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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

...

  • 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
    Abhishek Rathore: representing ICRISAT, GOBii and EiB module 5

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

...

  • 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. 

...

TimeTopicSpeaker
9.00 amWelcomeHugo 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 amPotatoHannele Lindqvist Kreuze
9.40 amSweetpotatoDorcus Gemenet
9.50 amYamRanjana Agre 
10.00 amCIAT crops

Luis Augusto

10.10 amBanana, IITATrushar Shah
10.20 amBanana, BioversityCatherine Breton
10.30 amBreak
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 amHaplotyping in F1 populations (30 mins)Marcelo Mollinari
12.30 pm

Haplotyping in general populations

Umesh Rosyara
1 -2 pmLunch
2.00 pmPresentations to help lead break-out groups
2.00 pmFile formats - ploidyverse Lindsay Clark
2.30 pmData storage - GOBiiLiz Jones
2.50 pmGenotyping technology methodsEng 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 pmReport back and discussion
5 pmWrap up

...

TimeTopicSpeaker
9.00 amDaily logisticsDorcus Gemenet
General Quantitative Genetics
9.05 amQuantitative genetics of autopolyploids. Breeding values and dominanceJeffJeff Endelman
9.30 amAnalysis and statistics for a complex polyploidsAntonio 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 amQTLpoly (demo)Marcelo Mollinari
GWAS and GS
12.00 pmGWAS and genomic prediction using GAPIT, FarmCPU, and/or rrBLUP (demo 1 hr)Lindsay Clark
1.00 pmLunch
2.00 pmGWASPoly (discussion, demo 1 hr)Umesh/Jeff
3 pmBreak out discussion - how do we capture these tools. What are the gaps, needs, resources, priorities  (3 groups)
4.30 pmReport back



Day 3 Friday May 10th - Hands-on training in tools and databases, opportunities for further break-out discussions and consulting sessions

Dorcus

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

  • GATK - Trushar
  • Variant discovery with no reference available - Lindsay
  • vcf filtering tools - Lindsay
  • Calling pipelines (ClusterCall, FitTetra, SuerMASSA, updog, polyRAD, ... ) - Marcelo
Marcelo9.30 pm

In parallel to the Carpentries, the morning will be reserved for developing proposals, defining collaborations, and small group consultations

4 pmTour of CIP potato and sweet potato Genebank tour (45 mins)

Marcelo Mollinari