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Advances in Tomato Breeding and Molecular Research

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 20 February 2025 | Viewed by 8308

Special Issue Editors

Dr. Silvana Grandillo

E-Mail Website
Guest Editor
CNR (National Research Council of Italy) Institute of Biosciences and BioResources (IBBR), Research Division of Portici, Via Universita' 133, 80055 Portici (Naples), Italy
Interests: tomato genetics; genomics; breeding; fruit quality; QTL; mapped genetic resources
Dr. Gianfranco Diretto

E-Mail Website
Guest Editor
ENEA (Italian National Agency for New Technologies, Energy and Sustainable Development), Biotechnologies and Agroindustry Division, Department for Sustainability, Casaccia Research Center, Post Bag 026 Via Anguillarese 301, 00123 S.M. di Galeria (Rome), Italy
Interests: secondary metabolism; metabolic engineering; carotenoids; metabolomics; transcriptomics; systems biology; genome editing, network biology
Special Issues, Collections and Topics in MDPI journals
Dr. Maria Cammareri

E-Mail Website
Guest Editor
CNR (National Research Council of Italy) Institute of Biosciences and BioResources (IBBR), Research Division of Portici, Via Universita' 133, 80055 Portici (Naples), Italy
Interests: plant genetics; genomics; plant breeding; Solanaceae; biodiversity exploitation; fruit quality; plant biotechnology; metabolic engineering
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Tomato (Solanum lycopersicum L., Solanaceae) is one of the most consumed and economically important fruit/vegetable crops worldwide, making a significant nutritional contribution to the human diet. In addition, tomato is also an established model plant for biological research, the primary model for fleshy-fruit development and composition, and a reference species for the family Solanaceae.

Several tomato features have contributed to make this important crop and its wild relatives one of the main models in classical genetics, and then a pioneer of genome analysis in plants and for the development of new molecular breeding strategies aimed at a more efficient exploitation of the rich genetic variation stored in unadapted germplasm.

The release of the tomato reference genome sequence in 2012 and the ever-improving and cost-effective sequencing technologies have triggered a rapid surge in genomic resources, which are greatly facilitating the exploitation of natural and induced genetic diversity, thus, accelerating quantitative trait locus (QTL) mapping, genome-wide association studies (GWAS), gene/allele functional identification and characterization, molecular breeding and generation of novel idiotypes, as well as other scientific discoveries. The use of advanced genetic resources, together with multi-omics approaches are revolutionizing our understanding of the regulatory networks underlying complex traits in tomato and enhancing the identification of candidate genes. In this context, hundreds of cultivated and wild tomato accessions have been re-sequenced, uncovering a vast amount of genetic variation and providing insights into the history of tomato domestication and breeding. A pan-genome of cultivated tomato and close wild relatives has revealed numerous new protein-coding genes, not captured by the reference genome. In addition, the application of third-generation (long-read) sequencing is shedding light upon the landscape of natural structural variants in tomato, demonstrating their widespread importance and potential value for future research and breeding.

The tomato research community can also benefit from vast genetic resources, including wild relatives, thousands of landraces, modern cultivars, several TILLING populations, mutant collections and populations of well-defined wild tomato introgression lines. In addition, the new genome-editing technologies have already proven to be a very powerful tool to characterize gene function in tomato and for crop improvement, also through de novo domestication of wild tomatoes. This rapidly evolving technology is expected to considerably enrich the allelic spectrum that can be employed in future breeding programs.

The deluge of resources and tools now available for the tomato clade, and largely stored in several databases, provide unprecedented opportunities to address the forthcoming breeding challenges imposed by climate change, related to evolving biotic and abiotic stress combinations, world population increase and new consumer demand for more flavorful and health-promoting tomato fruit.

The scope of this Special Issue is to bring together research articles, review articles as well as short communications that address the progress and current status in tomato molecular research and breeding, which can contribute to the development of climate-smart, highly nutritious and flavorful tomato varieties for sustainable agriculture.

