SSR genotyping

Abstract

SSR genotyping involves the use of simple sequence repeats (SSRs) as DNA markers. SSRs, also called microsatellites, are a type of repetitive DNA sequence ubiquitous in most plant genomes. SSRs contain repeats of a motif sequence 1-6 bp in length. Due to this structure SSRs frequently undergo mutations, mainly due to DNA polymerase errors, which involve the addition or subtraction of a repeat unit. Hence, SSR sequences are highly polymorphic and may be readily used for detection of allelic variation within populations. SSRs are present within both genic and nongenic regions and are occasionally transcribed, and hence may be identified in expressed sequence tags (ESTs) as well as more commonly in nongenic DNA sequences. SSR genotyping involves the design of DNA-based primers to amplify SSR sequences from extracted genomic DNA, followed by amplification of the SSR repeat region using polymerase chain reaction, and subsequent visualization of the resulting DNA products, usually using gel electrophoresis. These procedures are described in this chapter. SSRs have been one of the most favored molecular markers for plant genotyping in the last 20 years due to their high levels of polymorphism, wide distribution across most plant genomes, and ease of use and will continue to be a useful tool in many species for years to come.