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Tomato Fruit Traits and Breeding
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Tomato Fruit Traits and Breeding

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Horticultural Science and Ornamental Plants".

Deadline for manuscript submissions: closed (30 June 2024) | Viewed by 5338

Special Issue Editors

Dr. Gustavo Ruben Rodriguez

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Guest Editor
1. Head of Tomato Genetics and Breeding Group at Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, S2125ZAA Zavalla, Santa Fe, Argentina
2. Professor of Genetics at Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA Zavalla, Santa Fe, Argentina
Interests: tomato genetics; plant breeding; fruit quality; agrinformatics; plant biotechnology
Dr. María Inés Zanor

E-Mail
Guest Editor
1. Crop Molecular Physiology Group at Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET - UNR, Rosario 2000, Argentina
2. Professor of Biochemistry at Departamento de Química Biológica, Facultad de Ciencias, Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario 2000, Argentina
Interests: plant molecular biology; oxidative stress; transcription; metabolism

Special Issue Information

Dear Colleagues,

Tomato (Solanum lycopersicum L.) is one of the most important horticultural crops worldwide due to its level of production and consumption. It is broadly recognized as a model crop for studying the genetics and physiology of climacteric fleshy fruits, as well as for the breeding methods of autogamous plant species. Morphological fruit traits influence the crop yield and determine the final commercial destination, either for fresh market use or processing. Tomato plays an important role in human nutrition since it has a reservoir of health-beneficial compounds, such as vitamins, essential amino acids, carotenoids, phytosterols, and minerals. Lycopene, the main carotenoid in the red tomato fruit, together with other phenolic compounds, has been shown to exhibit anti-inflammatory, antioxidant, and cardioprotective properties.

Today, tomato breeding for yield and its morphological and nutritional components is assisted by biotechnologies, such as the maker-assisted selection for mendelian traits and quantitative trait loci (QTL) analysis, genome-wide association studies (GWAS), map-based cloning, omics analysis, and gene or genome editing. Furthermore, the big data analytics that are emerging from high-throughput pheno- and genotyping are revealing new approaches and bioinformatics tools that will have a colossal impact on tomato breeding.

To highlight the state-of-the-art and recent advances in the field of genetics and breeding for fruit traits in tomato, this Special Issue welcomes novel research articles based on the utilization of bioinformatics tools, omic approaches, gene editing, and breeding methods used to improve biochemical and morphological fruit traits.

Dr. Gustavo Ruben Rodriguez
Dr. María Inés Zanor
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. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). 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

  • bioinformatics
  • breeding methods
  • functional food
  • gene editing
  • morphology
  • nutritional content
  • omics
  • phenotyping
  • tomato genetics

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Published Papers (4 papers)

