- Use of Markers for Genetic
Selection of Desirable Traits
The hereditary information that defines all
living things is encoded in the chemical substance called deoxyribonucleic acid, or
DNA. This molecule is unique among chemicals in that it has 1) the ability to store
information, 2) the ability to be replicated accurately, and 3) the ability to mutate or
change the information stored in the molecule.
DNA molecules consist of long chains of
units called nucleotides. There are four different kinds of nucleotides: adenine (A),
thymine (T), guanine (G), and cytosine (C). DNA molecules almost always consist
of two chains twisted around one another to form a double helix. The nucleotides of
the two chains are arranged so that the A’s are always opposite T’s, and
G’s are always opposite C’s. It is this double helix structure that enables DNA
to meet the requirements of hereditary material: 1) The information in a DNA molecule lies
in the sequence of nucleotides in the chain, 2) when DNA is duplicated, the two strands
separate from one another and each serves as a template for the synthesis of a new strand,
with A’s opposite T’s and G’s opposite C’s, virtually guaranteeing
that the newly formed strand will be identical to the ones they replace, and 3) although
this process is almost perfect, mutations sometimes happen that change the nucleotide
sequence.
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DNA molecules typically consist of millions
of nucleotide pairs and are located in cell nuclei where they store the hereditary
information of the organism. In the simplest bacteria and viruses, thousands or even
millions of nucleotide pairs are required to encode the information which defines that
microorganism. In more complex organisms, such as birds and mammals, nucleotide pairs are
measured in the billions. In humans, for example, there are about three billion nucleotide
pairs in the egg or sperm contributed by each parent at the time of conception, and about
six billion pairs in the fertilized egg.
In bacteria and viruses, all DNA is present
as a single molecule. In higher organisms, the much greater quantity of DNA is subdivided
into smaller molecules that are contained in the chromosomes. In the DNA of an
average human chromosome, for example, there are 130 million nucleotide pairs. Chromosomes
structure and compress DNA molecules. If the total of 6 billion nucleotides in each cell
of a human were all present in a single molecule, that molecule would be over two meters
long.
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Genes Genes are sub-divisional elements of
the chromosome that define and transmit inheritable characteristics. Theoretically, there
is a gene for every inheritable trait, and thus an organism or individual resulting from
the union of two reproductive cells receives a set of genes from each of its parents. A
gene may consist of several thousand to tens of thousands or more DNA nucleotide pairs
(sometimes referred to as base pairs).
Genes are distributed along the DNA
molecules, often separated by long stretches of DNA of little or no known function. It has
been estimated that as little as 5% or less of the DNA in higher organisms has a genetic
function. That is, only a relatively small portion contains sequences that define the
enzymes and other proteins responsible for the life and characteristics of an animal or
plant. Much of the remaining 95% consists of sequences involved in replicating the DNA, in
regulating the activity of the genetic portion, and perhaps, even "junk"
sequences that are no more than relics reflecting the history of the species but which
have long since lost their function.
Thus, the DNA of even the simplest organism
is a complex sequence of nucleotide pairs arranged in an order that essentially defines
the species. Even within the species, there is diversity in the ordering of the
nucleotides that make each individual unique. This diversity in nucleotide sequence
provides the basis for much of the DNA-based science today.
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The technology of identifying individuals
on the basis of nucleotide sequences is referred to as DNA typing. This method is
based upon the fact that no two individuals are exactly alike with respect to their DNA.
The degree of genetic difference that exists between any two individuals depends on their
relationship to one another: identical twins are so similar that it would be difficult to
find differences in their DNA; other siblings would share many features of their DNA, but
would be much more easily identified. Unrelated members of the same population would be
even more dissimilar, and animals from populations that have been isolated from one
another for long periods of time are likely to be most dissimilar. Thus, the issue is not
whether or not differences are present in the DNA of animals of a particular species, but
whether or not technology is capable of finding and exploiting those differences.
In the last few years, new developments
have been made in the science of DNA typing, based on the invention of new equipment,
methods of study, and on the discovery of previously unknown features of the DNA itself.
Technical developments such as:
- Ability to clone DNA of higher organisms in bacteria,
- Mechanization in cloning specific DNA sequences, and,
- Determination of nucleotide sequence in the cloned
fragments.
These developments now enable scientists to
find DNA sequences that differ between virtually any two individuals, and to use those
sequences to identify the animal from which the sequences were obtained. The consequence
of this technology to animal breeders is profound. Even among species that show little
outward difference, it is now possible to identify specific animals, make sex
determinations, and to detect the presence of bacteria/viruses (gene probes).
Recently, a powerful new technique for DNA
analysis has been discovered which relies on the differences in length of short regions
along DNA molecules called "microsatellites" or STR’s [Short Tandem
Repeats]. A microsatellite is a simple DNA sequence that is repeated several times at
various points in the organism’s DNA. The number of repeat units present in a
particular microsatellite is often variable. For example, a STR at one point on a DNA
molecule may have eight repeats of the sequence ATTG in one case and ten repeats at the
same point in another case. There may be six or eight different repeat unit lengths in
that specific location in the population as a whole. In higher organisms, there are
hundreds of thousands of different microsatellite locations in the DNA and the number of
repeat units at any particular location is often highly variable. These two features make
them ideal for a variety of genetic applications since the high degree of variability
essentially provides a fingerprint or very specific marker by which the trait or
gene location may be tagged.
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Microsatellites/markers are found in all
species studied except bacteria. They can be used in a wide variety of applications
including pedigree analysis, identification of individual animals, determining parentage,
and selective breeding to minimize effects of inbreeding. They can also be used as markers
to indicate the presence of genes that are otherwise difficult to detect, and as markers
for quantitative traits such as disease resistance or growth rate. In shrimp culture, a
good example can be found with Taura Syndrome Virus (TSV), the most devastating shrimp
disease of white shrimp in recent years. We find this disease to be manifested as a
discontinuous trait, since some shrimp survive and others don’t. DNA typing will
reveal differences between those animals with resistance to TSV and those that are less
resistant. Computerized digital comparisons of DNA typing from a sample population against
a reference species library (of markers) reveals the variations involved, allowing
selection of only those broodstock animals with desired traits. Such technology will
revolutionize shrimp aquaculture and promote overall industry growth through
domestication, greater production efficiency, and increased profits.
Technically, DNA typing is done using a
process involving Polymerase Chain Reaction or PCR. This is a method for multiplying DNA
fragments that may be found in a single cell and producing enough of it for analysis or
assessment of the fragment for use as a location marker.
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