Analysis of SSR and SNP markers

Abstract The advent of innovative next-generation sequencing (NGS) techniques has allowed the huge generation of a large amount of sequence information in a short time span, which is pocket friendly too; sequencing the genomes and transcriptomes of reference and nonreference plants has become much easier. The sequencing outcomes have been successfully utilized for sequence-based marker development. In this chapter, we discuss the two most popular codominant DNA markers namely microsatellite [simple sequence repeats (SSRs)] and single-nucleotide polymorphism (SNP). SSRs are popular due to their hypervariability and multiallelic nature, while SNP is a biallelic and most abundant type of marker. This chapter covers the approaches on sequence data generation, data mining, and general pipelines used toward downstream processing of sequence data for SSR marker and high-quality SNPs’ identification and their consecutive usages.