Tropical shrimp aquaculture is facing a disease crisis that may be propelled, in part, by an interaction between management practices that cause inbreeding, and the amplification by inbreeding of susceptibility to disease and other stresses. Data are reviewed and re-analysed that show interaction between inbreeding and stress to be exceptionally strong in shrimp.

Broodstocks accumulate inbreeding and lose genetic diversity ("genetic erosion") when they experience bottlenecks or are chronically too small. The mechanism is simple: accidental, random mating among biological relatives in small populations. The main focus of this presentation, however, is a very different cause of genetic erosion which is neither accidental, nor random, nor related to population size: the genetic lock.

The genetic lock is a practice that leads to inbreeding at farm level when "locked" post-larvae (PLs) produced by large, well-managed hatcheries are used as breeders by "copy hatcheries". Lock-copy broodstock management is widespread in SE Asia and likely to increase. Gene flow through the lock-copy system is numerically simulated and analysed to reveal genetic statistical signatures of its various stages.

We have relatively few, marker-based estimates of accumulated inbreeding in any non-pedigreed shrimp aquaculture system, whether locked, copied, well-managed or otherwise. The expected value of accumulated inbreeding, as usually estimated, is zero whatever the true genealogy of the population. Simulation shows that, fortunately, locked PLs can be distinguished from copies in broodstocks and farm ponds, given appropriate analysis of genetic markers. Estimation of inbreeding already accumulated at farm level is also feasible.

Culture of stocks certified to be free of specified pathogens (SPF stocks) is strongly recommended and only SPF stocks can now be legally imported into most jurisdictions. These recommendations are appropriate, beneficial and necessary. But insofar as they increase the value of proprietary, high-quality SPF strains, such regulations may also increase the use of genetic locks and the likelihood of copying, and thus inbreeding at farm level. Intellectual property rights are fundamental to science-based economic innovation. Breeders will, and should, continue to protect their genetic improvement programs with genetic locks that generate inbreeding when copied, especially in regions where judicial sanctions are ineffective. The intellectual property value of disease-resistant strains will be extremely high.

The current consensus that inbreeding is unimportant may therefore be out of date. Inbreeding may be amplifying the severity of diseases, including the major current threats: WSSV, IHHNV and EMS (or AHPND). The regulatory objective should be to encourage biosecurity and genetic progress while at the same time discouraging copying and consequent inbreeding.