Lettuce (Lactuca sativa L.) is among the topmost cultivated crops in CEA for food production in the US (USDA-NASS, 2019). Lettuce has seven morphological types, namely, crisphead subdivided into Batavia and iceberg, butterhead including Boston and bibb, romaine or cos lettuce, Latin, and leaf or cutting lettuce, which are most common in field production worldwide (Ryder, 1999); however, in the US, the most popular types are crisphead, romaine, and leaf lettuce (USDA-NASS, 2022). More ancient types of lettuce include stem lettuce also known as “stalk” or “asparagus” lettuce and the oil seed type (Hayes, 2018). Traditionally, the crop has been improved for field adaptation (Hayes, 2018). While romaine and icebergs have been historically improved through breeding for head weight and morphology for field production, the most cultivated types in CEA are romaine, butterhead, and leaf lettuce and their subtypes. CE growers may require cultivars that offer novel morphological types than those grown in fields. A combination of leaf and crisphead lettuce commonly known as “crunchleaf” or “summercrisp” is currently desired by the industry.

Several key traits important for field production including high water- and nutrient-use efficiency (WUE and NUE) and resistance to biotic and abiotic stresses are also important in CEA (Sandoya, 2019). The CEA industry will benefit from lettuce cultivars improved for unique traits including nutritional value, new leaf shapes and colors, and the ability to adapt to new horticultural technologies including light use efficiency and mechanical harvesting. Variations in phylloquinone, tocopherols (alpha and gamma), and ascorbic acid (vitamin C) content in hydroponically grown lettuce demonstrate the opportunity to enhance metabolites beneficial for human health (Murray et al., 2023). Similarly, genetic variability within L. sativa for morphological traits like leaf shape, color, and texture can be utilized to develop cultivars for niche markets (Sandoya, 2019). Opportunities exist to create newer shapes and color variations from green to red that could be beneficial to CEA producers.

Major concerns for lettuce producers are diseases caused by plant pathogens. Most of the genetic studies in L. sativa and related species have been conducted for disease resistance. There is extensive germplasm testing either in a greenhouse (or lab-associated assay) or on the field for diseases such as downy mildew (DM) caused by Bremia lactucae. There are at least 51 genes and 15 QTLs controlling DM resistance (Parra et al., 2016). However, the fungus rapidly evolved overcoming host resistance into different races, of which 10 races are present in the US and 23 races are in the European Union (IBEB, 2024) while the B. lactucae race structure in other lettuce-producing regions of the world is unknown (Wu et al., 2018). The resistance to DM is widespread across several chromosomes in the lettuce genome and multiple germplasms of L. sativa and wild types of L. serriola and L. saligna (see Parra et al., 2016 for details). Further resistant loci were relatively recently identified in L. sativa (Parra et al., 2016; Simko et al., 2021). Other diseases including Fusarium wilt, Verticillium wilt, Sclerotinia drop, and Corky root rot are a concern to field producers due to their soil-borne nature (Raid and Sandoya-Miranda, 2024). It is expected that the pathogens causing these diseases, Fusarium oxysporum f. sp. lactucae, Verticillium dahliae, and Rizhorhapis suberifaciens, would be less problematic when the crop is produced hydroponically or in soilless substrates. However, a soilborne disease, Pythium wilt (Davis, 2018), has been reported on lettuce cultivated in CEA (Tsoukas et al., 2023). The disease has become problematic in fields and the pathogen has been identified and reclassified as Globisporangium uncilunatum (syn P. uncinulatum) (Slinski et al., 2024). Several of these soilborne pathogens are believed to be seed-borne. Further investigation on the survival of these pathogens from contaminated seeds on specific media (water, growing media including rockwool, vermiculite, etc.) can reveal the potential outbreaks of these pathogens.

While powdery mildew (PM) caused by Golonovinomyces cichoracearum is not a significant problem in the field except during conducive conditions, the disease is more problematic in greenhouses (Simko et al., 2014). The intent of year-round production in CEA creates the need for improved germplasm with resistance. There are few resistance sources for PM in the wild and cultivated lettuce, especially in butterhead lettuce (Lebeda, 1985, 1994; Lebeda et al., 2014; Simko et al., 2014). Resistance to other diseases concerning the CEA lettuce industry needs further investigation. There are no known sources of resistance against P. uncilunatum or any Pythium spp. and C. latucae-sativae (Raid, 2018). It remains unknown if F. oxysporum f. sp. lactucae, V. dahlia, or R. suberifaciens will cause disease outbreaks on lettuce in soilless media.

Lettuce is best adapted to temperatures below 28°C during the day and 23°C at night (Hayes, 2018). Higher temperatures could lead to early bolting and tipburn. Similarly, the crop suffers damage when exposed to longer periods of cold temperatures below 18°C during the day and 10°C, at night, respectively (Hayes, 2018). The rising temperatures across the globe are affecting both marketability and promoting physiological disorders (Lafta et al., 2017, 2021; Raid and Sandoya-Miranda, 2024). The need for cooling or heating of CEA operations results in increased production costs. The development of cold- and heat-tolerant cultivars is desired for both field and CEA production. Genetic variability has been identified within L. sativa for heat tolerance in romaine, butterhead, crisphead, and leaf lettuce (Lafta et al., 2017, 2021; Kreutz et al., 2021; Raid and Sandoya-Miranda, 2024). However, the genetics underlying the trait are yet to be identified. Further efforts are underway to identify germplasm that tolerate warmer temperatures in greenhouses to improve heat tolerance. Selection against bolting and tipburn is beneficial to both field and CEA lettuce production. While genetic variation is present for bolting (Rosental et al., 2021), tipburn, a physiological disorder, is partially controlled by a genetic component (Hayes, 2006; Macias-González et al., 2019) and needs further research.

