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Although domesticated tomato is cultivated by wild tomato, there are a lot of differences between cultivated tomato and wild tomato, such as shape, physiological function and life history. Many studies show that wild tomato has better salt resistance and drought resistance. In addition to, domesticated tomato’s fruit is bigger and has more nutritious than wild tomato. The different features are closely related to differentially expressed genes. We identified 126 up-regulated differentially expressed genes and 87 down-regulated differentially expressed genes in cultivated tomato and wild tomato by RNA-Seq. These differentially expressed genes may be associated with salt resistance, drought resistance and fruit nutrition. These differentially expressed genes also further highlight the large-scale reconstruction between wild and cultivated species. In this paper, we mainly study GO enrichment analysis and pathway analysis of the differentially expressed genes. After GO and pathway enrichment analysis, a set of significantly enriched GO annotations and pathways were identified for the differentially expressed genes. What’s more, we also identified long non-coding RNAs and mRNAs in the two species and analyzed its essential features. In addition to, we construct a co-expression network of long non-coding RNAs and mRNAs, and annotate mRNAs associated with long non-coding RNAs as target genes, and speculate the regulation function of long non-coding RNAs. In total, our results reveal the effects of artificial and natural selection on tomato’s transcript, providing scientific basis for tomato’s research in the future. [ABSTRACT FROM AUTHOR]

The Arabidopsis thaliana NAC transcription factor JUNGBRUNNEN1 (AtJUB1) regulates growth by directly repressing GA3ox1 and DWF4, two key genes involved in gibberellin (GA) and brassinosteroid (BR) biosynthesis, respectively, leading to GA and BR deficiency phenotypes. AtJUB1 also reduces the expression of PIF4, a bHLH transcription factor that positively controls cell elongation, while it stimulates the expression of DELLA genes, which are important repressors of growth. Here, we extend our previous findings by demonstrating that AtJUB1 induces similar GA and BR deficiency phenotypes and changes in gene expression when overexpressed in tomato (Solanum lycopersicum). Importantly, and in accordance with the growth phenotypes observed, AtJUB1 inhibits the expression of growth-supporting genes, namely the tomato orthologs of GA3ox1, DWF4 and PIF4, but activates the expression of DELLA orthologs, by directly binding to their promoters. Overexpression of AtJUB1 in tomato delays fruit ripening, which is accompanied by reduced expression of several ripeningrelated genes, and leads to an increase in the levels of various amino acids (mostly proline, β-alanine, and phenylalanine), γ-aminobutyric acid (GABA), and major organic acids including glutamic acid and aspartic acid. The fact that AtJUB1 exerts an inhibitory effect on the GA/BR biosynthesis and PIF4 genes but acts as a direct activator of DELLA genes in both, Arabidopsis and tomato, strongly supports the model that the molecular constituents of the JUNGBRUNNEN1 growth control module are considerably conserved across species. [ABSTRACT FROM AUTHOR]

Tomato yellow leaf curl disease is a major constraint for tomato production worldwide and availability of new resistant materials is of great importance for breeding programmes. A phenotypic survey was undertaken to evaluate the level of resistance to the main tomato yellow leaf curl disease-inducing virusesTomato yellow leaf curl virusandTomato yellow leaf curl Sardinia virus, in several commercial tomato cultivars, never characterised before. Seven weeks post inoculation, two cultivars resulted in high resistant phenotypes to both begomoviruses, and four were tolerant to at least one of them. In the two highly resistant hybrids (SJ12, RFT112), symptoms were completely absent and viral DNA was from 102to 105fold lower than in susceptible plants. Molecular marker analysis revealed that these genotypes harbour the resistant genesTy-1/Ty-3andTy-2.Given their high resistance, they can be considered good candidates for cultivation and breeding in areas where incidence of TYLCD is very elevated. [ABSTRACT FROM AUTHOR]

Phenotypic plasticity is the phenomenon that one particular genotype produces different phenotypes under different environmental conditions, but its underlying molecular and genetic mechanisms are poorly understood. Plastic traits may be under the control of genes whose expression is modulated by environmental cues. In this study, we investigated phenotypic plasticity in tomato (Solanum lycopersicum) and its ancestral species S. pimpinellifolium by comparing the global gene expression of young seedlings grown under two distinct growth conditions. Our results show that more than 7000 genes exhibited differential expression in response to environmental changes from phytotron to a plastic greenhouse, and 98 environmentally sensitive genes displayed the same patterns of expression response across the two tomato species. We also found that growth conditions had a remarkable impact on transcriptome complexity, attributable to alternative splicing (AS), in which 665 splice variants showed differential expression in response to the environmental changes. Moreover, more splice variants and AS events per gene were detected in plastic greenhouse-grown seedlings than their phytotron counterparts, and these seedlings also had higher percentages of intron retention events. The identification of the conserved environmentally-sensitive genes and the splice variants in this study will be useful for further analysis of gene regulation of environmental response in tomato and other crops. [ABSTRACT FROM AUTHOR]

Exposure to salinity induces a burst in ethylene synthesis in the wild tomato halophyte plant species Solanum chilense . In order to gain information on the role of ethylene in salt adaptation, plants of Solanum chilense (accession LA4107) and of cultivated glycophyte Solanum lycopersicum (cv. Ailsa Craig) were cultivated for 7 days in nutrient solution containing 0 or 125 mM NaCl in the presence or absence of the inhibitor of ethylene synthesis (aminovinylglycine (AVG) 2 μM). Salt-induced ethylene synthesis in S. chilense occurred concomitantly with an increase in stomatal conductance, an efficient osmotic adjustment and the maintenance of carbon isotope discrimination value (Δ 13 C). In contrast, in S. lycopersicum , salt stress decreased stomatal conductance and Δ 13 C values while osmotic potential remained higher than in S. chilense . Inhibition of stress-induced ethylene synthesis by AVG decreased stomatal conductance and Δ 13 C in S. chilense and compromised osmotic adjustment. Solanum chilense behaved as an includer and accumulated high amounts of Na in the shoot but remained able to maintain K nutrition in the presence of NaCl. This species however did not stimulate the expression of genes coding for high-affinity K transport but genes coding for ethylene responsive factor ERF5 and JREF1 were constitutively more expressed in S. chilense than in S. lycopersicum . It is concluded that ethylene plays a key role in salt tolerance of S. chilense . [ABSTRACT FROM AUTHOR]

