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Cassavabase general presentation PAG 2016

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Overview of cassavabase roles and latest developments at PAG 2016 San Diego

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Cassavabase general presentation PAG 2016

  1. 1. Unlocking breeding potential of African crops through data management an example with CASSAVABASE Guillaume Bauchet Plant and Animal Genome Conference San Diego January 2016 gjb99@cornell.edu
  2. 2. OUTLINE http://nextgencassava.org/ CASSAVABASE , What  for? CASSAVABASE , a  user  perspective CASSAVABASE , search,  manage,  analyze CASSAVABASE , a  view
  3. 3. The  Central  data  store  for  NEXTGEN CASSAVA : Genomic  selection  in  African  cassava  breeding  programs http://nextgencassava.org/
  4. 4. NEXTGEN CASSAVA
  5. 5. What are the major challenges?
  6. 6. ● Multi trait and Multi breeding environments for cassava phenotypic data collection ● Large scale production of genomic data using GBS ● Integrate Genomic Selection tool via web interface What are the major challenges? ● Make the most of this resource for cassava breeders: speed up the analysis and decision making
  7. 7. What are the needs? ● Search various data types (phenotypes and germplasm) in a large datastore ● Manage data and daily breeding activity through comprehensive interface ● Analyse and retrieve data for genomic assisted breeding What are our solutions? ● Integrate phenomic & genomic data with breeding tools ● Use Perl with the Bio::Chado::Schema and Natural Diversity module as database architecture ● Retrieve genomic information ● Sequence visualization ● Open source https://github.com/solgenomics/
  8. 8. http://cassavabase.org/
  9. 9. New search bar Navigation bar always visible on top Expandable search box
  10. 10. Caroussel
  11. 11. New responsive design
  12. 12. CASSAVABASE by numbers 2016: + 80,000 accessions, 2,5 billion genetic observations 2014: +360 registered users
  13. 13. From Phenotype to Genotype to Breeding: Harvesting the fruits of CASSAVABASE
  14. 14. CASSAVABASE, an Office perspective: Search Search breeding program, location, trial, trait, year, accession
  15. 15. CASSAVABASE, a field perspective: Manage Phenotypes Define phenotypic traits via Cassava trait dictionaryin CASSAVABASE Data collection via FieldBook app* Design trials, barcodes & field maps in CASSAVABASE* Data uploading in CASSAVABASE via .xls and .txt file * *See Alex Ogbonna PAG presentation “Managing Phenotypic Data through Cassavabase with Fieldbook App” “ Data analysis in CASSAVABASE -Sum. stat -ANOVA -BLUP -GS In CASSAVABASE
  16. 16. Design genotyping Trial in CASSAVABASE TASSEL pipeline Data filtering & imputation GBS data uploading In CASSAVABASE GS Analysis & Visualization in CASSAVABASE GBS facility @ Cornell CASSAVABASE, a lab perspective: Manage Genotypes
  17. 17. CASSAVABASE an office perspective: Manage Breeding programs, trial, accession
  18. 18. CASSAVABASE : Analyze with SolGS Phenotypic values Population Structure GEBV vs phenotypes See Isaak Tecle PAG presentation & poster 342 “solGS: A Web-based Solution for Genomic Selection” GEBV
  19. 19. CASSAVABASE : Analyze with SolGS
  20. 20. CASSAVABASE from the Office: Analyze phenotypes QC to phenotypes Single trial
  21. 21. CASSAVABASE from the Office: Analyze phenotypes QC to phenotypes Single trial
  22. 22. CASSAVABASE tools: Analyze pedigree
  23. 23. CASSAVABASE from the Office: Analyze phenotypes data_2011_B1 4 6 8 10 r= 0.68 p<0.001 r= 0.66 p<0.001 4 6 8 10 14 r= 0.70 p<0.001 4681012 r= 0.63 p<0.001 46810 data_2011_B2 r= 0.76 p<0.001 r= 0.79 p<0.001 r= 0.73 p<0.001 data_2011_B3 r= 0.76 p<0.001 46810 r= 0.68 p<0.001 4681014 data_2012_B1 r= 0.75 p<0.001 4 6 8 10 12 4 6 8 10 4 6 8 12 46812 data_2012_B2 30 31 32 33 34 35 36 37 -1.5-0.50.51.5 Fitted values Residuals Residuals vs Fitted 26 9 15 -2 -1 0 1 2 -1012 Theoretical Quantiles Standardizedresiduals Normal Q-Q 26 9 15 30 31 32 33 34 35 36 37 0.00.40.81.2 Fitted values Standardizedresiduals Scale-Location 269 15 0.0 0.1 0.2 0.3 0.4 0.5 -2-1012 Leverage Standardizedresiduals Cook's distance Residuals vs Leverage 9 26 15 ANOVA, h2, BLUP, GxE QC phenotypes Multiple trials
  24. 24. JBrowse CASSAVABASE tools: Analyze sequence Variant effects prediction
  25. 25. VIGS tool CASSAVABASE tools: Analyze sequence BLAST
  26. 26. CASSAVABASE, a User perspective: support & interaction
  27. 27. CASSAVABASE, a User perspective: support & interaction -> Provide support on technical issues ( data management) -> Gather user request for tool improvement and new developments (pedigree queries, VIGS) -> 2016: Install Mirror site @ IITA Ibadan, Nigeria Weekly meetings with users in Africa: Wiki, FB pages & mailing list:
  28. 28. CASSAVABASE Upcoming developments Search: Integrate trait & values in the wizard search Manage: extract data subset according to their phenotypic values, conditionnal choices Analyze: -Phenotypic analysis developments (ANOVA, GxE) -Pedigree analysis -Jbrowse: Mutation prediction of genetic variants -SolGS: Jobs queuing, trial selection improvement
  29. 29. Lukas Mueller Alex Ogbonna Bryan Ellerbrock Naama Menda Isaak Tecle Nick Morales AKNOWLEDGEMENTS Jeremy Edwards BMGF Chiedozie Egesi Peter Kulakow Robert Kawuki Ismail Rabbi
  30. 30. Questions?

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