Tomato Organs Research Articles

Ameliorative Effects of Organic Fertilizer, Trichoderma and Silicon on Productivity and Quality of Tomato Grown under Contaminated soil Conditions

The present study was carried out during the summer seasons of 2017 and 2018 in Talkha city, Dakahlia Governorate, Egypt near El-Mansoura-Damietta highway and El Delta Company for Fertilizers and Chemical Industries, where lead (Pb) and copper (Cu) levels in the soil exceed the permissible levels. Therefore, the aim of this study was to alleviate the adverse effects of heavy metals (HMs) on tomato plant (Solanumlycopersicum L.) Super Strain B F1. Twelve treatments were conducted which were the interactions between two silicon (Si) foliar spraying (without or 300 ppm Si) and six soil amendments : 100% chemical fertilizers (CF), 50% farmyard manure (FYM), 100% FYM, 100% CF+ Trichoderma spp. (T.), 50% FYM + T. and 100% FYM + T. Data indicate that Pb and Cu were accumulated in tomato organs to hazardous levels in the following descending order : roots > shoots > fruits and shoots > roots > fruits, respectively which consequently severely reduced tomato plant growth and fruit yield and fruit quality. Results also, showed that the application of Si treatment sole or in combination with soil amendments markedly enhanced plant height, dry weight, total chlorophyll, number of fruits/plant, total yield/fed, Vitamin C, acidity %, TSS and taste index, where as, reduced Pb and Cu concentrations in different plant organs, bio-concentration factor (BCF) and translocation factor (TF). However, Si + FYM + T. treatment was superior in these respects, therefore increased the net return. Also, negative correlations were obtained between fruit yield and BCF of Pb or Cu and between taste index and TF of Pb or Cu.

Crop Organ Segmentation and Disease Identification Based on Weakly Supervised Deep Neural Network

Object segmentation and classification using the deep convolutional neural network (DCNN) has been widely researched in recent years. On the one hand, DCNN requires large data training sets and precise labeling, which bring about great difficulties in practical application. On the other hand, it consumes a large amount of computing resources, so it is difficult to apply it to low-cost terminal equipment. This paper proposes a method of crop organ segmentation and disease recognition that is based on weakly supervised DCNN and lightweight model. While considering the actual situation in the greenhouse, we adopt a two-step strategy to reduce the interference of complex background. Firstly, we use generic instance segmentation architecture—Mask R-CNN to realize the instance segmentation of tomato organs based on weakly supervised learning, and then the disease recognition of tomato leaves is realized by depth separable multi-scale convolution. Instance segmentation algorithms usually require accurate pixel-level supervised labels, which are difficult to collect, so we propose a weakly supervised instance segmentation assignment to solve this problem. The lightweight model uses multi-scale convolution to expand the network width, which makes the extracted features richer, and depth separable convolution is adopted to reduce model parameters. The experimental results showed that our method reached higher recognition accuracy when compared with other methods, at the same time occupied less memory space, which can realize the real-time recognition of tomato diseases on low-performance terminals, and can be applied to the recognition of crop diseases in other similar application scenarios.

Eicosapolyenoic fatty acids alter oxylipin gene expression and fatty acid hydroperoxide profiles in tomato and pepper roots

Eicosapolyenoic fatty acids (EP), such as arachidonic acid (AA), are abundant in oomycetes and can serve as microbe-associated molecular patterns (MAMPs) to elicit host defense responses. Solanaceous plants have multiple enzymes that convert EP into biologically active oxylipins. We evaluated expression of genes involved in oxylipin production in tomato and pepper seedlings with roots treated with AA and in tomato seedlings inoculated with Phytophthora capsici. AA treatment of tomato and pepper roots significantly increased expression of 9-lipoxygenase (9-LOX), 9-divinyl ether synthase (9-DES), α-dioxygenase (α-DOX), 13-lipoxygenase (13-LOX), and 13-allene oxide synthase (13-AOS), with 9-DES and α-DOX having the largest increases in expression. A similar pattern of expression was observed for 9-LOX, 9-DES, and α-DOX in tomato roots inoculated with P. capsici. Expression of 13-LOX and 13-AOS in tomato roots inoculated with P. capsici did not consistently follow the pattern observed in AA-treated tomato and pepper roots. AA treatment of tomato roots increased production of 9-LOX products of LA and AA, with no change in 13-LOX products of LA. These results implicate the 9-oxylipin and α-dioxygenase pathways in EP signal-response coupling, and establish that the EP response in tomato and pepper roots, generally the primary site of attack by soil-borne oomycetes, parallels that in other vegetative organs of potato and tomato.

