The Digital Orchard: Advanced Data-Driven Technologies in Apple Breeding and Genetic Modification

Dr Fazeel Abid¹Zhao Zhang²Ghulam Farooque¹Rana Muhammad Zulqarnain³Jawad Rasheed^4,5,6,7*Onur Osman⁸Shtwai Alsubai⁹Leila Jamel¹⁰

• ¹The University of Lahore, Lahore, Pakistan
• ²China Agriculture University, Beijing, China
• ³Saveetha School of Engineering, Chennai, India
• ⁴Istanbul Sabahattin Zaim University, Istanbul, Türkiye
• ⁵Istanbul Nisantasi University, Istanbul, Türkiye
• ⁶Istanbul Medipol University, Istanbul, Türkiye
• ⁷Applied Science Private University, Amman, Jordan
• ⁸Istanbul Topkapi Universitesi, Istanbul, Türkiye
• ⁹Prince Sattam bin Abdulaziz University, Al Kharj, Saudi Arabia
• ¹⁰Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia

The apple (Malus × domestica), a globally significant perennial fruit crop, faces immense pressure from climate change, evolving pathogens, and consumer demand for novel traits. Also, remains constrained by slow trait selection despite technological advances. Further, the traditional breeding methods are slow and resource-intensive, hampered by the apple’s long juvenile period and high heterozygosity. This systematic literature review (SLR) synthesizes the state of the art in advanced data-driven technologies for accelerating apple breeding and genetic modification. Following the PRISMA-EcoEvo protocol, 47 selected studies were analyzed from databases including Web of Science, Scopus, and PubMed. Our thematic synthesis reveals a paradigm shift towards a “digital breeding” model, characterized by the convergence of three core technological pillars. First, high-throughput phenotyping (HTP), which leverages sensor modalities such as RGB-D, hyperspectral imaging, and LiDAR, is automating the collection of trait data at an unprecedented scale. Second, machine learning (ML) and deep learning (DL) algorithms are being deployed for diverse applications, including cultivar identification with over 96% accuracy, non-destructive quality prediction, and genomic selection, thereby boosting predictive ability for key traits by up to 18%. Third, precise and efficient genome editing, predominantly using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/ CRISPR-associated protein 9 (Cas9), is enabling the rapid introduction of desirable traits, such as disease resistance, enhanced shelf life, and improved nutrient uptake. Demonstrated transgene-free editing protocols are accelerating the path to commercialization. We further explore the integration of these pillars through the agricultural internet of things (AIoT) and discuss emerging frontiers, including federated learning for data privacy, explainable AI (XAI) for model transparency, and the implications of recent regulatory frameworks. This review identifies critical research gaps, including the need for standardized open-access datasets and integrated end-to-end system validation. It concludes that the synergistic application of these technologies is poised to revolutionize the speed, precision, and resilience of apple improvement programs worldwide.