Pedigree-based evaluation of classical, ancestral, and new inbreeding coefficients in Carora and Criollo Limonero dairy cattle populations

Abstract

ABSTRACT Background and Aim: Inbreeding is a major concern in livestock breeding because it can reduce genetic diversity, impair fitness, and compromise long-term population sustainability. Conventional pedigree-based inbreeding coefficients often fail to distinguish between recently accumulated inbreeding and historical ancestral inbreeding that may have undergone genetic purging. Consequently, evaluating both new and ancestral inbreeding provides a more comprehensive assessment of genetic risk. This study aimed to investigate the temporal dynamics of classical, new, and ancestral inbreeding coefficients in two native Venezuelan dairy cattle breeds, Carora and Criollo Limonero, and to compare their effective population sizes using multiple pedigree-based approaches. Materials and Methods: Pedigree records comprising 80,467 Carora cattle and 3,559 Criollo Limonero cattle born between 1984 and 2023 were analyzed. Classical, recursive, Ballou, Kalinowski (new and ancestral), and ancestral history coefficient (AHC) inbreeding estimates were calculated using GRain version 2.2 through gene-dropping simulations. Pedigree completeness, effective population size, regression analyses, and Pearson correlation analyses were performed to evaluate temporal trends, relationships among inbreeding estimators, and differences between breeds. Results: All pedigree-based inbreeding coefficients increased over time in both breeds, with ancestral inbreeding exhibiting the greatest increase. Using the AHC method, ancestral inbreeding increased from 0.26% to 8.59% in Carora cattle and from 0.13% to 4.17% in Criollo Limonero cattle. Regression analyses demonstrated significant temporal increases for all inbreeding measures (p < 0.001). Pearson correlation coefficients among inbreeding estimators ranged from 0.28 to 0.98 in Carora cattle and from 0.25 to 0.99 in Criollo Limonero cattle (p < 0.001), with the strongest associations observed between classical and new Kalinowski coefficients and between Ballou and AHC estimates. Effective population size varied substantially according to the estimation method, with ancestral Kalinowski estimates producing the largest values and AHC the smallest. Despite its considerably larger pedigree, the Carora breed exhibited consistently higher ancestral inbreeding than the Criollo Limonero breed. Conclusion: Pedigree purging approaches provided substantially greater insight into long-term genetic diversity than conventional pedigree inbreeding coefficients alone. The marked accumulation of ancestral inbreeding, particularly in the Carora breed, indicates that classical methods may underestimate genetic risk in native Venezuelan dairy cattle. Integrating ancestral and new inbreeding estimators into breeding and conservation programs could improve mating strategies, preserve genetic diversity, and support the long-term sustainability of locally adapted cattle populations. Future studies incorporating genomic information are warranted to validate pedigree-based evidence of genetic purging and optimize conservation management.