Abstract
Although several maize genome assemblies are publicly available, those of lines important to European breeding programs are underrepresented. Using PacBio long-read sequencing, we assembled high-quality chromosome-level genomes of 29 key lines of European breeding relevance, encompassing Northern flint and European flint lines used for adaptation to Northern European climate, lines derived from European landraces of tropical origin, and American temperate dent lines adapted to European regions. Genome assembly sizes range from 2.17 to 2.35 gigabases, with scaffold N50s ranging from 219 to 254 megabases. Completeness assessment revealed BUSCO scores ranging from 97.7 to 98.5 and merqury completeness scores ranging from 96.62 to 98.30. Calling structural variants and SNPs relative to the B73 reference sequence revealed the expected separation of inbred groups. Flint lines contribute the highest number of novel variants, thus emphasizing the importance of sequencing flint material to complete the maize pangenome. These high-quality genome assemblies therefore provide new opportunities to understand the dynamics of maize structural variation, and to identify the functional variations underlying maize phenotypic diversity.
Similar content being viewed by others
Data availability
All raw sequencing data, assembled genomes, and variant data (VCF files) have been deposited in publicly accessible repositories. The PacBio HiFi and Hi-C sequencing reads, as well as the genomes assembled from these data, have been uploaded to the European Nucleotide Archive (ENA) at www.ebi.ac.uk/ena as part of the SeqOccIn project, PRJEB600751634, and are accessible under project PRJEB6781231. Structural Variants and SNPs are available to European Variation Archive (EVA) and accessible under the accession PRJEB10659932. Variant data are linked to the nucleotide data through the sharing of a single BioSample ID. Variant data are also available at data.gouv.fr repository (https://doi.org/10.57745/7AUTOL)33.
Code availability
All the codes used for the analysis can be found on the SeqOccIn project’s GitHub page, following the path Data paper/Zea mays data paper: https://github.com/GeTPlaGe/SeqOccIn/tree/main/Data%20paper/Zeamays. The pipeline used for aligning reads and calling variants is available here: https://github.com/SeqOccin-SV/SeqOccinVariants.
References
Wrigley, C. W. & Nirmal, R. C. The major cereal grains: Corn, rice, and wheat, https://doi.org/10.1002/0471238961.23080501.a01.pub3 (2017).
Wang, Q. & Dooner, H. K. Remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus. Proceedings of the National Academy of Sciences 103, 17644–17649, https://doi.org/10.1073/pnas.0603080103 (2006).
Stitzer, M. C., Anderson, S. N., Springer, N. M. & Ross-Ibarra, J. The genomic ecosystem of transposable elements in maize. PLOS Genetics 17, e1009768, https://doi.org/10.1371/journal.pgen.1009768 (2021).
Ou, S. et al. Differences in activity and stability drive transposable element variation in tropical and temperate maize. Genome Research 34, 1140–1153, https://doi.org/10.1101/gr.278131.123 (2024).
Wallace, J. G. et al. Association mapping across numerous traits reveals patterns of functional variation in maize. PLoS Genetics 10, e1004845, https://doi.org/10.1371/journal.pgen.1004845 (2014).
Zhou, P., Hirsch, C. N., Briggs, S. P. & Springer, N. M. Dynamic patterns of gene expression additivity and regulatory variation throughout maize development. Molecular Plant 12, 410–425, https://doi.org/10.1016/j.molp.2018.12.015 (2019).
Ricci, W. A. et al. Widespread long-range cis-regulatory elements in the maize genome. Nature Plants 5, 1237–1249, https://doi.org/10.1038/s41477-019-0547-0 (2019).
Marand, A. P. et al. The genetic architecture of cell type-specific cis regulation in maize. Science 388, https://doi.org/10.1126/science.ads6601 (2025).
Fagny, M. et al. Identification of key tissue-specific, biological processes by integrating enhancer information in maize gene regulatory networks. Frontiers in Genetics 11, https://doi.org/10.3389/fgene.2020.606285 (2021).
Springer, N. M. et al. The maize w22 genome provides a foundation for functional genomics and transposon biology. Nature Genetics 50, 1282–1288, https://doi.org/10.1038/s41588-018-0158-0 (2018).
