Parentage assignment using SNP markers, inbreeding and population size for the Brazilian Red Sindhi cattle

Abstract

Brazilian Red Sindhi was originated from a very small number of founders and showed a consistent growth during the last three decades. One relevant herd was kept without proper birth recording and the reconstruction of parentage was possible for this herd through the use of a panel with 3894 SNP markers. Pedigree errors were also identified and corrected for animals sampled in various herds distributed in different Brazilian regions. A panel containing 71 SNP markers was indicated as the minimum number for the effective parentage verification within the Red Sindhi population in Brazil. Corrected genealogy was used for the description of inbreeding and effective population size, which was accessed with the paired increases in coancestry approach. Average inbreeding was high (F = 9.03%) for 15,217 inbred animals (54.1% of the total). Nevertheless, a trend of decrease with time was observed for this parameter with the average individual increases in inbreeding approach (∆Fi). This population went through a bottleneck during the 1980s and beginning of the 1990s, reaching a minimum population size of Ne=55.86. After that period, a consistent increase in the number of breeders and animals has raised the effective population size to the current value of Ne=87.55.