Kaix
05-03-2006, 10:33 AM
DNA testing for ornamental fish
In economically important animals and food fish species (e.g. pig, cattle, sheep, salmon, tilapia and rainbow trout), DNA testing techniques have also been used for identifying superior animals which grow faster, produce high-quality products, show strong disease resistance and other preferred phenotypes (2). However, the application of DNA testing technology in the ornamental fish industry is just beginning. Here I briefly introduce the very complicated subject of DNA testing techniques and their applications in the ornamental fish industry.
What can DNA testing do for ornamental fish industry?
1. Identification of species, varieties and interesting traits
Although traditional morphological taxonomy has been successful in distinguishing species/varieties for many fish groups, this approach can be problematic due to genetic and phenotypic variation in characters used for identification. Furthermore, successful use of many morphologically-based keys requires significant expertise and many keys are specific to certain genders or life stages. DNA testing provides a solution to these limitations in species/varieties identification.
For example, the dragon fish is one of the most expensive ornamental fish in the word. There are three natural colour varieties, namely the green, golden and red. However, the colour of young fish (up to several months of age) is hardly distinguishable. Temasek Life Sciences Lab (Singapore) has developed a PCR-based DNA testing method for differentiating golden from red and green dragon fish. On two per cent agarose gel (6), individuals showing one band are golden; two bands are shown either by green or red dragon fish. The accuracy of DNA testing is 100 per cent. The DNA testing procedure lasts ca. 4 hours. However, the DNA testing method cannot differentiate between green and red individuals.
For identification of species, the DNA sequence in the COX1 gene of the maternally-inherited mtDNA is a good choice. Currently, an international consortium is trying to barcode most of the species on earth using DNA sequences. DNA testing for identification of interesting traits is very complicated, but it is feasible. With the large number of DNA markers, and high-density linkage maps, DNA markers can be identified and used for identifying interesting traits. However, the development of a large number of DNA markers and construction of high-density linkage maps is very costly.
2. Identification of sex
Although many ornamental fish species have been raised in captivity for many years, experienced farmers are still unable to ascertain the gender of each fish in some of these species. This is a major obstacle in any selective breeding programmes for ornamental fish. Temasek Life Sciences Lab has developed a number of DNA makers, which can be used for identifying sex in several fish species. One PCR-based DNA testing method was developed for identifying the sex of green dragon fish (the efficiency of the method is 82.6 per cent) but the sex-associated DNA marker did not work in the more expensive golden or red varieties. Molecular sexing in fish is much more difficult than in mammals and, so far, no single universal sex-associated DNA marker has been identified for any fish species, presumably due to the complex nature of sex determination systems in fish.
3. Estimation of genetic diversity
Genetic diversity is the basis of genetic improvement. Experiences from livestock breeding and food fish breeding clearly show that loss of genetic diversity and inbreeding cause a reduction in production and low fitness. In ornamental fish species, their genetic diversity is difficult to identify without DNA testing methods, due to the fact that fish produce a lot of eggs, are difficult to tag, and pedigree information is (usually) either not available or incomplete. For example, right now, dragon fish farmers place 20 to 30 fish into the ponds without knowing the relationship of fish, and hope to see some babies every few months.
With a tiny scale from each fish and polymorphic DNA markers (e.g. microsatellites (7)), DNA testing can be easily conducted to give information about the relationship among fish, their genetic diversity and inbreeding. With this information, farmers can properly design mating plans to avoid inbreeding, maintain high genetic diversity and produce superior fish over other farmers who do not have such information. The Temasek Life Sciences Lab has developed a number of polymorphic DNA markers (microsatellites, mtDNA, RAPD, AFLP () for ornamental fish species (dragon fish, guppy, pufferfish, swordtail and koi). It has already conducted DNA testing on captive-bred dragon fish populations for some fish farms.
4. Reconstruction of pedigree
One major problem in conducting selective breeding programmes in fish is the maintenance of pedigree information. Offspring from different families have to be isolated and reared under the same environmental conditions until they are big enough to be tagged. This traditional approach is not only space-intensive, but also labour-intensive.
