Genetic Variability and Conservation Challenges in Lithuanian Dairy Cattle Populations

The purpose of the study was to investigate the genetic variability of open Lithuanian Red and Red-and-White (LRWP) and Lithuanian Black-and-White (LBWP) dairy cattle populations and indicate the differences from the old genotypes of Lithuanian Black-and-White (LBW) and Lithuanian Red cattle (LR), which are currently under a conservation program. In order to gain a better understanding of the populations under conservation and to minimize the potential influence of other breeds, a distinct subgroup was formed that comprised animals whose father and mother belonged to the same breed (LR_pure and LBW_pure). The genetic variability was estimated using the number of founders, pedigree completeness, number of males and females in reproduction and age distribution, generation interval (GI), inbreeding coefficient (F) and effective population size (Ne). The highest average pedigree completeness values in the second generations of the old genotype LR and LBW were 100%. Higher ages of females in the populations under conservation were related to a higher GI and their longer life expectancy. In 2021, the reproductive age of bulls used for insemination within these populations ranged from 5.1 to 27.8 years. The proportions of males producing offspring in their older age indicate that the semen was used from the national gene bank of commercial artificial insemination companies. The GI (>5) in LR and LBW females was higher than that in LRWP and LBWP. The analysis of the data over the 15-year period showed that the GI of males in LRWP and LBWP decreased equally by 38%, while in LR_pure population, it increased by 80%. A high (9.24%) average inbreeding coefficient (F) was found in inbred animals of LR_pure population, while in LBW_pure, it was 5.35% in 2021. The coefficient of inbreeding varied within the different cattle populations. In the open LR population, it ranged from 1.48% to 2.7%, while in the LRWP population, it fell between 2.12% and 3.72%. The lowest effective population size (Ne) concerning the rate of inbreeding was observed in LBW_pure (23) and LR_pure (59), with the highest Ne identified in the LBWP population (462). When considering Ne based on the number of parents, LR_pure displayed the lowest Ne (42), while the highest Ne was found in LBWP (4449). An analysis of local cattle populations reveals that LR faces the most critical situation. This particular population has been steadily declining for a number of years, necessitating additional measures and efforts to safeguard the LR’s ancestral genetic makeup. The results of the LBWP analysis also highlight a concerning trend. Even in very large populations with open breeding programs, the effective population size per generation can experience a significant decrease