Research & Development

Single Nucleotide Polymorphisms (SNPs) Genotyping in Plant Biotechnology

Mankind, in his quest to improve food quality, has been looking for various forms of crop. Plant breeders and farmers have created new varieties through traditional plant breeding in which the selection and evaluation of the new varieties can take several years to achieve. With the discovery of DNA, a new area of modern plant biotechnology began through the development of molecular marker systems which facilitates the selection and evaluation process greatly. SNPs, the most prevalent kind of DNA sequence variation across alleles, have been discovered in several plant species for recent improvements in genome technology. SNPs were discovered and used to advance the understanding of genetic variation and crop development which has hastened the natural breeding process.
A single nucleotide polymorphisms, SNPs, is a variation at a single position in a DNA sequence (A, C, G, and T) among individuals. If more than 1% of a population does not carry the same nucleotide at a specific position in the DNA sequence, then this variation can be classified as an SNP. If an SNP occurs within a gene, then the gene is described as having more than one allele.

The detection technologies of SNP have evolved with the discovery of new techniques on reporter systems, fluorescent probes, development of enzymatic assays, use of highly sensitive instruments, and mostly the accelerated high-throughput sequencing technology and bioinformatics tool. The techniques for detection can be divided into two main groups: in vitro and in silico techniques.
The application of SNPs on genetic diversity is essential for illuminating the relationships between varieties. SNPs can be used to discover new genes and their functions by affecting gene expression, transcriptional, and translational promoter activities which are responsible for phenotypic variations such as the color of different plants or fruits, fruit size, ripening, flowering time adaptation, crop quality, grain yield, or tolerance to various abiotic and biotic factors. Rapid progress in sequence technologies, including SNP genotyping and genome sequencing, has given powerful approaches to mapping complex features and then identifying genes which is an important advantage in creating experimental populations of germplasm collections in a short time. The most obvious advantages of SNP markers are that they are flexible and fast and provide data management convenience. As the most common type of SNPs can also be specified at the genome-wide locus, which can reveal the selection of variants at the target locus.
The development and advancement of SNP technology are extensive for both evolutionary and molecular geneticists, plant breeders, and industry and will be valuable for us to understand and develop crop species. The integration of genomic technologies with traditional breeding can have a big impact in dealing with current and future environmental challenges more effectively.

Mohsina Afreen
Associate Scientist, ASRBC.