For CEA, lettuce should be efficient in several factors including nutrient uptake and utilization. Lettuce cultivars with high WUE have been identified (Eriksen et al., 2016; Macias-González et al., 2021). Nitrogen and phosphorus uptake are known to be genetically controlled in lettuce (Macias-González et al., 2021; Kreutz et al., 2022). The genetics of WUE and nitrogen uptake are complex involving multiple loci distributed across the genome (Macias-González et al., 2021). It is important to note that these genetics are described for field lettuce and only phosphorus uptake has been investigated in hydroponic settings (Kreutz et al., 2023). Salinity is posing a concern in areas that are aquifer-dependent or close to saltwater. Salt intrusion into aquifers has affected the crop by higher salt levels in soils (Miceli et al., 2003). Lettuce cultivars tolerant to salinity could alleviate this problem (Xu and Mou, 2015; Eriksen et al., 2016) and could be used for saltwater-based aquaponics systems in CEA.

Most genetic studies in lettuce have been conducted using biparental mapping populations. There are few publicly available molecular markers for use in marker-assisted selection (MAS) specifically for disease resistance (Michelmore, 2018). These markers are limited to single locus inherited traits. Limited genome-wide association studies (GWAS), including resistance for bacterial leaf spot, DM, and shelf life, have been conducted using diverse germplasm sets (Sthapit Kandel et al., 2020; Kandel et al., 2022; Simko et al., 2022). As more phenotypic traits are mapped using GWAS populations, genomic selection (GS) will be employed to breed lettuce for polygenic traits.

Spinach (Spinacia oleracea L.) is widely recognized for its exceptional nutritional profile. It is packed with essential vitamins (A, C, K, and folate), minerals (iron and calcium), antioxidants (lutein, zeaxanthin, and flavonoids), and dietary fiber (Drewnowski and Gomez-Carneros, 2000; USDA FoodData Central, 2024). Traditionally, spinach is grown in open fields in the US, predominantly in California (April to October) and Arizona (November to March). Growing consumer demand for nutritious foods, particularly leafy greens like spinach, has spurred advancements in cultivation methods. There is a growing shift towards year-round production in CEA to meet the demand while minimizing environmental impact (Garcia et al., 2023). Breeding spinach specifically for CEA has become vital to meet the growing shift. Key breeding objectives include optimizing yield, maintaining or enhancing the nutritional profile under controlled conditions, and developing varieties that meet consumer demands for health-promoting vegetables.

Tomato breeding has specialized based on the market, product type, and cultural requirements such as fresh market, processing, CEs, or home garden (McKenzie, 2014). For varietal development, unique breeding strategies are needed for specific growing conditions and market challenges. Breeding tomatoes for CEs is evolving to meet the demands of production facilities such as indoor farms, vertical farms, greenhouses, and their modified forms. Most single-tier CE farms currently grow indeterminate tomatoes that can grow for an extended period and determinate large-fruited tomatoes, with or without grafting. Introducing tomatoes to vertical farms is yet to be realized due to a lack of optimized cultivars. Kozai (2013) recommended plant height to be approximately 30 cm to optimize space and ensure multi-tier production in platforms established for leafy vegetables. Modifications in plant architecture, morphology, and size are implemented to develop dwarf plants that fit in CEA. Various genes—DWARF (D), SELF-PRUNING (sp), miniature (mnt), and Dumpy (dpy)—contribute to reducing plant stature (Bishop et al., 1996; Pnueli et al., 1998; Koka et al., 2000; Martí et al., 2006). Moreover, meristem traits such as side shoots and branching need optimization. Canopy reduction results in smaller fruit size and hence breeding efforts need to retain fruit size while selecting for decreased canopy. The development of dwarf tomatoes began with the release of Dwarf Champion and more recently with Micro-Tom (Livingston Seed Company, 1896; Scott and Harbaugh, 1989). While Micro-Tom was a concept product, Micro-Tina and Micro-Gemma were released with improved sweetness (Scott et al., 2000). Recently, the performance of dwarf cultivars was tested for plant growth, yield, and CEA fitness (Langenfeld and Bugbee, 2023). Extended greenhouse production times can be compensated by shorter crop cycles and increased planting density in vertical and indoor farms. Plant performance under hybrid or fully electric lighting needs consideration to develop new CEA varieties. CEs also offer opportunities for the implementation of robotics and automation. Therefore, developing traits granting process mechanization such as synchronous maturity and longer pedicels for harvesting ease is essential. Synchronous maturity is a polygenic trait predominantly used in the processing tomato industry for mechanical harvest (Lukyanenko, 1991). Golden 2-like 2 (GLK2) gene has been widely used in modern breeding programs to control uniform fruit ripening. Genes terminating flower (tmf) and jointless (j) reduce the number of flowers in the inflorescences of lateral shoots and can be used in maintaining the quality and yield of fruits in dwarf plants in CEs (Molinero-Rosales et al., 1999; MacAlister et al., 2012). Dwarf and early varieties help in spreading the risk over multiple cycles.