Differences in the sucrose synthase gene SUS1 expression pattern between Solanum lycopersicum and wild tomato species

Plant sucrose synthase (SUS) reversibly hydrolyzes sucrose, incorporating sucrose into different metabolic pathways. SUS1 homologous genes were characterized in 12 accessions of cultivated tomato Solanum lycopersicum and wild tomato species (Solanum section Lycopersicon). In total, 34 non-synonymous SNPs were found; among them, 17 caused radical amino acid substitutions, mostly in the wild species. The SUS1-based phylogenetic tree topology was represented by two clusters of red-fruited and green-fruited species, where S. pennellii and S. habrochaites showed the highest divergence. SUS1 transcription was detected in source and sink organs of one cultivated and four wild tomato species; it was the highest in buds and flowers, but lower in mature green fruit of the final size. In leaves and roots, the level of SUS1 expression corresponded to species evolutionary history, whereas no correlation was found between SUS1 levels and fruit size and sugar composition. Our findings suggest that SUS1-mediated reversible sucrose hydrolysis is important for maintaining the balance between sucrose and its monomers not only in fruits, but also in the other tomato organs.

Downregulation of the auxin transporter gene SlPIN8 results in pollen abortion in tomato

SlPIN8 is expressed specifically within tomato pollen, and that it is involved in tomato pollen development and intracellular auxin homeostasis. The auxin (IAA) transport protein PIN-FORMED (PIN) plays key roles in various aspects of plant development. The biological role of the auxin transporter SlPIN8 in tomato development remains unclear. Here, we examined the expression pattern of the SlPIN8 gene in vegetative and reproductive organs of tomato. RNA interference (RNAi) transgenic lines specifically silenced for the SlPIN8 gene were generated to identify the role of SlPIN8 in pollen development. We found that SlPIN8 mRNA is expressed specifically within tomato pollen. In the anthers, the highest mRNA expression and β-glucuronidase (GUS) activity of promoter-SlPIN8-GUS was detected during late stages of anther development, when pollen maturation occurred. The downregulation of SlPIN8 did not drastically affect the vegetative growth of tomato. However, in SlPIN8-RNAi transgenic plants, approximately 80% of the pollen grains were identified to be abnormal and lack viability; they were shriveled and flattened. Furthermore, the downregulation of SlPIN8 affected the gene expression of some anther development-specific proteins. SlPIN8-RNAi transgenic plants induced seedless fruits because of defective pollen function rather than defective female gametophyte function. In addition, SlPIN8 was found to localize to the endoplasmic reticulum, consistent with the changes in the auxin levels of SlPIN8-RNAi lines, whereas the level of free IAA was increased in SlPIN8-overexpressing protoplasts, indicating that SlPIN8 is involved in intracellular auxin homeostasis.

Detection of Key Organs in Tomato Based on Deep Migration Learning in a Complex Background

In the current natural environment, due to the complexity of the background and the high similarity of the color between immature green tomatoes and the plant, the occlusion of the key organs (flower and fruit) by the leaves and stems will lead to low recognition rates and poor generalizations of the detection model. Therefore, an improved tomato organ detection method based on convolutional neural network (CNN) has been proposed in this paper. Based on the original Faster R-CNN algorithm, Resnet-50 with residual blocks was used to replace the traditional vgg16 feature extraction network, and a K-means clustering method was used to adjust more appropriate anchor sizes than manual setting, to improve detection accuracy. The test results showed that the mean average precision (mAP) was significantly improved compared with the traditional Faster R-CNN model. The training model can be transplanted to the embedded system, which lays a theoretical foundation for the development of a precise targeting pesticide application system and an automatic picking device.

