Translator Disclaimer
19 August 2016 Microsatellites in the Tree Foetidia mauritiana (Lecythidaceae) and Utility in Other Foetidia Taxa from the Mascarene Islands
Author Affiliations +

Trees that belong to the family Lecythidaceae are often used as indicators of disturbance in lowland tropical forests, in particular because they are usually among the most common trees in these rich but fragile ecosystems (Mori et al., 2007). In addition to their ecological significance, some species may also be economically important, such as the Brazil nut tree Bertholletia excelsa Bonpl. For these reasons, polymorphic genetic markers have been developed for several species of several subfamilies of Lecythidaceae, mostly in taxa occurring as large trees in the Amazon Basin (e.g., Bertholletia Bonpl. [Reis et al., 2009], Cariniam Casar. [Guidugli et al., 2009, 2010], and Lecythis Loefl. [Rodrigues et al., 2015]), but also in a few other taxa found in the Old World (e.g., Barringtonia J. R. Forst. & G. Forst. [Xie et al., 2015]). However, to our knowledge, polymorphic markers are not yet available for the representatives of Lecythidaceae in the biodiversity hotspot formed by Madagascar and the Indian Ocean islands.

Out of 18 species that make up the genus Foetidia Comm, ex Lam. (subfamily Foetidioideae), 17 are endemic to island biotas in Madagascar, the Comoros, and the Mascarene Islands, while one species is found only on the African continent in Tanzania (Prance, 2008; Labat et al., 2011). The endemic species F. mauritiana Lam. was common in drier areas of Mauritius and Réunion where precipitation is low and temperatures are high, relative to the wet conditions generally found on these two tropical islands. However, for this species as for many indigenous taxa adapted to dry tropical habitats, populations have undergone rapid decline in less than 400 years since human settlement, and those few remaining stands are left in highly fragmented landscapes on both islands. This species is considered endangered in Réunion and Mauritius. There is an urgent need to protect and restore natural communities in tropical dry habitats on the Indian Ocean islands as well as worldwide (Miles et al., 2006). A European Union–supported project, Life+ Corexrun, was launched in 2009 on Réunion; it aims at both reintroducing 48 indigenous plant species (including F. mauritiana) and controlling invasions by alien plants within and around semi-dry forest stands.

METHODS AND RESULTS

Genomic DNA of F. mauritiana was extracted with the DNeasy Plant Mini Kit (QIAGEN, Hilden, North Rhine-Westphalia, Germany). Production of a microsatellite-enriched library was outsourced to the high-throughput platform set up by Genoscreen (Lille, Nord-Pas-de-Calais-Picardie, France). Following the method described in Malausa et al. (2011), 1 µg of genomic DNA was mechanically fragmented, ligated to standard adapters (Adap-F: GTTTAAGGCCTAGCTAGCAGAATC and Adap-R: GATTCTGCTAGCTAGGCCTT), and enriched by addition of eight biotin-labeled oligoprobes corresponding to the following microsatellite motifs: (TG)n, (TC)n, (AAC)n, (AAG)n, (AGG)n, (ACG)n, (ACAT)n, and (ACTC)n. Enriched DNA was isolated using Dynabeads (Invitrogen, Waltham, Massachusetts, USA) and amplified by PCR with primers corresponding to the library adapters (PCR protocol not communicated by Genoscreen). Sequencing was carried out through 454 GS-FLX Titanium pyrosequencing (Roche Applied Science, Penzberg, Bavaria, Germany). Sequences were analyzed using the bioinformatics program QDD (Meglécz et al., 2010), which detects microsatellite sequences and designs primers in flanking regions. We then selected 13 primer pairs among the microsatellite sequences (dinucleotide repeats), because they had adequate flanking regions for designing primers (see Table 1 for locus information, primers, and GenBank accession numbers). Eight additional microsatellite loci are provided in this paper, although population testing was not conducted for these markers (Appendix 1).

Table 1.

