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This study was carried out in order to determine some morphological characteristics of 240 tomato genotypes at S2 level and to demonstrate the usability of these materials in breeding programs. Accordingly, the average fruit weight was between 553.11 g and 74.83 g. The mean pericarp thickness, carpel number, and soluble dry matter content of the genotypes were 7.38 mm, 3.6 pieces and 4.04% brix, respectively. While the fruit color of 165 genotypes was determined as red, the longitudinal section shape of the fruit was determined as slightly flattened in 106 genotypes. The flowering period of the genotypes was determined as medium flowering. The leaf posture of the genotypes was determined as attitude, and the leaf width was determined as medium and broad leaves. Based on these measurements and observations, tomato genotypes were also investigated using the Principal Component Analysis (PCA) methods. According to the PCA results, the first component explained 24.2% of the total variance, and the number of fruit carpels, average fruit weight, and fruit width were the most highly explained parameters. The second and third main components constituted 13.1% and 11.2% of the total. Based on the results of fruit characterization studies, genotypes 233, 447, 126, 22, 391, 118, 71, 100, 340, 102 were determined as superior. Overall, a high degree of phenotypic variation was detected among the characterized tomato genotypes. [ABSTRACT FROM AUTHOR]

High temperature stress is one of the major environmental factors that affect the growth and development of plants. Although WRKY transcription factors play a critical role in stress responses, there are few studies on the regulation of heat stress by WRKY transcription factors, especially in tomato. Here, we identified a group I WRKY transcription factor, SlWRKY3, involved in thermotolerance in tomato. First, SlWRKY3 was induced and upregulated under heat stress. Accordingly, overexpression of SlWRKY3 led to an increase, whereas knock-out of SlWRKY3 resulted in decreased tolerance to heat stress. Overexpression of SlWRKY3 accumulated less reactive oxygen species (ROS), whereas knock-out of SlWRKY3 accumulated more ROS under heat stress. This indicated that SlWRKY3 positively regulates heat stress in tomato. In addition, SlWRKY3 activated the expression of a range of abiotic stress-responsive genes involved in ROS scavenging, such as a SlGRXS1 gene cluster. Further analysis showed that SlWRKY3 can bind to the promoters of the SlGRXS1 gene cluster and activate their expression. Collectively, these results imply that SlWRKY3 is a positive regulator of thermotolerance through direct binding to the promoters of the SlGRXS1 gene cluster and activating their expression and ROS scavenging. [ABSTRACT FROM AUTHOR]

Tomato (Solanum lycopersicum) is one of the most important vegetable crops in the world and abiotic stresses often cause serious problems in tomato production. It is thus important to identify new regulators in stress response and to devise new approaches to promote stress tolerance in tomato. Previous studies have shown that small secreted peptides (SSPs) are important signal molecules regulating plant growth and stress response by mediating intercellular communication. However, little is known about tomato SSPs, especially their roles in responding to abiotic stresses. Here we report the identification of 1,050 putative SSPs in the tomato genome, 557 of which were classified into 38 known SSP families based on their conserved domains. GO and transcriptome analyses revealed that a large proportion of SlSSPs might be involved in abiotic stress response. Further analysis indicated that stress response related cis-elements were present on the SlCEP promotors and a number of SlCEPs were significantly upregulated by drought treatments. Among the drought-inducible SlCEPs, SlCEP10 and SlCEP11b were selected for further analysis via exogenous application of synthetic peptides. The results showed that treatments with both SlCEP10 and SlCEP11b peptides enhanced tomato drought stress tolerance, indicating the potential roles of SlSSPs in abiotic stress response. [ABSTRACT FROM AUTHOR]

Tomato is one of the most cultivated vegetables in the world. In this context, intensive tomato breeding studies are carried out around the world and new cultivars are emerging every day, which leads to great competition. In particular, resistance or tolerance levelstolerance levels to some important diseases and pests are considered important in cultivar breeding and in determining the commercial value of cultivars. In this context, the determination of resistance levels to 70 tomatoes, Meloidogyne incognita, Tomato Yellow leaf curling virus (Tylcv), Verticillium wilt, Fusarium oxysporum radicis, Tomato spotted wilt virus (TSWV), Fusarium Wilt, which have the potential to become parent lines at S8 level due to their agromorphological characteristics formed the subject of this study. When the results of the study are examined, tomato genotypes showed resistance/sensitive levels according to combinations of alleles as 58 genotypes of RR (homozygous resistant), 10 Rr (heterozygous), 2 rr(sensitive) to Meloidogyne incognita, 45 RR (homozygous resistant), 15 Rr (heterozygous),10 rr (sensitive)to Verticillium dahliae, 10 to, 52 RR (homozygous resistant), 13 Rr (heterozygous), 5 rr (sensitive) to Tomato Spotted Wilt Virus, 46 RR (homozygous resistant) 18 Rr (heterozygous), 6 rr (sensitive) to Tomato Yellow leaf Curl Virus, Fusarium oxysporum (Fusarium wilt) 49 RR (homozygous resistant), 13 Rr (heterozygous), 8 rr (sensitive), Fusarium oxysporum radicis (Frl) 52 Their resistances were determined as RR (homozygous resistant), 12 Rr (heterozygous), 6 rr (sensitive). [ABSTRACT FROM AUTHOR]

Leaf-color mutations have been studied extensively in plants. However, to better understand the complex mechanisms underlying the formation of leaf color, it is essential to continue discover novel genes involved in the process of leaf color development. In this study, we identified a variegated-leaf (vg) mutant in tomato that exhibited defective phenotypes in thylakoids and photosynthesis. To clone the vg locus, an F 2 population was constructed from the cross between the vg mutant (Solanum lycopersicum) and the wild tomato LA1589 (S. pimpinellifolium). Using the map-based cloning approach, the vg locus was mapped on chromosome 7 and narrowed down to a 128 kb region that contained 21 open reading frames (ORFs). The expression levels of ORF9, ORF10, and ORF13 were significantly lower in vg than in the wild-type plants, while the ORF11 transcript level was elevated in vg. We then mutagenized ORF9, ORF10, and ORF13 by the CRISPR/Cas9 system in the wild-type tomato background and found that only the ORF10 mutation reproduced the phenotype of variegated leaves, indicating that ORF10 represents VG and its down-regulated expression was responsible for the variegated leaf phenotype. ORF10 encodes a thylakoid formation protein and its mutant lines showed reduced levels of chlorophyll synthesis and photosynthesis. Taken together, these results suggest that VG is necessary for chloroplast development, chlorophyll synthesis, and photosynthesis in tomato. [ABSTRACT FROM AUTHOR]