Identification and Characterization of Sterol Acyltransferases Responsible for Steryl Ester Biosynthesis in Tomato.

Steryl esters (SEs) serve as a storage pool of sterols that helps to maintain proper levels of free sterols (FSs) in cell membranes throughout plant growth and development, and participates in the recycling of FSs and fatty acids released from cell membranes in aging tissues. SEs are synthesized by sterol acyltransferases, a family of enzymes that catalyze the transfer of fatty acil groups to the hydroxyl group at C-3 position of the sterol backbone. Sterol acyltransferases are categorized into acyl-CoA:sterol acyltransferases (ASAT) and phospholipid:sterol acyltransferases (PSAT) depending on whether the fatty acyl donor substrate is a long-chain acyl-CoA or a phospolipid. Until now, only Arabidopsis ASAT and PSAT enzymes (AtASAT1 and AtPSAT1) have been cloned and characterized in plants. Here we report the identification, cloning, and functional characterization of the tomato (Solanum lycopersicum cv. Micro-Tom) orthologs. SlPSAT1 and SlASAT1 were able to restore SE to wild type levels in the Arabidopsis psat1-2 and asat1-1 knock-out mutants, respectively. Expression of SlPSAT1 in the psat1-2 background also prevented the toxicity caused by an external supply of mevalonate and the early senescence phenotype observed in detached leaves of this mutant, whereas expression of SlASAT1 in the asat1-1 mutant revealed a clear substrate preference of the tomato enzyme for the sterol precursors cycloartenol and 24-methylene cycloartanol. Subcellular localization studies using fluorescently tagged SlPSAT1 and SlASAT1 proteins revealed that SlPSAT1 localize in cytoplasmic lipid droplets (LDs) while, in contrast to the endoplasmic reticulum (ER) localization of AtASAT1, SlASAT1 resides in the plasma membrane (PM). The possibility that PM-localized SlASAT1 may act catalytically in trans on their sterol substrates, which are presumably embedded in the ER membrane, is discussed. The widespread expression of SlPSAT1 and SlASAT1 genes in different tomato organs together with their moderate transcriptional response to several stresses suggests a dual role of SlPSAT1 and SlASAT1 in tomato plant and fruit development and the adaptive responses to stress. Overall, this study contributes to enlarge the current knowledge on plant sterol acyltransferases and set the basis for further studies aimed at understanding the role of SE metabolism in tomato plant growth and development.

Effects of salicylic acid, Epi-brassinolide and calcium on stress alleviation and Cd accumulation in tomato plants

Salicylic acid (SA), Epi-brassinolide (EBL) and calcium (Ca) play crucial roles in plant development and mediate plant response to biotic and abiotic stress. This study was aimed to investigate the possible mediatory role of SA, EBL, Ca or their combination in protecting tomato plants from cadmium (Cd) toxicity. According to the results, Cd stress resulted in a significant reduction of plant dry mass, photosynthetic pigment content as well as photosynthetic rate. Exogenous application of SA decreased the malondialdehyde (MDA) level by 39.27% and increased catalase (CAT) activity by 81.17%. SA and EBL treatment significantly increased chlorophyll a (Chl a), chlorophyll b (Chl b) content, photosynthetic rate (Pn) as well as water use efficiency (WUE). SA+EBL (1:1)/Ca+SA+EBL (1:1:1) treatment obviously alleviated Cd-induced growth inhibition, the dry mass of different tomato organs were significantly increased (p < 0.05). Especially in Ca+SA+EBL treated plants, the dry mass of roots, stems and leaves increased by 141.18%, 128.57% and 118.52%, respectively. Besides, SA+EBL and Ca+SA+EBL treatments reduced the MDA level, but increased photosynthetic pigment concentration and photosynthetic efficiency. CAT activity was increased by 62.92% in Ca+SA+EBL treated plants, the WUE was increased by 557.76% in SA+EBL pretreated plants. Moreover, exogenous application of SA, SA+EBL and Ca+SA+EBL significantly decreased Cd accumulation in tomato organs (p < 0.05) compared with Cd-stressed plants. Taken together, our results indicated that exogenous application of SA, EBL and Ca individually or in combination could alleviate Cd toxicity in tomato plants, although the extent varies.

