Genetic structure of a small closed population of the New Zealand white rabbit through pedigree analyses

Abstract

The genetic structure of a small population of New Zealand White rabbits maintained at the Sheep Breeding and Research Station, Sandynallah, The Nilgiris, India, was evaluated through pedigree analyses. Data on pedigree information (n=2503) for 18 yr (1995-2012) were used for the study. Pedigree analysis and the estimates of population genetic parameters based on the gene origin probabilities were performed. The analysis revealed that the mean values of generation interval, coefficients of inbreeding and equivalent inbreeding were 1.49 yr, 13.23 and 17.59%, respectively. The proportion of population inbred was 100%. The estimated mean values of average relatedness and individual increase in inbreeding were 22.73 and 3.00%, respectively. The percentage increase in inbreeding over generations was 1.94, 3.06 and 3.98 estimated through maximum generations, equivalent generations and complete generations, respectively. The number of ancestors contributing the majority of 50% genes (f_a50) to the gene pool of reference population was only 4, which might have led to reduction in genetic variability and increased the amount of inbreeding. The extent of genetic bottleneck assessed by calculating the effective number of founders (f_e) and the effective number of ancestors (f_a), as expressed by the f_e/f_a ratio was 1.1, which is indicative of the absence of stringent bottlenecks. Up to 5th generation, 71.29% pedigree was complete, reflecting the well maintained pedigree records. The maximum known generations were 15, with an average of 7.9, and the average equivalent generations traced were 5.6, indicating a fairly good depth in pedigree. The realized effective population size was 14.93, which is very critical, and with the increasing trend of inbreeding the situation has been assessed as likely to become worse in future. The proportion of animals with the genetic conservation index (GCI) greater than 9 was 39.10%, which can be used as a scale to use such animals with higher GCI to maintain balanced contribution from the founders. From the study, it was evident that the herd was completely inbred, with a very high inbreeding coefficient, and the effective population size was critical. Recommendations were made to reduce the probability of deleterious effects of inbreeding and to improve genetic variability in the herd. The present study can help in carrying out similar studies to meet the demand for animal protein in developing countries.