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<p>Table beet (<i>Beta vulgaris var. rubra et lutea</i>) is a flavonoid-rich root vegetable, but the coordinated regulation of flavonoid biosynthesis across varieties (red vs. yellow) and developmental stages (rosette vs. fleshy root enlargement) remains unclear. Here, we performed integrated LC-MS/MS-based metabolomic and RNA-seq transcriptomic analyses on 12 samples of red and yellow table beets at these two stages. A total of 374 flavonoid metabolites were detected. The relative abundance of detected flavonoid metabolites was highest in red beets at the fleshy root enlargement stage (RG3) and lowest in yellow beets at the rosette stage (YG2). Several characteristic flavonoids showed stage- and variety-associated accumulation patterns, including quercetin and rutin in RG3 and isoquercitrin and trifolin in YG3. Transcriptome sequencing identified 5503, 3253, 2661, and 6793 differentially expressed genes (DEGs) in RG3_vs_RG2, YG2_vs_RG2, YG3_vs_RG3, and YG3_vs_YG2, respectively, with enrichment in flavonoid biosynthesis-related pathways. Integrated analysis revealed strong correlations between flavonoid biosynthesis-related structural genes and metabolites, suggesting that CHS, CHI, F3H, CYP75B1, FLS, and LAR may contribute to stage- and variety-associated differences in flavonoid accumulation. We also identified MYB, bHLH, and WRKY family members as candidate regulators. These results provide a gene-metabolite framework for understanding flavonoid accumulation in table beet and offer candidate resources for high-flavonoid breeding.</p>

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Integrative Analysis of the Metabolome and Transcriptome Reveals the Mechanisms of Flavonoid Biosynthesis in Red and Yellow Varieties of Table Beets at Two Developmental Stages

  • 期刊论文

  • 发表日期：

    2026年7月18日

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  • Shuo Chen,
  • Naixin Liu,
  • Qin Zhou,
  • Yanan Liu,
  • Mengpu Jin

摘要

Table beet (Beta vulgaris var. rubra et lutea) is a flavonoid-rich root vegetable, but the coordinated regulation of flavonoid biosynthesis across varieties (red vs. yellow) and developmental stages (rosette vs. fleshy root enlargement) remains unclear. Here, we performed integrated LC-MS/MS-based metabolomic and RNA-seq transcriptomic analyses on 12 samples of red and yellow table beets at these two stages. A total of 374 flavonoid metabolites were detected. The relative abundance of detected flavonoid metabolites was highest in red beets at the fleshy root enlargement stage (RG3) and lowest in yellow beets at the rosette stage (YG2). Several characteristic flavonoids showed stage- and variety-associated accumulation patterns, including quercetin and rutin in RG3 and isoquercitrin and trifolin in YG3. Transcriptome sequencing identified 5503, 3253, 2661, and 6793 differentially expressed genes (DEGs) in RG3_vs_RG2, YG2_vs_RG2, YG3_vs_RG3, and YG3_vs_YG2, respectively, with enrichment in flavonoid biosynthesis-related pathways. Integrated analysis revealed strong correlations between flavonoid biosynthesis-related structural genes and metabolites, suggesting that CHS, CHI, F3H, CYP75B1, FLS, and LAR may contribute to stage- and variety-associated differences in flavonoid accumulation. We also identified MYB, bHLH, and WRKY family members as candidate regulators. These results provide a gene-metabolite framework for understanding flavonoid accumulation in table beet and offer candidate resources for high-flavonoid breeding.