The functional analysis of SlNCED1 in tomato pollen development.

Abscisic acid (ABA) regulates plant growth and development, but the role of ABA in the development of reproductive organs in tomato has rarely been addressed. In the present study, the role of ABA in the regulation of male and female gametogenesis as well as pollen development and germination is tested in tomato. qRT-PCR and in situ hybridization analysis of 9-cis-epoxycarotenoid dioxygenase (SlNCED1), a key enzyme in the ABA biosynthetic pathway, showed high expression of SlNCED1 primarily in the meristem during gametogenesis and mainly in ovule, stigma, anther/pollen and vascular tissues during floral organ development. SlNCED1 expression and ABA accumulation in anther peak at stages 13-14, suggesting that ABA plays a role in the primary formation of pollen grains. Over expression and suppression of SlNCED1 led to the abnormal development of anther/pollen, especially in SlNCED1-OE lines, which have serious pollen deterioration. The percentage of pollen germination in wild type is 91.47%, whereas it is 6.85% in OE transgenic lines and 38.4% at anthesis in RNAi lines. RNA-Seq of anthers shows that SlNCED1-OE can significantly enhance the expression of SlPP2Cs and down-regulate the expression of SlMYB108 and SlMYB21, which are anther/flower-specific transcriptional factors in tomato. Finally, anther transcriptome data indicate that SlNCED1 is involved in ABA-mediated regulation in pollen/anther metabolism, cell wall modification, and transcription levels. These results support an important role for ABA in the development of reproductive organs in tomato and contribute to the elucidation of the underlying regulatory mechanisms.

Dynamic of accumulation and redistribution of various carbohydrate forms and nitrogen in organs of tomatoes under treatment with retardants

The regulation of plant growth and development under application of antigibberellin compounds is accompanied by changes in the donor-acceptor system that in turn affects the accumulation and redistribution of carbohydrates and nitrogen-containing compounds. We studied the influence of tebuconazole 0.025% (EW-250) and 0.05% and 0.07% esphon (2-CEPA) on growth processes, leaf apparatus and content of various carbohydrate forms and total nitrogen content in vegetative organs of tomato hybrids Bobkat and Solerosso. A field-based micro-trial setup was established from 2013 to 2017. The plants were treated via foliar spraying with aqueous solution of retardants at the time of initiation of budding. Phytometric measurements were determined every 10 days, the content of various carbohydrate forms and total nitrogen in organs of plants was determined by using biochemical methods in a fixed dry material (the content of sugars and starch – by iodometric method, and the total nitrogen content – by Kjeldahl). It was found that both retardants reduced the linear growth of tomato plants. The results indicate that 2-CEPA treatment significantly decreased the plant height of both hybrids. Application of drugs increased the number of leaves per plant. The leaf dry matter weight increased, the most significant effect was created by EW-250. The leaf area of the retardant-treated tomatoes hybrid Solerosso increased and decreased in the hybrid Bobcat. Application of antigibberellin compounds intensified the outflow of sugars and remobilization of starch in roots and stems of both tomato hybrids. The content of starch, reducing and non-reducing sugars in leaves of hybrid Solerosso was higher after EW-250 treatment. 2-CEPA increased the content of reducing form of sugars, and EW-250 increased non-reducing form in the hybrid Bobkat. EW-250 intensified the accumulation of carbohydrates in fruits due to reducing sugars in both tomato hybrids, whereas 2-CEPA reduced their content compared with control. Growth inhibitors increased the starch content in fruits at the beginning of vegetation and intensified its reutilization at the end. This process was most intensive was in variant of EW-250-treated plants regardless of hybrids. We proved that there was a clear tendency to decrease the ratio of sugar content to starch in almost all organs of both tomato hybrids during the growing season. The most significant was the reduction of this ratio after EW-250 treatment. At the fruitification phase, the proportion of starch in retardant-treated plants increased compared to the control. The increased accumulation of carbohydrates in tomato fruits treated with EW-250 caused an increase in the average weight of the fruit. We have found that the total nitrogen content in vegetative organs decreased in the control and in the experimental variant of both tomato hybrids during vegetation. EW-250 accelerated the outflow of total nitrogen from roots and stems and increased its content in leaves. This drug retarded the accumulation of this element in fruit. Such changes in the dynamics of total nitrogen under the influence of tebuconazole resulted in enhanced formation of fruit on tomato plants. We concluded that the antigibberellin compounds EW-250 and 2-CEPA due the action on growth processes and leaf apparatus of tomato plants, changed the character of donor-acceptor relation through an increase in outflow of plastic substances from vegetative organs to fruits, which optimized the crop production.

