Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.


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 amYamAgre Ranjana
10.00 amCIAT crops

Luis Augusto

10.10 amBanana, IITATrushar Shah
10.20 amBanana, BioversityCatherine
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)

EXPAND to make longer or separate session Friday - GATK - Trushar

Marcelo - has many calling pipelines - would need - 2-3 hrs

Lindsay - calling with no reference available

Lindsay Clark
12.00 amHaplotyping in populationsUmesh Rosyara
12.30 pm

Building highly dense multilocus, multidose markers in polyploids (30 mins)

Marcelo Mollinari
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 - Jeff

(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

10  
TimeTopicSpeaker
9.00 amDaily logisticsGOBii - data management and analysis of genomics dataDorcus Gemenet
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

11.30am

GOBii - data management and analysis of genomics data

Liz Jones
12.30pm00pmLunch
1.30 pmAfternoon reserved for developing proposals, defining collaborations, and small group consultations

Tour of CIP potato and sweet potato Genebank tour (45 mins)Dorcus

...