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 Jones and Dorcus Gemenet |
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 (30 mins) | Marcelo Mollinari |
| 12.30 pm | 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 |
| 2.30 pm | Data storage - GOBii | Liz Jones |
| 2.50 pm | Genotyping technology methods | Eng NG |
| 3.10 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 |
...
| Time | Topic | Speaker |
|---|---|---|
| 9.00 am | Daily logistics | Dorcus Gemenet |
| General Quantitative Genetics | ||
| 9.05 am | Quantitative genetics of autopolyploids. Breeding values and dominance | JeffJeff Endelman |
| 9.30 am | Analysis and statistics for a complex polyploids | Antonio Augusto Franco Garcia |
| Linkage and QTL mapping in bi-parental populations | ||
| 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 | QTLpoly (demo) | Marcelo Mollinari |
| GWAS and GS | ||
| 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 | GWASPoly (discussion, demo 1 hr) | Umesh/Jeff |
| 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 | Improving breeding through data management and analysis tools - GOBii and Excellence in Breeding module 5. Open seminar. | 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. Open to CIP community. | Lindsay Clark Umesh Rosyara | |||
| 9.30 am | In parallel to The Carpentries, this morning is also reserved for developing proposals, defining collaborations, and small group consultations | ||||
| 12.00pm | Lunch | ||||
| 1.00 pm | Genotyping and variant calling - expanded session
| Marcelo | 9.30 pm | In parallel to the Carpentries, the morning will be reserved for developing proposals, defining collaborations, and small group consultations | Marcelo Mollinari |
| 4 pm | Tour of CIP potato and sweet potato Genebank tour (45 mins) | Dorcus Gemenet |