biostudies-arrayexpressBalázs KalaposTriticum aestivumhttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17093A wheat–Thinopyrum chromosome substitution line (GLA3) was characterized at the genomic level using genotyping-by-sequencing (GBS). In the GLA3 line, a Thinopyrum-derived group 3 chromosome (3J) replaces wheat chromosome 3D. To confirm the chromosomal composition, identify the homoeologous relationships of the alien chromosome, and detect potential chromosomal rearrangements or deletions, GBS read coverage analysis was performed. Short reads from the GLA3 introgression line were aligned to the wheat (Triticum aestivum IWGSC RefSeq v2.1) and Thinopyrum intermedium (v3.1) reference genomes, revealing the absence of chromosome 3D and the presence of Thinopyrum group 3 chromatin predominantly of J-genome origin.biostudies-arrayexpressSample Collection - Young leaf samples were collected from hydroponically grown seedlings of the GLA3 introgression line for genomic DNA extraction. Samples were immediately processed or stored at –20 °C until use.Growth Protocol - Wheat (Triticum aestivum genotype Mv9kr1) and the wheat–Thinopyrum 3J(3D) chromosome substitution line GLA3 were grown hydroponically under standard greenhouse conditions. Root tip meristems were used for cytogenetic analyses, and young leaves were collected for genomic DNA extraction at the seedling stage.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.Nucleic Acid Extraction - Genomic DNA was extracted from young leaves of the GLA3 introgression line using the BioSprint DNA kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. DNA concentration and quality were assessed prior to library construction.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 GLA3 introgression line and the parental wheat genotype MV9. Chromosomes exhibiting read densities significantly deviating from the expected range (166.7–230.9 reads/Mb for wheat chromosomes) were identified as absent or introgressed. The 3D chromosome of wheat was confirmed absent (7 reads/Mb; 96–97% reduction), whereas elevated read densities for Thinopyrum group 3 chromosomes (3J, 3St, 3V) indicated the presence of alien chromatin.UnknownTranscriptomicsNextSeq 2000genotyping by high throughput sequencingTriticum aestivumBalázs KalaposfalseGBS-based genomic characterization of a wheat–Thinopyrum 3J(3D) chromosome substitution line (GLA3)A wheat–Thinopyrum chromosome substitution line (GLA3) was characterized at the genomic level using genotyping-by-sequencing (GBS). In the GLA3 line, a Thinopyrum-derived group 3 chromosome (3J) replaces wheat chromosome 3D. To confirm the chromosomal composition, identify the homoeologous relationships of the alien chromosome, and detect potential chromosomal rearrangements or deletions, GBS read coverage analysis was performed. Short reads from the GLA3 introgression line were aligned to the wheat (Triticum aestivum IWGSC RefSeq v2.1) and Thinopyrum intermedium (v3.1) reference genomes, revealing the absence of chromosome 3D and the presence of Thinopyrum group 3 chromatin predominantly of J-genome origin.2026-05-19T00:00:00Z2026-05-19T21:24:13.044Z2026-05-19T21:23:57.798ZE-MTAB-17093ERP193609EFO_0002944EFO_0004170EFO_0003789EFO_0002771EFO_0005518EFO_0003816EFO_0004184