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Key message <p><b>This study provides the first integrated analysis of chlorophyll, carotenoid, and anthocyanin pathways underlying stem color differentiation in</b> <Emphasis Type="BoldItalic">G. elata</Emphasis><b>, identifying</b> <Emphasis Type="BoldItalic">PSY</Emphasis> <b>and</b> <i>F3’H</i> <b>as key candidate genes for color regulation in this mycoheterotrophic orchid.</b></p> Abstract <p><i>Gastrodia elata</i> is a mycoheterotrophic orchid of medicinal and economic value, yet the molecular basis of its stem color variation remains poorly understood. Here, pigment quantification, non-targeted metabolomics, and comparative transcriptomics were integrated to investigate stem color differentiation between green <i>G. elata</i> (GG) and red <i>G. elata</i> (RG). Pigment analysis revealed significantly higher total chlorophyll in GG (9.202 μg g<sup>−1</sup> DW vs. 1.59 μg g<sup>−1</sup> DW in RG), with a low chlorophyll a/b ratio (0.177) and predominance of chlorophyll b contributing to its yellow-green appearance. In contrast, total carotenoid content in RG was 1.78 times that in GG, with β-carotene levels 3.2-fold higher, primarily accounting for the orange-red coloration. Metabolomic profiling identified 21 anthocyanin compounds in both varieties, dominated by cyanidin derivatives. Transcriptome analysis identified 134 differentially expressed genes, with KEGG enrichment in carotenoid biosynthesis, porphyrin metabolism, and secondary metabolite biosynthesis pathways. Key candidate genes included phytoene synthase (<i>PSY</i>, <i>Gae_04381</i>), which showed higher expression in RG, and flavonoid 3’-hydroxylase (<i>F3’H</i>, <i>Gae_15605</i>), the only gene with statistically significant differential expression (P &lt; 0.05, ~ threefold higher in RG). qRT-PCR validation confirmed RNA-seq reliability. These findings demonstrate that stem coloration in G. elata is co-regulated by chlorophyll, carotenoid, and anthocyanin, and provide candidate genes for marker-assisted breeding of specific color varieties.</p>

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Transcriptome sequencing provides new insight into the biosynthesis pathway of pigments in stems of Gastrodia elata

  • 期刊论文

  • 发表日期：

    2026年6月16日

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  • Shanshan Luo,
  • Linshuang Tang,
  • Mingyan Tan,
  • Xinyun Liu,
  • Xiaofeng Wang,
  • Bin He,
  • Mingjin Huang

摘要

Key message

This study provides the first integrated analysis of chlorophyll, carotenoid, and anthocyanin pathways underlying stem color differentiation in G. elata, identifying PSY and F3’H as key candidate genes for color regulation in this mycoheterotrophic orchid.

Abstract

Gastrodia elata is a mycoheterotrophic orchid of medicinal and economic value, yet the molecular basis of its stem color variation remains poorly understood. Here, pigment quantification, non-targeted metabolomics, and comparative transcriptomics were integrated to investigate stem color differentiation between green G. elata (GG) and red G. elata (RG). Pigment analysis revealed significantly higher total chlorophyll in GG (9.202 μg g−1 DW vs. 1.59 μg g−1 DW in RG), with a low chlorophyll a/b ratio (0.177) and predominance of chlorophyll b contributing to its yellow-green appearance. In contrast, total carotenoid content in RG was 1.78 times that in GG, with β-carotene levels 3.2-fold higher, primarily accounting for the orange-red coloration. Metabolomic profiling identified 21 anthocyanin compounds in both varieties, dominated by cyanidin derivatives. Transcriptome analysis identified 134 differentially expressed genes, with KEGG enrichment in carotenoid biosynthesis, porphyrin metabolism, and secondary metabolite biosynthesis pathways. Key candidate genes included phytoene synthase (PSY, Gae_04381), which showed higher expression in RG, and flavonoid 3’-hydroxylase (F3’H, Gae_15605), the only gene with statistically significant differential expression (P < 0.05, ~ threefold higher in RG). qRT-PCR validation confirmed RNA-seq reliability. These findings demonstrate that stem coloration in G. elata is co-regulated by chlorophyll, carotenoid, and anthocyanin, and provide candidate genes for marker-assisted breeding of specific color varieties.