Using of SNP markers to estimate inbreeding, coancestry and effective population size in Sicilian cattle breeds

Abstract

Maintaining the highest levels of genetic diversity and limiting the increase in inbreeding is the premise of most conservation programs. The aim of this work was to estimate the inbreeding (F), coancestry (f) and effective population size (Ne) in two Sicilian cattle breeds, Cinisara (CIN) and Modicana (MOD). Rate of molecular inbreeding and coancestry were used to estimate the Ne. A total of 144 animals were genotyped using the Illumina Bovine SNP50K v2 BeadChip. The average molecular F and f coefficients were 0.68±0.024 and 0.67±0.03 in CIN and 0.69±0.020 and 0.70±0.03 in MOD cattle breeds, respectively. The results were not unexpected considering the reduced number of reared animals and the farming system, where natural mating is the common practice and the exchange of bulls among flocks is quite unusual; therefore, mating with close relatives can be quite frequent. Rates of molecular inbreeding (ΔF) and coancestry (Δf) per year were 0.004 and 0.022 in CIN and 0.007 and 0.010 in MOD cattle breeds, respectively. Ne values estimated from the ΔF were about 19 animals in CIN and 12 animals in MOD, and those calculated from the Δf, were about 4 and 8 animals in CIN and MOD cattle breeds, respectively. In animal breeding, the recommendation is to maintain a Ne of at least 50 to 100. High values of F and f in local breeds, with low population size, as CIN and MOD, can compromise the viability of the populations. The control of F and f would restrict inbreeding depression, the probability of losing beneficial rare alleles, and therefore the risk of extinction. The information generated from this study has important implications for the development of conservation programs.