Functional genomics of tomato: opportunities and challenges in post-genome NGS era

Next-Generation Sequencing of Local Romanian Tomato Varieties and Bioinformatics Analysis of the Ve Locus

Genetic variability is extremely important, not only for the species’ adaptation to environmental challenges, but also for the creation of novel varieties through plant breeding. Tomato is an important vegetable crop, as well as a model species in numerous genomic studies. Its genome was fully sequenced in 2012 for the ‘Heinz 1706’ variety, and since then, resequencing efforts have revealed genetic variability data that can be used for multiple purposes, including triggering mechanisms of biotic and abiotic stress resistance. The present study focused on the analysis of the genome variation for eight Romanian local tomato varieties using next-generation sequencing technique, and as a case study, the sequence analysis of the Ve1 and Ve2 loci, to determine which genotypes might be good candidates for future breeding of tomato varieties resistant to Verticillium species. The analysis of the Ve locus identified several genotypes that could be donors of the Ve1 gene conferring resistance to Verticillium race 1. Sequencing for the first time Romanian genotypes enriched the existing data on various world tomato genetic resources, but also opened the way for the molecular breeding in Romania. Plant breeders can use these data to create novel tomato varieties adapted to the ever-changing environment.

All-flesh fruit in tomato is controlled by reduced expression dosage of AFF through a structural variant mutation in the promoter

The formation of locule gel is an important process in tomato and is a typical characteristic of berry fruit. In this study, we examined a natural tomato mutant that produces all-flesh fruit (AFF) in which the locule tissue remains in a solid state during fruit development. We constructed different genetic populations to fine-map the causal gene for this trait and identified SlMBP3 as the locus conferring the locule gel formation, which we rename as AFF. We determined the causal mutation as a 416-bp deletion in the promoter region of AFF, which reduces its expression dosage. Generally, this sequence is highly conserved among Solanaceae, as well as within the tomato germplasm. Using BC6 near-isogenic lines, we determined that the reduced expression dosage of AFF did not affect the normal development of seeds, whilst producing unique, non-liquefied locule tissue that was distinct from that of normal tomatoes in terms of metabolic components. Combined analysis using mRNA-seq and metabolomics indicated the importance of AFF in locule tissue liquefaction. Our findings provide insights into fruit-type differentiation in Solanaceae crops and also present the basis for future applications of AFF in tomato breeding programs.

Omics applications: towards a sustainable protection of tomato

Transcriptome data and gene expression analysis have a huge potential in the study of multiple relationships involving plants, pathogens, and pests, including the interactions with beneficial microorganisms such as endophytes or other functional groups. Next-generation sequencing (NGS) and other recent long-read-based sequencing approaches (i.e., nanopore and others) provide unprecedented tools allowing the fast identification of plant information processing systems, in situ and in real time, fundamental for crop management and pest regulation. Other -omics approaches such as metagenomics and metatranscriptomics allow high-resolution insights on the rhizosphere ecology. They may highlight key factors affecting belowground biodiversity or processes, modulating the expression of stress-responsive pathways. The application of miRNAs and other small RNAs is a relatively new field of application, with enormous potential for the selective activation of defense pathways. However, limitations concerning the stability of the RNA molecules and their effective delivery must be overcome.

Advances in Omics Approaches for Abiotic Stress Tolerance in Tomato

Tomato, one of the most important crops worldwide, has a high demand in the fresh fruit market and processed food industries. Despite having considerably high productivity, continuous supply as per the market demand is hard to achieve, mostly because of periodic losses occurring due to biotic as well as abiotic stresses. Although tomato is a temperate crop, it is grown in almost all the climatic zones because of widespread demand, which makes it challenge to adapt in diverse conditions. Development of tomato cultivars with enhanced abiotic stress tolerance is one of the most sustainable approaches for its successful production. In this regard, efforts are being made to understand the stress tolerance mechanism, gene discovery, and interaction of genetic and environmental factors. Several omics approaches, tools, and resources have already been developed for tomato growing. Modern sequencing technologies have greatly accelerated genomics and transcriptomics studies in tomato. These advancements facilitate Quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection (GS). However, limited efforts have been made in other omics branches like proteomics, metabolomics, and ionomics. Extensive cataloging of omics resources made here has highlighted the need for integration of omics approaches for efficient utilization of resources and a better understanding of the molecular mechanism. The information provided here will be helpful to understand the plant responses and the genetic regulatory networks involved in abiotic stress tolerance and efficient utilization of omics resources for tomato crop improvement.

