Lorenc, Michał 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 (3). pp. 370-382. ISSN 2079-7737 (Print), 2079-7737 (Online) (doi:10.3390/biology1020370)

Preview

PDF (Publisher's PDF - Open Access) 17915 VISENDI_Discovery_of_Single_Nucleotide_Polymorphisms_in_Complex_Genomes_2012.pdf - Published Version Available under License Creative Commons Attribution Non-commercial Share Alike. Download (154kB) | Preview

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.

Item Type:	Article
Uncontrolled Keywords:	single nucleotide polymorphisms; wheat; autoSNP; genome diversity; genotyping by sequencing; haplotype
Subjects:	S Agriculture > S Agriculture (General)
Faculty / School / Research Centre / Research Group:	Faculty of Engineering & Science Faculty of Engineering & Science > Natural Resources Institute Faculty of Engineering & Science > Natural Resources Institute > Agriculture, Health & Environment Department Faculty of Engineering & Science > Natural Resources Institute > Molecular Virology and Entomology Research Group
Last Modified:	03 Nov 2017 12:15
URI:	http://gala.gre.ac.uk/id/eprint/17915

Actions (login required)

View Item

Downloads