Higher functional-longevity genomic merit is associated with lower morbidity, shorter calving interval, and greater herd retention in Holstein cows matched for milk-production merit.

Extending functional longevity in high-producing dairy cows is important for improving economic efficiency, environmental sustainability, and animal welfare in modern dairy systems. This longitudinal controlled cohort study investigated the phenotypic expression of genomic functional longevity estimated breeding values (GFLEBV) in a stratified cohort of Holstein-Friesian cows managed under uniform conditions for more than 10 yr. Pregnant heifers were genomically classified into High-GFL_EBV (n = 18) and Low-GFL_EBV (n = 18) groups while being matched for genomic milk production estimated breeding values (GMPEBV), thereby minimizing confounding by production potential. Genomic stratification generated a 24.7-point difference in functional-longevity index between groups, corresponding to approximately 2.1 genetic standard deviations (High-GFL_EBV: 120.9 ± 6.2; Low-GFL_EBV: 96.2 ± 5.91), whereas genomic milk-production merit was comparable. Lifetime phenotypes included milk yield and milk composition traits derived from monthly standard milk performance testing, as well as reproductive performance, survival time, herd retention, and detailed veterinary diagnoses. Milk production trajectories were broadly comparable between groups across parities, indicating effective separation of functional longevity from production intensity. Across months in milk and parities 1 to 5, milk yield, energy-corrected milk, milk fat traits, lactose traits, and milk urea nitrogen showed no meaningful group differences. Milk protein percentage was greater in High-GFL_EBV cows, whereas protein yield remained similar. In contrast, somatic cell count was greater in Low-GFL_EBV cows, consistent with higher udder inflammatory burden despite similar overall lactation output. Age at first calving, lactation length, calf birth weight, and calf sex distribution were also comparable between groups, whereas High-GFL_EBV cows exhibited shorter calving intervals, indicating more favorable reproductive efficiency under similar production demands. Despite similar milk output, Low-GFL_EBV cows showed a consistently greater weighted disease burden beginning in lactation 1, characterized by mastitis clustering, transition-related disorders, and greater burdens of ketosis, digestive disorders, and infectious claw disease. This pattern progressed toward greater claw-related multimorbidity in lactation 2 and a more pronounced lameness-reproductive burden in lactation 3. Herd retention remained similar after lactation 1 (18 vs. 17 cows) but diverged thereafter; by lactations 2 to 6, the numbers of cows remaining were 18 versus 14, 17 versus 11, 14 versus 7, 10 versus 4, and 8 versus 2 for High- and Low-GFL_EBV groups, respectively. No Low-GFL_EBV cows remained beyond lactation 6, whereas High-GFL_EBV cows persisted into lactations 7 to 9. Survival analysis showed sustained separation of survival curves and longer median survival in High-GFL_EBV cows. Collectively, these findings provide long-term phenotypic evidence that GFLEBV is associated with more favorable health, reproductive, and survival outcomes under comparable milk production potential, supporting its relevance in breeding programs targeting improved lifetime performance.