황기의 유전체 기반 SSR 마커 개발
Development of Whole Genome Sequence-based Novel SSR Markers in Astragalus membranaceus (Fisch.)
1
조회
0
다운로드
2
인용
0
참고문헌
키워드
초록
Background: Although Astragalus membranaceus is a major medicinal herb used for food and medicinal purposes, genome-based research for its exploration is insufficient. The introduction of the genetic breeding system for medicinal crops, based on genomic analysis, will have a great impact not only on the establishment of the origin but also on understanding the existing traditional breeding system. Methods and Results: A. membranaceus from five accessions of Poongsung, Asung, Jecheon, Sancheong, and Jilin from China were used, which are cultivated in the test field. The produced nucleotide sequences were assembled de novo to obtain 450,449 contigs, and the repeat sequences were extracted using the selection criteria, two to six nucleotide sequences repeated five time or more. Finally, we obtained 147,766 simple sequence repeat (SSR) marker candidates. Using the CLC genomics workbench program, 949 SSR markers showing mutations for Astragalus in the 5 accessions were selected. From the designed primer sets, 99 were randomly selected and applied to the genomic DNA which was extracted from five cultivars and pooled. Ten primer sets showing more than two bands were finally selected as SSR markers, and were used for the genetic relationship analysis in 81 strains of A. membranaceus. Conclusions: The data of this study can be used as a marker when registering A. membranaceus varieties through pure line selection and line breeding in the future. It is thought that it can greatly contribute to securing intellectual property rights for domestic Astragalus breeding varieties.
Abstract
Background: Although Astragalus membranaceus is a major medicinal herb used for food and medicinal purposes, genome-based research for its exploration is insufficient. The introduction of the genetic breeding system for medicinal crops, based on genomic analysis, will have a great impact not only on the establishment of the origin but also on understanding the existing traditional breeding system. Methods and Results: A. membranaceus from five accessions of Poongsung, Asung, Jecheon, Sancheong, and Jilin from China were used, which are cultivated in the test field. The produced nucleotide sequences were assembled de novo to obtain 450,449 contigs, and the repeat sequences were extracted using the selection criteria, two to six nucleotide sequences repeated five time or more. Finally, we obtained 147,766 simple sequence repeat (SSR) marker candidates. Using the CLC genomics workbench program, 949 SSR markers showing mutations for Astragalus in the 5 accessions were selected. From the designed primer sets, 99 were randomly selected and applied to the genomic DNA which was extracted from five cultivars and pooled. Ten primer sets showing more than two bands were finally selected as SSR markers, and were used for the genetic relationship analysis in 81 strains of A. membranaceus. Conclusions: The data of this study can be used as a marker when registering A. membranaceus varieties through pure line selection and line breeding in the future. It is thought that it can greatly contribute to securing intellectual property rights for domestic Astragalus breeding varieties.
참고문헌 (31)
- Dong TTX, "Phylogeny of Astragalus in China : Molecular evidence from the DNA sequences of 5S rRNA spacer, ITS, and 18S rRNA", Journal of Agricultural and Food Chemistry, 51, pp.6709~6714 (2003)
- Du X, "Astragalus polysaccharides enhance immune responses of HBV DNA vaccination via promoting the dendritic cell maturation and suppressing Treg frequency in mice", International Immunopharmacology, 14, pp.463~470 (2012)
- Fu J, "Review of the botanical characteristics, phytochemistry, and pharmacology of Astragalus membranaceus(Huangqi)", Phytotherapy Research, 28, pp.1275~1283 (2014)
- Gil JS, "Development of genome-wide SSR markers from Angelica gigas Nakai using next generation sequencing", Genes, 8, pp.238~ (2017)
