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The Role of Genetics in EMS/AHPNS

Plus Growth Rates, FCRs and Feeds

A “Dan”dy Discussion from the Shrimp List


Dan Fegan ( Dan Fegan, owner and creator of the Shrimp List, initiated the following discussion with his long posting to the Shrimp List on June 25, 2013.


Daniel Gruenberg ( In that posting, Fegan said:


Similarly, there has been a lot of speculation that broodstock and genetic selection could be contributing factors to EMS/APHNS.  I am not convinced of that because we have seen mortalities in shrimp from almost every broodstock supplier regardless of their genetic selection.  I find it hard to believe that every single selection program, regardless of its breeding goals or level of selection pressure would end up with the same problem.


Dan, I don’t know if you have heard the latest from the field, but we see a clear relationship between postlarvae supplier/breeding programs and the AHPNS incidence rate.  Hence, I am not sure that the above statement is entirely accurate.  In any case, don’t you think it is possible that there is both vertical and horizontal transmission that accounts for such variation?  After changing from supplier X to supplier Y, I can tell you that for two farms I take care of, the EMS incidence decreased from 80% to less than 40%.  Currently, the 40% figure varies from 20% to 40%.  That is a clear and significant change from earlier in the year and from another supplier.


Dan Fegan ( Daniel, I wasn’t making a statement as such, but only giving my opinion based on the limited information I have available.  I do not doubt your experience with different broodstock suppliers, but I also do not think that this necessarily contradicts my opinion that broodstock and genetic selection are not contributing factors.


Differences in “incidence rate” (and I assume that you are using this in the epidemiological sense) between PL suppliers can arise from a number of factors that have nothing to do with broodstock or genetic selection.  To put it in another context, your observation is like saying that differences in infant mortality rates between children born in two hospitals is due to genetics.  While this is one possibility, it is more likely that it is associated with a number of other factors from the state of health of the mothers to the hygiene standards in the hospitals and the subsequent home environment and nutrition of the children.


In your case, I can see several possible differences that might also explain your observation without invoking breeding and genetics.  There may, for example, be differences in the production standards and quality control of both suppliers or they may differ in their biosecurity programs or location resulting in different levels of exposure to disease risk.  At the farm, from what you write, these ponds were stocked at different times which further raises the question about the relative risk of exposure of shrimp to diseases or conditions causing early mortality when stocked at different times.  (I am not using the term AHPNS as it is not clear from your mail if these losses were unequivocally confirmed as AHPNS).


All I am saying is that we could look at the same information and legitimately draw different conclusions (or no conclusion at all for lack of sufficient data) to develop working hypothesis.  We can then gather more evidence to “falsify” (in the scientific sense) the working hypothesis and use the additional information to revise and refine it.


In this case, we are both using different information or data and have drawn different conclusions on which to base our own working hypotheses.  This isn’t a big deal.  It’s how science works.  The information I have assessed leads me to believe that hatcheries, and specifically genetics and breeding, are unlikely to be contributing factors in AHPNS outbreaks.  I have taken into account your observations, and I believe there is still insufficient evidence to change my opinion.  I am, however, open to changing my opinion and hypothesis as further information comes to light that falsifies that hypothesis.


Daniel Gruenberg ( Hi Dan, we have a bit of a misunderstanding.  I agree with your statement that there is not enough data to drawn any conclusions.  I was questioning your premise, not your conclusions.


Your premise is that despite different broodstock breeding programs, they all got the same results.  I was just saying that we did not find all PL sources to be the same.  In sharp contrast at one farm I take care of in Petchaburi, Thailand, our current EMS rate is zero.  That farm gets its PLs from one supplier, but individual ponds are managed differently.  Once that farm changed to a new supplier—despite different ponds with different management methods—it has had no EMS for almost three months now.


Of course you are correct in saying that there can be factors other than genetics to explain this result.  On this point I cannot disagree with you.


I may have a disagreement with you about whether or not genetics are a “contributing factor”.  If you use these quoted words instead of “cause”, then we may have a fundamental disagreement.


EMS or no EMS, genetics are important!


Not only are they important, but I see too many hatcheries or breeders doing it wrong.  “Doing it wrong” can run the gamut from the worst case scenario of using brothers and sisters from pond production as broodstock, to mismanagement in the commercial breeding unit (for example, mixing progeny from the wrong families), to the method of doing selection, and to simple hatchery management issues.  I have visited many hatcheries, mostly in eastern Thailand, and it is exceedingly rare to see “everything” being done correctly.


The scientific data documenting inbreeding depression is abundantly clear.  Do you agree that?