While some CEs use sunlight and supplemental electric light, indoor vertical farms solely rely on electric lighting. Focus on genes eid1 and lnk2 involved in the circadian clock could help in breeding plants for altered photoperiod to reduce energy costs (Müller et al., 2018). Plants with high phenotypic plasticity can help plants adapt to different light sources and production systems such as hydroponics, aeroponics, or aquaponics. Shoot architecture including leaf number, area, and angle determines light capture, photosynthesis, and transpiration but is highly influenced by the environment. Plant responses due to growing conditions could help develop breeding strategies to capitalize on these traits. Inflorescence branching caused by FALSIFLORA and other genes could be used for smaller fruit types like cherry and grape, while tmf mutants causing unbranched inflorescences are desirable for Roma and large-fruited tomatoes (Molinero-Rosales et al., 1999; MacAlister et al., 2012).

Besides the traits useful to crop optimization in CEA, several fruit traits pertaining to consumers are significant, such as fruit striping, skin texture, nutritional quality, flavor, shape, size, and aroma. Various studies have inventoried metabolites in tomato fruits as previously reviewed (Rothan et al., 2019). Purple tomatoes with increased anthocyanin content have been developed by combining the dominant allele Atv with Aft or Abg in “Indigo rose” and “Sun Black” cultivars (Ooe et al., 2016; Blando et al., 2019). Genetic engineering has been applied to enhance anthocyanin production using genes encoding R2R3-MYB, bHLH, and WDR factors (Zhang et al., 2019). Overexpression of S. lycopersicum Anthocyanin 1 (ANT1) and SlAN2 originating from S. chilense resulted in enhanced anthocyanin production (Sun et al., 2020). Furthermore, increased anthocyanins using two snapdragon Delila (Del) and Rosea (Ros1) genes delayed overripening and reduced susceptibility to a postharvest disease gray mold (Zhang et al., 2013). The level of anthocyanins produced by genetic engineering using Del and Ros1 is higher than conventionally bred purple tomatoes using atv and Aft (Baranski et al., 2024). Therefore, both traditional and biotechnological breeding could be applied to increase nutritional compounds (Ilic and Misso, 2012). These resources could be used to develop varieties with novelty in consumer-related traits to minimize market competition and generate price premiums.

A wide range of tomato fruit colors appeal to consumers and some colored pigments are known to prevent cardiovascular disease and potentially reduce obesity (Gammone et al., 2015). Tomato fruit color is a multigenic trait. The red color of tomato is due to all-trans-lycopene, naringenin chalcone (NarCh), and yellow skin (Zhu et al., 2018). Mutation in recessive yellow (y) disrupts NarCh deposition resulting in transparent skin and pink-colored fruits. Loss of function of PSY1 leads to yellow fruit, and mutations in CRTISO and IDI1 genes in tangerine (t) and fruit carotenoid-deficient 1 mutants resulted in overall carotenoid reduction, giving orange color (Isaacson et al., 2002; Pankratov et al., 2016). Accumulation of carotene due to lycopene β-cyclase and ϵ-cyclase encoded by CrtL-b and CrtL-e genes also confers an orange color in ripe tomato fruits (Ronen et al., 2000). Brown-colored tomato fruits have been attributed to an inability in chlorophyll degradation due to mutation in STAY-GREEN1 (SGR1) coupled with lycopene accumulation during ripening (Barry et al., 2008). Genetics of carotenoid production is reviewed by Baranski et al. (2024). While S. lycopersicum mostly produces red tomatoes, fruits of some S. cheesmanii were reported to be yellow, yellow-green, orange, and purple, fruits of S. pimpinellifolium were reported to be red, fruits of S. habrochaites, S. peruvianum, S. pennellii, and S. chmielewskii were described to stay green, and fruits of S. neorickii were reported to be pale green (Peralta et al., 2021). Crimson (og^c ) gene, an alternative allele at Beta (β) locus, is widely used in fresh market breeding as it increases lycopene and provides deep red color in seed locules and pericarp. In addition to og^c , a dominant QTL (lyc12.1) from S. pimpinellifolium accession LA2093 increases lycopene by 50% to 70% without reducing β-carotene (Kinkade and Foolad, 2013). Recently, three color-related genes Phytoene Synthase 1 (PSY1), R2R3-MYB transcription factor (MYB12), and SGR1 were edited using multiplexed CRISPR-Cas9 to produce yellow, brown, pink, light yellow, pink-brown, yellow-green, and light green–green colors of fruits (Yang et al., 2022).

