Discovery of single nucleotide polymorphisms in complex genomes using SGSautoSNP

Lorenc, Michal T., Hayashi, Satomi, Stiller, Jiri, Lee, Hong, Manoli, Sahana, Ruperao, Pradeep, Visendi, Paul, Berkman, Paul J., Lai, Kaitao, Batley, Jacqueline and Edwards, David (2012) Discovery of single nucleotide polymorphisms in complex genomes using SGSautoSNP. Biology, 1 2: 370-382. doi:10.3390/biology1020370

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Author Lorenc, Michal T.
Hayashi, Satomi
Stiller, Jiri
Lee, Hong
Manoli, Sahana
Ruperao, Pradeep
Visendi, Paul
Berkman, Paul J.
Lai, Kaitao
Batley, Jacqueline
Edwards, David
Title Discovery of single nucleotide polymorphisms in complex genomes using SGSautoSNP
Journal name Biology   Check publisher's open access policy
ISSN 2079-7737
Publication date 2012-09
Sub-type Article (original research)
DOI 10.3390/biology1020370
Open Access Status DOI
Volume 1
Issue 2
Start page 370
End page 382
Total pages 13
Place of publication Basel, Switzerland
Publisher MDPI
Collection year 2013
Language eng
Abstract Single nucleotide polymorphisms (SNPs) are becoming the dominant form of molecular marker for genetic and genomic analysis. The advances in second generation DNA sequencing provide opportunities to identify very large numbers of SNPs in a range of species. However, SNP identification remains a challenge for large and polyploid genomes due to their size and complexity. We have developed a pipeline for the robust identification of SNPs in large and complex genomes using Illumina second generation DNA sequence data and demonstrated this by the discovery of SNPs in the hexaploid wheat genome. We have developed a SNP discovery pipeline called SGSautoSNP (Second-Generation Sequencing AutoSNP) and applied this to discover more than 800,000 SNPs between four hexaploid wheat cultivars across chromosomes 7A, 7B and 7D. All SNPs are presented for download and viewing within a public GBrowse database. Validation suggests an accuracy of greater than 93% of SNPs represent polymorphisms between wheat cultivars and hence are valuable for detailed diversity analysis, marker assisted selection and genotyping by sequencing. The pipeline produces output in GFF3, VCF, Flapjack or Illumina Infinium design format for further genotyping diverse populations. As well as providing an unprecedented resource for wheat diversity analysis, the method establishes a foundation for high resolution SNP discovery in other large and complex genomes.
Keyword Single nucleotide polymorphisms
Genome diversity
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Centre for Integrative Legume Research Publications
School of Agriculture and Food Sciences
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Created: Fri, 08 Mar 2013, 15:53:26 EST by Dr Dave Edwards on behalf of School of Agriculture and Food Sciences