BigOmics - High Throughput Genetic Diversity Analyses of Tropical Crops

From 04 Mar 2024 until 08 Mar 2024 - CIRAD, Montpellier, France (Face-to-face)

This advanced course is organized in the context of the EU Teaming project "Biopolis” between CIBIO and Univ. of Montpellier, and aims at presenting bioinformatics/population genomics tools to study crops and in particular to identify genes important in the domestication process/adaptation to local environment. This is an innovative course with a strong hands-on component and research mini-projects proposed by experts from Univ. Montpellier.

The general objective is to help participants getting familiar with the different forms of raw data from the latest sequencing technologies and their analysis, focusing on various tropical crops with diverse genomic constitutions and modes of reproduction, such as rice, sugarcane and banana, all of them intensively studied in Univ. Montpellier.

This advanced course will start with an in-person week at CIRAD on March 4-8. The program will include presentations on crops and on tools and hands-on sessions under guidance. Participants will be invited to conduct their own research mini-project on suspected introgressions among rice cultivar groups, trying to connect population diversity to gene diversity.

The research mini-project will go on until March 29 with regular remote interaction with instructors. Participants will be asked to deliver a short report and a brief oral presentation on their results at the end of the course on March 29.

PROGRAM
Day 01 | March 04, 2024
| Morning

Welcome and general introduction (Stéphanie SIDIBE-BOCS & Jean Christophe GLASZMANN)

| Afternoon

NGS from A to Z (Gautier SARAH, François SABOT)
Operational session for collective tools and individual computers

Day 02 | March 05, 2024
| Morning

Adaptive introgression in crop evolution (Concetta BURGARELLA)

Genetic diversity of Asian rice; the 3000 rice genomes (Jean Christophe GLASZMANN & Julien FROUIN)

| Afternoon

Rice mini-projects, introduction, principles, initiation (Jean Christophe GLASZMANN, Claire BILLOT, Stéphanie SIDIBE-BOCS & All participants)

Day 03 | March 06, 2024
| Morning

Sequence assembly and characterization of the highly polyploid sugarcane genome (Olivier GARSMEUR & Simon RIO)

| Afternoon

Comparative (pan)genomics, functional annotations, candidate genes 1 (Stéphanie SIDIBE-BOCS & South Green colleagues)

Rice mini-projects (All participants )

Day 04 | March 07, 2024
| Morning

Comparative (pan)genomics, functional annotations, candidate genes 2 (Stéphanie SIDIBE-BOCS & South Green colleagues)

Rice mini-projects (All participants)

| Afternoon

The banana crop and its genomic resources (Franc-Christophe BAURENS)

NGS characterization of the dynamic banana genome (Guillaume MARTIN (from Guadeloupe))

Day 05 | March 08, 2024
| Morning

Further analytical tools (Stéphanie SIDIBE-BOCS & tool referents Alexis DEREEPER, Alexandre SORIANO, Jean-François DUFAYARD, Aude GILABERT, Mathieu ROUARD)

Further analytical tools, practice (All participants)

| Afternoon

Participants evaluation

Conclusion

COURSE COORDINATOR

Jean Christophe Glaszmann - Cirad, Montpellier, France

COURSE INSTRUCTORS

Claire BILLOT, Cirad, Montpellier, France

Julien FROUIN , Cirad, Montpellier, France

Jean Christophe GLASZMANN, Cirad, Montpellier, France

Gautier SARAH, INRAE, Montpellier, France

Guilhem SEMPERE, Cirad, Montpellier, France

Stéphanie SIDIBE-BOCS, Cirad, Montpellier, France

LECTURES

Franc-Christophe BAURENS, Cirad, Montpellier, France

Concetta BURGARELLA, INRAE, Montpellier, France

Olivier GARSMEUR, Cirad, Montpellier, France

Guillaume MARTIN, Cirad, Neufchateau, Guadeloupe, France

Simon RIO, Cirad, Montpellier, France

François SABOT, IRD, Montpellier, France

SHORT COMMUNICATIONS

Alexis DEREEPER, IRD, Montpellier, France

Jean-Francois DUFAYARD, Cirad, Montpellier, France

Aude GILABERT, Cirad, Montpellier, France

Mathieu ROUARD, Alliance Bioversity-CIAT, Montpellier, France

Alexandre SORIANO, Cirad, Montpellier, France

SELECTION CRITERIA

The course will be open to a maximum number of 25 participants.

REGISTRATION

• Participation is free of charge for members from institutions involved in the BIOPOLIS Teaming project* (PhD students, Postdoc, Researchers), including travel, accommodation, lunch and dinner during the course)

• Other participants: 95€ (students) | 200€ (other participants)

CIBIO's TwinLabs members will have an additional discount of 20%

Includes registration and lunch on the days of the course

• Participants will be selected on a first-come, first-served basis

• Registration deadline: February 08, 2024

To apply, please fill the form available HERE

* CIBIO and 11 research units of the Univ. of Montpellier (AGAP, AMAP, CBGP, CEEM, CEFE, DIADE, IHPE, IPSIM, ISEM, LEPSE, MIVEGEC)