Genomic characterization and gene bank curation of Aegilops using genotyping-by-sequencing

In this study, Aegilops accessions preserved and maintained as single seed descent (SSD) at the Wheat Genetics Resource Center at Kansas State University were subjected to genotyping-by-sequencing. The DNA was extracted from the seedlings of individual plants and GBS library was made as described in the manuscript. The GBS data were utilized to detect variants using a reference-based pipeline, such as TASSEL GBS, in cases where genome assemblies were available. For the accessions without available genome assemblies, the sequence FASTQ files were aligned to a mock reference generated from the raw GBS data. The accessions with a higher amount of data were chosen to generate the mock reference. Variants were called using both GBS-SNP-CROP and bcfools pipeline. Subsequently, the SNP matrices were filtered and utilized for various analyses.