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Review

Novel Breeding Techniques and Strategies for Enhancing Greenhouse Vegetable Product Quality

by
Julia Weiss
1,* and
Nazim S. Gruda
1,2
1
Department of Agricultural Engineering, Universidad Politécnica de Cartagena, Paseo Alfonso XIII 48, 30203 Cartagena, Spain
2
Institute of Plant Sciences and Resource Conservation, Division of Horticultural Sciences, University of Bonn, 53113 Bonn, Germany
*
Author to whom correspondence should be addressed.
Agronomy 2025, 15(1), 207; https://doi.org/10.3390/agronomy15010207
Submission received: 19 December 2024 / Revised: 11 January 2025 / Accepted: 13 January 2025 / Published: 16 January 2025
(This article belongs to the Special Issue Conventional vs. Modern Techniques in Horticultural Crop Breeding)
Browse Figure
Versions Notes

Abstract

With its controlled environment, protected cultivation is advantageous and effective for breeding programs. This distinct setting also guarantees that fresh vegetables meet high quality standards. The controlled environment allows for precise monitoring and tuning of breeding efforts, a critical factor in continuously improving the quality of fresh vegetable production. Classical breeding strategies include hybridization, pedigree selection, backcrossing, recombination, and marker-assisted breeding. However, advanced techniques like phenomics and genome editing are revolutionizing the field. These methods accelerate phenotyping and aid in identifying traits and genetic variants linked to quality characteristics. Modern biotechnological tools, specifically genetic engineering and gene editing methods like CRISPR/Cas, have enhanced a wide array of traits in numerous vegetable species. These technological advancements have the potential to effectively address challenges associated with stress resistance, product quality, and shelf-life, thereby presenting promising prospects for the advancement of agriculture. The protracted process of developing new vegetable cultivars with reduced physiological issues through contemporary techniques is an enduring endeavor.

