Kidner Lab

Understanding DiversityBegonia "Mr S."Begonia bogneri

We are interested in determining the genetics underlying differences between species.  We would like to know how many genetic changes and what type of changes determine differences in plant growth and form. A combination of classical genetics and new sequencing technologies is being used to link the variation in form to variation in the sequence and expression of genes. We are particularly interested applying these techniques to tropical species, as the tropics contain most of the world’s diversity but have been genetically understudied.

Developing Begonia as a genetic system

As a study system we are working on Begonia, a species rich genus (1500+ species) found in wet rainforests throughout the world, with a focus on Section Gireoudia.  This is a group of about 66 Central American Begonia species, very variable in form and including many examples of convergent evolution, which makes it an excellent system to study the evolution of development. 

To discover the genetic architecture Begonia "L'escargote"of the differences between species - how many genes are involved in each trait, how strong their effects are and where the genes are, we have developed a genetic map using backcross populations of B. plebeja (a widespread species of dry tropical forests) and B. conchifolia (a species found in wet tropical forest in Costa-Rica and Panama).  

Some of the markers for the genetic map are based on sequences from the Begonia transcriptomes.  With the collaboration of The Genepool at the ULeaf variation in the backcross population ARB302niversity of Edinburgh we sequenced genes expressed in the meristems and developing leaves of B. plebeja, B. conchifolia and the Southeast Asian species B. venusta.  Analysis of the patterns of sequence variation in these genes suggests begonias underwent a whole genome duplication early in their history.  We are currently sequencing the genome from B. conchifolia to enable us to study the effects of this genome duplication in detail.

To discover how Section Gireoudia evolved and spread from South America to Central America and Mexico we are generating a dated phylogeny.  As this event is relatively recent most loci are not variable enough to give a strong phylogenetic signal.  We therefore used whole chloroplast genome sequencing with sample indexing.  Using the complete chloroplast genomes we are able to generate a robust backbone phylogeny and identify the most variable chloroplast regions to sequence from the rest of Section Gireoudia and related South American Begonia.

B. plebejaWe are also working on the understanding the ecology of Begonia and the factors controlling its evolution.  We are collecting data to relate species distributions to climate, soil and aspect, and looking for phylogenetic patterns.  We are documenting the ecophysiological responses (photosynthetic and related factors) of a large range of Begonia species and correlating this to variation in leaf anatomy.
B. multineura meristem
Fieldwork in Mexico and Costa Rica has increased the number of species in the living collection and allows us to determine the extent and effect of interspecific hybridisation in the wild. This data will provide an insight into speciation processes in a large tropical genus.

Current Projects and lab members

Generation of phylogenetic markers from transcriptomes in Inga
Collaboration with Toby Pennington (RBGE), Graham Stone (UoE), Tom Kusar and Phyllis Kusar (Univerity of Utah)

Generation of a Better Begonia Genome 
Collaboration with Aureliano Bombarely, Virginia Tech.

Candidate genes for the regulation of wood formation in Begonia burbidgei
Collaboration with Frederic Lens (Naturalis, Leiden), Andrew Groover (US Forrest Service/UC Davis)

The fate of duplicated genes in Begonia
Katie Emiliovana

Past Group MembersB. luxurians leaf primordia

Aliex Soler 20014 Chracterisation of the draft Begonia Genome
Mobina Shaukat Ali 2008 - 2012 Genetic architecture of variation between species in leaf structure and ecophysiology in Begonia
Nikki Harrison 2006 - 2012 Plastid genomes for phylogenetics
Alex Twyford 2007 - 2011 Hybridisation and introgression in Mexican Begonia
Saima Umbreen 2005 – 2011 ARP and KNOX genes and leaf form
Julie Bluhm Summer 2011 Microsatellite markers
Adrian Brennan 2010-2011 A genetic map of Begonia based on AFLPs and SNPs.
Aaron Marrubi Spring 2011 Candidate genes for stomatal patterning
Emily Johnston Spring 2011 CAM metabolism in Begonia
Chris White Spring 2010 QTL analysis of petal form
Stephen Wrigley 2010 – 2012 Ectopic leaves in hybrid Begonia
Qasim Hayat 2010 – Phylogenetic realtionships in Central Asian Artemisia
Iro Kouzali Summer 2010 Paternal chloroplast inheritance
Keith Gardner 2008-2010 Genetic map of Begonia
Ninette Rowlands – Summer 2009, CUC genes and leaf dissection in B. carolineifolia and B. heracleifolia
Stewart Nicholson – Summer 2009, Species delimitation in B. serconeura.
Samantha Dobbie –  Spring 2009 Transformation of Begonia
Olivia Moss –Summer 2008. Segregation of vegetative traits in an F1BC1 population.
Melanie Oakley - Spring 2008.  KNOX gene and Begonia leaf form
Neil Young –Summer 2007. Pollen germination in interspecific interspecific hybrids
Sergio  Piso-Martin – Spring 2007. – Methylation at the CYC and DIC loci in Linaria purpurea
Clare Rickerby – Spring 2007. KNOX1-like genes and leaf dissection
Rhydian Beydon-Davies –Spring 2007. Interspecific hybrids in Begonia
Andrew Matthews –Spring 2007. F1 fertility in Begonia
Emma Laidlaw –Summer 2006. Genetics of Leaf form in Begonia F1 hybrids
Katie Glass – Spring 2006. DNA fingerprinting in schools
Fatima Dahmani – Spring-summer 2006. KNOX1-like genes and compound leaves in Begonia
Rachel Kenneil – Summer 2005. QTL mapping of serrations in Arabidopsis
Claire Webster – Summer 2005. Sequencing and genotyping
Pierre Cattenoz – Spring-Summer 2005. ARP genes and leaf form in Begonia
Jack Cavers – Spring 2005. KNOX1 and ectopic leaflets in Begonia luxurians

B. rexRecent Publications

Catherine Kidner, Andrew Groover, Daniel Thomas, Katie Emelianova, Claudia Soliz-Gamboa, Frederic Lens (in press). Origins of secondary woodiness in Begonia (Begoniaceae): combining anatomy, phylogenetics, and stem transcriptomics. Bot. J. Linn. Soc.

