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Genetic Basis of Fruit Quality Traits
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Genetic Basis of Fruit Quality Traits

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (5 June 2020) | Viewed by 13583

Special Issue Editors

Dr. Amalia Barone

E-Mail Website
Guest Editor
Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici (Naples), Italy
Interests: tomato; fruit quality traits; genetics; genomics; molecular breeding
Dr. Julie Graham

E-Mail Website
Guest Editor
Cell and Molecular Sciences, The James Hutton Institute, Dundee, UK
Interests: fruit; ripening; genetics; genomics; molecular breeding; phenotyping

Special Issue Information

Dear Colleagues,

Quality is the result of the complex perception of many attributes evaluated by the consumer. Key to these are attractiveness and flavour. Other important aspects of fruit quality exist that relate to market quality, user quality, and biological quality; thus, its meaning is continuously expanding. In the last few years, the concept of fruit quality has focused on the nutritional value of fruits for human health, thus evidencing that “quality” is a very plastic term, depending on the expectations of consumers, and thus other traits are continuously added to the ‘quality’ objectives to be achieved. Fruit size, shape, color, and firmness are the first quality traits that attract the consumer. The organoleptic quality comes second but is not less important: it involves flavour, aroma, and texture. For fruit that also has a processing destination, the content of soluble solids, pH, viscosity, and shelf-life are also quality attributes. Last but not least, nutritional value and food safety are important quality parameters of consumers. The content of carbohydrates, proteins, lipids, vitamins, minerals, and phytochemicals, as well as the absence of natural toxicants, mycotoxins, and microbial contaminants in fruit, are key objectives for high-quality fruit. In order to reach this objective, many “traditional” and “innovative” genomics and metabolomics tools as well as plant imaging technologies have been made available, which could allow for a better understanding of fruit quality traits and the development of different and novel approaches to gain improvement in these traits. The forthcoming Special Issue aims to provide an overview of recent topics in plant genetics and genomics strategies to improve the fruit quality potential of many different plant species, including vegetables, berries, and tree crops.

Prof. Amalia Barone
Dr. Julie Graham
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. Genes is an international peer-reviewed open access monthly 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 2600 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

  • Vegetables, berry, and tree
  • Nutritional quality
  • Organoleptic quality
  • Post-harvest quality
  • Genomics
  • Transcriptomics
  • Metabolomics
  • QTL analysis
  • Genome editing
  • Genomic selection
  • TILLING and mutants
  • Phenotyping
  • Molecular breeding

Published Papers (4 papers)

