Trait discovery and editing in tomato

Characterization of tomato autophagy-related SlCOST family genes

Autophagy is a eukaryote-specific cellular process that can engulf unwanted targets with double-membrane autophagosomes and subject them to the vacuole or lysosome for breaking down and recycling, playing dual roles in plant growth and environmental adaptions. However, perception of specific environmental signals for autophagy induction is largely unknown, limiting its application in agricultural usage. Identification of plant-unique DUF641 family COST1 (Constitutively Stressed 1) protein directly links drought perception and autophagy induction, shedding light on manipulating autophagy for breeding stress tolerant crops. In this study, we performed a genome-wide analysis of DUF641/COST family in tomato, and identified five SlCOST genes SlCOST1, -2, -3, -4, and -5. SlCOST genes show both overlapping and distinct expression patterns in plant growth and stress responding. In addition, SlCOST1, -3, -4, -5 proteins demonstrate co-localization with autophagy adaptor protein ATG8e, and all five SlCOST proteins show interactions ATG8e in planta. However, only SlCOST1, the closest ortholog of Arabidopsis AtCOST1, can restore cost1 mutant to WT level, suggesting conserved role of COST1 and functional diversification of SlCOST family in tomato. Our study provides clues for future investigation of autophagy-related COST family and its promising implementations in breeding crops with robust environmental plasticity.

Tomato domestication rather than subsequent breeding events reduces microbial associations related to phosphorus recovery

Legacy phosphorus (P) is a reservoir of sparingly available P, and its recovery could enhance sustainable use of nonrenewable mineral fertilizers. Domestication has affected P acquisition, but it is unknown if subsequent breeding efforts, like the Green Revolution (GR), had a similar effect. We examined how domestication and breeding events altered P acquisition by growing wild, traditional (pre-GR), and modern (post-GR) tomato in soil with legacy P but low bioavailable P. Wild tomatoes, particularly accession LA0716 (Solanum pennellii), heavily cultured rhizosphere P solubilizers, suggesting reliance on microbial associations to acquire P. Wild tomato also had a greater abundance of other putatively beneficial bacteria, including those that produce chelating agents and antibiotic compounds. Although wild tomatoes had a high abundance of these P solubilizers, they had lower relative biomass and greater P stress factor than traditional or modern tomato. Compared to wild tomato, domesticated tomato was more tolerant to P deficiency, and both cultivated groups had a similar rhizosphere bacterial community composition. Ultimately, this study suggests that while domestication changed tomato P recovery by reducing microbial associations, subsequent breeding processes have not further impacted microbial P acquisition mechanisms. Selecting microbial P-related traits that diminished with domestication may therefore increase legacy P solubilization.

Enhancing Yield and Improving Grain Quality in Japonica Rice: Targeted EHD1 Editing via CRISPR-Cas9 in Low-Latitude Adaptation

The "Indica to Japonica" initiative in China focuses on adapting Japonica rice varieties from the northeast to the unique photoperiod and temperature conditions of lower latitudes. While breeders can select varieties for their adaptability, the sensitivity to light and temperature often complicates and prolongs the process. Addressing the challenge of cultivating high-yield, superior-quality Japonica rice over expanded latitudinal ranges swiftly, in the face of these sensitivities, is critical. Our approach harnesses the CRISPR-Cas9 technology to edit the EHD1 gene in the premium northeastern Japonica cultivars Jiyuanxiang 1 and Yinongxiang 12, which are distinguished by their exceptional grain quality-increased head rice rates, gel consistency, and reduced chalkiness and amylose content. Field trials showed that these new ehd1 mutants not only surpass the wild types in yield when grown at low latitudes but also retain the desirable traits of their progenitors. Additionally, we found that disabling Ehd1 boosts the activity of Hd3a and RFT1, postponing flowering by approximately one month in the ehd1 mutants. This research presents a viable strategy for the accelerated breeding of elite northeastern Japonica rice by integrating genomic insights with gene-editing techniques suitable for low-latitude cultivation.

New Advances in the Study of Regulation of Tomato Flowering-Related Genes Using Biotechnological Approaches

The tomato is a convenient object for studying reproductive processes, which has become a classic. Such complex processes as flowering and fruit setting require an understanding of the fundamental principles of molecular interaction, the structures of genes and proteins, the construction of signaling pathways for transcription regulation, including the synchronous actions of cis-regulatory elements (promoter and enhancer), trans-regulatory elements (transcription factors and regulatory RNAs), and transposable elements and epigenetic regulators (DNA methylation and acetylation, chromatin structure). Here, we discuss the current state of research on tomatoes (2017-2023) devoted to studying the function of genes that regulate flowering and signal regulation systems using genome-editing technologies, RNA interference gene silencing, and gene overexpression, including heterologous expression. Although the central candidate genes for these regulatory components have been identified, a complete picture of their relationship has yet to be formed. Therefore, this review summarizes the latest achievements related to studying the processes of flowering and fruit set. This work attempts to display the gene interaction scheme to better understand the events under consideration.

CRISPR/Cas9-mediated seamless gene replacement in protoplasts expands the resistance spectrum to TMV-U1 strain in regenerated Nicotiana tabacum

CRISPR/Cas-based genome editing is now extensively used in plant breeding and continues to evolve. Most CRISPR/Cas current applications in plants focus on gene knock-outs; however, there is a pressing need for new methods to achieve more efficient delivery of CRISPR components and gene knock-ins to improve agronomic traits of crop cultivars. We report here a genome editing system that combines the advantages of protoplast technologies with recent CRISPR/Cas advances to achieve seamless large fragment insertions in the model Solanaceae plant Nicotiana tabacum. With this system, two resistance-related regions of the N' gene were replaced with homologous fragments from the N'alata gene to confer TMV-U1 resistance in the T0 generation of GMO-free plants. Our study establishes a reliable genome-editing tool for efficient gene modifications and provides a detailed description of the optimization process to assist other researchers adapt this system for their needs.

GIFTdb: a useful gene database for plant fruit traits improving

Fruit traits are critical determinants of plant fitness, resource diversity, productive and quality. Gene regulatory networks in plants play an essential role in determining fruit traits, such as fruit size, yield, firmness, aroma and other important features. Many research studies have focused on elucidating the associated signaling pathways and gene interaction mechanism to better utilize gene resources for regulating fruit traits. However, the availability of specific database of genes related to fruit traits for use by the plant research community remains limited. To address this limitation, we developed the Gene Improvements for Fruit Trait Database (GIFTdb, http://giftdb.agroda.cn). GIFTdb contains 35 365 genes, including 896 derived from the FR database 1.0, 305 derived from 30 882 articles from 2014 to 2021, 236 derived from the Universal Protein Resource (UniProt) database, and 33 928 identified through homology analysis. The database supports several aided analysis tools, including signal transduction pathways, gene ontology terms, protein-protein interactions, DNAWorks, Basic Local Alignment Search Tool (BLAST), and Protein Subcellular Localization Prediction (WoLF PSORT). To provide information about genes currently unsupported in GIFTdb, potential fruit trait-related genes can be searched based on homology with the supported genes. GIFTdb can provide valuable assistance in determining the function of fruit trait-related genes, such as MYB306-like, by conducting a straightforward search. We believe that GIFTdb will be a valuable resource for researchers working on gene function annotation and molecular breeding to improve fruit traits.

