Abstract
From two cDNA libraries made of flowers of the evergreen Rhododendron simsii hybrid ‘Flamenco’ and the deciduous species Rhododendron luteum, 323 cDNA fragments were randomly sequenced and functions were assigned. Reliable homologies were found for 31% of the fragments. For mapping applications, EST-derived markers were developed on 127 sequences. Since polymorphisms are more prone to come about in introns, primers were selected to have an elevated probability to be intron-spanning. The utilised approach resulted in an overall polymorphism-generating efficiency of 35% (45 polymorphic markers). The transferability of these cDNA-based EST markers among plant species was confirmed within the Rhododendron genus. The markers developed here are currently screened for the construction of genetic linkage maps of four crossing populations of R. simsii hybrids.
References
Alexandrov NN, Troukhan ME, Brover VV, Tatarinova T, Flavell RB, Feldmann K (2006) Features of Arabidopsis genes and genome discovered using full-length cDNAs. Plant Mol Biol 60:69–85. doi:10.1007/s11103-005-2564-9
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402. doi:10.1093/nar/25.17.3389
Chamberlain DF, Hyam R, Argent G, Fairweather G, Walter KS (1996) The genus Rhododendron: its classification and synonymy. Royal Botanic Garden, Edinburgh, Scotland
Choi HK, Kim D, Uhm T, Limpens E, Lim H, Mun J-H et al (2004) A sequence-based genetic map of Medicago truncatula and comparison of marker collinearity with M. sativa. Genetics 166:1463–1502. doi:10.1534/genetics.166.3.1463
De Keyser E, Dendauw J, De Riek J, Van Bockstaele E (2001) Characterization of carotenoid biosynthesis in Rhododendron luteum. Commun Agric Appl Biol Sci 66:439–441
Dendauw J, De Riek J, Arens P, Vosman B, Van Bockstaele E, De Loose M (2001) Development of sequenced tagged microsatellite site (STMS) markers in azalea. Acta Hortic 546:193–197
De Riek J, Dendauw J, Mertens M, De Loose M, Heursel J, Van Bockstaele E (1999) Validation for criteria for the selection of AFLP markers to assess the genetic variation of a breeders’ collection of evergreen azaleas. Theor Appl Genet 99:1155–1165. doi:10.1007/s001220051320
De Schepper S, Debergh P, Van Bockstaele E, De Loose M (2001) Molecular chracterisation of flower colour genes in azalea sports (Rhododendron simsii hybrids). Acta Hortic 552:143–150
Dunemann F, Kahnau R, Stange I (1999) Analysis of complex leaf and flower characters in Rhododendron using a molecular linkage map. Theor Appl Genet 98:1146–1155. doi:10.1007/s001220051179
Eeckhaut T, De Keyser E, Van Huylenbroeck J, De Riek J, Van Bockstaele E (2007) Application of embryo rescue after interspecific crosses in the genus Rhododendron. Plant Cell Tissue Organ Cult 89:29–35. doi:10.1007/s11240-007-9209-4
Iqbal MJ, Paden DW, Rayburn AL (1995) Clonal stability of RAPD markers in three Rhododendron species. J Environ Hortic 13:43–46
Just BJ, Santos CAF, Fonseca MEN, Boiteux LS, Oloizia BB, Simon PW (2007) Carotenoid biosynthesis structural genes in carrot (Daucus carota): isolation, sequence characterization, single-nucleotide polymorphism (SNP) markers and genome mapping. Theor Appl Genet 114:693–704. doi:10.1007/s00122-006-0469-x
Komulainen P, Brown GR, Mikkonen M, Karhu A, Garcia-Gil MR, O’Malley D et al (2003) Comparing EST-based genetic maps between Pinus sylvestris and Pinus taeda. Theor Appl Genet 107:667–678. doi:10.1007/s00122-003-1312-2
Lem P, Lallemand J (2003) Grass consensus STS markers: an efficient approach for detecting polymorphism in Lolium. Theor Appl Genet 107:1113–1122. doi:10.1007/s00122-003-1308-y
Ner-Gaon H, Leviatan N, Rubin E, Fluhr R (2007) Comparative cross-species alternative splicing in plants. Plant Physiol 144:1632–1641. doi:10.1104/pp. 107.098640
Oliveira KM, Pinto LR, Marconi TG, Margarido GRA, Pastina MM, Teieira LHM et al (2007) Functional integrated genetic linkage map based on EST-markers for a sugarcane (Saccharum spp.) commercial cross. Mol Breed 20:189–208. doi:10.1007/s11032-007-9082-1
Park Y-H, Alabady MS, Ulloa M, Sickler B, Wilkins TA, Yu J et al (2005) Genetic mapping of new cotton fiber loci using EST-derived microsatellites in an interspecific recombinant inbred line cotton population. Mol Gen Genet 274:428–441
Pearson WR, Lipman DJ (1988) Proc Natl Acad Sci USA 85:2444–2448. doi:10.1073/pnas.85.8.2444
Perry DJ, Bousquet J (1998) Sequence-tagged-site (STS) markers of arbitrary genes: the utility of black spruce-derived STS primers in other conifers. Theor Appl Genet 97:735–743. doi:10.1007/s001220050950
Rowland LJ, Dhanaraj AL, Polashock JJ, Arora R (2003) Utility of blueberry-derived EST-PCR primers in related Ericaceae species. Hort Sci 38:1428–1432
Scariot V, De Keyser E, Handa T, De Riek J (2007a) Comparative study of the discriminating capacity and effectiveness of AFLP, STMS and EST markers in assessing genetic relationships among evergreen azaleas. Plant Breed 126:207–212. doi:10.1111/j.1439-0523.2007.01326.x
Scariot V, Handa T, De Riek J (2007b) A contribution to the classification of evergreen azalea cultivars located in the Lake Maggiore area (Italy) by means of AFLP markers. Euphytica 158:47–66. doi:10.1007/s10681-007-9425-3
Taylor C, Madsen K, Borg S, Moller MG (2001) The development of sequence-tagged sites (STSs) in Lolium perenne L.: the application of primer sets derived from other genera. Theor Appl Genet 103:648–658. doi:10.1007/PL00002920
Wei H, Fu Y, Arora R (2005) Intron-flanking EST-PCR markers: from genetic marker development to gene structure analysis in Rhododendron. Theor Appl Genet 111:1347–1356. doi:10.1007/s00122-005-0064-6
Wei H, Fu Y, Arora R (2006) Utilization of intron-flanking EST-specific markers in the phylogenetic analysis and parentage identification of Rhododendron species and hybrids. J Am Soc Hortic Sci 131:814–819
Acknowledgements
The authors wish to thank Veerle Buysens, Laurence Desmet and Ruud Derijcker for their assistance in DNA preparations and EST development. The whole staff of the biotech lab of ILVO was very much appreciated for their support and skilful assistance. This research was funded by IWT-Flanders (VIS-CO 30907) and the Ministry of Agriculture of Flanders.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
De Keyser, E., De Riek, J. & Van Bockstaele, E. Discovery of species-wide EST-derived markers in Rhododendron by intron-flanking primer design. Mol Breeding 23, 171–178 (2009). https://doi.org/10.1007/s11032-008-9212-4
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11032-008-9212-4