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Microsatellite Markers from Whole Genome and Transcriptomic Sequences

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Bioinformatics in Rice Research

Abstract

Microsatellites (MS) or simple sequence repeats (SSRs) is a DNA sequence set comprising of tandemly repeated motifs. SSRs with codominant inheritance, higher amounts, moderately conservative flanking sequences, and rich polymorphism are commonly distributed throughout the plants and animals’ genome. MS has already been employed in several crop plants for determining their seed lots’ genetic integrity and to evaluate the capacity of plant varieties to defend their intellectual property. Thus, the key objective of this chapter is to include a revised and comprehensive overview of the SSR marker and its applications in various biological domains. Additionally, we have discussed genomic occurrence and the advantage/disadvantages of employing microsatellites as genetic markers in agricultural research.

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Abbreviations

ESTs:

Expressed sequence tags

GNMS:

Genic non-coding microsatellite

InDel:

Insertion-deletion

MAB:

Marker-assisted backcrossing

MAS:

Marker-assisted selection

MFRs:

Microsatellite flanking regions

MS:

Microsatellites

NGS:

Next-generation sequencing

QTL:

Quantitative trait loci

SNP:

Single nucleotide polymorphism

SSRs:

Simple sequence repeats (SSRs)

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Gupta, M.K. et al. (2021). Microsatellite Markers from Whole Genome and Transcriptomic Sequences. In: Gupta, M.K., Behera, L. (eds) Bioinformatics in Rice Research. Springer, Singapore. https://doi.org/10.1007/978-981-16-3993-7_18

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