Plants have developed mechanisms to cope with stresses in their environments as they grow in diverse settings. Such means include releasing plant defense compounds upon attacks by pests or other stressors. Plants with these characteristics are essential as a plant germplasm source for breeding resistance against herbivores and insect pests. Therefore, this study aimed to screen germplasms for whitefly resistance and characterize the secondary metabolites responsible for this. Thirty local tomato accessions were screened for resistance against whiteflies (Bemisia tabaci Gennadius) in the screen house located at Tanzania Plant Health and Pesticides Authority (PTHPA) between January and April 2021. From this screening, seven local tomato cultivars: TZA3729, TZA5554, TZA5545, TZA5562, TZA5552, TZA3177 and TZA5157, showed resistance, and one accession (TZA5496) that showed susceptibility to whiteflies (negative control) and accession V1030462 that was a standard (positive control) were selected for the subsequent experiments. The experiment was conducted in July–October 2021 in the screen house at TPHPA and repeated in January–April 2022 using a completely randomized block design with three replications. From this experiment, three accessions: TZA3729, TZA5562 and TZA5157, showed resistance against whiteflies. However, accession TZA3729 was more resistant than TZA5562 and TZA5157 when compared to the resistant accession V1030462. Therefore, these accessions were further screened for secondary metabolites responsible for resistance against herbivores and insect pests—in this case, whiteflies. The GS-MS methanol extract results showed accession TZA3729 to possess a wide array of secondary plant metabolites responsible for plant self-defenses, such as diterpenes, Tetraterpenes, alkaloids, carotenoids and fatty acid esters. Therefore, the study recommends accession TZA3729 as a source of tomato plant germplasm for breeding tomatoes resistant to whiteflies. [ABSTRACT FROM AUTHOR]

This study was carried out to determine some morphological characteristics of 94 tomato genotypes at the S4 level and to reveal the relationships between these materials. In the study, leaf attitude, leaf length, leaf width, number of flowers, fruit color, fruit weight, fruit width, fruit length, the thickness of pericarp, fruit shape, fruit diameter, number of locules, and total soluble solid content (TTSC) were measured and observed in these genotypes. As a result of the phenotypic assessment, the maximum fruit weight values of the genotypes were observed as in G9 (317.59 g), G54 (310 g), G92 (292.85 g), G70 (287.01 g), and G110 (276.66 g); and the lowest fruit weight values were observed in G26 (18.302 g) and G8 (14.48 g). Average fruit length, fruit width, pericarp thickness, and the number of carpels were recorded (69.09 mm, 56.90 mm, 6.37 mm, and 4 carpels respectively). Tomato genotypes were also investigated using Cluster and Principal Component Analysis (PCA) method based on these measurements and observations. As a result of this analysis, five independent principal component axes were obtained. While these axes represent 69.28% of the total variation, the eigen values were ranged between 1.06 and 4.02. According to the PCA analysis results, genotypes G7, G81, G93, and G103 were prominent in terms of leaf length, fruit width, fruit weight, and carpel number parameters. Based on TSSC results, the G65 genotype was found to be the most prominent one, and the genotypes G12 and G114 exhibit promising results for fruit color. A high degree of morphological variation was detected among tomato genotypes. [ABSTRACT FROM AUTHOR]

Cold stress is considered as one of the major environmental factors that adversely affects the plant growth and distribution. Therefore, there arises an immediate need to cultivate effective strategies aimed at developing stress-tolerant crops that would boost the production and minimise the risks associated with cold stress. In this study, a novel cold-responsive protein1 (BoCRP1) isolated from Brassica oleracea was ectopically expressed in a cold susceptible tomato genotype Shalimar 1 and its function was investigated in response to chilling stress. BoCRP1 was constitutively expressed in all the tissues of B. oleracea including leaf, root and stem. However, its expression was found to be significantly increased in response to cold stress. Moreover, transgenic tomato plants expressing BoCRP1 exhibited increased tolerance to chilling stress (4 °C) with an overall improved rate of seed germination, increased root length, reduced membrane damage and increased accumulation of osmoprotectants. Furthermore, we observed increased transcript levels of stress responsive genes and enhanced accumulation of reactive oxygen species scavenging enzymes in transgenic plants on exposure to chilling stress. Taken together, these results strongly suggest that BoCRP1 is a promising candidate gene to improve the cold stress tolerance in tomato. [ABSTRACT FROM AUTHOR]

Four common landraces of tomato were investigated for the response in some physiological parameter and variation in gene expression. The results of the present study found that salinity stress is negatively affect germination percentage and ranged from 60% to 80% and the effect of salinity levels was found to be related to the exposure time to salinity treatment and the genotypic of tomato landraces. similar negative effect of salinity was reported the length of radical length. The amount of chlorophyll was highly influenced by salinity and was ranged between about 26 to 40 and was found to be largely dependent on genotypic characteristics of tomato landraces and the time of exposure to salinity. Moreover, it was found that the increase in salinity level significantly impacted the stomatal conductance of varied genotype of tomatos. Additionally, germination rate and germination rate were both affected by salinity with varied degrees. Based on the results (chlorophyll content, stomatal conductance and germination ability) presented in this study it was found that the landrace (111) and landrace (975) were both salt tolerant and the landrace of Quaresma (111) is highly sensitive to salinity. [ABSTRACT FROM AUTHOR]

E3 ubiquitin ligases are a central modifier of plant signaling pathways that act through targeting proteins to the degradation pathway. U-box E3 ubiquitin ligases are a distinct class of E3 ligases that utilize intramolecular interactions for its scaffold stabilization. U-box E3 ubiquitin ligases are prevalent in plants in comparison to animals. However, the evolutionary aspects, genetic organizations, and functional fate of the U-box E3 gene family in plant development, especially in tomato is not well understood. In the present study, we have performed in-silico genome-wide analysis of the U-box E3 ubiquitin ligase gene family in Solanum lycopersicum. We have identified 62 U-box genes with U-box/Ub Fusion Degradation 2 (UFD2) domain. The chromosomal localization, phylogenetic analysis, gene structure, motifs, gene duplication, syntenic regions, promoter, physicochemical properties, and ontology were investigated. The U-box gene family showed significant conservation of the U-box domain throughout the gene family. Duplicated genes discerned noticeable functional transitions among duplicated genes. The gene expression profiles of U-box E3 family members show involvement in abiotic and biotic stress signaling as well as hormonal pathways. We found remarkable participation of the U-box gene family in the vegetative and reproductive tissue development. It is predicted to be actively regulating flowering time and endosperm formation. Our study provides a comprehensive picture of distribution, structural features, promoter elements, evolutionary relationship, and gene expression of the U-box gene family in the tomato. We predict the crucial participation of the U-box gene family in tomato plant development and stress responses. [ABSTRACT FROM AUTHOR]

Due to climate change, economically important crop plants will encounter flooding periods causing hypoxic stress more frequently. This may lead to reduced yields and endanger food security. As roots are the first organ to be affected by hypoxia, the ability to sense and respond to hypoxic stress is crucial. At the molecular level, therefore, fine-tuning the regulation of gene expression in the root is essential for hypoxia tolerance. Using an RNA-Seq approach, we investigated transcriptome modulation in tomato roots of the cultivar 'Moneymaker', in response to short- (6 h) and long-term (48 h) hypoxia. Hypoxia duration appeared to have a significant impact on gene expression such that the roots of five weeks old tomato plants showed a distinct time-dependent transcriptome response. We observed expression changes in 267 and 1421 genes under short- and long-term hypoxia, respectively. Among these, 243 genes experienced changed expression at both time points. We identified tomato genes with a potential role in aerenchyma formation which facilitates oxygen transport and may act as an escape mechanism enabling hypoxia tolerance. Moreover, we identified differentially regulated genes related to carbon and amino acid metabolism and redox homeostasis. Of particular interest were the differentially regulated transcription factors, which act as master regulators of downstream target genes involved in responses to short and/or long-term hypoxia. Our data suggest a temporal metabolic and anatomic adjustment to hypoxia in tomato root which requires further investigation. We propose that the regulated genes identified in this study are good candidates for further studies regarding hypoxia tolerance in tomato or other crops. [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]

