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Background <p>Quinoa exhibits striking inflorescence color variation, with red inflorescences (RF) characterized by higher anthocyanin accumulation than green inflorescences (GF). However, the molecular mechanisms underlying this phenotype remain insufficiently understood. </p> Results <p>Integrated metabolomic and transcriptomic analyses revealed substantial differences in the anthocyanin biosynthetic pathway between RF and GF accessions. RF plants showed marked upregulation of key structural genes, including <i>ANS</i>, <i>3GGT</i>, and malonyltransferases (<i>MaTs</i>). Notably, MYB and bHLH transcription factors, including homologs of MdMYBA1, AtPAP1/2, and ZmbHLH125, were identified as master regulators, while the WD40 was significantly upregulated, supporting formation of the MYB-bHLH-WD40 (MBW) complex. Genes encoding transporters such as multidrug resistance-associated proteins (MRPs) and multidrug and toxic compound extrusion (MATE) proteins were also significantly upregulated, supporting the enhanced accumulation of malonylated cyanidin and petunidin derivatives. Regulatory analysis further revealed that abscisic acid (ABA) signaling appeared to indirectly influence anthocyanin biosynthesis by modulating transcription factor expression. Genomic analysis further showed that quinoa, as an allotetraploid species, possesses multiple paralogs of anthocyanin-related genes, potentially enhancing metabolic plasticity. </p> Conclusions <p>This study elucidates the metabolic, transcriptional, and genomic bases of inflorescence color formation in quinoa. The findings highlight that red panicle formation is driven by coordinated upregulation of biosynthetic genes (ANS, 3GGT, MaTs), transporters (MRP, MATE), and MBW transcription factors, with ABA signaling playing a key modulatory role. The findings provide valuable insight for improving pigment quality and advancing molecular breeding in this crop.</p>

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Integrated metabolite profiling and transcriptomic analysis reveal mechanisms underlying quinoa inflorescence color

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年4月18日

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  • Jialin Li,
  • Shance Niu,
  • Jiaxing Wei,
  • Chang Liu,
  • Zhifei Tang,
  • Lumeng Zheng,
  • Guojun Mu,
  • Wei Lv,
  • Xinbo Sun

摘要

Background

Quinoa exhibits striking inflorescence color variation, with red inflorescences (RF) characterized by higher anthocyanin accumulation than green inflorescences (GF). However, the molecular mechanisms underlying this phenotype remain insufficiently understood.

Results

Integrated metabolomic and transcriptomic analyses revealed substantial differences in the anthocyanin biosynthetic pathway between RF and GF accessions. RF plants showed marked upregulation of key structural genes, including ANS, 3GGT, and malonyltransferases (MaTs). Notably, MYB and bHLH transcription factors, including homologs of MdMYBA1, AtPAP1/2, and ZmbHLH125, were identified as master regulators, while the WD40 was significantly upregulated, supporting formation of the MYB-bHLH-WD40 (MBW) complex. Genes encoding transporters such as multidrug resistance-associated proteins (MRPs) and multidrug and toxic compound extrusion (MATE) proteins were also significantly upregulated, supporting the enhanced accumulation of malonylated cyanidin and petunidin derivatives. Regulatory analysis further revealed that abscisic acid (ABA) signaling appeared to indirectly influence anthocyanin biosynthesis by modulating transcription factor expression. Genomic analysis further showed that quinoa, as an allotetraploid species, possesses multiple paralogs of anthocyanin-related genes, potentially enhancing metabolic plasticity.

Conclusions

This study elucidates the metabolic, transcriptional, and genomic bases of inflorescence color formation in quinoa. The findings highlight that red panicle formation is driven by coordinated upregulation of biosynthetic genes (ANS, 3GGT, MaTs), transporters (MRP, MATE), and MBW transcription factors, with ABA signaling playing a key modulatory role. The findings provide valuable insight for improving pigment quality and advancing molecular breeding in this crop.