Genetic profiles from polymorphic DNA markers would allow retrospective assignment of offspring to family groups (their parents) even when all offspring are reared in same place.
Experience in food fish has shown that using one set of 8-18 polymorphic DNA markers, all offspring can be assigned to their parents with 99.999 per cent certainty. The reconstructed pedigree information can then be used for selective breeding, setting up proper mating among individuals to produce superior offspring.
5. Identification of individual fish: Genetic ID card
Traditionally, fish can be tagged by an electrical tag (e.g. PIT tag) containing a digital number. However, the electrical tag can only be implanted in relatively large fish. Furthermore, it is easily lost, removed and exchanged. Therefore, it is not the most reliable method for tagging fish.
Cells/tissues of each fish naturally contain a unique ‘fingerprint' embedded in its DNA, which could be used as the basis for labelling each individual. The same DNA in each fish is maintained throughout its whole lifespan and cannot be removed or changed. Therefore, by selecting the most variable parts of the DNA, it is possible to differentiate each individual with certainty.
One of the most variable parts of DNA is a special class of repetitive DNA called a microsatellite. Microsatellites consist of variable numbers of tandem repeats, ranging from two to six base pairs (9) in length, which are distributed evenly and widely in the genomes (10) of most vertebrate species. As microsatellite patterns are highly polymorphic (11) between individuals within a species, they can be used to generate genetic profiles or ‘fingerprints' unique to the individual animal, using PCR technology and high-resolution gel electrophoresis or capillary electrophoresis (12). A genetic ID card looks like a human ID card, but contains details about genetic information. The Temasek Life Sciences Lab is developing a genetic card for expensive ornamental fish species (e.g. dragon fish).
What are the benefits of DNA testing to the ornamental fish industry?
• Allows for knowledge-based decisions to be made for selective breeding programmes
• Increases performances of fish to ensure product quality
• Increases production efficiency to increase return on investment
• Accelerates development of new species, new strains and new varieties
• Protects intellectual property
• Conserves precious genetic materials more effectively
How much does a DNA testing cost ?
The cost of DNA testing could vary from S$8 to S$200 depending on how many DNA markers are used and how high the certainty of test is.
In economically important animals and food fish species (e.g. pig, cattle, sheep, salmon, tilapia and rainbow trout), DNA testing techniques have also been used for identifying superior animals which grow faster, produce high-quality products, show strong disease resistance and other preferred phenotypes (2). However, the application of DNA testing technology in the ornamental fish industry is just beginning. Here I briefly introduce the very complicated subject of DNA testing techniques and their applications in the ornamental fish industry.
What can DNA testing do for ornamental fish industry?
1. Identification of species, varieties and interesting traits
Although traditional morphological taxonomy has been successful in distinguishing species/varieties for many fish groups, this approach can be problematic due to genetic and phenotypic variation in characters used for identification. Furthermore, successful use of many morphologically-based keys requires significant expertise and many keys are specific to certain genders or life stages. DNA testing provides a solution to these limitations in species/varieties identification.
For example, the dragon fish is one of the most expensive ornamental fish in the word. There are three natural colour varieties, namely the green, golden and red. However, the colour of young fish (up to several months of age) is hardly distinguishable. Temasek Life Sciences Lab (Singapore) has developed a PCR-based DNA testing method for differentiating golden from red and green dragon fish. On two per cent agarose gel (6), individuals showing one band are golden; two bands are shown either by green or red dragon fish. The accuracy of DNA testing is 100 per cent. The DNA testing procedure lasts ca. 4 hours. However, the DNA testing method cannot differentiate between green and red individuals.
For identification of species, the DNA sequence in the COX1 gene of the maternally-inherited mtDNA is a good choice. Currently, an international consortium is trying to barcode most of the species on earth using DNA sequences. DNA testing for identification of interesting traits is very complicated, but it is feasible. With the large number of DNA markers, and high-density linkage maps, DNA markers can be identified and used for identifying interesting traits. However, the development of a large number of DNA markers and construction of high-density linkage maps is very costly.
