2020-01-02 Meeting notes EiB Polyploid Working Group

Owned by Elizabeth Jones
Last updated: Aug 09, 2020
3 min read

Video recording (sorry, I missed the first minute!). I tried inserting it directly into Confluence but it may be a bit glitchy.

Also can be found on YouTube (private link) where it should work better: https://youtu.be/1LUottSwY8Y

 

Below is the EiB Forum link. It can be accessed from the top right corner on the main EiB page. All registered users can post questions and I believe there’s automatic notification if there’s a response.

 https://excellenceinbreeding.org/forum

 

Agenda

  1. Eng – short update on EiB Module 3 mid density platform

  2. Feedback on DArTTag technology from 3 crops

    1. Bodo Raatz – beans

    2. Damien Platten – rice

    3. Moctar Kante – potato

 

Action items

Liz - to share questions with everyone for further follow up. Try the EiB site?  https://excellenceinbreeding.org/forum

Eng - For polyploids need more information on the read depth we will see under the standard contract, and what the costs will be for higher read depth

Bodo - Would be good to have standardized metrics to compare technology. He calls:

  • Assay success rate, and what filters we used for the SNP selection

  • % genotyping calls

  • % heterozygous calls

  • Mismatches between technical replicates

  • Mismatches between different genotyping platforms, GBS vs DarTag

  • Checking if the data makes biological sense, if we see clear blocks of sensible recombination  frequencies in segregating populations.

 

 

Main positives and negatives

  • Conversion rate from other technologies low (can be up to 50%) - especially a problem for trait specific markers. Need to submit double the number of sites to get the plex at the number you want.

  • Calls rate and quality of markers that do convert is high

  • Need consistency of reporting, sometimes get nucleotides, sometimes +-, needs to be consistent. Have had markers not named consistently. Also not obvious what the calls are compared with the submitted sequence for each allele. Working with DArT to resolve this.

  • Getting good read depth and calls with 384 panels for potato and but not really sure what the call rate will be for routine genotyping under the contract

  • Not yet getting vcf format which many users need

  • Bodo saw some issues with hets being resolved - might help to use posterior probabilities eg updog?

  • For rice have about 500 markers which is sub-optimal for GS or mapping, but has been working well for fingerprinting and background selection. Need to fill in gaps in another round of design.

 

Questions

Catherine: do you have the script to convert in vcf? Or can we receive a vcf from DArT?

Moira: For the technical control, does 384 samples really translate to 383?

Siva and Liz: Could you please elaborate on upfront costs? You mention EiB will provide support for set-up - how do we access these funds and what would they cover?

Liz: Is there a cost to update the panel every year?

Liz: what is the approx. cost of shipping DNA between Intertek (Sweden or Australia) and DArT that would be added to the invoice?

Moctar - getting good call rate with average 80 reads per sample locus. What would be the costs to achieve this? Standard genotyping under contract is around 10 calls for potato?

Liz: will other technologies be considered for medium density platforms under EiB M3?