Graphical Abstract

1. Introduction

Vegetables are healthy products with immense value. The leading vegetable crops cultivated worldwide are tomatoes, cucumbers, eggplants, and peppers, with estimated global production volumes of 187, 95, 60, and 37 million tons, respectively [1]. Their value lies in their diversity, providing various flavors and nutrients to meet multiple dietary needs, supporting health, disease prevention, and food security worldwide. Vegetables are essential for a balanced diet and help prevent health issues like cardiovascular diseases, diabetes, and obesity. They regulate blood pressure, reduce inflammation, inhibit cancer, and lower cholesterol [2,3,4,5].
The rising standard of living has also fueled an increased local demand for fresh vegetables, prompting out-of-season production [6,7]. Covering crops protects them from natural hazards and allows manipulation of the crop microenvironment. This enhances plant performance, extends production duration, induces early flowering, and improves production quality by optimizing resource use efficiency [8,9,10].
Protected cultivation is used for cultivating various crops, such as cut flowers, potted ornamentals, and fruits. However, the priority is off-season vegetables [11]. It allows growing vegetables in adverse conditions by modifying the natural environment to optimize plant growth. This method uses solar energy to enhance productivity per unit area, reducing land and water requirements for early and higher yields [8,9]. Ensuring a consistent vegetable supply during the off-season is crucial for managing year-round consumption patterns while offering improved income opportunities for smallholder farmers. Off-season cultivation, supported by well-constructed and maintained protective structures, enhances durability and reduces the risk of pests and diseases, minimizing the need for harmful chemical pesticides [12]. This approach enables growers to mitigate climate impacts, achieve higher returns, and benefit from early harvests, extended growing seasons, efficient fertilizer use, and eco-friendly pest and disease management [8]. Therefore, due to intensive production techniques and extended cropping periods, the vegetable yield surpasses the open field yield. Disadvantages may also accompany the above-mentioned advantages of greenhouse environments compared to field-grown vegetables, such as tip burn associated with higher growth rates, reduced polyphenol content in tomatoes or salad plants due to the absence of UV-B in glasshouse growing systems, or glucosinolate content in greenhouse-grown Chinese brassicas [7]. Breeding efforts, especially for greenhouse-grown vegetables, may contribute to alleviating these quality-related disadvantages. An additional concern when comparing the advantages of greenhouse versus field vegetable production is that greenhouse technology must be adapted to specific local climatic conditions. These adaptations require technical expertise, challenging smallholder vegetable producers in certain regions. Additionally, limited resources and lack of access to credit further complicate the ability of these farmers to invest in the necessary infrastructure, as experienced among smallholder vegetable producers, e.g., in Africa [13].
Growers use various covered structures tailored to the crop, climate, and desired benefits, classified into screen constructions and greenhouses. Screen constructions have permeable screens, while greenhouses use impermeable plastic films or glass. The first structures are located more in the coastal area, using the favorable maritime climate conditions. Climate control can be passive (screen constructions) or active (greenhouses), with hybrids also existing [8]. Passive control relies on natural interactions, while active control involves systems to manipulate the internal microclimate. Screenhouses reduce solar radiation and protect crops from harsh weather and harmful insects. They create a favorable microenvironment, and a misting system can further enhance growing conditions by lowering the vapor pressure deficit [14]. Naturally ventilated tunnels or greenhouses use impermeable films with vents for better climate control, and in northern Europe, these structures often use glass for higher light transmittance. Hi-tech greenhouses, the most advanced, feature extensive climate control systems, including shading, cooling, heating, dehumidifying, and artificial illumination [8,9].
In innovative horticulture, vegetables grown under protective coverings are recognized for their exceptional visual quality, significantly enhancing their market value [8,9,15]. However, producing high-quality vegetables faces challenges from abiotic and biotic factors, including shrinking arable land, urbanization, and climate change, all of which impact the quality of the produce [16]. The unpredictable impacts of climate change on ecosystems and agriculture require plants to adapt metabolically. Considering the relatively high production costs associated with protected cultivation, it is essential that the cultivars used deliver superior quality to ensure profitability and sustainability [17].
The first factor influencing produce quality is the genotype. According to Hanna (2009), selecting a high-yielding cultivar with desirable fruit qualities and a longer shelf-life is crucial for growers [18]. In the context of cultivation, it is essential to note the differences between indoor and outdoor settings, including the specific cultivar used. Although plants bred for a particular purpose are expected to thrive in a variety of conditions, there are still differences to be expected between outdoor and indoor cultivation, open fields, and protected cultivation. For instance, greenhouse cucumbers are typically tall with large leaves for fresh consumption, while field cucumbers are shorter with smaller leaves, mainly used for pickling [7,19]. Quality emphasis is particularly vital in protected cultivation, which provides a controlled environment for practical breeding. This setting allows for precise monitoring and adjustments, enhancing the quality and efficiency of vegetable production. Additionally, modern breeding strategies focus on reducing manual labor, time efficiency, and addressing climate variability, making controlled environments advantageous compared to open-field systems [20]. The physiological behavior, stress tolerance, and susceptibility of greenhouse vegetable cultivars also affect their visual, organoleptic, and nutritional quality [3,21].
Both classical and advanced breeding strategies are applied to improve vegetable quality attributes. The first step in classical breeding is the selection of parental traits, often from wild crop relatives. The combination of favorable genotypes through crossing is followed by several backcrossing steps to preserve the crop’s genetic background. In contrast, F1 hybrid breeding exploits the resulting heterosis impact on productivity and quality [22]. Modern phenomics methods aid in accelerating phenotyping, while molecular markers and genome-wide association studies help track traits and identify genetic variants associated with specific characteristics during the breeding process [23]. Next-generation sequencing facilitates efficient genotyping and transcriptome analysis, contributing to identifying genes related to quality traits [24]. The transgenic approach utilizes recombinant DNA technology and Agrobacterium-mediated genetic transformation as a standard transfer method [25]. RNA interference and DNA editing methods such as CRISPR/Cas9 enable precise genome alterations [26]. The following sections describe the successful use of the above breeding strategies for quality improvement in economically significant fruit and leaf vegetables.