The aim of this study is to assess the influence of covering with black polyethylene mulch on soil properties and also over plant physiological behavior. Analyzed gas-exchange parameters were: soil net CO2 exchange rate (NCER), soil respiration (Ce) and water humidity (W flux) as soil indicators and photosynthetic rate, transpiration, and stomatal conductance and also sugars leaf content as plant physiological indicators. Plant material was Prekos tomato variety cultivated in protected organic system at The Vegetable Research and Development Station Bacau (SCDL Bacău). Our analysis showed that black plastic mulch on the soil surface favored soil compaction especially on the space between tomato plant rows. The strong soil compactness state was reflected by the high bulk density values and other indicators as smooth soil surface and the cracks networks. In variant with no black plastic cover, soil gas-exchange showed that net CO2 exchange rate of was 7.94 µmol m-2s-1 and soil CO2 flux as soil respiration was 77.4 µmol m-2s-1 both higher in comparison with black polyethylene covering variant. In variant with black plastic cover because of higher soil moisture under polyethylene the water flux between air and soil are increased. Photosynthesis registered a slight increase, having the value of 10 µmol m-2s-1 in flowering phenophase (June) and about 11 µmol m-2s-1 in ripening phenophase (July) in uncovered with polyethylene variant. During the studied period, the variant uncovered with black plastic (polyethylene) registered a small variation of the photosynthesis rate but a higher mean value than covered variant. Covered variant registered a higher value in the flowering phenophase and a smaller value in ripening stage. [ABSTRACT FROM AUTHOR]

Currently, world, horticultural producers and processors are concerned to obtain high quality organic products in conditions of economic profitability. The main aim of the research is to highlight the physico -- chemical characteristics of some improved genotypes from the species Lycopersicon esculentum Mill. obtained in ecological system in the experimental field within USAMV Iasi in 2019. Thus, the aim was to highlight some qualitative parameters, respectively: titrable acidity, pH value, total dry matter content, soluble dry matter, vitamin c, carotene and lycopene content. The biological material was represented by 37 improved tomato genotypes in order to ensure competitive horticultural techniques. The 37 genotypes of Lycopersicon esculentum Mill. showed an average value of the total dry matter content of 7.07 ± 0.5%, showing an oscillating amplitude of the lower delimited values of 4.64% (G223) and 17.9% (G265). The average pH value was 4.4 with limits that fell within the range of variation [4.15 - 4.85]. The content of vitamin C ranged between 14 mg/ 100 g and 29 mg/ 100 g. Other components with antioxidant value that have been shown in important proportions are represented by carotenes (2.36 - 21.22 mg/ 100 g) and lycopene (3.01 - 33.7 mg/ 100 g). This research results strengthens the data in the literature referring to the bioactive compounds of tomatoes emphasizing that the study was conducted for different genotypes grown in organic conditions. [ABSTRACT FROM AUTHOR]

Solanum lycopersicum L., an important vegetable crop (Tomato) in most regions of the world, is affected by high temperature stress at various stages of its growth. Likely increase in periodicity of high temperature episodes under climate change conditions would further affect the tomato production. To sustain productivity and yields under climate change situations, there is an urgent need to develop suitable cultivrsa as an adaptation strateyg. For this endeavour, identification of high temperature tolerant lines for crop improvement is a prerequisite. Hence in the present study, temperature induction response (TIR) technique was employed to evaluate thermotolerance in 52 tomato genotypes. Two day old seedlings were subjected to an initial induction treatment i.e., gradual temperature increase from 33-43°C for 3 h followed by 50°C for 3 h as challenging temperature. Wide variability was seen for seedling survival and vigour. In genotypes IIHR-2202, IIHR-2836 and IIHR-2841 seedling survival was as high as 90%, while H-329, H-371, IIHR-2745 and H-335 showed least reduction in growth and also had better seedling vigour index. Of the 52 genotypes, 21 were identified as tolerant, 12 moderately tolerant and 19 susceptible. This TIR technique is simple, quick and less expensive than whole plant screening. Hence, it could be used by plant physiologists and plant breeders for screening seedlings at an early stage in the phenotyping and crop improvement programmes. [ABSTRACT FROM AUTHOR]

A newly discovered bacterial species, Pseudomonas floridensis, has emerged as a pathogen of tomato in Florida. This study compares the virulence and other attributes of P. floridensis to Pseudomonas syringae pv. tomato, which causes bacterial speck disease of tomato. Pseudomonas floridensis reached lower population levels in leaves of tomato as compared to the P. syringae pv. tomato strains DC3000 and NYT1. Analysis of the genome sequence of the P. floridensis type strain GEV388 revealed that it has just nine type III effectors including AvrPtoBGEV388, which is 66% identical to AvrPtoB in DC3000. Five of these effectors have been previously reported to be members of a 'minimal effector repertoire' required for full DC3000 virulence on Nicotiana benthamiana; however, GEV388 grew poorly on leaves of this plant species compared to the DC3000 minimal effector strain. The tomato Pto gene recognizes AvrPtoB in race 0 P. syringae pv. tomato strains, thereby conferring resistance to bacterial speck disease. Pto was also found to confer resistance to P. floridensis, indicating this gene will be useful in the protection of tomato against this newly emerged pathogen. [ABSTRACT FROM AUTHOR]

