A comprehensive analysis of canonical biological pathways linking milk yield and quality traits to key fertility indicators in Murciano-Granadina dairy does

Abstract

This study analyses relationships between milk yield, milk composition, and fertility in Murciano-Granadina dairy goats to test whether these associations reflect biological pathways underlying a production–fertility trade-off. Linear and non-linear patterns were examined using canonical discriminant analysis (CDA), regularized canonical correlation analysis (rCCA), and CHAID decision trees. The dataset included 32,693 artificial inseminations from 21,757 does and 29,390 milk records from 21,541 does; fertility was assessed using three indicators accounting for insemination timing and semen type. Mean fertility differed by semen preservation method, with fresh/chilled semen showing 18–20 percentage points higher fertility than frozen/thawed semen. Milk yield showed wide variability (8.7–6704.6 kg; mean 686.4 kg), whereas milk composition was relatively stable. After multicollinearity control (VIF > 178 to <5), CDA and rCCA revealed a low-dimensional structure dominated by a first canonical function, explaining 80.8–88.7% of discriminant variance and 97.3% of shared covariance. This dominant axis reflected an energy balance and metabolic partitioning pathway, with higher milk yield and solids concentration associated with reduced fertility; very high production (>2021 kg) consistently coincided with lower fertility, supporting a production–reproduction trade-off. A secondary axis represented an endocrine and lactation-timing pathway linking fertility to temporal variation in milk composition, while semen type constituted an autonomous semen-related pathway with the strongest standardized canonical coefficients. CHAID analysis identified non-linear relationships and biologically meaningful thresholds in milk traits, achieving ~44% classification accuracy and up to 87% reliability for high fertility. Optimal fertility was associated with intermediate ranges of milk yield and composition (protein 3.64–6.98%, fat 6.0–7.9%, dry matter 14–25%, lactose 5.6–6.5%, SCC < 5200 × 10³ cells/mL). Overall, milk yield and composition showed statistically robust but moderate associations with fertility, consistent with reproductive biology multifactorial nature of and gaining relevance when interpreted jointly with metabolic, endocrine, and semen-related factors.