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Plant Genotyping pp 29–47Cite as

Bioinformatics: Identification of Markers from Next-Generation Sequence Data

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1245))

Abstract

With the advent of sequencing technology, next-generation sequencing (NGS) technology has dramatically revolutionized plant genomics. NGS technology combined with new software tools enables the discovery, validation, and assessment of genetic markers on a large scale. Among different markers systems, simple sequence repeats (SSRs) and Single nucleotide polymorphisms (SNPs) are the markers of choice for genetics and plant breeding. SSR markers have been a choice for large-scale characterization of germplasm collections, construction of genetic maps, and QTL identification. Similarly, SNPs are the most abundant genetic variations with higher frequencies throughout the genome of plant species. This chapter discusses various tools available for genome assembly and widely focuses on SSR and SNP marker discovery.

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Authors and Affiliations

  1. School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia

    Pradeep Ruperao & David Edwards

  2. Australian Centre for Plant Functional Genomics, University of Queensland, Brisbane, QLD, Australia

    Pradeep Ruperao & David Edwards

  3. School of Plant Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia

    David Edwards

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  1. Pradeep Ruperao
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  1. School of Plant Biology, The University of Western Australia, Crawley, West Australia, Australia

    Jacqueline Batley

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Ruperao, P., Edwards, D. (2015). Bioinformatics: Identification of Markers from Next-Generation Sequence Data. In: Batley, J. (eds) Plant Genotyping. Methods in Molecular Biology, vol 1245. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1966-6_3

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  • DOI: https://doi.org/10.1007/978-1-4939-1966-6_3

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-1965-9

  • Online ISBN: 978-1-4939-1966-6

  • eBook Packages: Springer Protocols

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