Abstract
Microsatellites or Single Sequence Repeats (SSRs) are extensively employed in plant genetics studies, using both low and high throughput genotyping approaches. Motivated by the importance of these sequences over the last decades this review aims to address some theoretical aspects of SSRs, including definition, characterization and biological function. The methodologies for the development of SSR loci, genotyping and their applications as molecular markers are also reviewed. Finally, two data surveys are presented. The first was conducted using the main database of Web of Science, prospecting for articles published over the period from 2010 to 2015, resulting in approximately 930 records. The second survey was focused on papers that aimed at SSR marker development, published in the American Journal of Botany's Primer Notes and Protocols in Plant Sciences (over 2013 up to 2015), resulting in a total of 87 publications. This scenario confirms the current relevance of SSRs and indicates their continuous utilization in plant science.
Highlights
Ongoing technological advances in all fields of knowledge mean that we cannot be sure which technologies will survive the impact of innovation, and for how long
Advances in molecular genetics methodology have lead to widespread use of codominant molecular markers, especially Simple Sequence Repeats (SSRs) and, more recently, Single Nucleotide Polymorphisms (SNPs)
In barley and Avena species, SSRs were classified in two types: those with unique sequences on either flank and those intimately associated with retrotransposons and other dispersed repetitive elements
Summary
Ongoing technological advances in all fields of knowledge mean that we cannot be sure which technologies will survive the impact of innovation, and for how long. SSRs have been useful for generating integrated maps for plant species in which full-sib families are used for constructing linkage maps (Garcia et al, 2006; Souza et al, 2013; Pereira et al, 2013), and for combining genetic, physical, and sequence-based maps (Temnykh, 2001), providing breeders and geneticists with a tool to link phenotypic and genotypic variation (see Mammadov et al, 2012; Hayward et al, 2015 for review articles) These markers are enormously useful in studies of population structure, genetic mapping, and evolutionary processes. It is worth noting that a number of SSR search algorithms have been developed, including TRF (Benson, 1999), SSRIT (Temnykh, 2001), MISA (Thiel et al, 2003), SSRFinder (Gao et al, 2003), TROLL (Castelo et al, 2002) and SciRoKo (Kofler et al, 2007)
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