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Selective Breeding in Shrimp Farming

Article · April 2015

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Arul Victor Suresh

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 Elastomer tagging is one method that is used to identify which characters have passed onto the next generation
in breeding programmes. (Photo courtesy: Kona Bay vannamei breeding program, Hawaii)

Selective breeding has been used for ages by

Selective mankind for improving plant and animal production.
In shrimp farming, it has a relatively short history of
about 20 years and the gains are already impressive.
Breeding in Production of 15 g vannamei in 120-135 days at a
stocking density of 20 animals/sq.m was the norm
twenty years ago. Today 28 g shrimp can be produced
Shrimp Farming in the same duration at a stocking density of 50-100
animals/sq.m. While factors such as disease control,
pond technology, partial harvest, better feeds and
improvements in management knowledge have
A. Victor Suresh contributed to the phenomenal improvement in
United Research (Singapore) Pte. Ltd. &
shrimp farm productivity, selective breeding has played
Growel Feeds Pvt. Ltd., India
E-mail: avictor.suresh@gmail.com the most important role. Further improvements in
productivity will occur as we continue to select shrimp
for growth, disease resistance, and other desirable traits.
The purpose of this article is to provide a broad
understanding of selective breeding programs so that
farmers can make educated decisions concerning the
seed stocks they buy.

32 FISHING CHIMES|APRIL - MAY 2015

 HISTORY conditions are not optimal. While it has been possible
to rear the more popular tiger shrimp, Penaeus
Selective breeding requires that the lifecycle of monodon, from egg to maturity and breed them,
target animals should be closed under captivity, i.e. successful domestication to full commercial impact has
animals should be able to live under human been limited to only a handful of groups till date.
management from their birth/hatch onward and be This is partly due to the late start of tiger shrimp
able to breed and produce offspring that will survive breeding programmes and the limited number of
to produce another generation of animals. Without generations in captivity. Undoubtedly, selective
this ability, broodstock needs to be taken from wild breeding of tiger shrimp will become easier with
stocks every generation and selection of animals for successive generations. Domestication and selective
improvement cannot occur.Hence, closing of the breeding are also limited in other penaeid species due
lifecycle under captivity is an essential part of selective to the lack of widespread commercial interest in those
breeding, which is defined as the process whereby a species. So this article considers breeding of vannamei
population of living organisms is changed at the shrimp only.
genetic level, through generations of controlled
reproduction, to accentuate traits that ultimately U.S Government funded breeding programme:
benefit the interests of humans. Efforts to develop selectively bred stocks of vannamei
shrimp can be broadly divided into two, based on
Necessity for Breeding:For a period of time in where the efforts occurred. One is the large and highly
shrimp farming history, seed stocks were sourced from successful effort in the United States of America
the wild. Later on, due to increasing demand initially funded by the US government in what was
broodstock were sourced from the wild to produce known as the US Marine Shrimp Farming Programme
offspring in captivity. The third stage was selective (USMSFP). The primary objective of the program was
breeding, which occurred when the shrimp were to develop Specific Pathogen Free (SPF) stocks of
domesticated. The species of the Litopenaeus genera, vannamei shrimp for shrimp farming in the US.
namely L. vannamei and L . stylirostris (blue shrimp) Concerted efforts by multiple institutions since 1989
were the first ones to be domesticated widely due to led to the collection of adult vannamei from the wild,
the limited geographic range and seasonal which were taken through a systematic quarantine and
reproduction of the wild populations and the ease of disease surveillance system, after which they were bred
breeding them under captivity. L. vannamei are native and the domesticated. The disease-free stocks were
to the Pacific coast of the Americas between Mexico deposited in a Nuclear Breeding Center (NBC) located
and Peru, so farms located on the Caribbean and at the Oceanic Institute (OI) in Hawaii. The stocks
Atlantic coasts were forced to adopt domestication were perpetuated at the NBC and high health larvae
programmes. Even within the geographic range of L. (larvae free from listed pathogens) were supplied to
vannamei, wild adults often were not available, due to the farms. The programme screened for nine viruses,
seasonal factors such as cool offshore currents during
La Nina periods off Ecuador. On the other hand,
Penaeus monodon, has much wider geographic range
throughout the IndoPacific, which enabled farms Concerted efforts by multiple
throughout the region to use wild stocks without the institutions since 1989 led to the
necessity of domestication.
collection of adult vannamei from the
In terms of ease of breeding, L. vannamei reaches wild, which were taken through a
maturity when they were relatively small in size systematic quarantine and disease
(30-50 g) and are open thelycum breeders. surveillance system, after which they
Nevertheless, it was a challenge to induce reproduction were bred and the domesticated. The
in the wild adults under captive conditions. Now, disease-free stocks were deposited in a
populations of L. vannamei have been domesticated
for about 30 generations and they reproduce easily in
Nuclear Breeding Center (NBC) located
captivity, even when the diet and environmental at the Oceanic Institute (OI) in Hawaii.