Characteristics of 13 microsatellite loci developed in Foetidia mauritiana.

t01_01.gif

For biological validation, we selected the main wild populations on Réunion. This included 49 individuals sampled near the Lataniers River (mean elevation 330 m), 45 individuals on the southern slope of the Grande-Chaloupe River (545 m), and 27 individuals near the Tamarins River (270 m), for a total of 121 individuals (sampling authorized by the Parc National de La Réunion, the Office National des Forêts, the Département de La Réunion, and the Conservatoire du Littoral). Because the species is considered critically endangered on Réunion, we harvested no more than 1–2 leaves per individual tree, with the exception of three individuals (one per locality) from which voucher specimens were made (see Appendix 2). Plant genomic DNA was isolated with the DNeasy Plant Mini Kit (QIAGEN). Multiplex PCR was performed in a total volume of 15 µL containing 7.5 µL 2× Type-it Multiplex PCR Master Mix (QIAGEN), 1.5 µL 5× Q-Solution, 0.2 µM each primer, and 20–50 ng template DNA. The thermal cycling protocol was as follows: initial denaturation at 95°C for 5 min; 28 cycles of denaturation at 95°C for 30 s, primer annealing at 57°C for 90 s, extension at 72°C for 30 s; and final extension at 60°C for 30 min. PCR products were diluted in HPLC-grade water (1:10), denatured in formamide, and separated on a 16-capillary ABI PRISM 3130xl Genetic Analyzer (Applied Biosystems, Foster City, California, USA); GeneScan 500 LIZ (Applied Biosystems) was used for sizing alleles in the expected range of 80–300 bp.

Table 2.

Genetic properties of the 13 newly developed microsatellites of Foetidia mauritiana.a

t02_01.gif

Allele sizes were estimated using the Microsatellite Plugin version 1.4 implemented in Geneious version 8.1.7 (Biomatters, Auckland, New Zealand). The number of different alleles and observed and expected heterozygosity were calculated for each locus and population in GenAlEx (Peakall and Smouse, 2006, 2012). Hardy–Weinberg exact tests (9999 iterations) and linkage disequilibrium were analyzed in GENEPOP version 4.2 (Rousset, 2008). The presence of null alleles was estimated with MICRO-CHECKER version 2.2.3 (van Oosterhout et al., 2004). The minimum number of microsatellite loci necessary to discriminate individuals of F. mauritiana was assessed using the package poppr in R software (Kamvar et al., 2015).

Table 3.

Cross-species amplification (showing number of different alleles and size range) of the 13 newly developed microsatellites of Foetidia mauritiana.a

t03_01.gif

All microsatellite loci revealed polymorphisms in F. mauritiana populations on Réunion. The number of different alleles per locus ranged from two to 17 (Table 2). Four loci showed significant deviation from Hardy–Weinberg equilibrium: FmCIR27, FmCIR47, FmCIR16, and FmCIR3. No significant linkage disequilibrium was detected between pairs of loci. We found that the minimum number of loci necessary to discriminate individuals in the data set was eight (data not shown).

Transferability of the microsatellite loci was tested on 28 individuals of F. mauritiana and 30 individuals of F. rodriguesiana F. Friedmann sampled across Mauritius and Rodrigues, respectively (sampling authorized by the National Parks and Conservation Service of Mauritius). Conspecific populations on different islands were tested because they are expected to experience strong genetic isolation. Foetidia rodriguesiana is morphologically similar to F. mauritiana (Prance, 2008). Using the above-mentioned protocol, we found that all loci amplified in Foetidia populations found on other islands, with the exception of FmCIR31, which did not amplify in F. rodriguesiana (Table 3). Moreover, most loci were polymorphic in the Mauritius and Rodrigues populations.

CONCLUSIONS

We developed 13 polymorphic genetic markers for Foetidia, a widespread genus in the Indian Ocean islands biodiversity hotspot. They will aid in designing priority populations for conservation and implementing adaptive conservation plans for the genus. They may also be used to study mating systems and pollen and seed flow between lowland forest fragments.

ACKNOWLEDGMENTS

The authors thank S. Dafreville, T. M'sa, and J. Segrestin (laboratory assistance); P. Adolphe, S. Baret, L. Calichiama, M. Félicité, R. Lucas, H. Thomas (assistance on Réunion); and J. T. Genave, R. Parmananda, J.-C. Sevathian, and A. Waterstone (assistance on Mauritius and Rodrigues). This work was funded by the European Regional Development Fund (ERDF), by the Région Réunion, and by the Centre de Coopération International en Recherche Agronomique pour le Développement (CIRAD).

LITERATURE CITED

1.

Guidugli, M. C., T. de Campos, A. C. B. de Sousa, J. M. Feres, A. M. Sebbenn, M. A. Mestriner, E. P. B. Contel, and A. L. Alzate-Marin. 2009. Development and characterization of 15 microsatellite loci for Cariniana estrellensis and transferability to Cariniana legalis, two endangered tropical tree species. Conservation Genetics 10: 1001–1004. Google Scholar

2.