2. Classical Breeding Strategies for Quality Improvement in Fruit and Leaf Vegetables

Breeding for quality traits in vegetables is an intricate procedure, as the demand for quality attributes is often location-specific. One of the most consumed fruit vegetables is tomato. Its enhanced breeding success depends on the natural biodiversity supplied by wild species for quality improvement [27]. For instance, the susceptibility to blossom-end rot (BER), a physiological disorder that causes significant losses in tomatoes, is particularly low in wild tomato species. Introgression lines of Solanum pennellii into S. lycopersicum have shown significantly lower BER incidence, likely due to a higher expression of calcium movement-related genes in the pericarp and a slower fruit growth rate [28]. A longer shelf-life also characterizes fruits from wild tomato species, and hybrids with commercial varieties demonstrate overall quality improvement [29]. Wild ancestors can also serve as potential sources for pigment improvement, i.e., breeding anthocyanin-rich varieties by introgressing alleles from wild species like S. chilense into S. esculentum [30].
According to agricultural and plant breeding studies, landraces are pivotal in preserving genetic diversity within the tomato species. These traditional varieties have evolved and adapted to various environmental conditions, making them valuable reservoirs of gene variability. They are crucial for breeding programs to develop new tomato cultivars with enhanced characteristics like resistance to disease and increased yield and taste. Therefore, understanding and preserving these landraces are essential for ensuring resilience and sustainability by increasing quality traits. For example, Spanish landraces display a wide range of traits related to resistance to environmental stresses, fruit shape, color, ribbing, and sensory and organoleptic quality characteristics [31]. The specific local selection criteria and environmental conditions have led to the wide variability in existing varieties, with local names of the different varieties varying according to use or morphology, such as the heart-shaped “Corazon de toro” from the Alpujarra region in Granada [32], the mellow and sweet landrace “Muchamiel” from the coastal area of Valencia and Alicante, or the Mediterranean drought-resistant landrace group “long shelf-life” [33] These landraces tend to have lower productivity and disease susceptibility, requiring breeding efforts such as backcrossing and natural selection [34]. In modern farming, selecting tolerant cultivars enhances resilience against drought, pests, and salinity. RAF tomatoes, developed in Almeria, Spain, are a premium choice due to their natural aroma and fast ripening. The sweet taste is an attribute of the cultivar in combination with a moderate salinity, making it popular among gourmet consumers [16].
Marker-assisted selection is an advanced breeding tool for identifying certain traits while breeding using cultivars, landraces, and wild species. A significant milestone in establishing a foundation for sequencing-based approaches and understanding complex traits was completing the tomato genome sequencing project in 2012 [35]. Next-generation sequencing and high-throughput genotyping have led to the identification of Single Nucleotide Polymorphisms (SNPs) as valuable molecular markers for the identification of genes and Quantitative Trait Loci (QTLs) [36]. Furthermore, the Sol Genomics Network (SGN) (https://solgenomics.net/, accessed on 18 November 2024) serves as a valuable resource for accessing genomic and phenotypic data for Solanaceae, enabling breeders to design effective breeding strategies [37].
Significant genotypic variation exists among sweet pepper (Capsicum annuum L.) landraces, with preserved alleles for quality traits and local adaptation. These can be used for selective breeding and hybridization [38]. A wide variety of phenotypically different landraces, adapted to the specific agro-climate conditions, exist in Southern Europe, such as the early ripening, sweet green variety “Piñeira” from Lugo in Northwestern Spain or the thick and sweet Valencian “Trompa de Vaca” [39,40]. Greenhouse peppers may also be affected by BER. Developing parthenocarpic pepper lines is suggested as a breeding strategy to combat BER, as a significant decrease in BER incidence was observed in auxin-induced parthenocarpic fruits [41]. Factors such as water loss and chilling sensitivity influence post-harvest quality in peppers. QTLs and candidate genes have been identified that can be utilized for genotype selection to improve post-harvest characteristics [42].