MicroRNA1917 targets CTR4 splice variants to regulate ethylene responses in tomato.

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

Optimization of calcium and magnesium concentrations for fertigation of tomato with desalinated water

Desalinated water has become a legitimate alternative water resource for the irrigation of intensive crops in semiarid regions. The concentrations of calcium (Ca) and magnesium (Mg) in water (C Ca and C Mg , respectively) supplied from desalinated plants are much lower than the values typically found in irrigation water resources in semiarid regions. blossom-end rot (BER), a physiological disorder at the blossom-end part of the fruit resulting in tissue disintegration and dehydration, is considered a Ca-related disorder and therefore the optimization of C Ca has to consider not only total fruit production but also the occurrence of BER. There is a lack of information regarding the optimal C Ca and C Mg and Ca/Mg ratio in low-salinity water under Mediterranean conditions for high-quality yield of tomato fruits.The main objective of the research was to optimize C Ca and C Mg for the production of high tomato fruit yield with minimal occurrence of BER. A secondary objective was to determine critical levels of Ca, Mg and Ca/Mg ratio in leaves in relation to yield and the occurrence of BER.Tomato plants were grown in an inert media and fed with a wide range of C Ca and C Mg . Fruit yield was shown to decrease significantly when C Ca was at or below 0.40 mmol l –1 . In moderate C Mg (1.4 mmol l –1 ) treatment, BER was negatively correlated to Ca level up to and including 1.4 mmol l –1 and was not manifested above that level under the prevailing conditions. Elevating C Mg above 0.25 mmol l –1 enhanced BER occurrence. Concentrations of Ca and Mg in tomato organs increased with the respective mineral concentration in irrigation solution, whereas each element was reduced in organs as a function of the increased solution concentration of the other. The Ca concentration in diagnostic leaves (the diagnostic leaf is the fully developed youngest leaf) for optimal fruit yield with minimum BER was found to be 1.6%. The optimum C Ca for high fruit yield with minimal BER occurrence was found to be in the range of 1.5–2.5 mmol l –1 combined with C Mg at 0.25 mmol l –1 .

Novel SlFUL2 orthologous genes and analysis of their expression in wild and cultivated tomato of the section Lycopersicon

FRUITFULL (FUL) transcription factors, SlFUL1 and SlFUL2, are directly involved in the regulation of tomato fruit development. In the present study, complete sequences of novel SlFUL2 orthologous genes were isolated and structurally characterized in five accessions of domestic tomato Solanum lycopersicum and closely related wild species S. pimpinellifolium, having different morphological characteristics. In the studied genes, overall level of nucleotide sequence variation was 1.94%. Nine out of 11 exon-specific SNPs led to amino acid substitutions in the functionally important MADS, K, and C domains of the SlFUL2 orthologues. Considerable differences in the level and spatiotemporal dynamics of the expression patterns in different tomato organs at the species and intraspecific levels were observed.

