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
...
| 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) | Lindsay Clark | |
| 12.00 am | Haplotyping in F1 populations Umesh Rosyara(30 mins) | Marcelo Mollinari | |
| 12.30 pm | Building highly dense multilocus, multidose markers in polyploids (30 mins) | Marcelo Mollinari Haplotyping in general populations | Umesh Rosyara |
| 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 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 - Improving breeding through data management and analysis of genomics dataDorcus Gemenettools - GOBii and Excellence in Breeding module 5 | Liz Jones |
| 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 | |
| 1.00 pm | Genotyping and variant calling - expanded session GATK - Trushar Calling pipelines - Marcelo Calling with no reference available - Lindsay vcf filtering tools - Lindsay | Marcelo |
| 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 |
...