Tomato flavor is a fusion of sugars, acids, and numerous volatile organic compounds (VOCs). Selection for increased yield, fruit size, and disease resistance has impacted unintentional flavor loss in modern varieties (Folta and Klee, 2016). A breeding opportunity exists to revisit the lost flavor genes and leverage CEA produce for high-quality products (Figàs et al., 2015). The sources and genetics of tomato flavor have been previously studied (Pereira et al., 2021). Although not trivial, improvement in flavor could be achieved through manipulating VOCs without significantly impacting quality or yield with the help of automated phenotyping, SNP markers, and gene editing. While a clear understanding of flavor has not been established, several studies have discovered genomic regions and variants involved in flavor (Kuhalskaya et al., 2024). Genomic regions including genetic loci, candidate genes, and transcription factors (TFs) involved in flavor in tomato have also been reviewed (Kaur et al., 2023). These regions can be harnessed to develop specific flavors in novel varieties for CEA.

Pepper (Capsicum annuum L.) breeding for CEA mainly emphasizes plant growth and architecture, adaptability to environmental factors (temperature, humidity, and light efficiency), enhanced fruit quality, tolerance to biotic stresses, yield and productivity, WUE, amenable pollination and fruit set, and phenotypic plasticity, among others (Hummer, 2021; Goldstein and Ehrenreich, 2021). Breeding peppers (sweet, hot, and specialty type) for CEA requires an integrated approach to incorporate the targeted traits tailored for specific growing conditions. Breeding for targeted traits involves conventional breeding methods as well as advanced biotechnology approaches including MAS and genome editing. The genetic control of plant architecture is important in CEA breeding and candidate genes like MADS-box protein and WUSCHEL-like genes (Capanan11g001832 and Capana00g000667) are linked to inflorescence architecture in pepper (Lv et al., 2019). A single-base mutation in the CaBRI1 results in a dwarf phenotype (Yang et al., 2020). The FASCICULATE (FA) gene primarily known for its effects on fruit clustering also influences plant architecture and branching patterns (Elitzur et al., 2009). These findings offer insights into plant architecture and trait variation for breeding for CEA.

Enhancement in pepper fruit quality attributes like vitamin and antioxidant content as well as uniform fruit size and shape may generate added value at the retail level (Rouphael et al., 2018). Several genes and markers have been identified to improve fruit quality. The Capsanthin-capsorubin synthase (CCS) gene is a critical component in carotenoid biosynthesis, particularly in the production of red pigments (Lefebvre et al., 1998). This gene is closely associated with the dominant y⁺ allele, which results in red fruit coloration while its absence or mutation leads to the recessive y allele resulting in yellow or orange fruits (Popovsky and Paran, 2000). Gene Capana01g004285, encoding the BREVIS RADIX (BRX) protein, was linked to the locule number that influences fruit quality (Ma et al., 2022a). Additionally, Capana10g002229 was proposed to encode a polygalacturonase as a strong candidate gene associated with the deciduous character of ripe fruit impacting fruit softening and abscission (Hu et al., 2023). Furthermore, GS was explored for predicting fruit length, shape, width, weight, and pericarp thickness in pepper highlighting the potential of Reproducing Kernel Hilbert Space (RKHS) as a method with high prediction accuracies (Hong et al., 2020).

Damping off, PM, and bacterial spot are major disease concerns while aphids, whiteflies, and spider mites are the main pest issues observed in pepper production (Messelink et al., 2020). Wild relatives of pepper are valuable sources of resistant genes (Devi et al., 2021). Additionally, species in Capsicum have mechanisms such as osmoprotectant production, autophagy, and involvement of TFs and plasma membrane proteins in stress tolerance with identified genes and QTLs contributing to biotic stress tolerance (Jaiswal et al., 2019; Parisi et al., 2020). Numerous studies have pinpointed genomic regions associated with Phytophthora resistance (Siddique et al., 2019; Kumar et al., 2022; Ro et al., 2022; Kaur et al., 2024). The utilization of these genetic resources and markers is crucial in developing resilient and high-yielding varieties.

Early and continuous fruit sets can increase pepper productivity in CEA (Gautam et al., 2024). Multi-locus models in diverse populations have revealed eight GBS-derived SNP markers linked to multiple traits, indicating shared genetic control between plant height, width, and yield components (Lozada et al., 2021). QTL analyses have shown high heritability and identified 24 QTLs related to physiological traits influencing yield with pleiotropic effects observed on specific linkage groups (Alimi et al., 2013).

Breeding pepper for CEA could benefit from improving stress resilience and WUE. In bell peppers, two linked QTLs on chromosome 10 control post-harvest fruit water loss (PWL), a trait closely related to WUE (Popovsky-Sarid et al., 2017). These efforts advance the identification of the underlying genes increasing selection efficiency to develop water-efficient and drought-tolerant varieties (Lee et al., 2018).

Solanaceous vegetables (tomato, pepper, and eggplant) often require external pollinators to enhance fruit set and yield; therefore, selection of desirable flower types is necessary to facilitate improved pollination (Schubert, 2017; Folta, 2019). C. annuum and C. chinense produce single and multiple flowers per node, respectively, and have been the focus of genetic investigations. A study on recombinant inbred lines (RILs) between C. annuum and C. chinense identified four QTLs on chromosomes 1, 2, 7, and 11 accounting for 65% of the phenotypic variation in multiple-flower-per-node trait with five candidate genes involved in shoot and flower meristem development (Kim et al., 2022). Transcriptome analysis of different developmental stages of flowers identified several differentially expressed genes (DEGs) involved in flower development, nectar biosynthesis, and nectary development (Deng et al., 2020). The first flower node (FFN) trait important for evaluating fruit earliness was studied using bulked segregant analysis (BSA) and specific-locus amplified fragment sequencing identifying 393 high-quality SNP markers and 10 candidate regions on chromosome 12 associated with FFN (Zhang et al., 2018b). Further QTL mapping identified two major QTLs, Ffn2.1 and Ffn2.2 located in linkage group 2, associated with FFN consisting of 59 candidate genes including three DEGs (Zhang et al., 2019). Six QTLs were identified in an interspecific population developed from C. chinense and C. annuum controlling flower number per node. A candidate gene, Capana02g000700, encoding the homeotic protein APETALA2, significantly associated with flowering time (Zhu et al., 2019). These studies collectively reveal genetic mechanisms controlling flower type and can be used in breeding programs to improve pepper yield.

