Estimates of Effective Population Size and Inbreeding Level for Three Australian Pig Breeds

Abstract

Selective breeding may result in higher inbreeding levels which can lead to inbreeding depression and limit future genetic gain. This study quantified inbreeding levels and evaluated effective population sizes for Large White (LW), Landrace (LR) and Duroc (DU) populations in Australia. Pedigree data from 1994 to 2015 representing about 12 generations on average were explored with the software package PopRep by Groeneveld et al. (2009) which provides multiple population parameters. Pedigree completeness was highest in 2004 and 2005 when it reached about 95% and 80% in the third and sixth generation. Average inbreeding levels were highest for these years with averages of 0.031, 0.034 and 0.050 in LW, LR and DU, respectively. Two herds joined the across-herd genetic evaluations at that time and pedigree completeness varied from 80 to 90% and from 60 to 70% in the third and sixth generation in subsequent years leading to lower estimates of inbreeding levels. Estimates of effective population size varied from 64 to 98 in LW, from 52 to 108 in LR and from 42 to 61 in DU over time. These estimates of effective population size are imprecise and an underestimate of true effective population sizes given the limited time period considered and the extent of missing pedigree.