Can microplastics threaten plant productivity and fruit quality? Insights from Micro-Tom and Micro-PET/PVC

Solanum lycopersicum L., a crop grown worldwide with a high nutritional value for the human diet, was used to test the impact of microplastics on plant growth, productivity, and fruit quality. Two of the most represented microplastics in soils, polyethylene terephthalate (PET) and polyvinyl chloride (PVC), were tested. Plants were grown in pots with an environmentally realistic concentration of microplastics and, during the whole crop life cycle, photosynthetic parameters, number of flowers and fruits were monitored. At the end of the cultivation, plant biometry and ionome were evaluated, along with fruit production and quality. Both pollutants had negligible effects on shoot traits, with only PVC causing a significant reduction in shoot fresh weight. Despite an apparent low or no toxicity during the vegetative stage, both microplastics decreased the number of fruits and, in the case of PVC, also their fresh weights. The plastic polymer-induced decline in fruit production was coupled with wide variations in fruit ionome, with marked increases in Ni and Cd. By contrast there was a decline in the nutritionally valuable lycopene, total soluble solids, and total phenols. Altogether, our results reveal that microplastics can not only limit crop productivity but also negatively impact fruit quality and enhance the concentration of food safety hazards, thus raising concerns for their potential health risks for humans.

Diversity and genetic architecture of agro-morphological traits in a core collection of European traditional tomato

European traditional tomato varieties have been selected by farmers given their consistent performance and adaptation to local growing conditions. Here we developed a multipurpose core collection, comprising 226 accessions representative of the genotypic, phenotypic, and geographical diversity present in European traditional tomatoes, to investigate the basis of their phenotypic variation, gene×environment interactions, and stability for 33 agro-morphological traits. Comparison of the traditional varieties with a modern reference panel revealed that some traditional varieties displayed excellent agronomic performance and high trait stability, as good as or better than that of their modern counterparts. We conducted genome-wide association and genome-wide environment interaction studies and detected 141 quantitative trait loci (QTLs). Out of those, 47 QTLs were associated with the phenotype mean (meanQTLs), 41 with stability (stbQTLs), and 53 QTL-by-environment interactions (QTIs). Most QTLs displayed additive gene actions, with the exception of stbQTLs, which were mostly recessive and overdominant QTLs. Both common and specific loci controlled the phenotype mean and stability variation in traditional tomato; however, a larger proportion of specific QTLs was observed, indicating that the stability gene regulatory model is the predominant one. Developmental genes tended to map close to meanQTLs, while genes involved in stress response, hormone metabolism, and signalling were found within regions affecting stability. A total of 137 marker-trait associations for phenotypic means and stability were novel, and therefore our study enhances the understanding of the genetic basis of valuable agronomic traits and opens up a new avenue for an exploitation of the allelic diversity available within European traditional tomato germplasm.

The RLCK subfamily VII-4 controls pattern-triggered immunity and basal resistance to bacterial and fungal pathogens in rice

Receptor-like cytoplasmic kinases (RLCKs) mediate the intracellular signaling downstream of pattern-recognition receptors (PRRs). Several RLCKs from subfamily VII of rice (Oryza sativa) have important roles in plant immunity, but the role of RLCK VII-4 in pattern-triggered immune (PTI) signaling and resistance to pathogens has not yet been investigated. Here, we generated by multiplex clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9-mediated genome editing rice sextuple mutant lines where the entire RLCK VII-4 subfamily is inactivated and then analyzed the resulting lines for their response to chitin and flg22 and for their immunity to Xanthomonas oryzae pv. oryzae (Xoo) and Magnaporthe oryzae. Analysis of the rlckvii-4 mutants revealed that they have an impaired reactive oxygen system burst and reduced defense gene expression in response to flg22 and chitin. This indicates that members of the rice RLCK VII-4 subfamily are required for immune signaling downstream of multiple PRRs. Furthermore, we found that the rice RLCK VII-4 subfamily is important for chitin-induced callose deposition and mitogen-activated protein kinase activation and that it is crucial for basal resistance against Xoo and M. oryzae pathogens. This establishes that the RLCK VII-4 subfamily has critical functions in the regulation of multiple PTI pathways in rice and opens the way for deciphering the precise role of its members in the control of rice PTI.

Unraveling the Molecular Mechanisms of Tomatoes' Defense against Botrytis cinerea: Insights from Transcriptome Analysis of Micro-Tom and Regular Tomato Varieties

Botrytis cinerea is a devastating fungal pathogen that causes severe economic losses in global tomato cultivation. Understanding the molecular mechanisms driving tomatoes' response to this pathogen is crucial for developing effective strategies to counter it. Although the Micro-Tom (MT) cultivar has been used as a model, its stage-specific response to B. cinerea remains poorly understood. In this study, we examined the response of the MT and Ailsa Craig (AC) cultivars to B. cinerea at different time points (12-48 h post-infection (hpi)). Our results indicated that MT exhibited a stronger resistant phenotype at 18-24 hpi but became more susceptible to B. cinerea later (26-48 hpi) compared to AC. Transcriptome analysis revealed differential gene expression between MT at 24 hpi and AC at 22 hpi, with MT showing a greater number of differentially expressed genes (DEGs). Pathway and functional annotation analysis revealed significant differential gene expression in processes related to metabolism, biological regulation, detoxification, photosynthesis, and carbon metabolism, as well as some immune system-related genes. MT demonstrated an increased reliance on Ca2+ pathway-related proteins, such as CNGCs, CDPKs, and CaMCMLs, to resist B. cinerea invasion. B. cinerea infection induced the activation of PTI, ETI, and SA signaling pathways, involving the modulation of various genes such as FLS2, BAK1, CERK1, RPM, SGT1, and EDS1. Furthermore, transcription factors such as WRKY, MYB, NAC, and AUX/IAA families played crucial regulatory roles in tomatoes' defense against B. cinerea. These findings provide valuable insights into the molecular mechanisms underlying tomatoes' defense against B. cinerea and offer potential strategies to enhance plant resistance.

Optimization of Callus Induction and Shoot Regeneration from Tomato Cotyledon Explants

Cultivated tomato (Solanum lycopersicum L.) is one of the most important horticultural crops in the world. The optimization of culture media for callus formation and tissue regeneration of different tomato genotypes presents numerous biotechnological applications. In this work, we have analyzed the effect of different concentrations of zeatin and indole-3-acetic acid on the regeneration of cotyledon explants in tomato cultivars M82 and Micro-Tom. We evaluated regeneration parameters such as the percentage of callus formation and the area of callus formed, as well as the initiation percentage and the number of adventitious shoots. The best hormone combination produced shoot-like structures after 2-3 weeks. We observed the formation of leaf primordia from these structures after about 3-4 weeks. Upon transferring the regenerating micro-stems to a defined growth medium, it was possible to obtain whole plantlets between 4 and 6 weeks. This hormone combination was applied to other genotypes of S. lycopersicum, including commercial varieties and ancestral tomato varieties. Our method is suitable for obtaining many plantlets of different tomato genotypes from cotyledon explants in a very short time, with direct applications for plant transformation, use of gene editing techniques, and vegetative propagation of elite cultivars.

An Integrative Transcriptomics and Proteomics Approach to Identify Putative Genes Underlying Fruit Ripening in Tomato near Isogenic Lines with Long Shelf Life

The elucidation of the ripening pathways of climacteric fruits helps to reduce postharvest losses and improve fruit quality. Here, we report an integrative study on tomato ripening for two near-isogenic lines (NIL115 and NIL080) with Solanum pimpinellifolium LA0722 introgressions. A comprehensive analysis using phenotyping, molecular, transcript, and protein data were performed. Both NILs show improved fruit firmness and NIL115 also has longer shelf life compared to the cultivated parent. NIL115 differentially expressed a transcript from the APETALA2 ethylene response transcription factor family (AP2/ERF) with a potential role in fruit ripening. E4, another ERF, showed an upregulated expression in NIL115 as well as in the wild parent, and it was located physically close to a wild introgression. Other proteins whose expression levels changed significantly during ripening were identified, including an ethylene biosynthetic enzyme (ACO3) and a pectate lyase (PL) in NIL115, and an alpha-1,4 glucan phosphorylase (Pho1a) in NIL080. In this study, we provide insights into the effects of several genes underlying tomato ripening with potential impact on fruit shelf life. Data integration contributed to unraveling ripening-related genes, providing opportunities for assisted breeding.

