Use of biotechnology in characterization of animal biodiversity.
Genetic uniqueness of populations is measured by the relative genetic distances of such populations from each other. Polymorphism in gene products such as enzymes, blood group systems and leukocyte antigens, traditionally used for measuring genetic distance, is being rapidly replaced by polymorphism at the level of DNA, both nuclear and mitochondrial as a source of information for the estimation of genetic distances. The first DNA polymorphism to be used widely for genome characterization and analysis is the restriction fragment length polymorphism (RFLP), which detects variations ranging from gross rearrangements to single base changes. Minisatellite sequences of 60 or so bases repeated many hundreds or thousands of times at one unique locus within the genome are used to generate DNA fingerprints typical of individuals within species. Microsatellite repeats of simple sequences, the commonest being di-nucleotide repeats, are abundant in genomes of all higher organisms, including livestock.
Polymorphism of microsatellites takes the form of variation in the number of repeats at any given locus, and is generally revealed as fragment length variation in the products of polymerase chain reaction (PCR) amplification of genomic DNA using primers flanking the chosen repeat sequence and specific for a given locus. Ease of identification and of sequence determination and need for only small amounts of DNA, are some of the advantages of microsatellites. Additionally, because microsatellite polymorphism can be described numerically, they lend themselves to computerized data handling and analyses. Microsatellites can be used in non-PCR systems in a way similar to minisatellite probes. Microsatellite based data have helped in assessment of both between as well as within breed diversity and can predict the population bottlenecks and inbreeding levels, so it can be a valuable tool in biodiversity analysis.
The genetic characterization using microsatellite (simple short tandem repeat sequences) located in non coding regions of genomic DNA were used and sufficient data have been generated on different livestock and poultry breeds at the NBAGR and other laboratories in the country. This data should be used to know
l Genetic distinctness of breed/population in study
l Inbreeding level in the population
l Population bottleneck in the past
l Evolutionary pattern of the breeds or populations
l Genetic endangerment level
Complete sequencing of the genome is the ultimate form of genetic characterization. Sequencing has traditionally been expensive and laborious, but with the advent of automated sequencing this is changing rapidly. However, sequencing is unlikely to be used as a technique of choice for genetic characterization. A new marker type, single nucleotide polymorphism (SNP), is now on the scene and has gained high popularity, even though it is only a bi-allelic type of marker. The continued development of technology including new high throughput methods, for example those being applied to single nucleotide polymorphisms, will change the ease with which current questions can be answered as well as enable new analyses that are presently impossible to undertake. The increasing popularity of SNPs in recent years has been phenomenal because the recent SNP concept has basically arisen from the need of very high density genetic markers for the studies of multifactorial traits in farm animals.
In DNA-based selection the knowledge of which DNA sequences are associated with improvement in a given trait is required and selection is focused on those known DNA “markers” to make genetic improvement in the trait. Recently scientists have started to identify regions of DNA that influence these production traits. The molecular techniques are now being used to find differences in the sequence of the nucleotide base pairs in these regions. Tests were developed to identify these subtle differences in the DNA. This has allowed for the development of genetic markers which can be used to identify whether an animal is carrying a segment of DNA that is positively or negatively associated with the trait of interest.