1. An animal with less inbreeding will generally be less susceptible to disease than an inbreed one?

2. A stressed animal will be more likely to succumb to a disease challenge than a non-stressed animal?


In addition, there is a large body of evidence that early larval nutrition status has effects throughout the life span of the animal.  In other words, an animal that receives less stress and proper nutrition in the hatchery will generally outperform an animal that may suffer from subclinical, but significant, development issues.


Matt Briggs, a broodstock/hatchery specialist, probably sees more hatcheries than I do, and perhaps he can chime in here with his views, but from what I personally see, much can be done better.  Whether or not this has a direct cause/effect relationship with EMS cannot be stated without more data, but I believe it prudent to take this opportunity to improve the PL/hatchery business and the way shrimp are bred.


We should not just be content with “good enough” as farmers and stewards of both the environment and the food that humans will eventually eat.  We need to continuously strive for “the best”.


Dan Fegan ( Daniel, when I referred to getting the same results, I was referring to the occurrence of AHPNS, not the scale.  Although, again, I have to emphasize that this is based on reports of early mortality and not confirmed AHPNS cases (See we both keep falling into the EMS/AHPNS trap!).  You are the first one I know of to claim to see a significant (statistically?) difference between suppliers, although I stand by my earlier point that there are other factors involved.  However, with a viable, reproducible challenge mechanism for AHPNS, it should be possible to run challenges with the pathogen responsible for AHPNS to see what differences there may be between families and sources of broodstock as the basis for developing families that are more resistant or less susceptible to the disease, assuming that this trait is heritable.


While I agree with you about inbreeding depression being something that is deleterious, I have to disagree about the idea that less inbreeding means more fitness.  I am not a geneticist, but as far as I understand, animal breeding is basically a process of controlled inbreeding managed (by pedigree selection) to ensure that deleterious traits are lost or minimized and favorable ones are enhanced.


Having said that, I do agree with you that most of the small-scale breeding programs conducted in Asia are poorly managed and run a high risk of causing inbreeding depression.  Selecting only the fastest growing individuals from a pond for broodstock and using them in a mating program without ensuring that there is sufficient genetic diversity in the mating population will probably eventually result in inbreeding depression, probably fairly quickly.


On the issue of stress, I don’t think anyone would disagree, and since I started my shrimp career in larval feeds, I also agree with you on the importance of early larval (and broodstock) nutrition.  This is an area that could be vastly improved as you say, but resolving this would require a change (actually a change back) to focusing on PL quality (independent of broodstock source) rather than competing on price and replacement guarantees.


Providing extra PLs to make up for PLs that might die in transit or soon after stocking has, in my opinion, distorted the market by absolving many hatcheries of the need to focus on quality, especially when shipping to small-scale or distant farms.  The number of farm survivals I see quoted in excess of 100% and in the high 90% has meant that I simply don’t trust survival claims any more.


So to get back to my first mail, we are all on the same side and share the same goals.  As someone who has been active in dealing with many different stakeholders in improving the environmental, food safety and performance issues facing our industry, I am 100% behind your desire to strive for the best.


Dallas Weaver ( Dan, selective breeding for growth rate in aquatic animals (fish/shrimp) is probably a lot less important than most people think.  In the case of chicken breeding, taking a day off their growth cycle saves the metabolic energy of keeping their bodies warm and erect, which results in an improved FCR.  These FCR gains go directly to the bottom line—to profit.


In the case of shrimp that expend no energy to stay warm or erect, growth rate and FCR are not tightly coupled.  Most non-flow through culture systems are limited in how much feed can go into the water (pond) per day as a consequence of the impact of that feed on water quality (ranging from DO to ammonia, BOD, bacterial loads).  For aquatic species with reasonable social behavior (don’t kill and eat each other at higher densities), animals that grow half as fast with half the metabolic rate stocked at twice the density with the same feed rate per area will produce the same revenue per hectare.


The major economic advantage of faster growth rate is just the interest on working capital with no impact on FCR.  Selective breeding of aquatic animals should be for disease resistance, survival, FCR and pollution tolerance, not for growth rate.


I think we are letting our judgment be clouded by the long history and science of growing and breeding chickens where FCR and growth rate are coupled.  With shrimp selection for survival variables may impact FCR and costs far more than selection for growth rate.


Russ Allen ( Dallas you said:


The major economic advantage of faster growth rate is just the interest on working capital with no impact on FCR.

What you say about growth rate may be true for pond culture, but in my system, growth rate has by far the most effect on profitability.  I’d trade a little higher FCR any day for faster growth.