Beyond green and red: unlocking the genetic orchestration of tomato fruit color and pigmentation

Fruit color is a genetic trait and a key factor for consumer acceptability and is therefore receiving increasing importance in several breeding programs. Plant pigments offer plants with a variety of colored organs that attract animals for pollination, favoring seed dispersers and conservation of species. The pigments inside plant cells not only play a light-harvesting role but also provide protection against light damage and exhibit nutritional and ecological value for health and visual pleasure in humans. Tomato (Solanum lycopersicum) is a leading vegetable crop; its fruit color formation is associated with the accumulation of several natural pigments, which include carotenoids in the pericarp, flavonoids in the peel, as well as the breakdown of chlorophyll during fruit ripening. To improve tomato fruit quality, several techniques, such as genetic engineering and genome editing, have been used to alter fruit color and regulate the accumulation of secondary metabolites in related pathways. Recently, clustered regularly interspaced short palindromic repeat (CRISPR)-based systems have been extensively used for genome editing in many crops, including tomatoes, and promising results have been achieved using modified CRISPR systems, including CAS9 (CRISPR/CRISPR-associated-protein) and CRISPR/Cas12a systems. These advanced tools in biotechnology and whole genome sequencing of various tomato species will certainly advance the breeding of tomato fruit color with a high degree of precision. Here, we attempt to summarize the current advancement and effective application of genetic engineering techniques that provide further flexibility for fruit color formation. Furthermore, we have also discussed the challenges and opportunities of genetic engineering and genome editing to improve tomato fruit color.

Genetics and breeding of phenolic content in tomato, eggplant and pepper fruits

Phenolic acids and flavonoids are large groups of secondary metabolites ubiquitous in the plant kingdom. They are currently in the spotlight due to the numerous health benefits associated with their consumption, as well as for their vital roles in plant biological processes and in plant-environment interaction. Tomato, eggplant and pepper are in the top ten most consumed vegetables in the world, and their fruit accumulation profiles have been extensively characterized, showing substantial differences. A broad array of genetic and genomic tools has helped to identify QTLs and candidate genes associated with the fruit biosynthesis of phenolic acids and flavonoids. The aim of this review was to synthesize the available information making it easily available for researchers and breeders. The phenylpropanoid pathway is tightly regulated by structural genes, which are conserved across species, along with a complex network of regulatory elements like transcription factors, especially of MYB family, and cellular transporters. Moreover, phenolic compounds accumulate in tissue-specific and developmental-dependent ways, as different paths of the metabolic pathway are activated/deactivated along with fruit development. We retrieved 104 annotated putative orthologues encoding for key enzymes of the phenylpropanoid pathway in tomato (37), eggplant (29) and pepper (38) and compiled 267 QTLs (217 for tomato, 16 for eggplant and 34 for pepper) linked to fruit phenolic acids, flavonoids and total phenolics content. Combining molecular tools and genetic variability, through both conventional and genetic engineering strategies, is a feasible approach to improve phenolics content in tomato, eggplant and pepper. Finally, although the phenylpropanoid biosynthetic pathway has been well-studied in the Solanaceae, more research is needed on the identification of the candidate genes behind many QTLs, as well as their interactions with other QTLs and genes.

Genome-Wide Identification and Expression Analysis of Cysteine-Rich Polycomb-like Protein (CPP) Gene Family in Tomato

The cysteine-rich polycomb-like protein (CPP) gene family is a class of transcription factors containing conserved cysteine-rich CRC structural domains that is involved in the regulation of plant growth and stress tolerance to adversity. Relative to other gene families, the CPP gene family has not received sufficient attention. In this study, six SlCPPs were identified for the first time using the most recent genome-wide identification data of tomato. Subsequently, a phylogenetic analysis classified SlCPPs into four subfamilies. The analysis of cis-acting elements in the promoter indicates that SlCPPs are involved in plant growth and development and also stress response. We present for the first time the prediction of the tertiary structure of these SlCPPs proteins using the AlphaFold2 artificial intelligence system developed by the DeepMind team. Transcriptome data analysis showed that SlCPPs were differentially expressed in different tissues. Gene expression profiling showed that all SlCPPs except SlCPP5 were up-regulated under drought stress; SlCPP2, SlCPP3 and SlCPP4 were up-regulated under cold stress; SlCPP2 and SlCPP5 were up-regulated under salt stress; all SlCPPs were up-regulated under inoculation with Cladosporium fulvum; and SlCPP1, SlCPP3, and SlCPP4 were up-regulated under inoculation with Stemphylium lycopersici. We performed a virus-induced gene silencing experiment on SlCPP3, and the results indicated that SlCPP3 was involved in the response to drought stress. Finally, we predicted the interaction network of the key gene SlCPP3, and there was an interaction relationship between SlCPP3 and 10 genes, such as RBR1 and MSI1. The positive outcome showed that SlCPPs responded to environmental stress. This study provides a theoretical and empirical basis for the response mechanisms of tomato in abiotic stresses.

A 21-bp InDel in the promoter of STP1 selected during tomato improvement accounts for soluble solid content in fruits

Domestication and improvement are important processes that generate the variation in genome and phonotypes underlying crop improvement. Unfortunately, during selection for certain attributes, other valuable traits may be inadvertently discarded. One example is the decline in fruit soluble solids content (SSC) during tomato breeding. Several genetic loci for SSC have been identified, but few reports on the underlying mechanisms are available. In this study we performed a genome-wide association study (GWAS) for SSC of the red-ripe fruits in a population consisting of 481 tomato accessions with large natural variations and found a new quantitative trait locus, STP1, encoding a sugar transporter protein. The causal variation of STP1, a 21-bp InDel located in the promoter region 1124 bp upstream of the start codon, alters its expression. STP1 ^Insertion accessions with an 21-bp insertion have higher SSC than STP1 ^Deletion accessions with the 21-bp deletion. Knockout of STP1 in TS-23 with high SSC using CRISPR/Cas9 greatly decreased SSC in fruits. In vivo and in vitro assays demonstrated that ZAT10-LIKE, a zinc finger protein transcription factor (ZFP TF), can specifically bind to the promoter of STP1 ^Insertion to enhance STP1 expression, but not to the promoter of STP1 ^Deletion , leading to lower fruit SSC in modern tomatoes. Diversity analysis revealed that STP1 was selected during tomato improvement. Taking these results together, we identified a naturally occurring causal variation underlying SSC in tomato, and a new role for ZFP TFs in regulating sugar transporters. The findings enrich our understanding of tomato evolution and domestication, and provide a genetic basis for genome design for improving fruit taste.

Diversity of tomato leaf form provides novel insights into breeding

Tomato (Solanum lycopersicum L.) is cultivated widely globally. The crop exhibits tremendous morphological variations because of its long breeding history. Apart from the commercial tomato varieties, wild species and heirlooms are grown in certain regions of the world. Since the fruit constitutes the edible part, much of the agronomical research is focused on it. However, recent studies have indicated that leaf morphology influences fruit quality. As leaves are specialized photosynthetic organs and the vascular systems transport the photosynthetic products to sink organs, the architectural characteristics of the leaves have a strong influence on the final fruit quality. Therefore, comprehensive research focusing on both the fruit and leaf morphology is required for further tomato breeding. This review summarizes an overview of knowledge of the basic tomato leaf development, morphological diversification, and molecular mechanisms behind them and emphasizes its importance in breeding. Finally, we discuss how these findings and knowledge can be applied to future tomato breeding.