2. Identification of sex
Although many ornamental fish species have been raised in captivity for many years, experienced farmers are still unable to ascertain the gender of each fish in some of these species. This is a major obstacle in any selective breeding programmes for ornamental fish. Temasek Life Sciences Lab has developed a number of DNA makers, which can be used for identifying sex in several fish species. One PCR-based DNA testing method was developed for identifying the sex of green dragon fish (the efficiency of the method is 82.6 per cent) but the sex-associated DNA marker did not work in the more expensive golden or red varieties. Molecular sexing in fish is much more difficult than in mammals and, so far, no single universal sex-associated DNA marker has been identified for any fish species, presumably due to the complex nature of sex determination systems in fish.
3. Estimation of genetic diversity
Genetic diversity is the basis of genetic improvement. Experiences from livestock breeding and food fish breeding clearly show that loss of genetic diversity and inbreeding cause a reduction in production and low fitness. In ornamental fish species, their genetic diversity is difficult to identify without DNA testing methods, due to the fact that fish produce a lot of eggs, are difficult to tag, and pedigree information is (usually) either not available or incomplete. For example, right now, dragon fish farmers place 20 to 30 fish into the ponds without knowing the relationship of fish, and hope to see some babies every few months.
With a tiny scale from each fish and polymorphic DNA markers (e.g. microsatellites (7)), DNA testing can be easily conducted to give information about the relationship among fish, their genetic diversity and inbreeding. With this information, farmers can properly design mating plans to avoid inbreeding, maintain high genetic diversity and produce superior fish over other farmers who do not have such information. The Temasek Life Sciences Lab has developed a number of polymorphic DNA markers (microsatellites, mtDNA, RAPD, AFLP () for ornamental fish species (dragon fish, guppy, pufferfish, swordtail and koi). It has already conducted DNA testing on captive-bred dragon fish populations for some fish farms.
4. Reconstruction of pedigree
One major problem in conducting selective breeding programmes in fish is the maintenance of pedigree information. Offspring from different families have to be isolated and reared under the same environmental conditions until they are big enough to be tagged. This traditional approach is not only space-intensive, but also labour-intensive.
Genetic profiles from polymorphic DNA markers would allow retrospective assignment of offspring to family groups (their parents) even when all offspring are reared in same place.
Experience in food fish has shown that using one set of 8-18 polymorphic DNA markers, all offspring can be assigned to their parents with 99.999 per cent certainty. The reconstructed pedigree information can then be used for selective breeding, setting up proper mating among individuals to produce superior offspring.
5. Identification of individual fish: Genetic ID card
Traditionally, fish can be tagged by an electrical tag (e.g. PIT tag) containing a digital number. However, the electrical tag can only be implanted in relatively large fish. Furthermore, it is easily lost, removed and exchanged. Therefore, it is not the most reliable method for tagging fish.
Cells/tissues of each fish naturally contain a unique ‘fingerprint' embedded in its DNA, which could be used as the basis for labelling each individual. The same DNA in each fish is maintained throughout its whole lifespan and cannot be removed or changed. Therefore, by selecting the most variable parts of the DNA, it is possible to differentiate each individual with certainty.
One of the most variable parts of DNA is a special class of repetitive DNA called a microsatellite. Microsatellites consist of variable numbers of tandem repeats, ranging from two to six base pairs (9) in length, which are distributed evenly and widely in the genomes (10) of most vertebrate species. As microsatellite patterns are highly polymorphic (11) between individuals within a species, they can be used to generate genetic profiles or ‘fingerprints' unique to the individual animal, using PCR technology and high-resolution gel electrophoresis or capillary electrophoresis (12). A genetic ID card looks like a human ID card, but contains details about genetic information. The Temasek Life Sciences Lab is developing a genetic card for expensive ornamental fish species (e.g. dragon fish).
What are the benefits of DNA testing to the ornamental fish industry?
• Allows for knowledge-based decisions to be made for selective breeding programmes
• Increases performances of fish to ensure product quality
• Increases production efficiency to increase return on investment
• Accelerates development of new species, new strains and new varieties
• Protects intellectual property
• Conserves precious genetic materials more effectively
How much does a DNA testing cost ?
The cost of DNA testing could vary from S$8 to S$200 depending on how many DNA markers are used and how high the certainty of test is.