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Horticulturae
Special Issues
Genetics, Genomics and Breeding of Vegetable Crops
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Genetics, Genomics and Breeding of Vegetable Crops

A special issue of Horticulturae (ISSN 2311-7524). This special issue belongs to the section "Genetics, Genomics, Breeding, and Biotechnology (G2B2)".

Deadline for manuscript submissions: closed (30 April 2026) | Viewed by 9968

Special Issue Editors

Dr. André Ricardo Zeist

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Guest Editor
Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil
Interests: vegetable genetics; vegetable breeding; vegetable crop production
Dr. Tiago Benedito Dos Santos

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Guest Editor
Laboratório de Genética Molecular, Universidade do Oeste Paulista, UNOESTE, Presidente Prudente, SP, Brazil
Interests: plant molecular genetics; bioinformatics; abiotic stress in plants
Dr. Valdir Marcos Stefenon

E-Mail Website
Guest Editor
Agricultural Research Center, Federal University of Santa Catarina, Campus Universitário Reitor João David Ferreira Lima, s/nº Trindade, Florianópolis 88040-900, SC, Brazil
Interests: plant biotechnology; plant genomics; plant micropropagation
Dr. Juliano Tadeu Vilela de Resende

E-Mail Website
Guest Editor
Agronomy Department, Londrina State University, Londrina 86057-970, Brazil
Interests: vegetable breeding; pest and disease resistance

Special Issue Information

Dear Colleagues,

This Special Issue aims to highlight recent advances in the application of genetic, genomic, and classical breeding approaches to vegetable crops. Recognizing the growing importance of horticulture in the global context of food security and sustainability, we welcome contributions that explore one or more of these issues, including aspects of molecular genetics, functional genomics, or classical breeding. Topics of interest include but are not limited to, functional genomics, gene editing, molecular markers, genetic diversity studies, marker-assisted selection, classical breeding strategies, and the development and evaluation of genotypes aimed at improving productivity and resilience to biotic and abiotic stresses, particularly in the context of climate changes. We also invite the submission of articles emphasizing the impact of these technologies and methodologies on increasing productivity, enhancing nutritional quality, and improving the tolerance of vegetable crops. This Special Issue provides an opportunity to disseminate research and promote the integration of scientific and practical knowledge, contributing to the advancement and sustainability of the horticultural sector.

Dr. André Ricardo Zeist
Dr. Tiago Benedito Dos Santos
Dr. Valdir Marcos Stefenon
Dr. Juliano Tadeu Vilela de Resende
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 250 words) can be sent to the Editorial Office for assessment.

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. Horticulturae 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 2200 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

  • molecular markers
  • gene editing
  • genetic diversity
  • marker-assisted selection
  • tolerance to abiotic and biotic stresses
  • classical breeding
  • crop improvement strategies

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Published Papers (5 papers)