Sun, S. et al. Extensive intraspecific gene order and gene structural variations between mo17 and other maize genomes. Nature Genetics 50, 1289–1295, https://doi.org/10.1038/s41588-018-0182-0 (2018).
Yang, N. et al. Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement. Nature Genetics 51, 1052–1059, https://doi.org/10.1038/s41588-019-0427-6 (2019).
Lin, T., Song, Y., Lawrence, P., Kheshgi, H. S. & Jain, A. K. Worldwide maize and soybean yield response to environmental and management factors over the 20th and 21st centuries. Journal of Geophysical Research: Biogeosciences 126, https://doi.org/10.1029/2021jg006304 (2021).
Chen, J. et al. A complete telomere-to-telomere assembly of the maize genome. Nature Genetics 55, 1221–1231, https://doi.org/10.1038/s41588-023-01419-6 (2023).
Darracq, A. et al. Sequence analysis of european maize inbred line f2 provides new insights into molecular and chromosomal characteristics of presence/absence variants. BMC Genomics 19, https://doi.org/10.1186/s12864-018-4490-7 (2018).
Haberer, G. et al. European maize genomes highlight intraspecies variation in repeat and gene content. Nature Genetics 52, 950–957, https://doi.org/10.1038/s41588-020-0671-9 (2020).
Hufford, M. B. et al. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science 373, 655–662, https://doi.org/10.1126/science.abg5289 (2021).
Mayjonade, B. et al. Extraction of high-molecular-weight genomic dna for long-read sequencing of single molecules. BioTechniques 61, 203–205, https://doi.org/10.2144/000114460 (2016).
Workman, R. et al. High molecular weight dna extraction from recalcitrant plant species for third generation sequencing v1. https://doi.org/10.1038/protex.2018.059 (2018).
Cabanettes, F. & Klopp, C. D-GENIES: dot plot large genomes in an interactive, efficient and simple way. journal = PeerJ 6, https://doi.org/10.7717/peerj.4958 (2018).
Cheng, H., Concepcion, G. T., Feng, X., Zhang, H. & Li, H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nature Methods 18, 170–175, https://doi.org/10.1038/s41592-020-01056-5 (2021).
Durand, N. C. et al. Juicer provides a one-click system for analyzing loop-resolution hi-c experiments. Cell systems 3, 95–98 (2016).
Dudchenko, O. et al. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356, 92–95, https://doi.org/10.1126/science.aal3327 (2017).
Durand, N. C. et al. Juicebox provides a visualization system for hi-c contact maps with unlimited zoom. Cell Systems 3, 99–101, https://doi.org/10.1016/j.cels.2015.07.012 (2016).
Alonge, M. et al. Automated assembly scaffolding using ragtag elevates a new tomato system for high-throughput genome editing. Genome Biology 23, https://doi.org/10.1186/s13059-022-02823-7 (2022).
Bradnam, K. R. et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience 2, https://doi.org/10.1186/2047-217x-2-10 (2013).
Seppey, M., Manni, M. & Zdobnov, E. M. BUSCO: Assessing Genome Assembly and Annotation Completeness, 227–245 (Springer New York, 2019).
Rhie, A., Walenz, B. P., Koren, S. & Phillippy, A. M. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biology 21, https://doi.org/10.1186/s13059-020-02134-9 (2020).
Smolka, M. et al. Detection of mosaic and population-level structural variants with Sniffles2. Nature Biotechnology 42, https://doi.org/10.1038/s41587-023-02024-y (2024).
Kirsche, M. et al. Jasmine and Iris: population-scale structural variant comparison and analysis. Nature Methods 20, https://doi.org/10.1038/s41592-022-01753-3 (2023).
European nucleotide archive. https://www.ebi.ac.uk/ena/browser/view/PRJEB67812 (2025).
European variant archive. https://www.ebi.ac.uk/eva/?eva-study=PRJEB106599 (2026).
The 29 maize lines SNP and SV variant set. https://doi.org/10.57745/7AUTOL (2025).
Germplasm Resources Information Network (GRIN) — doi.org. https://doi.org/10.15482/USDA.ADC/1212393.
