• 제목/요약/키워드: Plant life

검색결과 6,719건 처리시간 0.031초

High-Throughput Development of Polymorphic Simple Sequence Repeat Markers Using Two Whole Genome Sequence Data in Peucedanum japonicum

  • Lee, Junki;Joh, Ho Jun;Kim, Nam-Hoon;Lee, Sang-Choon;Jang, Woojong;Choi, Beom Soon;Yu, Yeisoo;Yang, Tae-Jin
    • Plant Breeding and Biotechnology
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    • 제5권2호
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    • pp.134-142
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    • 2017

  • Resource plants are important and have strong potential for a variety of utilities as crops or pharmaceutical materials. However, most resource plants remain wild and thus their utility for breeding and biotechnology is limited. Molecular markers are useful to initiate genetic study and molecular breeding for these understudied resource plants. We collected various wild collections of Peucedanum japonicum which is indigenous resource plants utilized as oriental medicine and leafy vegetables in Korea. In this study, we produced two independent whole genome sequences (WGSs) from two collections and identified large scale polymorphic simple sequence repeat (pSSR) based on our pipeline to develop SSR markers based on comparison of two WGSs. We identified a total of 452 candidate pSSR contigs. To confirm the accuracy and utility of pSSR, we designed ten SSR primer pairs and successfully applied those to seven collections of P. japonicum. The WGS and pSSR candidates identified in this study will be useful resource for genetic research and breeding purpose for the valuable resource plant, P. japonicum.

  • https://doi.org/10.9787/PBB.2017.5.2.134 인용

Transcriptome profiling and comparative analysis of Panax ginseng adventitious roots

  • Jayakodi, Murukarthick;Lee, Sang-Choon;Park, Hyun-Seung;Jang, Woojong;Lee, Yun Sun;Choi, Beom-Soon;Nah, Gyoung Ju;Kim, Do-Soon;Natesan, Senthil;Sun, Chao;Yang, Tae-Jin
    • Journal of Ginseng Research
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    • 제38권4호
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    • pp.278-288
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    • 2014

  • Background: Panax ginseng Meyer is a traditional medicinal plant famous for its strong therapeutic effects and serves as an important herbal medicine. To understand and manipulate genes involved in secondary metabolic pathways including ginsenosides, transcriptome profiling of P. ginseng is essential. Methods: RNA-seq analysis of adventitious roots of two P. ginseng cultivars, Chunpoong (CP) and Cheongsun (CS), was performed using the Illumina HiSeq platform. After transcripts were assembled, expression profiling was performed. Results: Assemblies were generated from ~85 million and ~77 million high-quality reads from CP and CS cultivars, respectively. A total of 35,527 and 27,716 transcripts were obtained from the CP and CS assemblies, respectively. Annotation of the transcriptomes showed that approximately 90% of the transcripts had significant matches in public databases.We identified several candidate genes involved in ginsenoside biosynthesis. In addition, a large number of transcripts (17%) with different gene ontology designations were uniquely detected in adventitious roots compared to normal ginseng roots. Conclusion: This study will provide a comprehensive insight into the transcriptome of ginseng adventitious roots, and a way for successful transcriptome analysis and profiling of resource plants with less genomic information. The transcriptome profiling data generated in this study are available in our newly created adventitious root transcriptome database (http://im-crop.snu.ac.kr/transdb/index.php) for public use.

  • https://doi.org/10.1016/j.jgr.2014.05.008 인용 PDF KSCI

The Complete Chloroplast Genome Sequence and Intra-Species Diversity of Rhus chinensis

  • Kim, Inseo;Park, Jee Young;Lee, Yun Sun;Joh, Ho Jun;Kang, Shin Jae;Murukarthick, Jayakodi;Lee, Hyun Oh;Hur, Young-Jin;Kim, Yong;Kim, Kyung Hoon;Lee, Sang-Choon;Yang, Tae-Jin
    • Plant Breeding and Biotechnology
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    • 제5권3호
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    • pp.243-251
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    • 2017

  • Rhus chinensis is a shrub widely distributed in Asia. It has been used for traditional medicine and ecological restoration. Here, we report the complete chloroplast genome sequence of two R. chinensis genotypes collected from China and Korea. The assembled chloroplast genome of Chinese R. chinensis is 149,094 bp long, consisting of a large single copy (97,246 bp), a small single copy (18,644 bp) and a pair of inverted repeats (16,602 bp). Gene annotation revealed 77 protein coding genes, 30 tRNA genes, and 4 rRNA genes. A phylogenomic analysis of the chloroplast genomes with 11 known complete chloroplast genomes clarified the relationship of R. chinensis with the other plant species in the Sapindales order. A comparative chloroplast genome analysis identified 170 SNPs and 85 InDels at intra-species level of R. chinensis between Chinese and Korean collections. Based on the sequence diversity between Korea and Chinese R. chinensis plants, we developed three DNA markers useful for genetic diversity and authentication system. The chloroplast genome information obtained in this study will contribute to enriching genetic resources and conservation of endemic Rhus species.

  • https://doi.org/10.9787/PBB.2017.5.3.243 인용