Loss of genetic diversity due to hatchery culture practices in barramundi ( Lates calcarifer)

Many aquaculture hatchery practices are detrimental to the long-term viability of restocking and selective improvement programs. Small effective broodstock population sizes, differential broodstock contribution, differential larval/juvenile survival during metamorphosis and size-based grading, all have the potential to drastically reduce the level of genetic variation remaining in hatchery populations. Monitoring levels of genetic variation and maintaining detailed pedigrees on progeny is the key to circumventing these problems. In this study we used microsatellites, coupled with DNA parentage analyses, to track the loss of genetic diversity in two independent commercial barramundi ( Lates calcarifer) hatcheries over three mass spawning events, where up to two females and seven males had the opportunity to participate. Initial broodstock contributions were observed to be highly skewed, with significant differences observed in both the level of contribution by females to each mass spawning, as well as in the number of males participating and subsequently contributing to the genetic composition of cohorts. Effective population sizes were around half that of census sizes. We then examined whether differential family survival through metamorphosis (27 days post-hatch) and/or first size grading further influenced the retention of genetic diversity levels initially sampled during spawning. Parentage analyses indicated that some families that had been initially represented in cohorts had been lost, or that the contribution by particular broodstock had changed. In one cohort, as many as 55% of progeny were found to be sired by a single male individual. Size grading was also found to potentially impact on genetic diversity, with data suggesting that family representation in each of the grades was non-uniform and that some families were on average faster or slower growing than others. These results illustrate that hatchery management practices have the potential to significantly impact on the retention of genetic diversity in this species.