Evolution of Population Structure, Reproductive Performance, Inbreeding, and Genetic Diversity in Ecuadorian Charolais Cattle

Abstract

The objective was to evaluate the evolution of the population structure, reproductive performance, inbreeding, and genetic diversity in Charolais cattle. Official genealogical information from the Ecuadorian Charolais Association was divided into five populations: (a) historical (total), (b) 2008-2012 (natural mating period), (c) 2013-2017 (natural mating + artificial insemination period), (d) 2018-2022 (artificial insemination + embryo transfer period), and (e) the reference (known sires and dams) from which the population structure was evaluated using pedigree completeness and the generation interval (GI). Meanwhile, for genetic diversity (GD), inbreeding (F), average relatedness (AR), and the effective population size (Ne) were estimated. The gene origin probability (number of founders, effective number of founders/ancestors, and number of founder genomes) explaining genetic variability, reproductive efficiency, the number of offspring per sire and dam, and the average ages of parents at the birth of their offspring were determined. The database was analyzed using the ENDOG, POPREP, and CFC software programs. The results indicate that pedigree completeness and the GI decreased over time among populations, although the first generation showed higher values. The sire gametic pathway was greater in all populations. F increased over time, although not markedly. Although Ne variations were observed, the levels remained above the recommended limit value. The GD loss increased progressively over time although the most recent population was not significantly affected. Finally, the female reproductive efficiency increased over time as well. In conclusion, the Charolais cattle GI should be reduced. After 2012, the use of Assisted Reproductive Technologies and breeding schemes raised the GD loss. Finally, the F increased over time although it could be reduced using foreign genetic resources in the current Ecuadorian Charolais population.

Keywords: Charolais breed; beef cattle; demographic structure; genetic diversity loss; inbreeding; reproductive efficiency.

Figure 1

Average ages of breeding sires and dams in the Ecuadorian Charolais cattle population (2008–2022).

Figure 2

Evolution of the numbers of registered animals by type of Assisted Reproductive Technology (ART) used in the Ecuadorian Charolais population (2008–2022). NM: natural mating; AI: artificial insemination; ET: embryo transfer.

Figure 3

Distribution of dams by the number of offspring (calves/cow/year) from 2008 to 2022. Over the years, the percentage of cows with one calving (blue: a calf per cow/year) decreased drastically while the percentages of cows with two (orange), three (grey), and four (yellow) calves per year increased significantly over time, especially in the last two five-year periods analyzed.

Figure 4

Evolution of the generation interval (GI) regarding the different gametic pathways in Ecuadorian Charolais cattle from 2008 to 2022. Data from before 2008 were excluded because the Charolais Association began in 2008, including animals born and registered that year onwards.

Figure 5

Evolution of inbreeding (F and ΔF), average relatedness (AR), coancestry (C), and non-random mating (α) in Ecuadorian Charolais cattle population from 2008 to 2022. Data from before 2008 were excluded because the Charolais Association began in 2008, including animals born and registered that year onwards.

Figure 6

Evolution of Ecuadorian Charolais breed belonging to FF and PB herd books regarding the total animal population and inbreeding rate. Data from before 2008 were excluded because the Charolais Association began in 2008, including animals born and registered that year onwards.

Figure 7

Evolution of the effective size (Ne) in Ecuadorian Charolais cattle population. Data from before 2008 were excluded because the Charolais Association began in 2008, including animals born and registered that year onwards.