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Revardel E, Lepais O. Development and characterization of microsatellite markers for the French endemic Angelica heterocarpa (Apiaceae) and congeneric sympatric species. BMC Res Notes 2022; 15:15. [PMID: 35012643 PMCID: PMC8751362 DOI: 10.1186/s13104-021-05903-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 12/24/2021] [Indexed: 11/11/2022] Open
Abstract
Objective Angelica heterocarpa (Apiaceae) is a wild endemic French species with special conservation interest in the European Union. It belongs to Angelica complex genus which is widespread throughout the north temperate zone, and is sympatric with other congeneric species. The objective of this work is to develop and characterize microsatellite markers as a new tool for understanding the ecology and evolution of Angelica species complex. Results We identified simple sequence repeat (SSR) regions in a microsatellite‐enriched library from A. heterocarpa and A. sylvestris. All 16 selected SSR regions were found to amplify in these species and were highly polymorphic. Marker transferability was validated in A. razulii and A. archangelica. These markers will help us to better understand the evolutionary dynamic between rare endemics and widespread sister species, and be useful for conservation of the endemic species. Moreover, they can provide new tools for studying the numerous traditional medicinal herbs of the Angelica genus.
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Affiliation(s)
| | - Olivier Lepais
- University of Bordeaux, INRAE, BIOGECO, 33615, Pessac, France
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Liu Q, Lu Z, He W, Li F, Chen W, Li C, Chao Z, Tian E. Development and characterization of 16 novel microsatellite markers by Transcriptome sequencing for Angelica dahurica and test for cross-species amplification. BMC PLANT BIOLOGY 2020; 20:152. [PMID: 32268882 PMCID: PMC7140362 DOI: 10.1186/s12870-020-02374-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/31/2020] [Indexed: 05/31/2023]
Abstract
BACKGROUND Angelica dahurica (Apiaceae) is an important herb in traditional Chinese medicine. Because of its important medicinal and economic values, its wild resources were over-exploited and increasingly reduced. Meanwhile, the diversity of cultivars of A. dahurica has decreased as a result of long-term artificial cultivation. However, there are no population genetics studies of natural A. dahurica reported yet, especially for using microsatellite markers (SSRs) to investigate population genetics of the species. RESULTS Sixteen polymorphic EST-SSR loci were isolated from A. dahurica with transcriptome sequencing technology (RNA-Seq). The number of alleles varied from 2 to 15 per polymorphic locus over populations with the observed and expected heterozygosities ranging from 0.000 to 1.000 and from 0.000 to 0.829, respectively. Significant deviations from Hardy-Weinberg equilibrium were observed at 8 loci. Tests of linkage disequilibrium showed 11 informative locus pairs were significant across all populations. Cross-species amplification showed that 14 out of 16 SSR loci have the transferability in cultivar-A. dahurica cv. 'Hangbaizhi' and A. decursiva. CONCLUSIONS The 16 newly developed loci microsatellite primers with RNA-Seq will be useful for further investigating population genetics of A. dahurica, cultivars and other members of this genus.
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Affiliation(s)
- Qianqian Liu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095, China
| | - Zuyu Lu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 515005, China
| | - Wei He
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 515005, China
| | - Fang Li
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 515005, China
| | - Wenna Chen
- College of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, 056038, China
| | - Chan Li
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 515005, China
| | - Zhi Chao
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 515005, China.
| | - Enwei Tian
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 515005, China.
