The NF-Y gene family in Rosa: evolutionary divergence across three species and potential roles in heat tolerance and secondary metabolism
- 1School of Pharmacy, Hubei University of Science and Technology
- 2Key Laboratory of National Forestry and Grassland Administration on Osmanthus fragrans, Hubei University of Science and Technology
- 3College of Landscape Architecture, Central South University of Forestry and Technology
Abstract
Introduction: Plant pigmentation and secondary metabolism are intrinsically linked to pollinator attraction, environmental adaptation, and ornamental quality, yet the transcriptional regulators that coordinate multiple metabolic branches remain poorly understood. Nuclear Factor Y (NF-Y) transcription factors are well-established mediators of developmental and stress signaling, but their involvement in orchestrating plant metabolic networks has not been explored in the genus Rosa .
Methods: Here, we performed genome-wide identification and multi-omics characterization of 30, 30, and 29 NF-Y genes from R. chinensis , R. rugosa , and R. wichuraiana , respectively. We then conducted evolutionary analyses, orthology-based protein interaction modeling, promoter cis-element analysis, transcriptome profiling under heat stress, and integrated Weighted Gene Co-expression Network Analysis (WGCNA) with untargeted metabolomics.
Results: Evolutionary analyses revealed that segmental duplications drove family expansion under strong purifying selection, with the NF-YB and NF-YC subfamilies exhibiting distinct structural diversification. Orthology-based protein interaction modeling predicted the NF-YC subgroup I as a likely scaffold for heterotrimer assembly, while promoter cis-element analysis showed enrichment in hormone-responsive motifs (ABRE and MeJA), linking these genes to both environmental cues and metabolic signaling. Transcriptome profiling under heat stress demonstrated species-specific NF-Y expression dynamics, with the NF-YA subfamily contributing the most responsive members. Crucially, by integrating WGCNA with untargeted metabolomics, we associated multiple RcNF-Y genes with cultivar-dependent accumulation of flavonoids, terpenoids, and alkaloids—spanning the major classes of pigmentation-related and defense-related secondary metabolites. Among these, RcNF-YA4, RcNF-YA5 , and RcNF-YB12 were associated with flavonoid accumulation, whereas RcNF-YC2 was associated with terpenoid and alkaloid accumulation. This suggests that RcNF-YC2 may function as a potential hub bridging stress signaling with broad-spectrum metabolic regulation. Notably, the NF-Y members responding to heat stress and those linked to metabolic output showed limited overlap, implying functional specialization within the family.
Discussion: Collectively, our findings suggest a potential role of the rose NF-Y family in integrating thermal stress signals with diverse secondary metabolic pathways. This study prioritizes RcNF-YC2 as a candidate target for genetic or biotechnological improvement of fragrance and stress resilience in ornamental crops.
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BibTeX
@article{jiang2026gene,
title = {{The NF-Y gene family in Rosa: evolutionary divergence across three species and potential roles in heat tolerance and secondary metabolism}},
author = {Sainan Jiang and Jun Zhang and Jie Yang and Junlan Zhang and Wen Xing and Zeqing Li},
journal = {Frontiers in Plant Science},
year = {2026},
month = oct,
doi = {10.3389/fpls.2026.1944775},
url = {https://www.frontiersin.org/articles/10.3389/fpls.2026.1944775/full},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - The NF-Y gene family in Rosa: evolutionary divergence across three species and potential roles in heat tolerance and secondary metabolism
AU - Sainan Jiang
AU - Jun Zhang
AU - Jie Yang
AU - Junlan Zhang
AU - Wen Xing
AU - Zeqing Li
PY - 2026
DA - 2026/10/08
JO - Frontiers in Plant Science
DO - 10.3389/fpls.2026.1944775
UR - https://www.frontiersin.org/articles/10.3389/fpls.2026.1944775/full
AB - Introduction: Plant pigmentation and secondary metabolism are intrinsically linked to pollinator attraction, environmental adaptation, and ornamental quality, yet the transcriptional regulators that coordinate multiple metabolic branches remain poorly understood. Nuclear Factor Y (NF-Y) transcription factors are well-established mediators of developmental and stress signaling, but their involvement in orchestrating plant metabolic networks has not been explored in the genus Rosa . Methods: Here, we performed genome-wide identification and multi-omics characterization of 30, 30, and 29 NF-Y genes from R. chinensis , R. rugosa , and R. wichuraiana , respectively. We then conducted evolutionary analyses, orthology-based protein interaction modeling, promoter cis-element analysis, transcriptome profiling under heat stress, and integrated Weighted Gene Co-expression Network Analysis (WGCNA) with untargeted metabolomics. Results: Evolutionary analyses revealed that segmental duplications drove family expansion under strong purifying selection, with the NF-YB and NF-YC subfamilies exhibiting distinct structural diversification. Orthology-based protein interaction modeling predicted the NF-YC subgroup I as a likely scaffold for heterotrimer assembly, while promoter cis-element analysis showed enrichment in hormone-responsive motifs (ABRE and MeJA), linking these genes to both environmental cues and metabolic signaling. Transcriptome profiling under heat stress demonstrated species-specific NF-Y expression dynamics, with the NF-YA subfamily contributing the most responsive members. Crucially, by integrating WGCNA with untargeted metabolomics, we associated multiple RcNF-Y genes with cultivar-dependent accumulation of flavonoids, terpenoids, and alkaloids—spanning the major classes of pigmentation-related and defense-related secondary metabolites. Among these, RcNF-YA4, RcNF-YA5 , and RcNF-YB12 were associated with flavonoid accumulation, whereas RcNF-YC2 was associated with terpenoid and alkaloid accumulation. This suggests that RcNF-YC2 may function as a potential hub bridging stress signaling with broad-spectrum metabolic regulation. Notably, the NF-Y members responding to heat stress and those linked to metabolic output showed limited overlap, implying functional specialization within the family. Discussion: Collectively, our findings suggest a potential role of the rose NF-Y family in integrating thermal stress signals with diverse secondary metabolic pathways. This study prioritizes RcNF-YC2 as a candidate target for genetic or biotechnological improvement of fragrance and stress resilience in ornamental crops.
SN - 1664-462X
ER -