Alex  Twyford, Richard  Ennos, Chris  White, Mobina Shaukat Ali, Catherine Kidner (2014) The evolution of sex ratio differences and inflorescence architectures in Begonia (Begoniaceae). Am. J. Bot, 101: 308-17

Alex  Twyford,  Catherine Kidner, Richard Ennos (2013) Genetic differentiation and species cohesion in two widespread Central American Begonia species. Heredity (doi:10.1038)

Alex Twyford, Richard A. Ennos and Catherine A. Kidner (2013)  Development and Characterization of Microsatellite Markers for Central American Begonia sect. Gireoudia (Begoniaceae). Applications in Plant Sciences 1:1200499. doi: 10.3732

Adrian Brennan, Stephen Bridgett, Mobina Shaukat Ali, Nicola Harrison, Andrew Mathews, Jaume Pellicer, Alex Twyford, and Catherine Kidner (2012) Genomic resources for evolutionary studies in the large, diverse tropical genus Begonia. Tropical Plant Biology 5:261-276

Alex Twyford, Catherine Kidner, Nicola Harrison and Richard Ennos (2012) Population history and seed dispersal in widespread Central American Begonia species (Begoniaceae) inferred from plastome derived microsatellite markers. Bot. J. Linn. Soc. 171: 260-276
DOI: 10.1111/j.1095-8339.2012.01265.x

Nicola Harrison and Catherine Kidner (2011) Next-generation sequencing and systematics.  What can a billion base pairs of DNA sequence do for you? Taxon 60:1552-1566.

Angelo Dewitte, Alex Twyford, Daniel Thomas, Catherine Kidner and Jan Van Huylenbroeck (2011) The Origin of Diversity in Begonia: Genome dynamism, population processes and phylogenetic patterns. Biodiversity Book 2. p 27-52 InTech.

Catherine Kidner and Marja Timmermans (2010) Signalling sides: adaxial-abaxial patterning in leaves. Current Topics in Developmental Biology 91:141-68.

Catherine Kidner and Steven Wrigley (2010) Patches, pegs and piggies. New Phytol. 187:13-7.

Catherine Kidner and Saima Umbreen (2010) Why is leaf shape so variable? International Journal of Plant Developmental Biology 4: 64-75.

Kanae Nishii, Michael Möller, Catherine Kidner, Albert Spada, Raffaella Mantegazza, Chun-Neng Wang, Tochiyuka Nagata. (2010) A complex case of simple leaves: indeterminate leaves co-express ARP and KNOX1 genes. Dev Genes Evol. 220:25-40.

Catherine Kidner (2010) Plant Organ Primordia. In: Encyclopedia of Life Sciences (ELS). John Wiley & Sons, Ltd: Chichester. DOI: 10.1002/9780470015902.a0002055.pub2

Catherine Kidner (2010) Small RNAs controlling leaf shape. Journal of Genetics and Genomics 37:13-21.

Kanae Nishii, Michael Möller, Catherine Kidner, Albert Spada, Raffaella Mantegazza, Haung Hsu, Tochiyuka Nagata, Chun-Neng Wang (2009) A simple leaf with compound gene expression: Indeterminate leaves co-express ARP and KNOX genes. Mech. Dev. 126: S93-S93.

Catherine Kidner (2007) Leaf evolution: working with what's to hand. Evol Dev. 9:321-2.

Catherine Kidner and Marja Timmermans (2006c) Mixing and matching pathways in leaf polarity. Curr Opp Pl. Sci 2007 10:13-20.

Sophie Neale, Will Goodall-Copespeak and Catherine Kidner (2006b) The Evolution of  Diversity in Begonia. In: ‘Floriculture, Ornamental and Plant Biotechnology: Advances and Topical Issues’. J. A. Teixeira da Silva (Ed.) Global Science Books

Catherine Kidner and Marja Timmermans (2006a). In situ hybridization as a tool to study the role of miRNAs in plant development. In: ‘MicroRNA protocols’ Methods in Molecular Biology. Shao-Yao Ying (Ed). Humana press Inc.

Catherine Kidner and Robert Martienssen (2005b) The role of ARGONAUTE1(AGO1) in meristem formation and identity. Developmental Biology 280:504-17

Catherine Kidner and Robert Martienssen (2005a).  The developmental role of microRNA in plants.  Curr Opin Plant Biol. 8:38-44.

Catherine Kidner  and Robert Martienssen (2004) Spatially restricted microRNA directs leaf polarity via ARGONAUTE1. Nature. 428:81-4

Mary E. Byrne, Catherine A. Kidner and Robert A. Martienssen (2003) Plant stem cells: divergent pathways and common themes in shoots and roots. Curr. Opin .Genet. Dev.. 5:551-7.

Catherine Kidner, Marja Timmermans, Mary Byrne, and Robert Martienssen.  (2002) Developmental Genetics of the Angiosperm Leaf.  Advances in Botanical Research Vol 38: 192-234

Tom Volpe, Catherine Kidner, Ira Hall, Grace Teng, Shiv Grewel and Robert Martienssen. (2002) Regulation of Heterochromatic Silencing and Histone H3 Lysine-9 Methylation by RNAi. Science. 297: 1833-1837.  


Evo-devo research at RBGE

Kidner lab at Edinburgh University 

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