Inbreeding depression affecting stayability in Italian Holstein cows

Advances in selection and reproduction methods, particularly the implementation of genomic evaluations alongside assisted reproductive technologies, have substantially enhanced productivity and efficiency, notably within specialized dairy cattle populations. Nevertheless, the widespread use of a limited number of elite sires and dams has also led to increased levels of inbreeding, posing a risk to animal performance in production, reproduction, and functional longevity. The objective of this study was to evaluate the effect of inbreeding on stayability in the Italian Holstein population. Stayability, defined as the ability of cows to remain productive in the herd from one parity to another, was assessed across 5 periods: STAY12, from parity 1 to 2; STAY23, from parity 2 to 3; STAY34, from parity 3 to 4; STAY13, from parity 1 to 3; and STAY14, from parity 1 to 4. Individual inbreeding coefficients were estimated using 3 methods: pedigree information, diagonal elements of the genomic relationship matrix, and the proportion of the total length of runs of homozygosity (ROH) segments relative to the total autosomal genome covered by SNPs. Furthermore, different ROH length classes were evaluated separately to distinguish between the effects of recent and ancient inbreeding. Two datasets were extracted from the breeders' association database with no interference in the herds' usual management: one including both genotyped and nongenotyped individuals and another with only genotyped animals. The first, comprising 828,056 cows, was used to assess pedigree-measured inbreeding depression in the Italian Holstein population. The second, including 48,833 genotyped cows, was used to compare inbreeding measures. The effect of inbreeding was estimated as best linear unbiased estimates on the liability scale within a Bayesian framework. In the stayability analysis, milk yield level relative to contemporary group was included as an additional fixed effect to account for its influence. Estimates were converted to the probability scale, using a cumulative distribution function, and then used to compare models and assess survival probabilities according to varying levels of inbreeding. Increased inbreeding consistently resulted in decreased stayability. The magnitude of inbreeding depression was greater for traits involving cumulative periods, such as STAY13 and STAY14. The expected variation in stayability resulting from a 1-unit increase in the pedigree inbreeding coefficients (F_PED), ranged from -0.06% to -0.44%, depending on the model and trait. Models using genomic inbreeding captured larger effects of inbreeding depression. In these cases, the expected variation in stayability ranged from -0.22% to -1.60% per 1-unit increase in F_PED. Inbreeding estimated from the sum of ROH segments longer than 2 Mb were associated with reduced stayability, whereas shorter segments were not. This suggests that recent inbreeding contributes to inbreeding depression on this trait, whereas ancient inbreeding does not. It should be noted that part of the observed inbreeding depression may be attributable to voluntary culling related to the production level of cows within their herds. Thus, in a selection index that includes milk yield and penalizes future inbreeding, stayability should preferably be analyzed using a model that incorporates production level as a fixed effect.