The topics to be considered include, but are not limited to:

  • Germplasm characterization and utilization
  • Mapping and cloning of genes and QTL
  • “Omics” (genomics, transcriptomics, epigenomics, proteomics, metabolomics, phenomics, metagenomics, etc.) and multi-omics studies
  • Epigenetic regulation
  • Systems biology
  • Advanced breeding methods
  • Development of tools for marker-assisted selection
  • New plant breeding techniques for gene editing
  • Genomic selection
  • Domestication and evolution
  • Fruit quality and yield-enhancing traits
  • Primary and secondary metabolism
  • Biotic and abiotic stress tolerance and their interactions
  • Physiological mechanisms

Dr. Silvana Grandillo
Dr. Gianfranco Diretto
Dr. Maria Cammareri
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

 

Keywords

  • tomato
  • natural and induced variation
  • genetics
  • genomics
  • omics
  • molecular breeding
  • physiology and development
  • fruit quality
  • biochemistry and metabolism
  • biotic and abiotic stresses

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Published Papers (6 papers)

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Research

20 pages, 3712 KiB  
Article
Overexpression of SlALC Increases Drought and Salt Tolerance and Affects Fruit Dehiscence in Tomatoes
by Zihan Gao, Yuqing Tu, Changguang Liao, Pengyu Guo, Yanling Tian, Ying Zhou, Qiaoli Xie, Guoping Chen and Zongli Hu
Int. J. Mol. Sci. 2024, 25(17), 9433; https://doi.org/10.3390/ijms25179433 - 30 Aug 2024
Viewed by 519
Abstract
The bHLH transcription factors are important plant regulators against abiotic stress and involved in plant growth and development. In this study, SlALC, a gene coding for a prototypical DNA-binding protein in the bHLH family, was isolated, and SlALC-overexpression tomato (SlALC [...] Read more.
The bHLH transcription factors are important plant regulators against abiotic stress and involved in plant growth and development. In this study, SlALC, a gene coding for a prototypical DNA-binding protein in the bHLH family, was isolated, and SlALC-overexpression tomato (SlALC-OE) plants were generated by Agrobacterium-mediated genetic transformation. SlALC transgenic lines manifested higher osmotic stress tolerance than the wild-type plants, estimated by higher relative water content and lower water loss rate, higher chlorophyll, reducing sugar, starch, proline, soluble protein contents, antioxidant enzyme activities, and lower MDA and reactive oxygen species contents in the leaves. In SlALC-OE lines, there were more significant alterations in the expression of genes associated with stress. Furthermore, SlALC-OE fruits were more vulnerable to dehiscence, with higher water content, reduced lignin content, SOD/POD/PAL enzyme activity, and lower phenolic compound concentrations, all of which corresponded to decreased expression of lignin biosynthetic genes. Moreover, the dual luciferase reporter test revealed that SlTAGL1 inhibits SlALC expression. This study revealed that SlALC may play a role in controlling plant tolerance to drought and salt stress, as well as fruit lignification, which influences fruit dehiscence. The findings of this study have established a foundation for tomato tolerance breeding and fruit quality improvement. Full article
(This article belongs to the Special Issue Advances in Tomato Breeding and Molecular Research)
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20 pages, 6475 KiB  
Article
The YABBY Transcription Factor, SlYABBY2a, Positively Regulates Fruit Septum Development and Ripening in Tomatoes
by Hui Shen, Baobing Luo, Yingfeng Ding, Haojun Xiao, Guoping Chen, Zhengan Yang, Zongli Hu and Ting Wu
Int. J. Mol. Sci. 2024, 25(10), 5206; https://doi.org/10.3390/ijms25105206 - 10 May 2024
Viewed by 808
Abstract
The tomato fruit is a complex organ and is composed of various structures from the inside out, such as columella, septum, and placenta. However, our understanding of the development and function of these internal structures remains limited. In this study, we identified a [...] Read more.
The tomato fruit is a complex organ and is composed of various structures from the inside out, such as columella, septum, and placenta. However, our understanding of the development and function of these internal structures remains limited. In this study, we identified a plant-specific YABBY protein, SlYABBY2a, in the tomato (Solanum lycopersicum). SlYABBY2a exhibits relatively high expression levels among the nine YABBY genes in tomatoes and shows specific expression in the septum of the fruit. Through the use of a gene-editing technique performed by CRISPR/Cas9, we noticed defects in septum development in the Slyabby2a mutant fruits, leading to the inward concavity of the fruit pericarp and delayed septum ripening. Notably, the expression levels of key genes involved in auxin (SlFZY4, SlFZY5, and SlFZY6) and ethylene (SlACS2) biosynthesis were significantly downregulated in the septum of the Slalkbh10b mutants. Furthermore, the promoter activity of SlYABBY2a was regulated by the ripening regulator, SlTAGL1, in vivo. In summary, these discoveries provide insights into the positive regulation of SlYABBY2a on septum development and ripening and furnish evidence of the coordinated regulation of the auxin and ethylene signaling pathways in the ripening process, which expands our comprehension of septum development in the internal structure of the fruit. Full article
