Rice Functional Genomics Project

Status

The Plant Industry Rice Functional Genomics project was initiated in 1998 as one of the components of a special CSIRO research initiative "Genomics and Gene Discovery for Australia". This project was also a component of  "Genomics" program (1999-2002) of "GrianGene" (a joint venture between AWB Ltd, CSIRO and the Grains Research and Development Corporation). Rural Industries Research and Development Corporation (RIRDC) (2001-2004)  and the NSW Agricultural Genomics Centre (2001-2006) are funding this project. This project activity has been scaled down since July 2006. However, this web site is being maintained as an access point for information about our gene constructs, mutant lines and other resources.

Achievements

• We have shown that Ac/Ds based gene and enhancer trap systems are suitable for generating insertion mutants in rice. The systems involved production of immobile Ac (iAc) and Ds (enhancer or gene trap) transgenic lines by Agrobacterium-mediated transformation, genetic crossing to produce mutagenic populations containing both, iAc and Ds and screening of plants from subsequent generations for stable (devoid of iAc) Ds insertions in new genomic locations and for any phenotypes associated with these insertions. Regions flanking the Ds element have been cloned (limited scale) and sequenced to create a database of flanking sequences that represent disrupted genes which is BLAST searchable. 

• We have also explored the possibility of inducing transposition in callus cultures of proven Ds lines with an excision marker. This is achievable by transiently expressing transposase (TET) after co-cultivation with Agrobacterium harbouring an iAc construct containing gfp as a visual reporter gene and then selecting for excision⁺ GFP^- Ds⁺ regenerants.  We have shown that this transiently expressed transposase could induce Ds transposition.

• New generation gene constructs have been developed for TET system and T-DNA/Ds launch pads mapping to different chromomosomal regions have been produced which should facilitate chromosomal region-directed insertional mutagenesis.

• We have developed RGMIMS (Rice Gene Machine Information Management System) to manage data generated in this project.  RGMIMS automates and integrates multi-step experimental processes using a Web user interface. Built in barcoding utilities enables rapid data capture and tracking of biological resources.  Ontologies from Gramene and Plant Ontology consortium have been used to describe mutant phenotypes.  RGMIMS supports generic research processes in plant mutagenesis and could readily be adapted to general high throughput plant research.

• Our efforts in hosting an international workshop Towards Building a Global Rice Gene Machine  in 2002 have led to the formation of the International Rice Functional Genomics Consortium. We are one among 18 institutions (from 10 countries and two international agricultural research centres) represented on the Interim Steering Committee. The mandate of the IRFGC is to coordinate international rice functional genomics research and to build common strategies. We are taking an active part in this global initiative. In addition we have collaborations with researchers at five overseas laboratories (Brazil, Indonesia, Germany, Japan and India).

                                 
Members (Previous staff, students and visitors)

Narayana M Upadhyaya, Liz Dennis, Jim Peacock

Xue Rong Zhou, Qian-Hao Zhu (PDFs)

Leaka Henry (Bioinformatics support, CMIS)

Hui Wang, Jie Yang, Ramesh Bhat, Satya Nugroho, Marcia Margis, Kefan Peng,

Tsuneo Kato, Jie Yang (Visiting Scientists)

Dow-Won Yun, Song-Jin Kim, Song-Su Ma (Visitors)
Andrew Eamens (PhD Student)
Kerrie Ramm, Kathryn Smith, Shuting Pan, Limin Wu, Xueqin Wang, Weining Yu, Ramani Sivakumar, Shamsul Hoque, Suzhi Li  (TOs),
 

Publications
 

Refereed papers

1. Zhu Q-H, Upadhyaya NM, Gubler F, Helliwell CA (2009) Over-expression of miR172 causes loss of spikelet determinancy and floral organ abnormalities in rice (Oryza sativa) (submitted)

2. Krishnan A, Guiderdoni E, An G, Hsing Y-I, Han C-D, Lee MC, Yu S-M, Upadhyaya N, Ramachandran S, Zhang Q, Sundaresan V, Hirochika H, Leung H, Pereira A (2009) Mutant resources in rice for functional genomics of grasses. Plant Physiology 149:165-170.

3. Henry L,  Ramm K, Zhu Q-H, Upadhyaya NM (2008) RGMIMS - A web-based laboratory information management system for plant functional genomics research. Molecular Breeding 22:151-157

4. Xu, M, Ross Wilderman P, Morrone D, Xu J, Roy A, Margis-Pinheiro M, Upadhyaya NM, Coates RM, Peters RJ (2007) Functional characterization of the rice kaurene synthase-like gene family. Phytochemistry 68:312-326

5. Zhu Q-H, Dennis ES, Upadhyaya NM (2007) compact shoot and leafy head 1, a mutation affects leaf initiation and developmental transition in rice (Oryza sativa L.). Plant Cell Rep 421-427 ( doi: 10.1007/s00299-006-0259-6)
6. Zhu Q-H, Ramm K, Eamens AL Dennis ES, Upadhyaya NM (2006) Transgene structures suggest that multiple mechanisms are involved in T-DNA integration in plants. Plant Science 171:308–322 (doi:10.1016/j.plantsci.2006.03.019)

7. Upadhyaya NM, Zhu Q-H, Zhou X-R, Eamens AL, Hoque MS, Ramm K, Shivakkumar R, Smith KF, Pan S-T, Li Suzhi, Peng K, Kim SJ, Dennis ES (2006) Dissociation (Ds) constructs, mapped Ds launch pads and a transiently expressed transposase system suitable for localized insertional mutagenesis in rice. Theoretical and Applied Genetics 112:1326 1341 (http://dx.doi.org/10.1007/s00122-006-0235-0).

8. Hoque MS, Masle J, Udvardi MK, