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Metabolomic and transcriptomic analyses provide insights into metabolic networks during Fragaria nilgerrensis fruit development and ripening

Ai-Hua Wang,Bao-Hui Zhang,Chao Ma,Jie Wang,Chun-Ying Kang,Xing Zhang

Published 2025 in BMC Plant Biology

ABSTRACT

Fragaria nilgerrensis is a wild diploid strawberry species that represents a rich source of genetic variations with potential for enhancing fruit quality traits. However, the transcriptional regulation of changes in fruit quality relevant metabolites during F. nilgerrensis fruit development and ripening has not been investigated. Thus, this study analyzed the changes and accumulation of sugars, organic acids, phenolic acids and flavonoids at the four developmental stages of F. nilgerrensis fruit. D-sucrose, raffinose, D-trehalose, melibiose and isocitric acid increased as fruit developed. In terms of phenolic acids and flavonoids, cinnamic acid, hydroxycinnamic acid, coumarin, coniferin, anthocyanidins, rutin, and nicotiflorin accumulated as fruit developed. Conversely, contents of sinapoyl malate, coniferaldehyde, sinapinaldehyde, coniferyl alcohol, quercetin, gallocatechin, eriodictyol, luteolin, phloretin, and naringenin were decreased. The expression levels of key structural genes that corresponded with metabolite changes were identified. These genes included RFS (LOC101297814) and IDH(LOC101296705) in saccharide and organic acid metabolism, PAL (LOC101315259), BG (LOC101313585), F5H (LOC101307828), CCR (LOC101315149), CAD (LOC101306416 and LOC101309917), GT5 (LOC101296671), CHS(LOC101298162 and LOC101298456), LAR(LOC101306809), FLS(LOC101303260, LOC101309876, and LOC101302485), and ANR (LOC101292386) in phenylpropanoid and flavonoid biosynthesis pathways. Correlation analysis revealed that multiple transcription factor families were involved in the saccharide, phenylpropanoid and flavonoid biosynthesis, among which, AUX/IAA (LOC101298379), WRKY (LOC101302596), and AP2/ERF(LOC101295372)TFs were significantly correlated with saccharide synthesis. The effects of AP2/ERF (LOC101291560), AUX/IAA (LOC101298379), MYB (LOC105352442), and WRKY (LOC101302596 and LOC101295677) TFs were significantly correlated with cinnamic acid accumulation. This study identified key metabolites, structural genes, and transcription factors influencing fruit quality-related metabolic changes during fruit development in F. nilgerrensis. These findings may facilitate the utilization of wild strawberry resources for breeding novel cultivars.

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