Pangenome References for Crop Improvement: A Review of Structural Variation Missed by Single References
DOI:
https://doi.org/10.5281/zenodo.22666553Keywords:
Pangenome References for Crop Improvement; Agricultural biotechnology; Gene editing; Evidence synthesis; Biosafety regulationAbstract
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.
References
Alvez D, Dumitrescu A, et al. "Pangenome References for Crop Improvement: a field trial". Plant Biotechnol J 8(2014): 80-86. DOI: 10.1016/j.ssci.2025.107028
Brankovic K, Kowalczyk B, et al. "Pangenome References for Crop Improvement: a systematic review". Theor Appl Genet 10(2017): 91-98. DOI: 10.2196/48633
Castellani R, Ristic C, et al. "Pangenome References for Crop Improvement: a confined-trial evaluation". Front Plant Sci 12(2020): 102-110. DOI: 10.1371/journal.pone.0305949
Dumitrescu A, Andric D, et al. "Pangenome References for Crop Improvement: a benchmark comparison". Transgenic Res 14(2023): 113-122. DOI: 10.1371/journal.pdig.0000514
Eriksdottir B, Brankovic E, et al. "Pangenome References for Crop Improvement: a multi-generation study". GM Crops Food 16(2014): 124-134. DOI: 10.17219/acem/208596
Farkas I, Ionescu F, et al. "Pangenome References for Crop Improvement: a pilot deployment". Plant Cell Rep 18(2017): 135-146. DOI: 10.7759/cureus.104086
Grabowski P, Petrescu G, et al. "Pangenome References for Crop Improvement: a case study". Mol Plant 20(2020): 146-158. DOI: 10.1038/s41746-023-00852-5
Hendriksen W, Wojcik H, et al. "Pangenome References for Crop Improvement: a meta-analysis". J Exp Bot 22(2023): 157-170. DOI: 10.1016/j.mayocpiqo.2022.09.004
Ionescu F, Foscarini I, et al. "Pangenome References for Crop Improvement: a comparative trial". Crop Sci 24(2014): 168-182. DOI: 10.1177/08404704241291226
Jankowiak G, Grabowski J, et al. "Pangenome References for Crop Improvement: a stakeholder-survey study". Agron J 26(2017): 179-185. DOI: 10.1093/medlaw/fwad013
Kowalczyk N, Novotna K, et al. "Pangenome References for Crop Improvement: a field trial". Plant Physiol 28(2020): 190-197. DOI: 10.2196/89834
Lindqvist U, Urbanek L, et al. "Pangenome References for Crop Improvement: a systematic review". New Phytol 30(2023): 201-209. DOI: 10.1007/s10916-024-02104-9
Marchetti D, Doncheva M, et al. "Pangenome References for Crop Improvement: a confined-trial evaluation". Nat Biotechnol 32(2014): 212-221. DOI: 10.3389/fdgth.2026.1896184
Novotna E, Eriksdottir N, et al. "Pangenome References for Crop Improvement: a benchmark comparison". Sci Rep 34(2017): 223-233. DOI: 10.3390/diagnostics15162117
Ostrowski L, Lindqvist O, et al. "Pangenome References for Crop Improvement: a multi-generation study". PLoS One 36(2020): 234-245. DOI: 10.4103/jrpp.jrpp_20_65
Petrescu S, Szabo P, et al. "Pangenome References for Crop Improvement: a pilot deployment". BMC Plant Biol 38(2023): 245-257. DOI: 10.3389/fdgth.2026.1763884
Quintero B, Balogh Q, et al. "Pangenome References for Crop Improvement: a case study". Biotechnol Adv 40(2014): 256-269. DOI: 10.2196/48297
Ristic C, Castellani R, et al. "Pangenome References for Crop Improvement: a meta-analysis". Plant Mol Biol 42(2017): 267-281. DOI: 10.1007/s00330-025-12031-z
Szabo J, Jankowiak S, et al. "Pangenome References for Crop Improvement: a comparative trial". Field Crops Res 44(2020): 278-284. DOI: 10.3389/fdgth.2026.1699005
Tarasov Q, Quintero T, et al. "Pangenome References for Crop Improvement: a stakeholder-survey study". Euphytica 46(2023): 289-296. DOI: 10.3389/fdgth.2026.1834800
