Construction of the relationship between phytochemicals and gene expression in different Chaenomeles speciosa (Sweet) Nakai cultivars

Abstract

This study investigated the phytochemical profiles of four Chaenomeles speciosa cultivars (Xuan Mugua) (Zhimahong, Pingguohong, Luohanqi, Lengmugua) and conducted transcriptome analysis of two selected cultivars (Zhimahong, Lengmugua) across three developmental stages (fruit set, expansion, and maturation). Using HPLC-MS/MS and RNA-seq, we quantified phenolic acids, flavonoids, organic acids, and triterpenoids while identifying associated biosynthetic genes. Key findings revealed significant interspecific variations at full maturity: Zhimahong showed the highest ursolic acid content (1.82 mg/g DW), Pingguohong accumulated peak oleanolic acid (2.15 mg/g DW) and malic acid (34.7 mg/g DW), while Luohanqi exhibited maximal proanthocyanidin B2 (0.68 mg/g DW), chlorogenic acid (1.24 mg/g DW), epicatechin (0.92 mg/g DW), phloridzin (0.56 mg/g DW), and rutin (0.43 mg/g DW). Transcriptomic analysis identified 29,424 differentially expressed genes (DEGs, |log₂FC|≥1, P-Adjust<0.05) between Zhimahong and Lengmugua at maturation, including flavonoid biosynthesis genes CHS (LOC114843160) and CHI (LOC114826590), and triterpenoid-related FDFT1 (LOC114822340) and LUP4 (LOC114847190). Antioxidant assessment (ABTS method) across all cultivars demonstrated stage-dependent variation, with Luohanqi showing maximum activity (17.94 mg VE/g DW) during fruit expansion. These results provided molecular evidence for cultivar-specific phytochemical accumulation, identified key genetic targets for metabolic engineering, and established Luohanqi as the optimal cultivar for antioxidant-focused cultivation. The findings directly inform breeding programs and quality control strategies for Xuan Mugua industrial applications.