Review on application of SNP detection methods in animal research

Abstract: Single nucleotide polymorphism (SNP) is just a single base change in a DNA sequence, including transition, transversion, insertion or deletion of one base, and it is usual with an alternative of two possible nucleotides at a given position. It is also considered as the least frequent mutation in the biological genome, with the frequency of 1% or greater, and the mutation is widespread in the genome. SNP is usually bi-allelic mutation, which is liable to high-throughput automated analysis and genotyping. In addition, SNP is relative genetically stable than other mutations, such as simple sequence repeat (SSR), estimated to be between 1×10-9 and 5×10-9 per nucleotide per year at neutral positions in mammals. SNP is considered as the third generation of molecular marker, and it is very popular in both overseas and domestic scholars in many fields of research. In recent years, the methods for SNP quantification and genotyping are rapidly developed and so many new analytical techniques are renewed. The first type of genotyping and quantification technique is sequencing, such as Sanger sequencing, next generation sequencing and the third-generation sequencing. The sequencing technique can directly get the sequence information of the target fragment by comparing between sequences each other, and the detection rate can be reached to 100%. What's more, the information of mutation type and location can be clear at the same time. The allele-specific enzymatic techniques and allele-specific hybridization-based techniques are the second type of genotyping and quantification techniques. These techniques utilize the characteristics of subtle difference in thermal stability between perfectly matched and one-base mismatched in the sequences to design different detective methods and adopt corresponding detectors. The types of method include endonuclease digestion technique, oligo nucleotide ligation assay technique, allele-specific PCR technique, dynamic allele specific hybridization technique, Taqman, DNA chip technique and so on. These approaches have realized the high throughput beyond doubt, however, due to the enzymatic and hybridization theories, in order to achieve good results, the optimal condition of PCR reaction and the carefully designed probes and hybridisation protocols are of great importance. Besides the above SNP genotyping and quantification techniques, the chromatography and mass spectrometry techniques are also employed in the field, such as denaturing high performance liquid chromatograph and MALDI-TOF-MS. The two methods are all ultra-high-throughput screening and high efficient SNP detection methods. But they are too expensive to be widely used by most researchers. Although each technique is not perfect, researchers can choose one or two suitable methods to solve their scientific problems. With the rapid development in SNP typing and improvement of relevant databases, SNP has been extensively employed in genetic studies, such as genetic maps construction, population genetics structural analysis, genetic association studies, breed and individual identification and product traceability. We hope that this article will provide some references for the SNP genotyping and quantification techniques towards to the more robust, flexible and low-cost for further development.