Reference-derived Dairy-Affinity Score in Lacaune and Lacaune x Dagestan Mountain F1 sheep: derived data, marker lists and analysis scripts

This repository contains publication-safe derived data tables, analysis-specific SNP marker lists, author-generated scripts, software parameters, validation outputs, and figures supporting the study "Genome-wide dairy-meat differentiation in Lacaune sheep and projection of a reference-derived genomic coordinate into Lacaune x Dagestan Mountain F1 ewes". The reference cohort comprised 181 Lacaune sheep from the ISGC SNP50 HapMap and Sheep Breed Diversity resource, including 103 Dairy and 78 Meat Lacaune. The target cohort comprised 39 ewes recorded as first-generation Lacaune x Dagestan Mountain crosses. The deposited materials support verification of cross-platform marker harmonisation, reference-only PCA, independent F1 projection, ADMIXTURE model selection, Weir-Cockerham FST analysis, Dairy-Affinity Score construction and internal validation, sensitivity analyses, observed heterozygosity, runs of homozygosity, ROH-based autozygosity, and DAS associations with Ho and FROH. The repository does not redistribute individual-level Sheep HapMap genotypes, raw local genotype matrices, private identifier crosswalks, direct farm identifiers, or the complete proprietary 75,300-marker panel. Reference Sheep HapMap genotypes are available from the CSIRO Data Access Portal under DOI 10.4225/08/51870B1E8EE56 and remain subject to the source licence.