Phenotypic plasticity plays an important role in regulating plant growth and development functions that are influenced by the growing environment; hence, breeders must include this trait in their CEA breeding strategy. Phenotypic plasticity in pepper is influenced by various genetic markers and environmental factors. Variability in morphological and biochemical traits observed in C. baccatum accessions can enhance fruit length, diameter, fresh mass, and antioxidant activity (Constantino et al., 2020). In wild C. annuum populations, genetic differences leading to adaptive phenotypic plasticity based on water and light availability have been observed. Phenotypic plasticity is essential for plant fitness and is influenced by natural selection and genetic drift with selection gradients varying based on resource availability (Romero-Higareda et al., 2022). The genetic basis of phenotypic traits in C. annuum has been further elucidated through QTL identification associated with domestication and agronomic traits. These QTLs highlight the genetic architecture underlying traits such as fruit form, seedlessness, and growth habit, providing insights into domestication and exploiting wild alleles for crop improvement (Lopez-Moreno et al., 2023). Additionally, the marker effect networks have been proposed as a novel method to identify genetic markers associated with environmental adaptability. This approach was demonstrated in maize and can be adapted in pepper to understand how different markers co-vary across environments providing insights into phenotypic plasticity and environmental modulation of the genome (Coletta et al., 2023). Together, these studies underscore the complex interplay between genetic markers, environmental factors, and phenotypic plasticity in pepper, enabling breeding and conservation efforts. By exploiting these genetic resources and molecular breeding techniques, future research can focus on optimizing plant architecture, enhancing yield, and improving overall adaptability in CEs. This targeted breeding approach can potentially revolutionize pepper cultivation in CEA, leading to more efficient and productive systems that meet the growing demand for sustainable and high-density crop production.

Cucurbits such as cucumber (Cucumis sativus), melons (Cucumis melo), squash (Cucurbita spp.), and pumpkins are produced in fields, semi-controlled environments, and increasingly in CEs. For fruiting crops, a long harvesting season is highly desirable for CEA production. Most cucurbits display indeterminate vegetative growth when fruits are continuously removed (Loy, 2004). When not removed, fruits become dominant sinks for photosynthate, and this is accompanied by a slowing or cessation of vegetative growth (Valantin-Morison et al., 2006). Thus, crops with fruits harvested at an immature state like cucumber and summer squash will likely yield more in a CEA system than crops like pumpkin and melon that require full reproductive maturity. For CEA facilities to produce such fruits, niche markets will have to be developed that demand superior fruit quality as they will need to command a high price. Accompanying the increased quality, marketing efforts will be needed that allow for CEA-produced cucurbits to be differentiated in the marketplace via branding and labeling.

Cucurbits face a wide range of pest and disease pressures that can be avoided by growing them in CEs. Insect pests like the squash bug (Anasa tristis), squash vine borer (Melittia cucurbitae), and striped and spotted cucumber beetles (Acalymma spp.) can be excluded from cucurbits by using insect screening (Ingwell and Kaplan, 2019). This reduces both direct damage by insect pests and diseases that they transmit.

Among Cucurbitaceae, cucumber occupies the greatest CEA acreage currently (Pal, 2020). Published genomes and molecular markers are available for the major cucurbits to assist and accelerate breeding for CEA. Cucumber has a small genome with only seven chromosomes (Sun et al., 2006). Not only is it the most widely produced cucurbit in CEA, but also the crop with the most annotated genes. The cucumber genome was first sequenced in 2009 by Huang et al. Currently, three sequenced genomes have been published representing three of the major cultivar groups of cucumber. Approximately 22 QTLs have been mapped in cucumber including QTLs for important traits for CEA like fruit length, early flowering, parthenocarpy, gynoecy, and compact growth (Dey et al., 2023). Additionally, QTLs for important disease resistance traits have been mapped including for DM (Wang et al., 2016), PM (Nie et al., 2015; Xu et al., 2016), Fusarium wilt (Zhang et al., 2015), gummy stem blight (Liu et al., 2017), and cucumber mosaic virus (CMV) (Shi et al., 2018). Additionally, resistance to abiotic stresses such as low temperatures (Song et al., 2018), high temperatures (Dong et al., 2020), and salt stress also have mapped QTLs (Ahmad et al., 2023). Such extensive mapping and linked molecular markers should enable breeders to rapidly advance on breeding new cultivars especially well-suited for CEA.

