Transcriptomics and Metabolomics Revealed Genes Associated with the Formation of Different Fruit Colors in Fragaria pentaphylla

Yang, Xianan; Tian, Shiqi; Zhao, Chenxue; Li, Jianxin; Wang, Lianjun; Tang, Xuedong; Guo, Ruixue

doi:10.3390/horticulturae11091097

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Transcriptomics and Metabolomics Revealed Genes Associated with the Formation of Different Fruit Colors in Fragaria pentaphylla

by

Xianan Yang

^†,

Shiqi Tian

^†,

Chenxue Zhao

,

Jianxin Li

,

Lianjun Wang

,

Xuedong Tang

^* and

Ruixue Guo

^*

College of Horticulture, Jilin Agricultural University, Changchun 130118, China

^*

Authors to whom correspondence should be addressed.

^†

These authors contributed equally to this work.

Horticulturae 2025, 11(9), 1097; https://doi.org/10.3390/horticulturae11091097

Submission received: 19 August 2025 / Revised: 4 September 2025 / Accepted: 9 September 2025 / Published: 10 September 2025

(This article belongs to the Section Genetics, Genomics, Breeding, and Biotechnology (G2B2))

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Abstract

Fragaria pentaphylla, a unique wild strawberry species in China, is rich in various fruit colors and a valuable resource for studying color genes. Fruits of different colors from F. pentaphylla were selected as the experimental material. Liquid chromatography-mass spectrometry (LC-MS) and high-throughput RNA sequencing (RNA-seq) were employed to identify key genes responsible for the development of different fruit colors. Metabolite analysis revealed that 3249 metabolites were detected, including nine differential metabolites related to anthocyanin synthesis and five biological pathways. Additionally, an analysis combining transcriptome and metabolome data showed that the structural genes FpDFR, FpCHS, FpCHI, and FpUFGT were upregulated in red fruit, with significantly higher expression levels compared to pink and white fruits, actively promoting anthocyanin production in red fruit. Conversely, genes FpANR and FpLAR were upregulated in white fruit, enhancing catechin synthesis and inhibiting anthocyanin formation. The gene FpPAL was upregulated in pink fruit. Transcription factors FpbHLH18, FpMYB1, FpMYB24, and FpMYB114 collaborate with structural genes to enhance the synthesis of anthocyanins in red fruit. The findings improve our understanding of the molecular mechanisms that control anthocyanin production in F. pentaphylla. The identified key candidate genes may be utilized in the molecular breeding of strawberries.

Keywords: F. pentaphylla; fruit color; transcriptome analysis; metabolomic analysis; differential expression genes

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MDPI and ACS Style

Yang, X.; Tian, S.; Zhao, C.; Li, J.; Wang, L.; Tang, X.; Guo, R. Transcriptomics and Metabolomics Revealed Genes Associated with the Formation of Different Fruit Colors in Fragaria pentaphylla. Horticulturae 2025, 11, 1097. https://doi.org/10.3390/horticulturae11091097

AMA Style

Yang X, Tian S, Zhao C, Li J, Wang L, Tang X, Guo R. Transcriptomics and Metabolomics Revealed Genes Associated with the Formation of Different Fruit Colors in Fragaria pentaphylla. Horticulturae. 2025; 11(9):1097. https://doi.org/10.3390/horticulturae11091097

Chicago/Turabian Style

Yang, Xianan, Shiqi Tian, Chenxue Zhao, Jianxin Li, Lianjun Wang, Xuedong Tang, and Ruixue Guo. 2025. "Transcriptomics and Metabolomics Revealed Genes Associated with the Formation of Different Fruit Colors in Fragaria pentaphylla" Horticulturae 11, no. 9: 1097. https://doi.org/10.3390/horticulturae11091097

APA Style

Yang, X., Tian, S., Zhao, C., Li, J., Wang, L., Tang, X., & Guo, R. (2025). Transcriptomics and Metabolomics Revealed Genes Associated with the Formation of Different Fruit Colors in Fragaria pentaphylla. Horticulturae, 11(9), 1097. https://doi.org/10.3390/horticulturae11091097

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Transcriptomics and Metabolomics Revealed Genes Associated with the Formation of Different Fruit Colors in Fragaria pentaphylla

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