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Resources for Citrus Genomics, Genetics and Breeding Research

Resources for Citrus Genomics, Genetics and Breeding Research.

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Resources for Citrus Genomics, Genetics and Breeding Research

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  1. Resources for Citrus Genomics, Genetics and Breeding Research Jodi Humann, Morgan Frank, Sook Jung, Chun-Huai Cheng, Taein Lee, Heidi Hough, Katheryn Buble, Ping Zheng, Kristin Scott, Julia Piaskowski, Mirella Flores, Surya Saha, Lukas A. Mueller, Fred Gmitter, Jill Wegrzyn, Meg Staton, Stephen Ficklin, Albert Abbott, Dorrie Main jhumann@wsu.edu, dorrie@wsu.edu www.citrusgenomedb.org

  2. Why CGD? • Single website to view, search, and download citrus related genomics, genetics and breeding data • Easy-to-use interfaces • Multiple tools available • Can be tailored to suit the needs of the research community • Uses an open-source database platform with many groups worldwide developing new modules

  3. Species Overview Page

  4. Genetic Resources • Searchable markers, genetic maps, QTLs from published literature • MapViewer tool to view and compare genetic maps

  5. Marker Search

  6. Marker Search

  7. QTL Search

  8. QTL Search

  9. MapViewer

  10. MapViewer • Draggable section adjusts close-up view of linkage group • Marker and QTL info displayed when cursor hovers over name • Clicking on marker and QTL name opens a feature page with more details

  11. MapViewer – Control Panel

  12. MapViewer – Comparing Maps www.citrusgenomedb.org

  13. MapViewer – Dot Plot

  14. Genomic Resources • Citrus genomes • C. clementinacv. Clemenules, v0.9 and v1.0, JGI • Aligned SRA data to v1.0 from Wu et al. 2014 and M. Roose also available in JBrowse • C. sinensiscv. Ridge Pineapple, v1.0 and v1.1, JGI • C. sinensiscv. Valencia, v2.0, HZAU • C. maxima (C. grandis), v1.0, HZAU • C. ichangensis(C. cavaleriei) cv. XJC, v1.0, HZAU • C. medicacv. X2, v1.0, HZAU • C. reticulatacv. WM01, v1.0, HZAU • Atalantiabuxifoliacv. HKC, v1.0, HZAU • Liberibacter genomes • All complete genomes from NCBI • CLas (6), CLam (1), CLaf (1), CLso (1), L. crescens(2)

  15. Genomic Resources - Tools • Available for all genomes • Gene and Transcript search • Sequence search • JBrowse • BLAST+ • Synteny Viewer • Also have PathwayCyc for C. clementinaand C. sinensisgenomes • Provided by Lukas Mueller’s Lab, Boyce Thompson Institute, Cornell

  16. Gene and Transcript Search

  17. Gene and Transcript Search

  18. Sequence Search

  19. Sequence Search

  20. Gene and mRNA Feature Pages

  21. Gene and mRNA Feature Pages

  22. JBrowse

  23. BLAST+

  24. BLAST+

  25. BLAST+

  26. BLAST+

  27. Synteny Viewer Module provided by Fei Bioinformatics Lab, Boyce Thompson Institute

  28. Synteny Viewer

  29. Synteny Viewer

  30. www.citrusgenomedb.org PathwayCyc

  31. Breeding Information Management System (BIMS) • A secure and comprehensive online breeding management system • Allows breeders to store, manage, archive and analyze their private breeding program • Load data with provided templates • Import data from Field Book (Android App) • Users without accounts can also view and search the publicly available breeding data • USDA-GRIN phenotype data

  32. Breeding Information Management System (BIMS) • Future BIMS development • Users will be able to integrate private data with publicly available genomic, genetic and breeding data in the community database • Utilize user-provided pedigree, phenotype and genotype data in performing genomic analysis and making breeding decisions. • Use open-source new genomics tool and breeding decision tools with seamless access to HPC

  33. BIMS

  34. Sign up for the CGD Mailing list from the website www.citrusgenomedb.org Funding To learn more about BIMS: Database Resources for Crop Genomics, Genetics and Breeding Workshop Sunday, 1:30 PM Sunrise – Meeting House BIMS Poster - PE0116

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