Investigation of inbreeding rate and its influence on stillbirth in South African Holstein African dairy cattle

Abstract

There is no study done at the population level on stillbirth in Holstein dairy cattle population of South Africa. The current study was conducted to evaluate the inbreeding rate and its influence across generations on incidences of stillbirth in South African Holstein dairy population. The dataset included about 1 million Holstein dairy cattle born between the year of 1945 to 2020. Pedigree information included animal ID, sire ID, dam ID, breeder and farm region, other information included date of birth, calf sex, dam parity and age at parturition, calving date, herd, and birth status. Generation intervals were determined using ENDOG software (version 4.8), while General Linear Model (GLM) procedure at 5% significant level was used to model incidences of stillbirth. Phenotypic trends were determined using regression procedure, and SAS was used to analyse regression of inbreeding rate effect on the incidences of stillbirth per generation. Effective population size, inbreeding coefficients and inbreeding rate were estimated using Contribution Inbreeding Coancestry (CFC) software. The results indicated that dam parity, herd, calf sex, generation, birth season and birth year had a significant effect (P<0.05) on the incidences of stillbirth. The multiparous, autumn (3.397±0.067), summer (3.306±0.067), and female calves (3.516±0.046) had high incidences of stillbirth than primiparous, spring (3.073±0.067), winter (3.00±0.063 and male calves (2.922±0.028). Stillbirth incidences were observed to increase with birth year and generation, while decreasing with an increase in dam parity and dam age. Incidences of stillbirth was very different across the herds ranging from a minimum of 0% and a maximum of 100%, however most of the herds had zero incidences of stillbirth (3.736±0.251). This indicated that stillbirth problem in South African Holstein dairy population is at the herd level not at the population level. Inbreds were only 0.48% of the population, with an average inbreeding coefficient ranging from 2.48% to 24.60%. Average discreet generation equivalents (DGE) approximated one for most generations, with a range of 0.226 to 1.256, this highlight that majority of the generations were complete. Animals in the 1st to the 12th generation were closely related, while from the 12th to 14th generation they were less related to each other. Inbreeding coefficients ranged from 0.0020% to 0.1099%, with inbreeding rate increasing per generation and recording the lowest value (0.0479) and the highest (0.5536) in the 13th and 2nd generations respectively. Effective population size was observed to depend on the number of breeding males, with the 2nd generation showing lowest number of breeding males (23 sires) and the lowest effective population size (90.3), while the 13th generation had the highest number of breeding males (264 sires) and the highest effective population size (10447.7). The regression model was observed to be statistically significant (P<0.05) with R2 value of 88.61%, however the evaluated factors; number of individuals, no of inbreds, no of founders, average F, average F in the inbreds, effective population size and inbreeding rate were not significant on incidences of stillbirth. Inbreeding rate in the current study had a significant effect on stillbirth incidences in the South African Holstein population. Stillbirth incidences increased with effective population size with an R square of 12% but decreased with an increase in inbreeding rate and average inbreeding coefficients in the inbreds, with R square values of 13% and 20% respectively. Inbreeding contributed only 20% towards the stillbirth incidences indicating that stillbirth in the South African Holstein population is caused by other factors other than the inbreeding. Stillbirth incidences increased with effective population size and a reduced with an increase in average inbreeding coefficients in the inbreds. However, generations increased with stillbirth incidences and effective population size with R2 of 60% and 92% respectively, indicating that generation had 60% contribution to stillbirth incidences. Generation increased with a reduction in inbreeding rate and average inbreeding coefficients in the inbreds with R squares of 35% and 53% respectively. Stillbirth incidences in the South African Holstein population is not caused by the genetic factors such as inbreeding rate, this can be because stillbirth is a lowly heritable trait meaning it is more affected by environmental factors other than genetic factors.