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Research

18 pages, 3538 KiB  
Article
Genomic Dissection of a Wild Region in a Superior Solanum pennellii Introgression Sub-Line with High Ascorbic Acid Accumulation in Tomato Fruit
by Antonietta Aliberti, Fabrizio Olivieri, Salvatore Graci, Maria Manuela Rigano, Amalia Barone and Valentino Ruggieri
Genes 2020, 11(8), 847; https://doi.org/10.3390/genes11080847 - 24 Jul 2020
Cited by 6 | Viewed by 3044
Abstract
The Solanum pennellii introgression lines (ILs) have been exploited to map quantitative trait loci (QTLs) and identify favorable alleles that could improve fruit quality traits in tomato varieties. Over the past few years, ILs exhibiting increased content of ascorbic acid in the fruit [...] Read more.
The Solanum pennellii introgression lines (ILs) have been exploited to map quantitative trait loci (QTLs) and identify favorable alleles that could improve fruit quality traits in tomato varieties. Over the past few years, ILs exhibiting increased content of ascorbic acid in the fruit have been selected, among which the sub-line R182. The aims of this work were to identify the genes of the wild donor S. pennellii harbored by the sub-line and to detect genes controlling ascorbic acid accumulation by using genomics tools. A Genotyping-By-Sequencing (GBS) approach confirmed that no wild introgressions were present in the sub-line besides one region on chromosome 7. By using a dense single nucleotide polymorphism (SNP) map obtained by RNA sequencing (RNA-Seq), the wild region of the sub-line was finely identified; thus, defining 39 wild genes that replaced 33 genes of the ILs genetic background (cv. M82). The differentially expressed genes mapping in the region and the variants detected among the cultivated and the wild alleles evidenced the potential role of the novel genes present in the wild region. Interestingly, one upregulated gene, annotated as a major facilitator superfamily protein, showed a novel structure in R182, with respect to the parental lines. These genes will be further investigated using gene editing strategies. Full article
(This article belongs to the Special Issue Genetic Basis of Fruit Quality Traits)
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30 pages, 9439 KiB  
Article
Target-Genes Reveal Species and Genotypic Specificity of Anthocyanin Pigmentation in Citrus and Related Genera
by Chiara Catalano, Angelo Ciacciulli, Fabrizio Salonia, Maria Patrizia Russo, Paola Caruso, Marco Caruso, Giuseppe Russo, Gaetano Distefano and Concetta Licciardello
Genes 2020, 11(7), 807; https://doi.org/10.3390/genes11070807 - 16 Jul 2020
Cited by 7 | Viewed by 3043
Abstract
Background: Anthocyanin pigmentation characterizes a number of tissues of Citrus and its relatives. The gain and loss of pigmentation is intriguing and is inherited variously among species. Methods: Citrus germplasm was used to investigate the anthocyanin pigmentation of tissues never before considered, including [...] Read more.
Background: Anthocyanin pigmentation characterizes a number of tissues of Citrus and its relatives. The gain and loss of pigmentation is intriguing and is inherited variously among species. Methods: Citrus germplasm was used to investigate the anthocyanin pigmentation of tissues never before considered, including stamen, style and stigma, and of young leaves, petals, rind and flesh of 28 genotypes belonging to 14 species. Citrus genotypes encompassed citron, lemon, sweet orange, lime, and Citrus relatives included Microcitrus, Murraya, and Severinia. A relative qRT-PCR analysis was carried out on the structural and regulatory genes: phenylalanine ammonia-lyase (PAL), chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3′-hydroxylase (F3H), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS), uridine diphosphate glucose flavonoid glucosyl-transferase (UFGT), glutathione S-transferase (GST), Ruby and Noemi. Image analysis and a genomic approach were employed to evaluate how the red pigmentation is inherited among tissues and species. Results: Pigmentation of young leaves and petals is specific to citron and its hybrids. Ruby controls the pigmentation of petals, but not of leaves. The red color of the rind and flesh is a trait that particularly characterizes a diversity of sweet oranges, citron hybrids and Citrus relatives. Color expression depends on external factors and also on developmental stage. The coloration of stamen and style is citron-specific, while a red stigma is exclusive to Moro orange and its hybrids. Conclusion: It is hypothesized that there is a relationship among Citrus species and genes controlling anthocyanin pigmentation. Full article
(This article belongs to the Special Issue Genetic Basis of Fruit Quality Traits)
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14 pages, 1789 KiB  
Communication
Comparative Transcriptomic Analysis of Two Bottle Gourd Accessions Differing in Fruit Size
by Hongyuan Zhang, Jie Tan, Min Zhang, Shuping Huang and Xia Chen
Genes 2020, 11(4), 359; https://doi.org/10.3390/genes11040359 - 27 Mar 2020
Cited by 15 | Viewed by 2841
Abstract
The bottle gourd (Lagenaria siceraria) is an important horticultural and medicinal crop with high nutritional value. This study aimed at examining the molecular regulation of fruit size in bottle gourd. We performed transcriptome sequencing of two bottle gourd cultivars differing in [...] Read more.
The bottle gourd (Lagenaria siceraria) is an important horticultural and medicinal crop with high nutritional value. This study aimed at examining the molecular regulation of fruit size in bottle gourd. We performed transcriptome sequencing of two bottle gourd cultivars differing in their fruit size. The average fruit length and weight of the cultivar Hang (39.48 cm/624.4 g) were higher than those of the cultivar USA (10.34 cm/152.8 g) at maturity. Transcriptome sequencing and assembly resulted in 89,347 unigenes. A total of 1250 differentially expressed genes (DEG) were found between the two cultivars, including 422 upregulated genes and 828 downregulated genes in Hang as compared to USA. Genes related to cell wall metabolism, phytohormones, cell cycle, and cell division showed significant differential expression between the two cultivars. DEGs encoding transcription factors (TF) from nine TF families were also identified. The ethylene response factor family was the most enriched among these families. Our study provides a basis for further investigations of the molecular regulation of fruit size in bottle gourd. Full article
(This article belongs to the Special Issue Genetic Basis of Fruit Quality Traits)
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32 pages, 5067 KiB  
Article
Unraveling the Deep Genetic Architecture for Seedlessness in Grapevine and the Development and Validation of a New Set of Markers for VviAGL11-Based Gene-Assisted Selection
by Nallatt Ocarez, Nicolás Jiménez, Reynaldo Núñez, Rocco Perniola, Antonio Domenico Marsico, Maria Francesca Cardone, Carlo Bergamini and Nilo Mejía
Genes 2020, 11(2), 151; https://doi.org/10.3390/genes11020151 - 30 Jan 2020
Cited by 16 | Viewed by 3456
Abstract
Seedless inheritance has been considered a quasi-monogenic trait based on the VvAGL11 gene. An intragenic simple sequence repeat (SSR) marker, p3_VvAGL11, is currently used to opportunely discard seeded progeny, which represents up to 50% of seedlings to be established in the field. However, [...] Read more.
Seedless inheritance has been considered a quasi-monogenic trait based on the VvAGL11 gene. An intragenic simple sequence repeat (SSR) marker, p3_VvAGL11, is currently used to opportunely discard seeded progeny, which represents up to 50% of seedlings to be established in the field. However, the rate of false positives remains significant, and this lack of accuracy might be due to a more complex genetic architecture, some intrinsic flaws of p3_VvAGL11, or potential recombination events between p3_VvAGL11 and the causal SNP located in the coding region. The purpose of this study was to update the genetic architecture of this trait in order to better understand its implications in breeding strategies. A total of 573 F1 individuals that segregate for seedlessness were genotyped with a 20K SNP chip and characterized phenotypically during four seasons for a fine QTL mapping analysis. Based on the molecular diversity of p3_VvAGL11 alleles, we redesigned this marker, and based on the causal SNP, we developed a qPCR-HRM marker for high-throughput and a Tetra-ARMS-PCR for simple predictive analyses. Up to 10 new QTLs were identified that describe the complex nature of seedlessness, corresponding to small but stable effects. The positive predictive value, based on VvAGL11 alone (0.647), was improved up to 0.814 when adding three small-effect QTLs in a multi-QTL additive model as a proof of concept. The new SSR, 5U_VviAGL11, is more informative and robust, and easier to analyze. However, we demonstrated that the association can be lost by intragenic recombination and that the e7_VviAGL11 SNP-based marker is thus more reliable and decreases the occurrence of false positives. This study highlights the bases of prediction failure based solely on a major gene and a reduced set of candidate genes, in addition to opportunities for molecular breeding following further and larger validation studies. Full article
(This article belongs to the Special Issue Genetic Basis of Fruit Quality Traits)
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