Credit hours
In-class work per week |
Practice per week |
Credits |
Duration |
Total |
10 |
15 |
4 |
2 weeks |
60 hours |
Instructor
Maria Imaculada Zucchi
Maria Lucia Carneiro Vieira
Roberto Fritsche Neto
Objective
The goal of this class is to teach step-by-step how to prepare libraries for Genoytping-By-Sequencing (GBS). By the end of the course, the students should be able to 1) Describe the necessary steps to prepare libraries for GBS; 2) Assess the quality of DNA libraries digested with different restriction enzymes; 3) Prepare a GBS library to be send for Illumina sequencing. We will also discuss some of the possible applications of GBS generated data for studies for population genomics; 4) We will show approaches for data filtering and identification of SNPs markers.
Content
The course will cover theoretical and practical aspects of the development of GBS genomic libraries aiming the identification of SNP markers, data filtering using the pipeline of Stacks, and introducing population genomic analyses.
Bibliography
Elshire, R.J.; Glaubitz, J.C.; Sun, Q.; Poland, J.A.; Kawamoto, K.; Buckler, E.S.; Mitchell, S.E. 2011. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PloS One, 6(5), e19379.
Poland, J.; Brown, P.J.; Sorrells, M.E.; Jannink, J.C. 2012. Development of high-density genetic maps for Barley and Wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS One, 7(2): e32253.
N. Rochette & J. Catchen. Deriving genotypes from RAD-seq short-read data using Stacks. Nature Protocols. 2017.
J. Paris, J. Stevens, & J. Catchen. Lost in parameter space: a road map for Stacks. Methods in Ecology and Evolution2017.
J. Catchen, P. Hohenlohe, S. Bassham, A. Amores, and W. Cresko. Stacks: an analysis tool set for population genomics. Molecular Ecology. 2013.
J. Catchen, A. Amores, P. Hohenlohe, W. Cresko, and J. Postlethwait. Stacks: building and genotyping loci de novo from short-read sequences. G3: Genes, Genomes, Genetics, 1:171-182, 2011.