CRISPR/Cas genome editing in tomato improvement: Advances and applications

The narrow genetic base of tomato poses serious challenges in breeding. Hence, with the advent of clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein9 (CRISPR/Cas9) genome editing, fast and efficient breeding has become possible in tomato breeding. Many traits have been edited and functionally characterized using CRISPR/Cas9 in tomato such as plant architecture and flower characters (e.g. leaf, stem, flower, male sterility, fruit, parthenocarpy), fruit ripening, quality and nutrition (e.g., lycopene, carotenoid, GABA, TSS, anthocyanin, shelf-life), disease resistance (e.g. TYLCV, powdery mildew, late blight), abiotic stress tolerance (e.g. heat, drought, salinity), C-N metabolism, and herbicide resistance. CRISPR/Cas9 has been proven in introgression of de novo domestication of elite traits from wild relatives to the cultivated tomato and vice versa. Innovations in CRISPR/Cas allow the use of online tools for single guide RNA design and multiplexing, cloning (e.g. Golden Gate cloning, GoldenBraid, and BioBrick technology), robust CRISPR/Cas constructs, efficient transformation protocols such as Agrobacterium, and DNA-free protoplast method for Cas9-gRNAs ribonucleoproteins (RNPs) complex, Cas9 variants like PAM-free Cas12a, and Cas9-NG/XNG-Cas9, homologous recombination (HR)-based gene knock-in (HKI) by geminivirus replicon, and base/prime editing (Target-AID technology). This mini-review highlights the current research advances in CRISPR/Cas for fast and efficient breeding of tomato.

Plasticity of maternal environment-dependent expression-QTLs of tomato seeds

Seeds are essential for plant reproduction, survival, and dispersal. Germination ability and successful establishment of young seedlings strongly depend on seed quality and on environmental factors such as nutrient availability. In tomato (Solanum lycopersicum) and many other species, seed quality and seedling establishment characteristics are determined by genetic variation, as well as the maternal environment in which the seeds develop and mature. The genetic contribution to variation in seed and seedling quality traits and environmental responsiveness can be estimated at transcriptome level in the dry seed by mapping genomic loci that affect gene expression (expression QTLs) in contrasting maternal environments. In this study, we applied RNA-sequencing to construct a linkage map and measure gene expression of seeds of a tomato recombinant inbred line (RIL) population derived from a cross between S. lycopersicum (cv. Moneymaker) and S. pimpinellifolium (G1.1554). The seeds matured on plants cultivated under different nutritional environments, i.e., on high phosphorus or low nitrogen. The obtained single-nucleotide polymorphisms (SNPs) were subsequently used to construct a genetic map. We show how the genetic landscape of plasticity in gene regulation in dry seeds is affected by the maternal nutrient environment. The combined information on natural genetic variation mediating (variation in) responsiveness to the environment may contribute to knowledge-based breeding programs aiming to develop crop cultivars that are resilient to stressful environments.

Escaping drought: The pectin methylesterase inhibitor gene Slpmei27 can significantly change drought resistance in tomato

Drought stress will lead to a decrease in tomato yield and poor flavour, yield and quality, resulting in economic losses in agricultural production. Mining the key genes regulating tomato drought resistance is of great significance to improve the drought resistance of tomato plants. The cell wall can directly participate in the plant drought stress response as one of the main components of the cell wall, and the regulation of pectin content in plant drought resistance is still unclear. Here, the candidate gene Solyc08g006690 (Slpmei27) was obtained by fine mapping based on genome sequencing technology (BSA-seq) of late-maturing stress-resistant tomato mutants found in the field. Slpmei27 is expressed in the cell wall. The transient silencing of Slpmei27 by VIGS significantly improved the drought resistance of tomato. Meanwhile, Slpmei27 silencing could significantly change the cell wall structure of plants, change the stomatal pass rate, reduce the water loss rate of plants, improve the scavenging ability of reactive oxygen species, change the redox balance in plants, and thus improve the drought resistance of tomato. The promoter region of this gene contains a large number of hormone-response and stress-response binding sites. The promoter region of the Slpmei27 gene in the mutant could lower the expression of downstream genes. Through this study, the mechanism by which Slpmei27 improves tomato drought resistance was revealed, and the relationship between pectin methyl ester metabolism and plant drought resistance was established, providing a theoretical basis for the production of high-quality tomato materials with high drought resistance.

Next generation sequencing technologies to explore the diversity of germplasm resources: achievements and trends in tomato

Tomato is one of the major vegetable crops grown worldwide and a model species for genetic and biological research. Progress in genomic technologies made possible the development of forefront methods for high-scale sequencing, providing comprehensive insight into the genetic architecture of germplasm resources. This review revisits next-generation sequencing strategies and applications to investigate the diversity of tomato, describing the common platforms used for SNP genotyping of large collections, de novo sequencing, and whole genome resequencing. Significant findings in evolutionary history are outlined, thus discussing how genomics has provided new hints about the processes behind domestication. Finally, achievement and perspectives on pan-genome construction and graphical pan-genome development toward precise mining of the natural variation to be exploited for breeding purposes are presented.

Biotechnological Advances to Improve Abiotic Stress Tolerance in Crops

The major challenges that agriculture is facing in the twenty-first century are increasing droughts, water scarcity, flooding, poorer soils, and extreme temperatures due to climate change. However, most crops are not tolerant to extreme climatic environments. The aim in the near future, in a world with hunger and an increasing population, is to breed and/or engineer crops to tolerate abiotic stress with a higher yield. Some crop varieties display a certain degree of tolerance, which has been exploited by plant breeders to develop varieties that thrive under stress conditions. Moreover, a long list of genes involved in abiotic stress tolerance have been identified and characterized by molecular techniques and overexpressed individually in plant transformation experiments. Nevertheless, stress tolerance phenotypes are polygenetic traits, which current genomic tools are dissecting to exploit their use by accelerating genetic introgression using molecular markers or site-directed mutagenesis such as CRISPR-Cas9. In this review, we describe plant mechanisms to sense and tolerate adverse climate conditions and examine and discuss classic and new molecular tools to select and improve abiotic stress tolerance in major crops.

Systematic Annotation Reveals CEP Function in Tomato Root Development and Abiotic Stress Response

Tomato (Solanum lycopersicum) is one of the most important vegetable crops worldwide; however, environmental stressors severely restrict tomato growth and yield. Therefore, it is of great interest to discover novel regulators to improve tomato growth and environmental stress adaptions. Here, we applied a comprehensive bioinformatics approach to identify putative tomato C-TERMINALLY ENCODED PEPTIDE (CEP) genes and to explore their potential physiological function in tomato root development and abiotic stress responses. A total of 17 tomato CEP genes were identified and grouped into two subgroups based on the similarity of CEP motifs. The public RNA-Seq data revealed that tomato CEP genes displayed a diverse expression pattern in tomato tissues. Additionally, CEP genes expression was differentially regulated by nitrate or ammonium status in roots and shoots, respectively. The differences in expression levels of CEP genes induced by nitrogen indicate a potential involvement of CEPs in tomato nitrogen acquisition. The synthetic CEP peptides promoted tomato primary root growth, which requires nitric oxide (NO) and calcium signaling. Furthermore, we also revealed that CEP peptides improved tomato root resistance to salinity. Overall, our work will contribute to provide novel genetic breeding strategies for tomato cultivation under adverse environments.

