Inbreeding and its genetic and evolutionary consequences in red tilapia (Oreochromis spp.)

Managing inbreeding and effective population sizes in closed nucleus populations, such as red tilapia (Oreochromis spp.), is crucial to preserve genetic diversity and enhance selection response. This study aimed to assess these parameters (inbreeding, effective population sizes, and genetic diversity) in a red tilapia population undergoing selection for increased harvest body weight since 2016. The breeding program involved 75,950 individuals descended from 1200 dams and 600 sires. Traits including body weight, length, body colour, and survival were monitored from stocking to harvest. Our analysis employed different methods to estimate inbreeding and effective population size. Our results indicate that the pedigree-based inbreeding was effectively managed, stabilizing at an average rate of only 0.65% over eight generations. Effective population size (Ne), assessed through inbreeding rates between successive generations, ranged from 35 to 275, averaging 145 when evaluated via average coancestry. Genetic diversity based on the effective number of founders and ancestors in the population remained robust, with only about 3% loss in genetic diversity relative to the base population. These findings suggest that the current population will continue to respond to selection. Nonetheless, advanced technologies (e.g., using genotype and genomic mate allocation) are necessary to simultaneously improve genetic traits and control inbreeding in future genetic enhancement programs for this species.