Phenotypic determinants of milk yield and reproductive performance of stud British Alpine goats across agro-ecological zones in South Africa

Phenotypic determinants of milk production, reproductive performance, and dairy value of stud British Alpine dairy goats across South African agro-ecological zones (AEZs) were evaluated using 2422 performance records from 3037 pedigreed animals spanning 1960–2024, extracted from the national Integrated Registration and Genetic Information System (INTERGIS). Data were analysed using a restricted maximum likelihood (REML) mixed model, with breeder, AEZ, birth season, breed purity class, and parity as fixed effects; sire, dam, and animal as random effects; and genotype × AEZ interaction fitted to assess environment-specific breed expression. Phenotypic correlations were estimated, and principal component analysis (PCA) was applied to resolve major axes of multivariate variation. Mean separation was conducted using Tukey’s HSD (p < 0.05). Breeder was the dominant source of variation across most traits, highlighting herd-level management as the primary driver of phenotypic performance. Agro-ecological zone significantly influenced peak yield, milk persistency, litter size, birth difficulty, and dam longevity. Does in humid zones recorded the highest peak yield (2.55 ± 0.33 kg/day) and persistency (63.6 ± 2.9%), whereas dry sub-humid zones exhibited reduced peak yield (1.77 ± 0.34 kg/day) and the greatest birth difficulty (2.29 ± 0.17), reflecting a productivity–adaptability trade-off across environments. Birth season affected lactation milk yield (LMY), lactation value index (LVI), fat percentage, milk urea nitrogen (MUN), milk persistency, kidding ease score (KES), and litter size (LS); winter and spring kidding maximised LMY and LVI, while summer kidding increased litter size but reduced kidding ease and elevated MUN, indicating seasonal nutritional imbalances. Crossbred does (< 75% British Alpine) achieved the highest LMY, consistent with heterosis, but showed reduced milk persistency, whereas Studbook Proper does (> 93.75%) exhibited superior milk composition, lower SCC, and greater reproductive stability. Parity structured production and health trajectories, with reproductive efficiency peaking at parities 4–5 and SCC increasing markedly after the sixth parity. Phenotypic correlations revealed trade-offs between prolificacy and parturition ease, declining milk persistency over time, and increasing birth difficulty across years. PCA retained six components explaining 77.7% of total variation, confirming that performance is multidimensional and unsuited to single-trait selection. These findings demonstrate that AEZ, season, breed purity, parity, and management interact non-additively, underscoring the need for PCA-informed multi-trait selection indices to improve productivity, reproductive efficiency, and resilience of British Alpine dairy goats across South Africa.