Pedigree analysis of an ostrich breeding flock

Abstract

Pedigree records, maintained from 1978 to 2005 at the Oudtshoorn Research Farm, South Africa, of 40 074 birds of a pair-breeding ostrich flock were used to estimate the effective number of founders (fe), the effective number of ancestors (fa), the effective population size and the effective genome equivalents (fg) under random mating, to assess the genetic variability present in the population. The average level of completeness of the pedigrees was high (99.3%) in the first generation, and the average level of inbreeding (F), calculated from the pedigrees, was 0.51%. The reference population was defined as the 39 784 birds hatched from 1990 to 2005. The estimated measures of variability were fg = 47.3, fe = 59 and fa = 58, with an fe/fa ratio of 1.02. The numbers of ancestors responsible for 100%, 50% and 20% of the genes in the reference population were 254, 21 and 6, respectively. The largest individual contribution to the population hatched from 1990 to 2005 was from a male that was responsible for 4.85% of the genetic variability. The generation interval for the four selection pathways – calculated as the average age of parents when offspring that were kept for reproduction were born – were sire to son (7.74 ± 4.92), sire to daughter (7.77 ± 5.13), dam to son (7.50 ± 4.29) and dam to daughter (7.90 ± 4.92). The average generation interval of the reference population was 7.72 ± 4.79 years. The linear regressions of mean annual individual rate of inbreeding on year of birth for the two distinct periods 1995–2002 and 2003–2005 were 0.08% and -0.07% per year, respectively. The estimate of effective population size (Ne), computed via the increase in the individual rate of inbreeding, was 112.7. Estimates of Ne using the alternative methods of tracing the numbers of generations were 73.6, 177.4 and 95.3 for complete, maximum and equivalent complete generations. The results of this study indicated that the population under study was at an acceptable level of genetic variability.

Keywords: Effective number of founders and ancestors, effective population size, level and rate of inbreeding.