Changes in genetic diversity of Asian seabass in a 20-year breeding program

Abstract

Asian seabass (Lates calcarifer) has become a popular aquaculture species. In Singapore, a breeding program of Asian seabass started with 549 brooders in 2004. In the past 20-years, selection within families in each of 105 mass crosses was conducted with the assistance of molecular parentage using DNA markers. Growth, resistance to diseases, and omega-3 content of Asian seabass were improved. In this study, the genetic diversity in breeding nuclei from the founder broodstock (F0) to the fourth selected generation (F4) was estimated using 10 neutral microsatellites. In F0, F1, F2, F3, and F4, the expected and observed heterozygosity were largely maintained, and inbreeding indices were near zero. These data indicate that selection within families in mass–crosses between genetically distantly related broodstocks can avoid inbreeding. The average allele number (A) and effective population size (Ne) decreased from 10.0 to 7.1, and from 79.6 to 30.1 in F0 and in F4. The reasons for the reduction of A and Ne might be the non-contribution, and unequal contribution of broodstock to offspring and/or bottlenecks. Therefore, we recommend introducing some new Asian seabass genetic material to the breeding nucleus and improving the reproductive performance of brooders. Our study provides a better understanding of the changes in genetic diversity in an Asian seabass breeding program and highlights the importance of monitoring genetic diversity in different generations in a breeding program.