Genomics and bioinformatics resources for crop improvement

Abstract

Recent remarkable innovations in platforms for omics-based research and application development provide crucial resources to promote research in model and applied plant species. A combinatorial approach using multiple omics platforms and integration of their outcomes is now an effective strategy for clarifying molecular systems integral to improving plant productivity. Furthermore, promotion of comparative genomics among model and applied plants allows us to grasp the biological properties of each species and to accelerate gene discovery and functional analyses of genes. Bioinformatics platforms and their associated databases are also essential for the effective design of approaches making the best use of genomic resources, including resource integration. We review recent advances in research platforms and resources in plant omics together with related databases and advances in technology.

Fig. 1

Omic space and related resources in plants. Examples of resources related to each omics instance are represented in Arabidopsis, rice and soybean, as the model plant, as a model monocot and a sequenced crop, and as an important crop recently sequenced, respectively. These resources are accessible from the following URLs or citations. 1. http://www.arabidopsis.org/, 2. http://www.gramene.org/, 3. http://soybase.org/, 4. http://nazunafox.psc.database.riken.jp, 5. http://rarge.gsc.riken.jp/dsmutant/index.pl, 6. http://signal.salk.edu/tabout.html 7. http://tilling.fhcrc.org/, 8. Kolesnik et al. (2004), 9. http://www.postech.ac.kr/life/pfg/risd/, 10. http://tos.nias.affrc.go.jp/, 11. http://www.soybeantilling.org/psearch.jsp, 12. http://mulch.cropsoil.uga .edu/∼parrottlab/Mutagenesis/acds/index.php, 13. http://arabidopsis.org.uk/home.html, 14. http://abrc.osu.edu/, 15. http://www.shigen.nig.ac.jp/rice/oryzabase/top/top.jsp, 16. http://www .irri.org/grc/GRChome/home.htm, 17. http://www.legumebase.agr.miyazaki-u.ac.jp/index.jsp, 18. http://www.plantcyc.org:1555/ARA/server.html, 19. http://pathway.gramene.org/gramene/ricecyc.shtml, 20. http://www.plantcyc.org/, 21. http://mediccyc.noble.org/, 22. http://prime.psc.riken.jp/, 23. http://csbdb.mpimp-golm.mpg.de/csbdb/gmd/gmd.html, 24. http://ppdb.tc.cornell.edu/, 25. http://phosphat.mpimp-golm.mpg.de/, 26. http://cdna01.dna.affrc.go.jp/RPD/main_en.html, 27. http://proteome.dc.affrc.go.jp/Soybean/, 28. http://oilseedproteomics .missouri.edu/, 29. http://bioinfo.esalq.usp.br/cgi-bin/atpin.pl, 30. http://atpid.biosino.org/, 31. http://suba.plantenergy.uwa.edu.au/, 32.http://proteomics.arabidopsis.info/, 33. http://www .brc.riken.go.jp/lab/epd/catalog/cdnaclone.html, 34. http://rarge.gsc.riken.jp/, 35. http://cdna01.dna.affrc.go.jp/cDNA/, 36. http://rsoy.psc.riken.jp/, 37. http://www.arabidopsis.org/portals/expression/microarray/ATGenExpress.jsp, 38. https://www.genevestigator.com/gv/index.jsp, 39. http://bioinformatics.med.yale.edu/riceatlas/, 40. http://bioinformatics.towson.edu/SGMD/Default.htm, 41. http://soyxpress.agrenv.mcgill.ca/cgi-bin/soy/soybean.cgi, 42. http://mpss.udel.edu/at/, 43. http://mpss.udel.edu/rice/, 44. http://signal.salk.edu/, 45. http://rapdb.dna.affrc .go.jp/, 46. http://rice.plantbiology.msu.edu/, 47. http://www.phytozome.net/, 48. http://walnut.usc.edu/, 49. http://www.oryzasnp.org/, 50. http://www.soymap.org/, 51. http://1001genomes .org/, 52. http://rarge.gsc.riken.jp/rartf/, 53. http://arabidopsis.med.ohio-state.edu/, 54. http://datf.cbi.pku.edu.cn/, 55. http://drtf.cbi.pku.edu.cn/, 56. http://grassius.org/, 57. http://soybeantfdb .psc.riken.jp, 58. http://legumetfdb.psc.riken.jp/.