Cucumber displays a wide range of flowering habits (Dhall et al., 2023). The development of gynoecious cucumber varieties is a major factor in the success of cucumber as a greenhouse crop. Three different loci are thought to affect sex expression in cucumber: F confers female flowers with incomplete dominance, m is a recessive allele that confers andromonoecy, and a confers androecy. The genotype of gynoecious varieties is thought to be MMFFA/a. A second locus has also been uncovered that confers gynoecy and is a recessive allele called gy. Because the femaleness conferred by gy is thought to be more stable than F, it is the gene most commonly found in gynoecious cucumber varieties (Dhall et al., 2023). Additionally, most cucumber cultivars used in greenhouse production are parthenocarpic. The Pc gene confers parthenocarpy in cucumber and is thought to be incompletely dominant. Genomics research with this trait has revealed great complexity including epistatisis and multiple chromosomal locations, and appears to be inherited quantitatively (Sun et al., 2006).

Although CEA systems can exclude many important insect pests, breeding cucumbers for disease resistance remains a major priority for breeders. Diseases like DM, PM, bacterial wilt, Fusarium wilt, CMV, and watermelon mosaic virus (WMV) can all present challenges for growers in CEs (Singh et al., 2017). Extensive molecular genetics work has revealed QTLs for resistance and breeders use MAS to guide their efforts in breeding resistance to these diseases.

Currently, most cucumber production in CEA systems takes place in greenhouses and high tunnels; however, cucumber is an emerging crop for vertical farms or PFALs (plant factories with artificial lights). Bush cultivars with greatly reduced internode length are available in cucumber and are the most suitable cultivars for vertical farms. Classical genetics studies identified seven genes that affect cucumber plant height and growth patterns, giving breeders the ability to tailor growth habits to a wide variety of growing environments (Naegele and Wehner, 2016). A recessive gene thought to impart a compact or dwarf habit and an associated molecular marker were identified and mapped by Li et al. (2011). This finding should guide breeders to develop compact cucumber cultivars (Li et al., 2011). Other important traits in cucumber breeding include freedom from bitterness, lack of spines on fruits, heterosis when making hybrids, flesh thickness, and yield (Dey et al., 2023).

Most modern cultivars of summer squash and zucchini have a bushy appearance with short internodes and a thickened central stem. Only one bush gene has been named, Bu, and is incompletely dominant to vine habit (bu). The recessive allele confers a vining habit with long internodes (Loy, 2013). However, the genetics behind the bush trait are likely not as simple as a single gene. Three QTLs associated with the bush phenotype in Cucurbita pepo were identified (Xiang et al., 2018) and QTLs for the bush trait had been previously mapped in C. maxima (Zhang et al., 2015). Lateral branching is also an important trait for breeding squash for CEA (Loy, 2004). Freedom from lateral branching is desirable as it promotes airflow and light penetration into the plant canopy, allowing for easy access to fruits for harvest. Greenhouse cultivars of summer squash should be single-stemmed with a semi-bush habit that enables trellising and utilization of the vertical space in modern greenhouses. The glabrous trait, conditioned by a single recessive gene (gl-2), is also highly desirable for CEA summer squash cultivars. This gene reduces scratching of fruits during the post-harvest period and eases skin irritation for CEA workers caused by trichomes found along stems and leaves of non-glabrous summer squash cultivars (Xiao and Loy, 2007).

A wide range of fruit shapes are available in summer squash including straightneck or marrow, crookneck, discoid or scallop, and round (Paris, 1996). Preferences for fruit shape in summer squash vary greatly. A wide range of colors is also available and range from dark green to light green/gray, yellow, bicolor, and white. Color expression is affected both by genes that impact rind color and by flesh color. Striping, conferred by the L1/L2 gene complex, is also a feature of some cultivars of zucchini and yellow straight and crookneck squash. The B gene causes precocious yellow pigmentation and is found in some varieties of yellow summer squash and yellow or golden zucchini (Shifriss, 1965, 1996). When heterozygous, the B gene is known for generating bicolor fruit as in the cultivar “Zephyr”, which is both bicolor and has the L1 allele for broad normal stripes. When homozygous, the B gene turns Cucurbita fruits uniformly yellow before anthesis. In addition to the use of Cucurbita pepo as summer squash, globally, other species may be harvested immature and eaten as summer squash as in the case of Korean summer squash cultivars of Cucurbita moschata, Italian Cucurbita moschata cultivars (cv. Trombocino) (Andres, 2004), and bush cultivars of Cucurbita maxima in South America (cv. Zapallito de tronco) (López-Anido et al., 2003). Interspecific hybrids of C. maxima × C. moschata are used as rootstocks for grafting crops like melon (Yarsi et al., 2012), used as winter squash (cv. Tetsakuboto) (Queiroga et al., 2017), and may have use as summer squash. Parthenocarpy in summer squash is a highly desirable trait for the development of cultivars suitable for CEA production. Several parthenocarpic cultivars (cv’s Whitaker, Parthenon, and Golden Glory) are in the marketplace, and breeding efforts are underway globally for the generation of new cultivars (Martínez et al., 2014; Tian et al., 2023). Although molecular breeding in summer squash is not as developed as in other cucurbits, its genome has been sequenced and is available to molecular breeders (Xanthopoulou et al., 2019). Major QTLs for traits such as growth habit, early flowering, leaf morphology, fruit size, and flesh color have already been molecularly mapped (Montero-Pau et al., 2016).

