tomato
219900091
Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato
Structural variants (SVs) underlie important crop improvement and domestication traits. However, resolving the extent, diversity, and quantitative impact of SVs has been challenging. We used long read nanopore sequencing to capture 238,490 SVs in 100 diverse tomato lines. This panSV genome, along with 14 new reference assemblies, revealed large scale intermixing of diverse genotypes, as well as thousands of SVs intersecting genes and cis regulatory regions. Hundreds of SV gene pairs exhibit subtle and significant expression changes, which could broadly influence quantitative trait variation. By combining quantitative genetics with genome editing, we show how multiple SVs that changed gene dosage and expression levels modified fruit flavor, size, and production. In the last example, higher order epistasis among four SVs affecting three related transcription factors allowed introduction of an important harvesting trait in modern tomato. Our findings highlight the underexplored role of SVs in genotype to phenotype relationships and their widespread importance and utility in crop improvement.
Cell
Michael Alonge Xingang Wang Matthias Benoit Sebastian Soyk Lara Pereira Hamsini Suresh Srividya Ramakrishnan Florian Maumus Danielle Ciren Yuval Levy T Harel Gili Shalev-Schlosser Ziva Amsellem Hamid Razifard Ana L Caicedo Denise M Tieman Harry J Klee Melanie Kirsche Sergey S Aganezov T Rhyker Ranallo-Benavidez Zachary H Lemmon Jennifer Kim Gina Robitaille Melissa Kramer Sara Goodwin W Richard McCombie Samuel F Hutton Joyce van Eck Jesse A Gillis Yuval Eshed Fritz J Sedlazeck Esther van der Knaap Michael C Schatz Zachary B Lippman
212730521
Highly efficient homology directed repair using CRISPR/Cpf1 geminiviral replicon in tomato
Summary Genome editing via the homology directed repair (HDR) pathway in somatic plant cells is very inefficient compared with error prone repair by nonhomologous end joining (NHEJ) Here, we increased HDR based genome editing efficiency approximately threefold compared with a Cas9 based single replicon system via the use of de novo multi replicon systems equipped with CRISPR/LbCpf1 in tomato and obtained replicon free but stable HDR alleles. The efficiency of CRISPR/LbCpf1 based HDR was significantly modulated by physical culture conditions such as temperature and light. Ten days of incubation at 31 degC under a light/dark cycle after Agrobacterium mediated transformation resulted in the best performance among the tested conditions. Furthermore, we developed our single replicon system into a multi replicon system that effectively increased HDR efficiency. Although this approach is still challenging, we showed the feasibility of HDR based genome editing of a salt tolerant SlHKT1;2 allele without genomic integration of antibiotic markers or any phenotypic selection. Self pollinated offspring plants carrying the HKT1;2 HDR allele showed stable inheritance and germination tolerance in the presence of 100 mm NaCl. Our work may pave the way for transgene free editing of alleles of interest in asexually and sexually reproducing plants.
Plant biotechnology journal
Tien Van Vu Velu Sivankalyani Eun-Jung Kim Duong Thi Hai Doan Mil Thi Tran Jihae Kim Yeon Woo Sung Min-Woo Park Yang Jae Kang Jae-Yean Kim
210087010
Genomic Evidence for Complex Domestication History of the Cultivated Tomato in Latin America
Abstract The process of plant domestication is often protracted, involving underexplored intermediate stages with important implications for the evolutionary trajectories of domestication traits. Previously, tomato domestication history has been thought to involve two major transitions: one from wild Solanum pimpinellifolium L. to a semidomesticated intermediate, S. lycopersicum L. var. cerasiforme (SLC) in South America, and a second transition from SLC to fully domesticated S. lycopersicum L. var. lycopersicum in Mesoamerica. In this study, we employ population genomic methods to reconstruct tomato domestication history, focusing on the evolutionary changes occurring in the intermediate stages. Our results suggest that the origin of SLC may predate domestication, and that many traits considered typical of cultivated tomatoes arose in South American SLC, but were lost or diminished once these partially domesticated forms spread northward. These traits were then likely reselected in a convergent fashion in the common cultivated tomato, prior to its expansion around the world. Based on these findings, we reveal complexities in the intermediate stage of tomato domestication and provide insight on trajectories of genes and phenotypes involved in tomato domestication syndrome. Our results also allow us to identify underexplored germplasm that harbors useful alleles for crop improvement.