Acknowledgement: The author is grateful to DrJoão L. Rocha, a leading shrimp geneticist associated with many successful vannamei breeding
programmes around the world (Genearch, Brazil; PrimaGen, Indonesia; Texcumar, Ecuador; CAMACO, Panama)for providing study materials and going
through the first draft of the manuscript and correcting many errors. Dr George W. Chamberlain, whose companies Kona Bay Marine Resources and iAqua
run breeding programmes on vannamei and monodon, respectively, provided valuable inputs on the second draft of the manuscript.

VOL. 35 NO. 1 & 2|FISHING CHIMES 33

 Steps in the development of
selectively-bred shrimp stocks

Vannamei shrimp breeding programmes

one bacteria and three parasites and assured that the
high health larvae did not have the listed pathogens
when they were released from the NBC. Once SPF
was established, efforts went into selective breeding
of stocks. The breeding programme primarily focused
on growth improvement and development of Specific
Pathogen Resistant (SPR) stocks. The programme
accomplished the development of fast growing stocks,
and stocks resisting the Taura Syndrome Virus (TSV).
Broodstock developed by USMSFP were sold from
the NBC to US companies that wished to start their
own SPF programmes. These companies were located
in the states of Hawaii and Florida. These companies
then sent out their stocks to shrimp farming countries
around the world for propagation and use in shrimp
farming. Consolidation of these organisations also
occurred over time resulting in only a handful of
breeding companies. While all vannamei stocks used
in Asia can be traced to the founder stocks developed
by USMSFP, the commercial breeding programmes
have become more advanced and have achieved higher
acceptance by farms throughout Asia. that are on the Atlantic Ocean. So, domestication was
required for independence from the need to frequently
About the time USMSFP was initiated, many import broodstock from other countries.
shrimp farming countries in Latin America, notably
Mexico, Honduras, Panama, Ecuador, Colombia, In other Latin American countries, hatcheries found
Venezuela and Brazil embarked on their own vannamei it logistically easier and more seasonably reliable to
domestication programmes. The Pacific white shrimp, source adult animals from farms than from the ocean.
vannamei are non-native species in Venezuela and Brazil However, no systematic efforts were taken to exclude
pathogens when the broodstock were sourced. This
led to the development of stocks with pathogens. Some
breeding programs intentionally took animals that
While all vannamei stocks used in survived disease outbreaks and used them for breeding
Asia can be traced to the founder with the belief that they could produce stocks that
stocks developed by USMSFP, the were resistant to pathogens.
commercial breeding programs have According to some industry insiders, the approach
become more advanced and have of sourcing broodstock with pathogens was counter-
achieved higher acceptance by farms productive and resulted in the rapid evolution of the
throughout Asia. pathogens’ ability to cause harm.However, this
assertion has been disputed by others and trends

34 FISHING CHIMES|APRIL - MAY 2015

 emerging in the last few years show that the Latin
American approach to building disease resistance by
direct exposure to pathogens may have some merits.
Breeding programmes in Latin America are more
focused on the development of stocks that are tolerant
of pathogens because the large pond size (5-20 ha)
does not allow for intensive management of ponds.
Tight biosecurity, heavy aeration and periodic sludge
removal are not realistic in large ponds, therefore
farmers preferred pathogen-resistant stocks to
pathogen free stocks. Some breeding programmes have
achieved notable success in producing pathogen-
resistant stocks, the most important one being against
the white spot syndrome virus (WSSV). The recent Laboratory disease challenge trials indicate which
industry growth trends in Ecuador and some other families from a given genetic line have greater
Latin American countries have been attributed to the resistance to specific diseases. This data can be
used as one of criteria for selecting which families
development of resistance to WSSV in some stocks. to use for producing the next generation. In this
Whether these stocks have truly attained complete trial, survival of 30 L. vannamei families exposed to
resistance against WSSV is not confirmed, but these a 5-day WSSV challenge ranged from 8-64%. The
average survival of the top 15 families was 51%.
countries are able to coexist well with the occurrence [data courtesy of Kona Bay breeding program in
of the pathogen but without major catastrophes. Kauai, USA].

