Two-Hour Tutorial I |  Two-Hour Tutorial II

Genotyping-by-Sequencing Strategy
for
Genome-wide SNP Discovery and Genotyping

  1. Frank M You1, Sylvie Cloutier1, Ming-Cheng Luo2, Jan Dvorak2
  2. 1Cereal Research Centre, Agriculture and Agri.-Food Canada, Canada
  3. 2Department of Plant Sciences, University of California, Davis, USA

Abstract

With advances of next generation sequencing technology, genotyping-by-sequencing strategy (GBS) has increasingly become a standard genotyping method for small to large genomes. GBS takes advantage of the high throughput and multiplexing capacities of the NGS to produce genotyping information by direct genome sequencing. It is effective to identify genome-wide SNPs. It also has reduced ascertainment bias compared to other genotyping methods. The major objectives of this tutorial are (1) to introduce the basic principles and methods of GBS, (2) to introduce the GBS software pipeline we developed and its applications in plants, (3) to discuss the challenges and critical problems in GBS data analysis, and (4) to demonstrate how to use the pipeline for GBS data analysis from raw Illumina read mapping to the final SNP marker genotyping.

Speakerí»s Short Biography Dr. Frank You is a senior bioinformaticist at Cereal Research Centre, Agriculture and Agri-Food Canada (AAFC), Canada. He earned a BS in agronomy and computer science as well as a MS and Ph.D in plant genetics and breeding with statistical genetics. Since 2001, Dr. You had been a project bioinformaticist at the Department of Plant Sciences, University of California at Davis, and then joined AAFC in 2011. Dr. You has contributed more than 70 peer-reviewed papers in scientific journals, many of which are very top in the field, such as Nature and PNAS. His research interests include plant comparative and statistical genomics, quantitative genetics, genome assembly and annotation of complex genomes, gene expression and microarray data analysis, physical mapping and data analysis, high-throughput molecular marker design and development, bioinformatics software development.