ASSEMBLY-AWARE EVALUATION OF CATTLE GROWTH GWAS: REPRODUCIBILITY, REGIONAL RECURRENCE, AND PRIORITIES FOR YAK GENOMICS

Abstract

Genome-wide association studies (GWAS) have identified many cattle growth loci, but differences in phenotype, population, statistical model, reference assembly, and result availability can make apparent replication misleading. We assessed whether published cattle growth GWAS could support quantitative synthesis, identified defensible regional recurrence, and defined priorities for translating cattle evidence to yak. The audit drew on a 318-record livestock-genomics library, a PubMed horizon search updated to 28 August 2026, and direct source verification. A 13-study primary cattle inventory framed the audit: ten studies supplied complete extractable locus-level data, two supplied partial main-text coordinates, and one was retained at study and chromosome-summary levels. Two additional contemporary cattle GWAS were appraised narratively, together with seven yak growth GWAS. Coordinates were compared only within verified assemblies and were never pooled across species. The ten complete-source studies supplied 1,163 marker-test records after duplicate removal. Within the original nine study extraction, 399 of 450 records had verified assemblies and formed the primary coordinate-analysis subset; 33 coordinates recovered from main texts were retained for sensitivity analysis. Two independent populations supported a phenotype-compatible BTA1 region near VEPH1, indicating regional rather than causal-variant recurrence. Heterogeneous designs and incomplete effect reporting precluded quantitative meta-analysis of the seven yak GWAS. An assembly-aware, phenotype-compatible synthesis is therefore more defensible than cross species effect pooling. Cattle loci should guide yak validation only when supported by orthology or conserved synteny, compatible phenotypes, and independent functional evidence. This framework links regional prioritization to functional annotation, fine-mapping, metabolomic integration, and precision yak breeding.