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Plant-growth-promoting bacteria (PGPB) are gaining attention as a sustainable alternative to current agrochemicals. This study evaluated the impact of three Bacillus spp. (5PB1, 1PB1, FV46) and one Brevibacillus sp. (C9F) on the important crop tomato (Solanum lycopersicum) using the model cv. 'MicroTom'. The effects of these isolates were assessed on (a) seedlings' growth and vigor, and (b) adult potted plants. In potted plants, several photosynthetic parameters (chlorophylls (a and b), carotenoids and anthocyanins contents, transpiration rate, stomatal conductance, net CO2 photosynthetic rate, and intercellular CO2 concentration, and on chlorophyll fluorescence yields of light- and dark-adapted leaves)), as well as soluble sugars and starch contents, were quantified. Additionally, the effects on redox status were evaluated. While the growth of seedlings was, overall, not influenced by the strains, some effects were observed on adult plants. The Bacillus safensis FV46 stimulated the content of pigments, compared to C9F. Bacillus zhangzhouensis 5PB1 increased starch levels and was positively correlated with some parameters of the photophosphorylation and the gas exchange phases. Interestingly, Bacillus megaterium 1PB1 decreased superoxide (O2-) content, and B. safensis FV46 promoted non-enzymatic antioxidant defenses, increasing total phenol content levels. These results, conducted on a model cultivar, support the theory that these isolates differently act on tomato plant physiology, and that their activity depends on the age of the plant, and may differently influence photosynthesis. It would now be interesting to analyze the influence of these bacteria using commercial cultivars. [ABSTRACT FROM AUTHOR]

'Red Cloud' (RC) is a cultivar of tomato (Solanum lycopersicum L.) which one of the main agricultural products classified as cultivated plants, it is very important in many countries throughout the world. RC prefers open sunny areas. For this plant, temperature variations are important and have solutions to improve the effects of cold stress by many ways. This study was undertaken to determine the expression of FeSOD (iron superoxide dismutase) and SlNCED1 (a key enzyme in the ABA biosynthetic pathway) genes using qRT-PCR and some physiological features of RC under cold stress. For this purpose, after flowering and fruiting, the potted tomatoes were placed at 2, 4 and –1°C for 8, 12 and 24 h. To measure superoxide dismutase (SOD) enzyme activity, the extract of RC fruits was prepared, and the total protein content (TPrC) was analysed using the standard curve of Bovine Serum Albumin (BSA). Moreover, non-enzymatic antioxidants and total phenol contents (TPC) were measured by diphenyl-picrylhydrazyl (DPPH) and Folin Ciocalteu methods respectively. The results illustrated that all samples at 2°C and 12 h showed the lowest IC50 value, and also the highest amount of TPC was observed in 2–12 sample. Compared to the control, in all treatment groups, FeSOD and SlNCED1 genes expression were higher and much more significant at 4°C, 12 and 24 h, respectively. It has also been demonstrated that at lower temperatures, the TPrC raised and simultaneously, SOD showed the highest levels of activity. [ABSTRACT FROM AUTHOR]

Abstract The cellulose synthase gene superfamily, which includes the cellulose synthase (CesA) and cellulose synthase-like (Csl) gene families, plays a vital role in the biosynthesis of cellulose and hemicellulose in plants. However, these genes have not been extensively studied in tomato (Solanum lycopersicum), a model for Solanaceae plants and for fleshy fruit development. Here, we identified and systematically analyzed 38 CesA / Csl family members that contained cellulose synthase domain regions, and categorized their encoded proteins into 6 subfamilies (CesA, CslA, CslB, CslD, CslE, and CslG) based on phylogenetic analysis. Most CesA / Csl genes from tomato are closely related to those from Arabidopsis , but the families have distinct features regarding gene structure, chromosome distribution and localization, phylogeny, and deduced protein sequence, indicating that they arose via different evolutionary process. Furthermore, expression analysis of CesA / Csl genes in different tissues at various developmental stages showed that most CesAs were constitutively expressed with differential expression levels in various organs; three CslD genes were expressed specifically in flowers, and four CesA and five Csl putative genes were preferentially expressed in fruits. Our results provide insight into the general characteristics of the CesA / Csl genes in tomato, and lay the foundation for further functional studies of CesA / Csl genes in tomato and other Solanaceae species. Highlights • 38 CesA / Csl family members containing cellulose synthase domain were identified in Solanum lycopersicum. • 38 tomato CesA / Csl families were separated into the five subclasses. • The unique Csl genes were identified in Group II and V. • The tissue specific gene expression patterns of 28 CesA / Csl genes were studied. [ABSTRACT FROM AUTHOR]

Summary: Tomato (Solanum lycopersicum), which is used for both processing and fresh markets, is a major crop species that is the top ranked vegetable produced over the world. Tomato is also a model species for research in genetics, fruit development and disease resistance. Genetic resources available in public repositories comprise the 12 wild related species and thousands of landraces, modern cultivars and mutants. In addition, high quality genome sequences are available for cultivated tomato and for several wild relatives, hundreds of accessions have been sequenced, and databases gathering sequence data together with genetic and phenotypic data are accessible to the tomato community. Major breeding goals are productivity, resistance to biotic and abiotic stresses, and fruit sensorial and nutritional quality. New traits, including resistance to various biotic and abiotic stresses and root architecture, are increasingly being studied. Several major mutations and quantitative trait loci (QTLs) underlying traits of interest in tomato have been uncovered to date and, thanks to new populations and advances in sequencing technologies, the pace of trait discovery has considerably accelerated. In recent years, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene editing (GE) already proved its remarkable efficiency in tomato for engineering favorable alleles and for creating new genetic diversity by gene disruption, gene replacement, and precise base editing. Here, we provide insight into the major tomato traits and underlying causal genetic variations discovered so far and review the existing genetic resources and most recent strategies for trait discovery in tomato. Furthermore, we explore the opportunities offered by CRISPR/Cas9 and their exploitation for trait editing in tomato. Significance Statement: The pace of trait discovery in tomato has considerably accelerated in recent years thanks to advances in deep sequencing and other 'omics technologies. Here we review the genetic resources and current powerful forward genetic strategies, allowing discovery of QTLs, genes and mutations underlying remarkable traits in tomato. We also show how CRISPR/Cas9 GE now provides unprecedented opportunities for candidate gene validation, creation of new genetic diversity and breeding of improved tomato varieties. [ABSTRACT FROM AUTHOR]

Abstract Members of the LEUNIG gene family have recently emerged as key players in gene repression, affecting several developmental mechanisms in plants, especially flower development. LEUNIG proteins function via recruiting adaptor SEUSS proteins. Nevertheless, no systematic studies on the LEUNIG and SEUSS gene families have been undertaken in tomato (Solanum lycopersicum , a fleshy fruit-bearing model plant, belonging to the Solanaceae family). Here, we present the results of a genome-wide analysis of tomato LEUNIG and SEUSS genes. In our study, we identified three SlLUG and four SlSEU genes. All three SlLUG full-length proteins contained the LEUNIG canonical domains (LUFS and two WD40 repeats), and the four full-length SlSEU genes contained the Lim-binding domain. All the members of the SlLUG and SlSEU family proteins were localized to the nucleus. All the SlSEU and SlLUG genes were detected in the tomato tissues tested. Expression analysis showed that the SlLUGs and SlSEUs exhibited tissue-specific expression, and that they responded to exogenous plant hormone and stress treatment. Protein-protein interaction analysis showed that only SlLUGs, but not SlSEUs, interacted with SlYABBY. Only a weak interaction between SlLUG1 and SlSEU3 was observed among all the SlLUG and SlSEU proteins. Taken together, these findings may help elucidate the roles played by SlLUG and SlSEU family members in plant growth and development. Highlights • 3 SlLUGs and 4 SlSEUs genes have been identified in the tomato genome. • SlLUGs/SlSEUs genes preferentially expressed in sepal and anther. • Expression level of SlLUGs/SlSEUs genes was affected by hormone treatment. • There is weak interaction between SlLUG1 and SlSEU3. • Only SlLUGs could interact with SlYABBY transcription factors. [ABSTRACT FROM AUTHOR]

A fusion gene coding for trehalose-6-phosphate synthase/phosphatase (TPSP) derived from Escherichia coli was introduced into tomato plants (Solanum lycopersicum cv. Joyful) to generate overexpressing lines and enhance the level of trehalose in the seeds. Trehalose has been implicated in tolerance to abiotic stress in plants, so the response to heat stress of seeds from the transgenic lines and seeds from wild-type plants were compared. Wild-type heat-treated seeds had a germination rate of 17%, while four transgenic lines had germination rates over 50% following heat stress. In one heat-treated transgenic line, 100% of the seeds germinated, and therefore had a germination rate six times that of seeds from wild-type plants. Moreover, quantitative PCR revealed that the expression of diverse genes that respond to heat stress was enhanced in TPSP transgenic seeds compared to wild-type seeds 150 min after the onset of heat stress. The enhanced germination rate and expression of these genes in the transgenic seeds were essentially mimicked in wild-type seeds treated with 1 mM exogenous trehalose. Therefore, accumulated trehalose and associated metabolites may act as signaling molecules that enhance the expression of heat stress-responsive genes and confer heat-stress tolerance to seeds. [ABSTRACT FROM AUTHOR]

