Horticultural crops are unusually exposed to climate instability because their commercial value depends on delicate traits such as fruit expansion, texture, pigmentation, aroma, and appearance. Cold can disrupt membranes or trigger freezing injury, drought restricts growth and water supply, salinity disturbs ion balance, and heat can damage reproductive tissues and accelerate pigment loss. Plants already use interconnected hormonal, redox, transcriptional, and metabolic defenses, but domestication has narrowed useful diversity in many crops. Moreover, constitutively activating defense genes can consume energy, delay development, and reduce yield under normal conditions, while woody perennials remain difficult to transform and slow to evaluate. Based on these challenges, in-depth research is needed to connect molecular stress biology with field-ready precision breeding in horticultural crops.
Researchers from the School of Enology and Horticulture at Ningxia University, the Engineering Research Center of Grape and Wine of the Ministry of Education, the Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, and the State Key Laboratory of Efficient Production of Forest Resources conducted the review. Published (DOI: 10.1093/hr/uhag119) online on April 2, 2026, in Horticulture Research, the article examines how transcriptional regulation, epigenetic memory, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) genome editing, synthetic biology, and predictive breeding can be combined to build climate-resilient horticultural crops.
The review first traces how abscisic acid (ABA), reactive oxygen species (ROS), calcium signals, and transcription factors (TFs) such as C-repeat binding factor/dehydration-responsive element-binding (CBF/DREB), no apical meristem/Arabidopsis transcription activation factor/cup-shaped cotyledon (NAC), myeloblastosis (MYB), WRKY, and basic helix-loop-helix (bHLH) coordinate osmotic adjustment, antioxidant defense, membrane protection, and ion homeostasis. It emphasizes that annual vegetables and woody perennials solve similar problems differently: tomato and pepper rely largely on rapid metabolic adjustment, whereas grape and apple also use dormancy, structural isolation, and long-term epigenetic timing. Progressive histone H3 lysine 27 trimethylation at Dormancy-Associated MADS-box (DAM) loci, for example, can act as a seasonal “molecular hourglass” that helps prevent premature bud break. The authors then assess precision strategies beyond always-on gene overexpression. These include editing ScF3'H in potato to adjust flavonoid metabolism, knocking out VvBBX44 in grape to relieve repression of anthocyanin production, modifying cis-regulatory regions, and building stress-inducible synthetic promoters or Boolean logic gates. It also highlights short insulator sequences that may shield synthetic circuits from seasonal chromatin changes in long-lived crops, and tissue-specific designs that separate defense responses in leaves and roots from flavor and color pathways in fruit. The roadmap further combines pan-genomes, high-throughput phenotyping, artificial intelligence (AI), and machine learning (ML) to identify trait combinations that preserve resilience, yield, and quality across variable environments.
The authors said the review's central message can be summarized as follows: “Climate resilience will not come from switching on a single defense gene. Horticultural crops must sense when stress occurs, activate the right response in the right tissue, and return quickly to growth when conditions improve. Precision editing and synthetic networks can make that control more selective, while pan-genomics and AI can help breeders find combinations that would be difficult to identify through conventional selection alone. The real test, however, is whether these designs remain stable, productive, and acceptable across seasons and in farmers'fields.”
The proposed framework could guide breeding programs for vegetables, fruit trees, grapevines, berries, and tuber crops exposed to increasingly unpredictable weather. Stress-responsive promoters and cis-regulatory editing may reduce the growth penalties associated with permanent defense activation, while rapid-cycling rootstocks and improved transformation systems could shorten validation in perennial species. Pan-genomic resources may recover useful alleles lost during domestication, and field phenotyping combined with genotype-by-environment (G × E) modeling could identify designs that work under simultaneous stresses rather than controlled laboratory conditions alone. Translation will also require transparent regulation, multi-year field trials, consumer communication, and careful assessment of crop quality. Together, these steps could support horticultural systems that use water and nutrients more efficiently while maintaining reliable, nutritious harvests.
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References
DOI
10.1093/hr/uhag119
Original Source URL
https://doi.org/10.1093/hr/uhag119
Funding information
National Natural Science Foundation of China, grant 32472711; Science and Technology Leading Talent Cultivation Program of the Ningxia Hui Autonomous Region, grant 2025GKLRLX21; Ningxia Hui Autonomous Region Key Research and Development Program, grant 2023BCF01003; Ningxia Province Natural Science Foundation, grant 2024AAC02024.
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.