Genetic selection for flowering time traits during speciation of tomato

In the last decade, a coordinated network of knowledge about the Solanaceae family has been created by the International Solanaceae Genome Project (SOL), whose final purpose is to explain how a common set of genes/proteins can result in a wide range of morphologically and ecologically distinct organisms like those in the Solanaceae family. This taxon includes more than 3000 species many of which evolved in the Andean/Amazonian regions of South America. Their habitats vary dramatically, from rain forests to deserts to high mountains. Moreover, the Solanaceae is the third most valuable crop family exceeded only by the grasses (e.g. rice, maize, wheat) and legumes (e.g. soybean), and the most valuable in terms of vegetable crops. It includes, among others, tomato, potato, eggplant, pepper, petunia, tobacco. Among Solanaceae, tomato was selected as a reference since it provides the smallest diploid genome (950 Mb) for which homozygous inbreds are available, as well as an advanced BAC-based physical map to start the sequencing. It also offers the vantage of short generation time, routine transformation technology, and availability of rich genetic and genomic resources. In this project, we merged structural and functional genomic approaches, in order to study in tomato one of the most important characters in terms of fitness and adaptation: flowering. We have focused our efforts in the study of genes involved in the photoperiodic regulatory pathway, since some wild tomato species, that growth between 0 and -25 degrees of latitude and between 0 and 3700 m of elevation, show different photoperiodic responses. These genes are members of three gene families, whose orthologs in Arabidopsis and rice play a key role in the regulation of flowering in dependence of day length. They are the TCOL (tomato CONSTANS-like), the CRYPTOCHROME and the GIGANTEA gene families. In chapter 2 we provide structural information on the organization and expression of the CRY, COL and GI gene families in tomato and we analyse the microsynteny with Arabidopsis. We also identify four new COL and one new GI gene. In chapter 3 we investigate the sequence diversification of the three gene families during speciation in the tomato clade, using both sequencing and expression profiling approaches. In particular, we observed a high degree of diversifying selection for TCOL3, that presents also a geographical cline in the frequency of synonymous mutations, suggesting a role of this gene in adaptation to low latitudes. Finally, in chapter 4, we use four reverse genetic approaches (VIGS, RNAi, TILLING and overexpression) for a functional characterization of the tomato Cryptochrome gene family. Novel cry1b- and cry2- mutants and RNAi plants and CRY1a overexpressors are described for the first time and novel developmental and flowering phenotypes are attributed to the various genes.