Skim-based genotyping by sequencing

Golicz, Agnieszka A., Bayer, Philipp E. and Edwards, David (2015) Skim-based genotyping by sequencing. Methods in Molecular Biology, 1245 257-270. doi:10.1007/978-1-4939-1966-6_19


Author Golicz, Agnieszka A.
Bayer, Philipp E.
Edwards, David
Title Skim-based genotyping by sequencing
Journal name Methods in Molecular Biology   Check publisher's open access policy
ISSN 1064-3745
1940-6029
ISBN 9781493919659
9781493919666
Publication date 2015-01-01
Sub-type Article (original research)
DOI 10.1007/978-1-4939-1966-6_19
Open Access Status Not Open Access
Volume 1245
Start page 257
End page 270
Total pages 14
Place of publication New York, NY, United States
Publisher Humana Press
Language eng
Formatted abstract
Genotyping by sequencing (GBS) is a relatively new method used to determine the differences in the genetic makeup of individuals. Its novelty stems from a combination of two already available methods: genotyping and next-generation sequencing. Depending on the individual study design GBS protocols can take multiple forms, however most share a sequence of core steps that have to be undertaken. These include: sequencing of the DNA from the individuals of interest (usually two parents of a mapping population and their progeny), mapping of the sequencing reads to the reference sequence, SNP calling and filtering, SNP genotyping and imputation, followed by haplotype identification and downstream analysis. GBS has a range of applications from general marker discovery, haplotype identification, and recombination characterization to quantitative trait locus (QTL) analysis, genome-wide association studies (GWAS), and genomic selection (GS). It has already been applied to a range of plant species including: rice, maize, artichoke, and Arabidopsis thaliana. It is a promising approach which is likely to provide new and important insights into plant biology.
Keyword GBS
Genotyping
Haplotype identification
Imputation
Markers
Recombination
SNP calling
SNPs
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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