Molecular biology and evolution
Hamid Razifard Alexis Ramos Audrey L Della Valle Cooper Bodary Erika Goetz Elizabeth J Manser Xin-Zheng Li Lei Zhang Sofia Visa Denise M Tieman Esther van der Knaap Ana L Caicedo
212998497
Tomato WRKY81 acts as a negative regulator for drought tolerance by modulating guard cell H2O2 mediated stomatal closure
Abstract WRKY transcription factors (TFs) are key regulators in numerous plant biological processes and responses to stresses. Although a group III tomato WRKY, SlWKRY81, is induced by some biotic stressors, its role in drought response remains largely unknown. Here, we unveiled a critical role of SlWKRY81 in regulation of drought response by using agronomic, bioinformatics, genetic and pharmacological approaches. Drought gradually increased the transcript levels of SlWRKY81 and impaired leaf water potential and membrane stability in tomato. Analysis of plant phenotypes revealed that silencing of SlWRKY81 in tomato enhanced tolerance to drought, while its overexpression in Arabidopsis resulted in an opposite phenotype. Notably, the enhanced drought tolerance in SlWRKY81 silenced tomato plants was closely associated with a rapid and increased stomatal closure. Furthermore, such stomatal response in the SlWRKY81 silenced plants was sensitive to abscisic acid alongside drought induced enhanced accumulation of H2O2 in the guard cells. The results suggest that SlWRKY81 acts as a negative regulator of stomatal closure by suppressing SlRBOH1 derived H2O2 accumulation, which attenuates plant tolerance to drought. These results may have potential implications on improving plant drought tolerance through genetic manipulation.
Golam Jalal Ahammed Xin Li Youxin Yang Chao-Chao Liu Guozhi Zhou Hongjian Wan Yuan Cheng
209914591
Attention embedded residual CNN for disease detection in tomato leaves
Abstract Automation in plant disease detection and diagnosis is one of the challenging research areas that has gained significant attention in the agricultural sector. Traditional disease detection methods rely on extracting handcrafted features from the acquired images to identify the type of infection. Also, the performance of these works solely depends on the nature of the handcrafted features selected. This can be addressed by learning the features automatically with the help of Convolutional Neural Networks (CNN) This research presents two different deep architectures for detecting the type of infection in tomato leaves. The first architecture applies residual learning to learn significant features for classification. The second architecture applies attention mechanism on top of the residual deep network. Experiments were conducted using Plant Village Dataset comprising of three diseases namely early blight, late blight, and leaf mold. The proposed work exploited the features learned by the CNN at various processing hierarchy using the attention mechanism and achieved an overall accuracy of 98% on the validation sets in the 5 fold cross validation.
Appl. Soft Comput.
R Karthik M Hariharan Sundar Anand Priyanka Mathikshara Annie Johnson R Menaka
210709348
Tomato as Potential Source of Natural Additives for Meat Industry. A Review
Tomato industry produces huge amounts of by products that represent an environmental and economic problem. However, these by products contain multiple bioactive compounds, which would make them a renewable source for obtaining natural antioxidants and colourants (carotenoids) This is in line with the preferences of the current consumer who demands more natural and healthy products. However, the lipophilic character of carotenoids means that their extraction must be carried out using toxic organic solvents. To overcome environmental and health problems of organic solvents, the application of supercritical fluid extraction (SFE) for the extraction of lipophilic compounds such as lycopene was used successfully, achieving yields similar to those obtained with conventional techniques. Nonetheless, the extraction conditions must be carefully selected, to obtain high yields and at the same time maintain a high antioxidant capacity. On the other hand, the use of tomato and tomato extracts as natural additives in meat products are reduced in comparison with other natural antioxidant/colourant extracts. However, different researches conclude that the use of tomato improved nutritional quality, reduced lipid oxidation and increased stability during the shelf life period of meat products, while retaining or increasing sensory properties and overall acceptability, which converts tomato by products into a promising source of natural additives.
Antioxidants
Ruben Dominguez Patricia Gullon Mirian Pateiro Paulo E S Munekata Wangang Zhang J Lorenzo
215772135
YOLO Tomato: A Robust Algorithm for Tomato Detection Based on YOLOv3
Automatic fruit detection is a very important benefit of harvesting robots. However, complicated environment conditions, such as illumination variation, branch, and leaf occlusion as well as tomato overlap, have made fruit detection very challenging. In this study, an improved tomato detection model called YOLO Tomato is proposed for dealing with these problems, based on YOLOv3. A dense architecture is incorporated into YOLOv3 to facilitate the reuse of features and help to learn a more compact and accurate model. Moreover, the model replaces the traditional rectangular bounding box (R Bbox) with a circular bounding box (C Bbox) for tomato localization. The new bounding boxes can then match the tomatoes more precisely, and thus improve the Intersection over Union (IoU) calculation for the Non Maximum Suppression (NMS) They also reduce prediction coordinates. An ablation study demonstrated the efficacy of these modifications. The YOLO Tomato was compared to several state of the art detection methods and it had the best detection performance.