The expanding roles of APETALA2/Ethylene Responsive Factors and their potential applications in crop improvement

Understanding the molecular basis of the gene-regulatory networks underlying agronomic traits or plant responses to abiotic/biotic stresses is very important for crop improvement. In this context, transcription factors, which either singularly or in conjugation directly control the expression of many target genes, are suitable candidates for improving agronomic traits via genetic engineering. In this regard, members of one of the largest class of plant-specific APETALA2/Ethylene Response Factor (AP2/ERF) superfamily, which is implicated in various aspects of development and plant stress adaptation responses, are considered high-value targets for crop improvement. Besides their long-known regulatory roles in mediating plant responses to abiotic stresses such as drought and submergence, the novel roles of AP2/ERFs during fruit ripening or secondary metabolites production have also recently emerged. The astounding functional plasticity of AP2/ERF members is considered to be achieved by their interplay with other regulatory networks and signalling pathways. In this review, we have integrated the recently accumulated evidence from functional genomics studies and described their newly emerged functions in plants. The key structural features of AP2/ERF proteins and the modes of their action are briefly summarized. The importance of AP2/ERFs in plant development and stress responses and a summary of the event of their successful applications in crop improvement programs are also provided. Altogether, we envisage that the synthesized information presented in this review will be useful to design effective strategies for improving agronomic traits in crop plants.

Identification of Stress Associated microRNAs in Solanum lycopersicum by High-Throughput Sequencing

Tomato (Solanum lycopersicum) is one of the most important crops around the world and also a model plant to study response to stress. High-throughput sequencing was used to analyse the microRNA (miRNA) profile of tomato plants undergoing five biotic and abiotic stress conditions (drought, heat, P. syringae infection, B. cinerea infection, and herbivore insect attack with Leptinotarsa decemlineata larvae) and one chemical treatment with a plant defence inducer, hexanoic acid. We identified 104 conserved miRNAs belonging to 37 families and we predicted 61 novel tomato miRNAs. Among those 165 miRNAs, 41 were stress-responsive. Reverse transcription quantitative PCR (RT-qPCR) was used to validate high-throughput expression analysis data, confirming the expression profiles of 10 out of 11 randomly selected miRNAs. Most of the differentially expressed miRNAs were stress-specific, except for sly-miR167c-3p upregulated in B. cinerea and P. syringae infection, sly-newmiR26-3p upregulated in drought and Hx treatment samples, and sly-newmiR33-3p, sly-newmiR6-3p and sly-newmiR8-3p differentially expressed both in biotic and abiotic stresses. From mature miRNAs sequences of the 41 stress-responsive miRNAs 279 targets were predicted. An inverse correlation between the expression profiles of 4 selected miRNAs (sly-miR171a, sly-miR172c, sly-newmiR22-3p and sly-miR167c-3p) and their target genes (Kinesin, PPR, GRAS40, ABC transporter, GDP and RLP1) was confirmed by RT-qPCR. Altogether, our analysis of miRNAs in different biotic and abiotic stress conditions highlight the interest to understand the functional role of miRNAs in tomato stress response as well as their putative targets which could help to elucidate plants molecular and physiological adaptation to stress.

Application of CRISPR/Cas9-Mediated Gene Editing in Tomato

CRISPR-/Cas9-mediated gene editing has been demonstrated in a number of food crops including tomato. Tomato (Solanum lycopersicum) is both an important food crop and a model plant species that has been used extensively for studying gene function, especially as it relates to fruit biology. This duality in purpose combined with readily available resources (mutant populations, genome sequences, transformation methodology) makes tomato an ideal candidate for gene editing. The CRISPR/Cas9 system routinely used in our laboratory has been applied to various tomato genotypes and the wild species, Solanum pimpinellifolium. The vector system is based on Golden Gate cloning techniques. Cassettes that contain the neomycin phosphotransferase II (NPTII) selectable marker gene that confers resistance to kanamycin, a human codon-optimized Cas9 driven by the CaMV 35S promoter, and guide RNA (gRNA) under control of the Arabidopsis U6 polymerase promoter are assembled into a T-DNA vector. Generally, we design CRISPR/Cas9 constructs that contain two gRNAs per gene target. However, we have been successful with inclusion of up to eight gRNAs to simultaneously target multiple genes and regions. Introduction of CRISPR-/Cas9-designed constructs into tomato is accomplished by transformation methodology based on Agrobacterium tumefaciens infection of young cotyledon sections and selection on kanamycin-containing medium based on the presence of the NPTII gene. The approaches for the development of CRISPR/Cas9 constructs and genotypic analyses (PCR-based amplicon sequencing and T7 endonuclease) are detailed in this chapter.

