Understanding Diversity
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. We are particularly interested in studying this in tropical species, as the tropics contains most of the world’s diversity.
Begonia is one of the ten largest plant genera, with probably over 1,500 species. They are found throghout the tropics, originating in Africa about 60 million years ago and undergoing parallel radiations in South East Asia and tropical America. Almost all are herabaceous perrenials of wet rainforests, though some have adapted to drier enviroments or seasonally dry forests. The floral form is similar throughout the genus but leaves are particularly diverse in form, size and colour.
This diversity in form is part of the explaination for Begonia's horticultural success. They also have the advantage of easy propagation, by cuttings or seed and wide hybridisation. The ease with which many Begonia species hybridise has allowed us to use genetics to try to understand the numbers of genes controlling the differences between species and the effects of these genes.
Developing Begonia as a genetic system
As a study system we are focusing 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. Our prelimary focus is on vegetative form. Genes controlling leaf form have been isolated in several model species. We are cloning these genes from Begonia and using genetic association and expression analysis to determine if they are important in generating the variety of leaf forms we see in our species.
To discover the genetic architecture of the differences between species - how many genes are involved in each trait, how strong their effects are and where the genes are, we are developing a genetic map using an F1 backcross population 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 will be based on sequence from the Begonia transcriptome. We are sequencing genes expressed in the meristems and developing leaves of B. plebeja and B. conchifolia. This will allow us to compare the genes involved in Begonia development to those in other species and determine how different the two Begonia species are in their gene expression and sequences.
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 are therefore developing whole chloroplast genome sequencing using sample indexing on the Illumina Solexa sequencer in collaboration with ‘The Genepool’ at the University of Edinburgh This will provide large amounts of information for a robust framework phylogeny and enable us to identify the most variable chloroplast regions to sequence from the rest of the Gireoudias and related South American Begonias.
We are also working on the understanding the ecology of Begonia and the factors controling 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. Fieldwork we have planned in Mexico and Costa Rica will increase the number of species in the living collection and allow 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
The role of ARP and KNOX genes in leaf form variation
Saima Umbreen
Generation of genetic map for Begonia
Keith Gardner, Mobina Shaukat Ali
Begonia Transcriptome
Keith Gardner, Nikki Harrison, University of Edinburgh Genepool
QTL mapping of species level variation
Keith Gardner, Mobina Shaukat Ali, Alex Twyford
Correlations between leaf structure and ecophysiology
Mobina Shaukat Ali
Phylogenetic analysis and biogeography of Section Gireoudia
Nikki Harrison
Species barriers and hybridisation in Begonia
Alex Twyford
Begonia fieldwork
Alex Twyford, Keith Gardner, in collaboration with Mark Hughes
Past Group Members
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
Recent Publications
Catherine Kidner (in press) Small RNAs controlling leaf shape. Journal of Genetics and Genomics
Catherine Kidner and Saima Umbreen (in press) Why is leaf shape so variable? International Journal of Plant Developmental Biology.
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.