Bioinformatics: Identifi cation of markers from Next-Generation sequence data

Ruperao, Pradeep and Edwards, David (2015) Bioinformatics: Identifi cation of markers from Next-Generation sequence data. Methods in Molecular Biology, 1245 29-47. doi:10.1007/978-1-4939-1966-6_3


Author Ruperao, Pradeep
Edwards, David
Title Bioinformatics: Identifi cation of markers from Next-Generation sequence data
Journal name Methods in Molecular Biology   Check publisher's open access policy
ISSN 1064-3745
1940-6029
ISBN 9781493919659
Publication date 2015-01-01
Sub-type Article (original research)
DOI 10.1007/978-1-4939-1966-6_3
Open Access Status Not Open Access
Volume 1245
Start page 29
End page 47
Total pages 19
Editor Jacqueline Batley
Place of publication New York, NY, United States
Publisher Humana Press
Collection year 2016
Language eng
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.
Keyword Assembly tools
Genetic markers
Mapping tools
Microsatellites
Next-generation sequencing (NGS)
SGSautoSNP
SNPs
SSRPrimerII
SSRs
Q-Index Code CX
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Non HERDC
School of Agriculture and Food Sciences
 
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