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Date

Participants

Discussion topics

Time

Item

Presenter

Notes

· New public Confluence site allowing easier access https://gobiiproject.atlassian.net/wiki/x/A4AKB

Liz


· Slack channel now created


Liz


Review meeting agenda CIP May https://gobiiproject.atlassian.net/wiki/x/IgEIB

Tour of genebank facilities Friday?

Marcello

Carpentries Lindsay - Dorcus send out an email for interest. Need R and R studio set up - Lindsay will sedn out specifications

Umesh and Marcello and Trushar can help,

Liz talk earlier - Friday and then Lindsay

Get a number count closer to the time - Friday afternoon is good

Need for vcf filtering tools - Lindsay and Marcelo can cover

Read depth - how this affects calling dosage? sweet potato need 100X - Jeff’s talk will cover this and Lindsay will too

Small numbers of markers - eg amplicon technologies , KASP dosage for potato - Petra says can do now - Eng present on technologies for polyploids.

Luis has genotyped with the fluidigm system with Cassava - converted Illumina markers. 50/50 dosage

Review crop specialist needs – crop contacts https://gobiiproject.atlassian.net/wiki/x/KQEIB

Dorcus

Local arrangements

Recordings

Dorcus

Would be good to get recordings and can post them on the EiB website

Visa requirements for Americans?

Jeff

None - Dorcus will check - no, none needed

Dataset sharing site

Liz

Github?

Marcelo - Mapping section have a vcf F1 population with 2 hexaploid parents

Can also be used for haplotyping - Umesh will present haplotyping in populations

Dorcus have any tetraploid F1 datasets? No but have a GWAS panel

Marcelo has public datasets for F1 tetraploids

Linsday may use a different dataset for GWAS

Key datasets

Mapping - F1 triploids (Trushar), tetraploid (SolCAP) and hexaploid

GWAS - diversity population - tetraploid (Umesh has) and hexaploid (Dorcus has raw data)

Data types: vcf, Illumina chips (banana)

Challenge - don’t know the ploidy level (single dose markers?)

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