Development and characterization of microsatellite markers for the French endemic Angelica heterocarpa (Apiaceae) and congeneric sympatric species
BMC Research Notes volume 15, Article number: 15 (2022)
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.
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.
Angelica L. is a large complex genus comprising approximately 110 species confined in the northern hemisphere, with the majority in Eurasia . In this paper, four French native congeneric Angelica species are considered. Angelica heterocarpa Lloyd is endemic to southwestern French estuary banks. It is protected at national level in France and is listed as priority species in the Habitats Directive of European Union . Angelica sylvestris L. is common in open and forest habitats and is widely distributed among Europe and Asia. Despite different ecological niches, A. heterocarpa and A. sylvestris can live in neighboring riverbank locations. The observation of morphological intermediates questions the taxonomic relationship and potential for hybridization between these two species. Two other species are present in southwestern France: Angelica razulii Gouan, a Pyrenean endemic that shares hydrographic zones with A. heterocarpa and A. sylvestris, and Angelica archangelica L. that occurs naturally in estuaries from northern France and Europe and is cultivated in southwestern France for aromatic and pharmacological interests.
For the effective conservation of A. heterocarpa, genetic markers providing resolution at the population level are essential although, until now, not available. Here, we report the characterization of 16 new polymorphic microsatellite markers for A. heterocarpa and A. sylvestris and test their cross‐species transferability in A. razulii and A. archangelica.
Plant material was collected across natural populations in France or Germany: two for A. heterocarpa (N = 78), three for A. sylvestris (N = 98) and one for A. razulii (N = 50) and A. archangelica (N = 3) (Table 4 in Appendix 1). One or two leaflets were collected from each plant and preserved dried in silica gel. DNA was extracted with the Invitek extraction kit (Invitek, Berlin, Germany). Microsatellites markers were developed from sequences obtained from A. heterocarpa and A. sylvestris after enrichment by both traditional cloning and high throughput sequencing (GenoScreen, Lille, France) of microsatellite-enriched library . Sequences containing microsatellites were identified using the QDD software  and primers were designed using the Primer 3 software  using default parameters with 56 °C as annealing temperature. A total of 119 primers pairs for these SSR loci were tested for amplification and genotyping of 4 of each A. heterocarpa and A. sylvestris individuals using primer extended with M13 sequence for fluorescent labeling . All of them were found to amplify in the both species and among them, 16 showing polymorphisms and consistent peak profile were selected in the final genotyping protocol (Table 1).
Multiplexed PCR were achieved using Qiagen Microsatellite Type-It master mix (Qiagen, Hilden, Germany) and cycling conditions were: 15 min at 95 °C; 30 cycles of 30 s at 94 °C, 60 s at 56 °C, 45 s at 72 °C; and 60 °C for 30 min. The fluorescent‐labeled PCR products were run on an ABI 3730 DNA Analyzer (Applied Biosystems, Waltham, MA, USA) at the Genome Transcriptome Facility of Bordeaux. Genotype calling was carried out manually using GeneMapper Software (Applied Biosystems, Waltham, MA, USA).
Results and discussion
Overall, the developed microsatellite loci were highly polymorphic with a number of alleles per locus ranged from 2 to 21 with a mean of 8 alleles per locus in the five studied A. heterocarpa and A. sylvestris populations (Table 2). At the population level, the observed heterozygosity ranged from 0.54 to 0.60, and the expected heterozygosity ranged from 0.66 to 0.74. Four out of the 16 loci showed significant deviations from Hardy–Weinberg equilibrium (HWE) in more than one population after correcting for multiple testing (P < 0.001; Table 2).
The cross‐species transferability and polymorphism of the developed SSR markers were further tested in the two other congeneric species (Table 3). In A. razulii, only 7 out of the 16 loci amplified consistently and were polymorphic. On the 12 markers tested in A. archangelica, 7 amplified successfully and were polymorphic. Note that additional markers amplified inconsistently, suggesting presences of null alleles or limited transferability (3 markers for A. razulii and 4 for A. archangelica, Table 3).
These new polymorphic markers will allow investigating population genetic structure, reproductive system, and potential hybridization within the Angelica species complex. Moreover, as numerous Angelica species are traditional medicine herbs all over the Eurasia continent, including A. sylvestris and A. archangelica , these microsatellite markers complement the molecular markers previously developed for other congeneric species of particular pharmacological interest [8,9,10].