This study aims to investigate the role ofPaenibacillus terraeAY-38 to produce bioactive metabolites and to counteract pathogenic infections caused byB. cinerea. The pure culture ofP. terrae(AY-38) showed the secretion of significant amount of IAA (indole-3-acetic acid) (109.57 ± 3.2 µg mL−1). The AY-38 strain also produced siderophore and glucanase, while in the in vitro test, it showed significant antagonism toBotrytis cinerea. In the in vivo plant experiment, the sole application of AY-38 significantly improved plant growth (plant height and leaf area), while inB. cinereainfected plants, AY-38 inoculation not only decreased the disease incidence on leaves and fruits but also reprogramed the plants for higher growth. AY-38 treatments promoted and rescued plant growth by modulating the defence responses of endogenous hormones, such as jasmonic and salicylic acids. Our findings concluded thatP. terraepossesses great potential as a possible biocontrol agent againstB. cinerea-induced pathogenic infections. [ABSTRACT FROM PUBLISHER]

Endemic flora of the Galapagos Islands has adapted to thrive in harsh environmental conditions. The wild tomato species from the Galapagos Islands, Solanum cheesmaniae and S. galapagense, are tolerant to various stresses, and can be crossed with cultivated tomato. However, information about genetic diversity and relationships within and between populations is necessary to use these resources efficiently in plant breeding. In this study, we analyzed 3,974 polymorphic SNP markers, obtained through the genotyping-by-sequencing technique, DArTseq, to elucidate the genetic diversity and population structure of 67 accessions of Galapagos tomatoes (compared to two S. lycopersicum varieties and one S. pimpinellifolium accession). Two clustering methods, Principal Component Analysis and STRUCTURE, showed clear distinction between the two species and a subdivision in the S. cheesmaniae group corresponding to geographical origin and age of the islands. High genetic variation among the accessions within each species was suggested by the AMOVA. High diversity in the S. cheesmaniae group and its correlation with the islands of origin were also suggested. This indicates a possible influence of the movement of the islands, from west to east, on the gene flow. Additionally, the absence of S. galapagense populations in the eastern islands points to the species divergence occurring after the eastern islands became isolated. Based on these results, it can be concluded that the population structure of the Galapagos tomatoes collection partially explains the evolutionary history of both species, knowledge that facilitates exploitation of their genetic potential for the identification of novel alleles contributing to stress tolerance. [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]

The 7B-1 tomato (Solanum lycopersicum L. cv Rutgers) is a male-sterile mutant with enhanced tolerance to abiotic stress, which makes it a potential candidate for hybrid seed breeding and stress engineering. To underline the molecular mechanism regulating the male-sterility in 7B-1, transcriptomic profiles of the 7B-1 male-sterile and wild type (WT) anthers were studied using mRNA sequencing (RNA-Seq). In total, 768 differentially expressed genes (DEGs) were identified, including 132 up-regulated and 636 down-regulated transcripts. Gene ontology (GO) enrichment analysis of DEGs suggested a general impact of the 7B-1 mutation on metabolic processes, such as proteolysis and carbohydrate catabolic process. Sixteen candidates with key roles in regulation of anther development were subjected to further analysis using qRT-PCR and in situ hybridization. Cytological studies showed several defects associated with anther development in the 7B-1 mutant, including unsynchronized anther maturation, dysfunctional meiosis, arrested microspores, defect in callose degradation and abnormal tapetum development. TUNEL assay showed a defect in programmed cell death (PCD) of tapetal cells in 7B-1 anthers. The present study provides insights into the transcriptome of the 7B-1 mutant. We identified several genes with altered expression level in 7B-1 (including beta-1,3 glucanase, GA2oxs, cystatin, cysteine protease, pectinesterase, TA29, and actin) that could potentially regulate anther developmental processes, such as meiosis, tapetum development, and cell-wall formation/degradation. [ABSTRACT FROM AUTHOR]

Isolation and functional characterization of tissue- and stage-specific gene promoters is beneficial for genetic improvement of economically important crops. Here, we have characterized a putative promoter of a ripening-induced gene RIP1 ( Ripening induced protein 1) in tomato. Quantification of the transcript level of RIP1 showed that its expression is fruit preferential, with maximum accumulation in red ripe fruits. To test the promoter activity, we made a reporter construct by cloning 1450 bp putative RIP1 promoter driving the GUS (ß- glucuronidase) gene expression and generated stable transgenic lines in tomato and Arabidopsis. Histochemical and fluorometric assays validated the fruit-specific expression of RIP1 as the highest GUS activity was found in red ripe tomatoes. Similarly, we detected high levels of GUS activity in the siliques of Arabidopsis. On the contrary, weak GUS activity was found in the flower buds in both tomato and Arabidopsis. To characterize the specific regions of the RIP1 promoter that might be essential for its maximum activity and specificity in fruits, we made stable transgenic lines of tomato and Arabidopsis with 5′-deletion constructs. Characterization of these transgenic plants showed that the full length promoter is essential for its function. Overall, we report the identification and characterization of a ripening-induced promoter of tomato, which would be useful for the controlled manipulation of the ripening-related agronomic traits in genetic manipulation studies in future. [ABSTRACT FROM AUTHOR]

Tomato cultivars differ in their sensitivity to heat stress, and the sensitivity depends on the developmental stage of the plants. It is less known how heat stress affects tomato at the anthesis stage in terms of leaf physiology and fruit set and whether the ability of tomato to tolerate heat at different developmental stages is linked. To investigate photosynthetic gas exchange characteristics, carbohydrate content and fruit set during heat stress, a thermo-tolerant cultivar (' LA1994') and a thermo-sensitive cultivar ('Aromata') were studied at the seedling and anthesis stage. The photosynthetic parameters, maximum quantum efficiency of photosystem II ( Fv/ Fm), chlorophyll content, carbohydrate content and fruit set were determined in plants grown at 26/18 °C (control) and 36/28 °C (heat stress). The physiological responses including net photosynthetic rate ( PN), chlorophyll content and Fv/ Fm decreased in 'Aromata' at both developmental stages during heat stress, whereas they were unaltered in ' LA1994' during heat stress as compared to the respective control. This was accompanied by lower contents of glucose and fructose in mature leaves of 'Aromata' at the seedling stage under heat stress. In contrast, the glucose content increased while the fructose content was unaltered in mature leaves of ' LA1994' at the seedling stage under heat stress. High temperature induced a similar change in carbohydrate content in the young leaves of both cultivars at anthesis. The fructose and sucrose content were unaffected in the mature leaves of 'Aromata' but significantly increased in ' LA1994' under heat stress at anthesis. The heat stress treatment decreased pollen viability and inhibited fruit set due to flower wilting and abnormal abscission in 'Aromata', whereas fruit set was not inhibited in ' LA1994'. A decrease in chlorophyll content, photosynthesis and carbohydrate content in the mature leaves of tomato could be related to fruit set failure at high temperature. The results show that physiological responses to heat stress at the seedling stage correspond with the responses at the anthesis stage, demonstrating that screening for heat stress sensitivity can be carried out in young plants. [ABSTRACT FROM AUTHOR]

