Global Information Resources on Rice for Research and Development

Abstract

Abstract: Various issues concerning the progress of rice research are related to ambiguous germplasm identification, difficulty in tracing pedigree information, and lack of integration between genetic resources, characterization, breeding, evaluation and utilization data. These issues are the constraints in developing knowledge-intensive crop improvement programs. The rapid growth, development and the global spread of modern information and communication technology allow quick adoption in fundamental research. Thus, there is a need to provide an opportunity for the establishment of services which describe the rice information for better accessibility to information resources used by researchers to enhance the competitiveness. This work reviews some of available resources on rice bioinformatics and their roles in elucidating and propagating biological and genomic information in rice research. These reviews will also enable stakeholders to understand and adopt the change in research and development and share knowledge with the global community of agricultural scientists. The establishment like International Rice Information System, Rice Genome Research Project and Integrated Rice Genome Explorer are major initiatives for the improvement of rice. Creation of databases for comparative studies of rice and other cereals are major steps in further improvement of genetic compositions. This paper will also highlight some of the initiatives and organizations working in the field of rice improvement and explore the availability of the various web resources for the purpose of research and development of rice. We are developing a meta web server for integration of online resources such as databases, web servers and journals in the area of bioinformatics. This integrated platform, with acronym iBIRA, is available online at http://ibiranet.in. The resources reviewed here are the excerpts from the resources integrated in iBIRA.

Key words: bioinformatics , rice informatics , genomic resource , proteomic resource , agricultural database

Shri RAM1, N. LAXMAN RAO2. Global Information Resources on Rice for Research and Development[J]. RICE SCIENCE, 2012, 19(4): 327-334.