Deviation from HWE: Loci showing marked deficits in heterozygotes in most populations are likely affected by null alleles. However, this should be further investigate with larger sample size because the restricted sampled size of the present study hampered additional statistical test. In addition, more biological insight to support the fact that the species is expect to follow HWE is needed because population substructure or hybridization are likely affecting Angelica population and would resulted in departure from HWE.
Sample size limitation for A. archangelica: only 3 individuals have been included to test for transferability and polymorphism for this species. Amplification success and polymorphism should be assessed in a larger sample size to confirm monomorphic loci.
Availability of data and materials
The genotypic dataset supporting the conclusions of this article available in the Data INRAE repository under DOI, https://doi.org/10.15454/LFMP64. Sequences are accessible in Genbank under accession number MZ065559-MZ065574.
Polymerase chain reaction
Simple sequence repeat
Liao C, Gao Q, Katz-Downie DS, Downie SR. A systematic study of North American Angelica species (Apiaceae) based on nrDNA ITS and cpDNA sequences and fruit morphology. J Syst Evol. 2021. https://doi.org/10.1111/jse.12702.
Council Directive 92/43/EEC of 21 May 1992 on the conservation of natural habitats and of wild fauna and flora. Eur-Lex. 1992. http://data.europa.eu/eli/dir/1992/43/2013-07-01. Accessed 3 Jan 2022.
Malausa T, Gilles A, Meglécz E, Blanquart H, Duthoy S, Costedoat C, et al. High-throughput microsatellite isolation through 454 GS-FLX titanium pyrosequencing of enriched DNA libraries. Mol Ecol Resour. 2011;11:638–44. https://doi.org/10.1111/j.1755-0998.2011.02992.x.
Meglécz E, Costedoat C, Dubut V, Gilles A, Malausa T, Pech N, et al. QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects. Bioinformatics. 2010;26:403–4. https://doi.org/10.1093/bioinformatics/btp670.
Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. In: Misener S, Krawetz SA, editors. Bioinformatics methods and protocols. New Jersey: Humana Press; 2000. p. 365–86. https://doi.org/10.1385/1-59259-192-2:365.
Schuelke M. An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol. 2000;18:233–4.
Sarker SD, Nahar L. Natural medicine: the genus Angelica. Curr Med Chem. 2004;11:1479–500. https://doi.org/10.2174/0929867043365189.
Hao H-C, Chang J-Y, Chung F-Y. Internal transcribed spacer sequence analysis of Angelica from different habitats. Genom Med Biomark Heal Sci. 2012;4:43–4. https://doi.org/10.1016/J.GMBHS.2012.04.017.
Lu Y, Cheng T, Zhu T, Jiang D, Zhou S, Jin L, et al. Isolation and characterization of 18 polymorphic microsatellite markers for the “Female Ginseng” Angelica sinensis (Apiaceae) and cross-species amplification. Biochem Syst Ecol. 2015;61:488–92. https://doi.org/10.1016/J.BSE.2015.07.013.
Gil J, Um Y, Kim S, Kim O, Koo S, Reddy C, et al. Development of genome-wide SSR markers from Angelica gigas nakai using next generation sequencing. Genes. 2017;8:238. https://doi.org/10.3390/genes8100238.
The authors thank Henri Caron, Patrick Léger and Guillaume Lalanne-Tisné for their technical assistance in developing SSR markers and genotyping, and Conservatoire Botanique National Sud Atlantique, particularly Sandrine Loriot, Conservatoire Botanique National de Brest and Jean-Pierre Reduron for sampling natural populations. ABI 3730 capillary electrophoreses were performed at the Genome Transcriptome Facility of Bordeaux (Grants from Investissements d’avenir, Convention attributive d’aide EquipEx Xyloforest ANR-10-EQPX-16-01).
Funding were from support of Conservatoire Botanique National Sud Atlantique and University of Bordeaux.
Ethics approval and consent to participate
Plant leaflets of A. heterocarpa were collected by the Conservatoire Botanique National Sud-Atlantique and the Conservatoire Botanique National de Brest, which both have national agreement from the French Ministry of the environment with written authorization from the regional legal representatives of the Ministry.
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The authors declare that they have no competing interests.
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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 15, 15 (2022). https://doi.org/10.1186/s13104-021-05903-2
- Population genetics
- Genetic diversity
- Nuclear SSR
- Estuary riverbanks
- Angelica sylvestris
- Angelica razulii
- Angelica archangelica