion between Angelica roots.

• Journal of Plant Biotechnology
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• 제45권4호
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• pp.382-391
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• 2018

본 연구는 사과 대목 M.26 (Malus pumila Mill))의 효과적인 기내 대량번식하기 위해 신초 증식과 뿌리 형성에 적합한 배지조건을 확립하고, simple sequence repeat (SSR) 마커를 이용하여 증식된 소식물체의 유전적 다양성을 분석하고자 수행하였다. MS (Murashige and Skoog) 기본배지에 benzyladenin (BA, $0.5{\sim}5.0mg{\cdot}L^{-1}$)와 thidiazuron (TDZ, $0.01{\sim}0.1mg{\cdot}L^{-1}$)을 첨가하여 신초를 배양한 결과, $1.0mg{\cdot}L^{-1}$ BA 처리에서 절편체 당신초 수가 10.67개로 가장 많았으며 과수화 발생률은 BA 처리구보다 TDZ 처리구에서 높았다. M.26 신초 증식에 BA와 auxin과의 혼용처리 효과는 없었고, $1.0mg{\cdot}L^{-1}$ BA가 첨가된 MS 기본배지가 적합하였다. 신초 발근에 적합한 배지를 구명하고자 auxin인 indole-3-butyric acid (IBA)와 ${\alpha}$-naphthaleneacetic acid의 농도($0.5{\sim}5.0mg{\cdot}L^{-1}$), MS 배지의 무기염류(1/4 ~ 1배) 및 sucrose 농도($0{\sim}30g{\cdot}L^{-1}$)를 달리하여 처리한 결과, $1.0mg{\cdot}L^{-1}$ IBA, $15{\sim}20g{\cdot}L^{-1}$ sucrose가 첨가된 1/2 MS 배지에서 발근율(100%), 뿌리 수(10.45 ~ 13.60개/절편체), 뿌리 길이(7.41 ~ 8.33 cm) 및 신초 길이(4.93 ~ 5.38 cm)가 양호하였다. 15종의 SSR primer를 이용하여 증식된 20개의 소식물체를 분석한 결과, 총 30개의 대립유전자가 검출되었으며 모두 동일한 밴드 패턴을 보여 온실에서 자란 M.26 식물체와 유사하여 유전적으로 안정한 것으로 판단되었다.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2005년도 춘계 학술발표대회
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• pp.102-102
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• 2005

• 한국생명과학회:학술대회논문집
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• 한국생명과학회 2006년도 제47회 학술심포지움 및 추계국제학술대회
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• pp.40.2-40.2
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• 2006

• 원예과학기술지
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• 제34권3호
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• pp.453-460
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• 2016

The parentage of the horticulturally important pear cultivar 'Niitaka' was confirmed by determining its S-genotypes based on the S-RNase and $PpSFBB^{-{\gamma}}$ genes, and genotyping using simple sequence repeat (SSR) markers. Previous reports suggested that the cultivars 'Amanogawa' and 'Imamuraaki' were the parents of 'Niitaka', although the cultivars 'Chojuro' and 'Shinchu' were also examined as candidate parents, along with two other cultivars. In the present study, the S-genotype of 'Niitaka' was determined to be $S^3S^9$. The $S^9$-RNase of 'Niitaka' was found to be likely inherited from the parent 'Amanogawa' ($S^1S^9$) and the $S^3$-RNase from 'Chojuro' ($S^3S^5$) or 'Shinchu' ($S^3S^5$). Based on the S-genotypes, the cultivar 'Imamuraaki' ($S^1S^6$) had no contribution to the parentage of 'Niitaka' ($S^3S^9$). A total of 67 polymorphic SSR markers were used to further confirm the parentage of 'Niitaka'. Discrepancies were found at several SSR loci between 'Niitaka' and the cultivars 'Imamuraaki' and 'Shinchu', whereas 'Niitaka' inherited alleles from 'Amanogawa' and 'Chojuro' at all SSR loci. Therefore, our findings established that 'Amanogawa' and 'Chojuro' are the parents of pear cultivar 'Niitaka', and not 'Imamuraaki' as previously reported.

• 식물분류학회지
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• 제50권1호
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• pp.22-26
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• 2020

Chrysosplenium aureobracteatum Y. I. Kim & Y. D. Kim (Saxifragaceae) is a recently described endemic species growing in the central part of the Korean peninsula. It requires constant monitoring for conservation due to its limited distributions. There is also a need for molecular markers for proper assessments of the genetic differentiation of C. aureobracteatum from species morphologically similar to it. In this study, we developed microsatellite markers that can be used to evaluate the genetic diversity of this species, representing fundamental data with which to conserve the natural populations of the species. A total of 17 expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed by the Illumina pair-end sequencing of the transcriptomes of C. aureobracteatum. These markers were successfully applied to populations of C. aureobracteatum and to its most closely related species, C. barbatum, revealing high polymorphism in both species. The EST-SSR markers developed in this study were proven to be useful not only to monitor the population genetic structure of C. aureobracteatum for conservation purposes but also to study the genetic delimitation of the species from species closely related to it.

• 생명과학회지
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• 제20권4호
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• pp.632-638
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• 2010

총 20개의 감 SSR primer set을 사용하여 완전단감(PCNA) 12품종, 불완전단감(PVNA) 13품종, 불완전 떫은감(PVA) 15품종, 완전 떫은감(PCA) 8품종 등, 총 48개 유전자원의 유전적 연관성을 분석하였다. 획득된 114개의 다형성 밴드를 이용하여 UPGMA 방식으로 유사도 및 집괴분석을 수행한 결과 48개 품종들은 크게 2개의 그룹(cluster)으로 나뉘어졌으며, 제 1 cluster는 다시 4개의 subcluster를 형성하였다. 이는 탈삽의 특성을 기준으로 분류한 품종군과 대체로 일치 함을 알 수 있고, 품종군간의 유연관계에 있어서는 완전단감군은 불완전 단감군과, 그리고 완전 떫은감은 불완전 떫은감군과 유연관계가 더욱 높은 것으로 관찰되었다. 평균 유사도의 값은 0.499였고 품종간 가장 높은 유사도 값(0.954)를 나타낸 것은 '청도반시'와 '함안반시'였고, 가장 낮은 유사도 값(0.192)를 나타낸 것은 '대마반'과 '애탕'이었다. 본 연구에 사용된 2SSR primer 들은 유럽 감품종으로부터 개발되어 보고되었지만, 일본 및 국내 품종의 연구에서도 효과적으로 사용될 수 있었고, 이들 마커들을 통해, 48개 품종 중 청도반시(Cheongdo-Bansi)와 경산반시(Gyeongsan-Bansi)를 제외한 모든 품종간 구별이 가능하였다. 이는 향후 신품종 개발시 품종보호를 위한 품종 특이적 마커로 효율적으로 사용될 수 있음을 보여준다.