Growth and development are vital processes in the life cycles of plants. Brassinosteroids (BRs) are steroids that when exogenously applied can regulate several biological responses. The aim of this research was to investigate the possible interferences caused by the exogenous application of BR on growth and metabolism using two genotypes of the DWARF gene, MT-d and MT-D, that are BR-deficient and BR-efficient, respectively. The experiment had four treatments with two genotypes (BR-efficient and BR-deficient) and two levels of brassinosteroids (0 and 100 nM BR, described as − BR and + BR, respectively). This study revealed that the exogenous application of BR promoted improvement in growth, inducing increases in all variables of both genotypes evaluated. In general, BR-deficient plants sprayed with BR had effects more intense, confirming the benefits of this steroid on photosynthetic apparatus and gas exchange. The changes in the anatomical characteristics of the leaf are related to the contribution of BR on the influx and consequent fixation of CO2. In addition, modifications related to root anatomy occurred as a result of the BR action with the purpose of increasing the root protection and absorption of water and nutrients. Increases in photosynthetic pigments suggest that the role of BR is linked with chlorophyll biosynthesis and the maintenance of chloroplast integrity, resulting from associations with the increases found in the activities of antioxidant enzymes that modulate the accumulation of reactive oxygen species. [ABSTRACT FROM AUTHOR]

Limitations in access to electricity in rural areas and substantial cost of supplemental lightning necessitate breeding as response to low light conditions. Seven inbred lines of tomato (Solanum lycopersicum L.) and their F1 hybrids, including reciprocals, developed through a 7x7 full diallel cross were evaluated under two different levels of light. Mean square for light (L) effect was significant for total yield, average fruit weight and days to first flower. Variation attributable to Genotypes and genotype x light (GxL) interaction had significant effect on all studied traits except days to ripening for which GxL interaction was not significant. Diallel analysis across two environments indicated that general (GCA), specific (SCA) and reciprocal combining ability (REC) were significant for all characters implying importance of additive and non-additive gene action along with cytoplasmic effects on genetic expression of yield, yield components and earliness. Ratio of SCA variance to SCA variance and estimates of narrow sense heritability (h²n.s) demonstrated higher weight of additive effects in inheritance of yield, fruit number and days to ripening, while indicating predominance of non-additive effects for fruit weight and early flowering. Interactions GCAxL and SCAxL were significant for almost all studied features. A particular genotype could not be recommended for all traits, but variation among genotypes in response to ambient light was promising for feasibility of plant breeding for non-optimal light intensity and duration. [ABSTRACT FROM AUTHOR]

The NAC (NAM, ATAF1/2, and CUC2) transcription factor family participates in responses to various kinds of environmental stimuli in plants. However, the roles of NAC protein in cold resistance, especially in the cold resistance of tomatoes, are not completely understood. This study examined the roles of a tomato (Solanum lycopersicum) NAC transcription factor (SlNAC35) in resisting chilling using transgenic tomatoes. GUS staining and expression analysis revealed that SlNAC35 expression was induced at 4 °C, thereby suggesting its involvement in plant responses to chilling stress. Moreover, transgenic lines over-expressing SlNAC35 exhibited high chlorophyll content, fresh mass, and low accumulation of reactive oxygen species and membrane damage under chilling stress. These results indicated that SlNAC35 overexpression enhanced the chilling tolerance of transgenic tomatoes. High expressions of cold tolerance markers SlCOR518 and SlCOR413IM1 were observed under chilling stress in transgenic lines. This observation suggested that SlNAC35 overexpression enhanced the chilling tolerance of transgenic lines by involving the c-repeat binding factor-cold stress response (CBF-COR) signaling pathway and by regulating SlCOR expression. [ABSTRACT FROM AUTHOR]

Ethylene plays an important role in the grape rachis, where its production can be 10 times higher than in the berry. VvACS1 is the only rachis-specific ACC synthase (ACS) gene, and its expression is coincident with ethylene production in the rachis of Vitis vinifera ‘Thompson seedless’. VvACS1 was cloned and ectopically expressed in tomato ( Solanum lycopersicum ‘Moneymaker’). Lateral buds were increased in two- or four-week-old 35s∷ VvACS1 transgenic tomato plants after transplanting. Compared with wild-type (WT) plants, the transgenic tomato plants showed higher expression of the VvACS1 gene in the flowers, leaves, rachis, and fruits. There was no obvious difference of ACS activity in the fruit of tomato, and only increased ACS activity in the rachis of tomato. Ethylene production was decreased in flowers, leaves, and fruits (seven weeks after full bloom), while the relative expression of endogenous tomato ACS1 and ACS6 genes was not down-regulated by the ectopic expression of VvACS1 . These results imply that post-transcriptional or post-translational regulation of ACS may occur, resulting in lower ethylene production in the transgenic tomato plants. Moreover, expression of VvACS1 in tomato resulted in decreased auxin and increased zeatin contents in the lateral buds, as well as reduced or delayed formation of adventitious roots in lateral bud cuttings. RNA-Seq and qRT-PCR analyses of rooted lateral bud cuttings indicated that the relative expression levels of the genes for zeatin O -glucosyltransferase-like, auxin repressed/dormancy-associated protein, and ERF transcription factors were higher in transgenic tomatoes than in WT, suggesting that ethylene may regulate auxin transport and distribution in shoots and that adventitious root formation employs coordination between auxin and ethylene. [ABSTRACT FROM AUTHOR]

Agronomic performance of transgenic tomato overexpressing functional genes has rarely been investigated in the field. In an attempt to improve low-phosphate (P) stress tolerance of tomato ( Solanum lycopersicum ) plants and promote tomato fruit production in the field, an expression vector containing cDNA to an Arabidopsis 14-3-3 protein, General Regulatory Factor 9 ( GRF9 ), driven by a cauliflower mosaic virus 35S promoter, was transferred into tomato plants. Transgenic expression of GRF9 was ascertained by quantitative real-time PCR analysis. The degree of low-P tolerance in transgenic plants was found to be significantly greater than that in wild-type plants, and reflected in improved root development and enhanced P content under hydroponic conditions. For transgenic tomato, roots had higher P uptake, as evidenced by tissue P content and relative expression of the genes LePT1 and LePT2 in both normal and low-P hydroponic solutions. GRF9 overexpressors had greatly enhanced proton extrusion from roots and heightened activity of the plasma-membrane H + -ATPase (PM H + -ATPase) in roots under low-P hydroponic conditions. Thus, in addition to enhanced root development, higher expression of genes coding for phosphate transporters and improved capacity for acidification in the rhizosphere emerged as key mechanisms underpinning improved P acquisition in transgenic tomato plants in soil. Subsequent field trials measuring tomato fruit production at two P levels, indicated that GRF9 can indeed improve total tomato production and may play a role in early fruit maturity. Our results suggest that the heterologous Arabidopsis GRF9 gene can confer resistance to P deficiency in transgenic tomato plants and promote fruit production. [ABSTRACT FROM AUTHOR]

Summary: Steroidal glycoalkaloids (SGAs) are specialized anti‐nutritional metabolites that accumulate in Solanum lycopersicum (tomato) and Solanum tuberosum (potato). A series of SGA biosynthetic genes is known to be upregulated in Solanaceae species by jasmonate‐responsive Ethylene Response Factor transcription factors, including JRE4 (otherwise known as GAME9), but the exact regulatory significance in planta of each factor has remained unaddressed. Here, via TILLING‐based screening of an EMS‐mutagenized tomato population, we isolated a JRE4 loss‐of‐function line that carries an amino acid residue missense change in a region of the protein important for DNA binding. In this jre4 mutant, we observed downregulated expression of SGA biosynthetic genes and decreased SGA accumulation. Moreover, JRE4 overexpression stimulated SGA production. Further characterization of jre4 plants revealed their increased susceptibility to the generalist herbivore Spodoptera litura larvae. This susceptibility illustrates that herbivory resistance is dependent on JRE4‐mediated defense responses, which include SGA accumulation. Ethylene treatment attenuated the jasmonate‐mediated JRE4 expression induction and downstream SGA biosynthesis in tomato leaves and hairy roots. Overall, this study indicated that JRE4 functions as a primary master regulator of SGA biosynthesis, and thereby contributes toward plant defense against chewing insects. [ABSTRACT FROM AUTHOR]

