Project description:A 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.

2026-08-27 | E-MTAB-17546 | biostudies-arrayexpress

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