Invited speakers
- Marcelo Mollinari, Quantitative Geneticist, NCSU, sweetpotato MAPpoly
- Lindsay Clark, Geneticist, UI, developed polyRAD, ploidyverse
- Antonio Augusto Franco Garcia, Geneticist and Plant Breeder, USR, Brazil, sugarcane
- Jeffrey Endelman, UW, leads the potato variety development program, specialist in GS, GWAS
- Umesh Rosyara, CIMMYT, previously worked on Strawberry and Sour Cherry, developed GWASpoly
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Day 1 Wednesday May 8th: Crop Reports, sequencing, variant calling, marker design and data storage
Location:
| Time | Topic | Speaker |
|---|---|---|
| 9.00 am | Welcome | Hugo Campos |
| 9.20 am | Introductions and logistics | Liz and Dorcus |
Overview of CGIAR polyploid crops - genotyping methods, analysis methods, data storage, challenges (10 mins each?) | Moderator, Liz Jones | |
| 9.30 am | Potato | Hannele Lindqvist Kreuze |
| 9.40 am | Sweetpotato | Dorcus Gemenet |
| 9.50 am | Yam |
| Ranjana Agre | ||
| 10.00 am | CIAT crops | Luis Augusto |
| 10.10 am | Banana, IITA | Trushar Shah |
| 10.20 am | Banana, Bioversity | Catherine Breton |
| 10.30 am | Break | |
| 11.00 am | Genotype quality in polyploids (30 mins) | Jeff Endelman |
| 11.30 am | Variant and genotype calling issues. How various tools address this. Genotype calling with PolyRAD (30 mins) |
EXPAND to make longer or separate session Friday - GATK - Trushar
Marcelo - has many calling pipelines - would need - 2-3 hrs
Lindsay - calling with no reference available| Lindsay Clark | ||
| 12.00 am | Haplotyping in populations | Umesh Rosyara |
| 12.30 pm | Building highly dense multilocus, multidose markers in polyploids (30 mins) | Marcelo Mollinari |
| 1 -2 pm | Lunch | |
| 2.00 pm | Presentations to help lead break-out groups | |
| 2.00 pm | File formats - ploidyverse | Lindsay Clark |
| 2.10 pm | Data storage - GOBii | Liz Jones |
| 2.20 pm | Genotyping technology methods and needs - need to be specific about goals here - technology or analysis | Jeff / Luis / Eng |
| 2.30 pm | Breakout sessions and coffee 1) Genotyping technology needs - |
Eng (2) Data formats and storage - Liz (3) Data formats and ontology for markers -Lindsay | ||
| 4.30 pm | Report back and discussion | |
| 5 pm | Wrap up |
Day 2 Thursday May 9th - Tools for GWAS, Mapping, QTL mapping and GS
| Time | Topic | Speaker |
|---|---|---|
| 9.00 am | Daily logistics | Dorcus Gemenet |
| 9.05 am | Quantitative genetics of autopolyploids. Breeding values and dominance | Jeff |
| 9.30 am | Analysis and statistics for a complex polyploids | Antonio Augusto Franco Garcia |
| 10.00 am | Linkage mapping: Comparison of tools MAPpoly to build highly dense maps in autotetraploids, autohexaploids and autooctaploids (demo 1 hr) | Marcelo Mollinari |
| 11.00 am | GWASPoly (discussion, demo 1 hr) | Umesh/Jeff |
| 12.00 pm | GWAS and genomic prediction using GAPIT, FarmCPU, and/or rrBLUP (demo 1 hr) | Lindsay Clark |
| 1.00 pm | Lunch | |
| 2.00 pm | QTLPoly (demo 1 hr) | Marcelo Mollinari |
| 3 pm | Break out discussion - how do we capture these tools. What are the gaps, needs, resources, priorities (3 groups) | |
| 4.30 pm | Report back | |
Day 3 Friday May 10th - Hands-on training in tools and databases, opportunities for further break-out discussions and consulting sessions
| Time | Topic | Speaker | |
|---|---|---|---|
| 9.00 am | GOBii - data management and analysis of genomics data | Dorcus Gemenet | |
| 9.30 am | The Carpentries: https://carpentries.org/ A workshop directed at R novices, covering how to import data, manipulate a data frame, and make some plots | Lindsay Clark | |
| 12.00pm | Lunch | ||
| 1. | 3000 pm | Genotyping and variant calling - expanded session GATK - Trushar Calling pipelines - Marcelo Calling with no reference available - Lindsay | |
| 1.00 pm | Afternoon also reserved for developing proposals, defining collaborations, and small group consultations | ||
| 4 pm | Tour of CIP potato and sweet potato Genebank tour (45 mins) | Dorcus |
...