2019-04-04 Meeting notes EiB Polyploid Working Group
- Elizabeth Jones
- Marcelo Mollinari
- Lindsay Clark
Date
Apr 4, 2019
Participants
@Elizabeth Jones
@Lindsay Clark
@Catherine Breton and Matthiue
@Dorcus Gemenet
@Marcelo Mollinari
@endelman
@Umesh Rosyara
and more….
Discussion topics
Time | Item | Presenter | Notes |
|---|---|---|---|
| · New public Confluence site allowing easier access for everyone https://gobiiproject.atlassian.net/wiki/x/A4AKB | Liz | |
· Slack channel now created |
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| 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 send out specifications Umesh and Marcello and Trushar can help, Liz talk earlier - Friday and then Lindsay Get a number count for the genebank tour closer to the time - Friday afternoon is good Need for vcf filtering tools - Lindsay and Marcelo can cover Lindsay recommends an R package - VariantAnnotation (Bioconductor) 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 |
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| 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 (Marcelo) GWAS - diversity population - tetraploid (Umesh has) and hexaploid (Dorcus has raw data) Data types: vcf, Illumina chips (banana)
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Action items