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Gil J, Um Y, Kim S, Kim OT, Koo SC, Reddy CS, Kim SC, Hong CP, Park SG, Kim HB, Lee DH, Jeong BH, Chung JW, Lee Y. Development of Genome-Wide SSR Markers from Angelica gigas Nakai Using Next Generation Sequencing. Genes (Basel) 2017; 8:E238. [PMID: 28934115 PMCID: PMC5664088 DOI: 10.3390/genes8100238] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/17/2017] [Accepted: 09/18/2017] [Indexed: 12/19/2022] Open
Abstract
Angelica gigas Nakai is an important medicinal herb, widely utilized in Asian countries especially in Korea, Japan, and China. Although it is a vital medicinal herb, the lack of sequencing data and efficient molecular markers has limited the application of a genetic approach for horticultural improvements. Simple sequence repeats (SSRs) are universally accepted molecular markers for population structure study. In this study, we found over 130,000 SSRs, ranging from di- to deca-nucleotide motifs, using the genome sequence of Manchu variety (MV) of A. gigas, derived from next generation sequencing (NGS). From the putative SSR regions identified, a total of 16,496 primer sets were successfully designed. Among them, we selected 848 SSR markers that showed polymorphism from in silico analysis and contained tri- to hexa-nucleotide motifs. We tested 36 SSR primer sets for polymorphism in 16 A. gigas accessions. The average polymorphism information content (PIC) was 0.69; the average observed heterozygosity (HO) values, and the expected heterozygosity (HE) values were 0.53 and 0.73, respectively. These newly developed SSR markers would be useful tools for molecular genetics, genotype identification, genetic mapping, molecular breeding, and studying species relationships of the Angelica genus.
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Affiliation(s)
- Jinsu Gil
- Department of Industrial Plant Science & Technology, Chungbuk National University, Chungju 28644, Korea.
| | - Yurry Um
- Forest Medicinal Resources Research Center, National Institute of Forest Science, Yeongju 36040, Korea.
| | - Serim Kim
- Department of Industrial Plant Science & Technology, Chungbuk National University, Chungju 28644, Korea.
| | - Ok Tae Kim
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong 27709, Korea.
| | - Sung Cheol Koo
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong 27709, Korea.
| | - Chinreddy Subramanyam Reddy
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong 27709, Korea.
| | - Seong-Cheol Kim
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeju 63240, Korea.
| | | | - Sin-Gi Park
- TheragenEtex Bio Institute, Suwon 16229, Korea.
| | - Ho Bang Kim
- Life Sciences Research Institute, Biomedic Co., Ltd., Bucheon 14548, Korea.
| | - Dong Hoon Lee
- Department of Biosystems Engineering, Chungbuk National University, Chungju 28644, Korea.
| | - Byung-Hoon Jeong
- Korea Zoonosis Research Institute, Chonbuk National University, Iksan 54531, Korea.
| | - Jong-Wook Chung
- Department of Industrial Plant Science & Technology, Chungbuk National University, Chungju 28644, Korea.
| | - Yi Lee
- Department of Industrial Plant Science & Technology, Chungbuk National University, Chungju 28644, Korea.
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Guo JJ, Shang SB, Wang CS, Zhao ZG, Zeng J. Twenty microsatellite markers for the endangered Vatica mangachapoi (Dipterocarpaceae). APPLICATIONS IN PLANT SCIENCES 2017; 5:apps1600134. [PMID: 28224060 PMCID: PMC5315383 DOI: 10.3732/apps.1600134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 12/27/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY Microsatellite markers were developed for Vatica mangachapoi (Dipterocarpaceae), an endangered species indigenous to Southeast Asia and southern China. METHODS AND RESULTS Twenty microsatellite markers, including 12 polymorphic markers, were identified from V. mangachapoi using high-throughput sequencing. Polymorphism at each marker was evaluated using 87 individuals from three natural populations. The number of alleles per polymorphic locus ranged from six to 15, and the observed and expected heterozygosity varied from 0.000 to 0.926 and from 0.177 to 0.864, respectively. These markers were transferred successfully to the endangered species V. guangxiensis. CONCLUSIONS These markers may be used to investigate the genetic diversity and gene flow of V. mangachapoi and V. guangxiensis.
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Affiliation(s)
- Jun-Jie Guo
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, People’s Republic of China
| | - Shuai-Bin Shang
- Northwest Institute of Forest Inventory, Planning and Design, State Forestry Administration, Xi’an, Shaanxi 710048, People’s Republic of China
| | - Chun-Sheng Wang
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, People’s Republic of China
| | - Zhi-Gang Zhao
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, People’s Republic of China
| | - Jie Zeng
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, People’s Republic of China
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