In the present study, 21 thermo tolerant tomato (Solanum lycopersicum L.) genotypes were evaluated to delineate the extent of genetic diversity through 10 quantitative traits. The genotypes were categorized into 4 distinct clusters using D² statistics. Cluster IV had the maximum number (10) of genotypes, where all heat tolerant genotypes grouped together, followed by cluster I (5). Intra cluster analysis revealed that the cluster IV had highest distance, while the inter cluster distance was maximum between cluster III and cluster IV (6.53) indicating the presence of wide range of variability among genotypes of the cluster. Cluster IV recorded maximum cluster mean for yield (579.0), average fruit weight (33.33) and fruit set per cent (54.8) and the cluster III recorded highest mean value for days to 50 percent flowering (67.33). Principal component analysis showed that the first two principal components (PC's) accounting for 77.6 per cent of total variation. On the basis of inter cluster distance, cluster mean and principal component analysis observed in the present study, a crossing programme involving genotypes from cluster IV will be promising one for developing heat tolerant tomato hybrids. [ABSTRACT FROM AUTHOR]

Ethylene perception is regulated by receptors, and the downstream protein CONSTITUTIVE TRIPLE RESPONSE1 is a key suppressor of ethylene signalling. The non-conserved tomato (Solanum lycopersicum) microRNA1917 (SlymiR1917) mediates degradation of SlCTR4 splice variants (SlCTR4sv) but the molecular details of this pathway remain unknown. Sly-miR1917 and the targeted SlCTR4sv are ubiquitously expressed in all tomato organs. Overexpression of Sly-miR1917 enhances ethylene responses, including the triple response in etiolated seedlings, in the absence of ethylene, as well as epinastic petiole growth, accelerated pedicel abscission, and fruit ripening. Enhanced ethylene signalling in Sly-miR1917-overexpressing plants (1917-OE) is accompanied by up-regulation of ethylene biosynthesis and signalling genes, and increased ethylene emission. These phenotypes were recovered by repressing the positive ethylene regulator EIN2. Moreover, the Sly-miR1917-targeted SlCTR4 splice variant SlCTR4sv3, expressed specifically in the abscission zone, exhibited the opposite expression pattern to Sly-miR1917. Complementation of the Arabidopsis thaliana ctr-1 mutant and yeast two-hybrid and bimolecular fluorescence complementation assays suggested that SlCTR4sv3 functions in ethylene signalling. Co-expression of Sly-miR1917 and SlCTR4sv3 in Nicotiana benthamiana further suggested that Sly-miR1917 cleaves SlCTR4sv3 in vivo. Database homology searching revealed a Solanum tuberosum CTR-like splice variant containing a Sly-miR1917 binding sequence, and a homologue of mature SlymiR1917 in potato, indicating a conserved function for miR1917 and the regulatory miRNA-mediated ethylene network in solanaceous species. [ABSTRACT FROM AUTHOR]

The ripening stage at harvest time determines the tomato fruit quality. After the fruit achieves its maximum size several metabolic changes of typically climacteric fruits are produced. Two cultivated genotypes of Solanum lycopersicum (Caimanta and 804627), with normal and altered fruit ripening, respectively and two accession, LA1385 of S. lycopersicum var. cerasiforme and LA722 of S. pimpinellifolium , with genes that prolong fruit shelf life, were tested to: 1) characterize and make a comparatively analysis for the transcriptome at different fruit ripening stages in genotypes that differ in fruit shelf life by cDNA-AFLP; and 2) provide further insight into the relationship between the extreme phenotypic differences for ripening among the genotypes through changes at transcriptomic level. Fruits at the breaker stage (B) were evaluated for fruit weight, firmness and fruit shelf life. The elapsed days between mature green (MG) and breaker stages Days (MG-B) as well as the elapsed days between B and red ripe (RR) stages Days (B-RR) were recorded. Comparison among ripening stages showed a great polymorphism related to the changes in gene expression. For all genotypes the transition from B to RR stages had higher polymorphism than the transition from MG to B. It was observed a great genetic variability for the phenotypic traits in agreement with the changes of gene expression. Moreover, it was observed that the transcriptome expression profiles in the initial and intermediate stages during ripening (MG and B) are more important to characterize genotypes. The wild species which have long shelf life do not show as drastic changes in gene expression as the cultivar with altered ripening that carrythe nor gene. These results suggest that the expressed or silenced genes could be involved, in some way, in the determination of the phenotypic traits evaluated in this study. [ABSTRACT FROM AUTHOR]

Jasmonic acid (JA) and arbuscular mycorrhizal (AM) symbioses are known to protect plants against abiotic and biotic stresses, but are also involved in the regulation of root hydraulic conductance (L). The objective of this experiment was to elucidate the role of JA in the water relations and hormonal regulation of AM plants under drought by using tomato plants defective in the synthesis of JA (def-1). Our results showed that JA is involved in the uptake and transport of water through its effect on both physiological parameters (stomatal conductance and L) and molecular parameters, mainly by controlling the expression and abundance of aquaporins. We observed that def-1 plants increased the expression of seven plant aquaporin genes under well-watered conditions in the absence of AM fungus, which partly explain the increment of L by this mutation under well-watered conditions. In addition, the effects of the AM symbiosis on plants were modified by the def-1 mutation, with the expression of some aquaporins and plant hormone concentration being disturbed. On the other hand, methyl salicylate (MeSA) content was increased in non-mycorrhizal def-1 plants, suggesting that MeSA and JA can act together in the regulation of L. In a complementary experiment, it was found that exogenous MeSA increased L, confirming our hypothesis. Likewise, we confirmed that JA, ABA and SA are hormones involved in plant mechanisms to cope with stressful situations, their concentrations being controlled by the AM symbiosis. In conclusion, under wellwatered conditions, the def-1 mutation mimics the effects of AM symbiosis, but under drought conditions the def-1 mutation changed the effects of the AM symbiosis on plants. [ABSTRACT FROM AUTHOR]

With the completion of genome sequencing projects, the next challenge is to close the gap between gene annotation and gene functional assignment. Genomic tools to identify gene functions are based on the analysis of phenotypic variations between a wild type and its mutant; hence, mutant collections are a valuable resource. In this sense, T- DNA collections allow for an easy and straightforward identification of the tagged gene, serving as the basis of both forward and reverse genetic strategies. This study reports on the phenotypic and molecular characterization of an enhancer trap T- DNA collection in tomato ( Solanum lycopersicum L.), which has been produced by Agrobacterium-mediated transformation using a binary vector bearing a minimal promoter fused to the uidA reporter gene. Two genes have been isolated from different T- DNA mutants, one of these genes codes for a UTP-glucose-1-phosphate uridylyltransferase involved in programmed cell death and leaf development, which means a novel gene function reported in tomato. Together, our results support that enhancer trapping is a powerful tool to identify novel genes and regulatory elements in tomato and that this T- DNA mutant collection represents a highly valuable resource for functional analyses in this fleshy-fruited model species. [ABSTRACT FROM AUTHOR]

The transition from flowering to fruit production, namely fruit set, is crucial to ensure successful sexual plant reproduction. Although studies have described the importance of hormones (i.e. auxin and gibberellins) in controlling fruit set after pollination and fertilization, the role of micro RNA-based regulation during ovary development and fruit set is still poorly understood. Here we show that the micro RNA159/ GAMYB1 and -2 pathway (the miR159/ GAMYB1/2 module) is crucial for tomato ovule development and fruit set. MiR159 and Sl GAMYBs were expressed in preanthesis ovaries, mainly in meristematic tissues, including developing ovules. Sl MIR159-overexpressing tomato cv. Micro-Tom plants exhibited precocious fruit initiation and obligatory parthenocarpy, without modifying fruit shape. Histological analysis showed abnormal ovule development in such plants, which led to the formation of seedless fruits. Sl GAMYB1/2 silencing in Sl MIR159-overexpressing plants resulted in misregulation of pathways associated with ovule and female gametophyte development and auxin signalling, including AINTEGUMENTA-like genes and the miR167/ Sl ARF8a module. Similarly to Sl MIR159-overexpressing plants, Sl GAMYB1 was downregulated in ovaries of parthenocarpic mutants with altered responses to gibberellins and auxin. Sl GAMYBs likely contribute to fruit initiation by modulating auxin and gibberellin responses, rather than their levels, during ovule and ovary development. Altogether, our results unveil a novel function for the miR159-targeted Sl GAMYBs in regulating an agronomically important trait, namely fruit set. [ABSTRACT FROM AUTHOR]

