Assessing the inbreeding evolution and genetic diversity loss in Ecuadorian Nelore (Bos indicus) cattle.

Abstract

The Ecuadorian Nelore cattle are one of the main beef breeds whose have been traditionally raised in the tropics and subtropics from northern provinces (coastal region). The aim was to analyse the inbreeding evolution and genetic diversity loss by analysing official genealogical information from the Ecuadorian Association of Nelore Cattle. The total population included 3,846 cows and 1,687 bulls born between 1933-2021. Three databases were considered: historical (all individuals= 5,533), current (individuals born between 2012-2021= 521) and reference (individuals with known sire and dam within the current population= 340). Population structure variables: pedigree completeness index (PCI), number of equivalent (GEq), complete (GCom) and maximum (GMax) generations, and generation interval (GI). DG variables: inbreeding (F), inbreeding increment (ΔF), average relatedness (AR), co-ancestry (C), non-random mating (α), effective population size (Ne) and genetic conservation index (GCI). The gene origin probability variables: number of founders (f), effective number of founders (fe) and ancestors (fa), number of equivalent genomes (fg), fe/fa and fg/fa ratio, and DG loss. The databases were analyzed using ENDOG software. GMax, GEq, and GCom in the historical population were lower (3.98, 1.93 and 1.18) compared to the current population (7.97, 2.97 and 1.13), while the GI decreased from 7.23 to 6.99 years. Moreover, F=0.80 to 0.56%; AR=0.65 to 0.58%, ΔF= 0.28 to 0.12%, C= 0.32 to 0.29%, α=0.00485 to 0.00278; GCI=4.54 to 5.84, and Ne= 132.31 to 194.51 values were obtained (historical vs. current population). Gene origin probability was f=220, fa=76, fe=126.61, fg=38.39, fa/fe= 0.60, fg/fe=0.30 showing a GD loss due to unequal contribution of founders (0.39%) and bottleneck/genetic drift (1.30%). In conclusion, the current Nelore population showed an increase in PCI, as well as a slight reduction in GI. GD loss suggest lower recent inbreeding and bottlenecks/genetic drift. Therfore, this breed shows adequate genetic parameters necessary to preserve GD.