Recoloring tomato fruit by CRISPR/Cas9-mediated multiplex gene editing

Fruit color is an important horticultural trait, which greatly affects consumer preferences. In tomato, fruit color is determined by the accumulation of different pigments, such as carotenoids in the pericarp and flavonoids in the peel, along with the degradation of chlorophyll during fruit ripening. Since fruit color is a multigenic trait, it takes years to introgress all color-related genes in a single genetic background via traditional crossbreeding, and the avoidance of linkage drag during this process is difficult. Here, we proposed a rapid breeding strategy to generate tomato lines with different colored fruits from red-fruited materials by CRISPR/Cas9-mediated multiplex gene editing of three fruit color-related genes (PSY1, MYB12, and SGR1). Using this strategy, the red-fruited cultivar 'Ailsa Craig' has been engineered to a series of tomato genotypes with different fruit colors, including yellow, brown, pink, light-yellow, pink-brown, yellow-green, and light green. Compared with traditional crossbreeding, this strategy requires less time and can obtain transgene-free plants with different colored fruits in less than 1 year. Most importantly, it does not alter other important agronomic traits, like yield and fruit quality. Our strategy has great practical potential for tomato breeding and serves as a reference for improving multigene-controlled traits of horticultural crops.

Tomato salt tolerance mechanisms and their potential applications for fighting salinity: A review

One of the most significant environmental factors affecting plant growth, development and productivity is salt stress. The damage caused by salt to plants mainly includes ionic, osmotic and secondary stresses, while the plants adapt to salt stress through multiple biochemical and molecular pathways. Tomato (Solanum lycopersicum L.) is one of the most widely cultivated vegetable crops and a model dicot plant. It is moderately sensitive to salinity throughout the period of growth and development. Biotechnological efforts to improve tomato salt tolerance hinge on a synthesized understanding of the mechanisms underlying salinity tolerance. This review provides a comprehensive review of major advances on the mechanisms controlling salt tolerance of tomato in terms of sensing and signaling, adaptive responses, and epigenetic regulation. Additionally, we discussed the potential application of these mechanisms in improving salt tolerance of tomato, including genetic engineering, marker-assisted selection, and eco-sustainable approaches.

Coordinated transcriptional regulation of the carotenoid biosynthesis contributes to fruit lycopene content in high-lycopene tomato genotypes

Lycopene content in tomato fruit is largely under genetic control and varies greatly among genotypes. Continued improvement of lycopene content in elite varieties with conventional breeding has become challenging, in part because little is known about the underlying molecular mechanisms in high-lycopene tomatoes (HLYs). We collected 42 HLYs with different genetic backgrounds worldwide. High-performance liquid chromatography (HPLC) analysis revealed lycopene contents differed among the positive control wild tomato Solanum pimpinellifolium, HLYs, the normal lycopene cultivar "Moneymaker", and the non-lycopene cultivar NC 1Y at the pink and red ripe stages. Real-time RT-PCR analysis of expression of the 25 carotenoid biosynthesis pathway genes of each genotype showed a significantly higher expression in nine upstream genes (GGPPS1, GGPPS2, GGPPS3, TPT1, SSU II, PSY2, ZDS, CrtISO and CrtISO-L1 but not the well-studied PSY1, PDS and Z-ISO) at the breaker and/or red ripe stages in HLYs compared to Moneymaker, indicating a higher metabolic flux flow into carotenoid biosynthesis pathway in HLYs. Further conversion of lycopene to carotenes may be prevented via the two downstream genes (β-LCY2 and ε-LCY), which had low-abundance transcripts at either or both stages. Additionally, the significantly higher expression of four downstream genes (BCH1, ZEP, VDE, and CYP97C11) at either or both ripeness stages leads to significantly lower fruit lycopene content in HLYs than in the wild tomato. This is the first systematic investigation of the role of the complete pathway genes in regulating fruit lycopene biosynthesis across many HLYs, and enables tomato breeding and gene editing for increased fruit lycopene content.

Genome-wide association study of eigenvectors provides genetic insights into selective breeding for tomato metabolites

Background

Long-term domestication and intensive breeding of crop plants aim to establish traits desirable for human needs, and characteristics related to yield, disease resistance, and postharvest storage have traditionally received considerable attention. These processes have led also to negative consequences, as is the case of loss of variants controlling fruit quality, for instance in tomato. Tomato fruit quality is directly associated to metabolite content profiles; however, a full understanding of the genetics affecting metabolite content during tomato domestication and improvement has not been reached due to limitations of the single detection methods previously employed. Here, we aim to reach a broad understanding of changes in metabolite content using a genome-wide association study (GWAS) with eigenvector decomposition (EigenGWAS) on tomato accessions.

Results

An EigenGWAS was performed on 331 tomato accessions using the first eigenvector generated from the genomic data as a “phenotype” to understand the changes in fruit metabolite content during breeding. Two independent gene sets were identified that affected fruit metabolites during domestication and improvement in consumer-preferred tomatoes. Furthermore, 57 candidate genes related to polyphenol and polyamine biosynthesis were discovered, and a major candidate gene chlorogenate: glucarate caffeoyltransferase (SlCGT) was identified, which affected the quality and diseases resistance of tomato fruit, revealing the domestication mechanism of polyphenols.

Conclusions

We identified gene sets that contributed to consumer liking during domestication and improvement of tomato. Our study reports novel evidence of selective sweeps and key metabolites controlled by multiple genes, increasing our understanding of the mechanisms of metabolites variation during those processes. It also supports a polygenic selection model for the application of tomato breeding.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01327-x.

The tomato OST1-VOZ1 module regulates drought-mediated flowering

Flowering is a critical agricultural trait that substantially affects tomato fruit yield. Although drought stress influences flowering time, the molecular mechanism underlying drought-regulated flowering in tomato remains elusive. In this study, we demonstrated that loss of function of tomato OPEN STOMATA 1 (SlOST1), a protein kinase essential for abscisic acid (ABA) signaling and abiotic stress responses, lowers the tolerance of tomato plants to drought stress. slost1 mutants also exhibited a late flowering phenotype under both normal and drought stress conditions. We also established that SlOST1 directly interacts with and phosphorylates the NAC (NAM, ATAF and CUC)-type transcription factor VASCULAR PLANT ONE-ZINC FINGER 1 (SlVOZ1), at residue serine 67, thereby enhancing its stability and nuclear translocation in an ABA-dependent manner. Moreover, we uncovered several SlVOZ1 binding motifs from DNA affinity purification sequencing analyses and revealed that SlVOZ1 can directly bind to the promoter of the major flowering-integrator gene SINGLE FLOWER TRUSS to promote tomato flowering transition in response to drought. Collectively, our data uncover the essential role of the SlOST1-SlVOZ1 module in regulating flowering in response to drought stress in tomato and offer insights into a novel strategy to balance drought stress response and flowering.

CRISPR-based knock-out of eIF4E2 in a cherry tomato background successfully recapitulates resistance to pepper veinal mottle virus

The host susceptibility factors are important targets to develop genetic resistances in crops. Genome editing tools offer exciting prospects to develop resistances based on these susceptibility factors, directly in the cultivar of choice. Translation initiation factors 4E have long been known to be a susceptibility factor to the main genus of Potyviridae, potyviruses, but the inactivation of the eIF4E2 gene has only recently been shown to provide resistance to some isolates of pepper veinal mottle virus (PVMV) in big-fruit tomato plants. Here, using CRISPR-Cas9-NG, we show how eIF4E2 can be targeted and inactivated in cherry tomato plants. Three independent knockout alleles caused by indel in the first exon of eIF4E2, resulted in the complete absence of the eIF4E2 protein. All three lines displayed a narrow resistance spectrum to potyvirus, similar to the one described earlier for an eIF4E2 EMS mutant of M82, a big-fruit tomato cultivar; the plants were fully resistant to PVMV-Ca31, partially to PVMV-IC and were fully susceptible to two isolates of PVY assayed: N605 and LYE84. These results show how easily a resistance based on eIF4E2 can be transferred across tomato cultivar, but also confirm that gene redundancy can narrow the resistances based on eIF4E knockout.

