Like crops in general, apple trees are vulnerable to pathogens, which cause significant economic losses. These include the fungus Venturia inaequalis which causes apple scab, Erwinia amylovora, causing fire blight, Penicillium expansum leading to postharvest disease, and more (MacHardy, 1996; Malnoy et al., 2012; Luciano-Rosario et al., 2020). In general, highly produced commercial cultivars exhibit little to no resistance to those three diseases, which are managed through cultivation practices (Gessler et al., 2006; Holb, 2007; Kellerhals et al., 2012; Luciano-Rosario et al., 2020). Similarly, post-harvest losses from fungal growth can be considerable, with little genetic resistance, fungicides re the typical control method (Gupta and Saxena, 2023). There is great interest in identifying or developing disease resistant cultivars.

In addition to disease resistance, interesting marketable fruit traits are sought after, such as red fleshed fruits, tiny fruits, large sized fruits, or early ripening (Janick et al., 1996; Volz et al., 2009). Other preferred characteristics of fresh market apples such as fruit color, pattern, and texture are variable by region and across time (Janick et al., 1996). As apples intended for the fresh fruit market can undergo extensive storage to allow year-round sales of this seasonal fruit, longer shelf-life is a valuable trait (Janick et al., 1996). Consumers are also interested in obtaining nutritious foods (Rahman et al., 2021). Apples are high in a variety of compounds, including ascorbic acid, commonly known as vitamin C (overviewed in (Planchon et al., 2004)). Analysis of vitamin C content of apple indicates both genes and the environment factor into vitamin levels, with older cultivars tending to have much higher levels on average than newer varieties (Planchon et al., 2004).

Given the great diversity of apple cultivars as a group and the presence of genetically compatible wild relatives, there are abundant genetic resources available for potentially obtaining apples with desired genetically encoded traits. Apple germplasm collections in countries around the world are valuable resources for conserving and documenting this diversity (Supplementary Table S1). Phenotype screening of collections of wild and domestic apple have identified resistance to fire blight, apple scab, and other diseases, and some individuals even exhibit multiple resistance (Luby et al., 2002; Volk et al., 2008). An addition, extensive research identifying candidate genes or quantitative trait loci (QTLs) for fire blight and apple scab resistance now makes it possible to perform marker assisted seeding selection (MASS) in apple (Ru et al., 2015). Thus, trees and progeny can now be genotyped to track traits genetically. The long juvenile period and lack of self-compatibility of apples in general means is time-consuming to integrate traits and develop cultivars using naturally occurring plant maturation (Pereira-Lorenzo et al., 2018). This approach works well, and breeding efforts started in the 1940s have successfully bred in resistance to apple scab from wild M. floribunda into domestic apple (Crosby et al., 1992). Similar efforts to create additional scab-resistant apple cultivars have yielded numerous new varieties, but overall the market success of scab resistant cultivars developed to date has been low (Gessler et al., 2006).

Genetic engineering represents a second and faster option for changing domestic apple. Transformation of domestic cultivars occurred in the 1980s and wild apple is a more recent development (James et al., 1989; Zhang et al., 2021). A variety of genetic engineering approaches have been used in apple, including cisgenesis, transgenesis, RNA interference (RNAi), Viral Induced Gene Silencing (VIGS), and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR, see Table 1 and citations therein). The same apple scab resistance gene introgressed by traditional breeding with M. floribunda into domestic apple was transformed directly into Gala apples, maintaining the cultivar background and obtaining resistance in this single generation (Belfanti et al., 2004). Resistance to both apple scab and fire blight occurred with transfer of the Zea maize (corn) Leaf colour (Lc) gene, but the positive gravitropism of the branches meant the trees would be commercially unsuitable for fruit production (Flachowsky et al., 2010a).

