- ASICo Markers
- Genetic Tools for Shrimp Breeders
Hereditary information Hereditary information that defines
all living things is encoded in the chemical substance called DNA. DNA molecules
consist of long chains of units called nucleotides. These molecules almost always consist
of two chains twisted around one another to form a double helix.
In the simplest of organisms like bacteria
and viruses, all DNA is present as a single molecule which may be made up of
thousands or millions of nucleotide pairs required to encode the information
which defines that microorganism. In more complex organisms, like birds and mammals,
billions of nucleotide pairs make up the genetic information and these are
subdivided into many molecules. Each of these molecules is present in a chromosome which
contain further divisions known as genes. These divisions and subdivisions are
nature’s way of ordering life’s information which describes that particular
organism uniquely from any other.
In humans, there are about three
billion nucleotide pairs in the egg and the same number in the sperm such that at the time
of conception, the fertilized egg will consist of about six billion pairs. What is amazing
is that all this information is located in the nucleus of each cell of the organism. This
entire DNA sequence of a single sperm or egg is known as a genome. The
genome of L. vannamei consists roughly of two billion nucleotide pairs or 2/3rds
the size of the human genome. In shrimp, there are about 90 chromosomes, each with
about 22 million base pairs of DNA nucleotides per molecule. In humans, there are 23
chromosomes each with about 130 million base pairs contained in each molecule.
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Theoretically, for every heritable trait
or function which characterizes the life of an organism, there is at least one gene responsible
for that trait. For most organisms, less than 5% of the total genome has
a genetic function. The other 95% consists of sequences involved in replicating DNA,
in regulating the activity of the genetic portion, or even "junk" sequences that
are relics reflecting the evolution of the species, but which have long since lost their
function. In the DNA of a genome there are nucleotide pair combinations which repeat themselves
and form groupings known as "microsatellites". There may be
thousands or hundreds of thousands of microsatellites spread randomly throughout the
genome.
Microsatellites Microsatellites are present in all
plants and animals and in many bacteria. Some microsatellites can be found in the
same location along the genome of the same species or even closely related species. This
means, that if a suitable microsatellite is found for L. vannamei, for
example, we can identify and distinguish individuals of that species irrespective
of where those shrimp came from (Colombia, Panama, Mexico, Ecuador, and even highly
selected/isolated stocks like those kept in Brazil or Venezuela).
What makes a microsatellite suitable for
use as a genetic tool? When we look at a specific microsatellite from many
specimens of L. vannamei of diverse origins, some will show high degrees of
variations within the same location (locus or loci). This variation is good as it allows
us to use that microsatellite locus as a potential marker and the variation within that
locus to differentiate between animals, families, or even populations. The variation in
any locus is due to the different number of nucleotide components, and each different
number of repeat units comprises an allele (allelic variation). To the extent there is
variation in the same microsatellite location, this is known as a "polymorphic
locus".
Suitable or good polymorphic loci are those
from which we can determine finite differences down to an individual animal…that is,
we can tell brother and sister apart, full from half siblings, parents from off-spring,
and general relatedness or diversity within a population. In essence, we have found a way
to fingerprint each shrimp with the use of one or more polymorphic loci. Similar
technology is so definitive that it is used in forensics and in criminal cases to identify
a single human individual out of a world population of billions
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Finding these polymorphic loci and using
them as genetic guidance tools describes the research and development phase at ASICo.
To date, we have found more than 60 suitable loci applicable to L.. vannamei that
have been identified, qualified, and characterized as candidate microsatellite
markers.….more than what many seed or animal breeding companies usually start off
with. Is the genotypic approach new science? Not to the more mature agriculture
sectors (e.g., in the last 30 years chicken egg production has increased 300%; cow milk
production rose 250%; and daily weight gains in the pig industry grew by 200%, with most
of the gains across these sectors occurring in the last 10 years). Since 1988,
genetic/phenotypic selection in the salmon industry resulted in production benefits
(growth and cost savings) exceeding 50%. What is new about this science is its application
to specific targets within the L. vannamei industry.
