Agenda: Polyploid Genomics Data Management and Analysis May 8-10th (field tour on 7th) CIP, Lima, Peru
- Elizabeth Jones
- Marcelo Mollinari
- Lindsay Clark
- Dorcus Gemenet
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
Crop and CGIAR center representatives
- Hannele Lindqvist-Kreuze, CIP: Potato (local)
- Dorcus Gemenet, CIP: Sweetpotato
- Trushar Shah, IITA: Banana
- Catherine Breton, Bioversity: Banana
- Ranjana Bhattacharjee, IITA: Yam
- Agre Paterne, IITA: Yam
- Luis Augusto, CIAT: Forages/Cassava
Local representatives
- John Schoper, Leader; Genetics, Genomics and Crop Improvement Sciences Division
- Hugo Campos, Director of Research
- Noel Anglin, Leader for Conserving Biodiversity for the Future
- Michael Freidman, Science Officer, RTB Program
- Bert de Boeck, Statistician
- Elisa Salas, Data Manager/Potato breeder
- Ciro Rosales, System Analyst
- Federico Diaz, Sweetpotato breeder
- Wolfgang Gruneberg, Sweetpotato breeder
Other representatives (self-sponsored)
- Elizabeth Jones, GOBii, module 5 (funded by GOBii)
- Eng NG, HTPG, module 3 (funded by module 3)
- Moira Sheehan, Breeding Insight (funded by BI)
- Tim Millar, Plant and Food Research (funded by PFR, GOBii)
Tuesday May 7th: Optional field tour to see CIP Sweetpotato trials
Details of tour to follow. Lunch will be provided. The tour will be to Huaral in Peru, about 2 hours drive from Lima. we will spend approximately 2 hours in the field and then back to Lima after lunch. Viviana will send out further logistical details.
Please arrive Monday May 6th if you would like to attend this tour.
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 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 |
Day 2 Thursday May 9th - Tools for GWAS, Mapping, QTL mapping and GS
| Time | Topic | Speaker |
|---|---|---|
| 9.00 am | Daily logistics | Dorcus Gemenet |
| General Quantitative Genetics | ||
| 9.05 am | Quantitative genetics of autopolyploids. Breeding values and dominance | Jeff 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://swc-uiuc.github.io/2019-05-10-cip/ 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 | Tour of CIP potato and sweet potato Genebank tour (45 mins) | Dorcus Gemenet |
| 2:00 pm | Genotyping and variant calling - expanded session
| Marcelo Mollinari |