Given the long juvenile period of apple trees, one goal of genetic engineering was to produce precocious flowering, which could then be used to shorten generation times and obtain accelerated breeding. This approach required some optimization, as it was challenging to obtain trees that flowered, but not too early. Transgenic addition of LEAFY (LFY) from Arabidopsis thaliana (Arabidopsis) led to a more compact and columnar tree form, but no early flowering (Flachowsky et al., 2010b). Overexpression of one FLOWERING LOCUS T homolog from domestic apple (MdFT1) led to very early flowering with blooms observed while trees were still undergoing in vitro cultivation (Trankner et al., 2010). Use of BpMADS4 from Betula pendula Roth. (silver birch) led to the creation of several events, one of which was used to rapidly breed fire blight resistance from an ornamental cultivar of apple to a fruit-bearing cultivar, with five generations occurring in just 7 years (Flachowsky et al., 2007; Schlatholter et al., 2018). This same BpMADS4 event was also used for introgression of resistance to blue mold from wild M. sieversii to Gala (Luo et al., 2020). Individuals with or without the BpMADS4 gene can be identified by DNA testing, allowing for genotyping in each generation (Luo et al., 2020).

In general, genetic engineering approaches are most straightforward with single genes of large influence, but it is possible to target multiple genes at once in apple with RNAi or CRISPR (Klocko et al., 2016; Jacobson et al., 2023). Unlike their conventionally bred counterparts, engineered trees are subject to many regulations, and are challenging to bring to the commercial market.

Apples and apple products are globally produced and traded, with apples grown in over 90 countries (Nations, 2025). Nearly all apples are conventional crops, produced without genetic engineering, but there is potential for engineered apples to become more prevalent. Currently, non-browning apples obtained by RNAi are grown in Canada and the United States (Waltz, 2015; Duford, 2024). One challenge to wider usage of engineered apples is that regulations regarding definitions and guidelines for genetically engineered crops and crop products are still under development and vary greatly by country and region. Some countries, such as the United States, have guidelines but until recently had no labeling requirements for GMO crops and products. Starting in mid-2025, the United States will now require labeling of foods with ingredients produced by recombinant DNA technology, including Arctic™ apple (Becker, 2023). By contrast, Europe has implemented labeling and monitoring of GMOs, which also included gene-edited crops (Ruffell, 2018). However, a recent decision by the Council of the European Union updated the guidelines to better encompass current plant breeding and modification techniques, which opens up the possibility for future new crop adoptions (Union, 2025). How apple trees such as the fire-blight resistant individuals with the resistance gene introgressed from compatible relatives via genetically accelerated breeding, but which lack transgenes, would be regulated remains to be seen. It is possible that consumers may be in favor of trees produced with these new technologies. There is growing interest in food produced fewer pesticides or fungicides, and if apples produced by new technologies meet consumer needs and desires then regulations may adapt to meet market demand (Rahman et al., 2021).

As science moves quickly, some recent innovations in plant gene targeting offer potential options for achieving transgene-free genome-edited apple trees. It is now possible perform transient CRISPR editing in apple, or to use excision to remove transgenes after edits (Malnoy et al., 2016; Osakabe et al., 2018; Dalla Costa et al., 2020). These approaches, while not highly efficient, are likely to be faster than using breeding to separate transgenes from edits and would allow for maintaining the overall genetic background of the cultivar used. It is possible that if the targeted changes are small and the transgenes are not stably integrated, apple trees produced with this approach could get approval in the European Union or elsewhere. As the field of biotech crops continues to develop, both in terms of science and regulations, it will be interesting to see what is possible, and which possibilities reach consumers. Both growers and consumers may also be a significant influence in the marketability of engineered apples. Transgenic virus-resistant Carica papaya (papaya) trees were created and are credited with saving the Hawaiian papaya industry, which at the time was mostly small farmers (Gonsalves, 2006). More recently, the engineered “PinkGlow” Ananas comosus (pineapple) was released in the United States as a novelty item and is popular with consumers (Jay, 2024). Perhaps as more engineered fruits enter the global market apples could be part of the portfolio.