Salinity threatens productivity of economically important crops such as tomato (Solanum lycopersicum L.). WRKY transcription factors appear, from a growing body of knowledge, as important regulators of abiotic stresses tolerance. Tomato SlWRKY3 is a nuclear protein binding to the consensus CGTTGACC/T W box. SlWRKY3 is preferentially expressed in aged organs, and is rapidly induced by NaCl, KCl, and drought. In addition, SlWRKY3 responds to salicylic acid, and 35S::SlWRKY3 tomatoes showed under salt treatment reduced contents of salicylic acid. In tomato, overexpression of SlWRKY3 impacted multiple aspects of salinity tolerance. Indeed, salinized (125 mM NaCl, 20 days) 35S::SlWRKY3 tomato plants displayed reduced oxidative stress and proline contents compared to WT. Physiological parameters related to plant growth (shoot and root biomass) and photosynthesis (stomatal conductance and chlorophyll a content) were retained in transgenic plants, together with lower Na+ contents in leaves, and higher accumulation of K+ and Ca2+. Microarray analysis confirmed that many stress-related genes were already up-regulated in transgenic tomatoes under optimal conditions of growth, including genes coding for antioxidant enzymes, ion and water transporters, or plant defense proteins. Together, these results indicate that SlWRKY3 is an important regulator of salinity tolerance in tomato. [ABSTRACT FROM AUTHOR]

Fruit set is a developmental transition from ovaries to fruitlets that determines yield potential. Cell wall invertase (CWIN) is essential for fruit and seed set, but the underlying molecular basis remains elusive. We addressed this issue by using CWIN-elevated transgenic tomato, focusing on ovaries and fruitlets at 2 d before and after anthesis, respectively. RNAseq analyses revealed that ovaries and fruitlets exhibited remarkable differences in their transcriptomic responses to elevated CWIN activity. Ovaries 2 d before anthesis were far more responsive to elevated CWIN activity compared with the fruitlets. We identified several previously unknown pathways that were up-regulated by elevated CWIN activity during fruit set. The most notable of these were expression of genes for defence, ethylene synthesis and the cell cycle along with a large number of cell wall-related genes. By contrast, expression of photosynthetic, protein degradation and some receptor-like kinase genes were generally decreased as compared with the wild type ovaries. GC-MS analyses revealed that 22 out of 24 amino acids exhibited reduced levels in the RNAi ovaries as compared with that in the wild type, probably owing to a down-regulated expression of protein degradation genes. Overall, the data indicate that (i) ovaries are much more sensitive to metabolic intervention than fruitlets; (ii) high CWIN activity could promote fruit set by improving resistance against pathogens and altering cell cycle and cell wall synthesis. [ABSTRACT FROM AUTHOR]

Sterol glycosyltransferases (SGTs) catalyze the glycosylation of the free hydroxyl group at C-3 position of sterols to produce sterol glycosides. Glycosylated sterols and free sterols are primarily located in cell membranes where in combination with other membrane-bound lipids play a key role in modulating their properties and functioning. In contrast to most plant species, those of the genus Solanum contain very high levels of glycosylated sterols, which in the case of tomato may account for more than 85% of the total sterol content. In this study, we report the identification and functional characterization of the four members of the tomato (Solanum lycopersicum cv. Micro-Tom) SGT gene family. Expression of recombinant SlSGT proteins in E. coli cells and N. benthamiana leaves demonstrated the ability of the four enzymes to glycosylate different sterol species including cholesterol, brassicasterol, campesterol, stigmasterol, and b-sitosterol, which is consistent with the occurrence in their primary structure of the putative steroid-binding domain found in steroid UDP-glucuronosyltransferases and the UDP-sugar binding domain characteristic for a superfamily of nucleoside diphosphosugar glycosyltransferases. Subcellular localization studies based on fluorescence recovery after photobleaching and cell fractionation analyses revealed that the four tomato SGTs, like the Arabidopsis SGTs UGT80A2 and UGT80B1, localize into the cytosol and the PM, although there are clear differences in their relative distribution between these two cell fractions. The SlSGT genes have specialized but still largely overlapping expression patterns in different organs of tomato plants and throughout the different stages of fruit development and ripening. Moreover, they are differentially regulated in response to biotic and abiotic stress conditions. SlSGT4 expression increases markedly in response to osmotic, salt, and cold stress, as well as upon treatment with abscisic acid and methyl jasmonate Stress-induced SlSGT2 expression largely parallels that of SlSGT4. On the contrary, SlSGT1 and SlSGT3 expression remains almost unaltered under the tested stress conditions. Overall, this study contributes to broaden the current knowledge on plant SGTs and provides support to the view that tomato SGTs play overlapping but not completely redundant biological functions involved in mediating developmental and stress responses. [ABSTRACT FROM AUTHOR]

Background: Cultivated tomato (Solanum lycopersicum L.) is the second most important vegetable crop after potato and a member of thirteen interfertile species of Solanum genus. Domestication and continuous selection for desirable traits made cultivated tomato species susceptible to many stresses as compared to the wild species. In this study, we analyzed and compared the genomes of wild and cultivated tomato accessions to identify the genomic regions that encountered changes during domestication. Results: Analysis was based on SNP and InDel mining of twentynine accessions of twelve wild tomato species and forty accessions of cultivated tomato. Percentage of common SNPs among the accessions within a species corresponded with the reproductive behavior of the species. SNP profiles of the wild tomato species within a phylogenetic subsection varied with their geographical distribution. Interestingly, the ratio of genic SNP to total SNPs increased with phylogenetic distance of the wild tomato species from the domesticated species, suggesting that variations in gene-coding region play a major role in speciation. We retrieved 2439 physical positions in 1594 genes including 32 resistance related genes where all the wild accessions possessed a common wild variant allele different from all the cultivated accessions studied. Tajima's D analysis predicted a very strong purifying selection associated with domestication in nearly 1% of its genome, half of which is contributed by chromosome 11. This genomic region with a low Tajima's D value hosts a variety of genes associated with important agronomic trait such as, fruit size, tiller number and wax deposition. Conclusion: Our analysis revealed a broad-spectrum genetic base in wild tomato species and erosion of that in cultivated tomato due to recurrent selection for agronomically important traits. Identification of the common wild variant alleles and the genomic regions undergoing purifying selection during cultivation would facilitate future breeding program by introgression from wild species. [ABSTRACT FROM AUTHOR]

Phytophthora infestans, causing late blight on Solanaceae, is a serious threat to potato and tomato crops worldwide. P. infestans populations sampled on either potato or tomato differ in genotypes and pathogenicity, suggesting niche exclusion in the field. We hypothesized that such niche separation can reflect differential host exploitation by different P. infestans genotypes. We thus compared genotypes and phenotypes in 21 isolates sampled on potato ( n = 11) or tomato ( n = 10). Typing at 12 microsatellite loci assigned potato isolates to the 13_A2, 6_A1 and 1_A1 lineages, and tomato isolates to the 23_A1, 2_A1 and unclassified multilocus genotypes. Cross-inoculations on potato and tomato leaflets showed that all isolates were pathogenic on both hosts. However, tomato isolates performed much better on tomato than did potato isolates, which performed better on potato than did tomato isolates, thus revealing a clear pattern of local adaptation. Potato isolates were significantly fitter on potato than on tomato, and are best described as potato specialists; tomato isolates appear to be generalists, with similar pathogenicity on both hosts. Niche separation in the field may thus result mainly from the large fitness gap on tomato between generalists and unadapted potato specialists, while the small, but significant fitness difference on potato between both types of isolates may prevent population invasion by generalists. Extreme specialization to potato seems very costly relative to performance loss on the alternative host. This study therefore shows that local adaptation and niche separation, commonly expected to involve and generate specialists, can occur with generalists. [ABSTRACT FROM AUTHOR]

Light plays a key role in the regulation of many physiological processes required for plant and chloroplast development. Plant cryptochromes (crys) play an important role in monitoring, capturing, and transmitting the light stimuli. In this study, we analyzed the effects of CRY2 overexpression on transcription of tomato chloroplast genome by a tiling array, containing about 90 000 overlapping probes (5-nucleotide resolution). We profiled transcription in leaves of wild-type and CRY2-overexpressing plants grown in a diurnal cycle, to generate a comprehensive map of chloroplast transcription and to monitor potential specific modulations of the chloroplast transcriptome induced by the overexpression of CRY2. Our results demonstrate that CRY2 is a master gene of transcriptional regulation in the tomato chloroplast. In fact, it modulates the day/night mRNA abundance of about 58% of the 114 ORFs. The effect of CRY2 includes a differential extension of some transcripts at their 5′-end, according to the period of the day. We observed that the influence of CRY2 on chloroplast transcription is not limited to coding RNA; a great number of putative noncoding micro RNA also showed differential accumulation pattern. To our knowledge, this is the first study that highlights how a photoreceptor affects the day/night transcription of the chloroplast genome. [ABSTRACT FROM AUTHOR]