DIFFERENT SHADING ENVIRONMENTS IMPACT GROWTH AND YIELD OF THREE MINI-TOMATO CULTIVARS

ABSTRACT Our study was conducted in the experimental field of the Department of Technology and Social Sciences (DTCS) of the State University of Bahia - UNEB, Juazeiro-BA. The experimental design was comprised of randomized blocks, sub-subdivided in plots, with four replicates comprising the plots of three different shading methods, gray shading screen (GS), red shading screen (RS), and blue shading screen (BS), and the control treatment with no shading. The subplots comprised three mini-tomato cultivars (“Sweet Million”, “Red Sugar”, and “Shani”), and sub-subplots consisted of seven sampling times. The traits evaluated were: dry matter accumulation in leaves, stems, roots, and fruits, total dry matter, shoot length, root length, total number of fruits, and overall yield. The results of the growth analysis showed that dry matter accumulation in organs of mini tomatoes was similar in all treatments and that the highest total dry matter accumulation occurred under RS. In all treatments, fruit was the preferential drainage; however, the cultivar “Red Sugar” showed higher dry matter accumulation in other plant organs. “Red Sugar” also showed the highest number of fruits per plant; however, when we evaluated total productivity, “Sweet Million” and “Shani” showed similar, higher values than “Red Sugar”.

Callus Induction from Various Organs of Dragon Fruit, Apple and Tomato on some Mediums.

Dragon fruit (Hylocereus spp.), apple (Malus sylvestris Mill.) and tomato (Solanum lycopersicum L.) are high potential sources of antioxidant compounds such as phenolics. The compounds have the capability of protecting cells and tissues against free radicals. Secondary metabolite produced by callus cell culture from plant organs also acts as a source of antioxidants. This study aimed to determine the optimal ratio of sucrose and 2,4-D in Murashige and Skoog (MS) medium for callus induction from different plant organ explants. With all of characteristic, callus can be used further for the development of natural cell regeneration agent. This study was conducted using analytical technique. Suitable explants were obtained. They were developed in various concentrations of combination between MS medium and 2,4-D. Callus growth, including their weight and surface was then measured and analyzed by using one-way analysis of variance (ANOVA). Callus was able to grow from its explants in 5-7 days after induction process. They were clear in color and had friable texture. The highest value of fresh weight of dragon fruit callus was obtained through MS supplemented with 1 μL L-1 2,4-D and 30 g sucrose. However, apple and tomato callus induction and growth maintenance reached optimal medium on MS supplemented with 30 g sucrose and 2 μL L-1 2,4-D. Callus of apple, dragon fruit and tomato was maintained upon MS supplemented with 30-40 g sucrose and 1-2 μL L-1 2,4-D for optimum induction and growth. The optimization of growth medium will give advantages for further development of natural cell regeneration agent.

Solanum lycopersicum (tomato) hosts robust phyllosphere and rhizosphere bacterial communities when grown in soil amended with various organic and synthetic fertilizers

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 (R2=0.52, p=0.005) and negatively (R2=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.

Genome-wide identification, characterization and expression profiling of LIM family genes in Solanum lycopersicum L.

LIM domain proteins, some of which have been shown to be actin binding proteins, are involved in various developmental activities and cellular processes in plants. To date, the molecular defense-related functions of LIM family genes have not been investigated in any solanaceous vegetable crop species. In this study, we identified 15 LIM family genes in tomato (Solanum lycopersicum L.) through genome-wide analysis and performed expression profiling in different organs of tomato, including fruits at six different developmental stages. We also performed expression profiling of selected tomato LIM genes in plants under ABA, drought, cold, NaCl and heat stress treatment. The encoded proteins of the 15 tomato LIM genes were classified into two main groups, i.e., proteins similar to cysteine-rich proteins and plant-specific DAR proteins, based on differences in functional domains and variability in their C-terminal regions. The DAR proteins contain a so far poorly characterized zinc-finger-like motif that we propose to call DAR-ZF. Six of the 15 LIM genes were expressed only in flowers, indicating that they play flower-specific roles in plants. The other nine genes were expressed in all organs and at various stages of fruit development. SlβLIM1b was expressed relatively highly at the later stage of fruit development, but three other genes, SlWLIM2a, SlDAR2 and SlDAR4, were expressed at the early stage of fruit development. Seven genes were induced by ABA, five by cold, seven by drought, eight by NaCl and seven by heat treatment respectively, indicating their possible roles in abiotic stress tolerance. Our results will be useful for functional analysis of LIM genes during fruit development in tomato plants under different abiotic stresses.