Light-Intercepting Characteristics and Growth of Tomatoes Cultivated in a Greenhouse Using a Movable Bench System

The objective of this study was to investigate the growth and light-intercepting characteristics of tomatoes when movable benches are used in their cultivation. We cultivated tomatoes in a greenhouse (168 m2) during summer (9 July–9 September 2018) under different furrow distances (F1.0 = 1.0 m and F1.6 = 1.6 m) and movable benches (M indicates that the furrow distance = 0.4–0.8 m). Compared to the other treatments, when the movable bench was used to the change furrow distance depending on the plant growth stage (M treatment), the percentage of canopy light interception increased to ~90% at the early stage of plant growth (~20 days after transplanting). The percentage of canopy light interception for different treatments increased in the order of M > F1.0 > F1.6, and it increased towards the end of cultivation. In addition, the yield per unit area exhibited the same trend. Therefore, the solar radiation inside a greenhouse can be efficiently intercepted by plants when movable benches are used. This indicated that it was possible to increase plant yield per unit area using movable benches in plant cultivation.

DNA methylation in tomato fruit ripening

Fleshy fruit, the most economical and nutritional value unique to flowering plants, is an important part of our daily diet. Previous studies have shown that fruit ripening is regulated by transcription factors and the plant hormone ethylene, but recent research has also shown that epigenetics also plays an essential role, especially DNA methylation. DNA methylation is the process of transferring -CH3 to the fifth carbon of cytosine residues under the action of methyltransferase to form 5-methylcytosine (5-mC). So far, most works have been focused on tomato. Tomato ripening is dynamically regulated by DNA methylation and demethylation, but the understanding of this mechanism is still in its infancy. The dysfunction of a DNA demethylase, DEMETER-like DNA demethylases 2 (DML2), prevents the ripening of tomato fruits, but immature fruits ripen prematurely under the action of DNA methylation inhibitors. Additionally, studies have shown that the relationship between fruit quality and DNA methylation is not linear, but the specific molecular mechanism is still unclear. Here, we review the recent advances in the role of DNA methylation in tomato fruit ripening, the interaction of ripening transcription factors and DNA methylation, and its effects on quality. Then, a number of questions for future research of DNA methylation regulation in tomato fruit ripening is proposed.

Unraveling Cuticle Formation, Structure, and Properties by Using Tomato Genetic Diversity

The tomato (Solanum lycopersicum) fruit has a thick, astomatous cuticle that has become a model for the study of cuticle formation, structure, and properties in plants. Tomato is also a major horticultural crop and a long-standing model for research in genetics, fruit development, and disease resistance. As a result, a wealth of genetic resources and genomic tools have been established, including collections of natural and artificially induced genetic diversity, introgression lines of genome fragments from wild relatives, high-quality genome sequences, phenotype and gene expression databases, and efficient methods for genetic transformation and editing of target genes. This mini-review reports the considerable progresses made in recent years in our understanding of cuticle by using and generating genetic diversity for cuticle-associated traits in tomato. These include the synthesis of the main cuticle components (cutin and waxes), their role in the structure and properties of the cuticle, their interaction with other cell wall polymers as well as the regulation of cuticle formation. It also addresses the opportunities offered by the untapped germplasm diversity available in tomato and the current strategies available to exploit them.

Genome-Wide Identification and Evolutionary Analysis of the SRO Gene Family in Tomato

SRO (SIMILAR TO RCD ONE) is a family of plant-specific small molecule proteins that play an important role in plant growth and development and environmental responses. However, SROs still lack systematic characterization in tomato. Based on bioinformatics methods, SRO family genes were identified and characterized from cultivated tomatoes and several wild tomatoes. qRT-PCR was used to study the expression of SRO gene in cultivated tomatoes. Phylogenetic and evolutionary analyses showed that SRO genes in angiosperms share a common ancestor and that the number of SRO family members changed as plants diverged and evolved. Cultivated tomato had six SRO members, five of which still shared some degree of identity with the ancestral SRO genes. Genetic structure and physicochemical properties showed that tomato SRO genes were highly conserved with chromosomal distribution. They could be divided into three groups based on exon-intron structure, and cultivated tomato contained only two of these subclades. A number of hormonal, light and abiotic stress-responsive cis-regulatory elements were identified from the promoter of the tomato SRO gene, and they also interacted with a variety of stress-responsive proteins and microRNAs. RNA-seq analysis showed that SRO genes were widely expressed in different tissues and developmental stages of tomato, with significant tissue-specific features. Expression analysis also showed that SRO genes respond significantly to high temperature and salt stress and mediate the tomato hormone regulatory network. These results provide a theoretical basis for further investigation of the functional expression of tomato SRO genes and provide potential genetic resources for tomato resistance breeding.

Multiplex Genome-Editing Technologies for Revolutionizing Plant Biology and Crop Improvement

Multiplex genome-editing (MGE) technologies are recently developed versatile bioengineering tools for modifying two or more specific DNA loci in a genome with high precision. These genome-editing tools have greatly increased the feasibility of introducing desired changes at multiple nucleotide levels into a target genome. In particular, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) [CRISPR/Cas] system-based MGE tools allow the simultaneous generation of direct mutations precisely at multiple loci in a gene or multiple genes. MGE is enhancing the field of plant molecular biology and providing capabilities for revolutionizing modern crop-breeding methods as it was virtually impossible to edit genomes so precisely at the single base-pair level with prior genome-editing tools, such as zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). Recently, researchers have not only started using MGE tools to advance genome-editing applications in certain plant science fields but also have attempted to decipher and answer basic questions related to plant biology. In this review, we discuss the current progress that has been made toward the development and utilization of MGE tools with an emphasis on the improvements in plant biology after the discovery of CRISPR/Cas9. Furthermore, the most recent advancements involving CRISPR/Cas applications for editing multiple loci or genes are described. Finally, insights into the strengths and importance of MGE technology in advancing crop-improvement programs are presented.

Complex cellular and molecular events determining fruit size

The understanding of plant organ-size determination represents an important challenge, especially because of the significant role of plants as food and renewable energy sources and the increasing need for plant-derived products. Most of the knowledge on the regulation of organ growth and the molecular network controlling cell division and cell expansion, the main drivers of growth, is derived from arabidopsis. The increasing use of crops such as tomato for research is now bringing essential information on the mechanisms underlying size control in agronomically important organs. This review describes our current knowledge, still very scarce, of the cellular and molecular mechanisms governing tomato fruit size and proposes future research to better understand the regulation of growth in this important crop.

Scientometric and Methodological Analysis of the Recent Literature on the Health-Related Effects of Tomato and Tomato Products

The health benefits of tomato, a vegetable consumed daily in human diets, have received great attention in the scientific community, and a great deal of experiments have tested their utility against several diseases. Herein, we present a scientometric analysis of recent works aimed to estimate the biological effects of tomato, focusing on bibliographic metadata, type of testers, target systems, and methods of analysis. A remarkably variable array of strategies was reported, including testers obtained by standard and special tomatoes, and the use of in vitro and in vivo targets, both healthy and diseased. In vitro, 21 normal and 36 cancer human cell lines derived from 13 different organs were used. The highest cytotoxic effects were reported on cancer blood cells. In vivo, more experiments were carried out with murine than with human systems, addressing healthy individuals, as well as stressed and diseased patients. Multivariate analysis showed that publications in journals indexed in the agriculture category were associated with the use of fresh tomatoes; conversely, medicine and pharmacology journals were associated with the use of purified and formulate testers. Studies conducted in the United States of America preferentially adopted in vivo systems and formulates, combined with blood and tissue analysis. Researchers in Italy, China, India, and Great Britain mostly carried out in vitro research using fresh tomatoes. Gene expression and proteomic analyses were associated with China and India. The emerging scenario evidences the somewhat dichotomic approaches of plant geneticists and agronomists and that of cell biologists and medicine researchers. A higher integration between these two scientific communities would be desirable to foster the assessment of the benefits of tomatoes to human health.