Ascorbate (AsA) is very important in scavenging reactive oxygen species in plants. AsA can reduce photoinhibition by xanthophyll cycle to dissipate excess excitation energy. GGP is an important enzyme in AsA biosynthesis pathway in higher plants. In this study, we cloned a gene, SlGGP-LIKE , that has the same function but different sequence compared with SlGGP . The function of SlGGP-LIKE gene in response to oxidative stress was investigated using transgenic tobacco plants overexpressed SlGGP-LIKE under methyl viologen treatment. After oxidative stress treatment, transgenic tobacco lines exhibited higher levels of reduced AsA content and APX activity than WT plants. Under oxidative stress, transgenic tobacco plants accumulated less ROS and exhibited lower degrees of REC and MDA. Consequently, relatively higher levels of Pn, Fv/Fm, de-epoxidation status of xanthophyll cycle and D1 protein were maintained in transgenic tobacco plants. Hence, overexpression of SlGGP-LIKE gene enhances AsA biosynthesis and can alleviate the photoinhibition of PSII under oxidative stress. [ABSTRACT FROM AUTHOR]

SUMOylation is an important post-translational modification process that regulates different cellular functions in eukaryotes. SIZ/PIAS-type SAP and Miz1 (SIZ1) proteins exhibit SUMO E3 ligase activity, which modulates SUMOylation. However, SIZ1 in tomato has been rarely investigated. In this study, a tomato SIZ1 gene ( SlSIZ1) was isolated and its molecular characteristics and role in tolerance to drought stress are described. SlSIZ1 was up-regulated by cold, sodium chloride (NaCl), polyethylene glycol (PEG), hydrogen peroxide (H2O2) and abscisic acid (ABA), and the corresponding proteins were localized in the nucleus. The expression of SlSIZ1 in Arabidopsis thaliana (Arabidopsis) siz1-2 mutants partially complemented the phenotypes of dwarf, cold sensitivity and ABA hypersensitivity. SlSIZ1 also exhibited the activity of SUMO E3 ligase to promote the accumulation of SUMO conjugates. Under drought stress, the ectopic expression of SlSIZ1 in transgenic tobacco lines enhanced seed germination and reduced the accumulation of reactive oxygen species. SlSIZ1 overexpression conferred the plants with improved growth, high free proline content, minimal malondialdehyde accumulation and increased accumulation of SUMO conjugates. SlSIZ1 is a functional homolog of Arabidopsis SIZ1 with SUMO E3 ligase activity. Therefore, overexpression of SlSIZ1 enhanced the tolerance of transgenic tobacco to drought stress. [ABSTRACT FROM AUTHOR]

The rapid development of omics sequencing technology has facilitated the identification of thousands of long non-coding (lnc)RNAs in plant species, but the role of lncRNAs in plant-pathogen interactions remains largely unexplored. We used comparative transcriptome analysis of Phytophthora infestans-resistant and -susceptible tomatoes to identify differentially expressed genes (DEGs) and lncRNAs (DELs), and examine lncRNA-mRNA networks. A total of 1037 DEGs and 688 DELs were identified between P. infestans-resistant and -susceptible tomatoes. The co-localization networks, including 128 DEGs and 127 DELs, were performed. We found that lncRNA16397 acted as an antisense transcript of SlGRX22 to regulate its expression, and also induced SlGRX21 expression when lncRNA16397 was overexpressed. In addition, disease symptoms and reactive oxygen species (ROS) accumulation in tomatoes overexpressing lncRNA16397 and SpGRX were fewer and lower than those in wild-type after P. infestans infection. This result suggests that tomato lncRNA16397 induces SlGRX expression to reduce ROS accumulation and alleviate cell membrane injury, resulting in enhanced resistance to P. infestans. Our results provide insight into lncRNAs involved in the response of tomato to P. infestans infection, demonstrate that the lncRNA16397-GRXs network is an important component of the P. infestans network in tomato, and provide candidates for breeding to enhance biotic stress-resistance in tomato. [ABSTRACT FROM AUTHOR]

We determined the crossover (CO) distribution, frequency and genomic sequences involved in interspecies meiotic recombination by using parent-assigned variants of 52 F6 recombinant inbred lines obtained from a cross between tomato, Solanum lycopersicum, and its wild relative, Solanum pimpinellifolium. The interspecific CO frequency was 80% lower than reported for intraspecific tomato crosses. We detected regions showing a relatively high and low CO frequency, so-called hot and cold regions. Cold regions coincide to a large extent with the heterochromatin, although we found a limited number of smaller cold regions in the euchromatin. The CO frequency was higher at the distal ends of chromosomes than in pericentromeric regions and higher in short arm euchromatin. Hot regions of CO were detected in euchromatin, and COs were more often located in non-coding regions near the 50 untranslated region of genes than expected by chance. Besides overrepresented CCN repeats, we detected poly-A/T and AT-rich motifs enriched in 1-kb promoter regions flanking the CO sites. The most abundant sequence motifs at CO sites share weak similarity to transcription factor-binding sites, such as for the C2H2 zinc finger factors class and MADS box factors, while InterPro scans detected enrichment for genes possibly involved in the repair of DNA breaks. [ABSTRACT FROM AUTHOR]

The influence of the planting season on the nutritional as well as the aromatic composition of Hezuo 903 tomato was investigated by combining use of nutrition analysis, sensory evaluation, electronic nose and electronic tongue analysis, gas chromatography-mass spectrometry (GC-MS) and GC-MS-olfactometry (GC-MS-O) method. The results suggested that in-season tomato contained higher levels of reducing sugar, vitamin C and lycopene than off-season tomato. In-season tomato showed a better overall flavor and acceptability than off-season tomato. Significant difference was observed in both composition and concentration of the typical volatile and aroma-active compounds in two samples. E-2-Hexenal and methyl salicylate were only found in off-season tomato, and phenylacetaldehyde detected merely in in-season tomato. In addition, significantly higher levels of 6-methyl-5-hepten-2-one ( P < 0.01) and 2-isobutylthiazole ( P < 0.01) were detected in off-season tomato than in-season tomato, which showed a negative effect on the overall flavor of tomato. Our result indicated that the planting season affected the composition and concentration of both non-volatile and volatile compounds of tomato fruit. [ABSTRACT FROM AUTHOR]