In conclusion, the brief history of vannamei breeding

has seen two major approaches: one was oriented to the management, genetic gains might be minimal or even
development of fast-growing, pathogen-free stocks while negative. Targeted selective breeding programmes are
the other targeted the development of pathogen- a way of accelerating gains in desirable traits and
resistant stocks. The strengths and limitations of both avoiding the negative effects of inbreeding.
approaches are now better understood and the obvious
path for the future is to combine the efforts to produce Specific Pathogen Free (SPF) refers to the production
fast-growing, pathogen-free stocks that are also resistant of animals that are free of a specified list of pathogens.
to pathogens. The process involves biosecurity controls and systematic
surveillance and exclusion of pathogens as per a set of
protocols. Typically, the protocol requires primary and
......trends emerging in the last few years secondary quarantine steps spanning at least two
show that the Latin American approach generations before a population can be declared SPF.
to building disease resistance by direct
exposure to pathogens may have some Technically SPF status is guaranteed only until an
animal is within the premises of the Nucleus Breeding
merits.

Typically, the protocol requires primary

DOMESTICATION, SPF, SPR & BREEDING and secondary quarantine steps spanning
PROGRAMMES at least two generations before a
population can be declared SPF.
The terms “Domestication”, “SPF”, “SPR” &
“Breeding Programmes”are often misunderstood in the
shrimp farming sector, so distinguishing each term is Center that operates the SPF program. Once it leaves
important. the facility, it should be protected against infections
along the way and in every facility that receives, holds
Domestication, as explained in the previous section, or handles the animal until it is harvested. Since
involves the completion of the life cycle of an animal facilities like multiplication centers and hatcheries that
under human management. Domestication paves the handle SPF animals are not likely to be as biosecure as
way for production of stocks generation after generation the NBC, distinction has in the past been by what is
from one or more parental lines. Some degree of genetic referred to as High Health animals. These are animals
selection – intended or inadvertent — occurs during that are offspring of SPF broodstock produced in a
the domestication process, but without scrupulous hatchery with a good pathogen control programme.
VOL. 35 NO. 1 & 2|FISHING CHIMES 37
 Studying performance of different families in net cages suspended in ponds is a common practice in selective
breeding (photo courtesy: Generach, Brazil)

The term is not commonly used at present because of specified pathogens. As stated earlier, SPR stocks are
the practical difficulties in defining a High Health commonly available for TSV resistance from most
program for universal implementation. commercial SPF vannamei breeding companies.
Additionally, some SPF vannamei breeding companies
Breeding programme means that-animals within
have developed stocks with resistance to IHHNV,
the programme are mated as per a plan devised by a
IMNV, and WSSV. Efforts are also underway to
geneticist who wants to achieve specific traits in the
develop stocks resistant to EMS.
target organisms. The traits could be related to the
appearance of the organism or its ability to resist one In a form of convergent evolution, South American
or more pathogens, growth, feed efficiency, breeding programmes are also developing stocks
reproductive capacity, etc. Development of a single resistant to a wide range of pathogens, but not
trait is a long and painstaking process involving more necessarily SPF. These South American stocks are yet
than one generation of breeding, so breeding programs to be available in the open market but used within
require investment of time and money to be rewarding. programmes that have developed the stocks.
At the same time, breeding is a process that builds
value in the stocks continuously that the rewards are BASICS OF GENETICS
generally more than worth the efforts invested.
Aquaculturists need to understand what certain
As stated above, ability to resist pathogens can be genetic terms mean to understand breeding
achieved through selective breeding programmes or programmes better.
through natural selection. The term Specific Pathogen
Resistant (SPR)means that stocks are resistant to Traits are characteristics that are targeted for

