Taurine-indicine ancestry differentiation in Girolando dairy cattle: analysis code, result tables, figures and supplementary material

Reproducibility package for a two-layer genomic study of taurine-indicine differentiation relevant to Girolando (Gir x Holstein) dairy cattle. Version 1.2.0 rebuilds the functional layer on a panel of 108 genes (100 candidate genes, 7 RNA-seq control genes and HSPA1B, analysed with HSPA1A) with coordinates audited against Ensembl 113 and NCBI Gene, and adds the Cattle QTLdb overlap, the RNA-seq control genes and exploratory sensitivities; the ancestry layer is unchanged from version 1.1.0. Ancestry layer: Hudson Fst over 17,424,271 testable autosomal SNVs between 301 Holstein (1000 Bull Genomes Project, breed verified in BioSample) and 12 Gir (Embrapa Dairy Cattle, PRJNA1493839); 285,289 fixed differences define the ancestry-informative markers; panels of 25 to 500 markers are validated on held-out references, composite breeds and independent array animals. Functional layer: fixed and replicated differences within +-15 kb of 99 autosomal candidate genes in 89 units (88 with SNV data), enrichment against random windows and length-matched genes, SNV-weighted and per-unit comparisons, SnpEff and motifbreakR annotation, a cross with heat-stress transcriptomes and the Cattle QTLdb overlap. Contents: analysis code, result tables, figures with legends and Electronic Supplementary Material (Online Resources 1-16). The article text is not included. This record supersedes the earlier deposit 10.5281/zenodo.22185575. Versions under that deposit used a previous sample breed assignment (1.0.x) or previous gene coordinates (1.1.0). Version 1.2.1 is an editorial correction of the header of the supplementary material; the analyses, code, tables and figures are identical to version 1.2.0, which it replaces.