A study was conducted at Zifta district, Gharbia governorate, at middle delta region of Egypt during seven successive seasons of 2009-2015 to study the genetic variability and heritability for some plant and fruit characteristics in tomato. Fifteen F7 lines were selected from 4 F2 generations of six generations of selection. The estimated coefficient of variance (C. V %) values (degree of homogeneity) differed among the studied genotypes for the same character and from trait to another of the same genotype. The selected genotypes were enough homogenous for the studied traits and then it could be considered as new lines. A great diversity and significant differences were observed among the fifteen selected genotypes for all studied traits. The fines S.209, K.111-1, K.111-6, AL. 3-1-3 and EUR. 2-2 were considered the best fines for yield and fruit quality traits, and could be used in breeding programs to develop new focal F1 hybrids of tomato. The results showed high values for genotypic coefficient of variation (G. C. V %) compared with the phenotypic coefficient of variation (P. C. V %) and high heritability in broad sense (h2bs) ·for all studied traits. The G. V. C% vs P. C. V% and (h2bs)values were 18.43 vs 22.08% and 0. 70 for (days to 50% flowering), 20.09 vs 22.46 and 0.8( for plant height ),22.94 vs 24.80 and 0.86( for number of branches), 16.67 vs 17.26 and 0.93 (for early yield), 18.25 vs 18.53 and 0.94 (for total yield), 16.59 vs 19.22 and 0. 75 (for fruit firmness), indicating small environmental effects and large additive genetic components of the phenotypic variation for these traits and can be improved through selection programs. [ABSTRACT FROM AUTHOR]

Modern commercial tomato varieties are substantially less flavorful than heirloom varieties. To understand and ultimately correct this deficiency, we quantified flavor-associated chemicals in 398 modern, heirloom, and wild accessions. A subset of these accessions was evaluated in consumer panels, identifying the chemicals that made the most important contributions to flavor and consumer liking. We found that modern commercial varieties contain significantly lower amounts of many of these important flavor chemicals than older varieties. Whole-genome sequencing and a genome-wide association study permitted identification of genetic loci that affect most of the target flavor chemicals, including sugars, acids, and volatiles. Together, these results provide an understanding of the flavor deficiencies in modern commercial varieties and the information necessary for the recovery of good flavor through molecular breeding. [ABSTRACT FROM AUTHOR]

Background: Tomatoes provide a significant dietary source of the carotenoids, lycopene and β-carotene. During ripening, carotenoid accumulation determines the fruit colors while chlorophyll degradation. These traits have been, and continue to be, a significant focus for plant breeding efforts. Previous work has found strong evidence for a relationship between CYC-B gene expression and the orange color of fleshy fruit. Other work has identified a point mutation in SGR that impedes chlorophyll degradation and causes brown flesh color to be retained in some tomato varieties. Methods: We crossed two inbred lines, KNY2 (orange) and KNB1 (brown) and evaluated the relationship between these genes for their effect on fruit color. Phenotypes of F2 generation plants were analyzed and a novel 'orange-brown' fruit color was identified. Results: We confirm two SNPs, one in CYC-B and another in SGR gene sequence, associated with segregation of 'orange-brown' fruit color in F2 generation. The carotenoid and chlorophyll content of a fleshy fruit was assessed across the different phenotypes and showed a strong correlation with expression pattern of carotenoid biosynthesis genes and SGR function. The orange-brown fruit has high β-carotene and chlorophyll. Our results provide valuable information for breeders to develop tomato fruit of a novel color using molecular markers. [ABSTRACT FROM AUTHOR]

Gametogenesis is a key step in the production of ovules or pollen in higher plants. The molecular aspects of gametogenesis are well characterized in the model plant Arabidopsis; however, little information is known in tomato, which is a model plant for fleshy fruit development. In this study, we characterized a tomato (Solanum lycopersicum L.) γ-ray mutant, sexual sterility (Slses), that exhibited both male and female sterility. Morphological analysis revealed that the Slses mutant forms incomplete ovules and wilted anthers devoid of pollen grains at the anthesis stage. Genetic and next-generation sequencing analyses revealed that the Slses mutant carried a 13 bp deletion within the first exon of a homolog of SPOROCYTELESS/NOZZLE (SPL/NZZ), which plays an important role in gametogenesis in Arabidopsis. Complementation analysis in which the complete SlSES genomic region was introduced into the Slses mutant fully restored normal phenotypes, demonstrating that Solyc07g063670 is responsible for the Slses mutation. SlSES probably act as a transcriptional repressor because of an EAR motif at the C-terminal region. Gene expression levels of WUSCHEL (SlWUS) and INNER NO OUTER (SlINO), both of which are required for ovule development, were dramatically reduced in the early stages of pistil development in the Slses mutant, suggesting a positive regulatory role for SlSES in the transcription of gametogenesis genes and differences in the regulation of INO (SlINO) and integument development by SPL/NZZ (SLSES) between Arabidopsis and tomato. Taken together, our results indicate that SlSES is a novel tomato gametogenesis gene essential for both male and female gametogenesis. [ABSTRACT FROM AUTHOR]

Solanum lycopersicum (tomato) is an important agronomic crop and a major model fruit-producing plant. To facilitate basic and applied research, comprehensive experimental resources and omics information on tomato are available following their development. Mutant lines and cDNA clones from a dwarf cultivar, Micro-Tom, are two of these genetic resources. Large-scale sequencing data for ESTs and full-length cDNAs from Micro-Tom continue to be gathered. In conjunction with information on the reference genome sequence of another cultivar, Heinz 1706, the Micro-Tom experimental resources have facilitated comprehensive functional analyses. To enhance the efficiency of acquiring omics information for tomato biology, we have integrated the information on the Micro-Tom experimental resources and the Heinz 1706 genome sequence. We have also inferred gene structure by comparison of sequences between the genome of Heinz 1706 and the transcriptome, which are comprised of Micro-Tom full-length cDNAs and Heinz 1706 RNA-seq data stored in the KaFTom and Sequence Read Archive databases. In order to provide large-scale omics information with streamlined connectivity we have developed and maintain a web database TOMATOMICS (http://bioinf.mind.meiji.ac.jp/tomatomics/). In TOMATOMICS, access to the information on the cDNA clone resources, full-length mRNA sequences, gene structures, expression profiles and functional annotations of genes is available through search functions and the genome browser, which has an intuitive graphical interface. [ABSTRACT FROM AUTHOR]

