Tropical Plant Biology

, Volume 5, Issue 4, pp 261–276 | Cite as

Genomic Resources for Evolutionary Studies in the Large, Diverse, Tropical Genus, Begonia

  • Adrian Christopher Brennan
  • Stephen Bridgett
  • Mobina Shaukat Ali
  • Nicola Harrison
  • Andrew Matthews
  • Jaume Pellicer
  • Alex David Twyford
  • Catherine Anne KidnerEmail author


Begonia is one of the ten largest angiosperm genera with over 1,500 species found throughout the tropics. To use this group as a model for the evolution of diversity in tropical herbaceous plants, we have produced three species transcriptomes, physical genome size measures, and two backcross genetic maps. We chose to focus on two Central American species, B. conchifolia and B. plebeja, and one SE Asian species, B. venusta, allowing us to pose questions at widely different evolutionary scales within the genus. We used next generation sequencing of cDNA libraries to produce annotated transcriptome databases for each of the three species. Though Begonia is functionally diploid, transcriptome analysis suggested a genome duplication occurred at or near the base of the Begonia clade. The genetic maps were built from first generation backcrosses in both directions between B. plebeja and B.conchifolia using 105 SNP markers in genes known to regulate development that were identified from the transcriptomes and the map bulked out with 226 AFLP loci. The genetic maps had 14 distinct linkage groups each and mean marker densities of between 3.6 and 5.8 cM providing between 96 and 99 % genomic coverage within 10 cM. We measured genome size 1C value of 0.60 and 0.63 pg for B. conchifolia and B. plebeja corresponding to recombination rates of between 441 and 451 Kb per cM in the genetic maps. Altogether, these new data represent a powerful new set of molecular genetic tools for evolutionary study in the genus Begonia.


Begonia Genetic map Transcriptome Tropical diversity Genome duplication 



Mark Hughes, Neil Watherston, Keith Gardner, Michelle Hollingsworth, Laura Forrest, at RBG Edinburgh, Andrew Hudson at University of Edinburgh, Ilia Leitch at RBG Kew, David Menzies and Ewan Donaldson at Glasgow Botanic Gardens.

Funding was Provided by

Biological and Biotechnology Research Council (UK), M. L. MacIntyre Begonia Trust, Rural and Environmental Research and Analysis Directorate (RERAD) grant to Royal Botanic Gardens, Edinburgh. ACB was supported during the writing of this study by funding from FP7-REGPOT 2010-1, Grant No. 264125 EcoGenes.

Supplementary material

12042_2012_9109_MOESM1_ESM.docx (13 kb)
Supplementary note 1 AFLP protocol and primers (DOCX 13 kb)
12042_2012_9109_MOESM2_ESM.xls (82 kb)
Supplementary table 1 Mapping details (XLS 82 kb)
12042_2012_9109_MOESM3_ESM.docx (17 kb)
Supplementary table 2 Mapping details (DOCX 16.9 KB)
12042_2012_9109_Fig8_ESM.jpg (199 kb)
Supplementary figure 1

GO terms for tri-scriptome contigs (JPEG 199 kb)

12042_2012_9109_MOESM4_ESM.tif (210 kb)
High resolution image (TIFF 209 kb)


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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Adrian Christopher Brennan
    • 1
    • 7
  • Stephen Bridgett
    • 2
  • Mobina Shaukat Ali
    • 3
    • 7
  • Nicola Harrison
    • 3
    • 4
    • 7
  • Andrew Matthews
    • 5
  • Jaume Pellicer
    • 6
  • Alex David Twyford
    • 3
    • 7
  • Catherine Anne Kidner
    • 3
    • 7
    Email author
  1. 1.Estación Biológica de Doñana (EBD-CSIC)SevillaSpain
  2. 2.GenepoolUniversity of EdinburghEdinburghUK
  3. 3.Royal Botanic Garden EdinburghEdinburghUK
  4. 4.East Malling ResearchKentUK
  5. 5.Queen Mary, University of LondonLondonUK
  6. 6.Royal Botanic Gardens, KewKewUK
  7. 7.Institute of Molecular Plant SciencesUniversity of EdinburghEdinburghUK

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