The Tools for Genomics-Assisted Breeding in Polyploids: Development of a Community Resource will hold its fourth Tools for Polyploids Training Workshop on January 10-11th 2024. The workshop will be held as a hybrid meeting with the in-person meeting held at San Diego State University, in San Diego, CA, USA. It is designed to help those involved in any aspect of polyploid crop breeding incorporate the power of genomic data into a breeding program to accelerate breeding gain. Thus, all those involved in polyploid crop breeding and genetics are invited to attend. The schedule of events will be the following:
The full schedule for the sessions listed below can be found here.
- Computational Support: The purpose of these sessions is two-fold. First, to review and answer questions about the software tools presented in the previous Training Workshops. The key part of these sessions will be short 15-minute reviews of the software tools with the opportunity to ask questions. It is strongly suggested that you view the presentations from the previous workshops that are available on our YouTube channel before the session. Second, to aid participants with any software installation or use issues. These questions will be fielded at all 3 sessions. It is recommended that all participants download the programs they would like to use along with the associated dummy datasets before these sessions. The web page and Slack channel set up for the Tools for Genomics-Assisted Breeding of Polyploids project have links to resources to learn R and all the relevant programs. The Slack channel is managed by a team that can help you troubleshoot any problems you might have working with the computational tools discussed.
The Tools for Polyploids Training Workshop is a 2-day event with snacks and lunch provided. For those registering for the in-person event, there will be a $100 registration fee. The link to the payment page is at the bottom of this page.
We have previously covered software tools to call genotypes, to haplotype, to create maps, to discover and characterize QTL, and implement genomic selection to accelerate polyploid crop breeding progress. Every year this software is improving as our developers work closely with our breeding partners to satisfy their needs. All the software is designed to work with clonally propagated highly heterozygous crops. Thus, beyond working well with polyploid crops it also works well with clonally propagated diploid crops. This year we will:
- December 5 - Genotype Calling and Mapping Tools
- December 12 - QTL Analysis Tools
- December 19 - Haplotyping, Genomic Selection, and Visualization Tools
- Introduce the new software COMA for optimizing crossing plans to maximize the predicted merit of F1 progeny while limiting inbreeding.
- Highlight the improvements made in mapping and QTL discovery software including faster processing speeds, the ability to map triploid crosses, the ability to screen for non-additive effects, and the ability to analyze multiparental populations among other improvements.
- Updates on polyBreedR
- Introduce a polyploid version of Reads2Map, a software to optimize your genotype calling pipeline.
- Explore the new functionalities of VIEWpoly, a visualization tool to display the results of multiple analytical results from mapping, QTL discovery, sequencing, and haplotyping to facilitate the interpretation and use of this information.
- Updates on MChap, a program to characterize haplotypes from sequencing data.
- There will also be user oral and poster presentations about the exciting ongoing research in polyploid breeding and genetics.
We will be tracking the knowledge and satisfaction of the Tools for Polyploids Training Workshops; thus, it is imperative that you complete the pre-conference and post-conference surveys. The information from the pre-conference survey is to establish the organization type, expertise, crop type, major traits of interest, and experience with specific software of the Training Workshop participants. The survey results will be summarized without identifying individual responses. These will be kept confidential.
Training Workshop Guides
Need information on public transportation, parking options, and hotel recommendations? Download our travel guide here.
The deadline for submitting abstracts is November 27, 2023. Each presenter will be given a poster board with a usable area measuring 36" x 36." Use the links above for full details on abstract submissions and poster presentation guidelines.
This project is awarding 25 travel grants of $1,000 each which are on a reimbursement basis. Your application is due November 27, 2023. Please read our travel grant FAQ before applying.
Registration and Survey Form – Begin the registration process below.
Registration for in-person attendance must be done by December 8, 2023, and for virtual attendance by January 8. Shortly after you are registered you will receive an email to confirm your registration and to receive the Zoom link for the virtual meeting.
**For those attending in person, a $100 registration fee is required to cover expenses such as catering. Please use this link to continue to the payment page. This fee is non-refundable.**
Please click the "Next" button to proceed to the Registration and Survey Form. Once you start, the form takes roughly 10 minutes to complete. You can save your progress and come back later.