Antimicrobial peptides (AMPs) are produced by all living organisms and play an important role in innate immunity because they are readily available and non-specific against invading pathogenic microorganisms. Snakin-2 (SN2) from tomato is a short, cationic peptide that forms lethal pores in biomembranes of microbes. In plant cells, SN2 is produced as a prepeptide with a signal sequence for ER targeting and an acidic region to decrease toxicity in the producing organism. Gene expression analysis by qRT-PCR in tomato plants demonstrated that SN2 is constitutively expressed, mostly in leaves and flowers. After fungal infection, wounding, or external application of phytohormones (such as methyl jasmonate, MeJa) operating in the JA-dependent defense response, a systemic reaction with an elevated expression of the SN2 gene is triggered in all parts of tomato plants. Abiotic stress factors like extreme temperatures or dehydration do not affect SN2 expression. Upon wounding, the expression of SN2 and LoxD are strongly enhanced in tomato fruits. Furthermore, we provide evidence that the protein level of bioactive SN2 is also increased upon application of methyl jasmonate in tomato seedlings. [ABSTRACT FROM AUTHOR]

Key message : QTL and codominant genetic markers for fruit cracking have been identified in a tomato genetic map derived from a RIL population, providing molecular tools for marker-assisted breeding of this trait. Abstract: In tomato, as well as in other fleshy fruits, one of the main disorders that widely limit quality and production is fruit cracking or splitting of the epidermis that is observed on the fruit skin and flesh at any stage of fruit growth and maturation. To elucidate the genetic basis of fruit cracking, a quantitative trait loci (QTL) analysis was conducted in a recombinant inbred line (RIL) population derived from a cross between tomato ( Solanum lycopersicum) and the wild-relative species S. pimpinellifolium. The RIL population was evaluated for fruit cracking during three consecutive growing seasons. Construction of a high-density linkage map based on codominant markers, covering more than 1000 cM of the whole genome, led to the identification of both main and epistatic QTL controlling fruit cracking on the basis of a single-environment as well as multiple-environment analysis. This information will enhance molecular breeding for novel cracking resistant varieties and simultaneously assist the identification of genes underlying these QTL, helping to reveal the genetic basis of fruit cracking in tomato. [ABSTRACT FROM AUTHOR]

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The Ethylene-Responsive Factors (ERFs) comprise a large family of transcriptional factors that play critical roles in plant immunity. Gray mold disease caused by Botrytis cinerea, a typical necrotrophic fungal pathogen, is the serious disease that threatens tomato production worldwide. However, littler is known about the molecular mechanism regulating the immunity to B. cinerea in tomato. In the present study, virus-induced gene silencing (VIGS)-based functional analyses of 18 members of B3 group (also called Group IX) in tomato ERF family were performed to identify putative ERFs that are involved in disease resistance against B. cinerea. VIGS-based silencing of either SlERF.B1 or SlERF.C2 had lethal effect while silencing of SlERF.A3 (Pit4) significantly suppressed vegetative growth of tomato plants. Importantly, silencing of SlERF.A1, SlERF.A3, SlERF.B4, or SlERF.C3 resulted in increased susceptibility to B. cinerea, attenuated the B. cinerea-induced expression of jasmonic acid/ethylene-mediated signaling responsive defense genes and promoted the B. cinerea-induced H2O2 accumulation. However, silencing of SlERF.A3 also decreased the resistance against Pseudomonas syringae pv. tomato (Pst) DC3000 but silencing of SlERF.A1, SlERF.B4 or SlERF.C3 did not affect the resistance to this bacterial pathogen. Expression of SlERF.A1, SlERF.A3, SlERF.B4, or SlERF.C3 was induced by B. cinerea and by defense signaling hormones such as salicylic acid, methyl jasmonate, and 1-aminocyclopropane-1-carboxylic acid (an ethylene precursor). SlERF.A1, SlERF.B4, SlERF.C3, and SlERF.A3 proteins were found to localize in nucleus of cells and possess transactivation activity in yeasts. These data suggest that SlERF.A1, SlERF.B4, and SlERF.C3, three previously uncharacterized ERFs in B3 group, and SlERF.A3, a previously identified ERF with function in immunity to Pst DC3000, play important roles in resistance against B. cinerea in tomato. [ABSTRACT FROM AUTHOR]

Due to the intimate association between plants and their microbial symbionts, an examination of the influence of agricultural practices on phytobiome structure and diversity could foster a more comprehensive understanding of plant health and produce safety. Indeed, the impact of upstream crop producti006Fn practices cannot be overstated in their role in assuring an abundant and safe food supply. To assess whether fertilizer type impacted rhizosphere and phyllosphere bacterial communities associating with tomato plants, the bacterial microbiome of tomato cv. ‘BHN602’ grown in soils amended with fresh poultry litter, commercially available sterilized poultry litter pellets, vermicompost or synthetic fertilizer was described. Culture independent DNA was extracted from bulk and rhizosphere soils, and washes of tomato blossoms and ripe fruit. PCR amplicons of hypervariable regions of the 16S rRNA gene were sequenced and profiled using the QIIME pipeline. Bulk and rhizosphere soil, and blossom and fruit surfaces all supported distinct bacterial communities according to principal coordinate analysis and ANOSIM ( R = 0.87, p = 0.001 in year 1; R = 0.93, p = 0.001 in year 2). Use of microbiologically diverse organic fertilizers generally did not influence bacterial diversity, community structure or relative abundance of specific taxa on any plant organ surface. However, statistically significant differences in sand and silt contents of soil ( p < 0.05) across the field and corresponding shifts in water activity were positively ( R 2 = 0.52, p = 0.005) and negatively ( R 2 = 0.48, p = 0.009) correlated with changes in bacterial community structure in the rhizosphere, respectively. Over two harvest seasons, this study demonstrated that the application of raw poultry manure, poultry litter pellets and vermicompost had little effect on the tomato microbiome in the rhizosphere and phyllosphere, when compared to synthetically fertilized plants. Plant anatomy, and other factors related to field location, possibly associated with edaphic and air characteristics, were more influential drivers of different tomato organ microbiomes than were diverse soil amendment applications. [ABSTRACT FROM AUTHOR]

Targeted manipulation of phenylalanine (Phe) synthesis is a potentially powerful strategy to boost biologically and economically important metabolites, including phenylpropanoids, aromatic volatiles and other specialized plant metabolites. Here, we use two transgenes to significantly increase the levels of aromatic amino acids, tomato flavour-associated volatiles and antioxidant phenylpropanoids. Overexpression of the petunia MYB transcript factor, ODORANT1 ( ODO1), combined with expression of a feedback-insensitive E. coli 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase ( AroG), altered the levels of multiple primary and secondary metabolites in tomato fruit, boosting levels of multiple secondary metabolites. Our results indicate that coexpression of AroG and ODO1 has a dual effect on Phe and related biosynthetic pathways: (i) positively impacting tyrosine (Tyr) and antioxidant related metabolites, including ones derived from coumaric acid and ferulic acid; (ii) negatively impacting other downstream secondary metabolites of the Phe pathway, including kaempferol-, naringenin- and quercetin-derived metabolites, as well as aromatic volatiles. The metabolite profiles were distinct from those obtained with either single transgene. In addition to providing fruits that are increased in flavour and nutritional chemicals, coexpression of the two genes provides insights into regulation of branches of phenylpropanoid metabolic pathways. [ABSTRACT FROM AUTHOR]