Tomato (Solanum lycopersicum) is one of the highest-value vegetable crops worldwide. Understanding the genetic regulation of primary metabolite levels can inform efforts aimed toward improving the nutrition of commercial tomato cultivars, while maintaining key traits such as yield and stress tolerance. We identified 388 suggestive association loci (including 126 significant loci) for 92 metabolic traits including nutrition and flavor-related loci by genome-wide association study from 302 accessions in two different environments. Among them, an ascorbate quantitative trait locus TFA9 (OMATO RUIT SCORBATEON CHROMOSOME ) co-localized with SlbHLH59, which promotes high ascorbate accumulation by directly binding to the promoter of structural genes involved in the D-mannose/L-galactose pathway. The causal mutation of TFA9 is an 8-bp InDel, named InDel_8, located in the promoter region of SlbHLH59 and spanned a 5’UTR Py-rich stretch motif affecting its expression. Phylogenetic analysis revealed that differentially expressed SlbHLH59 alleles were selected during tomato domestication. Our results provide a dramatic illustration of how ascorbate biosynthesis can be regulated and was selected during the domestication of tomato. Furthermore, the findings provide novel genetic insights into natural variation of metabolites in tomato fruit, and will promote efficient utilization of metabolite traits in tomato improvement. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • The heat stress priming and acclimation system for acquired and maintenance of acquired thermotolerance of tomato have been established. • Antioxidant enzymes act as indicators predicting intension of acquired and maintenance of acquired thermotolerance. • The relationships between basal, acquired and maintenance of acquired thermotolerance of tomato are illuminated. Abstract Heat stress seriously threats the crop production. Understanding different types of thermotolerance and illustrating the relationship of these types were essential. The activities of different antioxidant enzymes were determined after heat priming and acclimation for a heat resistant (R) and sensitive tomato genotype. We optimized the treatments for priming in acquired thermotolerance (AT) and acclimation in maintenance of acquired thermotolerance (MT). Then the intension of basal thermotolerance (BT), AT and MT were tested by using lethal temperature (45 °C). The peak of antioxidant enzyme activity (AEA) was identity with the priming time, indicating AEA can predict the optimal-priming time of AT and MT. Moderate high-temperature induced stronger thermotolerance than warmer high-temperature, but the priming time was longer than warmer high-temperature. Moreover, S needed longer priming time than R, due to the slowly AEA increasing and the AT of S also showed weaker than that of R. When the first-optimized-priming combined with secondary-priming for a reasonable duration, its thermotolerance further enhanced. Surprisingly, these optimized-acclimation treatments showed no difference in MT, suggesting secondary-priming could supply gaps produced by the first-optimized-priming of warmer high-temperature. In addition, R also responded the secondary-priming quickly than S, due to the quickly AEA increasing. While, after optimized-acclimations, thermotolerance of S showed no difference with R, suggesting secondary-priming can also narrow the thermotolerance-gap between S and R. Results from this study will accelerate screening of heat tolerant cultivars and provide insights into the choice of tomato cultivars in the changing temperatures environment. [ABSTRACT FROM AUTHOR]

Highlights • Resequencing of "Caimanta" and "LA0722" reveals polymorphisms across the tomato genome. • Multiple sequence comparisons revealed several features relevant for breeding goals. • Development of DNA markers for easily accessed genotyping platforms. • Linkage map construction as genetic reference for QTL detection and resource for MAS. Abstract Next generation sequencing technologies have become affordable for most plant breeding programs. In this study we sequenced the entire genome of the Solanum lycopersicum L. cultivar Caimanta and S. pimpinellifolium L. accession LA0722 with assembly relative to the Heinz 1706 reference version SL2.50. We present 1) analysis of the amount and distribution of polymorphism in "Caimanta" and "LA0722", 2) examination of alleles in candidate genes affecting disease resistance, fruit shape, fruit weight and fruit quality and 3) development of molecular markers to construct a genetic linkage map based on a F 2 population. A total of 1,397,518 polymorphisms were detected in the comparison between "Caimanta" and "LA0722". A resistant allele for Rx4/ Xv3 was detected by sequence, and confirmed through inoculation. - We developed a set of insertion/deletion (InDel) DNA markers that can be multiplexed and scored using easily accessed genotyping platforms. These markers were used to construct a genetic linkage map. We demonstrate that the whole genome sequencing of parental lines can be successfully used to reveal phenotypes and characterize a reference population through easily accessed genotyping strategies. [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]

Highlights • COD and BADH transgenic tomato plants can synthesis and accumulate glycinebetaine. • Glycinebetaine enhances the fruit development and size in transgenic tomato plants. • Glycinebetaine regulates the source-sink metabolism and phytohormones to increase the fruit development and size. • Glycinebetaine affects the expression of fruit development-related genes in transgenic tomato plants. • The transcriptome analysis indicated that glycinebetaine promotes tomato fruit development in multiple ways. Abstract Glycinebetaine has been widely considered as an effective protectant against abiotic stress in plants, and also found to promote plant growth under normal growing conditions, especially during the reproductive stage. Betaine aldehyde dehydrogenase (BADH) and choline oxidase (COD) are two key enzymes which have been used to confer glycinebetaine synthesis in plant which normally does not synthesis glycinebetaine. In this study, we used the tomato (Solanum lycopersicum, cv 'Moneymaker') plants of wild-type and the transgenic lines codA (L1, L2) and BADH (2, 46), which were transformed with codA and BADH , respectively, to study the impact of glycinebetaine on tomato fruit development. Our results showed that the codA and BADH transgenes induced the formation of enlarged flowers and fruits in transgenic tomato plants. In addition, the transgenic tomato plants had a higher photosynthetic rate, higher assimilates content, and higher leaf chlorophyll content than the wild-type plants. We also found that the enlargement of fruit size was related to the contents of phytohormones, such as auxin, brassinolide, gibberellin, and cytokinin. Additionally, qPCR results indicated that the expressions levels of certain genes related to fruit growth and development were also elevated in transgenic plants. Finally, transcriptome sequencing results revealed that the differences in the levels of gene expression in tomato fruit between the transgenic and wild-type plants were observed in multiple pathways, predominantly those of photosynthesis, DNA replication, plant hormone signal transduction, and biosynthesis. Taken together, our results suggest that glycinebetaine promotes tomato fruit development via multiple pathways. We propose that genetic engineering of glycinebetaine synthesis offers a novel approach to enhance the productivity of tomato and other crop plants. [ABSTRACT FROM AUTHOR]

Nucleotide binding site leucine-rich repeat (NLR) proteins of the plant innate immune system are negatively regulated by the miR482/2118 family miRNAs that are in a distinct 22-nt class of miRNAs with a double mode of action. First, they cleave the target RNA, as with the canonical 21-nt miRNAs, and second, they trigger secondary siRNA production using the target RNA as a template. Here, we address the extent to which the miR482/2118 family affects expression of NLR mRNAs and disease resistance. We show that structural differences of miR482/2118 family members in tomato (Solanum lycopersicum) are functionally significant. The predicted target of the miR482 subfamily is a conserved motif in multiple NLR mRNAs, whereas for miR2118b, it is a noncoding RNA target formed by rearrangement of several different NLR genes. From RNA sequencing and degradome data in lines expressing short tandem target mimic (STTM) RNAs of miR482/2118, we confirm the different targets of these miRNAs. The effect on NLR mRNA accumulation is slight, but nevertheless, the tomato STTM lines display enhanced resistance to infection with the oomycete and bacterial pathogens. These data implicate an RNA cascade of miRNAs and secondary siRNAs in the regulation of NLR RNAs and show that the encoded NLR proteins have a role in quantitative disease resistance in addition to dominant gene resistance that has been well characterized elsewhere. We also illustrate the use of STTM RNA in a biotechnological approach for enhancing quantitative disease resistance in highly bred cultivars. [ABSTRACT FROM AUTHOR]