De novo Transcriptome Sequencing and Development of Abscission Zone-Specific Microarray as a New Molecular Tool for Analysis of Tomato Organ Abscission.

Abscission of flower pedicels and leaf petioles of tomato (Solanum lycopersicum) can be induced by flower removal or leaf deblading, respectively, which leads to auxin depletion, resulting in increased sensitivity of the abscission zone (AZ) to ethylene. However, the molecular mechanisms that drive the acquisition of abscission competence and its modulation by auxin gradients are not yet known. We used RNA-Sequencing (RNA-Seq) to obtain a comprehensive transcriptome of tomato flower AZ (FAZ) and leaf AZ (LAZ) during abscission. RNA-Seq was performed on a pool of total RNA extracted from tomato FAZ and LAZ, at different abscission stages, followed by de novo assembly. The assembled clusters contained transcripts that are already known in the Solanaceae (SOL) genomics and NCBI databases, and over 8823 identified novel tomato transcripts of varying sizes. An AZ-specific microarray, encompassing the novel transcripts identified in this study and all known transcripts from the SOL genomics and NCBI databases, was constructed to study the abscission process. Multiple probes for longer genes and key AZ-specific genes, including antisense probes for all transcripts, make this array a unique tool for studying abscission with a comprehensive set of transcripts, and for mining for naturally occurring antisense transcripts. We focused on comparing the global transcriptomes generated from the FAZ and the LAZ to establish the divergences and similarities in their transcriptional networks, and particularly to characterize the processes and transcriptional regulators enriched in gene clusters that are differentially regulated in these two AZs. This study is the first attempt to analyze the global gene expression in different AZs in tomato by combining the RNA-Seq technique with oligonucleotide microarrays. Our AZ-specific microarray chip provides a cost-effective approach for expression profiling and robust analysis of multiple samples in a rapid succession.

Genome-wide identification and expression profiling analysis of trihelix gene family in tomato

The trihelix family, classified as GT factors due to their binding specificity for GT elements, constitutes a plant-specific transcription factor family with a conserved trihelix DNA binding domain. In the present study, the comprehensive analysis of 36 putative GT factors was performed in tomato. SlGT members can be classified into six subgroups (GT-1, GT-2, SH4, SIP1, GT-γ and GT-δ). Expression analysis of SlGT gene transcripts showed the distinct expression patterns of SlGT genes in various tomato organs. All the SlGT genes were regulated in response to various abiotic stresses and hormone treatments by the quantitative real-time PCR (qRT-PCR) analysis. Several SlGT genes, including SlGT-27 and SlGT-34, were highly regulated by multiple abiotic stresses and phytohormone treatments. Taken together, our results presented here would be providing a useful platform for molecular clone and functional identification of SlGT genes in tomato.

Identification and expression analysis of the LRR-RLK gene family in tomato (Solanum lycopersicum) Heinz 1706.

As the largest subfamily of receptor-like kinases (RLKs), leucine-rich repeat receptor-like kinases (LRR-RLKs) regulate the growth, development, and stress responses of plants. Through a reiterative process of sequence analysis and re-annotation, 234 LRR-RLK genes were identified in the genome of tomato (Solanum lycopersicum) 'Heinz 1706', which were further grouped into 10 major groups based on their sequence similarity. In comparison to the significant role of tandem duplication in the expansion process of this gene family in other species, only approximately 12% (29 out of 234) of SlLRR-RLK genes arose from tandem duplication. Using the multiple expectation maximization for motif elicitation (MEME) method, the motif composition and arrangement were found to be variably conserved within each SlLRR-RLK group, indicating their different extent of functional divergence. Expression profiling analyses by qRT-PCR data revealed that SlLRR-RLK genes were differentially expressed in various tomato organs and tissues, and some SlLRR-RLK genes exhibited preferential expression in fruits at distinct developmental stages, suggesting that SlLRR-RLK may take important roles in fruit development and ripening process. The results of this study provide an overview of the LRR-RLK gene family in tomato Heinz 1706, one important species of Solanaceae, and will be helpful for future functional analysis of this important protein family in fleshy fruit-bearing species.