Marker-based guidance can reasonably yield
more than 20% greater production/revenues in the next 2-3 years. This will come about from
greater survival (resistance, hardiness, and/or healthier stocks), or from faster
growing animals (quicker pond turn-over or premium market sized product), or from a
combination of attributes. Realization of these benefits for L. vannamei
comes with the cost of pioneering the specific associative applications for targets of
economic importance. The use of such genetic tools and markers are highly complementary
to all existing phenotypic or traditional breeding programs. In fact, breeding
selection over the last twenty years with molecular genetics has resulted in more than
twice the results of gain when using a combination of genotypic and phenotypic programs
(compared to phenotypic programs alone), or accomplished the same results in less than
half the time.
Microsatellite Markers – The Tool:
Much genetic research today is devoted to
developing genetic maps; some of genes, some of chromosomes, and some of the entire
genome. This process may take years to accomplish since decoding the DNA sequence of even
the shrimp requires thousands of man-days. A genetic map is much like an atlas which shows
the locations of genes or DNA fragments that have been identified, some of which expresses
themselves as desirable traits for the farmer. It is possible, however, to find
microsatellites throughout the shrimp genome without knowledge of the genome or genetic
functions/mechanisms that make the genes operative within the shrimp. When these markers
are identified and characterized, each can be used as a signpost to help locate genes that
expresses the desired trait. Just as it is easier to find San Diego if you know it is near
Los Angeles, it is easier to find a gene location if you start with a marker nearby.
Markers are related to traits as a function of the distance they are from the gene
responsible for that trait.
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Microsatellite Markers - The Ability to
Fingerprint and Tag:
Good markers are those which, in the same
genomic location, have variation among different animals within the same species. This
allows us to track genetic diversity among families and populations, establish pedigree
lines centered around desired expression of certain traits, and determine vertical and
horizontal lineage should true bio-secure measures ever be implemented at the breeding
center. Similarly, these markers allow us to build unique profiles on developed strains or
to track family/population lines. That is, from pleopod samples, stock identification can
be made irrespective of where those stocks came from.
Microsatellite Markers - Marker Assisted
Selection:
The primary value of markers is to assist
in the breeding process and to improve the breeding prediction. Phenotypic breeding
programs are fine and have been around for centuries, but these are based upon the
probabilities of occurrence. A very good line may be developed but what happens to that
investment (time and money) should the breeding center be affected by storm or disease? Is
the investment lost if the lines can’t be reconstructed? Is the industry willing to
bet its future business on probabilities of occurrence or start taking control over the
factors which impact its livelihood? DNA sequence is definitive….it is either black
or white in content and the information cannot be interpreted in more than one way once it
is sequenced. This produces breeding tools and guidance which is informational based.
Over the next thirty years the pressure for
applying genetic improvement will intensify for several reasons. First, population growth
will widen the gap between demand and supply from wild fisheries. Ocean catches have
stablized at approximately 100 million tons per year and future supplies must come from
aquaculture. It is estimated that total aquaculture production by 2025 will exceed 60
million metric tons, up from 15 million tons in 1990 (Hempel, 1993).
Second, most aquaculture systems are higher
than normal population density monocultures. These are prone to far greater commercial
losses from disease outbreaks. Losses from existing diseases and new pathogens have been
well documented in the shrimp industry over the last 10 years. In most cases, the greatest
losses have occurred with wild stocks of unknown lineage. The development of strains
genetically resistant to pathogens or which may express greater stress
resistance/hardiness is one approach for addressing this problem.
Third, future production growth will most
likely shift to intensification wherein output is a consequence of production efficiency
per unit area rather than increases in area of production. Efficient use of capital,
environmental pressures, and unit cost of administration will mandate earlier return on
investment, higher utilization of existing facilities, better food conversion efficiency,
and reduced exposure to crop failure from accidental loss or disease as the primary rules
of operation. Genetic improvement produces domesticated stocks more suitable for captive
culture in artificial production environments.
Finally, as with most maturing industries,
as production of any given species increases, competition sets in and there is generally a
convergence of product price with cost of production. This can be seen clearly in the
cases of salmon, tilapia, catfish, oyster, and shrimp aquaculture. Such convergence should
be anticipated for any species under consideration for captive culture. As a consequence,
only the highly efficient and competitive entities will tend to survive and remain
profitable in the narrow window between profit and loss. Genetic improvement is expected
to be one of the most important tools for increasing commercial competitiveness among the
industry survivors.
Genetic improvement through selective
breeding provides the capability of culturing a better quality animal in less time, with
greater survival, and at less cost than animals removed from the wild.
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