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Background In wine grape production, management practices have been adopted to optimize grape and wine quality attributes by producing, or screening for, berries of smaller size. Fruit size and composition are influenced by numerous factors that include both internal (e.g. berry hormone metabolism) and external (e.g. environment and cultural practices) factors. Combined physiological, biochemical, and transcriptome analyses were performed to improve our current understanding of metabolic and transcriptional pathways related to berry ripening and composition in berries of different sizes. Results The comparison of berry physiology between small and large berries throughout development (from 31 to 121 days after anthesis, DAA) revealed significant differences in firmness, the rate of softening, and sugar accumulation at specific developmental stages. Small berries had significantly higher skin to berry weight ratio, lower number of seeds per berry, and higher anthocyanin concentration compared to large berries. RNA-sequencing analyses of berry skins at 47, 74, 103, and 121 DAA revealed a total of 3482 differentially expressed genes between small and large berries. Abscisic acid, auxin, and ethylene hormone pathway genes were differentially modulated between berry sizes. Fatty acid degradation and stilbenoid pathway genes were upregulated at 47 DAA while cell wall degrading and modification genes were downregulated at 74 DAA in small compared to large berries. In the late ripening stage, concerted upregulation of the general phenylpropanoid and stilbenoid pathway genes and downregulation of flavonoid pathway genes were observed in skins of small compared to large berries. Cis-regulatory element analysis of differentially expressed hormone, fruit texture, flavor, and aroma genes revealed an enrichment of specific regulatory motifs related to bZIP, bHLH, AP2/ERF, NAC, MYB, and MADS-box transcription factors. Conclusions The study demonstrates that physiological and compositional differences between berries of different sizes parallel transcriptome changes that involve fruit texture, flavor, and aroma pathways. These results suggest that, in addition to direct effects brought about by differences in size, key aspects involved in the regulation of ripening likely contribute to different quality profiles between small and large berries. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2660-z) contains supplementary material, which is available to authorized users.

[EN] Background: Domestication modifies the genomic variation of species. Quantifying this variation provides insights into the domestication process, facilitates the management of resources used by breeders and germplasm centers, and enables the design of experiments to associate traits with genes. We described and analyzed the genetic diversity of 1,008 tomato accessions including Solanum lycopersicum var. lycopersicum (SLL), S. lycopersicum var. cerasiforme (SLC), and S. pimpinellifolium (SP) that were genotyped using 7,720 SNPs. Additionally, we explored the allelic frequency of six loci affecting fruit weight and shape to infer patterns of selection. Results: Our results revealed a pattern of variation that strongly supported a two-step domestication process, occasional hybridization in the wild, and differentiation through human selection. These interpretations were consistent with the observed allele frequencies for the six loci affecting fruit weight and shape. Fruit weight was strongly selected in SLC in the Andean region of Ecuador and Northern Peru prior to the domestication of tomato in Mesoamerica. Alleles affecting fruit shape were differentially selected among SLL genetic subgroups. Our results also clarified the biological status of SLC. True SLC was phylogenetically positioned between SP and SLL and its fruit morphology was diverse. SLC and “cherry tomato” are not synonymous terms. The morphologically-based term “cherry tomato” included some SLC, contemporary varieties, as well as many admixtures between SP and SLL. Contemporary SLL showed a moderate increase in nucleotide diversity, when compared with vintage groups. Conclusions: This study presents a broad and detailed representation of the genomic variation in tomato. Tomato domestication seems to have followed a two step-process; a first domestication in South America and a second step in Mesoamerica. The distribution of fruit weight and shape alleles supports that domestication of SLC occurred in the Andean region. Our results also clarify the biological status of SLC as true phylogenetic group within tomato. We detect Ecuadorian and Peruvian accessions that may represent a pool of unexplored variation that could be of interest for crop improvement., We are grateful to the gene banks for their collections that made this study possible. We thank Syngenta Seeds for providing genotyping data for 42 accessions. We would like to thank the Supercomputing and Bioinnovation Center (Universidad de Malaga, Spain) for providing computational resources to process the SNAPP phylogenetic tree. This research was supported in part by the USDA/NIFA funded SolCAP project under contract number to DF and USDA AFRI 2013-67013-21229 to EvdK and DF.