European nucleotide archive. https://www.ebi.ac.uk/ena/browser/view/PRJEB60075 (2023).
Byrne, P. F. et al. Sustaining the future of plant breeding: The critical role of the usda-ars national plant germplasm system. Crop Science 58, 451–468, https://doi.org/10.2135/cropsci2017.05.0303 (2018).
Camus-Kulandaivelu, L. et al. Maize adaptation to temperate climate: Relationship between population structure and polymorphism in the dwarf8 gene. Genetics 172, 2449–2463, https://doi.org/10.1534/genetics.105.048603 (2006).
Bouchet, S. et al. Adaptation of maize to temperate climates: Mid-density genome-wide association genetics and diversity patterns reveal key genomic regions, with a major contribution of the vgt2 (zcn8) locus. PLoS ONE 8, e71377, https://doi.org/10.1371/journal.pone.0071377 (2013).
Acknowledgements
We thank “La Région Occitanie” and European Union for funding the project as part of the Occitanie Region’s “Regional Research and Innovation Platforms” call for projects under the FEDER-FSE MIDI-PYRENEES ET GARONNE 2014-2020 Operational Program. We thank KWS, Maisadour, Euralis, Caussade semences, Syngenta, RAGT and Limagrain for their financial support and their inputs for choosing the genetic material analyzed. We thank Valérie Combes for sample preparation, Delphine Madur and Nathalie Rivière for genotype validation, Gaëtan Givry for EVA data submission and Jorge Duarte and Johann Joets for insightful discussions on maize genome scaffolding. We are grateful to Cyril Bauland for expertise in maize germplasm accession nomenclature. We thank Carine Palaffre and French maize inbred lines seed bank (CRB, INRAE Saint Martin de Hinx), the U.S. National Plant Germplasm System (NPGS)35 and the USDA Agricultural Research Service Germplasm Resources Information Network (GRIN)36 for providing seeds with traced seedlots, as well as Adrienne Ressayre and Christine Dillmann (GQE-Le Moulon) for providing seeds of F252 and MBS847, and Silvio Salvi (University of Bologna) for early access to seeds from the GF111 inbred line, Carlotta Balconi (CREA-Research Centre for Cereal and Industrial Crops) for providing access to Lo3, and CSIC (Consejo Superior de Investigaciones Científicas) for authorizing the use of EM1197. GeT core facility https://doi.org/10.15454/1.5572370921303193E12 is supported by France Génomique National infrastructure, funded as part of “Investissement d’avenir” program managed by the French Agence Nationale pour la Recherche (contract ANR-10-INBS-09). We are grateful to the genotoul bioinformatics platform Toulouse Occitanie (Bioinfo Genotoul, https://doi.org/10.15454/1.5572369328961167E12) for providing computing and storage resources.
Author information
Authors and Affiliations
Contributions
C.D., D.M., and Ch.G. conceived and supervised the whole “SeqOccIn” project. Cl.V. and A.C. conceived the maize-related sub-project of the “SeqOccIn” project. C.D., D.M., Ch.G., Cl.V. and A.C. secured funding. C.I. coordinated data generation and quality control. C.I., C.M., C.E., E.D. produced sequence data. Ch.K., T.F. and Cl.K. supervised bioinformatic analyses. C.B., A.D.F., T.F., J.D., S.N., Cl.V. and Ch.K. analysed the results. S.P. and A.C. coordinated the selection of the inbred lines with private partners. Cl.K. and Ca.V. secured data and submitted them to public databases. C.I., Cl.V., Ch.K., S.N. and T.F. wrote the original draft of the manuscript. All authors reviewed the manuscript.
Corresponding authors
Ethics declarations
Competing interests
The authors declare no competing interests.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary information
Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
About this article
Cite this article
Marcuzzo, C., Birbes, C., Eché, C. et al. High-quality chromosome-scale genome assemblies of 29 maize inbred lines of European breeding relevance. Sci Data (2026). https://doi.org/10.1038/s41597-026-07055-z
Received:
Accepted:
Published:
DOI: https://doi.org/10.1038/s41597-026-07055-z