38 FISHING CHIMES|APRIL - MAY 2015

 Graphs illustrating Genetic x Environmental Interactions. The graph on the left shows that performance
of families for growth (as measured by harvest weight) at low stocking density is highly correlated to
performance at high stocking density. In other words, families performing well at low stocking density
would also perform well at high stocking density, therefore there is no interaction between genetics and
stocking density for growth. The graph on the right shows that there is poor correlation between survival
of families in low stocking environment and high stocking density environment. In other words, high
survival of a family in low stocking density does not mean that the same family would survive equally well
in high stocking density. This indicates there is interaction between genetics and stocking density for
survival (Data courtesy: Dr.João L. Rocha)

attainment or improvement through breeding. Traits expression. In cases where both alleles contribute
should be identifiable or quantifiable. Examples of equally, the offspring will have brownish black eyes.
traits commonly used in today’s breeding programmes
are: growth rate, multiple pathogen resistance, and SELECTIVE BREEDING PROGRAMMES:
reproductive performance. HOW DO THEY WORK?

Traits targeted in a breeding program must be Selective breeding is the means by which one or
heritable, i.e. passable from parents to offspring. more traits is attained or improved through crossing
Heritability of a trait ranges from 0 to 100%. When of selected individuals or families. In agriculture,target
it is 0%, the trait is not heritable at all. When it is traits can be divided into two types: one that is
100%, the trait is fully heritable. The higher the qualitative and another that is quantitative.Qualitative
heritability, the fewer the generations required for traits(for example, a fish with red eye)are typically
breeding to achieve its targets. Geneticists consider controlled by a single gene and can be achieved with
heritability levels above 20% to be suitable for a mating between individuals that possess the trait. It
attainment through breeding programmes. is also easy to identify the fish with the allele that
codes for the trait (any fish that has a red eye will have
Traits are coded by one or more genes. Each gene the allele) and use it in breeding. In two rounds of
has one or more forms called alleles. To understand let breeding, the way the alleles are expressed, i.e.
us take a simplified hypothetical example: eye colour dominant or recessive, can be established to develop a
in a population may be black or brown coded by an sound breeding program.
allele for whatever factor that causes eye black or brown
respectively. An individual will have two alleles of each Quantitative traits, for example, weight gain, are
gene, one derived from the father and other one derived controlled by many, many genes, so identifying fish or
from the mother and will pass one of the two alleles to shrimp that has superior alleles for all the genes is not
the offspring. The alleles may be the same (homozygous, practically possible. Further, redistribution of alleles
for example Black, Black) or different (heterozygous, occur every generation, so there is no guarantee that an
for example, Black, Brown) and expression of the gene
will depend on whether one allele dominates over the
other or both alleles contribute equally to the expression. The higher the heritability, the fewer
If the allele for black eye colour dominates over allele generations required for breeding to
for brown eye colour, for example, an individual will achieve its targets. Geneticists consider
have black eye colour even if he derives an allele for heritability levels above 20% to be
brown eye colour from one of the parents. Two alleles
suitable for attainment through
of brown eye colour will be needed for the expression of
brown eye colour. The allele for brown eye colour is breeding programs.
called a recessive allele because it requires two alleles for

VOL. 35 NO. 1 & 2|FISHING CHIMES 39

 Table 1: Some prominent SPF vannamei breeding companies that derived parental stocks from USMSFP

Company/Brand name Location Status of Permission

for import into India

Shrimp Improvement Systems USA, Singapore On the Approved List

Kona Bay Marine Resources USA On the Approved List
Oceanic Institute USA On the Approved List
SyAqua (acquired by Gold Coin) Thailand On the Approved List
CP Thailand On the Approved List
Global Gen Indonesia On the Approved List
Prima Gen Indonesia Never applied
Genearch Brazil Never applied