Urbanek Z, Zielinski U, et al. "Pangenome References for Crop Improvement: a field trial". Front Genome Ed 8(2014): 300-308. DOI: 10.2196/69678
Vasquez A, Alvez V, et al. "Pangenome References for Crop Improvement: a systematic review". CRISPR J 10(2017): 311-320. DOI: 10.7759/cureus.46454
Wojcik H, Hendriksen W, et al. "Pangenome References for Crop Improvement: a confined-trial evaluation". Plant Cell 12(2020): 322-332. DOI: 10.1016/j.ssci.2025.107028
Zielinski O, Ostrowski Z, et al. "Pangenome References for Crop Improvement: a benchmark comparison". Trends Biotechnol 14(2023): 333-344. DOI: 10.2196/48633
Andric V, Vasquez A, et al. "Pangenome References for Crop Improvement: a multi-generation study". Plant Biotechnol J 16(2014): 344-356. DOI: 10.1371/journal.pone.0305949
Balogh E, Emmerich B, et al. "Pangenome References for Crop Improvement: a pilot deployment". Theor Appl Genet 18(2017): 355-368. DOI: 10.1371/journal.pdig.0000514
Chiriac F, Farkas C, et al. "Pangenome References for Crop Improvement: a case study". Front Plant Sci 20(2020): 366-380. DOI: 10.17219/acem/208596
Doncheva M, Marchetti D, et al. "Pangenome References for Crop Improvement: a meta-analysis". Transgenic Res 22(2023): 377-383. DOI: 10.7759/cureus.104086
Emmerich T, Tarasov E, et al. "Pangenome References for Crop Improvement: a comparative trial". GM Crops Food 24(2014): 388-395. DOI: 10.1038/s41746-023-00852-5
Foscarini C, Chiriac F, et al. "Pangenome References for Crop Improvement: a stakeholder-survey study". Plant Cell Rep 26(2017): 399-407. DOI: 10.1016/j.mayocpiqo.2022.09.004
Alvez D, Dumitrescu A, et al. "Pangenome References for Crop Improvement: a field trial". Mol Plant 28(2020): 410-419. DOI: 10.1177/08404704241291226
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
Marchetti D, Doncheva M, et al. "Pangenome References for Crop Improvement: a confined-trial evaluation". Field Crops Res 12(2020): 542-554. DOI: 10.2196/69678
Novotna E, Eriksdottir N, et al. "Pangenome References for Crop Improvement: a benchmark comparison". Euphytica 14(2023): 553-566. DOI: 10.7759/cureus.46454
Ostrowski L, Lindqvist O, et al. "Pangenome References for Crop Improvement: a multi-generation study". Front Genome Ed 16(2014): 564-578. DOI: 10.1016/j.ssci.2025.107028
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
Ristic C, Castellani R, et al. "Pangenome References for Crop Improvement: a meta-analysis". Trends Biotechnol 22(2023): 597-605. DOI: 10.1371/journal.pdig.0000514
Szabo J, Jankowiak S, et al. "Pangenome References for Crop Improvement: a comparative trial". Plant Biotechnol J 24(2014): 608-617. DOI: 10.17219/acem/208596
Tarasov Q, Quintero T, et al. "Pangenome References for Crop Improvement: a stakeholder-survey study". Theor Appl Genet 26(2017): 619-629. DOI: 10.7759/cureus.104086
Urbanek Z, Zielinski U, et al. "Pangenome References for Crop Improvement: a field trial". Front Plant Sci 28(2020): 630-641. DOI: 10.1038/s41746-023-00852-5
Vasquez A, Alvez V, et al. "Pangenome References for Crop Improvement: a systematic review". Transgenic Res 30(2023): 641-653. DOI: 10.1016/j.mayocpiqo.2022.09.004
Wojcik H, Hendriksen W, et al. "Pangenome References for Crop Improvement: a confined-trial evaluation". GM Crops Food 32(2014): 652-665. DOI: 10.1177/08404704241291226
Zielinski O, Ostrowski Z, et al. "Pangenome References for Crop Improvement: a benchmark comparison". Plant Cell Rep 34(2017): 663-677. DOI: 10.1093/medlaw/fwad013
Andric V, Vasquez A, et al. "Pangenome References for Crop Improvement: a multi-generation study". Mol Plant 36(2020): 674-680. DOI: 10.2196/89834