Hank Bauman ( Dallas you said:


For aquatic species with reasonable social behavior (don’t kill and eat each other at higher densities), animals that grows half as fast with half the metabolic rate stocked at twice the density with the same feed rate per area will produce the same revenue per hectare.


Not with shrimp where larger sizes usually command a higher price.


David Griffith ( Dallas you said:


Animals that grows half as fast with half the metabolic rate stocked at twice the density with the same feed rate per area will produce the same revenue per hectare.


But they will cost correspondingly more in fixed costs.  Growth rate and production cost are not just about FCR.


Dallas Weaver ( Russ, given that your system is probably limited in square feet of tank area and that tank area is a larger fraction of the total capital cost than the biofiltration system, you are correct.  In a way, that outcome is just a byproduct of dealing with a 2-D animal.  A similar problem occurs with flat fish culture that is also area limited.  You also have a heat cost per square meter, which also favors shifting towards max growth rates.


Volume limited species, such as most of the fish species, are usually biofilter limited and growth rate becomes less important than FCR and survival.  That is why the optimum temperature for maximum profit is often less than the maximum growth rate temperature.  You grow them a little slower at higher density while operating at the FCR minimum instead of the growth rate maximum (not the same temperatures).


I was thinking of the more general class of culture systems such as ponds, not of our real love, super intensive, high technology, biosecure systems.


Dallas Weaver ( Hank, I have never done the experiments with shrimp, but with most of the fish species tested, the growth rates and FCR are almost independent of density at constant water quality.  Most of the observed impacts of density on growth rates are indirectly related to water quality and when you eliminate the water quality variation the density variation also disappears.  With fish, this independence of density is valid up to very high levels where social interaction or just physical interactions become a problem—bigger fish pushing the smaller fish away from the food or too many fish per cubic meter for the animals to see the feed (sight feeders).


The misleading information in a lot of the literature is a result of the water quality not staying constant as the experiment changes the densities.  The prime variable driving water quality is the feed input, which is related to FCR and density.


Hank Bauman ( Dallas, I think you’re responding to David Griffith’s post.  Mine was related to shrimp size and price differences.


Billy Setio ( Dear All, in my last three growout cycles, I have been increasing the feeding rate while maintaining the same stocking density of 130PL/m2.  This shortens the growout period without increasing the FCR or decreasing the size of the animals at harvest and brings down the total cost of production by at least 15%.  So I think growth is very important in outdoor ponds, and it plays an important role in absorbing fixed costs, especially if the selling price is not that good.


I’m now in the fourth growout cycle and pushing even harder to reach 2.5 grams of growth a week, but having a difficult time controlling water quality after 70 days of growout.  Not all the ponds produce 18-20 gram animals, but at least I’m showing that the growout cycle can be shortened to less than 90 days and still produce 18-20 gram animals.  Just like Russ said, even with a higher FCR, revenues are higher (depending on selling price, of course) and energy costs are a lot lower.


So what I learned from this little experiment is that maintaining water quality will give better growth, which in the end provides better survival and shorter growout periods.  Shrimp reach market size in as little as 50 days (10 grams), so if problems arise, I, at least, have a crop that I can market.


Daniel Gruenberg ( Dallas, at any given temperature, if you feed for maximum growth, most of the data available says that your corresponding FCR minima will also coincide with that feeding level.


When you add temperature variation to the mix, there are confounding factors that while temperature increases metabolism, a relatively larger portion of the energy budget goes into maintaining basal metabolism instead of growth.  The temperature that gives maximum growth and minimum FCR usually defines ideal temperature for fish.


Then you have the issue of feed energy content.  My old friend Reid Hole, who used to head R&D at Nutreco, would show me data that maximum growth and minimum FCR occur together.  However, this relationship only remained true when the energy budget was accounted for and total energy had to be increased accordingly for each increase in temperature.


At the end of the day, how much feed you put into the system and how much of that feed ends up as saleable product determine your profitability.  In that sense, it is like saying what is more important, your hourly wage or the number of hours you work?  They are both variables in the same income equation, so I don’t think you can say any one parameter is more important than the other.


As it relates to shrimp farming, large size usually happens with larger biomass and a higher price per kilogram, so you have multiplying factors that affect your income.  In this sense, I agree with Hank that growth is important.  The most important point is that in ponds, where 99%+ of prawns are grown today, you can improve both FCR and growth by feeding optimally and managing ponds correctly—and there is still a lot of room for improvement.


Pamindangan Farms Bocuan Orapopo ( Personally, I would rather have 1,000 kilograms of 20-gram shrimp than 2,000 kilograms of 10-gram shrimp, both in terms of revenue, profit and almost everything else.