(This article belongs to the Special Issue Advances in Tomato Breeding and Molecular Research)
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14 pages, 2687 KiB  
Article
ERECTA Modulates Seed Germination and Fruit Development via Auxin Signaling in Tomato
by Daoyun Chen, Yuqing Xu, Jiawei Li, Hiroshi Shiba, Hiroshi Ezura and Ning Wang
Int. J. Mol. Sci. 2024, 25(9), 4754; https://doi.org/10.3390/ijms25094754 - 26 Apr 2024
Cited by 1 | Viewed by 1196
Abstract
Tomato (Solanum lycopersicum) breeding for improved fruit quality emphasizes selecting for desirable taste and characteristics, as well as enhancing disease resistance and yield. Seed germination is the initial step in the plant life cycle and directly affects crop productivity and yield. [...] Read more.
Tomato (Solanum lycopersicum) breeding for improved fruit quality emphasizes selecting for desirable taste and characteristics, as well as enhancing disease resistance and yield. Seed germination is the initial step in the plant life cycle and directly affects crop productivity and yield. ERECTA (ER) is a receptor-like kinase (RLK) family protein known for its involvement in diverse developmental processes. We characterized a Micro-Tom EMS mutant designated as a knock-out mutant of sler. Our research reveals that SlER plays a central role in controlling critical traits such as inflorescence development, seed number, and seed germination. The elevation in auxin levels and alterations in the expression of ABSCISIC ACID INSENSITIVE 3 (ABI3) and ABI5 in sler seeds compared to the WT indicate that SlER modulates seed germination via auxin and abscisic acid (ABA) signaling. Additionally, we detected an increase in auxin content in the sler ovary and changes in the expression of auxin synthesis genes YUCCA flavin monooxygenases 1 (YUC1), YUC4, YUC5, and YUC6 as well as auxin response genes AUXIN RESPONSE FACTOR 5 (ARF5) and ARF7, suggesting that SlER regulates fruit development via auxin signaling. Full article
(This article belongs to the Special Issue Advances in Tomato Breeding and Molecular Research)
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17 pages, 3419 KiB  
Article
Candidate Gene Identification and Transcriptome Analysis of Tomato male sterile-30 and Functional Marker Development for ms-30 and Its Alleles, ms-33, 7B-1, and stamenless-2
by Kai Wei, Xin Li, Xue Cao, Shanshan Li, Li Zhang, Feifei Lu, Chang Liu, Yanmei Guo, Lei Liu, Can Zhu, Yongchen Du, Junming Li, Wencai Yang, Zejun Huang and Xiaoxuan Wang
Int. J. Mol. Sci. 2024, 25(6), 3331; https://doi.org/10.3390/ijms25063331 - 15 Mar 2024
Cited by 1 | Viewed by 1267
Abstract
Male sterility is a valuable trait for hybrid seed production in tomato (Solanum lycopersicum). The mutants male sterile-30 (ms-30) and ms-33 of tomato exhibit twisted stamens, exposed stigmas, and complete male sterility, thus [...] Read more.
Male sterility is a valuable trait for hybrid seed production in tomato (Solanum lycopersicum). The mutants male sterile-30 (ms-30) and ms-33 of tomato exhibit twisted stamens, exposed stigmas, and complete male sterility, thus holding potential for application in hybrid seed production. In this study, the ms-30 and ms-33 loci were fine-mapped to 53.3 kb and 111.2 kb intervals, respectively. Tomato PISTILLATA (TPI, syn. SlGLO2), a B-class MADS-box transcription factor gene, was identified as the most likely candidate gene for both loci. TPI is also the candidate gene of tomato male sterile mutant 7B-1 and sl-2. Allelism tests revealed that ms-30, ms-33, 7B-1, and sl-2 were allelic. Sequencing analysis showed sequence alterations in the TPI gene in all these mutants, with ms-30 exhibiting a transversion (G to T) that resulted in a missense mutation (S to I); ms-33 showing a transition (A to T) that led to alternative splicing, resulting in a loss of 46 amino acids in protein; and 7B-1 and sl-2 mutants showing the insertion of an approximately 4.8 kb retrotransposon. On the basis of these sequence alterations, a Kompetitive Allele Specific PCR marker, a sequencing marker, and an Insertion/Deletion marker were developed. Phenotypic analysis of the TPI gene-edited mutants and allelism tests indicated that the gene TPI is responsible for ms-30 and its alleles. Transcriptome analysis of ms-30 and quantitative RT-PCR revealed some differentially expressed genes associated with stamen and carpel development. These findings will aid in the marker-assisted selection for ms-30 and its alleles in tomato breeding and support the functional analysis of the TPI gene. Full article