Eggplant ranks as the fifth most economically significant plant in the Solanaceae family, and an extensive public germplasm collection of cultivated species and wild relatives of eggplants is hosted by the World Vegetable Center [43]. The characterization of thirty-one eggplant landraces from Spain revealed an exciting scope of fruit peel color from black-purple, striped, and white, to reddish, information that could be useful in future plant breeding programs [44]. Understanding the diversity of fruit peel colors could also provide insight into variations in phenolic content and susceptibility to browning among eggplant varieties, both essential factors in breeding efforts. Commercial varieties lag behind landraces in phenolic content and browning, suggesting room for improvement through breeding [45], while an increment in chlorogenic acid content was achieved by allele introgression from the wild relative S. incanum [46].
Successful classical breeding strategies for improving cucumber (Cucumis sativus L.) involve the pedigree method, backcross breeding, and F1 hybrid development [47]. Additionally, next-generation sequencing data analysis, the publication of a cucumber reference genome, and genome-wide expression studies are utilized to understand complex traits [48]. The various cucumber types, such as the Dutch greenhouse cucumber and the Mediterranean type, differ in size, shape, spine wart size and density, peel color, and pattern. Depending on market needs, different peel colors are demanded. Fruit peel color is controlled by the combinatory effect of six significant genes controlling chlorophyll and flavonoid production and chloroplast development. Molecular markers linked to these genes permit the selection of color phenotypes such as green and white skin, light green skin, yellow-green skin, and uniform coloring [49]. Shelf-life is another essential attribute of cucumber quality. Molecular mechanisms underlying shelf-life were dissected through RNAseq, leading to the identification of critical genes involved in ethylene and chlorophyll metabolism and cell wall degradation, as well as the development of molecular markers allowing genotype screens for post-harvest behavior [50]. The trait “bitterness” is due to the production of cucurbitacin. Gene-based markers were developed to detect allelic variation in the Bi (Bitter) gene for marker-assisted selection of non-bitter cucumbers [51]. QTLs for the quality parameters size, shape, firmness, and crispness were mapped, and the corresponding molecular markers can be used in selecting these attributes [52].
Lettuce (Lactuca sativa L.) is the most economically significant leafy vegetable [53]. The lettuce database (https://db.cngb.org/lettuce/ (accessed on 1 November 2021)) has significantly contributed to lettuce breeding by compiling sequencing, phenotypic, and multi-omics data, offering tools for data mining and exploration [54]. Lettuce germplasm, spanning wild species and traditional varieties, have considerable genotypic diversity in crucial nutritional compounds like carotenoids and ascorbic acid, but also post-harvest changes [44,55,56]. Although lettuce landraces play only a marginal role in the market, landraces such as “Cua d’oreneta” (swallow tail), “Enciam negre” (black lettuce) from Catalonia, Spain, are highly appreciated and tend to have higher total sugars, dry matter, and chlorophyll content [57]. Browning of fresh-cut lettuce is a significant quality issue and was found to be related to the expression level of the scopoletin biosynthesis gene, which can be used as a marker for browning prognostication [58]. The calcium-related physiological disorder “tip burn” is another lettuce quality issue. Genetic variability was found to be exceptionally high in cultivars of the Crisphead type and significantly associated with the degree of head closure, which may be used as an indicator to select against tip burn susceptibility [59].
Another popular leafy vegetable for greenhouse production is spinach (Spinacia oleracea L.) [60]. Early bolting is a quality-relevant attribute in spinach and is provoked by environmental and genetic factors. The comparison of transcriptomes from early- and late-bolting spinach cultivars discovered a function of genes associated with the signaling pathway vernalization or the circadian clock, among others, a valuable discovery for molecular breeding programs [61].
Studies analyzing the genetic diversity of rocket salad (Eruca vesicaria) collections using molecular markers have demonstrated significant variation within and between wild and cultivated populations, offering valuable resources for identifying promising candidates for future breeding programs [21,62,63].