Key message: The transcriptomic profile in the leaves of miR482b-overexpressing tomato plants revealed that miR482b may suppress alpha-linolenic acid metabolism, cysteine and methionine metabolism, plant-pathogen interaction, and the MAPK pathway to reduce resistance to Phytophthora infestans.Abstract: Our previous study showed that tomato miR482b acted as a negative regulator during tomato resistance to Phytophthora infestans by silencing NBS-LRR genes. To investigate pathways related to miR482b, the transcriptomic profile of tomato plants that overexpressed miR482b was constructed. A total of 47,124,670 raw sequence reads from the leaves of miR482b-overexpressing tomato plants were generated by Illumina sequencing. A total of 746 genes in miR482b-overexpressing tomato plants were found to show significantly differential expression relative to those in wild-type tomato plants, including 132 up-regulated genes and 614 down-regulated genes. GO and KEGG enrichment analyses showed that plant-pathogen interaction, the MAPK pathway, and the pathways related to JA and ET biosynthesis were affected by miR482b in tomato. qRT-PCR results showed that all the enriched genes in these pathways were down-regulated in tomato plants that overexpressed miR482b and up-regulated in tomato plants that overexpressed an NBS-LRR gene (Soly02g036270.2, the target gene of miR482b). After P. infestans infection, the expression of the enriched genes showed a time-dependent response, and the genes played different roles between resistant tomato (Solanum pimpinellifolium L3708) and tomato susceptible to P. infestans (S. lycopersicum Zaofen No. 2). Our results have, therefore, demonstrated that miR482b is an important component of defense response network. This will also help to identify candidate genes involved in plant-pathogen interaction. [ABSTRACT FROM AUTHOR]

Highlights • Differential responses between root-to-shoot following reductions in gibberellins (GA) were observed. • GA reductions effected more shoot than roots metabolism in tomato plants. • Our results suggest that GAs plays a more direct role in plant metabolism than previously thought. • Manipulations in the biosynthetic pathways of GAs could potentially increase plant fitness and stress tolerance. Abstract The ability to adapt to the environment is crucial for plant survival and thus a refined communication system capable of integrating endogenous and exogenous signals and further relaying this information to different parts of the plant is a key component of such adaptability. Given that they grow in highly distinct environments it is arguably unsurprising that roots and shoots display different responses to a given environmental condition. Accordingly, a higher sensitivity of roots to gibberellins (GAs) allows rapid adjustments in growth and development possibly triggering (a) stress tolerance mechanism(s). Here we investigated the differential metabolic responses between root and shoot following reductions of the endogenous GA content using tomato (Solanum lycopersicum L.) plants deficient in GA biosynthesis (gib3 , moderately deficient, gib2 , intermediate deficiency and gib1 , extremely deficient in GAs). GA depletion impedes shoot growth to a greater extent than root growth in all mutants. Moreover, the greater the reduction in GA content the greater the extent of a disturbance at the metabolic level. Low leaf carbohydrate contents were observed in plants displaying higher root growth, suggesting an enhanced flow of photoassimilate to support root growth. Large increases in amino acids contents of either roots or shoot were observed. The increased amino acid content was coupled to reduced levels of TCA cycle intermediates suggesting that these changes are directly linked to early reactions of nitrogen assimilation. The combined data are discussed in terms of our current understanding of the interaction between GA and primary metabolism and their crosstalk in environmental responses. [ABSTRACT FROM AUTHOR]

Summary: The tomato PROCERA gene encodes a DELLA protein, and loss‐of‐function mutations derepress growth. We used CRISPR/Cas9 and a single guide RNAs (sgRNA) to target mutations to the PROCERADELLA domain, and recovered several loss‐of‐function mutations and a dominant dwarf mutation that carries a deletion of one amino acid in the DELLA domain. This is the first report of a dominant dwarf PROCERA allele. This allele retains partial responsiveness to exogenously applied gibberellin. Heterozygotes show an intermediate phenotype at the seedling stage, but adult heterozygotes are as dwarfed as homozygotes. [ABSTRACT FROM AUTHOR]

Summary: Carotenoids are critically important to plants and humans. The ORANGE (OR) gene is a key regulator for carotenoid accumulation, but its physiological roles in crops remain elusive. In this study, we generated transgenic tomato ectopically overexpressing the Arabidopsis wild‐type OR (AtORWT) and a 'golden SNP'‐containing OR (AtORHis). We found that AtORHis initiated chromoplast formation in very young fruit and stimulated carotenoid accumulation at all fruit developmental stages, uncoupled from other ripening activities. The elevated levels of carotenoids in the AtOR lines were distributed in the same subplastidial fractions as in wild‐type tomato, indicating an adaptive response of plastids to sequester the increased carotenoids. Microscopic analysis revealed that the plastid sizes were increased in both AtORWT and AtORHis lines at early fruit developmental stages. Moreover, AtOR overexpression promoted early flowering, fruit set and seed production. Ethylene production and the expression of ripening‐associated genes were also significantly increased in the AtOR transgenic fruit at ripening stages. RNA‐Seq transcriptomic profiling highlighted the primary effects of OR overexpression on the genes in the processes related to RNA, protein and signalling in tomato fruit. Taken together, these results expand our understanding of OR in mediating carotenoid accumulation in plants and suggest additional roles of OR in affecting plastid size as well as flower and fruit development, thus making OR a target gene not only for nutritional biofortification of agricultural products but also for alteration of horticultural traits. [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 Fruit quality formation involves a series of physiological and biochemical changes during fruit ripening. Sucrose metabolism plays not only important roles in fruit ripening to establish energy status and nutritional quality but also a non-nutritive role in gene expression. In carbon metabolism and fruit ripening, cell wall invertases (CWINs) perform essential regulatory functions. Knowledge regarding the gene expression changes that occur following the repression of CWIN activity in fruit through the overexpression of a cell-wall inhibitor of β-fructosidase (CIF) under a fruit-specific promoter is limited. To further explore the molecular mechanism of sucrose regulation, global expression profiling of the fruits of transgenic tomato (Solanum lycopersicum) plants carrying a cell wall invertase inhibitor (SlCIF1) gene was performed using a microarray. In total, 622 and 833 differentially expressed genes (DEGs) were identified. The expression of the SlHSP17. 7 gene was increased by thousands of times in the transgenic- SlCIF1 tomato. Then, SlHSP17.7-RNA interference (RNAi) lines were generated by introducing pB7GWIWG2 (I)-SlHSP17.7 into wild-type chmielewskii tomatoes (WT). The sucrose and fructose contents significantly decreased in the RNAi fruits compared with those in the WT. Furthermore, 14 sugar metabolism related genes were also decreased synergistically by silencing SlHSP17. 7 gene. Our data indicate that the posttranslational modulation of CWIN activity by SlCIF1 contributes to earlier bloom times. SlHSP17. 7 and sugar can interact to regulate the development of tomato fruit and affect the quality of tomato, providing a different insight into improving the quality of tomato. Highlights • Differentially expressed genes were identified in transgenic- SlCIF1 by microarray. • The expression of SlHSP17. 7 gene was significantly increased in the transgenic- SlCIF1 tomato. • SlHSP17.7 regulates the pathway of sugar metabolism in SlHSP17.7-RNAi tomato. • A sophisticated regulatory model including SlCIF1 and SlHSP17.7 was set up involved in the pathway of sugar metabolism. [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]

