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DNA barcode identification of cultivated and wild tropical fruit species

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Abstract

With the rapid growth of the fruit industry worldwide, it is important to assess adulteration to ensure the authenticity and the safety of fruit products. The DNA barcoding approach offers a quick and accurate way of identifying and authenticating species. In this study, we developed reference DNA barcodes (rbcL, ITS2, and trnH-psbA) for 70 cultivated and wild tropical fruit species, representing 43 genera and 26 families. In terms of species recoverability, rbcL has a greater recoverability (100%) than ITS2 (95.7%) and trnH-psbA (88.6%). We evaluated the performance of these barcodes in species discrimination using similarity BLAST, phylogenetic tree, and barcoding gap analyses. The efficiency of rbcL, ITS2, and trnH-psbA in discriminating species was 80%, 100%, and 93.6%, respectively. We employed a multigene-tiered approach for species identification, with the rbcL region used for primary differentiation and ITS2 or trnH-psbA used for secondary differentiation. The two-locus barcodes rbcL + ITS2 and rbcL + trnH-psbA demonstrated robustness, achieving species discrimination rates of 100% and 94.3% respectively. Beyond the conventional species identification method based on plant morphology, the developed reference barcodes will aid the fruit agroindustry and trade, by making fruit-based product authentication possible.

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All data generated in this study are available within the paper and also as supplementary information.

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Acknowledgements

We thank Ahmad Farhan Nuri Rasli, Mohamad Izham Mohd Ariffin, Mohamad Aidil Noordin, Sharifah Talib, Ghazali Jaafar, Yahya Marhani, Ramli Ponyoh, Yasri Baya, Soo Pei Sin, and late Suryani Che Seman for their excellent assistance in the field and laboratory.

Funding

This study was supported by The Government of Malaysia under the 11th Malaysia Plan.

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Authors and Affiliations

  1. Forest Research Institute Malaysia, 52109, Kepong, Selangor Darul Ehsan, Malaysia

    Lee Hong Tnah, Soon Leong Lee, Chai Ting Lee, Kevin Kit Siong Ng, Chin Hong Ng & Ngah Zawiah

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  1. Lee Hong Tnah
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Correspondence to Lee Hong Tnah.

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The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Additional information

Accession Numbers: GenBank accessions of rbcL (OK052728–OK052798), ITS2 (OK052867–OK052949) and trnH-psbA (OK052799–OK052866).

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Tnah, L.H., Lee, S.L., Lee, C.T. et al. DNA barcode identification of cultivated and wild tropical fruit species. 3 Biotech 14, 7 (2024). https://doi.org/10.1007/s13205-023-03848-w

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