References

Altschul S F, Madden T L, Sch?ffer A A, Zhang J, Zhang Z, Miller W, Lipman D J. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search program. Nucl Acid Res, 25(17): 3389–3402.
Bruskiewich R M, Cosico A B, Eusebio W, Portugal A M, Ramos L M, Reyes M T, Sallan M A, Ulat V J, Wang X, McNally K L, Sackville Hamilton R, McLaren C G. 2003. Linking genotype to phenotype: The International Rice Information System (IRIS). Bioinformatics, 19(Suppl 1): i63–i65.
Dash S, Van Hemert J, Hong L, Wise R P, Dickerson J A. 2012. PLEXdb: Gene expression resources for plants and plant pathogens. Nucl Acids Res, 40 (Database issue): D1194–D1201.
Fox P N, Skovmand B. 1996. The International Crop Information System (ICIS): Connects genebank to breeder to farmer’s field. In: Cooper M, Hammer G L. Plant Adaptation and Crop Improvement. Wallingford (UK): CAB International: 317–326.
Hamada K, Hongo K, Suwabe K, Shimizu A, Nagayama T, Abe R, Kikuchi S, Yamamoto N, Fujii T, Yokoyama K, Tsuchida H, Sano K, Mochizuki T, Oki N, Horiuchi Y, Fujita M, Watanabe M, Matsuoka M, Kurata N, Yano K. 2011. OryzaExpress: An integrated database of gene expression networks and omics annotations in rice. Plant Cell Physiol, 52(2): 220–229.
IRGSP (International Rice Genome Sequencing Project). 2005. The map-based sequence of the rice genome. Nature, 436: 793–800.
Jung K H, Dardick C, Bartley L E, Cao P, Phetsom J, Canlas P, Seo Y S , Shultz M, Ouyang S, Yuan Q, Frank B C, Ly E, Zheng L, Jia Y, Hsia A P, An K, Chou H H, Rocke D, Lee G C, Schnable P S, An G, Buell C R, Ronald P C. 2008. Refinement of light-responsive transcript lists using rice oligonucleotide arrays: Evaluation of gene-redundancy. PLoS One, 3(10): e3337.
Komatsu S, Kojima K, Suzuki K, Ozaki K, Higo K. 2004. Rice Proteome Database based on two-dimensional polyacrylamide gel electrophoresis: Its status in 2003. Nucl Acids Res, 32(Database issue): D388–D392.
Lee T H, Kim Y K, Pham T T, Song S I, Kim J K, Kang K Y, An G, Jung K H, Galbraith D W, Kim M, Yoon U H, Nahm B H. 2009. RiceArrayNet: A database for correlating gene expression from transcriptome profiling, and its application to the analysis of coexpressed genes in rice. Plant Physiol, 151: 16–33.
McLaren C G, Bruskiewich R M, Portugal A M, Cosico A B. 2005. The International Rice Information System (IRIS): A platform for meta-analysis of rice crop data. Plant Physiol, 139: 637–642.
Nagamura Y, Anotnio B A. 2010. Current status of rice informatics resources and breeding applications. Breeding Sci, 60: 549–555.
Nagamura Y, Antonio B A, Sato Y, Miyao A, Namiki N, Yonemaru J, Minami H, Kamatsuki K, Shimura K, Shimizu Y, Hirochika H. 2011. Rice TOGO browser: A platform to retrieve integrated information on rice functional and applied genomics. Plant Cell Physiol, 52(2): 230–237.
Nakano M, Nobuta K, Vemaraju K, Tej S S, Skogen J W, Meyers B C. 2006. Plant MPSS databases: Signature-based transcriptional resources for analyses of mRNA and small RNA. Nucl Acids Res, 34(Database issue): D731–D735.
Ohyanagi H, Tanaka T, Sakai H, Shigemoto Y, Yamaguchi K, Habara T, Fujii Y, Antonio B A, Nagamura Y, Imanishi T, Ikeo K, Itoh T, Gojobori T, Sasaki T. 2006. The Rice Annotation Project Database (RAP-DB): Hub for Oryza sativa ssp. japonica genome information. Nucl Acids Res, 34(Database issue): D741–D744.
Que Y X, Chen T S, Lin J W, Han X Y. 2008. Development of one SCAR marker for detection of sugarcane smut resistance. Proc China Assoc Sci Technol, 4: 147–150.
Rice P, Longden I, Bleasby A. 2000. EMBOSS: The European molecular biology open software suite. Trends Genet, 16: 276–277.
Rund Q. 2000. Enhanced farm research analyst: Tools for on-farm crop production research. In: Proceedings of ESRI Conference, 2000: 985. Available at http://proceedings.esri.com/library/ userconf/proc00/professional/papers/PAP985/p985.htm
Sasaki T, Burr B. 2000. International Rice Genome Sequencing Project: The effort to completely sequence the rice genome. Curr Opin Plant Biol, 3: 138–141.
Sato Y, Antonio B A, Namiki N, Takehisa H, Minami H, Kamatsuki K, Sugimoto K, Shimizu Y, Hirochika H, Nagamura Y. 2011. RiceXPro: A platform for monitoring gene expression in japonica rice grown under natural field conditions. Nucl Acids Res, 39(Database issue): D1141–D1148.
Soderlund C, Haller K, Pampanwar V, Ebbole D, Farman M, Orbach M J, Wang G L, Wing R, Xu J R, Brown D, Mitchell T, Dean R. 2006. MGOS: A resource for studying Magnaporthe grisea and Oryza sativa interactions. Mol Plant Microbe Interact, 19(10): 1055–1061.
Tanaka T, Antonio B A, Kikuchi S, Matsumoto T, Nagamura Y, Numa H, Sakai H, Wu J, Itoh T, Sasaki T, et al. 2008. The Rice Annotation Project Database (RAP-DB): 2008 update. Nucl Acids Res, 36(Database issue): D1028–D1033.
Xue J, Zhao S J, Liang Y L, Hou C X, Wang J H. 2008. Bioinformatics and its application in agriculture. In: International Federation for Information Processing, Vol. 259, Computer and Computing Technologies in Agriculture, 2: 977–982.

[1]	Srivastava Deepti, Shamim Md, Kumar Mahesh, Mishra Anurag, Pandey Pramila, Kumar Deepak, Yadav Prashant, Harrish Siddiqui Mohammed, Narayan Singh Kapildeo. Current Status of Conventional and Molecular Interventions for Blast Resistance in Rice [J]. Rice Science, 2017, 24(6): 299-321.
[2]	PAN Cun-hong, LI Ai-hong, DAI Zheng-yuan, ZHANG Hong-xi, LIU Guang-qing, WANG Zi-bin, MA Yu-yin, YIN Yue-jun, ZHANG Ya-fang, ZUO Shi-min, CHEN Zong-xiang, PAN Xue-biao. InDel and SNP Markers and Their Applications in Map-based Cloning of Rice Genes [J]. RICE SCIENCE, 2008, 15(4): 251-258 .