Abstract
BackgroundDomestication 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.ResultsThirty 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).ConclusionCompared 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 materialThe online version of this article (doi:10.1186/s12870-014-0279-2) contains supplementary material, which is available to authorized users.
Highlights
Domestication and selection of crops have notably reshaped fruit morphology
The 30 candidates included 12 genes involved in meristem maintenance, 6 in floral organ identity and 5 in floral meristem identity
Six other candidates were previously characterized as involved in tomato fruit morphology and two non-coding sequences were included
Summary
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 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. Understanding the evolutionary basis of plant variation can be reached through the identification of the molecular mechanisms responsible for the large diversity in plant architecture [1,2]. Evolutionary changes in fruit shape and size has played a key role in the morphological diversification of plant species [3]. Meristem regulation growth is hypothesized to play a major role in sculpting the plant and fruit morphology [4,5]. We hypothesized that variation in genes controlling meristem development and expressed very early in flower/fruit development could be good candidates for fruit size variation
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
