2019-02-07 Meeting notes EiB Polyploid Working Group
- Elizabeth Jones
Date
Feb 7, 2019
Participants
Gemenet, Dorcus (CIP) <D.Gemenet@cgiar.org>; Rouard, Mathieu (Bioversity-France) <m.rouard@cgiar.org>; Breton, Catherine (Bioversity-France) <C.Breton@cgiar.org>; Salas, Elisa (CIP) <E.SALAS@CGIAR.ORG>; De Boeck, Bert (CIP) <B.DeBoeck@cgiar.org>;@Elizabeth Jones
Unable to attend:
Arnaud, Elizabeth (Bioversity-France) <e.arnaud@cgiar.org>; Lindqvist-Kreuze, Hannele (CIP) <h.lindqvist-kreuze@cgiar.org>; Dreher, Kate (CIMMYT) <K.Dreher@cgiar.org>;
Added Abhishek
Goals
To submit an EiB Module 5 Polyploid WG proposal, define CGIAR polyploid needs and plan an in-person meeting at CIP
Discussion topics
Time | Item | Presenter | Notes |
|---|---|---|---|
| Fill out Working group proposal |
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| Contact for in-person meeting |
| Dorcas Gemenet will coordinate meeting - from Nairobi!
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| Budget for in-person meeting |
| $25K? Liz will follow up with Kelly on COP total budget. Estimate costs for 12-15 people to attend from overseas. Dorcas will get estimates for CIP costs - CIP hostels? Cost for 12-15 people for 4 nights, cost for 1-2 small meeting rooms and cost for a field trial trip From CIP: Hannalele, Elisa, some breeders, small cost |
| Additional attendees |
| Lindsay Clark, Ph.D., University of Illinois, Urbana-Champaign
I recently published an R package called polyRAD, which can be used for calling genotypes from sequencing read depth in polyploids. It outputs genotype posterior probabilities, which can be helpful because of the uncertainty that is generally seen unless read depth is extremely high. My students and I are working on methods for using these probabilities in GWAS and GS. Additionally, I’m collaborating with folks at various institutions on a project called “ploidyverse” where we try to make sure our software for polyploids is interoperable. Anyway, if you would like to chat about anything or would be interested in collaboration, let me know!
polyRAD on GitHub: https://github.com/lvclark/polyRAD polyRAD manuscript: https://doi.org/10.1534/g3.118.200913 ploidyverse: https://ploidyverse.github.io/index.html
David Byrne who is interested in such community. Since January, I have been working to organize a structure and objectives for the Tools for Polyploid proposal that is entitled, “Tools for Polyploids: Development of a Community Resource”.
The project includes a Computational/Genomics group, a Breeder Validation group divided by crops (Rose, Potato, Sweetpotato, Blueberry, Blackberry and Turf) each with 1 or 2 scientists to coordinate activities for breeders of that crop, and an Outreach group that will be coordinated by a post doc and will consist of all of the PIs in the project. Each crop group will have a post doc or doctoral position to work on analysis for the crop and other crops as needed. Beyond the Validation crops we want to include breeders of other polyploid crops in the training phase of the project. The idea is to offer general training and breeding program specific consulting to guide in the development of a dataset or the analysis of an existing dataset. I have enclosed the following documents for your information.
Robin Buell - https://plantbiology.natsci.msu.edu/directory/robin-buell/ Has worked with David Douches lab on potato
Jeffery Endelman, software package ClusterCall Jeffery Endelman (https://horticulture.wisc.edu/directory/jeffrey-endelman/) is Genomic Prediction expert as some experience in term of potato (autotetraploid). Also his program has been working to optimize genotyping (GBS) for tetraploids and making cluster calls in SNP genotypes ( R package ClusterCall was developed). I developed GWASpoly package to perform GWAS in autopolyploids ( https://doi.org/10.3835/plantgenome2015.08.0073 )https://potatobreeding.cals.wisc.edu
Umesh Rosyara, software package GWASpoly
Haplotype construction / Phasing / imputation Lachlan J.M. Coin, software package polyHap https://researchers.uq.edu.au/researcher/3012 Dr. Lachlan Coin (https://researchers.uq.edu.au/researcher/3012 ) from UQ, Australia has written polyHap program that can do haplotyping in polyploids. I know he worked with potato and sweet potato in development of computational tools.
Linkage map construction, JHI https://www.hutton.ac.uk/staff/christine-hackett Software Program TetraploidMap
General Genetics / Genomics Dave Douches https://www.canr.msu.edu/people/douches_david
Antonio Augusto Franco Garcia augusto.garcia@usp.br – sugar cane genetics recommended by Hugo
Richard Finkers at WUR working in potato and who might be interested to come to CIP. Roeland E. Voorrips https://www.wur.nl/en/Persons/Roeland-dr.ir.-RE-Roeland-Voorrips.htm Industry partners? Potato company...Simplot (more biotech) People in polyploid reference genome management or pangenomes? Also need people in genotyping space so can have better methods for polyploids - - link with module 3. |
| Other ways to engage the polyploid community Seminars at GOBii/EiB seminar series Conference sponsorship Sabbaticals Slack as a communication tools Where to store meeting notes etc? |
| Invite others outside of CGIAR and affiliates to this meeting? Yes. Can also add people as needed to the monthly meeting. Star says have plenty open slots in GOBii/EiB seminar series we can invite people to. Do we need a separate CGIAR meeting for polyploids as there seem to be communities already? Yes, would be good to review data types and challenges in CGIAR. But connect with other groups. RTB have cluster 1 - to connect bioinformatics and GS in all crops - cassava, banana, etc - should connect with this group - what are their objectives. Connect via Dorcas and Hannalele Add request for conference sponsorship to proposal to WG proposal and also request sabbatical Slack is OK for chat - but free system only keeps 10,000 messages so need to keep meeting minutes somewhere else. Can demo at our next meeting We can keep meeting notes in a public space - cloud version (no login needed) or add attendees to confluence site |