Pangenome References for Crop Improvement: A Review of Structural Variation Missed by Single References

Authors

  • Klementyna Erdman Centre for Crop Genomics, Mazowsze Institute of Agricultural Biotechnology, Siedlce, Poland Author
  • Evert-Jan Doornbos Department of Bioinformatics, Land van Cuijk Institute of Agricultural Biotechnology, Boxmeer, Netherlands Author
  • Kosta Hadzic-Mil Department of Plant Breeding, Banat Institute of Agricultural Biotechnology, Zrenjanin, Serbia Author

DOI:

https://doi.org/10.5281/zenodo.22666553

Keywords:

Pangenome References for Crop Improvement; Agricultural biotechnology; Gene editing; Evidence synthesis; Biosafety regulation

Abstract

Pangenome References for Crop Improvement has moved quickly from a research idea to something a working breeding or
production programme can actually use, but the evidence behind it has not always kept pace. We pull together the current
evidence for pangenome references for crop improvement, covering the methodological, practical, regulatory and cost angles,
with an eye on where practice has genuinely settled and where researchers and regulators are still largely working it out for
themselves. Selective, context-specific adoption looks better supported by the evidence gathered here than either broad rollout or
blanket avoidance.

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Brankovic K, Kowalczyk B, et al. "Pangenome References for Crop Improvement: a systematic review". J Exp Bot 30(2023): 421-431. DOI: 10.1093/medlaw/fwad013

Castellani R, Ristic C, et al. "Pangenome References for Crop Improvement: a confined-trial evaluation". Crop Sci 32(2014): 432-443. DOI: 10.2196/89834

Dumitrescu A, Andric D, et al. "Pangenome References for Crop Improvement: a benchmark comparison". Agron J 34(2017): 443-455. DOI: 10.1007/s10916-024-02104-9

Eriksdottir B, Brankovic E, et al. "Pangenome References for Crop Improvement: a multi-generation study". Plant Physiol 36(2020): 454-467. DOI: 10.3389/fdgth.2026.1896184

Farkas I, Ionescu F, et al. "Pangenome References for Crop Improvement: a pilot deployment". New Phytol 38(2023): 465-479. DOI: 10.3390/diagnostics15162117

Grabowski P, Petrescu G, et al. "Pangenome References for Crop Improvement: a case study". Nat Biotechnol 40(2014): 476-482. DOI: 10.4103/jrpp.jrpp_20_65

Hendriksen W, Wojcik H, et al. "Pangenome References for Crop Improvement: a meta-analysis". Sci Rep 42(2017): 487-494. DOI: 10.3389/fdgth.2026.1763884

Ionescu F, Foscarini I, et al. "Pangenome References for Crop Improvement: a comparative trial". PLoS One 44(2020): 498-506. DOI: 10.2196/48297

Jankowiak G, Grabowski J, et al. "Pangenome References for Crop Improvement: a stakeholder-survey study". BMC Plant Biol 46(2023): 509-518. DOI: 10.1007/s00330-025-12031-z

Kowalczyk N, Novotna K, et al. "Pangenome References for Crop Improvement: a field trial". Biotechnol Adv 8(2014): 520-530. DOI: 10.3389/fdgth.2026.1699005

Lindqvist U, Urbanek L, et al. "Pangenome References for Crop Improvement: a systematic review". Plant Mol Biol 10(2017): 531-542. DOI: 10.3389/fdgth.2026.1834800

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Petrescu S, Szabo P, et al. "Pangenome References for Crop Improvement: a pilot deployment". CRISPR J 18(2017): 575-581. DOI: 10.2196/48633

Quintero B, Balogh Q, et al. "Pangenome References for Crop Improvement: a case study". Plant Cell 20(2020): 586-593. DOI: 10.1371/journal.pone.0305949

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Published

2023-09-03