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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

...

TimeTopicSpeaker
9.00 amWelcomeHugo 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 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 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 pmLunch
2.00 pmPresentations to help lead break-out groups
2.00 pmFile formats - ploidyverse Lindsay Clark
2.10 pmData storage - GOBiiLiz Jones
2.20 pmGenotyping technology methods and needs - need to be specific about goals here - technology or analysisJeff / 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 pmReport back and discussion
5 pmWrap up

...

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

TimeTopicSpeaker
9.00 amGOBii - Improving breeding through data management and analysis of genomics dataDorcus Gemenettools - GOBii and Excellence in Breeding module 5Liz 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

12.00pmLunch
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 pmAfternoon also reserved for developing proposals, defining collaborations, and small group consultations
4 pmTour of CIP potato and sweet potato Genebank tour (45 mins)Dorcus

...