Genetic variability of a small captive population of the cobia (Rachycentron canadum) through pedigree analyses

Abstract

The genealogical information of a small captive population of the cobia fish was evaluated to assess the genetic variability and the status of inbreeding through pedigree analyses. Pedigree data (n = 238) for 6 years (2010–2016) were analyzed and offspring born from 2015 to 2016 were considered as reference population to compute the population genetic parameters based on the gene origin probabilities using the program ENDOG (version 4.8). Molecular marker based FAP (Family Assignment Program, version 3.6) was used for parentage assignment. The pedigree completeness was 68% for the parent, 29% for the grandparents and 7% for the great-grandparents generations with a mean equivalent to complete generations of 2.66. Mean generation interval, computed from four pathways, was 2.38 years. Considering the reference population into account the coefficients of average inbreeding and average relatedness were computed as 9.6% and 9.9%, respectively. The mean values of individual increase in inbreeding (rate of inbreeding) were 6.5% and 2.5% for the reference population and for the whole pedigree, respectively. Realized effective population size was computed from the individual increase in inbreeding and from the individual increase in coancestry as 7.7 and 10.6, respectively. The effective numbers of founders (fe), ancestors (fa), founder genomes (fg) and non-founder genomes (nfe) for the reference population were computed as 6, 6, 3.8 and 11.1, respectively. About 85% of total genetic variation was explained by 7 most influential ancestors, with a maximum individual contribution of 33.5%. Though the genetic bottleneck, as expressed by the fe/fa ratio as 1.0, was not evident, the loss of genetic variability caused by genetic drift was evident by fg/fe ratio which was 0.64 for the reference population. The analysis revealed the evidences on loss of genetic diversity with a very critical effective population size. Recommendations were made to improve the genetic variability in the herd. The present study signifies the importance of maintaining the pedigree and can help in carrying out similar studies on captive-bred fish species where small populations are inevitable.