Tomato (Solanum lycopersicum) diageotropica (dgt) mutants, containing a single mutation in the Cyclophilin1 (SlCyp1) gene, are auxin-insensitive, exhibiting a pleiotropic phenotype including lack of geotropism, abnormal xylem structure, lack of lateral roots (LRs), and elevated shoot-to-root ratio. SlCyp1 is a putative peptidyl-prolyl isomerase that can traffic from shoot to root, where it induces changes in auxin response, LR formation, and xylem development, suggesting it has a role as a long-distance signaling molecule. Here, we explored the mechanism underlying SlCyp1 function in the phloem. Expression of SlCyp1 under a phloem-specific (AtSuc2) promoter in dgt plants partially restored the wild-type phenotype, including lateral root development, root branching, and xylem morphology. The observed developmental changes were associated with physiological alternations at the whole-plant level, including a reduction in shoot-to-root ratio, enhanced transpiration, and elevated photosynthetic rates. Conversely, phloemspecific expression of SlCyp1 active-site mutants did not restore the wild-type phenotype. Local inhibition of cyclophilin functioning in the target tissue reduced auxin sensitivity, suggesting that its enzymatic activity in the distant organ is required for its action as a long-distance signalling agent. The data presented suggest that SlCyp1 is a signal molecule trafficking from shoot to root where its activity is required for auxin-mediated lateral root development. [ABSTRACT FROM AUTHOR]

Water scarcity constitutes a crucial constraint for agriculture productivity. High-throughput approaches in model plant species identified hundreds of genes potentially involved in survival under drought, but few having beneficial effects on quality and yield. Nonetheless, controlled water deficit may improve fruit quality through higher concentration of flavor compounds. The underlying genetic determinants are still poorly known. In this study, we phenotyped 141 highly diverse small fruit tomato accessions for 27 traits under two contrasting watering conditions. A subset of 55 accessions exhibited increased metabolite contents and maintained yield under water deficit. Using 6100 single nucleotide polymorphisms (SNPs), association mapping revealed 31, 41, and 44 quantitative trait loci (QTLs) under drought, control, and both conditions, respectively. Twenty-five additional QTLs were interactive between conditions, emphasizing the interest in accounting for QTLs by watering regime interactions in fruit quality improvement. Combining our results with the loci previously identified in a biparental progeny resulted in 11 common QTLs and contributed to a first detailed characterization of the genetic determinants of response to water deficit in tomato. Major QTLs for fruit quality traits were dissected and candidate genes were proposed using expression and polymorphism data. The outcomes provide a basis for fruit quality improvement under deficit irrigation while limiting yield losses. [ABSTRACT FROM AUTHOR]

The objective of this study was to investigate the phenotypic and molecular variability in a F2 generation derived from a SCH (Second Cycle Hybrid) in order to detect QTLs for some fruit traits of tomato. Genome coverage at different levels was achieved by three types of molecular markers (polypeptides, sequence-related amplified polymorphism-SRAP and amplified restriction fragment polymorphism - AFLP). Different degrees of polymorphism were detected by SRAP and AFLP at the DNA structure level and also by polypeptides at the DNA expression level. The first two markers, associated with phenotypic variation, detected QTLs involved in important agronomic traits such as fruit shelf life, soluble solids content, pH, and titratable acidity. New gene blocks originated by recombination during the first cycle of crossing were detected. This study confirmed that the observed phenotypic differences represent a new gene rearrangement and that these new gene blocks are responsible for the presence of the genetic variability detected for these traits. [ABSTRACT FROM AUTHOR]

Ascorbate (AsA) is an important antioxidant that can scavenge reactive oxygen species to protect plant cells against oxidative stress. Guanosine 5'-diphosphate (GDP)-L-galactose phosphorylase (GGP) is a key enzyme in the AsA biosynthetic pathway. To investigate the functions of GGP in AsA synthesis and oxidative stress tolerance in tomato, antisense lines with a reduced expression of SlGGP were obtained. Photobleaching after treatment of leaf disks with methyl viologen was more severe in transgenic lines compared to wild type (WT) plants. Moreover, compared with the WT plants, the transgenic plants showed a higher content of hydrogen peroxide, superoxide anion, malondialdehyde, as well as ion leakage, but a lower content of AsA and chlorophylls, ascorbate peroxidase activity, net photosynthetic rate, and maximal photochemical efficiency of photosystem II. Results of real-time quantitative polymerase chain reaction show that suppression of the SlGGP gene in the transgenic plants reduced their oxidative stress tolerance. [ABSTRACT FROM AUTHOR]

In the present study, effect of different levels of nitrogen (N 0 , deprived; N 25 , sub-optimum; N 75 , optimum and N 150 , supra-optimum) in Solanum lycopersicum L. seedlings under NaCl (NaCl 1 , 0.3 g kg −1 sand and NaCl 2 , 0.5 g kg −1 sand) stress was investigated. Biomass accumulation, pigments, K + concentration, nitrate and nitrite contents were declined by NaCl in dose dependent manner. As compared to control (N 75 without NaCl), fresh weight declined by 4% and 11%, and dry weight by 7 and 13% when seedlings were grown under N 75 +NaCl 1 and N 75 +NaCl 2 combinations, respectively. Furthermore, fluorescence parameters (JIP-test): the size and number of active reaction centres of photosynthetic apparatus (F v /F 0 ), efficiency of water splitting complex (F 0 /F v ), quantum yield of primary photochemistry (φP 0 or Phi_P 0 ), yield of electron transport per trapped excitation (Ψ 0 or Psi_0), the quantum yield of electron transport (φE 0 ), and performance index of PS II (PI ABS ) and parameters related to energy fluxes per reaction centre (ABS/RC, TR 0 /RC, ET 0 /RC and DI 0 /RC) were also affected by NaCl. However, toxic effect of NaCl on photosystem II photochemistry was ameliorated by N. The lower dose (NaCl 1 ) of NaCl exerts damaging effect on oxidation side of PS II, while higher dose (NaCl 2 ) damages PS II reaction centre and its reduction side. Moreover, control seedlings (N 75 without NaCl) when exposed to NaCl 1 and NaCl 2 exhibited a significant enhancement in respiration rate by 6 and 16%, Na + accumulation by 111 and 169% in shoot, and 141 and 223% in root and ammonium contents by 19 and 34% respectively. Nitrate and ammonium assimilating enzymes such as nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS) and glutamate synthase (GOGAT) were adversely affected by NaCl stress while glutamate dehydrogenase (GDH) showed reverse trend. N addition caused further enhancement in free proline, and activity of Δ 1 -pyrroline-5-carboxylate synthetase (P5CS), while activity of proline dehydrogenase (ProDH) decreased. The results indicate that different levels of N significantly modulated NaCl-induced damaging effects in tomato seedlings. Furthermore, the results suggest that after N addition Na + , nitrite, nitrate, ammonium contents, nitrogen metabolic enzymes, proline content, and activity of P5CS are favourably regulated, which might be associated with mitigation of NaCl stress and effect was more pronounced with supra-optimum level of N (N 150 ). [ABSTRACT FROM AUTHOR]

The tomato resistance protein Sw-5b differs from the classical coiled-coil nucleotide-binding leucine-rich repeat ( CC- NB- LRR) resistance proteins by having an extra N-terminal domain ( NTD). To understand how NTD, CC and NB- LRR regulate autoinhibition and activation of Sw-5b, we dissected the function(s) of each domain., When viral elicitor was absent, Sw-5b LRR suppressed the central NB- ARC to maintain autoinhibition of the NB- LRR segment. The CC and NTD domains independently and additively enhanced the autoinhibition of NB- LRR., When viral elicitor was present, the NB- LRR segment of Sw-5b was specifically activated to trigger a hypersensitive response. Surprisingly, Sw-5b CC suppressed the activation of NB- LRR, whereas the extra NTD of Sw-5b became a positive regulator and fully activated the resistance protein, probably by relieving the inhibitory effects of the CC. In infection assays of transgenic plants, the NB- LRR segment alone was insufficient to confer resistance against Tomato spotted wilt tospovirus; the layers of NTD and CC regulation on NB- LRR were required for Sw-5b to confer resistance., Based on these findings, we propose that, to counter the negative regulation of the CC on NB- LRR, Sw-5b evolved an extra NTD to coordinate with the CC, thus developing a multilayered regulatory mechanism to control autoinhibition and activation. [ABSTRACT FROM AUTHOR]

Isoprenoids consist of a large class of compounds that are present in all living organisms. They are derived from the 5C building blocks isopentenyl diphosphate ( IDP) and its isomer dimethylallyl diphosphate ( DMADP). In plants, IDP is synthesized in the cytoplasm from mevalonic acid via the MVA pathway, and in plastids from 2- C-methyl- d-erythritol-4-phosphate through the MEP pathway. The enzyme IDP isomerase ( IDI) catalyzes the interconversion between IDP and DMADP. Most plants contain two IDI enzymes, the functions of which are characteristically compartmentalized in the cells. Carotenoids are isoprenoids that play essential roles in photosynthesis and provide colors to flowers and fruits. They are synthesized in the plastids via the MEP pathway. Fruits of Solanum lycopersicum (tomato) accumulate high levels of the red carotene lycopene. We have identified mutations in tomato that reduce overall carotenoid accumulation in fruits. Four alleles of a locus named FRUIT CAROTENOID DEFICIENT 1 ( fcd1) were characterized. Map-based cloning of fcd1 indicated that this gene encodes the plastidial enzyme IDI1. Lack of IDI1 reduced the concentration of carotenoids in fruits, flowers and cotyledons, but not in mature leaves. These results indicate that the plastidial IDI plays an important function in carotenoid biosynthesis, thus highlighting its role in optimizing the ratio between IDP and DMADP as precursors for different downstream isoprenoid pathways. [ABSTRACT FROM AUTHOR]

