African and European Haplotypes Carry Different Slick PRLR Alleles in Criollo and Senepol Cattle — analysis code, figures and supporting data
Abstract
Analysis code, configuration, intermediate result tables and figure-generating scripts supporting the manuscript "African and European Haplotypes Carry Different Slick PRLR Alleles in Criollo and Senepol Cattle" (submitted to Animal Genetics). What the study does. The slick coat phenotype of tropically adapted cattle arises from independent truncating mutations of the prolactin receptor (PRLR). Allele counts locate such a variant but do not source it. This work phases the receptor gene without the minor-allele-frequency filter that phasing normally applies, so that each carrier haplotype can be read at the causal site itself, and then assigns every carrier haplotype to a reference panel separately by functional class of site, keeping N'Dama distinct from the sanga populations rather than pooling them as "African". Three truncating alleles segregating in Criollo cattle of the Caribbean and northern South America are resolved: SLICK1 (c.1382del, p.Ala461ValfsTer2) sits on a West African taurine (N'Dama) background in four of five carrier haplotypes, whereas SLICK2 (c.1489C>T, p.Arg497*) and SLICK3 (c.1394C>A, p.Ser465*) sit on European taurine backgrounds. A fourth truncating allele, SLICK5 (c.1396A>T, p.Lys466*), fails a panel-specificity test and is reported as excluded rather than assigned. Referred to its lineage-matched British control, the Senepol carries about six percentage points more West African ancestry, which keeps an African route into tropically adapted taurine cattle open. Files. The manuscript, the Supporting Information, the graphical abstract, the reference list and the README are provided as standalone files. The complete reproducible tree is in slick_ancestry_analysis_code_and_data.zip: scripts/lib/hap_ancestry/ — locus-agnostic engine for haplotype ancestry assignment by functional class (likelihood assignment, site resampling, haplotype network). Everything locus-specific lives in a single YAML. scripts/ — supervised ancestry estimation, titration calibration, lineage-paired controls, background-homozygosity control, panel-specificity filter, informativeness analysis, data acquisition, panel labelling and every figure script. config/slick.yaml — focal sites, reference panels, consequence classes. data/genotypes/ — genotypes at the three focal sites for all 1,880 phased samples, plus the panel labels; these are the inputs that regenerate Figure 1. tables/ and figures/ — the tables and figures of the article and of the Supporting Information. What this archive does not contain. The primary sequence data are public and are referenced by accession rather than redeposited: European Nucleotide Archive ERP150979, PRJEB39353 and PRJEB39924; SRA PRJNA604048; GEO GSE192471 (Senepol liver RNA-seq); Dryad doi:10.5061/dryad.th092 (high-density array genotypes); the WIDDE portal; and CLARITY doi:10.5281/zenodo.17909700 (physical-genetic map). Reference assembly ARS-UCD1.2. What changed in version 1.1.0. This version accompanies a restructured manuscript. The Summary was rewritten; the two figures that had been supplementary were promoted into the body and the supplementary material now holds tables and text only; the figure set was consolidated from eight candidates into six multi-panel figures, so that the assay calibration and the sensitivity of the ancestry estimate to the number of ancestry axes now appear together as one figure, and the population ranking now appears alongside the paired controls; two pairs of Results subsections were merged under single headings; part of the methodology that had lived only in the supplementary file was moved into Materials and methods, because a figure in the body needs its method in the body; and the haplotype network was redrawn in a vertical, single-column layout. The scientific results are unchanged. See README.md for the software environment, the data sources, and how to go from the public accessions to each reported number.
