W362 Genotyping-by-sequencing: a Case Study in Barley

Date: Saturday, January 14, 2012
Time: 10:45 AM
Room: Golden West
Yong-Bi Fu , Plant Gene Resources of Canada, Saskatoon, SK, Canada
Next-generation DNA sequencing (NGS) technologies can survey sequence variation on a genome-wide scale, but their utility for crop genetic diversity analysis is poorly known. Many challenges remain in their applications, including sampling complex genomes, identifying single-nucleotide polymorphisms (SNPs), and analyzing missing data. This presentation will illustrate a practical application of the Roche 454 GS FLX Titanium technology in combination with genomic reduction and an advanced bioinformatics tool to analyze the genetic relationships of 16 diverse barley (Hordeum vulgare L.) landraces. A full 454 run generated roughly 1.7 million sequence reads with a total length of 612 Mbp. Application of the computational pipeline called DIAL (de novo identification of alleles) identified 2,578 contigs and 3,980 SNPs. Sanger sequencing of four barley samples confirmed 85 of the 100 selected contigs and 288 of the 620 putative SNPs, and identified 735 new SNPs and 39 new indels. Several diversity analyses revealed the eastern and western division in the barley samples. The division is compatible with those inferred with 156 microsatellite alleles of the same 16 samples and consistent with our current knowledge about cultivated barley. The NGS application not only provides a new informative set of genomic resources for barley research, but also helps to illustrate the feasibility of genotyping-by-sequencing with NGS technologies for crop diversity studies.