Flowering of higher plants is orchestrated by complex regulatory networks through integration of various environmental signals such as photoperiod, temperature, light quality and developmental cues. In Arabidopsis, transcription of the flowering integrator gene FLOWERING LOCUS T ( FT) that several flowering pathways converge to is directly regulated by more than ten transcription factors. However, very little is known about the transcriptional regulation of the FT homolog SINGLE FLOWER TRUESS ( SFT) in the day-neutral plant tomato ( Solanum lycopersicum). Previously, we showed that the zinc finger transcription factor Sl ZFP2 plays important roles in regulation of seed germination and fruit ripening in tomato and also found that overexpression of Sl ZFP2 impacted flowering and branching. Here, we characterized in detail the early flowering and high branching phenotypes by overexpression of this transcription factor. Our data showed that overexpression of Sl ZFP2 accelerated flowering in an SFT-dependent manner as demonstrated by elevated SFT expression in the leaves and the transcription factor's binding ability to SFT promoter in vitro and in vivo. Furthermore, overexpression of the Sl ZFP2 gene in the sft plants failed to rescue the mutant's late flowering. Through analysis of grafting phenotype, growth response of branches to auxin application and transcriptome profiling by RNA sequencing, we also showed that overexpression of Sl ZFP2 affected shoot apical dominance through multiple regulatory pathways. Our results suggest that the transcription factor Sl ZFP2 has potential applications in genetic modification of plant architecture and flowering time for tomato production and other crops as well. [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]

Salt stress was applied to tomato commercial genotypes to study adverse effects on their phenotypic traits. Three were saline tolerant (San Miguel, Romelia and Llanero), two were mildly tolerant (Perfect peel HF1 and Heinz 1350) whereas the remaining were sensitive. Genotyping cultivars using 19 polymorphic SSRs out of 25 tested produced a total of 70 alleles with an average of 3.68 alleles per locus and PIC values ranging from 0.22 (SSR 26, 92, 66 and TG35) to 0.82 (SSR 356). Principal component analysis (PCA) showed two contrasting panels discriminating tolerant and sensitive groups and one panel with scattered genotypes. STRUCTURE analysis clustered genotypes within three groups in accordance with their salt stress behavior. The success of tomato salt-tolerance breeding programs can be enhanced through molecular characterization of diversity within commercial cultivars that adapt differently to stress conditions. To this end, we combined phenotypes and SSR marker-genotypes to seek sources of salt tolerance that might be tomato species-specific. We integrated and represented genotype-phenotype associations from multiple loci into a multi-layer network representation. It is a systemic view linking discriminating genotypes to salt stress phenotypes, which may guide strategies for the introgression of valuable traits in target tomato varieties to overcome salinity. [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]

Boron (B) is an essential plant nutrient, but when present in excess it is toxic. Morphological measurements were made to assess the impact of B toxicity on the growth of two different tomato hybrids, Losna and Ikram. Contrasting long and short-term B responses in these tomato hybrids, were observed. Losna showed less toxicity symptoms, maintaining higher growth and showing much less B content in both root and shoot tissues compared to Ikram. Root morphological differences did not explain the tolerance between the two hybrids. Under excess B supply, a significant inhibition on net nitrate uptake rate was observed in Ikram, but not in Losna. This effect may be explained by a decrease of nitrate transporter transcripts in Ikram, which was not measured in Losna. There was a different pattern of B transporter expression in two tomatoes and this can explain the contrasting tolerance observed. Indeed, Losna may be able to exclude or efflux B resulting in less accumulation in the shoot. Particularly, SlBOR4 expression showed significant differences between the tomato hybrids, with higher expression in Losna explaining the improved B-tolerance. [ABSTRACT FROM AUTHOR]

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Tomato ( Solanum lycopersicum L.) is a major vegetable cultivated worldwide and has been used as a model plant for basic research. Since tomato genome sequences were uncovered in 2012, genome-wide molecular markers have been developed. However, these markers have not been often used to explore genetic variations in commercial tomato cultivars. In this study, we collected 62 F 1 tomato cultivars from 16 private seed companies to investigate genetic relationships using SSR and InDel markers. A total of 242 SSR and 76 InDel primer sets were tested for polymorphism using a subset of eight cultivars representing diverse morphological characteristics. Based on the clear polymorphism and simple banding pattern, 6 SSR and 35 InDel markers were selected for further analysis. The polymorphic information content (PIC) values of the 41 markers ranged from 0.243 to 0.375 with an average of 0.350. Principal component analysis revealed that the 62 cultivars were separated into three clusters representing fresh market, grape, and cherry tomatoes. We found two major clusters consisting of fresh market (cluster I) and both grape and cherry (cluster II) in the unweighted pair group mean algorithm (UPGMA) dendrogram. In cluster II, the grape and cherry cultivars were divided into two sub-clusters. This genetic differentiation was validated by pairwise estimates of F st and Nei’s standard genetic distance. In addition, the estimates of allelic richness ( A ) and expected heterozygosity ( He ) suggest high levels of genetic diversity in each of the three sub-populations. These results will benefit the tomato research community in developing new elite cultivars. The core set of SSR and InDel markers will also be a useful tool for cultivar identification and seed purity test. [ABSTRACT FROM AUTHOR]

Whiteflies damage tomatoes mostly via the viruses they transmit. Cultivated tomatoes lack many of the resistances of their wild relatives. In order to increase protection to its major pest, the whitefly Bemisia tabaci and its transmitted Tomato Yellow Leaf Curl Virus (TYLCV), we introgressed a trichome-based resistance trait from the wild tomato Solanum pimpinellifolium into cultivated tomato, Solanum lycopersicum. The tomato backcross line BC5S2 contains acylsucrose-producing type-IV trichomes, unlike cultivated tomatoes, and exhibits increased, yet limited protection to whiteflies at early development stages. Treatment of young plants with methyl jasmonate (MeJA) resulted in a 60% increase in type-IV trichome density, acylsucrose production, and enhanced resistance to whiteflies, leading to 50% decrease in the virus disease incidence compared to cultivated tomato. Using transcriptomics, metabolite analysis, and insect bioassays we established the basis of this inducible resistance. We found that MeJA activated the expression of the genes involved in the biosynthesis of the defensive acylsugars in young BC5S2 plants leading to enhanced chemical defenses in their acquired type-IV trichomes. Our results show that not only constitutive but also these inducible defenses can be transferred from wild into cultivated crops to aid sustainable protection, suggesting that conventional breeding strategies provide a feasible alternative to increase pest resistance in tomato. [ABSTRACT FROM AUTHOR]