Genetic diversity of tomato response to heat stress at the QTL and transcriptome levels

Tomato is a widely cultivated crop, which can grow in many environments. However, temperature above 30°C impairs its reproduction, subsequently impacting fruit yield. We assessed the impact of high-temperature stress (HS) in two tomato experimental populations, a multi-parental advanced generation intercross (MAGIC) population and a core-collection (CC) of small-fruited tomato accessions. Both populations were evaluated for 11 traits related to yield components, phenology and fruit quality in optimal and HS conditions. HS significantly impacted all traits in both populations, but a few genotypes with stable yield under HS were identified. A plasticity index was computed for each individual to measure the extent of the heat impact for each trait. Quantitative trait loci (QTL) were detected in control and HS conditions as well as for plasticity index. Linkage and genome-wide association analyses in the MAGIC and CC populations identified a total of 98 and 166 QTLs, respectively. Taking the two populations together, 69 plasticity QTLs (pQTLs) were involved in tomato heat response for 11 traits. The transcriptome changes in the ovary of six genotypes with contrasted responses to HS were studied, and 837 genes differentially expressed according to the conditions were detected. Combined with previous transcriptome studies, these results were used to propose candidate genes for HS response QTLs.

A consensus and saturated genetic map provides insight into genome anchoring, synteny of Solanaceae and leaf- and fruit-related QTLs in wolfberry (Lycium Linn.)

BACKGROUND

Lycium Linn. (Solanaceae) is a genus of economically important plants producing fruits and leaves with high nutritional value and medicinal benefits. However, genetic analysis of this plant and molecular breeding for quality improvement are limited by the lack of sufficient molecular markers.

RESULTS

In this study, two parental strains, 'Ningqi No. 1' (Lycium barbarum L.) and 'Yunnan Gouqi' (Lycium yunnanense Kuang et A.M. Lu), and 200 F₁ hybrid individuals were resequenced for genetic analysis. In total, 8,507 well-selected SNPs were developed, and a high-density genetic map (NY map) was constructed with a total genetic distance of 2,122.24 cM. A consensus genetic map was established by integrating the NY map and a previously published genetic map (NC map) containing 15,240 SNPs, with a total genetic distance of 3,058.19 cM and an average map distance of 0.21 cM. The 12 pseudochromosomes of the Lycium reference genome were anchored using this consensus genetic map, with an anchoring rate of 64.3%. Moreover, weak collinearities between the consensus map and the pepper, potato, and tomato genomes were observed. Twenty-five stable QTLs were identified for leaf- and fruit-related phenotypes, including fruit weight, fruit longitude, leaf length, the fruit index, and the leaf index; these stable QTLs were mapped to four different linkage groups, with LOD scores ranging from 2.51 to 19.37 and amounts of phenotypic variance explained from 6.2% to 51.9%. Finally, 82 out of 188 predicted genes underlying stable QTLs for fruit-related traits were differentially expressed according to RNA-seq analysis.

CONCLUSIONS

A chromosome-level assembly can provide a foundation for further functional genomics research for wolfberry. The genomic regions of these stably expressed QTLs could be used as targets for further fine mapping and development of molecular markers for marker-assisted selection (MAS). The present study provided valuable information on saturated SNP markers and reliable QTLs for map-based cloning of functional genes related to yield and morphological traits in Lycium spp.

High-Throughput Chlorophyll and Carotenoid Profiling Reveals Positive Associations with Sugar and Apocarotenoid Volatile Content in Fruits of Tomato Varieties in Modern and Wild Accessions

Flavor and nutritional quality has been negatively impacted during the course of domestication and improvement of the cultivated tomato (Solanum lycopersicum). Recent emphasis on consumers has emphasized breeding strategies that focus on flavor-associated chemicals, including sugars, acids, and aroma compounds. Carotenoids indirectly affect flavor as precursors of aroma compounds, while chlorophylls contribute to sugar production through photosynthesis. However, the relationships between these pigments and flavor content are still unclear. In this study, we developed a simple and high-throughput method to quantify chlorophylls and carotenoids. This method was applied to over one hundred tomato varieties, including S. lycopersicum and its wild relatives (S. l. var. cerasiforme and S. pimpinellifolium), for quantification of these pigments in fruits. The results obtained by integrating data of the pigments, soluble solids, sugars, and aroma compounds indicate that (i) chlorophyll-abundant varieties have relatively higher sugar accumulations and (ii) prolycopene is associated with an abundance of linear carotenoid-derived aroma compounds in one of the orange-fruited varieties, "Dixie Golden Giant". Our results suggest the importance of these pigments not only as components of fruit color but also as factors influencing flavor traits, such as sugars and aroma.

An auxin-mediated regulatory framework for wound-induced adventitious root formation in tomato shoot explants

Adventitious roots (ARs) are produced from non-root tissues in response to different environmental signals, such as abiotic stresses, or after wounding, in a complex developmental process that requires hormonal crosstalk. Here, we characterized AR formation in young seedlings of Solanum lycopersicum cv. 'Micro-Tom' after whole root excision by means of physiological, genetic and molecular approaches. We found that a regulated basipetal auxin transport from the shoot and local auxin biosynthesis triggered by wounding are both required for the re-establishment of internal auxin gradients within the vasculature. This promotes cell proliferation at the distal cambium near the wound in well-defined positions of the basal hypocotyl and during a narrow developmental window. In addition, a pre-established pattern of differential auxin responses along the apical-basal axis of the hypocotyl and an as of yet unknown cell-autonomous inhibitory pathway contribute to the temporal and spatial patterning of the newly formed ARs on isolated hypocotyl explants. Our work provides an experimental outline for the dissection of wound-induced AR formation in tomato, a species that is suitable for molecular identification of gene regulatory networks via forward and reverse genetics approaches.

Mapping of Quantitative Trait Loci (QTL) Associated with Plant Freezing Tolerance and Cold Acclimation

Most agronomic traits are determined by quantitative trait loci (QTL) and exhibit continuous distribution in natural or especially built segregating populations. The genetic architecture and the hereditary characteristics of these traits are much more complicated than those of oligogenic traits and need adapted strategies for deciphering. The model plant Arabidopsis thaliana is widely studied for quantitative traits, especially via the utilization of genetic natural diversity. Here we describe a QTL-mapping protocol for analyzing freezing tolerance after cold acclimation in this species, based on its specific genetic tools. Nevertheless, this approach can be applied for the elucidation of complex traits in others species.

Differential expression of SlKLUH controlling fruit and seed weight is associated with changes in lipid metabolism and photosynthesis-related genes

The sizes of plant organs such as fruit and seed are crucial yield components. Tomato KLUH underlies the locus fw3.2, an important regulator of fruit and seed weight. However, the mechanism by which the expression levels of KLUH affect organ size is poorly understood. We found that higher expression of SlKLUH increased cell proliferation in the pericarp within 5 d post-anthesis in tomato near-isogenic lines. Differential gene expression analyses showed that lower expression of SlKLUH was associated with increased expression of genes involved in lipid metabolism. Lipidomic analysis revealed that repression of SlKLUH mainly increased the contents of certain non-phosphorus glycerolipids and phospholipids and decreased the contents of four unknown lipids. Co-expression network analyses revealed that lipid metabolism was possibly associated with but not directly controlled by SlKLUH, and that this gene instead controls photosynthesis-related processes. In addition, many transcription factors putatively involved in the KLUH pathway were identified. Collectively, we show that SlKLUH regulates fruit and seed weight which is associated with altered lipid metabolism. The results expand our understanding of fruit and seed weight regulation and offer a valuable resource for functional studies of candidate genes putatively involved in regulation of organ size in tomato and other crops.

