Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera(1) and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium(2), and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness

Auxin/indole-3-acetic acid (Aux/IAA) proteins are transcriptional regulators that mediate many aspects of plant responses to auxin. While functions of most Aux/IAAs have been defined mainly by gain-of-function mutant alleles in Arabidopsis thaliana, phenotypes associated with loss-of-function mutations have been scarce and subtle. We report here that the downregulation of IAA9, a tomato (Solanum lycopersicum) gene from a distinct subfamily of Aux/IAA genes, results in a pleiotropic phenotype, consistent with its ubiquitous expression pattern. IAA9-inhibited lines have simple leaves instead of wild-type compound leaves, and fruit development is triggered before fertilization, giving rise to parthenocarpy. This indicates that IAA9 is a key mediator of leaf morphogenesis and fruit set. In addition, antisense plants displayed auxin-related growth alterations, including enhanced hypocotyl/stem elongation, increased leaf vascularization, and reduced apical dominance. Auxin dose-response assays revealed that IAA9 downregulated lines were hypersensitive to auxin, although the only early auxin-responsive gene that was found to be upregulated in the antisense lines was IAA3. The activity of the IAA3 promoter was stimulated in the IAA9 antisense genetic background, indicating that IAA9 acts in planta as a transcriptional repressor of auxin signaling. While no mutation in any member of subfamily IV has been reported to date, the phenotypes associated with the downregulation of IAA9 reveal distinct and novel roles for members of the Aux/IAA gene family. INTRODUCTIONThe phytohormone auxin is central to a myriad of aspects of plant growth and developmental processes. At the cellular level, auxin controls cell division, extension, and differentiation. On a wholeplant level, auxin plays an essential role in processes such as apical dominance, lateral/adventitious root formation, tropisms, fruit set and development, vascular differentiation, and embryogenesis (Friml, 2003). While it is clear that auxin plays a pivotal role in plant growth and development, the molecular effectors by which this hormone exerts its effect are still relatively unknown. For example, in the process of fruit set, the onset of ovary development into fruit and its subsequent development are naturally triggered by signals from successful fertilization. These processes can be initiated in the absence of pollination and fertilization by exogenous auxin or auxin transport inhibitors (Gustafson, 1937;Beyer and Quebedeaux, 1974) or by the ovaryspecific expression of Agrobacterium tumefaciens indoleacetamide monoxygenase (iaaM) or root loci B (rolB) genes, which confer higher auxin production or increased auxin sensitivity, respectively (Ficcadenti et al., 1999;Carmi et al., 2003). The molecular mediators by which auxin impacts this process are still unknown.The recent discovery that the F-box protein Transport Inhibitor Response1 functions as an auxin receptor represents a major breakthrough (Dharmasiri et al., 2005;Kepinski and Leyser, 2005) in understanding ho...

(M.L.); 0000-0002-5725-885X (J.P.); 0000-0001-7707-7776 (J.-P.R.).The plant hormone ethylene plays a key role in climacteric fruit ripening. Studies on components of ethylene signaling have revealed a linear transduction pathway leading to the activation of ethylene response factors. However, the means by which ethylene selects the ripening-related genes and interacts with other signaling pathways to regulate the ripening process are still to be elucidated. Using tomato (Solanum lycopersicum) as a reference species, the present review aims to revisit the mechanisms by which ethylene regulates fruit ripening by taking advantage of new tools available to perform in silico studies at the genomewide scale, leading to a global view on the expression pattern of ethylene biosynthesis and response genes throughout ripening. Overall, it provides new insights on the transcriptional network by which this hormone coordinates the ripening process and emphasizes the interplay between ethylene and ripening-associated developmental factors and the link between epigenetic regulation and ethylene during fruit ripening.As a developmental process, fruit ripening is coordinated by a complex network of endogenous and exogenous cues. Indeed, the making of a fruit is a genetically regulated process unique to plants involving three distinct stages: fruit set, development, and ripening. Fruit development is characterized by a series of developmental transitions tightly coordinated by a network of interacting genes and signaling pathways. Among these, ripening has received the greatest attention from both geneticists and breeders. From the scientific point of view, fruit ripening is seen as a process in which the biochemistry and physiology of the organ are developmentally altered to influence the appearance, texture, flavor, and aroma (Giovannoni, 2004). Since most of the fruit sensory and nutritional quality traits are elaborated at the ripening stage, deciphering the key genetic and molecular factors regulating ripening becomes a major task toward improving overall fruit quality (Carrari and Fernie, 2006). In addition, the control of fruit ripening is also instrumental to maintain the quality attributes of the fruit during the postharvest shelf life.Based on their mode of ripening, fleshy fruits are divided into two categories, climacteric and nonclimacteric, depending on the presence or absence of the climacteric rise in respiration and of autocatalytic ethylene production (Lelièvre et al., 1997). In climacteric fruit, the plant hormone ethylene is the major cue that controls most aspects of ripening. By contrast, the ripening of nonclimacteric fruit does not strictly depend on ethylene, and the nature of the triggers of ripening in this type of fruit remains yet to be elucidated. Since the upstream components of the ethylene transduction pathway are common to all ethylene responses, the apparent simplicity of the ethylene signaling pathway cannot account for the wide diversity of ethylene responses. A plausible hypothesis is that dif...

