Gene(s) responsible for variation in epidermal hair (trichome) distribution amongst Antirrhinum species

Trichomes are hair-like structures found on the surface of virtually all terrestrial plants (Yang et al., 2015). They are epidermal outgrowths that can occur on all of the aerial parts of a plant, varying markedly in size, shape, distribution, and in their ability to produce secondary metabolites. About 30% of all vascular plants carry the glandular trichomes capable of producing secondary metabolites (Glas et al., 2012). Trichomes are vitally important to plants as a defence mechanism, they are highly significant commercially, and they are of interest to plant biologists in that they serve as an excellent model system to study all aspects of plant differentiation at the single-cell level (Hulskamp, 2004). The simple, non-glandular trichomes found in Arabidopsis have been studied extensively. However the glandular trichomes of the kind found on the surface of Antirrhinum are much less well understood. The primary aim of the research reported here is to identify the gene(s) responsible for variation in epidermal hair (trichome) distribution between Antirrhinum species. Following an introduction which provides essential background on trichomes and on Antirrhinum, the thesis is presented in four parts. The first part describes a RAD-seq experiment used to produce linkage maps for the eight chromosomes making up the Antirrhinum genome and estimates the position of the Hairy gene on linkage group 8. The results are cross-validated against maps produced independently by the Xue group. It also describes novel methods developed to address a number of problems that arose during the course of the analysis, and explores the value of imputation methods in helping to overcome gaps and inconsistencies in the data. The second part presents the findings from a fine-mapping Pool-seq experiment designed to estimate the position of Hairy more precisely. The findings suggest that Hairy lies on one of a small number of scaffolds, with Scaffold 1097 being the most likely candidate. Also covered are the findings of another experiment to estimate the position of the gene that determines whether flowers are pale or dark. In this case the results indicate that the gene lies on one of a small number of scaffolds on linkage group 5. The third part presents the results of an RNA-seq experiment which, when combined with the results of the Pool-seq experiment provides evidence that Hairy might be a glutaredoxin gene on Scaffold 1097. Finally the interim results of three experiments designed to confirm that the gene identified as Hairy controls the distribution of trichomes in Antirrhinum are presented