Sequence resources

WHOLE GENOME SEQUENCE RESOURCES

De novo assembled genomes of the Flint lines DK105, EP1 and F7 as well as PE0075 (a DH line derived from the landrace PE) were generated using NRGene´s DeNovoMAGIC. Structural and functional annotation of the four genomes is completed. The four high-quality genomes, Zm-DK105-REFERENCE-TUM-1.0 (Zm00016a.1), Zm-EP1-REFERENCE-TUM-1.0 (Zm00010a), Zm-F7-REFERENCE-TUM-1.0 (Zm00011a) and Zm-PE0075-REFERENCE-TUM-1.0 (Zm00017a.1) were released in collaboration with the Maize Genetics and Genomics Database (MaizeGDB; http://www.maizegdb.org) and NCBI (BioProjects PRJNA360920 and PRJNA360923) in accordance with guidelines set forth by the Toronto Agreement for prepublication data sharing (Nature 2009 461:168).

Haberer G, Kamal N, Bauer E, Gundlach H, Fischer I, Seidel MA, Spannagl M, Marcon C, Ruban A, Urbany C, Nemri A, Hochholdinger F, Ouzunova M, Houben A, Schön CC, Mayer KFX (2020) European maize genomes highlight intraspecies variation in repeat and gene content. Nature Genetics 52:950-957, doi.org/10.1038/s41588-020-0671-9

Six Kemater DH lines were sequenced using PacBio HiFi long-reads and de novo assembled.

Urzinger S, Avramova V, Frey M, Urbany C, Scheuermann D, Presterl T, Reuscher S, Ernst K, Mayer M, Marcon C, Hochholdinger F, Brajkovic S, Ordas B, Westhoff P, Ouzunova M, Schön CC (2025) Embracing native diversity to enhance maximum quantum efficiency of photosystem II in maize (Zea mays L.). Plant Physiology 197:kiae670, doi.org/10.1093/plphys/kiae670

Urzinger S, Würstl L, Avramova V, Urbany C, Scheuermann D, Presterl T, Reuscher S, Mayer M, Brajkovic S, Ouzunova M, Ordas B, Westhoff P, Schön CC (2025) Structural variation at lhcb6 underlies genetic variation in photosystem II maximum quantum efficiency in maize. Scientific Reports accepted

Guffanti F, Scheuermann D, Urbany C, Reuscher S, Presterl T, Ouzunova M, Salvi S, Callot C, Schön CC (2026) Genetic architecture and functional consequences of lateral root length in maize (Zea mays L.). J Exp Bot, doi.org/10.1093/jxb/erag130

WGS data of 15 Kemater lines have been deposited in the NCBI Sequence Read Archive (https://www.ncbi.nlm.nih.gov/sra/, BioProject: PRJNA1133950).

29 Petkuser lines were sequenced at 30 x (n=7) or ~50X (n=22) coverage and assembled to contigs. Seven lines of PE were chosen to cover most of the diversity of the landrace and used as reference panel for haplotype construction. The remaining lines represent parents of bi-parental crosses for QTL fine mapping.

Illumina sequence data from 30 diverse Dent and Flint inbred lines from Europe and the US and from one Teosinte accession were generated. The average genome coverage of these 31 lines is 18.9 x. Sequence data are available from the NCBI Sequence Read Archive under BioProject number PRJNA260788 (http://www.ncbi.nlm.nih.gov/bioproject/PRJNA260788). For a description of the plant material see Unterseer et al. (2014).

Unterseer S, Bauer E, Haberer G, Seidel M, Knaak C, Ouzunova M, Meitinger T, Strom TM, Fries R, Pausch H, Bertani C, Davassi A, Mayer KFX, Schön C-C (2014) A powerful tool for genome analysis in maize: development and evaluation of the high density 600 k SNP genotyping array. BMC Genomics 15:823, doi:10.1186/1471-2164-15-823

SKIM-SEQUENCE RESOURCES

340 DH lines derived from the landrace PE sequenced at low coverage (skim-seq at 0.5X). For those lines, a library of haplotypes was built using GenoMagic developed by the company NRGene, based on their similarity to a reference panel of 51 maize genotypes for which a reference genome or a contig assembly was available.

Variant calls for chromosome 1 for 321 lines (after quality filtering) are available via https://github.com/tpook92/HBimpute. For a detailed description of this dataset see Pook et al. 2021.

Pook T, Nemri A, Gonzalez Segovia EG, Simianer H, Schoen CC (2021) Increasing calling accuracy, coverage, and read depth in sequence data by the use of haplotype blocks. PLOS Genetics, doi.org/10.1371/journal.pgen.1009944

RNA-SEQUENCES

21 DH lines diverging for cold tolerance derived from the European flint landrace “Petkuser Ferdinand Rot” showed highly variable transcriptomic responses with respect to cold treatment, cold tolerance and growth rate at cold in an RNA-seq experiment. The sequencing data has been deposited in the NCBI Sequencing Read Archive under BioProject accession number PRJNA556806 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA556806).

Frey F, Pitz M, Schön CC, Hochholdinger F. (2020) Transcriptomic diversity in seedling roots of European flint maize in response to cold. BMC Genomics 21, 300, doi.org/10.1186/s12864-020-6682-1

Transcriptom atlas of European Flint lines RNA-seq data were generated for the maize flint lines DK105, EP1, F7, and PE0075, as well as for the maize reference line B73. For these five lines, an expression atlas spanning a broad range of maize organs across the entire life cycle was established. Up to four biological replicates were collected for each of 30 tissues, resulting in nearly 600 RNA-seq samples in total. This dataset was used to support the generation of high-quality, evidence-based gene annotations for the genome assemblies of DK105, EP1, F7, and PE0075 (manuscript in preparation). The sequencing data will be made publicly available alongside the release of the updated genome annotations. In addition, a comprehensive differential gene expression analysis based on this dataset is currently in progress.