Tomato mosaic virus (ToMV) is one of the most economically important viruses on tomato (Solanum lycopersicum L.) in Bulgaria, easily transmitted mechanically and by seeds. Breeding, based on genetic controlled resistance, is the most effective and successful approach for combating the ToMV-tomato problem due to the dominant monogenic genetic control, governed by three single genes for resistance (Tm-1, Tm-2 and Tm-22). The aim of the current study was to investigate the reliability of some SCAR, CAPS and AS molecular markers for identification of Tm genes for resistance in tomato breeding lines. Parallel to molecular study, screening tests with three ToMV pathotypes (0, 1 and 2) were carried out as control tests. The resistance to the three pathotypes was found in 6 breeding lines. Twenty ToMV resistant plants were subjected to molecular analysis. The CAPS marker revealed the presence of Tm-22 allele in homozygous condition in 12 ToMV resistant plants, whereas the AS markers (AS1, AS2 and AS3) confirmed this result only in two plants. The remaining 10 reacted as heterozygous with genotype Tm-2/Tm-22. Another eight ToMV resistant plants were determined by CAPS marker as heterozygous for Tm-22 gene (tm-2/Tm-22), which was confirmed only in two plants by AS markers. The results obtained for the remaining six plants by AS markers were rather contradictory. Successful application of CAPS marker for genotyping the Tm-2 locus as well as confusing behavior of AS 2 marker during genotyping the Maritsa VCRI tomato breeding lines is discussed. [ABSTRACT FROM AUTHOR]

Inorganic nitrogen is a key element for plant growth under salt stress. A comparative study including physiological responses, ion content, transcript regulation of ammonium/nitrate transporters ( AMTs / NRTs ) as well as key enzymes for nitrogen assimilation was undertaken in wild salt-tolerant tomatoes ( Solanum pennellii ) and cultivated tomatoes ( Solanum lycopersicon ) exposed to 100 mM NaCl for 1 and 7 days. In comparison to S. lycopersicon , S. pennellii was more salt tolerant as evidenced by its higher survival rate, lower biomass reduction, and less salt injury (reduced electrolyte leakage and proline accumulation). In root tissues of both species, salt exposure (7 days) reduced the mRNA expression levels of low affinity nitrate transporters ( NRT1.1 and NRT1.2 ). This was associated with a decline in both nitrate content and expression level of the nitrate reductase gene ( NR ). Salt-stressed root tissues of S. pennellii showed relatively higher mRNA expression of the high affinity ammonium transporters ( AMT1.1 and AMT1.2 ) compared to S. lycopersicon. The root ammonium content was increased only in S. lycopersicon going hand in hand with a reduction in mRNA level of cytosolic glutamine synthetase ( GS1 ) after 7 days of salt stress, whereas the expression level of GS1 was unchanged in S. pennellii , suggesting a lower salt-induced inhibition in ammonium assimilation in this species. Our comparative study demonstrated that the salt-tolerant and salt-sensitive tomato species show differential contribution of the nitrogen transporters and key genes associated with nitrogen assimilation under salt stress. While the reduction in the expression of key components of NO 3 − uptake ( NRT1.1, NRT1.2 ) and assimilation ( NR gene) in both species, likely contributed to the reduction in plant growth under salt stress, the observed salt tolerance for S. pennellii was associated with relative higher mRNA expression of ammonium uptake and assimilation genes. These results provide crucial knowledge for tomato breeding employing salt-tolerant wild species in salt-induced nitrogen- deficient environments. [ABSTRACT FROM AUTHOR]

The aluminum-activated malate transporter (ALMT) family of proteins transports malate and/or inorganic anions across plant membranes. To demonstrate the possible role of ALMT genes in tomato fruit development, we focused on SlALMT4 and SlALMT5, the two major genes expressed during fruit development. Predicted proteins were classified into clade 2 of the family, many members of which localize to endomembranes. Tissue-specific gene expression was determined using transgenic tomato expressing the β-glucuronidase reporter gene controlled by their own promoters. Both the genes were expressed in vascular bundles connecting to developing seeds in fruit and in the embryo of mature seeds. Further, SlALMT5 was expressed in embryo in developing seeds in fruit. Subcellular localization of both proteins to the endoplasmic reticulum (ER) was established by transiently expressing the green fluorescent protein fusions in plant protoplasts. SlALMT5 probably localized to other endomembranes as well. Localization of SlALMT5 to the ER was also confirmed by immunoblot analysis. The transport function of both SlALMT proteins was investigated electrophysiologically in Xenopus oocytes. SlALMT5 transported malate and inorganic anions such as nitrate and chloride, but not citrate. SlALMT4 also transported malate, but the results were less consistent perhaps because it did not localize strongly to the plasma membrane. To elucidate the physiological role of SlALMT5 further, we overexpressed SlALMT5 in tomato. Compared with the wild type, overexpressors exhibited higher malate and citrate contents in mature seeds, but not in fruit. We conclude that the malate transport function of SlALMT5 expressed in developing fruit influences the organic acid contents in mature seeds. [ABSTRACT FROM AUTHOR]

The spatiotemporal localization of the plant hormone auxin acts as a positional cue during early leaf and flower organogenesis. One of the main contributors to auxin localization is the auxin efflux carrier PIN-FORMED1 (PIN1). Phylogenetic analysis has revealed that PIN1 genes are split into two sister clades; PIN1 and the relatively uncharacterized Sister-Of-PIN1 ( SoPIN1 ). In this paper we identify entire-2 as a loss-of-function SlSoPIN1a (Solyc10g078370) mutant in Solanum lycopersicum. The entire-2 plants are unable to specify proper leaf initiation leading to a frequent switch from the wild type spiral phyllotactic pattern to distichous and decussate patterns. Leaves in entire-2 are large and less complex and the leaflets display spatial deformities in lamina expansion, vascular development, and margin specification. During sympodial growth in entire-2 the specification of organ position and identity is greatly affected resulting in variable branching patterns on the main sympodial and inflorescence axes. To understand how SlSoPIN1a functions in establishing proper auxin maxima we used the auxin signaling reporter DR5: Venus to visualize differences in auxin localization between entire-2 and wild type. DR5: Venus visualization shows a widening of auxin localization which spreads to subepidermal tissue layers during early leaf and flower organogenesis, showing that SoPIN1 functions to focus auxin signaling to the epidermal layer. The striking spatial deformities observed in entire-2 help provide a mechanistic framework for explaining the function of the SoPIN1 clade in S.lycopersicum . [ABSTRACT FROM AUTHOR]

The article provides information on the molecular structure of uracil in tomatoes, focusing on pharmaceutical sciences, substituted pyrimidines and chemotherapeutic agents of plant growth. Topics include growth and flowering of tomato, repulsion between the oxygen atoms and complementary base pair in the RNA formation.

