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Striking increases in fruit size distinguish cultivated descendants from small-fruited wild progenitors for fleshy fruited species such as Solanum lycopersicum (tomato) and Prunus spp. (peach, cherry, plum, and apricot). The first fruit weight gene identified as a result of domestication and selection was the tomato FW2.2 gene. Members of the FW2.2 gene family in corn (Zea mays) have been named CNR (Cell Number Regulator) and two of them exert their effect on organ size by modulating cell number. Due to the critical roles of FW2.2/CNR genes in regulating cell number and organ size, this family provides an excellent source of candidates for fruit size genes in other domesticated species, such as those found in the Prunus genus. A total of 23 FW2.2/CNR family members were identified in the peach genome, spanning the eight Prunus chromosomes. Two of these CNRs were located within confidence intervals of major quantitative trait loci (QTL) previously discovered on linkage groups 2 and 6 in sweet cherry (Prunus avium), named PavCNR12 and PavCNR20, respectively. An analysis of haplotype, sequence, segregation and association with fruit size strongly supports a role of PavCNR12 in the sweet cherry linkage group 2 fruit size QTL, and this QTL is also likely present in sour cherry (P. cerasus). The finding that the increase in fleshy fruit size in both tomato and cherry associated with domestication may be due to changes in members of a common ancestral gene family supports the notion that similar phenotypic changes exhibited by independently domesticated taxa may have a common genetic basis. Electronic supplementary material The online version of this article (doi:10.1007/s11032-013-9872-6) contains supplementary material, which is available to authorized users.

Modern breeding for fruit plants require bioinformatics support to store and rationalize the abundance of available phenotypic and genotypic data. Critical requirements are standardization and database interoperability, necessary to avoid the creation of "data islands" that won't serve beyond the specific scope of the project (or task) that generated it. It is moreover necessary to intensify the connection between scientific genetics research and application to breeding. The FruitBreedomics project aims specifically to connect academia and breeders, with focus on apple and peach, two of the most important fruit crops in Europe and in the world. We here present a bioinformatics facility that has been designed for long term storage and fruition of all the data produced and collected during the project. The design choices focused on (re)use of available database schema and data harmonization. The database currently stores almost a million single phenotypic entries covering 111 traits linked to fruit quality and fruit yield. Three types of genetic data (SSR, SNP array datasets, and haplotype blocks) are stored, together with information about more than 13 thousands trees. The infrastructure contains also ad hoc "push button" integrated analytical tools to help both the breeder and the scientist.

Gametophytic self-incompatibility (GSI) is the main mechanism that controls fertilization in many rosaceous species, including those belonging to the subtribe Pyrinae (formerly the Maloideae). In natural conditions, S-specificities are subject to frequency-dependent balancing selection; the genetic imprint left by this kind of selection is visible on the S-RNase gene in terms of high sequence diversity, evidence of positive selection, and shared ancestral polymorphisms: thus, some alleles have been maintained almost unaltered during evolution in different but related species, as is the case of Malus and Pyrus species. We have questioned whether the same expected features can be extended to whole S haplotypes, thus including not only the female S determinant (the S-RNase) but also its male counterpart, most likely provided by S-locus F-box Brothers (SFBB) genes - even though direct functional evidence is still needed. On the one side, coevolution between female and male S genes has been postulated several times, given that the generation of any new Sspecificity requires a coordinated change on both sides in order to maintain the full S-haplotypes functionality. But on the other side, recent models for S-RNase-based GSI suggest a key difference between the control of female and male S functions: while the first entirely depends on the single S-RNase gene, the second might likely be provided by multiple SFBB genes acting in a collaborative mode. Even though this hypothesis makes it necessary to re-discuss the mode of coevolution between the female and male S genes, it might provide a suitable explanation for the complex phylogenetic profiles of SFBB genes, which are only in part in agreement with that of the S-RNase. Phylogenetic and segregation analyses of S-locus genes, together with the increasing amount of genomic information available for apple and pear, provide a valuable tool for understanding both the molecular mechanism of SRNase-based GSI, and the complex evolutionary pattern of S-haplotypes.

Retrotransposons have been found to comprise the most common class of transposable elements in eukaryotes and to occur in high copy number in plant genomes. Several of these elements have been sequenced and were found to display a high degree of heterogeneity and insertional polymorphism, both within and between species. The dispersion, ubiquity and prevalence of retrotransposons in plant genomes provide an excellent basis for the development of marker systems and, hence, may be good molecular candidates in distinguishing among apple clones, when they represent bud mutations of the original variety, considering that the random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) used thus far in fingerprinting analyses have failed to meet discrimination expectations. The technique called sequence-specific amplified polymorphism (S-SAP), which makes it possible to identify dominant markers for the detection of variation in the DNA flanking the retrotransposon insertion site, was used in the present study to distinguish several clones of the cultivars 'Gala' and 'Braeburn' in apple fingerprinting. Moreover, our results suggest that the bud mutations, which have generated new patented varieties of 'Gala' and 'Braeburn', appear to derive from retrotransposon insertion.

Self-incompatibility has been investigated in the cultivar ‘Abbé Fétel’ (Pyrus communis) in order to assign a role to transglutaminase (TGase), an enzyme able to post-translationally forming cross-links among proteins. This enzyme is localised in the pollen cytoplasm where it regulates the polymerisation of cytoskeleton proteins. An extracellular form is also necessary for pollen tube growth. In the self-pollinated style of Abbè Fétel (A x A, incompatible system), the activity of TGase increased when the pollen tube stopped its growth inside the style and the enzyme was immuno-localised around the tube tip. On the contrary in Abbé Fétel styles pollinated with Williams pollen (A x W, compatible system), TGase activity decreased during pollen germination. The TGase gene has been cloned and sequenced from Abbé Fétel pollen and style showing that it shares a high homology with a sequence of apple, whose genome has been recently published, which presents the typical TGase catalytic sequence, and with the TGase of Arabidopsis. This enzyme was expressed during pollen germination inside the style to a similar extent in both systems (A x A and A x W) showing that it is only the activity to have been stimulated by some factor dependent on SI. A molecular approach to clone one of the S-RNase alleles of the cv Abbé Fétel has been performed. This protein, supplied to pollen in the germination medium, was able to inhibit the growth of 50% of the tubes of the homologous pollen. This approach will allow us to verify if an interaction between the two enzymes will occur during SI, as TGase, at least in animal cells, is also able to act as disulphide isomerase modifying the RNase structure.