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. 2025 Jul:356:112500.
doi: 10.1016/j.plantsci.2025.112500. Epub 2025 Apr 7.

Comprehensive metabolomics and transcriptomics analysis reveal the regulatory mechanism of StHY5 on anthocyanin accumulation in potato tubers

Huiling Zhang  1 , Jingjing Liu  2 , Yanan Zhao  2 , Enshuang Wang  3 , Jianhua Zhou  4 , Kaixin Chang  2 , Xijuan Zhao  5 , Botao Song  6
Affiliations

Comprehensive metabolomics and transcriptomics analysis reveal the regulatory mechanism of StHY5 on anthocyanin accumulation in potato tubers

Huiling Zhang et al. Plant Sci. 2025 Jul.

Abstract

Light is a key factor for inducing anthocyanin biosynthesis; however, its regulatory mode in potato anthocyanin biosynthesis remains unclear. Previous research identified a specific genotype that causes the tuber skin to gradually turn purple when exposed to light of different wavelengths. In the present study, we conducted metabolome and transcriptome analyses on tuber samples during anthocyanin accumulation. The metabolome data showed that the contents of naringenin chalcone, naringenin, dihydrokaempferol, and cyanidin gradually increased during anthocyanin accumulation. The transcriptome data showed that the expression levels of most structural genes increased gradually during anthocyanin accumulation, especially the StF3'H gene that promotes cyanidin formation. Moreover, the photo-responsive transcription factor StHY5 was specifically expressed at high levels before anthocyanin accumulation, occurring 2 h after light induction. Establishment of transgenic lines demonstrated that StHY5 overexpression could promote the accumulation of anthocyanin in potato tubers, along with a parallel increase in the transcription levels of StAN2, StMYBA1, StCHI, StF3H, StF3'H, and StDFR. Electrophoretic mobility shift and dual luciferase assays showed that StHY5 can enhance the promoter activity of the MYB transcription factors StAN2 and StMYBA1 as well as the structural genes StCHI and StF3H through binding to the G-box motif. StAN2 activated the expression of StF3'H (a newly identified purple gene locus in potato) and StDFR by binding to the MYB-binding site in the promoters, thereby promoting anthocyanin biosynthesis. This study provides a theoretical basis for revealing the molecular mechanism of light-regulated anthocyanin biosynthesis in potatoes.

Keywords: Anthocyanin biosynthesis; Light-responsive; Potato; StHY5.

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Conflict of interest statement

Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. Conflict of interest The authors have no competing interests. Figure S1 Cluster and enrichment analysis of gene expression patterns. (A) Cluster analysis of gene expression patterns in ‘FT033–5’ tubers during light exposure. (B) The KEGG enrichment analysis of genes in Cluster 2, Cluster 3 and Cluster4. Figure S2 Phenotype and related gene expression pattern of ‘Desiree’ tubers during light exposure. (A) Phenotype of ‘Desiree’ tubers exposed to light. Bars = 1.0 cm. (B) Anthocyanin content of the ‘Desiree’ tubers skin. (C) Relative expression of StHY5 in the skin of the ‘Desiree’ tubers. (D) Relative expression of structural genes in the ‘Desiree’ tubers skin. Date represent the means of three replicates. Significant differences (LSD) between means are indicated by asterisks (** P < 0.01). Figure S3 Characterization of StHY5. (A) Distribution of the main elements in StHY5 gene promoter. (B) The nucleic acid and amino acid sequences of StHY5. The bZIP domain is marked red. (C) The phylogenetic relationships of the HY5 proteins. Protein sequences: SpHY5 (XP_027775218.1), SlHY5 (NP_001234820.1), NtHY5 (XP_009588348.1), DsHY5 (MCD7454496.1), SmHY5 (AOW42601.1), ItHY5-like (XP_031101728.1), PfHY5 (KAI3454192.1), SiHY5 (XP_011081579.1), SsHY5 (XP_042067399.1), InHY5 (XP_019173932.1), MiHY5-like (XP_044480757.1), CrHY5 (KAI5669584.1), PvHY5 (XP_031286333.1), CiHY5-like (XP_042991654.1), CcHY5 (CDP13490.1), SsHY5-like (XP_042059950.1), LsHY5 (XP_023759627.1), EgrHY5 (XP_010048982.1), MrHY5 (UWT49860.1), RcHY5 (XP_024165510.1), ShHY5-like (XP_047948711.1), CmHY5-like (XP_022996780.1), SoHY5 (XP_021837612.1), AtHY5 (NP_001330553.1), CqHY5-like (XP_021758181.1), JrHY5-like (XP_035548793.1), DlHY5-like (QRV61374.1). (D) Subcellular localization of StHY5 in Nicotiana benthamiana leaves. The green color indicates that StHY5 is localized in the nucleus (lower panels), while GFP alone is localized in the nucleus and cytoplasm (upper panel). Bars = 25 μm. Figure S4 Growth status and related gene expression of StHY5-overexpressed transgenic plants. (A) PCR detection of transgenic plants using NPTII primer. (B) Expression analysis of StHY5 in transgenic seedlings. (C) Expression analysis of related genes in transgenic seedlings. (D) Growth status, plant height, and stem diameter of transgenic seedlings transplanted for one month. Bars = 5 cm. Significant differences (LSD) are indicated by asterisks (** p < 0.01).

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