Fungal diseases like PM, caused by Podoshpaera xanthii and Golovinomyces orontii, pose a significant challenge for summer squash growers in CEA systems (Lebeda et al., 2024). Recently, Lebeda et al. (2024) reviewed the PM of cucurbits. Currently, only one resistant locus, a single, incompletely dominant gene called Pm-0, has been incorporated into commercial cultivars of summer squash. Molecular markers for this locus are available commercially for summer squash breeders (Holdsworth et al., 2016). Other resistant loci have been described in other Cucurbita species, like Cucurbita moschata, but are not yet available in commercial cultivars (Park et al., 2020; Alavilli et al., 2022). Other challenges for summer squash production in CEA include DM (Lebeda and Cohen, 2011) and Choaenophora fruit rots (Emmanuel et al., 2021).

CEA production of melons (C. melo), primarily cantaloupes also called muskmelons or rockmelons, continues to increase globally (Cantliffe and Vansickle, 2003). Like cucumber, melon plants display a wide variety of flowering habits and the availability of gynoecious lines and male sterile lines assist in its breeding (Hanafi, 2014; Kesh and Kaushik, 2021). Extensive genomic tools are available to melon breeders and many QTLs have been mapped to the melon genome. Melon breeding is facilitated by commercially available molecular markers for important traits such as Fusarium wilt, PM, WMV, and Zucchini yellow mosaic virus (ZYMV) resistance (Shahwar et al., 2023). Because many modern cultivars were bred for disease resistance and long shelf life, opportunities exist to breed for exceptional eating quality for CEA systems. Crops like cantaloupe vary greatly in quality when grown under field conditions leading to dissatisfaction among consumers (Farcuh et al., 2020). Advantages of CEA for melon production include reduced pest and disease pressure (Ingwell and Kaplan, 2019), reduced fruit cracking (Saltveit, 2016), and a reduction in risk from food-borne pathogens by avoiding melon to soil contact (EFSA Panel, 2014), a significant problem in field-based melon production. Additional traits that would help facilitate CEA melon production include parthenocarpy, a dwarf or compact plant stature, and fruiting along the main stem rather than fruiting along lateral branches as is typical of melon cultivars. In the US, cantaloupe, honeydew, and watermelon are the primary classes of melons available in most grocery stores. Specialty melons like Asian melons, casaba melons, Hami melons, casaba melons, Galia melons, and the horned melon (Momordica charantia), are becoming more popular and may offer opportunities for CEA production (Duncan and Ewing, 2015). Watermelon, Citrullus lanatus, is predominantly produced in open fields in the US, while countries like South Korea extensively use greenhouses for its production (Park and Cho, 2012).

Strawberry has drawn significant attention to CEA growers in the US as new findings demonstrate doubled yields as compared to field production (NIAB, 2022). Low height profile, high market value, wide demand, and high nutritional content make strawberries a suitable candidate for CEA (Hernández-Martínez et al., 2023). The lack of CE-tailored breeding efforts remains an obstacle to the wide application of CE strawberry farming (Hoffman and Shi, 2020). In some European countries, Canada, and Japan, strawberry greenhouse operations using supplemental lighting are standard and cultivars are selected for these settings. In the US, strawberry breeding for CEA needs to focus on selecting plants that perform well under two lighting systems, hybrid and electric lighting, hydroponic and substrate-based production, single and multi-tiered platforms, and resistance to prevalent diseases and pests.

Robotic and automated harvesting technology is being highly investigated in the CE strawberry industry. Breeding efforts need to be geared towards selecting traits supporting mechanical and automated harvesting. In vertical and greenhouse production, fruits hang from tabletop systems supporting automated harvesting. Improving traits like uniform long trusses, and larger and uniform shapes to generate better-displayed fruits can facilitate automation in harvesting (Diamanti et al., 2011). Cultivars like “Camarosa” and “Florida Elyana” are susceptible to yield loss due to misshapen fruits (Chandler et al., 2009; Ariza et al., 2012). Misshapen fruits can result from biological factors like unsuccessful pollination, abnormal carpel development, abiotic factors like rain damage, high temperature, and external factors like insect and disease damages (Chandler et al., 2009). Misshapen fruits can hinder proper recognition during mechanical harvest. Shape uniformity is a complex trait influenced by genetic and environmental factors, but improvements are possible through manipulation of the genetic component (Chandler et al., 2009; Whitaker et al., 2020). A QTL on chromosome 2B controlling fruit uniformity identified in a multi-parental mapping population can be harnessed to select against misshapen fruits and improve fruit uniformity (Li et al., 2020a). Selection of plants for evenly distributed carpels with better pollination abilities and heat tolerance can improve fruit quality in CEs. Breeding efforts in pursuit of parthenocarpy could assist in developing high-quality fruits in CEs where pollinations are suboptimal. Increased peduncle length can help the fruits hang below the canopy. However, the genetic architecture of traits like peduncle length and runner production are time-consuming and labor-intensive to quantify in large breeding sets and are not completely understood. Axillary meristems in strawberries can develop into either runners or inflorescence determining the fate of fruit yield. While runnering is highly desirable for nursery, high runner production during fruit production is undesirable as it incurs an increased cost for trimming and photosynthate translocation to runners compromising fruit yield. Identification of genetic control of flowering and runnering in cultivated strawberry is important to the industry and research (Whitaker et al., 2020). Thus, plant selection is critical for the optimized production of fruits and runners. Integrated research of selecting plants with reduced runnering under modified CE growing conditions along with automated removal of runnering can increase fruit yield. Accessions of diploid woodland strawberry F. vesca show variation from no to extreme runner production. Recessive mutations in the Runnering (R) locus cause runnerless plants (Brown and Wareing, 1965). A 9-bp deletion in the FveGA20ox4 is responsible for the runnerless phenotype (Hawkins et al., 2016). Even when FveGA20ox4 is mutated, a nonsense mutation in the DELLA protein encoded by FveRGA1 was found responsible for constitutive runnering (Caruana et al., 2018). The genetics of runnering is completely different in F. anannassa from F. vesca and is controlled by perpetual flowering and runnering (PFRU) (Gaston et al., 2013). However, the causal gene for runnering in F. anannassa is not known.