Billy-san, kudos for your good work.  I know it is tough to manage ideal water quality parameters while you are pushing the limits of pellet feeding, but you seem to be doing a great job at it.  I assume that maintaining decent water quality in your scenario would involve management of sediments, sludge and other waste at the pond bottom, something that Dr. Weaver is an expert in.  In my ponds, I haven’t done much siphoning of wastes (afraid of spikes in NO2 and other water quality variables) and have resorted to regular central draining of the waste.  How do you manage your water after 70 days of growout to prevent mortalities?


John Birkett ( Dan, there are indications in Mexico that the new EMS outbreak (just to give a name to the new disease that we’re encountering) that some genetic lines perform better than others.  Well-maintained pedigree lines with renowned performance (that I can not mention in this forum) are performing worst than some other lines.  The pedigree lines are usually not inbred, but as a consequence of selecting only individual family lines, they have less allele diversity.  Thus, allele diversity depression is what makes your new generation more susceptible to a new pathogen or a change in environmental conditions, since you have probably separated out the ones that will survive your next outbreak, which happens in every culture that I know, like pigs, poultry and even plants.  Wild populations or more diverse allele populations are more likely to survive a new outbreak than pedigree lines.  Any pedigree line of dog, horse, pig, whatever will have less vigor when subjected to the range of wild pathogens in an open pen condition.


John Birkett ( Good insight Dallas.


John Birkett ( Daniel, it is worth pursuing the relationship between daily dollar per hectare sales and daily dollar per hectare costs, which depends on your target size shrimp, and includes FCR, growth, survival, days of growout and dollar per gram sales.  We have developed a formula that incorporates all this information, and it’s the only number that I use when doing genetic selection for group family traits.


Ramon Macaraig ( Daniel, my mathematical modeling on shrimp monoculture growth rates in intensive systems introduces a daily FCR derived from the product of two factors: the number of days it takes to grow a gram of shrimp times the grams of feed given per shrimp per day, plotted against the independent variable, body weight.  Tweaking my growth data led me to the following conclusions:


1. Healthy shrimp eat a finite amount of feed each day as a function of their size, regardless of feed quality and density.  For each molt cycle, the shrimp’s daily feed capacity probably does not change.  Thus, overfeeding just adds more nutrients to the water.


2. The daily conversion of feed to shrimp biomass depends on shrimp health, feed quality and the pond environment (mostly the amount of dissolved oxygen in the morning).


3. The herd (or is it school?) FCR is principally dependent on survival rate.  As mortalities pile up, the denominator does not increase as fast as the numerator and FCR soars.


Daniel Gruenberg ( Ramon, there are extreme limitations to any feeding guide that doesn’t take into account the myriad of variables that affect feed consumption behavior.  When we look at feeding behavior of both shrimp and fish, we see a variation of 200 to 300 percent on a day-to-day basis, so even the most sophisticated modeling can never model real behavior accurately, only “average” behavior.


Daniel Gruenberg ( Recently we have done a lot of work on digestibility in shrimp feeds and found that the size of the particles in the feces is a good indication of the completeness of digestion.  Not only did this help with our feed development program (we now use a twin screw extruder for our shrimp feeds as a result of this program), but we also use particle size to monitor EMS/AHPNS.  When digestion is decreased due to hepatopancreatic issues, it will first show up in larger particles in the fecal matter collected from the end of the intestine.


Dallas Weaver ( Daniel, uneaten feed on the bottom creates a potential fecal/oral loop for opportunistic pathogens.  The uneaten feed provides a home and energy supply for pathogens that may be eaten by our shrimp and infect them.  With land animals and humans, we know that diarrhea diseases kill more than any other disease class, however with our animals, we never hear anything about “shrimp diarrhea”?  Why is that?  It’s hard to study?  Over feeding can be a very major husbandry problem, making a feedback control system even more important.


Daniel Gruenberg ( Hi Dan, getting back to the genetic issue, thanks for chiming in.  No matter what opinions we exchange here we will never get around the fact there is still just too little accurate information out there to draw solid conclusions.  I am not saying that proper breeding can control EMS.  I am just saying that on the farm level, we see a clear difference in EMS rate between suppliers.  Period.


Daniel Gruenberg ( Dallas, I couldn’t agree with you more.  Our double-drain tank system allows inspection of the feces and continuously removes feed from the tank in minutes.  We often look at feces as in indication of health.


Sources: 1. The Shrimp List (a mailing list for shrimp farmers).  Subject: Thoughts on Shrimp Disease Investigations and the EMS Situation.  June 25 to July 1, 2013. 2. Bob Rosenberry, Shrimp News International, July 20, 2013.

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