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2 High‐throughput Genotyping Platforms
Sandhya Sharma1, Kuldeep Kumar2, Kishor Tribhuvan3, Rita1, Sandeep Kumar4, Priyanka Jain1, Swati Saxena1, Joshita Vijayan1, Harsha Srivastava1, and Kishor Gaikwad1
1 ICAR – National Institute for Biotechnology, New Delhi, India
2 ICAR – Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India
3 ICAR – Indian Institute of Agricultural Biotechnology, Ranchi, Jharkand, India
4 Xcelris Lab Pvt Ltd., Ahmedabad, Gujarat, India
2.1 Introduction
Single‐nucleotide polymorphisms (SNPs) are the most common genetic variations present in the genome. These are the genetic loci where variation exists for a single nucleotide. Even for variation to be called as SNPs, it should be present in more than 1% of the individuals within a population. SNPs may be present as change or InDel of a single base which has originated mainly due to mutation or replication error. SNPs may fall within coding, noncoding as well as intergenic regions. Due to degeneracy of the genetic code, it is not necessary that SNPs within a coding region will change the amino acid sequence of the protein. A synonymous (often silent mutation) SNP is one in which both types of alleles result in the same polypeptide sequence, whereas nonsynonymous SNPs create a distinct polypeptide sequence. A nonsynonymous change further may be missense or nonsense. The missense mutation results in a different amino acid, while a nonsense mutation will result in a premature stop codon, ultimately forming a truncated peptide. SNPs that are not in protein‐coding regions may still affect the gene splicing, transcription factor binding resulting in a change in expression dynamics of the gene. As SNPs can occur throughout the genome, they offer a good advantage of genome‐wide coverage and higher frequency which assist high‐resolution mapping compared to other marker systems. Automated genotyping techniques, high reproducibility, easy cost of genotyping, presence within a genic region, and gel‐free methodology are some advantages of SNP which other markers lack. Besides several advantages, SNPs also offer certain disadvantages, such as detection of SNPs mostly requires sequencing of the DNA, high‐throughput analysis is required in postsequencing steps, also the SNP‐based genotyping