(This article belongs to the Special Issue Advances in Tomato Breeding and Molecular Research)
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21 pages, 20779 KiB  
Article
Transcriptome Analysis and Metabolic Profiling Reveal the Key Regulatory Pathways in Drought Stress Responses and Recovery in Tomatoes
by Jinshuai Shu, Lili Zhang, Guiming Liu, Xiaoxuan Wang, Fuzhong Liu, Ying Zhang and Yuhui Chen
Int. J. Mol. Sci. 2024, 25(4), 2187; https://doi.org/10.3390/ijms25042187 - 11 Feb 2024
Viewed by 1938
Abstract
Drought stress is a major abiotic factor affecting tomato production and fruit quality. However, the genes and metabolites associated with tomato responses to water deficiency and rehydration are poorly characterized. To identify the functional genes and key metabolic pathways underlying tomato responses to [...] Read more.
Drought stress is a major abiotic factor affecting tomato production and fruit quality. However, the genes and metabolites associated with tomato responses to water deficiency and rehydration are poorly characterized. To identify the functional genes and key metabolic pathways underlying tomato responses to drought stress and recovery, drought-susceptible and drought-tolerant inbred lines underwent transcriptomic and metabolomic analyses. A total of 332 drought-responsive and 491 rehydration-responsive core genes were robustly differentially expressed in both genotypes. The drought-responsive and rehydration-responsive genes were mainly related to photosynthesis–antenna proteins, nitrogen metabolism, plant–pathogen interactions, and the MAPK signaling pathway. Various transcription factors, including homeobox-leucine zipper protein ATHB-12, NAC transcription factor 29, and heat stress transcription factor A-6b-like, may be vital for tomato responses to water status. Moreover, 24,30-dihydroxy-12(13)-enolupinol, caffeoyl hawthorn acid, adenosine 5′-monophosphate, and guanosine were the key metabolites identified in both genotypes under drought and recovery conditions. The combined transcriptomic and metabolomic analysis highlighted the importance of 38 genes involved in metabolic pathways, the biosynthesis of secondary metabolites, the biosynthesis of amino acids, and ABC transporters for tomato responses to water stress. Our results provide valuable clues regarding the molecular basis of drought tolerance and rehydration. The data presented herein may be relevant for genetically improving tomatoes to enhance drought tolerance. Full article
(This article belongs to the Special Issue Advances in Tomato Breeding and Molecular Research)
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14 pages, 9148 KiB  
Article
Identification of Hub Genes and Physiological Effects of Overexpressing the Photosynthesis-Related Gene Soly720 in Tomato under High-CO2 Conditions
by Shaowen Zheng, Lingbo Yang, Hao Zheng, Jiayue Wu, Zijian Zhou and Jieyun Tian
Int. J. Mol. Sci. 2024, 25(2), 757; https://doi.org/10.3390/ijms25020757 - 7 Jan 2024
Viewed by 1093
Abstract
Changes in the atmospheric CO2 concentration influence plant growth and development by affecting the morphological structure and photosynthetic performance. Despite evidence for the macro-effects of elevated CO2 concentrations on plant morphology and yield in tomato, the gene regulatory network and key [...] Read more.
Changes in the atmospheric CO2 concentration influence plant growth and development by affecting the morphological structure and photosynthetic performance. Despite evidence for the macro-effects of elevated CO2 concentrations on plant morphology and yield in tomato, the gene regulatory network and key genes related to cross-regulation have not been reported. To identify the hub genes and metabolic pathways involved in the response of tomato to CO2 enrichment, weighted gene co-expression network analysis was conducted using gene expression profiles obtained by RNA sequencing. The role of the photosynthesis-related gene Soly720 (Solyc01g007720) in CO2-enriched tomato plants was explored. Tomato plants responded to CO2 enrichment primarily through RNA-related pathways and the metabolism of amino acids, fatty acids, and carbohydrates. The hub genes in co-expression networks were associated with plant growth and development, including cellular components and photosynthesis. Compared to wild-type plants, transgenic plants overexpressing the Soly720 gene exhibited 13.4%, 5.5%, 8.9%, and 4.1% increases in plant height, stem diameter, leaf length, and leaf width, respectively, under high-CO2 conditions. The morphological improvements in transgenic plants were accompanied by enhancement of photosynthetic performance in terms of chlorophyll contents, photosynthetic characteristics, and key enzyme activities. This study elucidates the response network of tomato to CO2 enrichment and demonstrates the regulatory role of Soly720 in photosynthesis under high-CO2 conditions. Full article
(This article belongs to the Special Issue Advances in Tomato Breeding and Molecular Research)
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