3. Biotechnological Approaches for Quality Improvement

Modern biotechnology offers advantages over conventional vegetable breeding, such as a faster selection procedure, high precision in the targeted modification, and the possibility to exploit and combine genes [64]. A comprehensive overview of genes identified to be involved in commodity, flavor, and nutritional quality for vegetables of the Solanaceae and Cucurbitaceae families, which may be targets of genetic manipulation, is given by Gao et al. (2022) [65]. Gene identification is carried out through a transcriptomic analysis by RNA-seq, utilizing next-generation sequencing (NGS) technologies. It allows us to identify and quantify the expression of all genes represented in a biological sample. The generated data (1) provide information on the molecular mechanisms underlying diverse biological processes, including those related to vegetable quality parameters; (2) reveal gene expression patterns; (3) allow the development of molecular markers for the selection of specific quality attributes; and (4) help to identify genes that can be used in genetic engineering [66]. Table 1 lists examples of genes and pathways related to vegetable quality parameters identified through comparative transcriptome analysis.
For example, the primary differentially expressed genes in tomato fruits with higher versus lower blossom-end rot (BER) incidence were related to those genes that trigger a reduction or increase in oxidative stress. Identified genes may be used as expression markers for the selection of tomato cultivars less susceptible to BER [69]. Equally, the identification of PECTATE LYSATE (PL) genes as downregulated in long shelf-life versus short shelf-life romaine lettuce varieties shows the importance of these cell wall degrading enzymes in lettuce shelf-life and may be valuable expression markers for pre-harvest lettuce shelf-life detection [76].
Shelf-life determines the period of market acceptance of vegetables after harvest and during transport and storage, considering appearance and legal and safety aspects [77]. Influencing fruit maturation for better quality and extended shelf-life is one of the main objectives addressed during recent decades using genetic engineering [78]. Gene knockout and site-directed mutagenesis using the CRISPR/Cas9 system allowed a re-evaluation of gene function and the potential for quality improvement related to fruit maturation of known ripening-related genes, especially in the model fleshy fruit tomato. The commonly applied CAS9 RNA-guided nucleases (RGNs) of the CRISPR system create double-strand breaks (DSBs) in the target sequence, which are then repaired by either non-homologous end joining (NHEJ) or homology-directed repair (HDR). Large lesions caused by DSBs may lead to low editing efficiency due to genome rearrangements, extensive lesions, and cell death. A solution to this problem is the usage of nicking RGNs such as Cas9 nickases, which produce single-strand breaks, avoiding unwanted double-strand breaks and stimulating cellular repair mechanisms [79]. Another promising biotechnological tool for plant genome modulation is the large serine integrases (Int), which originate from bacteriophage–prokaryote interactions. This genome modulation system allows for reversible DNA insertions, deletions, and inversions [80]. Table 2 summarizes the outcomes of CRISPR/Cas9 gene editing related to tomato fruit maturation.
Among the examples listed in Table 2, a double CRISPR knockout of the pectin-degrading enzymes polygalacturonase and pectate lyase can be highlighted, which significantly increases fruit firmness and shelf-life [81]. Another example is the CRISPR/Cas9 targeting of the gene GREENFLESH (GF) in tomatoes. The gene encodes an Mg-dechelatase involved in chlorophyll degradation during ripening. The functional analysis of mutants indicated that fruits were vitamin E over-accumulating and showed a higher pathogen resistance, making the GF gene an interesting target for tomato breeding [89].
Carotenoid content in vegetables plays a critical role in human nutrition and health due to antioxidant properties and dietary sources of provitamin A. Carotenoids are therefore targets for improvement through genetic engineering. This may be achieved by introducing genes from other species, such as the transfer of the Arabidopsis lycopene beta-cyclase (β-Lcy) gene into bell peppers or the bacterial lycopene β-cyclase gene into tomatoes, resulting in increased b carotene levels [91,92]. Carotenoids are synthesized and sequestered in diverse types of plastids. Each plastid type has a unique regulatory network of carotenoid metabolism, a fact that needs to be considered when designing strategies for carotenoid enrichment in vegetables, addressing aspects such as the rate of biosynthesis and degradation or the sink strength of plastids [93]. A candidate gene is the enzyme phytoene synthase 1 (PSY1), which influences carotenoid pool size by affecting the metabolic flux into carotenoid biosynthesis, and it was shown that its expression level directly correlated with carotenoid content in tomato fruits [94]. Plastid number and size also directly affect sink strength as demonstrated by increased carotenoid contents in tomato fruits of the high-pigment (hp) mutant, carrying a mutation in the gene UV-DAMAGED DNA-BINDING PROTEIN 1 (DDB) [95].
Cucumber lacks an efficient genetic transformation system. However, a comprehensive revision of the key factors of successful transformation concerning genotype and explant selection, hormone addition to growth medium, and co-cultivation and selection methods represents promising starting points for future research [96].
Qualitative improvements in lettuce have been achieved through various gene introductions, such as the overexpression of the γ-tocopherol methyltransferase (γ-TMT) gene from Arabidopsis thaliana [97]. Cao et al. (2022) applied CRISPR/Cas9 gene editing combined with Agrobacterium rhizogenes-mediated transformation in spinach, paving the way for future genome editing in this crop [98]. Mutation of the enzyme myrosinase in Brassica juncea (mustard greens) using the CRISPR/Cas12a system resulted in non-pungent leaves [99].
This brief review highlighted the effective use of strategies to enhance the quality of economically significant fruit and leafy vegetables. The CRISPR/Cas gene editing technology is considered a relatively low-cost method, amenable also to small companies [100]. However, advancing genetically edited food encounters several obstacles, including the need for robust safety research, international regulation variations, and public perception and acceptance challenges. Safety research must be bolstered, international regulations must be aligned, and public awareness and understanding must be increased to enable the widespread adoption of gene-edited food [101]. The EU’s regulations on GMOs are considered outdated by scientists and organizations such as the Union of European Academies for Sciences Applied to Agriculture, Food, and Nature, and they suggest these rules should be reevaluated [102]. Another significant concern is the potential impact of gene editing technology on agricultural production in developing countries, where genetically modified (GM) crops face opposition and skepticism, particularly among smallholder farmers. Farmers are worried about GM crops’ environmental and public health effects and fear that genetic modification could undermine the sustainability of their agricultural systems. These concerns are partly driven by a lack of access to accurate information about the benefits of GM crops, such as their higher nutritional value, increased yield, and reduced chemical input. Additionally, a lack of trust in scientists and government institutions further exacerbates these concerns [103].

