Unveiling the genetic basis of floral scent formation in roses using weighted gene co-expression and protein-protein interaction network analyses
Abstract Rosa species hold considerable economic and medicinal importance, used in traditional medicine, essential oils, and landscaping. However, the mechanisms of floral scent formation in roses are not well understood, hindering genetic improvement. To bridge this gap, we conducted a combined tra...
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Nature Portfolio
2025-07-01
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| Series: | Scientific Reports |
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| Online Access: | https://doi.org/10.1038/s41598-025-08137-5 |
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| author | Chan Xu Yuan Chen Qiaoli Xie Zongli Hu Hang Guo Guoping Chen Shibing Tian |
| author_facet | Chan Xu Yuan Chen Qiaoli Xie Zongli Hu Hang Guo Guoping Chen Shibing Tian |
| author_sort | Chan Xu |
| collection | DOAJ |
| description | Abstract Rosa species hold considerable economic and medicinal importance, used in traditional medicine, essential oils, and landscaping. However, the mechanisms of floral scent formation in roses are not well understood, hindering genetic improvement. To bridge this gap, we conducted a combined transcriptome and metabolome analysis, identifying nine key fragrance compounds. Using Weighted Gene Co-expression Network Analysis (WGCNA), we linked 574 genes to these compounds. From these, we identified candidate genes through differential expression, functional annotations, and protein-protein interaction (PPI) networks. We predicted candidate genes, NUDIX1, NUDIX2, GERD, AFS1, AFS2, CYP82G1, HMG1, NCED2, CCD7, PSY, ICMEL2, MAD1, and MAD2 that might terpenoid-related genes, as well as potential benzenoid/phenylpropanoid-related candidate genes, DET2, DET3, ICS2, PAL1, UGT74B1, MYB330, GST, CAD1, HST, PCBER1, LAC15, CSE, PER25, PER47, PER63, FBA, LNK2, PRE1, and PRE6. Additionally, three function-unknown genes, LOC112167529, LOC112174760, and LOC112183447, were predicted as candidate genes potentially involved in the formation of floral scent. |
| format | Article |
| id | doaj-art-74aa4aa188a543f0b1f6663f286fbe1c |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
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| series | Scientific Reports |
| spelling | doaj-art-74aa4aa188a543f0b1f6663f286fbe1c2025-08-20T03:45:23ZengNature PortfolioScientific Reports2045-23222025-07-0115111310.1038/s41598-025-08137-5Unveiling the genetic basis of floral scent formation in roses using weighted gene co-expression and protein-protein interaction network analysesChan Xu0Yuan Chen1Qiaoli Xie2Zongli Hu3Hang Guo4Guoping Chen5Shibing Tian6College of Bioengineering, Chongqing UniversityInstitute of Vegetables and Flowers, Chongqing Academy of Agricultural SciencesCollege of Bioengineering, Chongqing UniversityCollege of Bioengineering, Chongqing UniversityInstitute of Vegetables and Flowers, Chongqing Academy of Agricultural SciencesCollege of Bioengineering, Chongqing UniversityInstitute of Vegetables and Flowers, Chongqing Academy of Agricultural SciencesAbstract Rosa species hold considerable economic and medicinal importance, used in traditional medicine, essential oils, and landscaping. However, the mechanisms of floral scent formation in roses are not well understood, hindering genetic improvement. To bridge this gap, we conducted a combined transcriptome and metabolome analysis, identifying nine key fragrance compounds. Using Weighted Gene Co-expression Network Analysis (WGCNA), we linked 574 genes to these compounds. From these, we identified candidate genes through differential expression, functional annotations, and protein-protein interaction (PPI) networks. We predicted candidate genes, NUDIX1, NUDIX2, GERD, AFS1, AFS2, CYP82G1, HMG1, NCED2, CCD7, PSY, ICMEL2, MAD1, and MAD2 that might terpenoid-related genes, as well as potential benzenoid/phenylpropanoid-related candidate genes, DET2, DET3, ICS2, PAL1, UGT74B1, MYB330, GST, CAD1, HST, PCBER1, LAC15, CSE, PER25, PER47, PER63, FBA, LNK2, PRE1, and PRE6. Additionally, three function-unknown genes, LOC112167529, LOC112174760, and LOC112183447, were predicted as candidate genes potentially involved in the formation of floral scent.https://doi.org/10.1038/s41598-025-08137-5RosaFloral scentWGCNAPPIHub gene |
| spellingShingle | Chan Xu Yuan Chen Qiaoli Xie Zongli Hu Hang Guo Guoping Chen Shibing Tian Unveiling the genetic basis of floral scent formation in roses using weighted gene co-expression and protein-protein interaction network analyses Scientific Reports Rosa Floral scent WGCNA PPI Hub gene |
| title | Unveiling the genetic basis of floral scent formation in roses using weighted gene co-expression and protein-protein interaction network analyses |
| title_full | Unveiling the genetic basis of floral scent formation in roses using weighted gene co-expression and protein-protein interaction network analyses |
| title_fullStr | Unveiling the genetic basis of floral scent formation in roses using weighted gene co-expression and protein-protein interaction network analyses |
| title_full_unstemmed | Unveiling the genetic basis of floral scent formation in roses using weighted gene co-expression and protein-protein interaction network analyses |
| title_short | Unveiling the genetic basis of floral scent formation in roses using weighted gene co-expression and protein-protein interaction network analyses |
| title_sort | unveiling the genetic basis of floral scent formation in roses using weighted gene co expression and protein protein interaction network analyses |
| topic | Rosa Floral scent WGCNA PPI Hub gene |
| url | https://doi.org/10.1038/s41598-025-08137-5 |
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