The effect of hypoxia on the antioxidant system during the storage of tomato fruits was investigated using plants with different expression levels of the encoding gene for the MT-sHSP23.6 protein. Fruits from two 'Micro-Tom' tomato plant genotypes (wild type and high expression of MT-sHSP23.6) were harvested at the breaker stage and subjected to normoxia (23 °C, dark) and hypoxia (daily nitrogen flow of 0.098 Mpa/10 min, 23 °C, darkness) treatments for 5 and 8 days, respectively. We evaluated the color tone (Hueº) of the fruits, as well as the components of the enzymatic antioxidant system, reactive oxygen species, non-enzymatic antioxidant system components and radical scavenging activity. Fruits from plants with high MT-sHSP23.6 expression had the highest activity for all the antioxidant enzymes under hypoxia conditions (25, 20, 76, and 48% higher than wild type for SOD, CAT, APX, and GPOD, respectively). They also had the lowest concentrations of superoxide anion under both normoxia and hypoxia storage. At the end of the normoxia storage period, the genotype with high MT-sHSP23.6 expression had the highest accumulation of lycopene (13%), whereas at the end of hypoxia storage, the wild type genotype had the highest lycopene accumulation (39%). Higher accumulation of phenolic compounds was observed in the post-hypoxia period for plants subjected to the hypoxia treatment in high MT-sHSP23.6 expression genotype (12% on the fourth day and 9% on the eighth day). In addition, ascorbic acid concentration was considerably higher on the third and fourth storage days (47% and 8%, respectively). During the hypoxia period, the genotype with high MT-sHSP23.6 expression exhibited the highest radical scavenging activity. High MT-sHSP23.6 expression stimulated the enzymatic antioxidant system during the hypoxia period and led to higher accumulation of phenolic compounds and ascorbic acid, evidence that this protein may be related to tolerance mechanisms in plants subjected to post-harvest abiotic stresses. [ABSTRACT FROM AUTHOR]

Abstract FK506-protein also called FKBP protein belongs to PPIase (peptidylprolylcis-trans isomerase) super family of immune suppressive drugs that act as molecular protein chaperones. In plants, FKBPs are ubiquitous and involved in various biological and physiological processes like plant germination, development, stress response and hormonal signaling. Here, we identified 24 FKBP family genes in tomato by using different tools and bioinformatic approaches. The specific structure, domain organisation, cis-regulatory elements, phylogenetic analysis, multiple sequence alignment, tissue-specific expression patterns and expression under abiotic and phytohormone stresses of all genes were investigated. The genes are clustered on ten tomato chromosomes and are categorised into two sub-classes; single and multiple domains protein gene. One of the main features of tomato FKBPs is their large fractions localized in chloroplast (in silico analysis) and clustered together phylogenetically. Tissue-specific expression analysis using available RNA-seq data revealed the spatiotemporal expression of the FKBPs , but few genes were observed with relatively high expressions in certain developmental stages. However, the quantitative expression profile of all genes under hormone stress provided a supporting evidence for their potential role in hormone signal pathways. Our prediction not only providing the foundation for better understanding the complex physiological regulation of FKBP gene family in tomato but also providing the potential aids to accelerate tolerance and survival in tomato under stressful condition. Highlights • A total of 24 tomato FKBP genes were identified. • Bioinformatics analysis of FKBP gene family in tomato plant • The transcript levels in seedlings revealed that several genes involved in abiotic stress • Expression profiling of 24 candidate tomato FKBP genes in various tissues [ABSTRACT FROM AUTHOR]

Abstract Plant RNA silencing systems are organized as a network, regulating plant developmental pathways and restraining invading viruses, by sharing cellular components with overlapping functions. Host regulatory networks operate either at the transcriptional level via RNA-directed DNA methylation, or at the post-transcriptional stage interfering with mRNA to restrict viral infection. However, viral-derived proteins, including suppressors of RNA silencing, favour virus establishment, and also affect plant developmental processes. In this investigation, we report that Tomato leaf curl New Delhi virus-derived AC4 protein suppresses RNA silencing activity and mutational analysis of AC4 showed that Asn-50 in the SKNT-51 motif, in the C-terminal region, is a critical determinant of its RNA silencing suppressor activity. AC4 showed interaction with host AGO4 but not with AGO1, aggregated around the nucleus, and influenced cytosine methylation of the viral genome. The possible molecular mechanism by which AC4 interferes in the RNA silencing network, helps virus establishment, and affects plant development is discussed. Highlights • Expression or silencing status of AC4 influences viral DNA cytosine methylation. • AC4 is an RNA silencing suppressor and Asn-50 in the SKNT-51 motif is crucial for suppressor activity. • Interaction with AGO4 and sub-cellular localization imply AC4 regulates PTGS and TGS. • Molecular evidence for the role of AC4 in silencing suppression [ABSTRACT FROM AUTHOR]

Background: In living organisms, small heat shock proteins (sHSPs) are triggered in response to stress situations. This family of proteins is large in plants and, in the case of tomato (Solanum lycopersicum), 33 genes have been identified, most of them related to heat stress response and to the ripening process. Transcriptomic and proteomic studies have revealed complex patterns of expression for these genes. In this work, we investigate the coregulation of these genes by performing a computational analysis of their promoter architecture to find regulatory motifs known as heat shock elements (HSEs). We leverage the presence of sHSP members that originated from tandem duplication events and analyze the promoter architecture diversity of the whole sHSP family, focusing on the identification of HSEs. Results: We performed a search for conserved genomic sequences in the promoter regions of the sHSPs of tomato, plus several other proteins (mainly HSPs) that are functionally related to heat stress situations or to ripening. Several computational analyses were performed to build multiple sequence motifs and identify transcription factor binding sites (TFBS) homologous to HSF1AE and HSF21 in Arabidopsis. We also investigated the expression and interaction of these proteins under two heat stress situations in whole tomato plants and in protoplast cells, both in the presence and in the absence of heat shock transcription factor A2 (HsfA2). The results of these analyses indicate that different sHSPs are up-regulated depending on the activation or repression of HsfA2, a key regulator of HSPs. Further, the analysis of protein-protein interaction between the sHSP protein family and other heat shock response proteins (Hsp70, Hsp90 and MBF1c) suggests that several sHSPs are mediating alternative stress response through a regulatory subnetwork that is not dependent on HsfA2. Conclusions: Overall, this study identifies two regulatory motifs (HSF1AE and HSF21) associated with the sHSP family in tomato which are considered genomic HSEs. The study also suggests that, despite the apparent redundancy of these proteins, which has been linked to gene duplication, tomato sHSPs showed different up-regulation and different interaction patterns when analyzed under different stress situations. [ABSTRACT FROM AUTHOR]

New cultivation techniques associated with the use of genetic materials with high productive potential have provided the need for studies related to the accumulation of dry matter and nutrients by tomato plants. The objective of this study was to evaluate the accumulation of dry matter and macronutrients by the tomato 'Caeté' in Chapada do Apodi-CE. The accumulation of dry matter and nutrients in the vegetative part (stems and leaves) and in the fruits was quantified by sampling the plants at 14, 28, 42, 56, 70, 84 and 99 days after the transplant (DAT). The total accumulation of macronutrients in the plant followed the accumulation of dry matter, with greater demands in the fruiting phase. The accumulation of macronutrients at 99 DAT followed by the following decreasing order: K> N> Ca> S> Mg> P. [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]