BACKGROUND: Tomato is sensitive to ozone. Fruit growth and composition are altered under ozone stress by modification of reproductive development. Fifty-one-day-old plants were exposed to three concentrations of ozone (200, 350 and 500 ??gm?3) for 4 h. RESULTS: Ozone reduced well-developed fruit number and fruit size, but it did not significantly affect flowering rate and fruit setting rate. The effect of ozone depends on organ developmental stage at the time of ozone application, as flowers and young fruits at the time of ozone exposurewere more affected. Contents of total soluble sugars (total SS), total organic acids (total OA) and ascorbic acid (AsA) increased in fruits harvested from ozone-treated plants. Tomato fruit composition was altered under ozone stress, leading to a lower sugar:acid ratio. These changes weremostly due to increased contents of malic acid, ascorbate and glucose despite a decrease in sucrose. CONCLUSION: Acute ozone exposure up to 500 ??gm?3 greatly influences tomato fruit quality. As final fruit yield was not significantly reduced, it highlighted that there may be compensatory mechanisms present in the reproductive structures of tomato. Further research would be necessary to determine how reproductive traits are affected by repeated ozone exposure or longer-term exposure.

International audience; Sweet cherry (Prunus avium L.) is a rosaceous fruit crop cultivated in temperate regions of the world for its highly valued fruits. In today’s marketplace, large fruit is highly desirable and directly related to grower profitability; therefore, the development of new cherry varieties with large fruit is a major breeding goal. To elucidate the genetic control of fruit size in sweet cherry and thereby enable marker‐assisted breeding, we undertook a fine mapping – candidate gene analysis of two previously identified fruit size QTLs located on linkage groups 2 and 6 (G2 and G6)(Zhang et al. 2010) in two sweet cherry populations. A total of 14 simple sequence repeats were developed from the peach genomic regions syntenic to the G2 and G6 fruit size QTLs and used to further narrow the sweet cherry QTL regions. Genome annotations of the peach sequence in these syntenic regions identified cell number regulator genes (CNR, Guo et al. 2010) as likely candidate genes for both the G2 and G6 fruit size QTLs. The CNR gene family, first described in maize based upon homology to the tomato fruit weight gene fw2.2, is hypothesized to contain genes involved in cell number regulation that ultimately affect plant growth and organ size. Sequencing of the CNR candidate genes from the parents of the mapping populations and a panel of diverse sweet cherry selections for G2 and G6 identified 3 and 2 allelic variants, respectively. These findings agree with the previously described functional haplotypes for these two fruit size QTLs. Comparisons of sweet cherry fruit weights based on their CNR genotypes further support our hypothesis that the phenotypic differences in fruit size associated with the G2 and G6 QTLs are caused by allelic variants of the CNR genes.

International audience; Changes in elastic and plastic components of mango (Mangifera indica L. cv 'Cogshall') fruit growth were analyzed with a model of fruit growth over time and in response to various assimilate Supplies. The model is based on water relations (water potential and osmotic and turgor pressures) at the fruit level. Variation in elastic fruit growth was modeled as a function of the elastic Modulus and variation in turgor pressure. Variation in plastic fruit growth was modeled using the Lock-hart (1965) equation. In this model, plastic growth parameters (yield threshold pressure and cell wall extensibility) varied during fruit growth. Outputs of the model were diurnal and seasonal fruit growth, and fruit turgor pressure. These variables were simulated with good accuracy by the model, particularly the observed increase in fruit size with increasing availability of assimilate supply. Shrinkage was sensitive to the Surface conductance of fruit peel, the elasticity modulus and the hydraulic conductivity of fruit, whereas fruit growth rate was highly sensitive to parameters linked to changes in wall extensibility and yield threshold pressure, regardless of the assimilate Supply. According to the model, plastic growth was generally zero during the day and shrinkage and swelling were linked to the elastic behavior of the fruit. During the night, plastic and elastic growths were positive, resulting in fruit expansion

International audience; In order to screen for putative candidate genes linked to tomato fruit weight and to sugar or acid content, genes and QTLs involved in fruit size and composition were mapped. Genes were selected among EST clones in the TIGR tomato EST database (http://www.tigr.org/tdb/tgi/Igi/) or corresponded to genes preferentially expressed in the early stages of fruit development. These clones were located on the tomato map using a population of introgression lines (ILs) having one segment of Lycopersicon pennellii (LA716) in a L. esculentum (M82) background. The 75 ILs allowed the genome to be segmented into 107 bins. Sixty-three genes involved in carbon metabolism revealed 79 loci. They represented enzymes involved in the Calvin cycle, glycolysis, the TCA cycle, sugar and starch metabolism, transport, and a few other functions. In addition, seven cell-cycle-specific genes mapped into nine loci. Fourteen genes, primarily expressed during the cell division stage, and 23 genes primarily expressed during the cell expansion stage, revealed 24 and 26 loci, respectively. The fruit weight, sugars, and organic acids content of each IL was measured and several QTLs controlling these traits were mapped. Comparison between map location of QTLs and candidate gene loci indicated a few candidate genes that may influence the variation of sugar or acid contents. Furthermore, the gene/QTL locations could be compared with the loci mapped in other tomato populations.