individual with superior alleles will pass all superior

alleles to its offspring. So, rather than relying only on
individual selection for performance traits, geneticists Quantitative traits, for example, weight
also rely heavily on what is known as family selection. gain, are controlled by many, many
genes, so identifying fish or shrimp that
As the name implies, families instead of individual has superior alleles for all the genes is not
animals are selected for breeding based on their practically possible.
performance record in a family selection programME.
Families are created by mating a single male with a
single female and then identifying the offspring by
placing in tagged containers or tagging the animals SPF VANNAMEI BREEDING COMPANIES &
with a mark. Injectable elastomer marking is the most SELECTIVE BREEDING
common method of tagging penaeid shrimp, but more
sophisticated breeding programs use genetic markers All SPF vannamei breeding companies have derived
to increase selection intensity. their founding stocks from the USMSFP and many
have implemented selective breeding programmes to
Breeding programmes depend on geneticists who
improve growth, disease resistance, and reproductive
are adept in the use of sophisticated computer
performance. These programmes have been active over
programs to manage selective breeding as data need
dozens of generations and at different locations
to be compiled on thousands of individuals belonging
(including some in Asia and Brazil), so it is reasonable
to multiple families and analysed for decisions to be
to expect that the stocks sold by different companies
made on what families should be selected for further
have distinct performance characteristics. There has
development. Breeding programmes must maintain
also been some consolidation in the breeding
a sufficient number of families and carefully select
companies likely resulting in the amalgamation of
mating pairs to minimise the rate of inbreeding.
stocks. Companies hold the details of their
One of the key considerations in a selective breeding programmes secret, so the performance of the stocks
program is the environment in which the selection at the hatchery level or at the farm level are currently
occurs. Performance of shrimp is dictated by many known only through subjective feedback from the
environmental factors such as temperature, salinity, hatcheries and farms. Objective evaluation of stocks
stocking density, etc. Shrimp selected for performance of different companies is quite limited at this time.
in one set of conditions may not perform well in other
In today’s world, the majority of shrimp production
conditions. There is also need for breeding
is still in the hands of independent farmers who are
programmes to develop stocks that perform well in a
dependent on independent hatchery operators for their
specific environment, for example, low temperature.
seed stocks and the hatchery operators, in turn, rely
Consequently geneticists need to study performance
on broodstock suppliers for the spawners. The
of their animals under different variables of
breeding efforts of many broodstock suppliers are
environmental conditions and calculate what is known
oriented to two objectives. One is to keep running
as Genetic x Environmental Interaction to guide their
their selection programme. A large number of families
breeding programmes.
are perpetuated in this program. The second objective
40 FISHING CHIMES|APRIL - MAY 2015
 is to produce stocks that will be reared into adult size and broadcast pathogens from one area to a wider area,
and sent out to hatcheries for spawning (or the PL and on the other, create inbred stocks that are likely to
may be sent out to multiplication centers in the be more sensitive to pathogens.
recipient country for rearing to adult size). Typically
only a few families are used for this purpose due to WHAT CAN FARMERS DO TO ENSURE
space as well as proprietary considerations. By limiting THAT THEY GET QUALITY PL?
the number of families sent out, the breeding company Currently India allows only SPF vannamei
limits the chances that the recipients of the stocks can broodstock to be imported into the country and
establish their own breeding programmes. If a recipient stipulates that only such imported broodstock be used
begins a breeding programme with members of the for seed production. The broodstock suppliers are
same family, the programme will suffer from authorised after going through a process to ascertain
inbreeding depression in a few generations. the origin and SPF status of the stocks. The stocks are
In most countries that import SPF vannamei, local quarantined upon receipt in the country. These steps
programmes exist that mature and spawn the first or reduce the likelihood of defective stocks imported into
second generation offspring of genuine SPF broodstock. the country. But, clandestine programmes that illegally
These programmes generally rely on shrimp reared in use pond-reared broodstock are more difficult to control.
farm ponds to develop their broodstock. These So, farmers can only use vigilance in their stock selection.
programmes present a great threat to the sustainability 1. Develop close and long-term relationships
of shrimp farming because on one hand they perpetuate with their hatchery suppliers
One of the key considerations in a selective 2. Select hatcheries that are quality oriented and
breeding program is the environment in genuinely interested in the long-term survival of
shrimp farming
which the selection occurs. Performance of
shrimp is dictated by many environmental 3. Insist on quality and pathogen testing of the
factors such as temperature, salinity, seeds they buy
stocking density, etc. 4. Avoid purchase of PL that are priced
suspiciously below general market prices.

VOL. 35 NO. 1 & 2|FISHING CHIMES 41

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