Expanding Alternative Splicing Identification by Integrating Multiple Sources of Transcription Data in Tomato

Tomato (Solanum lycopersicum) is an important vegetable and fruit crop. Its genome was completely sequenced and there are also a large amount of available expressed sequence tags (ESTs) and short reads generated by RNA sequencing (RNA-seq) technologies. Mapping transcripts including mRNA sequences, ESTs, and RNA-seq reads to the genome allows identifying pre-mRNA alternative splicing (AS), a post-transcriptional process generating two or more RNA isoforms from one pre-mRNA transcript. We comprehensively analyzed the AS landscape in tomato by integrating genome mapping information of all available mRNA and ESTs with mapping information of RNA-seq reads which were collected from 27 published projects. A total of 369,911 AS events were identified from 34,419 genomic loci involving 161,913 transcripts. Within the basic AS events, intron retention is the prevalent type (18.9%), followed by alternative acceptor site (12.9%) and alternative donor site (7.3%), with exon skipping as the least type (6.0%). Complex AS types having two or more basic event accounted for 54.9% of total AS events. Within 35,768 annotated protein-coding gene models, 23,233 gene models were found having pre-mRNAs generating AS isoform transcripts. Thus the estimated AS rate was 65.0% in tomato. The list of identified AS genes with their corresponding transcript isoforms serves as a catalog for further detailed examination of gene functions in tomato biology. The post-transcriptional information is also expected to be useful in improving the predicted gene models in tomato. The sequence and annotation information can be accessed at plant alternative splicing database (http://proteomics.ysu.edu/altsplice).

SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases

Database URL

https://solgenomics.net/tools/solcyc/.

Use of Natural Diversity and Biotechnology to Increase the Quality and Nutritional Content of Tomato and Grape

Improving fruit quality has become a major goal in plant breeding. Direct approaches to tackling fruit quality traits specifically linked to consumer preferences and environmental friendliness, such as improved flavor, nutraceutical compounds, and sustainability, have slowly been added to a breeder priority list that already includes traits like productivity, efficiency, and, especially, pest and disease control. Breeders already use molecular genetic tools to improve fruit quality although most advances have been made in producer and industrial quality standards. Furthermore, progress has largely been limited to simple agronomic traits easy-to-observe, whereas the vast majority of quality attributes, specifically those relating to flavor and nutrition, are complex and have mostly been neglected. Fortunately, wild germplasm, which is used for resistance against/tolerance of environmental stresses (including pathogens), is still available and harbors significant genetic variation for taste and health-promoting traits. Similarly, heirloom/traditional varieties could be used to identify which genes contribute to flavor and health quality and, at the same time, serve as a good source of the best alleles for organoleptic quality improvement. Grape (Vitis vinifera L.) and tomato (Solanum lycopersicum L.) produce fleshy, berry-type fruits, among the most consumed in the world. Both have undergone important domestication and selection processes, that have dramatically reduced their genetic variability, and strongly standardized fruit traits. Moreover, more and more consumers are asking for sustainable production, incompatible with the wide range of chemical inputs. In the present paper, we review the genetic resources available to tomato/grape breeders, and the recent technological progresses that facilitate the identification of genes/alleles of interest within the natural or generated variability gene pool. These technologies include omics, high-throughput phenotyping/phenomics, and biotech approaches. Our review also covers a range of technologies used to transfer to tomato and grape those alleles considered of interest for fruit quality. These include traditional breeding, TILLING (Targeting Induced Local Lesions in Genomes), genetic engineering, or NPBT (New Plant Breeding Technologies). Altogether, the combined exploitation of genetic variability and innovative biotechnological tools may facilitate breeders to improve fruit quality tacking more into account the consumer standards and the needs to move forward into more sustainable farming practices.

In Silico identification and annotation of non-coding RNAs by RNA-seq and De Novo assembly of the transcriptome of Tomato Fruits

The complexity of the tomato (Solanum lycopersicum) transcriptome has not yet been fully elucidated. To gain insights into the diversity and features of coding and non-coding RNA molecules of tomato fruits, we generated strand-specific libraries from berries of two tomato cultivars grown in two open-field conditions with different soil type. Following high-throughput Illumina RNA-sequencing (RNA-seq), more than 90% of the reads (over one billion, derived from twelve dataset) were aligned to the tomato reference genome. We report a comprehensive analysis of the transcriptome, improved with 39,095 transcripts, which reveals previously unannotated novel transcripts, natural antisense transcripts, long non-coding RNAs and alternative splicing variants. In addition, we investigated the sequence variants between the cultivars under investigation to highlight their genetic difference. Our strand-specific analysis allowed us to expand the current tomato transcriptome annotation and it is the first to reveal the complexity of the poly-adenylated RNA world in tomato. Moreover, our work demonstrates the usefulness of strand specific RNA-seq approach for the transcriptome-based genome annotation and provides a resource valuable for further functional studies.

Functional genomics of tomato for the study of plant immunity

Tomato (Solanum lycopersicum), along with many other economically valuable species, belongs to the Solanaceae family. Understanding how plants in this family defend themselves against pathogens offers the opportunity of improving yield and quality of their edible products. The use of functional genomics has contributed to this purpose through both traditional and recently developed techniques that allow determination of changes in transcript abundance during pathogen attack. Such changes can implicate the affected gene as participating in plant defense. Testing the involvement of these candidate genes in defense has relied largely on posttranscriptional gene silencing, particularly virus-induced gene silencing. We discuss how functional genomics has played a key role in our current understanding of the defense response in tomato and related species and what are the challenges and opportunities for the future.