4. Conclusions

Greenhouse production offers a controlled environment that enhances the effectiveness of breeding programs. Nevertheless, genotype-environment interactions are crucial, impacting quality traits and emphasizing the need for adaptable varieties across diverse environments. Various methods exist to improve the quality of fruit and leaf vegetables, including classical breeding and biotechnological approaches. Classical breeding relies on genetic diversity and techniques like marker-assisted selection to enhance quality traits. Molecular tools like SNP markers aid precise trait mapping. Modern biotechnology, especially genetic engineering and gene editing techniques like CRISPR/Cas, has been instrumental in improving various traits in a range of vegetables. These advancements can potentially address challenges related to stress resistance, product quality, and shelf-life, offering promising opportunities for the future of agriculture. Breeding new vegetable cultivars with fewer physiological problems, improved flavor, higher levels of healthy compounds, and better nutritional quality using modern methods will be a long-term effort.

Author Contributions

Conceptualization, J.W. and N.S.G. writing—original draft preparation, J.W. and N.S.G. writing—review and editing, J.W. and N.S.G.; visualization, J.W. and N.S.G. All authors have read and agreed to the published version of the manuscript.

Funding

This research received no external funding.

Acknowledgments

N.S.G. was supported by a grant for the requalification of the Spanish University System, Maria Zambrano modality (Grants funded by Ministerio de Universidades and by the ‘European Union NextGenerationEU/PRTR’). Many thanks to Michał Słota, Contentfarmers, for designing the graphical abstract.

Conflicts of Interest

The authors declare no conflicts of interest.