Guidugli, M. C., K. A. Guerrieri, M. A. Mestriner, E. P. B. Contel, C. A. Martinez, and A. L. Alzate-Marin. 2010. Genetic characterization of 12 heterologous microsatellite markers for the giant tropical tree Cariniana legalis. Genetics and Molecular Biology 33: 131–134. Google Scholar

3.

Kamvar, Z. N., J. C. Brooks, and N. J. Grünwald. 2015. Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality. Frontiers in Genetics 6: 208. Google Scholar

4.

Labat, J.-N., E. Bidault, and G. Viscardi. 2011. A new critically endangered species of Foetidia (Lecythidaceae, subfamily Foetidioideae) recently discovered in Mayotte, Comoros archipelago. Adansonia 33: 263–269. Google Scholar

5.

Malausa, T., A. Gilles, E. Meglécz, H. Blanquart, S. Duthoy, C. Costedoat, et al. 2011. High-throughput microsatellite isolation through 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries. Molecular Ecology Resources 11: 638–644. Google Scholar

6.

Meglécz, E., C. Costedoat, V. Dubut, A. Gilles, T. Malausa, N. Pech, and J-F. Martin. 2010. QDD: A user-friendly program to select microsatellite markers and design primers from large sequencing projects. Bioinformatics 26: 403–404. Google Scholar

7.

Miles, L., A. C. Newton, R. S. DeFries, C. Ravilious, I. May, S. Blyth, V. Kapos, and J. E. Gordon. 2006. A global overview of the conservation status of tropical dry forests. Journal of Biogeography 33: 491–505. Google Scholar

8.

Mori, S. A., C.-H. Tsou, C.-C. Wu, B. Cronholm, and A. A. Anderberg. 2007. Evolution of Lecythidaceae with an emphasis on the circumscription of neotropical genera: Information from combined ndhF and trnL-F sequence data. American Journal of Botany 94: 289–301. Google Scholar

9.

Peakall, R., and P. E. Smouse. 2006. GenAlEx 6: Genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6: 288–295. Google Scholar

10.

Peakall, R., and P. E. Smouse. 2012. GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics (Oxford, England) 28: 2537–2539. Google Scholar

11.

Prance, G. T. 2008. A revision of Foetidia (Lecythidaceae subfamily Foetidioideae). Brittonia 60: 336–348. Google Scholar

12.

Reis, A. M. M., A. C. Braga, M. R. Lemes, R. Gribel, and R. G. Collevatti. 2009. Development and characterization of microsatellite markers for the Brazil nut tree Bertholletia excelsa Humb. & Bonpl. (Lecythidaceae). Molecular Ecology Resources 9: 920–923. Google Scholar

13.

Rodrigues, A. B., C. T. Florence, E. Mariano-Neto, and F. A. Gaiotto. 2015. First microsatellite markers for Lecythis pisonis (Lecythidaceae). an important resource for Brazilian fauna. Conservation Genetics Resources 7: 437–439. Google Scholar

14.

Rousset, F. 2008. GENEPOP'007: A complete reimplementation of the GENEPOP software for Windows and Linux. Molecular Ecology Resources 8: 103–106. Google Scholar

15.

van Oosterhout, C., W. F. Hutchinson, D. P. M. Willis, and P. Shipley. 2004. MICRO-CHECKER: Software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Resources 4: 535–538. Google Scholar

16.

Xie, H., Y. Yuan, X. Fang, Y. Liu, C. Yang, J. Jin, F. Tan, and Y. Huang. 2015. Development of EST-SSR markers in Barringtonia (Lecythidaceae) and cross-amplification in related species. Applications in Plant Sciences 3: 1500080. Google Scholar

Appendices

Appendix 1.

Eight additional microsatellite loci identified in Foetidia mauritiana.a

tA01_01.gif

Appendix 2.

Voucher information for Foetidia populations used in this study.

tA02_01.gif
Florent Martos, Gérard Lebreton, Eric Rivière, Laurence Humeau, and Marie-Hélène Chevallier "Microsatellites in the Tree Foetidia mauritiana (Lecythidaceae) and Utility in Other Foetidia Taxa from the Mascarene Islands," Applications in Plant Sciences 4(8), (19 August 2016). https://doi.org/10.3732/apps.1600034
Received: 17 March 2016; Accepted: 1 May 2016; Published: 19 August 2016
JOURNAL ARTICLE
PAGES


SHARE
ARTICLE IMPACT
Back to Top