Genetic diversity of Caracu cattle reveals contrasting trends between general and closed populations

Abstract The conservation of genetic diversity and control of inbreeding rate are fundamental factors in animal breeding programs, especially programs for adapted cattle breeds such as Caracu. However, there are still knowledge gaps regarding the population structure of this breed as a whole and the genetic dynamics in subpopulations, like closed populations reared in experimental farms in Brazil. Within this context, this study aimed to evaluate the population structure of the Caracu cattle breed by investigating inbreeding levels and genetic diversity based on pedigree analyses. Two populations were analyzed: a general population (183,326 animals; 1900–2023) and a closed subpopulation selected exclusively for body weight for more than four decades and maintained by the Institute of Animal Science, Sertãozinho, São Paulo, Brazil (4,892 animals; 1977–2023). Population structure and pedigree depth were evaluated through the estimation of several parameters, like generation intervals, equivalent complete generations, pedigree depth, inbreeding levels, and diversity loss. The mean inbreeding coefficient of the general population was higher (2.6%) than that of the subpopulation (2.35%), with maximum values of 44.3% and 25%, respectively. The subpopulation exhibited greater pedigree completeness, higher average coancestry, and lower genetic diversity, indicating cumulative losses due to genetic bottlenecks and unequal founder contributions. In the general population, kinship network analysis revealed the presence of highly connected individuals, suggesting intensive use of certain sires and the formation of distinct family clusters. In contrast, a more uniform kinship structure was observed in the subpopulation. The results provide important support for the design of mating strategies and the improvement of conservation and breeding programs for the Caracu breed.