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Table 1. Identification of metabolic/signaling pathways and genes involved in selected vegetable quality attributes using comparative transcriptome analysis.
Table 1. Identification of metabolic/signaling pathways and genes involved in selected vegetable quality attributes using comparative transcriptome analysis.
Quality AttributeBiological Samples for RNA SeqPathways/Terms of Differentially Expressed GenesOutstanding Differentially Expressed Genes Reference
Tomato
Fruit flavor Off-vine ripened tomato fruits treated with ethylene (Off)
versus
Fruits matured on the vine to the red stage (On)		Malic acid metabolism
Lipoxygenase activity
Synthesis of specific volatiles
Ethylene biosynthesis, signaling, response and regulation
Ripening-associated transcription factors
Auxin response genes 		Up in (Off)
MALATE DEHYDROGENASE 1 (MDH1); LOXC, BCAT1, AADC1A, ACS2, ACO1, NR, RIN, TAGL1, UL1 ERF.E4, ARF2A, Aux/IAA3, Aux/IAA9, SAUR69
UP in (On)
MADS1, ERF.E1, ERF.B3, NAC4, Aux/IAA1, Aux/IAA2, Aux/IAA4, Aux/IAA8, Aux/IAA13, Aux/IAA35, TPL6		[67]
Shelf lifespanLong shelf-life cultivars (LS)
versus
Short shelf-life cultivars (SS) 		Ethylene biosynthesis and response
Cell wall loosening
Cell wall 		Up in (LS)
ERF2, ERF, ACO1, ACO4, ACS6, ACS2, XTH3, XTH7, XTH23, 1,3;1,4-β-D-Gluc-like, pGlcT1, CELLULASE, PGH1, PL5, PL-like 1, PL-like 2		[68]
Blossom-end rot (BER)Blossom-end fruit tissue-26 days after pollination Fruits sprayed weekly after pollination with:
Apogee 1 (Pro1exadione calcium) (A)
versus
Abscisic acid 1 (AA)
versus
Water 2 (control)
versus
Gibberellins 4 + 7 (GA4 + 7) 3 (G)
(BER incidence: 1 = 0; 2 = medium; 3 = high)		Transcriptional regulation
Hormone
Oxidation-reduction
Protein metabolism
Lipid
Defense response
Detoxification
Nutrient
Cell wall		UP in (A); (AA) (low BER):
SRO2, DREB, MAF1, ERF109, ERF110, CBFq, NAC-NOR, MeJA, WAT1, AREB, PYL9, TAS14, TOC23, Class-III ADH; FBNL2, 2PIIFs, SRP 7S, UBLCP1, 2CIPKs, RABA5a, DNAJC2, SDF2, PP2-A13, MSR-B5, 2 GDSL, AAE7, LTP1, 2 JRLs 19, STO, PRP6, LGL, TAT, Td, MTP1, CCH
UP in (G) (high BER)
TIFY10A, RBOH, AO, SOBIR1, PME3		[69]
Fruit color Yellow-color fruit (YF)
versus
Green-color fruit (GF)
versus
Red-color fruit (RF)		Phenylpropanoid biosynthesis
Flavonoid biosynthesis
Flavone biosynthesis
Flavonol biosynthesis
Carotenoids		Up in (GF)
PSY2, PDS, PDS Z-ISO, ZDS
UP in (RF)
PSY1		[70]
Pepper
Storage toleranceResistant to storage (R)
versus
Non-resistant to storage (NR)		Ethylene and response
Cell wall
Polygalacturonase		UP in (R)
POLYGALACTURONASE INHIBITOR (PGI), CELLULOSE SYNTHASE (CESA), ERF1B-LIKE
Down in (R)
POLYGALACTURONASE (PG), ERF3-LIKE, ERF096-LIKE, ERFRAP2-13-LIKE		[71]
Fruit shapeAnthesis ovaries of:
Flat-shaped
versus
blocky-shaped
versus
horn-shaped
versus
helical-shaped (H)
versus
slender-shaped (S)		OFP-TRM pathway
IQD-CaM pathway
Amino acid transport and metabolism
Lipid transport and metabolism
Cell wall/membrane/envelope biogenesis
Hormone
Development
Cell proliferation/division
Cytoskeleton
Cell wall		Up in (S) (compared to other shapes)
IQD14
Down in (S) (compared to other shapes)
IQD25, EXO84A, NEDD1, SWEET1, SWEET10
Up in (H) (compared to other shapes)
MLP28, CYCA2;4, ECA2, ATK4, FLA11
Down in (H) (compared to other shapes)
CYCA2;1, SWEET, CC1, LRX, PLL		[72]
Eggplant
Seedless fruits Natural parthenocarpic lines (P)
versus
Non-parthenocarpic lines (NP)		Auxin signaling
Auxin distribution
Auxin-dependent cell division
Inactivation of IAA,
Interference of auxin signaling		UP in (P)
CALCIUM-BINDING PROTEIN PBP1, E2FB, NAC DOMAIN-CONTAINING PROTEINS, AGAMOUS-LIKE MADS-BOX PROTEIN
Down in (P)
GH3.1, SMALL AUXIN-UP PROTEIN 58. AUX/IAA, PP6-ARS-B, CYP83B1, SAPK2, GIBBERELLIN 3-BETA-DIOXYGENASE, COL HOMOLOG		[73]
Fruit brightnessDull peel (DP)
Versus
Glossy peel (GP)		Cuticle cutin and wax content
