biostudies-arrayexpressBalázs KalaposTriticum aestivumhttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17546A wheat × D.villosum pre-breeding population was analyzed using Genotyping-by-sequencing (GBS) combined with a skim-seq pipeline to identify and characterize D.villosum introgressions. Read coverage analysis based on a combined T. aestivum– D.villosum reference genome enabled high-resolution detection of major chromosomal introgressions and copy-number changes. To identify wheat- D.villosum introgressions, the Chinese Spring reference genome (IWGSC RefSeq v2.1) (IWGSC, 2021) and the Dasypyrum villosum (Zhang et al., 2023) reference genome were used as a reference during read coverage analyzis. During the assembly process, unique identifiers were assigned to all chromosomes or pseudomolecules to maintain distinctiveness. Prior to alignment, the Illumina short reads from 33 lines, 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 v2.2.1 (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 ‘Chinese Spring’) and the wheat– D. villosum 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 FilesSequence Alignment - Raw Illumina reads from the wheat × D.villosum pre-breeding lines were quality-filtered and aligned to two reference genomes: (1) the Triticum aestivum reference genome (IWGSC RefSeq v2.1) and (2) the Dasypyrum villosum (Zhang et al., 2023) using HISAT2 v2.2.1. Read alignment, normalization, and filtering followed the bioinformatic pipeline described by Adhikari et al. (2022). To assess chromosome-specific read distribution, the number of aligned reads per megabase (Mb) was calculated for each chromosome based on read alignment to the respective reference genome and chromosome lengths in Mb. Normalized GBS read coverage values were plotted along individual chromosomes to visualize the presence or absence of specific chromosomal segments and to identify introgressed alien chromatin.Data 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 D.villosum pre-breeding lines and the parental wheat genotype Chinese Spring.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000genotyping by high throughput sequencingTriticum aestivumBalázs KalaposfalseGBS-based identification of Dasypyrum villosum introgressions in a wheat pre-breeding populationA wheat × D.villosum pre-breeding population was analyzed using Genotyping-by-sequencing (GBS) combined with a skim-seq pipeline to identify and characterize D.villosum introgressions. Read coverage analysis based on a combined T. aestivum– D.villosum reference genome enabled high-resolution detection of major chromosomal introgressions and copy-number changes. To identify wheat- D.villosum introgressions, the Chinese Spring reference genome (IWGSC RefSeq v2.1) (IWGSC, 2021) and the Dasypyrum villosum (Zhang et al., 2023) reference genome were used as a reference during read coverage analyzis. During the assembly process, unique identifiers were assigned to all chromosomes or pseudomolecules to maintain distinctiveness. Prior to alignment, the Illumina short reads from 33 lines, 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 v2.2.1 (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.2026-08-27T00:00:00Z2026-08-27T01:00:43.645Z2026-08-25T21:29:10.088ZE-MTAB-17546ERP204256EFO_0002944EFO_0004170EFO_0003789EFO_0002771EFO_0004917EFO_0005518EFO_0003816EFO_0004184