Comprehensive assessment of the genetic diversity and population structure of cultured populations of golden pompano, Trachinotus ovatus (Linnaeus, 1758), by microsatellites

Golden pompano, Trachinotus ovatus , belongs to the family Carangidae. Within one decade, this species has rapidly become one of the most important cultured marine fish species in South China. However, the lack of a comprehensive genetic diversity assessment hinders the conservation of natural resources and management of cultured populations. Thus, we sampled one wild population and six cultured populations of golden pompano, which represented the whole cultured population, to assess the genetic diversity and population structure. The level of genetic diversity was low compared with those of other cultured fish, as the values of allelic richness, number of effective alleles and expected heterozygosity in the combined whole sample were 3.709, 2.592, and 0.591, respectively. These populations were little differentiated (Fst = 0.02091, p value = 0.00), and the whole sample did not show an explicit population structure at the individual level. The effective population size in each cultured population was small and in the whole sample was acceptable for a closed selection system. The pedigree reconstruction showed no evidence of artificial disturbance in mating. This general survey of cultured golden pompano populations showed the common characteristics of domestication with wild inputs. However, the low level of and potential decrease in genetic diversity should receive close attention in future breeding programs. In addition, we recommend wide surveys of natural resources and the establishment of closed breeding systems to increase genetic gain.