Strawberries are enjoyed by consumers for their flavor and nutritional benefits. While flavor preference is subjective, its components like sugar–acid balance, texture, aroma, and appearance can be improved through genetics and breeding. In addition to sugars and sugar–acid balance, breeding and selecting plants for high VOCs such as γ-D-galactone; 5-hepten-2-one, 6-methyl, and multiple medium-chain fatty acid esters can enhance fruit flavors and quality. Two QTLs on linkage group 6A controlling different esters production can be used to manipulate aroma strawberries (Fan et al., 2021). Breeding for enhanced VOCs has also been the focus of open-field strawberry breeding programs (Chambers et al., 2014). A negative correlation between soluble sugars and yield requires a need for their balance (Cockerton et al., 2021). Higher concentrations of VOCs enriching flavor and sweetness are observed in ripe fruits with shorter post-harvest shelf life. In field breeding, cultivars are bred for firm skin to withstand long-distance transit, reduce fruit damage during handling, and create a barrier for insects and diseases leaving behind cultivars with superior flavor but coupled with low firmness or disease susceptibility (Moya-León et al., 2019; Zacharaki et al., 2024). Breeding new cultivars with high flavors can capitalize on allowing fruits to ripen longer as these facilities are in or near consumers for CEA. A few QTLs have been reported for SSC; however, their presence and stability across breeding germplasms and environments are low (Gezan et al., 2017; Verma et al., 2017b; Natarajan et al., 2020). Similar growing environments across CEA can be leveraged to discover and use the genomic regions controlling SSC in selecting new cultivars. Furanones like furaneol and mesifurane are attributed to the sweet, caramel odor in strawberries (Ulrich et al., 1997). Genes quinone oxidoreductase (FaQR) and o-methyl transferase (FaOMT) on chromosomes 1C and 7D are evidenced to be involved in the production of furaneol and mesifurane, respectively (Barbey et al., 2021; Raab et al., 2006). Genes alcohol dehydrogenase (ADH), SAAT, and FaAAT2 are reported to confer ester production (Wolyn and Jelenkovic, 1990; Aharoni et al., 2004; Cumplido-Laso et al., 2012) The production of methyl anthranilate, providing grape aroma in strawberries, is modulated by two genes anthranilic acid methyl transferase (FanAAMT) and anthranilate synthase alpha subunit 1 (FaASa1) (Pillet et al., 2017; Barbey et al., 2021; Fan et al., 2022). Similarly, fatty acid desaturase 1 (FaFAD1) and three QTLs on LGVII-1 and 6B and 7B have been tagged to control two lactones, γ-decalactone and γ-dodecalactone, which confer peachy flavor (Sánchez-Sevilla et al., 2014; Oh et al., 2021; Rey-Serra et al., 2022). Linalool and nerolidol that provide floral and citrus-like aroma in strawberries were revealed to be modulated by nerolidol synthase 1 (FaNES1) located in chromosome 3C (Aharoni et al., 2004; Fan et al., 2022). Regulation of these genes by controlling the aromatic compound syntheses through marker-assisted breeding and precision breeding could help to develop consumer-desired flavors.

One of the most prevalent diseases in strawberry in CEA is PM. Characterization of pathogen races causing the disease in CEA in the US is needed. In field production, PM is caused by Podosphaera apahanis. Inheritance of PM resistance using natural infections in fields and greenhouse study revealed low disease rating correlations between two environments when disease pressure is low and high when the disease pressure is high (Nelson et al., 1995). Quantitative analysis revealed that non-additive dominance was more prominent than additive variance caused by two additive genes with one considerable epistatic gene causing susceptibility (Hsu et al., 2011). Four stable QTLs and a few transients have been observed in Hapil cultivar to confer PM resistance that could be further investigated for CE breeding (Cockerton et al., 2018). Additionally, three FveMLO and 12 FaMLO susceptibility genes have been identified that could serve as candidates for gene editing and improving host resistance to PM in strawberries (Tapia et al., 2021). Gray mold (Botrytis cinerea) could become a threat to CEA strawberry production. However, no known source of resistance has been identified and requires further investigation on host resistance (Petrasch et al., 2019).