The genetics of leaf shape variation in Begonia

With just over 2000 species, Begonia is one of the largest vascular plant genera. The vast morphological diversity, detailed phylogeny and extensive distribution data makes it an ideal model to study the evolution of diversity in tropical herbaceous plants. Specifically, their diverse leaf morphology allows them to be excellent subjects for studying the drivers of leaf shape variation in a non-model system. Studies in a range of model plants and crops have identified the key genes regulating leaf shape and shown them to be largely conserved across angiosperms (with a number of interesting exceptions). This study describes the genetic and evolutionary patterns observed in leaf form across Begonia. I have used a morphometric approach to quantify leaf shape in Begonia and subsequently plotted shape metrics across the phylogeny to identify patterns across the different clades and sections. I showed that although establishing metrics to quantify all species of Begonia collectively proved to be a challenging task, Elliptical Fourier Analysis (EFA) was adequate in scoring smaller clades and identifying patterns of change within these sections. Genome mining was then done to obtain orthologs for key leaf developmental genes in 11 Begoniaceae genomes. The expression patterns of these orthologous genes in six different tissues from B. conchifolia and B. plebeja were plotted to predict whether changes in function may have occurred. The drastic expansion of gene copy number and the variation in DGE expression patterns suggest that novel morphologies may have risen as the result of key leaf developmental gene regulators being altered. QTL analysis of leaf shape trait genes identified a number of candidates for asymmetry, dissection index (a CUC-like gene on chromosome 3) and EFA PCs. The nature of genetic differences between sister species in generating morphological differences was then analysed in B. luxurians and B. parviflora. The range of changes that can occur from gene sequence variation, copy number, expression patterns are also present in this sister pair of species. The search for candidate genes responsible for the compound leaf form in B. luxurians identified changes in hormone signalling genes, NAC TFs, an AS1-like gene. Interestingly, KNOX I expression was not observed. The development of ectopic leaflets was linked to the downregulation of a trichome inhibitor and the upregulation of key meristem and polarity genes.