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 (Bos taurus taurus versus Bos taurus indicus) differentiation in Girolando (Gir x Holstein) dairy cattle. The genome-wide ancestry layer screens 16,290,370 variants from the 1000 Bull Genomes Project (Run 8, TAUIND subset, ARS-UCD1.3) for Holstein x Gir differentiation, retains 51,548 ancestry-informative markers at an empirically calibrated Fst threshold, and compresses them into a 50-marker XGBoost classifier whose markers lie outside the candidate genes. The panel-restricted functional layer takes a 73-gene candidate set through variant-effect annotation, Cattle QTLdb positional validation, ancestry-contrast association analysis and transcription-factor binding-site disruption screening, and intersects the result with differential expression from 28 public bovine heat-stress RNA-seq samples across four tissues. The deposit contains the analysis code (Python and R) for every reported result, the robustness round (accuracy confidence intervals, bootstrap panel-composition stability, empirical threshold calibration, density control and marker localisation), the result tables, the figures with their published legends, and the Electronic Supplementary Material (Online Resources 1-17). It does not redistribute controlled-access genotypes from the 1000 Bull Genomes Consortium nor the public raw reads from NCBI SRA/GEO. README.md documents how to obtain each input and which analyses can be reproduced from the derived statistics included here alone.