The actin depolymerizing factor (ADF) proteins have growth, development, defense-related and growth regulatory functions in plants. The present study used genome-wide analysis to investigate ADF family genes in tomato. Eleven tomato ADF genes were identified and differential expression patterns were found in different organs. SlADF6 was preferentially expressed in roots, suggesting its function in root development. SlADF1, SlADF3 and SlADF10 were predominately expressed in the flowers compared to the other organs and specifically in the stamen compared to other flower parts, indicating their potential roles in pollen development. The comparatively higher expression of SlADF3 and SlADF11 at early fruit developmental stages might implicate them in determining final fruit size. SlADF5 and SlADF8 had relatively higher levels of expression five days after the breaker stage of fruit development, suggesting their possible role in fruit ripening. Notably, six genes were induced by cold and heat, seven by drought, five by NaCl, and four each by abscisic acid (ABA), jasmonic acid (JA) and wounding treatments. The differential expression patterns of the SlADF genes under different types of stresses suggested their function in stress tolerance in tomato plants. Our results will be helpful for the functional characterization of ADF genes during organ and fruit development of tomato under different stresses. [ABSTRACT FROM AUTHOR]

Key message: Genetic interactions of UFD gene support its specific function during reproductive development of tomato; in this process, UFD could play a pivotal role between inflorescence architecture and flower initiation genes. Abstract: Tomato ( Solanum lycopersicum L.) is a major vegetable crop that also constitutes a model species for the study of plant developmental processes. To gain insight into the control of flowering and floral development, a novel tomato mutant, unfinished flower development ( ufd), whose inflorescence and flowers were unable to complete their normal development was characterized using double mutant and gene expression analyses. Genetic interactions of ufd with mutations affecting inflorescence fate ( uniflora, jointless and single flower truss) were additive and resulted in double mutants displaying the inflorescence structure of the non- ufd parental mutant and the flower phenotype of the ufd mutant. In addition, ufd mutation promotes an earlier inflorescence meristem termination. Taken together, both results indicated that UFD is not involved in the maintenance of inflorescence meristem identity, although it could participate in the regulatory system that modulates the rate of meristem maturation. Regarding the floral meristem identity, the falsiflora mutation was epistatic to the ufd mutation even though FALSIFLORA was upregulated in ufd inflorescences. In terms of floral organ identity, the ufd mutation was epistatic to macrocalyx, and MACROCALYX expression was differently regulated depending on the inflorescence developmental stage. These results suggest that the UFD gene may play a pivotal role between the genes required for flowering initiation and inflorescence development (such as UNIFLORA, FALSIFLORA, JOINTLESS and SINGLE FLOWER TRUSS) and those required for further floral organ development such as the floral organ identity genes. [ABSTRACT FROM AUTHOR]

We present a resource for fine mapping of traits derived from the wild tomato species Solanum pennellii ( LA0716). The population of backcross inbred lines ( BILs) is composed of 446 lines derived after a few generations of backcrosses of the wild species with cultivated tomato (cultivar M82; LA3475), followed by more than seven generations of self-pollination. The BILs were genotyped using the 10K SOL- CAP single nucleotide polymorphism ( SNP) -Chip, and 3700 polymorphic markers were used to map recombination break points relative to the physical map of Solanum lycopersicum. The BILs carry, on average, 2.7 introgressions per line, with a mean introgression length of 11.7 Mbp. Whereas the classic 76 introgression lines ( ILs) partitioned the genome into 106 mapping bins, the BILs generated 633 bins, thereby enhancing the mapping resolution of traits derived from the wild species. We demonstrate the power of the BILs for rapid fine mapping of simple and complex traits derived from the wild tomato species. [ABSTRACT FROM AUTHOR]

A screening under salt stress conditions of a T- DNA mutant collection of tomato ( Solanum lycopersicum L.) led to the identification of the altered response to salt stress 1 ( ars1) mutant, which showed a salt-sensitive phenotype. Genetic analysis of the ars1 mutation revealed that a single T- DNA insertion in the ARS1 gene was responsible of the mutant phenotype. ARS1 coded for an R1- MYB type transcription factor and its expression was induced by salinity in leaves. The mutant reduced fruit yield under salt acclimation while in the absence of stress the disruption of ARS1 did not affect this agronomic trait. The stomatal behaviour of ars1 mutant leaves induced higher Na+ accumulation via the transpiration stream, as the decreases of stomatal conductance and transpiration rate induced by salt stress were markedly lower in the mutant plants. Moreover, the mutation affected stomatal closure in a response mediated by abscisic acid (ABA). The characterization of tomato transgenic lines silencing and overexpressing ARS1 corroborates the role of the gene in regulating the water loss via transpiration under salinity. Together, our results show that ARS1 tomato gene contributes to reduce transpirational water loss under salt stress. Finally, this gene could be interesting for tomato molecular breeding, because its manipulation could lead to improved stress tolerance without yield penalty under optimal culture conditions. [ABSTRACT FROM AUTHOR]

Cold is a serious threat that limits the productivity of tomato as it is a cold-sensitive crop. The cold tolerant gene DREB1A plays crucial roles in the survival of plants under cold stress. We have developed cold stress tolerant transgenic plants of tomato by the overexpression of an Arabidopsis DREB1A gene. They were obtained by using EHA-105 strain of Agrobacterium harboring pBIH binary vector that contained DREB1A controlled by an inducible promoter Lip9 and hygromycin phosphotransferase gene (hpt) as a plant selectable marker. Sequential 15 day old in vitro seedlings, 48 h preculture period, Agrobacterium density (OD600 nm = 0.2), 3 min infection period and 60 μM acetosyringone yielded 15?18% TE. T0 transformants were identified by PCR and then they were self-pollinated to generate T1 progeny that was evaluated by gene expression and cold tolerance analyses. AtDREB1A transcript expression was detected by RT-PCR and stable integration of AtDREB1A gene was confirmed by Southern blotting. Morphological analyses of T2 generations demonstrated that there were no significant differences among transgenic and NT plants under normal growth conditions. The T2 transgenic lines exhibited more cold stress tolerance when exposed to 4°C as compared to their NT counterparts. These findings clearly indicate that transgenic tomato plants over-expressing Arabidopsis DREB1A gene enhanced protection and provided cold tolerance under controlled conditions in transgenic containment. [ABSTRACT FROM AUTHOR]

Fusarium crown and root rot is a severe fungal disease of tomato caused by Fusarium oxysporum f. sp. radicis-lycopersici (FORL). In this study, the genomic location of the FORL-resistance locus was determined using a set of molecular markers on chromosome 9 and an F2 population derived from FORL-resistant inbred 'AV107-4' ( Solanum lycopersicum) × susceptible 'L3708' ( Solanum pimpinellifolium). Bioassay performed using Korean FORL strain KACC 40031 showed single dominant inheritance of FORL resistance in the F2 population. In all, 13 polymerase chain reaction-based markers encompassing approximately 3.6-72.0 Mb of chromosome 9 were developed based on the Tomato-EXPEN 2000 map and SolCAP Tomato single nucleotide polymorphism array analysis. These markers were genotyped on 345 F2 plants, and the FORL-resistance locus was found to be present on a pericentromeric region of suppressed chromosomal recombination in chromosome 9. The location of the FORL-resistance locus was further confirmed by testing these markers against diverse commercial tomato and stock cultivars resistant to FORL. A restriction fragment length polymorphism marker, PNU-D4, located at approximately 6.1 Mb of chromosome 9 showed the highest match with the resistance locus and was used for conducting high-resolution melting analysis for marker-assisted selection of FORL resistance. [ABSTRACT FROM AUTHOR]