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Research

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22 pages, 4460 KB  
Article
Multicharacteristic Selection of Purple-Flesh Sweetpotato Genotypes with High Productivity and Anthocyanin Content
by Jorge Andrés Betancur González, Andre Junior Ribeiro, Dalvan Beise, Edson Perez Guerra, Juliano Galina, Tiago Olivoto and André Ricardo Zeist
Horticulturae 2025, 11(12), 1486; https://doi.org/10.3390/horticulturae11121486 - 9 Dec 2025
Viewed by 774
Abstract
The development of improved, better-adapted purple-fleshed sweetpotato genotypes can enhance public health, diversify market opportunities, and increase incomes for Brazilian farmers while making biofortified foods more accessible and strengthening food security. Breeding programs should simultaneously target yield and quality traits to secure acceptance [...] Read more.
The development of improved, better-adapted purple-fleshed sweetpotato genotypes can enhance public health, diversify market opportunities, and increase incomes for Brazilian farmers while making biofortified foods more accessible and strengthening food security. Breeding programs should simultaneously target yield and quality traits to secure acceptance from both producers and consumers. This study aimed to identify promising purple-fleshed sweetpotato genotypes by evaluating multiple traits: root yield, postharvest quality, and anthocyanin content. We carried out two field trials, with predicted genetic gains of 127% for the number of marketable roots and 90.6% for total root yield in the first stage, and 13.1% for total yield, 14.5% for marketable yield, and 9.4% for dry matter of marketable roots in the second stage. Beginning with 1048 experimental genotypes, we preselected 21 promising lines. In the first trial (augmented block design), we chose 28 high-yielding genotypes. In the second trial, 12 genotypes from the breeding program were tested using an alpha-lattice design, with the cultivar SCS370 Luiza serving as a control in both experiments. We assessed traits including propagation potential, total root number, total and marketable yield, number of marketable roots, average mass and dry matter of marketable roots, resistance to insect damage, external appearance, pulp color, root spatial distribution in the soil, average root diameter, number of perforations, soluble solids, and anthocyanin content. Genotype selection was guided by the multi-trait genotype–ideotype distance index. In the final selection, 21 genotypes stood out as highly promising: U1-46, U1-145, U2-08, FA-08, U2-100, F06-32, B-77, U2-D, U2-47, FA-143, U1-123, U1-113, U2-49, F06-25, F06-199, FA-120, U1-55, LP-75, U2-74, F06-57, and U1-47, combining a mean total root yield of 27.392 t ha−1 and anthocyanin levels between 0.174 and 0.804 mg 100 g−1. These genotypes constitute promising candidates for incorporation into breeding pipelines targeting markets for purple-fleshed sweetpotato, with favorable implications for both producer income and nutritional outcomes. Full article
(This article belongs to the Special Issue Genetics, Genomics and Breeding of Vegetable Crops)
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15 pages, 1256 KB  
Article
Solanum lycopersicoides Introgression Lines Used as Rootstocks Uncover QTLs Affecting Tomato Morphological and Fruit Quality Traits
by Aylin Kabas, Selman Uluisik, Hayri Ustun, Jaime Prohens and Ibrahim Celik
Horticulturae 2025, 11(11), 1364; https://doi.org/10.3390/horticulturae11111364 - 13 Nov 2025
Cited by 1 | Viewed by 1137
Abstract
Tomato (Solanum lycopersicum) is the most important vegetable crop globally; however, its production is often hindered by soil-borne biotic and abiotic stresses. The use of rootstocks provides an effective strategy to mitigate these soil-related challenges. Hence, the development of new rootstock [...] Read more.
Tomato (Solanum lycopersicum) is the most important vegetable crop globally; however, its production is often hindered by soil-borne biotic and abiotic stresses. The use of rootstocks provides an effective strategy to mitigate these soil-related challenges. Hence, the development of new rootstock cultivars remains crucial to meet the demands of rapidly changing environmental conditions. Wild tomato species represent valuable genetic resources for rootstock improvement and are increasingly utilized in rootstock breeding programs. Nevertheless, the genetic mechanisms, particularly quantitative trait loci (QTL), underlying rootstock–scion interaction, remain poorly understood. In this study, 38 introgression lines (ILs) derived from S. lycopersicoides were used as rootstock and grafted with the commercial cultivar ‘Torry F1’ to evaluate their effects on morphological and fruit quality traits under greenhouse conditions. The evaluations included assessments of morphological and fruit quality traits for QTL analysis. A total of 19 QTLs were identified, associated with 11 traits such as yield, antioxidant capacity, flavonoid content, and fruit color parameters (L*, a*, b*, C*, h°), with the phenotypic variance explained ranging from 12% to 61%. Of these QTLs, seven favorable alleles originated from S. lycopersicoides, notably including a major yield-associated locus (Fy5.1). In addition, the identification of a QTL for scion stem thickness (Tsc3.1) highlights the genetic contribution of the rootstock to scion development. This study represents the first evaluation of the rootstock potential of S. lycopersicoides ILs and provides novel insights into the genetic basis of rootstock–scion interaction in tomato. The identified QTLs offer valuable information for future breeding efforts aimed at developing improved rootstock cultivars for sustainable tomato production. Full article
(This article belongs to the Special Issue Genetics, Genomics and Breeding of Vegetable Crops)
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16 pages, 1258 KB  
Article
Genome-Wide Association Analysis of Traits Related to Nitrogen Deficiency Stress in Potato
by Carmen Iribar, Alba Alvarez-Morezuelas, Leire Barandalla and Jose Ignacio Ruiz de Galarreta
Horticulturae 2025, 11(8), 889; https://doi.org/10.3390/horticulturae11080889 - 1 Aug 2025
Cited by 3 | Viewed by 1192
Abstract
Potato (Solanum tuberosum L.) crop yields may be reduced by nitrogen deficiency stress tolerance. An evaluation of 144 tetraploid potato genotypes was carried out during two consecutive seasons (2019 and 2020), with the objective of characterizing their variability in key physiological and [...] Read more.
Potato (Solanum tuberosum L.) crop yields may be reduced by nitrogen deficiency stress tolerance. An evaluation of 144 tetraploid potato genotypes was carried out during two consecutive seasons (2019 and 2020), with the objective of characterizing their variability in key physiological and agronomic parameters. Physiological parameters included chlorophyll content and fluorescence, stomatal conductance, NDVI, leaf area, and perimeter, while agronomic characteristics such as yield, tuber fresh weight, tuber number, starch content, dry matter, and reducing sugars were evaluated. To genotype the population, the GGP V3 Potato array was used, generating 18,259 high-quality SNP markers. Marker–trait association analysis was conducted using the GWASpoly package in R, applying Q + K linear mixed models to enhance precision. This methodology enabled the identification of 18 SNP markers that exhibited statistically significant associations with the traits analyzed in both trials and periods, relating them to genes whose functional implication has already been described. Genetic loci associated with chlorophyll content and tuber number were detected across non-stress and stress treatments, while markers linked to leaf area and leaf perimeter were identified specifically under nitrogen deficiency stress. The genomic distribution of these markers revealed that genetic markers or single-nucleotide polymorphisms (SNPs) correlated with phenotypic traits under non-stress conditions were predominantly located on chromosome 11, whereas SNPs linked to stress responses were mainly identified on chromosomes 2 and 3. These findings contribute to understanding the genetic mechanisms underlying potato tolerance to nitrogen deficiency stress, offering valuable insights for the development of future marker-assisted selection programs aimed at improving nitrogen use efficiency and stress resilience in potato breeding. Full article
(This article belongs to the Special Issue Genetics, Genomics and Breeding of Vegetable Crops)
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20 pages, 2048 KB  
Article
Effect of Tm-2a, Sw-5 and Ty-1 Gene Introduction on the Agronomic Performance and Metabolic Profile of Traditional Muchamiel-Type Tomato Varieties
by Alicia Sánchez, Juana Cava, Virginia Hernández, Pilar Flores, Santiago García-Martínez, Pedro Carbonell, Elena Sánchez, Nuria López, Elia Molina, José Fenoll and Pilar Hellín
Horticulturae 2025, 11(7), 838; https://doi.org/10.3390/horticulturae11070838 - 15 Jul 2025
Viewed by 1262
Abstract
The introduction of virus resistance genes into traditional tomato varieties offers a strategy to preserve genetic diversity and enhance commercial viability. However, the homozygous presence of these genes has been associated with negative effects on yield and fruit quality. This two-year study evaluated [...] Read more.
The introduction of virus resistance genes into traditional tomato varieties offers a strategy to preserve genetic diversity and enhance commercial viability. However, the homozygous presence of these genes has been associated with negative effects on yield and fruit quality. This two-year study evaluated the impact of introducing the Tm-2a, Sw-5 and Ty-1 genes, which are associated with resistance to ToMV, TSWV and TYLCV, respectively, on the agronomic yield, fruit characteristics and metabolic profile of Muchamiel-type cultivars. Four hybrids were obtained by crossing two breeding lines carrying the resistance genes in homozygosis (UMH1139 and UMH1200) with two traditional susceptible varieties (MC1 and MC2). Hybrids matched or exceeded the agronomic performance of their parents. Fruit morphology of the hybrids was similar to traditional parents. The presence of Ty-1 correlated with reduced organic acid concentration, though hybrids exhibited higher levels than the homozygous line, UMH1200. No negative effects on soluble sugars or secondary metabolites were observed. Genotypes carrying resistance genes, breeding lines and hybrids exhibited higher flavonoid contents, suggesting a potential role in virus response. Hybrids maintained or improved the bioactive profile of traditional varieties. These findings support the development of Muchamiel-type hybrids that combine the presence of virus resistance genes in heterozygosity with the desirable traits of traditional tomatoes. Full article
(This article belongs to the Special Issue Genetics, Genomics and Breeding of Vegetable Crops)
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Review

