Ancestral inbreeding evaluation in the tropically adapted Criollo Limonero dairy cattle

Abstract

The Criollo Limonero (Bos taurus) dairy cattle from the Zulia State (Venezuela) has been genetically managed using groups of animals in a circular mating system to reduce the inbreeding effects. Methodologies such as ‘pedigree purging’ analyse ancestral inbreeding as the historical accumulation of inbreeding by tracing the genetic contribution of common ancestors across generations. The objective was to evaluate the traditional, ancestral and current inbreeding values in the Criollo Limonero cattle using the traditional inbreeding (F_classic), Ballou (fa_Ballou), Kalinowski (Fa_Kal), and ancestral history coefficient (AHC). The genealogical database consisted of 3,559 registered individuals (1,178 bulls and 2,381 cows) born between 1969-2023 (total population), and 462 animals born between 2014-2023 (current population). The databases were analysed using the GRAIN v.2.2 package. The inbreeding results in the historical population were 1.30, 1.67, 0.12, and 1.72% for F_classic, fa_Ballou, Fa_Kal, and AHC, respectively, while in the current population were 2.05, 3.98, 0.34, and 4.17%. The comparative analysis revealed an increase in inbreeding values from the historical to the current population, with the most drastic increase observed in the AHC. In conclusion, the generalised increase in all inbreeding coefficients shows an accelerated genetic diversity loss in the Criollo Limonero cattle, especially marked in ancestral inbreeding (fa_Ballou and AHC). Furthermore, the difference between Fa_Kal and other methods suggests the existence of methodological limitations in determining historical inbreeding, considering that Fa_Kal quantifies recent inbreeding by tracing shared ancestors within the pedigree, focusing on direct parental contributions. Unlike the AHC (which tracks deep ancestral bottlenecks) the Fa_Kal is sensitive to immediate family structures but may overlook historical genetic overlaps. This trend highlights accelerated genetic erosion, likely driven by restricted breeding groups and/or founder effects. Finally, diversifying sire lines and implementing genetic/genomic selection are necessary to reduce the genetic diversity loss in Criollo Limonero cattle.