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Background <p>Diversification of cropping systems with orphan crops directly concerns food security issues. <i>Chenopodium</i> species display a high degree of morphological semblance, which makes their taxonomic identification intricate and challenging.</p> Methods and results <p>DNA barcoding of <i>Chenopodium quinoa</i> was made to characterize crop material imported through international trade for the prevailing cropping system. The phylogenetic reconstruction analysis using standard DNA barcodes <i>rbcL</i> and <i>matK</i> did not yield an optimal divergence threshold to resolve C. <i>quinoa</i> from other closely related <i>Chenopodium species</i>. Hence, identifying candidate DNA barcodes for resolving taxonomic diversity is a pressing need. Therefore, this study explored several candidate regions with low intraspecific but high interspecific divergence, and fourteen hypervariable regions were identified as candidate DNA barcodes. These hypervariable regions exhibit significant nucleotide diversity. The phylogenetic analysis revealed that candidate DNA barcodes possess an optimal divergence threshold compared to standard DNA barcodes and have shown more potential to delineate <i>C. quinoa</i> accessions as residents of an evolutionary distinct clade from other <i>Chenopodium</i> species. Mini-barcodes were developed from two hypervariable regions: the trnT(UGU)-trnL(UAA) intergenic spacer region and the rpl32-trnL region. These proved to have significant qualitative and quantitative identity accuracy for two <i>C. quinoa and C. album</i> seed experimental mixtures.</p> Conclusion <p>The standard DNA barcodes were insufficient to discriminate <i>C. quinoa</i> from other <i>Chenopodium</i> species whereas the candidate DNA barcodes and developed mini-barcodes showed high accuracy in species discrimination and germplasm authentication.</p>

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Identification of plastome-derived mini barcodes by DNA metabarcoding and comparative effectiveness to decipher their strength and resolving power for taxonomic topology-based phylogenetic determination of Chenopodium quinoa

  • 期刊论文

  • 发表日期：

    2026年3月6日

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  • Zakia Habib,
  • Siddra Ijaz,
  • Imran Ul Haq,
  • Irfan Afzal,
  • Ghulam Muhammad Ali

摘要

Background

Diversification of cropping systems with orphan crops directly concerns food security issues. Chenopodium species display a high degree of morphological semblance, which makes their taxonomic identification intricate and challenging.

Methods and results

DNA barcoding of Chenopodium quinoa was made to characterize crop material imported through international trade for the prevailing cropping system. The phylogenetic reconstruction analysis using standard DNA barcodes rbcL and matK did not yield an optimal divergence threshold to resolve C. quinoa from other closely related Chenopodium species. Hence, identifying candidate DNA barcodes for resolving taxonomic diversity is a pressing need. Therefore, this study explored several candidate regions with low intraspecific but high interspecific divergence, and fourteen hypervariable regions were identified as candidate DNA barcodes. These hypervariable regions exhibit significant nucleotide diversity. The phylogenetic analysis revealed that candidate DNA barcodes possess an optimal divergence threshold compared to standard DNA barcodes and have shown more potential to delineate C. quinoa accessions as residents of an evolutionary distinct clade from other Chenopodium species. Mini-barcodes were developed from two hypervariable regions: the trnT(UGU)-trnL(UAA) intergenic spacer region and the rpl32-trnL region. These proved to have significant qualitative and quantitative identity accuracy for two C. quinoa and C. album seed experimental mixtures.

Conclusion

The standard DNA barcodes were insufficient to discriminate C. quinoa from other Chenopodium species whereas the candidate DNA barcodes and developed mini-barcodes showed high accuracy in species discrimination and germplasm authentication.