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May 27, 2014


Full Copy of Roger Doyle’s Paper on Inbreeding


Shrimp News: For a full copy of Roger Doyle’s paper on inbreeding in shrimp, Click HereBelow I have provided parts of the abstract and introduction, some definitions, some excerpts and parts of the paper’s conclusion.  It’s a long technical paper, but important reading for anyone who purchases shrimp seedstock.


Abstract: The disease crisis facing shrimp aquaculture may be propelled, in part, by an interaction between management practices that cause inbreeding and the amplification by inbreeding of susceptibility to disease and environmental stresses.  The study describes and numerically simulates gene flow from Penaeus (Litopenaeus) vannamei hatcheries that employ a “Breeder Lock” [defined below] to discourage use of their PLs as breeders, through “copy hatcheries” [defined below] that breed the locked PL to inbred shrimp in farm ponds.   Re-analysis of published data shows that inbreeding depression under stress is exceptionally strong in shrimp.


Introduction: Discussion of the current shrimp disease crisis focuses on the microbiology of pathogens and the regulations needed to limit their spread locally and across national boundaries.  In this study I take the perspective of a geneticist and evolutionary biologist and suggest that a disease crisis that has microbiological roots may be amplified and accelerated by an agro-economic system in which shrimp breeders, hatcheries and farmers induce critical levels of inbreeding at the farm level. The inbreeding is now manifesting itself as increasing susceptibility to disease and frequency of epidemics over vast areas of Asia, Central and South America, Africa and the Middle East.


The purpose of this study is neither to review comprehensively existing research on inbreeding in aquaculture nor disease problems in aquaculture, both of which are large and important topics.  The purpose is more focused: to propose and, as far as possible with current information, to document a three-way connection between the effect of inbreeding in stressful conditions (especially disease stress), aquaculture practices that lead to inbreeding and technical issues with widely used procedures for estimating inbreeding that have caused inbreeding to be underestimated.


The Results and Discussion section of the study is divided into five sub-sections:


• Description of a Breeder Lock aquaculture system that induces inbreeding in farmed shrimp populations.


• Numerical simulation of gene flow through this system and demonstration that batches of locked and copied postlarvae (PL) can be distinguished with appropriate use of genetic markers.


• Review of the effect of inbreeding on susceptibility to stress in general and shrimp disease in particular.


• Explanation of why we currently have so little information about inbreeding in shrimp hatcheries and farms and (mistakenly) believe inbreeding to be minimal.


 • Possible policy initiatives that could reduce inbreeding and/or its effects.


Breeder Lock: A reciprocal cross between two, large full-sib families of breeders that produces non-inbred offspring intended to be used for growout.  The lock comes into effect when these hybrid offspring are matured and mated among themselves in copy hatcheries that produce inbred offspring with reduced fitness.


Copy Hatcheries: Hatcheries that use as broodstock breeder locked PL without authorization or knowledge of their biological relatedness or inbreeding status.


Estimates of The Global Extent of Shrimp Copying: There is as yet no individual estimate for any shrimp species, but people directly involved in the tropical shrimp industry believe copying to be substantial.  The following estimates have been offered as personal communications with permission to cite the source by name: Thailand, conservatively, 50% copied (Mr. Robins McIntosh); Ecuador greater than 90% copied, Honduras around 50% copied, Mexico greater than 90% copied, Nicaragua around 50% copied, Panama less than 10% copied, Venezuela greater than 90% copied (José B. Martinez, Panama).  These estimates are in general agreement with consensus estimates developed during a recent international workshop in 2014 on the possible connection between inbreeding and shrimp disease.


If they were offered verifiable information by authorized breeders and hatcheries, farmers could, if they chose to do so, avoid the copy distribution channel.  Certificates of Authenticity have been offered by some breeders, but this strategy fails when the certificates are counterfeit.  Certificates offered to date have been missing the essential element of verifiability.  Verification of the location of a population is technically easy in principle.  Certificates from breeders attesting that a particular batch is 100% heterozygous for two particular alleles at a particular locus (both specified in the certificate) would be sufficient to verify that the batch is a first-generation hybrid and minimally inbred.


Conclusions: In this study, I suggest that disease crises in tropical shrimp aquaculture may be growing more severe and more frequent owing to an agro-economic system that generates genetic erosion at farm level.  Genetic erosion results from a pattern of human behavior in which breeders protect intellectual property through the breeder lock (expressed only when broodstock is “copied”), copying hatcheries sell inbred offspring and farmers stock their ponds with seed animals they are unable to evaluate.  The resulting inbreeding and low genotypic diversity increase susceptibility to disease, which leads to more infected individuals and farms and thus, by standard epidemiological reasoning, increases the frequency and severity of epidemics.


The hypothesis is not that inbreeding triggers shrimp diseases—which have myriad environmental and other immediate causes—but that inbreeding increases the prevalence and severity of disease, and that inbreeding is accumulating regionally.


The extent of broodstock copying, the true level of inbreeding in farms and the magnitude of inbreeding depression in shrimp may be obtainable by relatively simple adjustments to current procedures and re-interpretation of existing data.


Source: Aquaculture Research.  Inbreeding and Diseases in Tropical Shrimp Aquaculture: a Reappraisal and Caution.  Roger Doyle (email, Genetic Computation Ltd., 1-4630 Lochside Drive, Victoria, British Columbia V8Y2T1, Canada).  Early View (Online Version of Record published before inclusion in an issue).  Published online on May 9, 2014.

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