Background: Tomato leaf mold is a common disease in tomato cultivation. This disease is caused by Cladosporium fulvum, which has many physiological races and differentiates rapidly. Cf genes confer resistance to C. fulvum, and the C. fulvum-tomato pathosystem is a model for the study of gene-for-gene interactions. Plants carrying the Cf-19 gene show effective resistance to C. fulvum in the field, and can be used in breeding and resistance mechanism studies as new resistant materials. In this study, we used F2 bulk specific-locus amplified fragment sequencing (SLAF-seq) and parental resequencing methods to locate and characterize the Cf-19 gene. Results: A total of 4108 Diff_markers and three association regions were found in association analysis. A 2.14-Mb region containing seven Cf-type genes was identified in further analysis based on data from SLAF-seq and parental resequencing. Two candidate genes, Solyc01g006550.2.1 and Solyc01g005870.1.1, were screened out by quantitative real-time PCR (qRT-PCR) analysis. Sequence analysis showed that Solyc01g006550.2.1 (an allelic locus of Cf-0) in CGN18423 was a novel homologue of the Cladosporium resistance gene Cf-9 (Hcr9s) in the Cf-4/9 locus. The marker P7, which cosegregated with the resistant trait, was developed based on sequence mutation of the Solyc01g006550.2.1 locus in CGN18423. Conclusions: The Cf-19 gene was mapped to the short arm of chromosome 1. The candidate genes Solyc01g006550.2.1 and Solyc01g005870.1.1 showed related amino acid sequence structures and expression patterns. Solyc01g006550.2.1 had a close evolutionary relationship with the functional Hcr9 members Cf-4 and Cf-9, and was very different from non-functional members. The results from this study will facilitate the breeding of cultivars carrying the Cf-19 gene and provide a basis for further gene cloning, resistance gene evolution and plant resistance mechanism studies. [ABSTRACT FROM AUTHOR]

To investigate the putative crosstalk between JA and ABA in Solanum lycopersicum plants in response to drought, suppressor of prosystemin-mediated responses2 (spr2, JA-deficient) and flacca (flc, ABA-deficient) mutants together with the naphthalene/salicylate hydroxylase (NahG) transgenic (SA-deficient) line were used. Hormone profiling and gene expression of key enzymes in ABA, JA and SA biosynthesis were analyzed during early stages of drought. ABA accumulation was comparable in spr2 and wild type (WT) plants whereas expression of 9-cis-epoxycarotenoid dioxygenase 1 (NCED1) and NCED2 was different, implying a compensation mechanism between NCED genes and an organ-specific regulation of NCED1 expression. JA levels and 12-oxo-phytodienoic acid reductase 3 (OPR3) expression in flc plants suggest that ABA regulates the induction of the OPR3 gene in roots. By contrast, ABA treatment to flc plants leads to a reduction of JA and SA contents. Furthermore, different pattern of SA accumulation (and expression of isochorismate synthase and phenylalanine ammonia lyase 1) was observed between WT seedlings and mutants, suggesting that SA plays an important role on the early response of tomato plants to drought and also that JA and ABA modulate its biosynthesis. Finally, hormone profiling in spr2 and NahG plants indicate a crosstalk between JA and SA that could enhance tolerance of tomato to water stress. [ABSTRACT FROM AUTHOR]

The aim of this study was to assess the effect of the mutant genes B, og, hp, and t on the fruit color of tomato genotypes. Two tomato lines (TOM-498 and TOM-499) with BB genotype composition (high β-carotene homozygous) were used in hybrid combinations with 7 tomato lines with different genotype compositions in loci og, hp, or t-Floradade, TOM-596, TOM-544, NC-8276, NC-2Y, Florida 7775, and Florida 7781. A randomized complete block design with 24 treatments and four replications was used. Both external and internal fruit color were assessed with a Minolta CR-400 colorimeter in the CIE L*, a* and b* mode. Hue and chroma readings were taken at four different points (epidermis, pericarp, placenta, and columella) of the fruit. For high β-carotene heterozygous hybrids B /B, hue angle indicated an orange color (since these hybrids did not come to equal the genotypes of normal coloring, red), even when genes promoting lycopene synthesis ( og, hp) were deployed as heterozygous genotypes. Fruit of high β-carotene heterozygous hybrids, without t, og, or hp, had chroma values similar to fruit of homozygous high β-carotene lines. The use of the og allele in heterozygosity led to higher chroma values in high β-carotene heterozygous genotypes in relation to the values found in high β-carotene heterozygous genotypes not bearing the og gene. The og homozygous lines had hue values that did not differ from those in normal genotypes in the epidermis and pericarp, but showed a significant shift towards red in the placenta and in the columella. [ABSTRACT FROM AUTHOR]

The objective was to estimate the combining ability of lines and heterosis in industrial tomato genotypes for the identification of those with good potential for breeding programs. Ten lines of industrial tomato, 45 hybrids derived from a complete diallel and two commercial check cultivars were evaluated. The combining ability of tomato lines and heterosis of hybrid combinations for fruitquality related traits were estimated. Non-additive effects predominated in the genetic control of all traits. The parent lines RVTD-04, RVTD-10 and RVTD-08 had an exceptionally high presence of favorable alleles for most traits. High genetic divergence between the parents was observed, contributing positively to significant heterosis values. The above lines can be used in breeding programs to develop tomato hybrids with high performance for characteristics related to industrial processing. [ABSTRACT FROM AUTHOR]

A detailed study of the diurnal compositional changes was performed in tomato (Solanum lycopersicum cv. Moneymaker) leaves and fruits. Plants were cultivated in a commercial greenhouse under two growth conditions: control and shaded. Expanding fruits and the closest mature leaves were harvested during two different day/night cycles (cloudy or sunny day). High-throughput robotized biochemical phenotyping of major compounds, as well as proton nuclear magnetic resonance and mass spectrometry metabolomic profiling, were used to measure the contents of about 70 metabolites in the leaves and 60 metabolites in the fruits, in parallel with ecophysiological measurements. Metabolite data were processed using multivariate, univariate, or clustering analyses and correlation networks. The shaded carbon-limited plants adjusted their leaf area, decreased their sink carbon demand and showed subtle compositional modifications. For source leaves, several metabolites varied along a diel cycle, including those directly linked to photosynthesis and photorespiration. These metabolites peaked at midday in both conditions and diel cycles as expected. However, transitory carbon storage was limited in tomato leaves. In fruits, fewer metabolites showed diel fluctuations, which were also of lower amplitude. Several organic acids were among the fluctuating metabolites. Diel patterns observed in leaves and especially in fruits differed between the cloudy and sunny days, and between the two conditions. Relationships between compositional changes in leaves and fruits are in agreement with the fact that several metabolic processes of the fruit appeared linked to its momentary supply of sucrose. [ABSTRACT FROM AUTHOR]

Tomato plants colonised with the arbuscular mycorrhizal ( AM) fungus Glomus fasciculatum show systemic induced resistance to the foliar pathogen Alternaria alternata, as observed in interactions of other AM-colonised plants with a range of pathogens. The role of jasmonic ( JA) and salicylic ( SA) acid in expression of this mycorrhiza-induced resistance ( MIR) against A. alternata was studied by measuring: (i) activity of enzymes reported to be involved in their biosynthesis, namely lipoxygenase ( LOX) and phenylammonia lyase ( PAL); and (ii) levels of methyl jasmonate (Me JA) and SA. Transcript abundance of some defence genes associated with JA and SA response pathways were also studied. Both LOX and PAL activity increased twofold in response to pathogen application to control plants. AM-colonised plants had three-fold higher LOX activity compared to control plants, but unlike controls, this did not increase further in response to pathogen application. Higher LOX activity in AM-colonised plants correlated with four-fold higher Me JA in leaves of AM-colonised plants compared to controls. Treatment of plants with the JA biosynthesis inhibitor salicylhydroxamic acid ( SHAM) led to 50% lower Me JA in both control and AM-colonised plants and correlated with increased susceptibility to A. alternata, suggesting a causal role for JA in expression of MIR against the pathogen. Genes involved in JA biosynthesis ( OPR3) and response ( COI1) showed six- and 42-fold higher expression, respectively, in leaves of AM-colonised plants compared to controls. AM-colonised plants also showed increased expression of the SA response gene PR1 and that of the wound-inducible polypeptide prosystemin. Our results suggest that the systemic increase in JA in response to AM colonisation plays a key role in expression of MIR against A. alternata. [ABSTRACT FROM AUTHOR]

Identification of the polymorphisms controlling quantitative traits remains a challenge for plant geneticists. Multiparent advanced generation intercross ( MAGIC) populations offer an alternative to traditional linkage or association mapping populations by increasing the precision of quantitative trait loci ( QTL) mapping. Here, we present the first tomato MAGIC population and highlight its potential for the valorization of intraspecific variation, QTL mapping and causal polymorphism identification. The population was developed by crossing eight founder lines, selected to include a wide range of genetic diversity, whose genomes have been previously resequenced. We selected 1536 SNPs among the 4 million available to enhance haplotype prediction and recombination detection in the population. The linkage map obtained showed an 87% increase in recombination frequencies compared to biparental populations. The prediction of the haplotype origin was possible for 89% of the MAGIC line genomes, allowing QTL detection at the haplotype level. We grew the population in two greenhouse trials and detected QTLs for fruit weight. We mapped three stable QTLs and six specific of a location. Finally, we showed the potential of the MAGIC population when coupled with whole genome sequencing of founder lines to detect candidate SNPs underlying the QTLs. For a previously cloned QTL on chromosome 3, we used the predicted allelic effect of each founder and their genome sequences to select putative causal polymorphisms in the supporting interval. The number of candidate polymorphisms was reduced from 12 284 (in 800 genes) to 96 (in 54 genes), including the actual causal polymorphism. This population represents a new permanent resource for the tomato genetics community. [ABSTRACT FROM AUTHOR]

