Abstract
Amplified fragment length polymorphisms (AFLPs) are a useful molecular tool for studying species with little available genetic information; however, since universal primers are used contaminant DNA from non-target organisms may also be amplified. Cambium tissue may contain fewer biotic contaminants or plant defense chemicals, than the more commonly used leaf tissue, and therefore be more suitable for use as a source of DNA when using universal primers. On the other hand, cambium tissue can be difficult to identify, yields low DNA and requires the bark of the tree to be damaged, thereby increasing the risk of introducing disease. We show that within two tropical tree species, there are few differences between AFLP profiles obtained from either cambium or leaf tissue from the same tree. We studied 50 Brosimum alicastrum individuals at 119 AFLP loci and 40 Swietenia macrophylla individuals at 112 AFLP loci. The matrix of Sørensen similarity indices between individual AFLP profiles for cambium samples was strongly correlated to the matrix for leaf samples in each species (Mantel test; B. alicastrum r = 0.815, P < 0.001; S. macrophylla r = 0.895, P < 0.001). The phylogenetic relationship between the trees studied did not differ dependent on tissue type used and therefore shows that both tissues can be used within a single study without introducing substantial error.
References
Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3:e3376. doi:10.1371/journal.pone.0003376
Blears MJ, De Grandis SA, Lee H, Trevors JT (1998) Amplified fragment length polymorphism (AFLP): a review of the procedure and its applications. J Ind Microbiol Biotechnol 21:99–114
Chase MW, Hills HH (1991) Silica gel: an ideal material for field preservation of leaf samples for DNA studies. Taxonomy 40:215–220
Cloutier D, Hardy OJ, Caron H, Clampi AY, Degen B, Kanashiro M, Schoen DJ (2007) Low inbreeding and high pollen dispersal distances in populations of two Amazonian forest tree species. Biotropica 39:406–415
Colpaert N, Cavers S, Bandou E, Caron H, Gheysen G, Lowe AJ (2005) Sampling tissue for DNA analysis of trees: trunk cambium as an alternative to canopy leaves. Silvae Genetica 54:265–269
Donini P, Elias ML, Bougourd SM, Koebner RMD (1997) AFLP fingerprinting reveals pattern differences between template DNA extracted from different plant organs. Genome 40:521–526
Doyle JJ, Doyle JT (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull, Botanical Soc Am 19:11–15
Duminil J, Caron H, Scotti I, Cazal SO, Petit RJ (2006) Blind population genetics survey of tropical rainforest trees. Mol Ecol 15:3505–3513. doi:10.1111/j.1365-294X.2006.03040.x
Fay MF, Lledó MD, Kornblum MM, Crespo MB (1999) From the waters of Babylon? Populus euphratica in Spain is clonal and probably introduced. Biodivers Conserv 8:769–778
Fisher RA (1918) The correlation between relatives on the supposition of Mendelian inheritance. Trans R Soc Edin 52:399–433
Franceschi VR, Krokene P, Christiansen E, Krekling T (2005) Anatomical and chemical defenses of conifer bark against bark beetles and other pests. New Phytol 167:353–375. doi:10.1111/j.1469-8137.2005.01436.x
Grubb FE (1969) Procedures for detecting outlying observations in samples. Technometrics 11:1–21
Hanson TR, Brunsfeld SJ, Finegan B, Waits LP (2008) Pollen dispersal and genetic structure of the tropical tree Dipteryx panamensis in a fragmented Costa Rican landscape. Mol Ecol 17:2060–2073. doi:10.1111/j.1365-294X.2008.03726.x
Jones CJ, Edwards KJ, Castaglione S, Winfield MO, Sala F, Van de Wiel C, Bredemeijer G, Vosman B, Matthes M, Daly A et al (1997) Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories. Mol Breed 3:381–390
Khanuja SPS, Shasany AK, Darokar MP, Kumar S (1999) Rapid isolation of DNA from dry and fresh samples of plants producing large amounts of secondary metabolites and essential oils. Plant Mol Biol Rep 17:1–7
Legendre P, Legendre L (1998) Ecological resemblance. Numerical ecology, 2nd edn. Elsevier BV, Amsterdam, The Netherlands
Mueller UG, Wolfenbarger LLR (1999) AFLP genotyping and fingerprinting. Trends Ecol Evol 14:389–394
Nei M, Li H (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76:5269–5273
Pearce RB (1996) Antimicrobial defences in the wood of living trees. New Phytol 132:203–233
Rosenberg MS, Anderson CD (2011) PASSaGE: Pattern analysis, spatial statistics and geographic exegesis. Version 2. Methods in Ecology and Evolution 2:229–232. doi:10.1111/j.2041-210X.2010.00081.x
Saar DE, Polans NO, Sørensen PD, Duvall MR (2001) Angiosperm DNA contamination by endophytic fungi: detection and methods of avoidance. Plant Mol Biol Report 19:249–260
Vos P, Hogers R, Bleeker M, Reijans M, Van De Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M et al (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414
Wilkinson T, Wetten A, Prychid C, Fay MF (2003) Suitability of cryopreservation for the long-term storage of rare and endangered plant species: a case history for Cosmos atrosanguineus. Annals of Botany 91:65–74
Zytynska SE, Fay MF, Penny D, Preziosi RF (2011) Genetic variation in a tropical tree species influences the associated epiphytic plant and invertebrate communities in a complex forest ecosystem. Phil Trans R Soc B 366:1329–1336
Acknowledgements
We thank Waldo Etherington and Mr Tec for tree climbing. We dedicate this work to the late Nicodemus ‘Chapal’ Bol from Las Cuevas Research Station, and thank Isidro Bol for tree identification and leaf collection. We thank Robyn Cowan for molecular assistance. We also thank Jennifer Rowntree and two anonymous referees for comments on the manuscript. This work was funded by a Natural Environment Research Council PhD studentship to S.E.Z.
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by S. González-Martínez
Electronic supplementary material
Below is the link to the electronic supplementary material.
Table S1
DNA purity from leaf and cambium samples (DOC 28 kb)
Fig. 4
DNA (microgram) obtained from 1 g of dried tissue. Error bars represent ± 1 standard error. C cambium, L leaf, BA Brosimum alicastrum, SM Swietenia macrophylla (JPEG 1868 kb)
Rights and permissions
About this article
Cite this article
Zytynska, S.E., Fay, M.F. & Preziosi, R.F. Comparing the use of leaf and cambium tissue in a single genetic study of tropical trees. Tree Genetics & Genomes 8, 431–437 (2012). https://doi.org/10.1007/s11295-011-0453-8
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11295-011-0453-8