The extent of genetic variability among 19 accessions of tomato was studied using genetic variability parameters. Four-week old seedlings were transplanted in a well levelled field with 0.6 x 0.6 spacing and replicated three times in randomized complete block design. High significant differences among the accessions for all attributes studied. Cluster analysis based on 37 agro-morphological attributes separated accessions into two distinct groups according to the fruit types. Values for genotypic and phenotypic coefficients of variation showed variability among the accessions. Correlation analysis showed fruit/plant is positively and significantly correlated to plant height, number of branches/plant and leaf length. Very high genetic advance and heritability estimates for leaf length, leaf width, days to flower, days to 50% flowering, number of fruits/plant, fruit length, fruit diameter, fruit weight and 1000 seed weight suggest simple inheritance system and thus amenability for these attributes to selection in tomato improvement. [ABSTRACT FROM AUTHOR]

Highlights • The presence of the glycans at the sites N94 and N112 was crucial for the activity of R-TBN1. • Hyperglycosylated mutant D36S/E104N was twice as active as R-TBN1 wt; the partial demannosylation shifted the substrate specificity of R-TBN1. • R-TBN1 was posttranslationally modified by high-mannose glycans, when produced in N. benthamiana. • Highly homologous nucleases R-HBN1 and R-ABN1 were glycosylated in a similar way as R-TBN1. • N. benthamiana can glycosylate foreign plant non-specific nucleases mainly by high-mannose type of glycosylation. Abstract A unique analysis of an enzyme activity versus structure modification of the tomato nuclease R-TBN1 is presented. R-TBN1, the non-specific nuclease belonging to the S1-P1 nuclease family, was recombinantly produced in N. benthamiana. The native structure is posttranslationally modified by N -glycosylation at three sites. In this work, it was found that this nuclease is modified by high-mannose type N -glycosylation with a certain degree of macro- and microheterogeneity. To monitor the role of N -glycosylation in its activity, hypo- and hyperglycosylated nuclease mutants, R-TBN1 digested by α-mannosidase, and R-TBN1 deglycosylated by PNGase F were prepared. Deglycosylated R-TBN1 and mutant N94D/N112D were virtually inactive. Compared to R-TBN1 wt, both N94D and N112D mutants showed about 60% and 10% of the activity, respectively, while the N186D, D36S, and D36S/E104 N mutants were equally or even more active than R-TBN1 wt. The partial demannosylation of R-TBN1 did not affect the nuclease activity; moreover, a little shift in substrate specificity was observed. The results show two facts: 1) which sites must be occupied by a glycan for the proper folding and stability and 2) how N. benthamiana glycosylates the foreign nuclease. At the same time, the modifications can be interesting in designing the nuclease activity or specificity through its glycosylation. [ABSTRACT FROM AUTHOR]

The site-directed mutagenesis of tomato allene oxide synthase LeAOS3 (CYP74C3) on the "F/L toggle" site resulted in a partial conversion of LeAOS3 into epoxyalcohol synthase. [ABSTRACT FROM AUTHOR]

Parthenocarpy and fruit malformations are common among independent transgenic tomato lines, expressing genes encoding different pathogenesis-related (PR) protein and antimicrobal peptides. Abnormal phenotype developed independently of the expression and type of target genes, but distinctive features during flower and fruit development were detected in each transgenic line. We analyzed the morphology, anatomy, and cytoembryology of abnormal flowers and fruits from these transgenic tomato lines and compared them with flowers and fruits of wild tomatoes, line YaLF used for transformation, and transgenic plants with normal phenotype. We confirmed that the main cause of abnormal flower and fruit development was the alterations of determinate growth of generative meristem. These alterations triggered different types of anomalous growth, affecting the number of growing ectopic shoots and formation of new flowers. Investigation of the ovule ontogenesis did not show anomalies in embryo sac development, but fertilization did not occur and embryo sac degenerated. Nevertheless, the ovule continued to differentiate due to proliferation of endothelium cells. The latter substituted embryo sac and formed pseudoembryonic tissue. This process imitated embryogenesis and stimulated ovary growth, leading to the development of parthenocarpic fruit. We demonstrated that failed fertilization occurred due to defective male gametophyte formation, which was manifested in blocked division of the nucleus in the microspore and arrest of vegetative and generative cell formation. Maturing pollen grains were overgrown microspores, not competent for fertilization but capable to induce proliferation of endothelium and development of parthenocarpic ovary. Thus, our study provided new data on the structural transformations of reproductive organs during development of parthenocarpic fruits in transgenic tomato. [ABSTRACT FROM AUTHOR]

Reductions in growth and quality due to powdery mildew (PM) disease cause significant economic losses in tomato production. Oidium neolycopersici was identified as the fungal species responsible for tomato PM disease in South Korea in the present study, based on morphological and internal transcribed spacer DNA sequence analyses of PM samples collected from two remote regions (Muju and Miryang). The genes involved in resistance to this pathogen in the tomato accession 'KNU-12' (Solanum lycopersicum var. cerasiforme) were evaluated, and the inheritance of PM resistance in 'KNU-12' was found to be conferred via simple Mendelian inheritance of a mutant allele of the PM susceptibility locus Ol-2 (SlMlo1). Full-length cDNA analysis of this newly identified mutant allele (Slmlo1.1) showed that a 1-bp deletion in its coding region led to a frameshift mutation possibly resulting in SlMlo1 loss-of-function. An alternatively spliced transcript of Slmlo1.1 was observed in the cDNA sequences of 'KNU-12', but its direct influence on PM resistance is unclear. A derived cleaved amplified polymorphic sequence (dCAPS) and a high-resolution melting (HRM) marker were developed based on the 1-bp deletion in Slmlo1.1, and could be used for efficient marker-assisted selection (MAS) using 'KNU-12' as the source for durable and broad-spectrum resistance to PM. [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]

Phylogenetics and population genetics are central disciplines in evolutionary biology. Both are based on the comparison of single DNA sequences, or a concatenation of a number of these. However, with the advent of next-generation DNA sequencing technologies, the approaches that consider large genomic data sets are of growing importance for the elucidation of evolutionary relationships among species. Among these approaches, the assembly and alignment-free methods which allow an efficient distance computation and phylogeny reconstruction are of great importance. However, it is not yet clear under what quality conditions and abundance of genomic data such methods are able to infer phylogenies accurately. In the present study we assess the method originally proposed by Fan et al. for whole genome data, in the elucidation of Tomatoes' chloroplast phylogenetics using short read sequences. We find that this assembly and alignment-free method is capable of reproducing previous results under conditions of high coverage, given that low frequency k-mers (i.e. error prone data) are effectively filtered out. Finally, we present a complete chloroplast phylogeny for the best data quality candidates of the recently published 360 tomato genomes. [ABSTRACT FROM AUTHOR]

