2019-10-17 Meeting Notes EiB Polyploid Working Group

EiB M5 updates

Liz

•Two new positions have been posted related to Module 5.

• https://www.cimmyt.org/careers/jobs/eib-module-leader-software-and-data-management/

•https://www.cimmyt.org/careers/jobs/eib-biometrics-group-lead/

• Kelly Robbins will stay very active in Excellence in Breeding and the CoPs, but these two roles will take on the leadership of the software and biometrics components of Module 5

•The bioinformatics component of Module 5 will be led by Liz Jones (Director of GOBii) and Kelly Robbins moving forward

•Deputy Director, Excellence in Breeding https://www.cimmyt.org/careers/jobs/deputy-director-for-excellence-in-breeding/

Bioinformatics component

Liz

•Bioinformatics needs very important to polyploid crops

•No actual resources…yet

•Broker resources – internal or contracted preferred resources

•Proposals for new tools

•Alexis wants to support getting Galaxy tools published – Lindsay has some tools that she would like wrapping in Galaxy but can’t work on this until next year

Marker ontologies

Elisa

•We could just start an email exchange around this – Elisa, Liz and Guillaume? Also include Japanese group working in this space. BMS?

PAG meeting attendees

Liz

Dorcus, Moira, Star, Liz, Ranjana, Hannale, Marcelo, Jeff, Eng going

Have a meeting while we are there with a dinner??

EiB contract for medium density

Eng

Still under negotiation but people can submit with the EiB pricing in the meantime. Intertek have a DNA extraction lab now in Australia.

Still need H11 and H12 for Intertek and G12 and H12 for DArT -leave 2 wells empty to meet needs of both.

Have rice and potato plexes, working on beans and wheat and then maize. Based on sample forecast. Can get to the other crops (eg Yam) next year

EiB M3 has funds for marker synthesis; Design costs $10 target and each crop can have 1,00-4,000 targets (prefer closer to $1,000).

Crop needs to submit a list of targets and 100 bp flanking sequence. We don’t currently have support in EiB M3 for marker design and so this needs to come from crop resources, or helps if already have a chip to select from.

DArT formats

Jeff

Now being provided in the standard 2 row DArT format ie instead of 0s, 1s get a read count

Jeff doesn’t think he needs a fasta file. Luis thinks this could be useful

DArT genotyping in potato

Jeff

Potato - submitted 1587 targets, DArT returned 853 SNPs. Only 1 trait marker worked - and matched KASP data (they will need the other trait markers for future projects).

Depth was higher than we will probably get for a routine genotyping run.

Using Updog for geno calling - have new ‘proportional normal’ priors which seem to work better. Most markers seem to be working well and match the SNP chip data, but need to spend more time on them to get final success %s.

Do we need a ref genome? Jeff thinks so as need to provide a ref positive validation sample to DArT.

Dorcus - How to assess marker quality without existing SNP chip? Use a segregating population (or two to see background effects)

Lindsay says she has a new algortihm that could help with scoring.