REVIEW article
Front. Plant Sci.
Sec. Plant Metabolism and Chemodiversity
This article is part of the Research TopicGenomic and Metabolomic Diversity in Fruit Plants: Impacts of Breeding TechniquesView all 4 articles
From data to decisions: a paradigm shift in fruit agriculture through the integration of multi-omics, modern phenotyping, and cutting-edge bioinformatic tools
Provisionally accepted
- 1Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), Málaga, Spain
- 2Instituto de Hortofruticultura Subtropical y Mediterranea, Málaga, Spain
- 3Universidad de Malaga, Málaga, Spain
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Fruit agriculture is undergoing a profound transformation driven by multi-omics, high-throughput phenotyping, and machine learning–driven bioinformatics. However, we demonstrate that this technological revolution has paradoxically created a 'valley of death' where most of genomic discoveries fail to reach farmers' fields. While we can now identify beneficial alleles in days and edit genomes in weeks, it still takes 10 years and 14,5 million euros to deliver a single improved cultivar to European markets - the same timeline as 30 years ago. This review exposes how data abundance has shifted, not eliminated, the fundamental bottlenecks in fruit crop improvement. We critically assess how these tools reshape genetic and metabolic diversity, emphasizing both their transformative promises and structural limitations. We highlight three persistent gaps: the challenge of integrating heterogeneous multi-omics datasets, the phenotyping bottleneck for complex traits, and the tension between innovation and biodiversity conservation. By framing fruit breeding as a "data-to-decisions" challenge, we outline the systemic changes needed for sustainable, resilient, and high-quality fruit production.
Keywords: Fruit breeding, Multi-omics integration, high-throughput phenotyping, Machinelearning, genomic selection, CRISPR, genetic diversity, agricultural biotechnology
Received: 17 Sep 2025; Accepted: 24 Nov 2025.
Copyright: © 2025 Pacheco Ruiz, Osorio and Vallarino. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Sonia Osorio
Jose G. Vallarino
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