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Background  Domestication and selection of crops have notably reshaped fruit morphology. With its large phenotypic diversity, tomato ( Solanum lycopersicum ) illustrates this evolutive trend. Genes involved in flower meristem development are known to regulate also fruit morphology. To decipher the genetic variation underlying tomato fruit morphology, we assessed the nucleotide diversity and selection footprints of candidate genes involved in flower and fruit development and performed genome-wide association studies.    Results  Thirty candidate genes were selected according to their similarity with genes involved in meristem development or their known causal function in  Arabidopsis thaliana . In tomato, these genes and flanking regions were sequenced in a core collection of 96 accessions (including cultivated, cherry-type and wild relative accessions) maximizing the molecular diversity, using the Roche 454 technology. A total amount of 17 Mb was sequenced allowing the discovery of 6,106 single nucleotide polymorphisms (SNPs). The annotation of the 30 gene regions identified 231 exons carrying 517 SNPs. Subsequently, the nucleotide diversity ( π ) and the neutral evolution of each region were compared against genome-wide values within the collection, using a SNP array carrying 7,667 SNPs mainly distributed in coding sequences.  About half of the genes revealed footprints of selection and polymorphisms putatively involved in fruit size variation by showing negative Tajima’s D and nucleotide diversity reduction in cultivated tomato compared to its wild relative. Among the candidates,  FW2.2  and  BAM1  sequences revealed selection footprints within their promoter regions suggesting their potential involvement in their regulation. Two associations co-localized with previously identified loci:  LC  (locule number) and  Ovate  (fruit shape).    Conclusion  Compared to whole genome genotypic data, a drastic reduction of nucleotide diversity was shown for several candidate genes. Strong selection patterns were identified in 15 candidates highlighting the critical role of meristem maintenance genes as well as the impact of domestication on candidates. The study highlighted a set of polymorphisms putatively important in the evolution of these genes.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-014-0279-2) contains supplementary material, which is available to authorized users.

Genes involved in floral meristem in tomato exhibit drastically reduced genetic diversity and signature of selection