Summary: High‐throughput RNA sequencing has proven invaluable not only to explore gene expression but also for both gene prediction and genome annotation. However, RNA sequencing, carried out on tens or even hundreds of samples, requires easy and cost‐effective sample preparation methods using minute RNA amounts. Here, we present TranSeq, a high‐throughput 3′‐end sequencing procedure that requires 10‐ to 20‐fold fewer sequence reads than the current transcriptomics procedures. TranSeq significantly reduces costs and allows a greater increase in size of sample sets analyzed in a single experiment. Moreover, in comparison with other 3′‐end sequencing methods reported to date, we demonstrate here the reliability and immediate applicability of TranSeq and show that it not only provides accurate transcriptome profiles but also produces precise expression measurements of specific gene family members possessing high sequence similarity. This is difficult to achieve in standard RNA‐seq methods, in which sequence reads cover the entire transcript. Furthermore, mapping TranSeq reads to the reference tomato genome facilitated the annotation of new transcripts improving >45% of the existing gene models. Hence, we anticipate that using TranSeq will boost large‐scale transcriptome assays and increase the spatial and temporal resolution of gene expression data, in both model and non‐model plant species. Moreover, as already performed for tomato (ITAG3.0; www.solgenomics.net), we strongly advocate its integration into current and future genome annotations. [ABSTRACT FROM AUTHOR]

A conventional breeding approach was framed to combine lycopene enhancing mutant gene, dg or hp-2 dg and anthocyanin synthesizing gene, Aft in one genotype in maximizing the accumulation of both lycopene and anthocyanin pigment in tomato fruit. This breeding scheme involves one crossing, Alisa Craig AftAft  × BCT-115 dgdg followed by two selfings for selection of the desirable double homozygous genotype, AftAft dgdg , the “Purple tomato” based on morphological marker characters conditioned by two genes, dark green fruit of dgdg due to very high total chlorophyll content (18.19 mg/100 g fresh weight) and purple colour for anthocyanin pigment of Aft - gene. Lycopene content in ripe fruits of BCT-115 dgdg (6.22 mg/100 g fresh weight) was 62.41% higher compared to Alisa Craig Aft / Aft while that of Alisa Craig AftAft had high anthocyanin content (14.51 mg/ 100 g fresh weight) contrary to nil in BCT 115 dgdg . Segregation pattern confirmed the expected 3:1 ratio for single dominant Aft gene and 1:3 ratio for single recessive dg gene. The F 2 segregates could be grouped into 5 phenotypic classes in the ratio of 6:3:3:3:1 instead of usual 9:3:3:1 in digenic segregation due to variable expression of anthocyanin in the homozygous ( Aft Aft ) and heterozygous ( Aft aft ) genotype. Of the selfed progeny of the 34 desirable F 2 segregates (dark green fruit with intense anthocyanin pigmentation) clustered in the Group-1 family (F 3 population), 9 segregates bred true confirming the presence of two targeted genes in homozygous condition, AftAft dgdg , the “Purple tomato line”. This breeding approach proved to be a viable option to develop a new variety “Purple tomato” with unique combination of high lycopene (6.13 mg/100 g fresh weight), anthocyanin (20.73 mg/100 g fresh weight) and ascorbic acid (31.56 mg/100 g fresh weight) contents. [ABSTRACT FROM AUTHOR]

Summary: Genomic imprinting is a conspicuous feature of the endosperm, a triploid tissue nurturing the embryo and synchronizing angiosperm seed development. An unknown subset of imprinted genes (IGs) is critical for successful seed development and should have highly conserved functions. Recent genome‐wide studies have found limited conservation of IGs among distantly related species, but there is a paucity of data from closely related lineages. Moreover, most studies focused on model plants with nuclear endosperm development, and comparisons with properties of IGs in cellular‐type endosperm development are lacking. Using laser‐assisted microdissection, we characterized parent‐specific expression in the cellular endosperm of three wild tomato lineages (Solanum section Lycopersicon). We identified 1025 candidate IGs and 167 with putative homologs previously identified as imprinted in distantly related taxa with nuclear‐type endosperm. Forty‐two maternally expressed genes (MEGs) and 17 paternally expressed genes (PEGs) exhibited conserved imprinting status across all three lineages, but differences in power to assess imprinted expression imply that the actual degree of conservation might be higher than that directly estimated (20.7% for PEGs and 10.4% for MEGs). Regardless, the level of shared imprinting status was higher for PEGs than for MEGs, indicating dissimilar evolutionary trajectories. Expression‐level data suggest distinct epigenetic modulation of MEGs and PEGs, and gene ontology analyses revealed MEGs and PEGs to be enriched for different functions. Importantly, our data provide evidence that MEGs and PEGs interact in modulating both gene expression and the endosperm cell cycle, and uncovered conserved cellular functions of IGs uniting taxa with cellular‐ and nuclear‐type endosperm. [ABSTRACT FROM AUTHOR]

In a previous study, when resistant tomato plants (cv. Motelle) carrying the Sm gene were challenged with S. lycopersici , the SLNLC1 gene was significantly upregulated. In this study, to verify the function of the SLNLC1 gene response to disease resistance against S. lycopersici , virus-induced gene silencing (VIGS) was used to downregulate the expression level of the SLNLC1 gene in resistant tomato plants inoculated with S. lycopersici . After inoculation with S. lycopersici , a susceptible phenotype was observed in the silenced SLNLC1 -resistant plants. Through microscopy, impaired hypersensitive response (HR) and decreased ROS accumulation were also observed in the silenced SLNLC1 plants. In addition, the production of lignin and callose were decreased in the silenced SLNLC1 plants. Taken together, these results indicated that silencing the SLNLC1 gene attenuated the resistance of tomato plants resistant to S. lycopersici. [ABSTRACT FROM AUTHOR]

We assembled three complete mitochondrial genomes (mitogenomes), two of Solanum lycopersicum and one of Solanum pennellii, and analyzed their intra- and interspecific variations. The mitogenomes were 423,596–446,257 bp in length. Despite numerous rearrangements between the S. lycopersicum and S. pennellii mitogenomes, over 97% of the mitogenomes were similar to each other. These mitogenomes were compared with plastid and nuclear genomes to investigate genetic material transfers among DNA-containing organelles in tomato. In all mitogenomes, 9,598 bp of plastome sequences were found. Numerous nuclear copies of mitochondrial DNA (NUMTs) and plastid DNA (NUPTs) were observed in the S. lycopersicum and S. pennellii nuclear genomes. Several long organellar DNA fragments were tightly clustered in the nuclear genome; however, the NUMT and NUPT locations differed between the two species. Our results demonstrate the recent occurrence of frequent endosymbiotic gene transfers in tomato genomes. [ABSTRACT FROM AUTHOR]

Plants are sessile organisms, hence to face environmental constrains they developed strategies that rely on the activation of stress-response genes under the control of specific transcription factors. The plant hormone ethylene mediates physiological, developmental and stress responses through the activation of Ethylene Response Factors (ERFs) which belong to a large multigene family of transcription factors. While an increasing number of studies supports the involvement of ERFs in abiotic stress responses, so far the specific role of ERF family members in different abiotic stress conditions remains unexplored. The present work investigates the expression profile of a set of ERFs, representative of different ERF types, in tomato plants subjected to cold, heat, salt, drought and flooding conditions. The study revealed that a group of ERFs is preferentially associated with cold and heat stress responses while another set is expressed in response to salt, water and flooding stresses. Transactivation assays indicated that ERFs can regulate the expression of abiotic stress genes regardless of whether or not they harbor conserved GCC or DRE cis -elements in their promoter region. The outcome of the study provides clue on which ERFs should be targeted when aiming to improve adaptation to a particular stress type. [ABSTRACT FROM AUTHOR]