Background: ATP-binding cassette proteins have been recognized as playing a crucial role in the regulation of growth and resistance processes in all kingdoms of life. They have been deeply studied in vertebrates because of their role in drug resistance, but much less is known about ABC superfamily functions in plants. Results: Recently released plant genome sequences allowed us to identify 803 ABC transporters in four vascular plants (Oryza. sativa, Solanum lycopersicum, Solanum tuberosum and Vitis vinifera) and 76 transporters in the green alga Volvox carteri, by comparing them with those reannotated in Arabidopsis thaliana and the yeast Saccharomyces cerevisiae. Retrieved proteins have been phylogenetically analysed to infer orthologous relationships. Most orthologous relationships in the A, D, E and F subfamilies were found, and interesting expansions within the ABCG subfamily were observed and discussed. A high level of purifying selection is acting in the five ABC subfamilies A, B, C, D and E. However, evolutionary rates of recent duplicate genes could influence vascular plant genome diversification. The transcription profiles of ABC genes within tomato organs revealed a broad functional role for some transporters and a more specific activity for others, suggesting the presence of key ABC regulators in tomato. Conclusions: The findings achieved in this work could contribute to address several biological questions concerning the evolution of the relationship between genomes of different species. Plant ABC protein inventories obtained could be a valuable tool both for basic and applied studies. Indeed, interpolation of the putative role of gene functions can accelerate the discovering of new ABC superfamily members. [ABSTRACT FROM AUTHOR]

Background: The basic helix-loop-helix (bHLH) proteins are a large superfamily of transcription factors, and play a central role in a wide range of metabolic, physiological, and developmental processes in higher organisms. Tomato is an important vegetable crop, and its genome sequence has been published recently. However, the bHLH gene family of tomato has not been systematically identified and characterized yet. Results: In this study, we identified 159 bHLH protein-encoding genes (SlbHLH) in tomato genome and analyzed their structures. Although bHLH domains were conserved among the bHLH proteins between tomato and Arabidopsis, the intron sequences and distribution of tomato bHLH genes were extremely different compared with Arabidopsis. The gene duplication analysis showed that 58.5% and 6.3% of SlbHLH genes belonged to low-stringency and high-stringency duplication, respectively, indicating that the SlbHLH genes are mainly generated via short low-stringency region duplication in tomato. Subsequently, we classified the SlbHLH genes into 21 subfamilies by phylogenetic tree analysis, and predicted their possible functions by comparison with their homologous genes of Arabidopsis. Moreover, the expression profile analysis of SlbHLH genes from 10 different tissues showed that 21 SlbHLH genes exhibited tissue-specific expression. Further, we identified that 11 SlbHLH genes were associated with fruit development and ripening (eight of them associated with young fruit development and three with fruit ripening). The evolutionary analysis revealed that 92% SlbHLH genes might be evolved from ancestor(s) originated from early land plant, and 8% from algae. Conclusions: In this work, we systematically identified SlbHLHs by analyzing the tomato genome sequence using a set of bioinformatics approaches, and characterized their chromosomal distribution, gene structures, duplication, phylogenetic relationship and expression profiles, as well predicted their possible biological functions via comparative analysis with bHLHs of Arabidopsis. The results and information provide a good basis for further investigation of the biological functions and evolution of tomato bHLH genes. [ABSTRACT FROM AUTHOR]

NAC (NAM, ATAF1,2, and CUC2) transcription factors play an important role in the responses of plants to various environmental stresses. To investigate the function of SlNAC1, which was found to be a member of the ATAF subfamily in tomato ( Solanum lycopersicum L.) plants under heat stress conditions, transgenic tomato plants were generated using an antisense technology. After a treatment at 40 °C for 48 h, in comparison with wild-type (WT) plants, the transgenic plants were severely wilted and exhibited a lower net photosynthetic rate and a maximal photochemical efficiency of photosystem II. Moreover, the transgenic plants displayed a higher ion leakage and malondialdehyde content and a lower proline content. The content of reactive oxygen species (superoxide anion radicals and hydrogen peroxide) were higher, and activities of ascorbate peroxidase and superoxide dismutase lower in the transgenic plants than in the WT plants. The transgenic plants also exhibited a lower accumulation of the transcripts of some heat shock protein genes ( Hsp70, Hsp90, sHsp17.4, and sHsp17.6). All of these results suggest that the suppression of SlNAC1 could obviously reduce heat resistance in the tomato plants, and this indicates that SlNAC1 played an important role in the thermal tolerance of the tomato plants. [ABSTRACT FROM AUTHOR]

Increasing cuticular wax accumulation in plants has been associated with improving drought tolerance in plants. In this study, a cDNA clone encoding the SlSHN1 transcription factor, the closest ortholog to WIN/SHN1 gene in Arabidopsis, was isolated from tomato plant. Expression analysis of SlSHN1 indicated that it is induced in response to drought conditions. The over-expression of SlSHN1 in tomato under the control of the constitutive CaMV 35S promoter produced plants that showed mild growth retardation phenotype with shiny and dark green leaves. Scanning electron microscopy showed that the over-expression of SlSHN1 in tomato resulted in higher cuticular wax deposition on leaf epidermial tissue when compared to non-transformed plants. Expression analysis in transgenic lines over-expressing SlSHN1 indicated that several wax-related synthesis genes were induced. Transgenic tomato plants over-expressing SlSHN1 showed higher drought tolerance when compared with wild type plants; this was reflected in delayed wilting of transgenic lines, improved water status and reduced water loss rate when compared with wild type plants. In conclusion, the SlSHN1 gene can modulate wax accumulation and could be utilized to enhance drought tolerance in tomato plant. [ABSTRACT FROM AUTHOR]

Background Decades of intensive tomato breeding using wild-species germplasm have resulted in the genomes of domesticated germplasm (Solanum lycopersicum) being intertwined with introgressions from their wild relatives. Comparative analysis of genomes among cultivated tomatoes and wild species that have contributed genetic variation can help identify desirable genes, such as those conferring disease resistance. The ability to identify introgression position, borders, and contents can reveal ancestral origins and facilitate harnessing of wild variation in crop breeding. Results Here we present the whole-genome sequences of two tomato inbreds, Gh13 and BTI-87, both carrying the begomovirus resistance locus Ty-3 introgressed from wild tomato species. Introgressions of different sizes on chromosome 6 of Gh13 and BTI-87, both corresponding to the Ty-3 region, were identified as from a source close to the wild species S. chilense. Other introgressions were identified throughout the genomes of the inbreds and showed major differences in the breeding pedigrees of the two lines. Interestingly, additional large introgressions from the close tomato relative S. pimpinellifolium were identified in both lines. Some of the polymorphic regions were attributed to introgressions in the reference Heinz 1706 genome, indicating wild genome sequences in the reference tomato genome. Conclusions The methods developed in this work can be used to delineate genome introgressions, and subsequently contribute to development of molecular markers to aid phenotypic selection, fine mapping and discovery of candidate genes for important phenotypes, and for identification of novel variation for tomato improvement. These universal methods can easily be applied to other crop plants. [ABSTRACT FROM AUTHOR]

Zinc finger genes comprise a large and diverse gene family. Based on their individual finger structures and spacing, zinc finger proteins are further divided into different families according to their specific molecular functions. Genes in the CCCH family encode zinc finger proteins containing a motif with three cysteines and one histidine. They play important roles in plant growth and development, and in response to biotic and abiotic stresses. However, the limited analysis of the genome sequence has meant that there is no detailed information concerning the CCCH zinc finger family in tomato ( Solanum lycopersicum). Here, we identified 80 CCCH zinc finger protein genes in the tomato genome. A complete overview of this gene family in tomato was presented, including the chromosome locations, gene duplications, phylogeny, gene structures and protein motifs. Promoter sequences and expression profiles of putative stress-responsive members were also investigated. These results revealed that, with the exception of four genes, the 80 CCCH genes are distributed over all 12 chromosomes with different densities, and include six segmental duplication events. The CCCH family in tomato could be divided into 12 groups based on their different CCCH motifs and into eight subfamilies by phylogenetic analysis. Analysis showed that almost all CCCH genes contain putative stress-responsive cis-elements in their promoter regions. Nine CCCH genes chosen for further quantitative real-time PCR analysis showed differential expression patterns in three representative tomato tissues. In addition, their expression levels indicated that these genes are mostly involved in the response to mannitol, heat, salicylic acid, ethylene or methyl jasmonate treatments. To the best of our knowledge, this is the first report of a genome-wide analysis of the tomato CCCH zinc finger family. Our data provided valuable information on tomato CCCH proteins and form a foundation for future studies of these proteins, especially for those members that may play important roles in stress responses. [ABSTRACT FROM AUTHOR]