Transcription factors are central to plant biology because they switch genes on and off in response to internal developmental programs and external stress. Among them, NF-Y factors are known to influence embryogenesis, flowering, seed development, drought tolerance, and immune responses. Yet most earlier studies examined NF-Y genes in only one or a few species, leaving major questions unanswered about when this family arose, how it expanded across lineages, and how its structure and functions changed over time. As more plant genomes become available, researchers now have a chance to reconstruct this deeper evolutionary history. Based on these challenges, further in-depth research is needed on the origin, diversification, and regulatory roles of NF-Y genes across major plant lineages.
Researchers from Hainan University, Lingnan Normal University, and Guizhou University reported (DOI: 10.1093/hr/uhaf304) in Horticulture Research on November 12, 2025 that a cross-species analysis of NF-Y transcription factors in 320 horticultural and representative plants uncovered an origin in charophytes, lineage-specific duplication patterns, conserved but shifting motif architectures, and broad stress- and development-related regulatory potential.
To build this evolutionary atlas, the team analyzed whole-genome data from 320 species, including 20 algae and 300 land plants spanning bryophytes, pteridophytes, gymnosperms, basal angiosperms, monocots, magnoliids, and eudicots. More than 70% of the sampled species were horticultural plants, including fruit trees, vegetables, ornamentals, medicinal plants, and beverage or spice plants. The researchers identified 15,392 nonredundant NF-Y genes, divided into 4,702 NF-YA, 6,302 NF-YB, and 4,388 NF-YC members. Land plants carried many more NF-Y genes than algal species, supporting the idea that the family expanded as plants adapted to terrestrial life. The study further showed that bryophytes, pteridophytes, and gymnosperms mainly expanded NF-Y genes through dispersed duplication, whereas angiosperms relied more on a combination of whole-genome or segmental duplication, dispersed duplication, and tandem duplication.
The team then examined motif conservation in representative species and found that core motifs were generally retained within each subfamily, while some genes in higher plants had lost motifs, suggesting evolutionary divergence and possible specialization. In Arabidopsis thaliana, expression profiling across abiotic stress, biotic stress, hormone treatments, tissues, and developmental stages revealed that NF-Y genes respond flexibly to changing conditions. The researchers also constructed a regulatory network involving 36 NF-Y genes, 2,473 downstream genes, and 261 upstream genes, showing that NF-Y genes sit within a dense transcriptional control system. Upstream regulators were enriched for AP2, Myb_DNA-binding, zf-Dof, and HLH families, while downstream targets were associated with development, metabolism, and stress-related processes. A dual-luciferase assay further confirmed that the transcription factor ERF115 positively regulates NF-YB2 in vivo, providing experimental support for one predicted interaction and suggesting a link between NF-Y signaling and tissue repair or regeneration.
This study moves NF-Y research from isolated species snapshots to a broad evolutionary landscape. Rather than simply showing that the family became larger over time, it reveals how NF-Y genes diversified through lineage-specific expansion, loss, and regulatory rewiring. By connecting deep evolutionary history with expression and network evidence in Arabidopsis, the work helps explain why NF-Y genes support so many plant traits, from seed formation to environmental adaptation.
The findings could prove valuable for crop and horticultural improvement. Because NF-Y genes are tied to development, flowering, reproduction, and resilience, this new atlas offers candidate targets for breeding and functional genomics in fruit, vegetable, ornamental, and medicinal plants. It also provides a comparative roadmap for identifying which NF-Y genes remained conserved and which evolved specialized roles in particular lineages. In practical terms, that means researchers may now be better equipped to pinpoint regulators associated with productivity, stress tolerance, and developmental plasticity. As plant science moves toward precision breeding and multi-omics crop design, this large-scale NF-Y framework offers a strong foundation for translating evolutionary knowledge into agricultural innovation.
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References
DOI
10.1093/hr/uhaf304
Original Source URL
https://doi.org/10.1093/hr/uhaf304
Funding information
This research was supported by the National Natural Science Foundation of China (32060392), Qian Ke He Cheng Guo ([2022] Zhong Dian 005), and the GZMARS-Forage Industry Technology System of Guizhou Province.
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.