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22 pages, 1322 KB  
Review
Virus-Induced Gene Silencing (VIGS) in Functional Genomics: Advances and Applications in Capsicum annuum L.
by Andrey Shingaliev, Alexandra Rekina, Mikhail Gorbachev, Ksenia Dudnikova and Maksim Dudnikov
Horticulturae 2025, 11(11), 1297; https://doi.org/10.3390/horticulturae11111297 - 29 Oct 2025
Cited by 4 | Viewed by 4979
Abstract
This article provides a comprehensive analysis of Virus-Induced Gene Silencing (VIGS), which is an effective tool for studying the functional genomics of organisms that are poorly amenable to genomic editing. The VIGS method is grounded in the plant’s post-transcriptional gene silencing (PTGS) machinery [...] Read more.
This article provides a comprehensive analysis of Virus-Induced Gene Silencing (VIGS), which is an effective tool for studying the functional genomics of organisms that are poorly amenable to genomic editing. The VIGS method is grounded in the plant’s post-transcriptional gene silencing (PTGS) machinery and utilizes recombinant viral vectors to trigger systemic suppression of endogenous plant gene expression, leading to visible phenotypic changes that enable gene function characterization. This article details the application of VIGS in model organisms (Arabidopsis thaliana, Nicotiana benthamiana) and a wide range of crops, with a special focus on the Solanaceae family, particularly pepper (Capsicum annuum L.). This review analyzes the design and structural elements of viral vectors used for VIGS, such as Tobacco Rattle Virus (TRV), Broad Bean Wilt Virus 2 (BBWV2), Cucumber Mosaic Virus (CMV), geminiviruses (CLCrV, ACMV), and satellite virus-based systems. It also critically examines the key factors that determine silencing efficiency. These factors encompass insert design, agroinfiltration methodology, plant developmental stage, agroinoculum concentration, plant genotype, and environmental factors (temperature, humidity, photoperiod). Particular attention is given to optimization strategies, such as the use of viral suppressors of RNA silencing (VSRs). This article concludes with the achievements in using VIGS to identify pepper genes governing fruit quality (color, biochemical composition, pungency), resistance to biotic (bacteria, oomycetes, insects) and abiotic (temperature, salt, osmotic stress) factors, as well as genes regulating plant architecture and development. The results obtained demonstrate the advantages and limitations of VIGS, alongside future perspectives for its integration with multi-omics technologies to accelerate breeding and advance functional genomics studies in pepper. Full article
(This article belongs to the Special Issue Genetics, Genomics and Breeding of Vegetable Crops)
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