ABSTRACT
The phenotype traits of livestock are determined by the genetic variation with environmental variation of individual animals. In the past, the classification of breed was depending on morphological characteristics to identify breed. However, in recent years, various genetic markers can be analyzed to identify different breeds and individual animals. These molecular genetic markers can be used to assess the genetic diversity as well as tracking the species origin and identification. Recently, a genome sequencing technology can be rapidly and accurately confirmed the various type of genetic markers in the entire genome area. Of these, developed SNP markers and the rapidly evolving SNP array technology are increasingly replacing genetic diversity analysis using microsatellite markers. Therefore, this review discussed the basic information for developing various molecular genetic markers and their use in genetic diversity studies of livestock animals.
Introduction
In general, many livestock breed present today have pass through the centuries of natural and human selection. Thus, different breeds were adopted to different environment condition and production criteria. As the results, livestock animals have different phenotypic characteristics that distinguish them from other subgroups in the same species; however, there are difficulties and limitations in distinguishing between different individuals and groups using their basic morphology or biological samples such as blood, tissue, and secretions. This problem has resolved by the genetic classification of individuals of different phenotypes by discovering their DNA profile and genomic level variation (Syvanen, 2001). Particularly, in mitochondrial DNA (mtDNA) and nuclear DNA. In fact, these patterns of genetic variation have various forms such as single nucleotide polymorphism (SNP), insertion and deletion (indel), simple tandem repeat (STR), copy number variation (CNV).
SNP markers versus MS markers
Despite the fact that the MS markers are high polymorphic, the MS typing technique is becoming limited use. Especially, because of the technical limit, the labor intensive and the cost of the experiment. One of the technical problems with MS markers is the inconsistency of allele sizes, which makes it difficult to contrast the results generated from various laboratories (Vignal et al., 2002). The reason for the different size of alleles is that allele sizes are measured differently depending on the condition of PCR reaction. For an example; Taq polymerase has synthesized different adenine number at the 3’ end of the PCR fragment, depending on the PCR amplification conditions (Brownstein et al., 1996). These additional nucleotide sequences lead to incorrect PCR amplification sizes (Ginot et al., 1996).