Integrating multi-omics data for crop improvement

Our agricultural systems are now in urgent need to secure food for a growing world population. To meet this challenge, we need a better characterization of plant genetic and phenotypic diversity. The combination of genomics, transcriptomics and metabolomics enables a deeper understanding of the mechanisms underlying the complex architecture of many phenotypic traits of agricultural relevance. We review the recent advances in plant genomics to see how these can be integrated with broad molecular profiling approaches to improve our understanding of plant phenotypic variation and inform crop breeding strategies.

Enhancement of Tobacco (Nicotiana tabacum L.) Seed Lipid Content for Biodiesel Production by CRISPR-Cas9-Mediated Knockout of NtAn1

Tobacco (Nicotiana tabacum L.) seed lipid is a promising non-edible feedstock for biodiesel production. In order to meet the increasing demand, achieving high seed lipid content is one of the major goals in tobacco seed production. The TT8 gene and its homologs negatively regulate seed lipid accumulation in Arabidopsis and Brassica species. We speculated that manipulating the homolog genes of TT8 in tobacco could enhance the accumulation of seed lipid. In this present study, we found that the TT8 homolog genes in tobacco, NtAn1a and NtAn1b, were highly expressed in developing seed. Targeted mutagenesis of NtAn1 genes was created by the CRISPR-Cas9-based gene editing technology. Due to the defect of proanthocyanidin (PA) biosynthesis, mutant seeds showed the phenotype of a yellow seed coat. Seed lipid accumulation was enhanced by about 18 and 15% in two targeted mutant lines. Protein content was also significantly increased in mutant seeds. In addition, the seed yield-related traits were not affected by the targeted mutagenesis of NtAn1 genes. Thus, the overall lipid productivity of the NtAn1 knockout mutants was dramatically enhanced. The results in this present paper indicated that tobacco NtAn1 genes regulate both PAs and lipid accumulation in the process of seed development and that targeted mutagenesis of NtAn1 genes could generate a yellow-seeded tobacco variety with high lipid and protein content. Furthermore, the present results revealed that the CRISPR-Cas9 system could be employed in tobacco seed de novo domestication for biodiesel feedstock production.

Application of Genome Editing in Tomato Breeding: Mechanisms, Advances, and Prospects

Plants regularly face the changing climatic conditions that cause biotic and abiotic stress responses. The abiotic stresses are the primary constraints affecting crop yield and nutritional quality in many crop plants. The advances in genome sequencing and high-throughput approaches have enabled the researchers to use genome editing tools for the functional characterization of many genes useful for crop improvement. The present review focuses on the genome editing tools for improving many traits such as disease resistance, abiotic stress tolerance, yield, quality, and nutritional aspects of tomato. Many candidate genes conferring tolerance to abiotic stresses such as heat, cold, drought, and salinity stress have been successfully manipulated by gene modification and editing techniques such as RNA interference, insertional mutagenesis, and clustered regularly interspaced short palindromic repeat (CRISPR/Cas9). In this regard, the genome editing tools such as CRISPR/Cas9, which is a fast and efficient technology that can be exploited to explore the genetic resources for the improvement of tomato and other crop plants in terms of stress tolerance and nutritional quality. The review presents examples of gene editing responsible for conferring both biotic and abiotic stresses in tomato simultaneously. The literature on using this powerful technology to improve fruit quality, yield, and nutritional aspects in tomato is highlighted. Finally, the prospects and challenges of genome editing, public and political acceptance in tomato are discussed.

A quick protocol for the identification and characterization of early growth mutants in tomato

Root system architecture (RSA) manipulation may improve water and nutrient capture by plants under normal and extreme climate conditions. With the aim of initiating the genetic dissection of RSA in tomato, we established a defined ontology that allowed the curated annotation of the observed phenotypes on 12 traits at four consecutive growth stages. In addition, we established a quick approach for the molecular identification of the mutations associated with the trait-of-interest by using a whole-genome sequencing approach that does not require the building of an additional mapping population. As a proof-of-concept, we screened 4543 seedlings from 300 tomato M₃ lines (Solanum lycopersicum L. cv. Micro-Tom) generated by chemical mutagenesis with ethyl methanesulfonate. We studied the growth and early development of both the root system (primary and lateral roots) and the aerial part of the seedlings as well as the wound-induced adventitious roots emerging from the hypocotyl. We identified 659 individuals (belonging to 203 M₃ lines) whose early seedling and RSA phenotypes differed from those of their reference background. We confirmed the genetic segregation of the mutant phenotypes affecting primary root length, seedling viability and early RSA in 31 M₄ families derived from 15 M₃ lines selected in our screen. Finally, we identified a missense mutation in the SlCESA3 gene causing a seedling-lethal phenotype with short roots. Our results validated the experimental approach used for the identification of tomato mutants during early growth, which will allow the molecular identification of the genes involved.

Enhanced resistance to fungal and bacterial diseases in tomato and Arabidopsis expressing BSR2 from rice

The overexpression of rice BSR2 would offer a simple and effective strategy to protect plants from multiple devastating diseases in tomato and Arabidopsis. Many devastating plant diseases are caused by pathogens possessing a wide host range. Fungal Botrytis cinerea and Rhizoctonia solani, as well as bacterial Pseudomonas syringae and Ralstonia pseudosolanacearum are four such pathogens that infect hundreds of plant species, including agronomically important crops, and cause serious diseases, leading to severe economic losses. However, reports of genes that can confer resistance to broad host-range pathogens via traditional breeding methods are currently limited. We previously reported that Arabidopsis plants overexpressing rice BROAD-SPECTRUM RESISTANCE2 (BSR2/CYP78A15) showed tolerance not only to bacterial P. syringae pv. tomato DC3000 but also to fungal Colletotrichum higginsianum and R. solani. Rice plants overexpressing BSR2 displayed tolerance to two R. solani anastomosis groups. In the present study, first, BSR2-overexpressing (OX) Arabidopsis plants were shown to be additionally tolerant to B. cinerea, R. solani, and R. pseudosolanacearum. Next, tomato 'Micro-Tom' was used as a model to determine whether such tolerance by BSR2 can be introduced into dicot crops to prevent infection from pathogens possessing wide host range. BSR2-OX tomato displayed broad-spectrum disease tolerance to fungal B. cinerea and R. solani, as well as to bacterial P. syringae and R. pseudosolanacearum. Additionally, undesirable traits such as morphological changes were not detected. Thus, BSR2 overexpression can offer a simple and effective strategy to protect crops from multiple destructive diseases.

Utilization of straw-based phenolic acids as a biofugicide for a green agricultural production

Phenolic compounds inhibit phytopathogenic fungal infections effectively. In this study, the antifungal effects of rice straw-derived phenolic acids (PAs) against Fusarium oxysporum were investigated. PAs can inhibit hyphal growth and spore germination, and p-coumaric acid (CA) is the main antifungal substance in PAs. PAs could induce the formation of hydrogen peroxide and increase the relative conductivity and extracellular K⁺ concentration. Observations using Scanning Electron Microscopy, Laser Scanning Confocal Microscopy and Transmission Electron Microscopy revealed that PAs could damage membrane permeability, which caused cytoplasm leakage. This phenomenon was verified by conductivity and the release of extracellular K⁺. The chlorophyll fluorescence maps of tomato leaves suggested that F. oxysporum damaged the tomato' photosynthetic system and that PAs reduced the area infected, thereby alleviating the damage. Moreover, PAs could decrease the disease incidence of tomato fruit. The results confirmed the feasibility of using PAs as a biofungicide and provide a way to increase the value of rice straw.