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Research

19 pages, 2632 KiB  
Article
Machine Learning-Based Tomato Fruit Shape Classification System
by Dana V. Vazquez, Flavio E. Spetale, Amol N. Nankar, Stanislava Grozeva and Gustavo R. Rodríguez 
Plants 2024, 13(17), 2357; https://doi.org/10.3390/plants13172357 - 23 Aug 2024
Viewed by 631
Abstract
Fruit shape significantly impacts the quality and commercial value of tomatoes (Solanum lycopersicum L.). Precise grading is essential to elucidate the genetic basis of fruit shape in breeding programs, cultivar descriptions, and variety registration. Despite this, fruit shape classification is still primarily [...] Read more.
Fruit shape significantly impacts the quality and commercial value of tomatoes (Solanum lycopersicum L.). Precise grading is essential to elucidate the genetic basis of fruit shape in breeding programs, cultivar descriptions, and variety registration. Despite this, fruit shape classification is still primarily based on subjective visual inspection, leading to time-consuming and labor-intensive processes prone to human error. This study presents a novel approach incorporating machine learning techniques to establish a robust fruit shape classification system. We trained and evaluated seven supervised machine learning algorithms by leveraging a public dataset derived from the Tomato Analyzer tool and considering the current four classification systems as label variables. Subsequently, based on class-specific metrics, we derived a novel classification framework comprising seven discernible shape classes. The results demonstrate the superiority of the Support Vector Machine model in terms of its accuracy, surpassing human classifiers across all classification systems. The new classification system achieved the highest accuracy, averaging 88%, and maintained a similar performance when validated with an independent dataset. Positioned as a common standard, this system contributes to standardizing tomato fruit shape classification, enhancing accuracy, and promoting consensus among researchers. Its implementation will serve as a valuable tool for overcoming bias in visual classification, thereby fostering a deeper understanding of consumer preferences and facilitating genetic studies on fruit shape morphometry. Full article
(This article belongs to the Special Issue Tomato Fruit Traits and Breeding)
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17 pages, 2155 KiB  
Article
Identification and Validation of Quantitative Trait Loci Associated with Fruit Puffiness in a Processing Tomato Population
by Françoise Dalprá Dariva, Su Subode, Jihuen Cho, Carlos Nick and David Francis
Plants 2024, 13(11), 1454; https://doi.org/10.3390/plants13111454 - 23 May 2024
Viewed by 838
Abstract
Physiological disorders impact the yield and quality of marketable fruit in tomato. Puffy fruit caused by cavities inside the locule can be problematic for processing and fresh market quality. In this paper, we used a recombinant inbred line (RIL) and three derived processing [...] Read more.
Physiological disorders impact the yield and quality of marketable fruit in tomato. Puffy fruit caused by cavities inside the locule can be problematic for processing and fresh market quality. In this paper, we used a recombinant inbred line (RIL) and three derived processing tomato populations to map and validate quantitative trait loci (QTLs) for fruit puffiness across environments. Binary interval mapping was used for mapping the incidence of fruit puffiness, and non-parametric interval mapping and parametric composite interval mapping were used for mapping severity. Marker–trait regressions were carried out to validate putative QTLs in subsequent crosses. QTLs were detected on chromosome (Chr) 1, 2, and 4. Only the QTL on Chr 1 was validated in progeny from subsequent crosses. This QTL explained up to 22.5% of the variance in the percentage of puffy fruit, with a significant interaction between loci on Chr 2 and 4, increasing the percentage of puffy fruit by an additional 15%. The allele responsible for puffy fruit on Chr 1 was inherited from parent FG02-188 and was dominant towards increased incidence and severity. Marker-assisted selection (MAS) for the QTL on Chr 1 was as efficient as genomic selection (GS) in reducing the incidence and severity of puffy fruit, despite the potential contribution of other loci. Full article
(This article belongs to the Special Issue Tomato Fruit Traits and Breeding)
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17 pages, 5471 KiB  
Article
Transcriptome and Metabolome Provide Insights into Fruit Ripening of Cherry Tomato (Solanum lycopersicum var. cerasiforme)
by Feng Pan, Qianrong Zhang, Haisheng Zhu, Junming Li and Qingfang Wen
Plants 2023, 12(19), 3505; https://doi.org/10.3390/plants12193505 - 9 Oct 2023
Cited by 3 | Viewed by 1708
Abstract
Insights into flavor formation during fruit ripening can guide the development of breeding strategies that balance consumer and producer needs. Cherry tomatoes possess a distinctive taste, yet research on quality formation is limited. Here, metabolomic and transcriptomic analyses were conducted on different ripening [...] Read more.
Insights into flavor formation during fruit ripening can guide the development of breeding strategies that balance consumer and producer needs. Cherry tomatoes possess a distinctive taste, yet research on quality formation is limited. Here, metabolomic and transcriptomic analyses were conducted on different ripening stages. The results revealed differentially accumulated metabolites during fruit ripening, providing candidate metabolites related to flavor. Interestingly, several key flavor-related metabolites already reached a steady level at the mature green stage. Transcriptomic analysis revealed that the expression levels of the majority of genes tended to stabilize after the pink stage. Enrichment analysis demonstrated that changes in metabolic and biosynthetic pathways were evident throughout the entire process of fruit ripening. Compared to disease resistance and fruit color genes, genes related to flavor and firmness may have a broader impact on the accumulation of metabolites. Furthermore, we discovered the interconversion patterns between glutamic acid and glutamine, as well as the biosynthesis patterns of flavonoids. These findings contribute to our understanding of fruit quality formation mechanisms and support breeding programs aimed at improving fruit quality traits. Full article
(This article belongs to the Special Issue Tomato Fruit Traits and Breeding)
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15 pages, 2571 KiB  
Article
An Integrative Transcriptomics and Proteomics Approach to Identify Putative Genes Underlying Fruit Ripening in Tomato near Isogenic Lines with Long Shelf Life
by Melisa Di Giacomo, Tatiana Alejandra Vega, Vladimir Cambiaso, Liliana Amelia Picardi, Gustavo Rubén Rodríguez and Javier Hernán Pereira da Costa
Plants 2023, 12(15), 2812; https://doi.org/10.3390/plants12152812 - 29 Jul 2023
Cited by 3 | Viewed by 1522
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Tomato Fruit Traits and Breeding)
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