EMBL-EBI
CABANA Workshop: Genotyping by Sequencing Applied to Plant Breeding
Date: 6 - 9 August 2019
This workshop will provide training around the experimental design and multiple applications of Genotyping by Sequencing (GBS) in plants. In addition, detailed computational analysis of GBS data and resources will be explored. Genomic analysis tools for GBS, such as Tassel, iPyrad, STACKS, as well as publicly available resources for plant data process and application will we implemented during the workshop.
The analysis of genomic variation is an essential part of plant genetics and crop improvement programs. DNA polymorphisms can be directly related to phenotype differences, be genetically linked to its causative factor, or indicate relationships between individuals in populations. Over the last years, the use of genotyping has enabled the characterization and mapping of genes and metabolic pathways in plants as well as the study of species diversity and evolution, marker-assisted selection (MAS), germplasm characterization and seed purity. Genotyping by sequencing (GBS) is a high throughput method to identify and genotype, at the same time, molecular markers as part of breeding activities, genetic mapping, and population genomics. Another advantage is that this method can be applied to organisms without reference genome and imputation of SNPs can be done as part of haplotype blocks. It was first published in 2011 and since then multiple crops have been improved including maize, potato, and rice.
Contact: Laura Brenes Guillén, Andrés Gatica-Arias - [email protected]
Venue: University of Costa Rica (UCR), Ciudad universitaria Rodrigo Facio Brenes
Region: San Jose
Country: Costa Rica
Organizer: European Bioinformatics Institute (EBI)
Host institutions: University of Costa Rica (UCR)
Target audience: This course is aimed at wet-lab researchers at within Latin America undertaking plant breeding and population genetics interested in applying next-generation sequencing to screen individuals. Please note this course will be taught in English, however the trainers are fluent in either Spanish or Portuguese, and can offer language support where feasible. A number of travel fellowships are available for this course - early-stage researchers and researchers from underrepresented groups are especially encouraged to apply for CABANA travel fellowships. You can apply for travel fellowships via the course application form. Knowledge in UNIX and NGS technologies is required. Therefore, these free resources should be studied beforehand: Basic introduction to the Unix environment: www.ee.surrey.ac.uk/Teaching/Unix Introduction and exercises for Linux: https://training.linuxfoundation.org/free-linux-training Basic R concept tutorials: www.r-tutor.com/r-introduction You may also find this video overview of GBS useful.
Capacity: 30
Event types:
- Workshops and courses
Scientific topics: Agricultural science, Genotyping
Activity log
