eorgekit / epicasscassvanet4dev

EpiCass Workshop

EpiCass & CassavaNet4Dev - Advanced Bioinformatics Workshop & Mini-symposium

EpiCass: Identification of epigenetic variations influencing viral resistance and yield in cassava (Manihot esculenta) farmers’ fields

CASSAVANET4DEV: In a race to prevent hunger: Cassava Bioinformatics for African cassava biotechnology.

Research on plant epigenetics helps to understand how endogenous, biotic, and abiotic factors might regulate plant growth, development, and interaction with the environment independent of changes in the genome sequence. Often, the epigenetic changes are heritable across several generations and harmonize plant growth and crop tolerance in response to environmental stimuli.

To take advantage of the knowledge of the epigenetic adaptation, it has the potential to provide a powerful toolbox for crop breeders; however, most mechanistic studies are based on information from model plant species due to the challenges that arise when working with crops in the field. EpiCass and CassavaNet4Dev are projects financed by the Swedish Research Council that will aim to sequence different field grown cassava genotypes under different conditions to study the DNA methylation profiles and potential methylation pattern related to ACMV resistance and yield variation in farmer’s fields and disseminate the technology, data acquired, knowledge gained and train African scientists in bioinformatics to learn how to analyze such data by including them in our data analysis efforts.

We organize a first workshop at different IITA Hubs in parallel sessions, training over 3 days students and researchers from IITA and NARs in NGS data analysis, informing them and cassava breeders during a mini-symposium about the potential of epigenetics in successful, accelerated breeding.

Objectives of the course topics offered

By the end of the course participants should be able to:

• Use Linux command-line as a tool for data analysis
• Describe and differentiate the different NGS data file formats
• Perform QC assessment on NGS data
• Explain the algorithmic concepts behind mapping and assembly
• Perform mapping using NGS data
• Perform sequence assembly using NGS data