Strawberry ripening is a highly coordinated developmental process in which fruit changes from firm and pale to soft, red, sweet, and aromatic. Unlike climacteric fruits such as tomato, strawberry ripening is mainly driven by abscisic acid (ABA), together with other hormones, epigenetic regulation, and TF networks. Previous studies had shown that Ripening Inducing Factor (RIF) plays an important role in this process, but the direct genes controlled by FaRIF and the proteins that modulate its activity in cultivated strawberry remained insufficiently understood. Based on these challenges, deeper investigation is needed into the regulatory networks that connect gene control with strawberry fruit ripening and quality formation.
The study was carried out by researchers from Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” Universidad de Málaga–Consejo Superior de Investigaciones Científicas, Unidad Asociada de I+D+i IFAPA-CSIC Biotecnología y Mejora en Fresa, Centro Nacional de Biotecnología, Eberhard Karls University, and the Institute of Botany, Chinese Academy of Sciences. Published (DOI: 10.1093/hr/uhaf362) in Horticulture Research on January 6, 2026, the work investigated how FaRIF controls ripening in cultivated strawberry (Fragaria × ananassa) through chromatin immunoprecipitation sequencing (ChIP-seq), RNA interference (RNAi)-based transcriptome analysis, TurboID-based proximity labeling, and promoter activation assays.
The researchers first examined four FaRIF homoeologs in the octoploid cultivated strawberry genome. Three full-length copies showed increased expression during receptacle ripening, while one truncated copy lacked much of the NAC domain and was likely nonfunctional. Using ChIP-seq, the team identified 13,620 high-confidence FaRIF binding sites, most located near promoter regions, revealing where this transcription factor (TF) acts directly in the genome. By integrating these binding data with RNAi transcriptome results, they separated direct from indirect targets and found that FaRIF mainly functions as a transcriptional activator. Its direct targets included genes involved in ABA biosynthesis and signaling, cell wall disassembly, carbohydrate metabolism, proline metabolism, phenolic compound pathways, and volatile-related regulation. Functional assays further validated FaRIF regulation of selected promoters, including FaNAC042, FaSCL8, FaβGal5, FaPRODH, FaPL2/plB, and FaAMY1. The study also showed that FaRIF interacts with NAC TFs such as FaNAC021 and FaNAC034, which can enhance the activation of shared target genes.
The authors said the results place FaRIF at the center of a broader ripening control system rather than within a single pathway. They said FaRIF links hormone signals with the physical and metabolic changes that make strawberries soften, color, sweeten, and develop flavor. By capturing both its in vivo DNA targets and nearby protein partners, the study gives researchers a more complete view of how ripening is switched on and adjusted. They also said the optimized ChIP-seq and TurboID workflows could help study other complex traits in strawberry and related fruit crops.
These findings may support future breeding and biotechnology approaches aimed at improving strawberry fruit quality without relying on a single trait marker. Because FaRIF connects ABA signaling, cell wall remodeling, sugar-related metabolism, color formation, and aroma-associated pathways, it provides a valuable entry point for understanding how multiple fruit-quality traits are coordinated. The identification of FaRIF-associated proteins, including FaNAC021 and FaNAC034, also suggests that ripening control depends on interaction networks as well as direct gene regulation. More broadly, the study offers a useful model for studying regulatory hubs in polyploid crops, where several related genome copies can shape important agricultural traits.
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References
DOI
10.1093/hr/uhaf362
Original Source URL
https://doi.org/10.1093/hr/uhaf362
Funding information
This work was mainly supported by the Spanish Ministry of Science and Innovation and Universities (MICIU; PID2021-123677OB-I00 and PID2024-155863OB-I00), Junta de Andalucía, EMBO Scientific Exchange Grant, Juan de la Cierva Program, and the Excellence Strategy of the German Federal and State Governments. Open access funding was provided by the University of Málaga/CBUA.
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.