Citation: Y. Guo (2024-08-07): Ancestral haplotype groups in a diversity panel of wild and domesticated barley (Hordeum vulgare). DOI:10.5447/ipk/2025/7

Abstract: Ancestral haplotype groups (AHG) were defined in a panel of 367 diverse barley genotypes, of which 251 are wild and 116 domesticated forms. Passport information of the barley genotypes and accession codes of the underlying Illumina short-read sequence data in the European Nucleotide Archive are provided in the file material_passport_data.tsv. All other files (n=63) are AHG matrix files in TSV format. AHGs were defined with IntroBlocker (https://wangzihell.github.io/IntroBlocker/, described in Wang et al. 2022, doi:10.1038/s41467-022-31581-0). Rows of the matrices correspond to genomic intervals in the reference genome sequence assemblies of barley cultivar Morex. The assembly version is MorexV3 (https://www.ebi.ac.uk/ena/browser/view/GCA_904849725, described in Mascher et al. 2021, doi:10.1093/plcell/koab077). The first three columns specify the coordinates of the windows: chromosome, start position, end position. The remaining columns correspond to barley genotypes. Values in the cells of the matrix are the numeric identifiers of haplotypes. If non-zeros entries in two cells are identical, it means that the corresponding genotypes share a haplotype in the corresponding genomic interval. Zero values (0) stand for missing data. The file names specify the parameters used in the respective IntroBlocker runs. Take the file "1Mb_200kb.400.chr2H.tsv" as an example, the meaning of file name is as follows. 1Mb_200kb: the genomic window size is 1 Mb (shift: 200 kb); 400: threshold (minimum number of observed single-nucleotide polymorphism) for defining AHGs; chr2H: barley chromosome 2H.

License: CC BY 4.0 (Creative Commons Attribution)

DOI: 10.5447/ipk/2025/7