Metacaspases play critical roles in developmentally regulated and environmentally induced programmed cell death in plants. In this study, we systematically identified and analyzed metacaspase gene family in tomato ( Solanum lycopersicum ). The results illustrated that tomato possesses eight metacaspase genes ( SlMC1 − 8 ) located on chromosomes 1, 3, 5, 9, and 10. SlMC1 − 6 belonged to type I metacaspases and had 5 exon/4 intron structures. SlMC7 and 8 were type II metacaspases and had 2 and 3 exons, respectively. Expression analysis revealed distinct expression patterns of SlMCs in various tomato tissues. Cis -regulatory element prediction showed that there were many hormone- and stress-related cis -regulatory elements in SlMCs promoter regions. Quantitative real-time PCR analysis further demonstrated that most of the SlMCs were regulated by drought, cold, salt, methyl viologen, and ethephon treatments. This study provides insights into the characteristics of SlMC genes and laid the foundation for further functional analysis of these genes in tomato. [ABSTRACT FROM AUTHOR]

Local translocation of small RNAs between cells is proved. Long distance translocation between rootstock and scion is also well documented in the homo-grafting system, but the process in distant-grafting is widely unexplored where rootstock and scion belonging to different genera. Micro RNAs are a class of small, endogenous, noncoding, gene silencing RNAs that regulate target genes of a wide range of important biological pathways in plants. In this study, tomato was grafted onto goji (Lycium chinense Mill.) to reveal the insight of miRNAs regulation and expression patterns within a distant-grafting system. Goji is an important traditional Chinese medicinal plant with enriched phytochemicals. Illumina sequencing technology has identified 68 evolutionary known miRNAs of 37 miRNA families. Moreover, 168 putative novel miRNAs were also identified. Compared with control tomato, 43 (11 known and 32 novels) and 163 (33 known and 130 novels) miRNAs were expressed significantly different in shoot and fruit of grafted tomato, respectively. The fruiting stage was identified as the most responsive in the distant-grafting approach and 123 miRNAs were found as up-regulating in the grafted fruit which is remarkably higher compare to the grafted shoot tip (28). Potential targets of differentially expressed miRNAs were found to be involved in diverse metabolic and regulatory pathways. ADP binding activities, molybdopterin synthase complex and RNA helicase activity were found as enriched terms in GO (Gene Ontology) analysis. Additionally, "metabolic pathways" was revealed as the most significant pathway in KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis. The information of the small RNA transcriptomes that are obtained from this study might be the first miRNAs elucidation for a distant-grafting system, particularly between goji and tomato. The results from this study will provide the insights into the molecular aspects of miRNA-mediated regulation in the medicinal plant goji, and in grafted tomato. Noteworthy, it would provide a basis how miRNA signals could exchange between rootstock and scion, and the relevance to diverse biological processes. [ABSTRACT FROM AUTHOR]

Glutathione (GSH) plays a critical role in plant growth, development and responses to stress. However, the mechanism by which GSH regulates tolerance to cadmium (Cd) stress still remains unclear. Here we show that inhibition of GSH biosynthesis by buthionine sulfoximine (BSO) aggravated Cd toxicity by increasing accumulation of reactive oxygen species (ROS) and reducing contents of nitric oxide (NO) and S -nitrosothiol (SNO) in tomato roots. In contrast, exogenous GSH alleviated Cd toxicity by substantially minimizing ROS accumulation and increasing contents of NO and SNO, and activities of antioxidant enzymes that eventually reduced oxidative stress. GSH-induced enhancement in Cd tolerance was closely associated with the upregulation of transcripts of several transcription factors such as ETHYLENE RESPONSIVE TRANSCRIPTION FACTOR 1 (ERF1) , ERF2 , MYB1 TRANSCRIPTION FACTOR- AIM1 and R2R3-MYB TRANSCRIPTION FACTOR- AN2 , and some stress response genes. In addition, GSH modulated the cellular redox balance through maintaining increased GSH: GSSG and AsA: DHA ratios, and also increased phytochelatins contents. Nonetheless, GSH-induced alleviation of Cd phytotoxicity was also associated with increased sequestration of Cd into cell walls and vacuoles but not with Cd accumulation. Under Cd stress, while treatment with BSO slightly decreased vacuolar fraction of Cd, combined treatment with BSO and GSH noticeably increased that fraction. Our results suggest that GSH increases tomato tolerance to Cd stress not only by promoting the chelation and sequestration of Cd but also by stimulating NO, SNO and the antioxidant system through a redox-dependent mechanism. [ABSTRACT FROM AUTHOR]

Natural mutants of the Non-ripening (Nor) gene repress the normal ripening of tomato fruit. The molecular mechanism of fruit ripening regulation by the Nor gene is unclear. To elucidate how the Nor gene can affect ripening and fruit quality at the protein level, we used the fruits of Nor mutants and wild-type Ailsa Craig (AC) to perform iTRAQ (isobaric tags for relative and absolute quantitation) analysis. The Nor mutation altered tomato fruit ripening and affected quality in various respects, including ethylene biosynthesis by down-regulating the abundance of 1-aminocyclopropane-1-carboxylic acid oxidase (ACO), pigment biosynthesis by repressing phytoene synthase 1 (PSY1), ζ-carotene isomerase (Z-ISO), chalcone synthase 1 (CHS1) and other proteins, enhancing fruit firmness by increasing the abundance of cellulose synthase protein, while reducing those of polygalacturonase 2 (PG2) and pectate lyase (PL), altering biosynthesis of nutrients such as carbohydrates, amino acids, and anthocyanins. Conversely, Nor mutation also enhanced the fruit’s resistance to some pathogens by up-regulating the expression of several genes associated with stress and defense. Therefore, the Nor gene is involved in the regulation of fruit ripening and quality. It is useful in the future as a means to improve fruit quality in tomato. [ABSTRACT FROM AUTHOR]