Elongation of fatty acids
Export of wax components		Down in (GP)
KCS6 (Β-KETOACYL-COA SYNTHASES) AND ABC TRANSPORTER PROTEINS		[74]
Cucumber
Shelf-lifeExtended shelf-life genotype (ES)
versus
Poor shelf-life genotype (PS)		Cell wall degradation
Chlorophyll metabolism
Ethylene metabolism		Down in (ES)
POLYGALATURONASE GENES, EXPANSIN-A4, XYCLOGLUCAN GENES (GLYCOSYLTRANSFERASE, ENDOTRANSGLUCOSYLASE/HYDROLASE PROTEIN) PECTINESTERASE, CHLOROPHYLL CATALYTIC ENZYMES, KEY GENES FOR ETHYLENE METABOLISM (ACO, ACS, EFTS)		[50]
Ascorbic acid (AsA) contentExocarp (EXC) (high AsA)
versus
Endocarp (ENC) (high AsA)
versus
Mesocarp (MC) (low AsA)		L-Galactose, D-Galacturonate, Myo-inositol and ascorbate recycling pathwayUp in (EX) and (ENC)
PHOSPHOMANNOMUTASE (PMM), GDP-MANNOSE-3′, 5′-EPIMERASE (GME), DEHYDROASCORBATE REDUCTASE (DHAR)		[75]
Leafy vegetables
Spinach bolting Early-bolting accessions (EB)
versus
Late-bolting accessions (LB)		Vernalization
Photoperiod/circadian clock
Gibberellin
Autonomous pathways
Aging pathways
Carbohydrate		UP in (LB)
FRUCTOSE-1, 6-BISPHOSPHATE ALDOLASE (FBA), TREHALOSE-6-PHOSPHATE SYNTHASE 1 (TPS1), COP1
UP in (EB)
FLOWERING PROMOTING FACTOR 1 (FPF1), TRANSCRIPTION FACTOR MADS-BOX, ELF, GI, CERTAIN AP2/ERF TFS, AGAMOUS-LIKE MADS-BOX PROTEIN		[61]
Lettuce shelf-lifeShort shelf-life cultivar (SSL)
versus
Long shelf-life (LSL)		Cell wall integrity
Cell enlargement
Cell wall degradation
Senescence
Jasmonic acid biosynthesis and signaling		Down in (LSL)
PECTATE LYSATE (PL) AND EXPANSIN (EXP) GENES
Up in (LSL)
SENESCENCE NEG. REGULATORS (SNAC83, LSWRKY48, AND LSWRKY70)
JA BIOSYNTHESIS GENES LSPLA1, LSLOX, LSAOS, LSAOC, LSKAT, LSJAR1, LSSAM-MTASE		[76]
Table 2. Outcomes of CRISPR/Cas9 gene editing related to tomato fruit maturation.
Table 2. Outcomes of CRISPR/Cas9 gene editing related to tomato fruit maturation.
CRISPR-Mutagenized GeneEffect on Fruit RipeningReference
Pectin degrading enzymes POLYGALACTURONASE (SlPG2A) and PECTATE LYASE (SlPL)Increased fruit firmness and shelf-life[81]
PECTATE LYASE (PL)Increased fruit firmness[82]
Transcription factors APETALA2a (AP2a), and FRUITFULL (FUL1/TDR4 and FUL2/MBP7)Orange-ripe phenotype[83]
Transcription factor NON-RIPENING (NOR)Delayed ripening[83]
Transcription factor ALCOBACA (ALC)–(NOR allele)Enhanced shelf-life[84]
Transcription factor TOMATO AGAMOUS LIKE 1 (TAGL1)Reduced ethylene biosynthesis, increased firmness, delayed ripening[85]
Transcription factors SBP box-Colourless non-ripening (SBP-CNR) and NAC-Non ripening (NAC-NOR) Delayed or partial non-ripening phenotypes [86]
MADS-box TF RINIncomplete-ripening fruits reduces red color pigmentation[87]
Transcription factor SlNAC4Inhibition of fruit softening[88]
GF locus (Mg-dechelatase)Reduced chlorophyll degradation, fruits accumulate carotenoids and chlorophylls.[89]
Ripening-related long non-coding RNA (lncRNA1459)Repression ripening, ethylene production, and lycopene accumulation [90]
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Weiss, J.; Gruda, N.S. Novel Breeding Techniques and Strategies for Enhancing Greenhouse Vegetable Product Quality. Agronomy 2025, 15, 207. https://doi.org/10.3390/agronomy15010207

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Weiss J, Gruda NS. Novel Breeding Techniques and Strategies for Enhancing Greenhouse Vegetable Product Quality. Agronomy. 2025; 15(1):207. https://doi.org/10.3390/agronomy15010207

Chicago/Turabian Style

Weiss, Julia, and Nazim S. Gruda. 2025. "Novel Breeding Techniques and Strategies for Enhancing Greenhouse Vegetable Product Quality" Agronomy 15, no. 1: 207. https://doi.org/10.3390/agronomy15010207

APA Style

Weiss, J., & Gruda, N. S. (2025). Novel Breeding Techniques and Strategies for Enhancing Greenhouse Vegetable Product Quality. Agronomy, 15(1), 207. https://doi.org/10.3390/agronomy15010207

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