musabase pag 2018

MUSABASE

Guillaume BauchetMueller lab

gjb99@cornell.du

Plant and Animal Genome, San Diego, 2018

Musabase: A Phenotyping and Breeding

Database for Bananas

https://btiscience.org/lukas-mueller/#lab-members

Mueller lab

- Bioinformatics

- Genomics

- Databases

MUSABASE

+ University of Queensland, Australia+ National Banana Breeding Program, India+ University of Malaya, Malaysia

Improvement of banana

for smallholder farmers

in the Great Lakes Region

of Africa

Project scope

Genomic Selection(Moses presentation)

But also:

-> Conventional breeding

-> Plant pathology

-> Parmer preferences

-> Germplasm Management

->Tissue culture

Project scope

Project scope

multiple data types…

- Phenotyping experiments- Participatory trials - Farmer surveys- Tissue culture- Sequencing data

…and a wealth of biological specificities!

- Various ploidy levels- Germplasm groups- Complex pedigrees- Plant and field size - Life cycle length

=> different tools and approaches!

=> Need for an “in situ” resource, a breeding information repository

The banana “digital ecosystem”

Ex situ conservation

Molecular data

Semantic data

Musabase

MUSABASE http://musabase.org/

MUSABASE

Field data collection: a demanding process…

MUSABASE

Field data collection: digitalize it!

Field data collection: digitalize it!

MUSABASE

Connecting dots between and within projects…

MUSABASE

Field

Lab

MGIS

Crop ontology

Field data collection: digitalize it!

MUSABASE

Barcoding

https://musabase.org/barcode

Field data collection: digitalize it!

MUSABASE

Ontologies: streamline management

http://submit.rtbbase.org/

Banana ontology Pipeline

Credits: EM-A Laporte, . Arnaud (Bioversity)

Field data collection: digitalize it!

MUSABASE

Ontologies: postcomposing

https://musabase.org/tools/composehttps://musabase.org/search/traits

Field data collection: digitalize it!

MUSABASE

Field geolocations

https://musabase.org/breeders/locations

Field data collection: digitalize it!

MUSABASE

Pedigree

David Lyon’s presentation

Field data collection: digitalize it!

MUSABASE

Surveys

https://odk.ona.io/

-> Need for dynamic data collection processes -Farmer surveys-Field procedure (crosses)-Lab procedure (tissue culture)

Field data collection: digitalize it!

MUSABASE

Wish list + Crossing tool

http://btract.sgn.cornell.edu/https://musabase.org/breeders/crosses/

Credits: Margaret Karanja, Trushar Shah (IITA)

MUSABASE

-> Link ex situ (MGIS) vs in situ (musabase) data

-> Link additional molecular resources (genome hub, gobii)

-> Additional tools for banana breeders

Perspectives: reach the “digital ecosystem”

https://brapi.org/

-> On site trainings

-> Data managers

MUSABASE

Perspectives: keep building partnership

Arusha Tanzania NARO Uganda IITA Uganda

BTI Cornell

-> Collaborations with Bioversity/Crop ontology colleagues + new partners

Connecting dots between and within projects…

MUSABASE

Questions?gjb99@cornell.edu

http://slideshare.net/solgenomicsField

Lab

MGIS

Crop ontology