The latest advances in our understanding of the relationship between ethylene and fruit ripening are reviewed. Considerable progress has been made in the characterisation of genes encoding the key ethylene biosynthetic enzymes, ACC synthase (ACS) and ACC oxidase (ACO) and in the isolation of genes involved in the ethylene signal transduction pathway, particularly those encoding ethylene receptors (ETR). These have allowed the generation of transgenic fruit with reduced ethylene production and the identification of the Nr tomato ripening mutant as an ethylene receptor mutant. Through these tools, a clearer picture of the role of ethylene in fruit ripening is now emerging. In climacteric fruit, the transition to autocatalytic ethylene production appears to result from a series of events where developmentally regulated ACO and ACS gene expression initiates a rise in ethylene production, setting in motion the activation of autocatalytic ethylene production. Differential expression of ACS and ACO gene family members is probably involved in such a transition. Finally, we discuss evidence suggesting that the NR ethylene perception and transduction pathway is specific to a defined set of genes expressed in ripening climacteric fruit and that a distinct ETR pathway regulates other ethylene‐regulated genes in both immature and ripening climacteric fruit as well as in non‐climacteric fruit. The emerging picture is one where both ethylene‐dependent and ‐independent pathways coexist in both climacteric and non‐climacteric fruits. Further work is needed in order to dissect the molecular events involved in individual ripening processes and to understand the regulation of the expression of both ethylene‐dependent and ‐independent genes.

Indole Acetic Acid 9 (IAA9) is a negative auxin response regulator belonging to the Aux/IAA transcription factor gene family whose downregulation triggers fruit set before pollination, thus giving rise to parthenocarpy. In situ hybridization experiments revealed that a tissue-specific gradient of IAA9 expression is established during flower development, the release of which upon pollination triggers the initiation of fruit development. Comparative transcriptome and targeted metabolome analysis uncovered important features of the molecular events underlying pollination-induced and pollination-independent fruit set. Comprehensive transcriptomic profiling identified a high number of genes common to both types of fruit set, among which only a small subset are dependent on IAA9 regulation. The fine-tuning of Aux/IAA and ARF genes and the downregulation of TAG1 and TAGL6 MADS box genes are instrumental in triggering the fruit set program. Auxin and ethylene emerged as the most active signaling hormones involved in the flower-to-fruit transition. However, while these hormones affected only a small number of transcriptional events, dramatic shifts were observed at the metabolic and developmental levels. The activation of photosynthesis and sucrose metabolism-related genes is an integral regulatory component of fruit set process. The combined results allow a far greater comprehension of the regulatory and metabolic events controlling early fruit development both in the presence and absence of pollination/fertilization.

In plants, genomic DNA methylation which contributes to development and stress responses can be actively removed by DEMETER-like DNA demethylases (DMLs). Indeed, in Arabidopsis DMLs are important for maternal imprinting and endosperm demethylation, but only a few studies demonstrate the developmental roles of active DNA demethylation conclusively in this plant. Here, we show a direct cause and effect relationship between active DNA demethylation mainly mediated by the tomato DML, SlDML2, and fruit ripeningan important developmental process unique to plants. RNAi SlDML2 knockdown results in ripening inhibition via hypermethylation and repression of the expression of genes encoding ripening transcription factors and rate-limiting enzymes of key biochemical processes such as carotenoid synthesis. Our data demonstrate that active DNA demethylation is central to the control of ripening in tomato.active DNA demethylation | DNA glycosylase lyase | epigenetic | tomato | fruit ripening G enomic DNA methylation is a major epigenetic mark that is instrumental to many aspects of chromatin function, including gene expression, transposon silencing, or DNA recombination (1-4). In plants, DNA methylation can occur at cytosine both in symmetrical (CG or CHG) and nonsymmetrical (CHH) contexts and is controlled by three classes of DNA methyltransferases, namely, the DNA Methyltransferase 1, Chromomethylases, and the Domain Rearranged Methyltransferases (5-7). Indeed, in all organisms, cytosine methylation can be passively lost after DNA replication in the absence of methyltransferase activity (1). However, plants can also actively demethylate DNA via the action of DNA GlycosylaseLyases, the so-called DEMETER-Like DNA demethylases (DMLs), that remove methylated cytosine, which is then replaced by a nonmethylated cytosine (8

SummaryArabidopsis thaliana has nine genes that constitute a family of putative carotenoid cleavage dioxygenases (CCDs). While five members of the family are believed to be involved in synthesis of the phytohormone abscisic acid, the functions of the other four enzymes are less clear. Recently two of the enzymes, CCD7/MAX3 and CCD8/MAX4, have been implicated in synthesis of a novel apocarotenoid hormone that controls lateral shoot growth. Here, we report on the molecular and genetic interactions between CCD1, CCD7/MAX3 and CCD8/ MAX4. CCD1 distinguishes itself from other reported CCDs as being the only member not targeted to the plastid. Unlike ccd7/max3 and ccd8/max4, both characterized as having highly branched phenotypes, ccd1 loss-of-function mutants are indistinguishable from wild-type plants. Thus, even though CCD1 has similar enzymatic activity to CCD7/MAX3, it does not have a role in synthesis of the lateral shoot growth inhibitor. Rather, it may have a role in synthesis of apocarotenoid flavor and aroma volatiles, especially in maturing seeds where loss of function leads to significantly higher carotenoid levels.

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