Sensors
Guoxu Liu Joseph Christian Nouaze Philippe Lyonel Touko Mbouembe Jae Ho Kim
209595498
Pretreatment with Trichoderma harzianum alleviates waterlogging induced growth alterations in tomato seedlings by modulating physiological, biochemical, and molecular mechanisms
Abstract We studied the role of Trichoderma harzianum (TH) in improving the physiological, biochemical, hormonal, and molecular parameters of tomato seedlings grown under waterlogging (WL, for 14 and 28 days) Pretreatment with TH significantly improved the growth of tomato by enhancing the chlorophyll synthesis and uptake of essential ions, including nitrogen, phosphorus, and potassium. A reduction in anthocyanin content was also ameliorated significantly by TH pretreatment. TH significantly mitigated the WL induced decline in height and in fresh and dry biomass accumulation. Accumulation of proline, flavonoids, anthocyanin, sugars, and soluble protein increased with TH pretreatment. At both growth periods (14 and 28 days after treatment [DAT] the accumulation of secondary metabolites, including total phenols and flavonoids, and the redox components (tocopherols) were increased significantly by TH pretreatment. Increased synthesis of metabolites maintained the antioxidant status of tomato, resulting in amelioration of WL induced oxidative effects on membranes. WL and TH treatments significantly increased ethylene production and decreased abscisic acid content at both growth periods. The accumulation of reactive oxygen species, like hydrogen peroxide, in TH treated seedlings was correlated with the upregulation of the Fe SOD gene. WL stress triggered the activity of sucrose synthase (SUS) lactate dehydrogenase (LDH) and pyruvate decarboxylase (PDC) which reached a maximum at 14 DAT, and TH pretreatment resulted in further enhancement above control and WL stressed levels. Quantitative RT PCR revealed differential expression of genes, where Fe SOD and ADH were upregulated due to TH treatment and ARE, ACO, ERF, and aquaporin were downregulated relative to control plants. Pretreatment of tomato seedlings with TH improved tolerance to WL by maintaining the antioxidant status, sugar metabolism, and expression of critical genes. These results suggest that TH pretreatment is an effective way to improve WL tolerance in tomato at vegetative stage.
Amr A Elkelish Haifa Abdulaziz Sakit Alhaithloul Sameer H Qari Mona H Soliman Mirza Hasanuzzaman
214204390
Active Packaging Poly(Vinyl Alcohol) Films Enriched with Tomato By Products Extract
Active films were prepared from poly(vinyl alcohol) (PVA) blended with itaconic acid (Ia) and with chitosan (Ch) enriched with tomato processing by products extract (TBE) in order to develop new bioactive formulations for food packaging. The effects of two biopolymers (Ch, Ia) and of the incorporated TBE containing phenolic compounds and carotenoids were studied regarding the physical and antimicrobial properties of films; in addition, their influence on the total phenolic content, viscosity, and flow behavior on the film forming solutions was investigated. The results showed increased physical properties (diameter, thickness, density, weight) of the films containing the TBE versus their control. TBE and Ch conferred significant antimicrobial effects to PVA films toward all the tested microorganisms, whereas the best inhibition was registered against S. aureus and P. aeruginosa, with a minimum inhibitory concentration of <0.078 mg DW/mL. The Ia PVA films also exhibited some antibacterial activity against P. aeruginosa (2.5 mg DW/mL) The total phenolic content of the film forming solutions presented the highest values for the TBE and Ch added PVA samples (0.208 mg gallic acid/100 mL film forming solution) These results suggest that the PVA Ch film containing TBE can be used for the development of intelligent and active food packaging materials.
Katalin Szabo Bernadette-Emoke Teleky Laura Mitrea Lavinia Florina Calinoiu Gheorghe Adrian Martau Elemer Simon Rodica-Anita Varvara Dan Cristian Vodnar
214786311
Exogenous Ascorbic Acid Induced Chilling Tolerance in Tomato Plants Through Modulating Metabolism, Osmolytes, Antioxidants, and Transcriptional Regulation of Catalase and Heat Shock Proteins
Chilling, a sort of cold stress, is a typical abiotic ecological stress that impacts the development as well as the growth of crops. The present study was carried to investigate the role of ascorbic acid root priming in enhancing tolerance of tomato seedlings against acute chilling stress. The treatments included untreated control, ascorbic acid treated plants (AsA; 0.5 mM) acute chilling stressed plants (4 degC) and chilling stressed seedlings treated by ascorbic acid. Exposure to acute chilling stress reduced growth in terms of length, fresh and dry biomass, pigment synthesis, and photosynthesis. AsA was effective in mitigating the injurious effects of chilling stress to significant levels when supplied at 0.5 mM concentrations. AsA priming reduced the chilling mediated oxidative damage by lowering the electrolyte leakage, lipid peroxidation, and hydrogen peroxide. Moreover, up regulating the activity of enzymatic components of the antioxidant system. Further, 0.5 mM AsA proved beneficial in enhancing ions uptake in normal and chilling stressed seedlings. At the gene expression level, AsA significantly lowered the expression level of CAT and heat shock protein genes. Therefore, we theorize that the implementation of exogenous AsA treatment reduced the negative effects of severe chilling stress on tomato.
Plants
Amr A Elkelish Sameer H Qari Yasser S A Mazrou Kh A A Abdelaal Yaser M Hafez Abdelghafar M Abu-Elsaoud Gaber El-Saber Batiha Mohamed A El-Esawi Nihal El Nahhas