- Henry RJ, "Next-generation sequencing for understanding and accelerating crop domestication", Briefings in Functional Genomics, 11, pp.51~56 (2012)
- 조익현, "미토콘드리아 DNA 염기서열 변이를 이용한 인삼 종 판별 연구", 한국약용작물학회지, 21(2), pp.91~96 (2013), 한국약용작물학회[DOI]
- Kajimura K, "Protective effect of Astragali radix by intraperitoneal injection against Japanese encephalitis virus infection in mice", Biological and Pharmaceutical Bulletin, 19, pp.855~859 (1996)
- Kilian B, "NGS technologies for analyzing germplasm diversity in genebanks", Briefings in Functional Genomics, 11, pp.38~50 (2012)
- Kim JE, "Whole-genome, transcriptome, and methylome analyses provide insights into the evolution of platycoside biosynthesis in Platycodon grandiflorus, a medicinal plant", Horticulture Research, 7, pp.112~ (2020)
- Jin Hee Kim, "Quantitative Evaluation of Radix Astragali through the Simultaneous Determination of Bioactive Isoflavonoids and Saponins by HPLC", UV and LC-ESI-MS, Bulletin of the Korean Chemical Society, pp.2007, 28(7)[DOI]
- 김세림, "Simple sequence repeat marker development from Codonopsis lanceolata and genetic relation analysis", Journal of Plant Biotechnology, 43(2), pp.181~188 (2016), 한국식물생명공학회[DOI]
- 이은정, "db", db마우스에서 Aspergillus awamori로 발효한 황기 추출물의 항당뇨 및 지질개선 효능, 2021, pp.29(4), 263~272[DOI]
- 이은송, "황기 재배지에서 토양의 물리적 특성에 따른 습해 정도와 재배적지 기준 설정", 한국약용작물학회지, 29(4), pp.273~281 (2021), 한국약용작물학회[DOI]
- 이기욱, "Bacillus spp.에 의한 황기의 생육촉진 및 토양병해 방제효과", 한국약용작물학회지, 29(2), pp.99~109 (2021), 한국약용작물학회[DOI]
- TW, "Immunomodulatory effects of aqueous extracted Astragali radix in methotrexate treated mouse spleen cells", Journal of Ethnopharmacology, 84, pp.193~198 (2003)
- Lei H, "Anti-aging effect of astragalosides and its mechanism of action", Acta Pharmacologica Sinica, 24, pp.230~234 (2003)
- Lei W, "Intraspecific and heteroplasmic variations, gene losses and inversions in the chloroplast genome of Astragalus membranaceus", Scientific Reports, 6, pp.21669~ (2016)
- Li J, "Long read reference genome-free reconstruction of a full-length transcriptome from Astragalus membranaceus reveals transcript variants involved in bioactive compound biosynthesis", Cell Discovery, 3, pp.17031~ (2017)
- Li R, "Developmental anatomy of anomalous structure and classification of commercial specifications and grades of the Astragalus membranaceus var. mongholicus", Microscopy Research and Technique, 81, pp.1165~1172 (2018)
- Liu K, "PowerMarker : An integrated analysis environment for genetic marker analysis", Bioinformatics, 21, pp.2128~2129 (2005)
- Mardis ER, "Next-generation DNA sequencing methods", Annual Review of Genomics and Human Genetics, 9, pp.387~402 (2008)
- Moose SP, "Molecular plant breeding as the foundation for 21st century crop improvement", Plant Physiology, 147, pp.969~977 (2008)
- Nybom H, "Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants", Molecular Ecology, 13, pp.1143~1155 (2004)
- Tian C, "Characterization and comparative analysis of complete chloroplast genomes of three species from the genus Astragalus(Leguminosae)", Frontiers in Genetics, 12, pp.705482~ (2021)
- 엄유리, "Identification of Korean Ginseng (Panax ginseng) Cultivars Using Simple Sequence Repeat Markers", Plant Breeding and Biotechnology, 4(1), pp.71~78 (2016), 한국육종학회[DOI]
- Untergasser A, "Primer3-new capabilities and interfaces", Nucleic Acids Research, 40, pp.e115~ (2012)
- Wang B, "Complete plastid genome of Astragalus membranaceus(Fisch.) Bunge var. membranaceus", Mitochondrial DNA Part B, 1, pp.517~519 (2016)
- Wang XJ, "Antioxidant activity of Qizhu tang", Acta Pharmacologica Sinica, 21, pp.1141~1144 (2000)
- Wang Z, "RNA-Seq : A revolutionary tool for transcriptomics", Nature Reviews Genetics, 10, pp.57~63 (2009)
- Zhang WJ, "Antiinflammatory activity of astragaloside IV is mediated by inhibition of NF-κB activation and adhesion molecule expression", Thrombosis and Haemostasis, 90, pp.904~914 (2003)
- Zhang YD, "Effect of astragaloside IV on inflammatory and hypertension", Acta Pharmacologica Sinica, 19, pp.333~337 (1984)