biostudies-arrayexpressBalázs KalaposTriticum timopheeviihttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17094A wheat × T. timopheevii pre-breeding population was analyzed using Genotyping-by-sequencing (GBS) combined with a skim-seq pipeline to identify and characterize T. timopheevii introgressions. Read coverage analysis based on a combined T. aestivum–T. timopheevii reference genome enabled high-resolution detection of major chromosomal introgressions and copy-number changes. Sequencing reads were aligned to this combined assembly, and chromosome identity and physical position could be extracted. An \"in silico wheat × T. timopheevii hybrid\" reference genome was constructed by combining the reference sequences of the donor and the recipient species. To identify wheat-T. timopheevii introgressions, we combined the Chinese Spring reference genome (IWGSC RefSeq v1.0) (IWGSC, 2018) with the draft genome assembly of T. timopheevii (GCA_963921465.1) (Grewal et al., 2024). During the assembly process, unique identifiers were assigned to all chromosomes or pseudomolecules to maintain distinctiveness. Prior to alignment, the Illumina short reads from 42 lines, along with the previously described control genotypes, were demultiplexed and adapter-trimmed with Stacks v2.68 (Rochette et al., 2019). The processed paired-end reads were then mapped separately to the combined reference genome using HISAT v2.1.0 (Kim et el., 2019) with the – no-spliced-alignment and – no-unal parameters. Following alignment, concordant unique reads were retrieved by filtering the sequence alignment map (SAM) outputs for the YT:Z:CP and NH:i:1 tags.biostudies-arrayexpressGrowth Protocol - Wheat (Triticum aestivum genotype Mv9kr1) and the wheat–T.timopheevii pre-breeding lines were grown in a high-input breeding nursery under field conditions. Root tip meristems were used for cytogenetic analyses, and young leaves were collected for genomic DNA extraction at the seedling stage.Nucleic Acid Extraction - Genomic DNA was extracted from young leaves of the pre-breeding lines and the control wheat lines using the BioSprint DNA kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. DNA concentration and quality were assessed prior to library construction.Sample Collection - Young leaf samples were collected from a high-input breeding nursery under field conditions for genomic DNA extraction. Samples were immediately processed or stored at –20 °C until use.Library Construction - GBS libraries were prepared using a modified double-digest RAD-seq (ddRAD-seq) protocol based on Yang et al. (2023). Genomic DNA was digested with restriction enzymes MspI and SphI. Adapter and index designs followed Poland et al. (2012). Size selection of 350–390 bp fragments was performed using a BluePippin system (1.5% gel cassette; Sage Science, Beverly, MA, USA). Equimolar sub-libraries were pooled prior to sequencing.Sequencing - Pooled equimolar libraries were sequenced on an Illumina NovaSeq 6000 platform using a paired-end 2 × 150 bp sequencing strategy at the Institute of Experimental Botany, Czech Academy of Sciences (Olomouc, Czechia).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Read coverage was normalized per chromosome by dividing the total number of mapped reads by the chromosome length in Mb (reads/Mb). Normalization and graphical visualization of read distribution were performed to compare chromosome-specific read densities between the T. timopheevii pre-breeding lines and the parental wheat genotype Mv9kr1.UnknownTranscriptomicsGenomicsProteomicsNextSeq 2000genotyping by high throughput sequencingTriticum timopheeviiBalázs KalaposfalseGBS-based identification of Triticum timopheevii introgressions in a wheat pre-breeding populationA wheat × T. timopheevii pre-breeding population was analyzed using Genotyping-by-sequencing (GBS) combined with a skim-seq pipeline to identify and characterize T. timopheevii introgressions. Read coverage analysis based on a combined T. aestivum–T. timopheevii reference genome enabled high-resolution detection of major chromosomal introgressions and copy-number changes. Sequencing reads were aligned to this combined assembly, and chromosome identity and physical position could be extracted. An \"in silico wheat × T. timopheevii hybrid\" reference genome was constructed by combining the reference sequences of the donor and the recipient species. To identify wheat-T. timopheevii introgressions, we combined the Chinese Spring reference genome (IWGSC RefSeq v1.0) (IWGSC, 2018) with the draft genome assembly of T. timopheevii (GCA_963921465.1) (Grewal et al., 2024). During the assembly process, unique identifiers were assigned to all chromosomes or pseudomolecules to maintain distinctiveness. Prior to alignment, the Illumina short reads from 42 lines, along with the previously described control genotypes, were demultiplexed and adapter-trimmed with Stacks v2.68 (Rochette et al., 2019). The processed paired-end reads were then mapped separately to the combined reference genome using HISAT v2.1.0 (Kim et el., 2019) with the – no-spliced-alignment and – no-unal parameters. Following alignment, concordant unique reads were retrieved by filtering the sequence alignment map (SAM) outputs for the YT:Z:CP and NH:i:1 tags.2026-05-28T00:00:00Z2026-05-28T11:19:49.126Z2026-05-26T13:23:42.02ZE-MTAB-17094ERP193974EFO_0002944EFO_0004170EFO_0003789EFO_0002771EFO_0005518EFO_0003816EFO_0004184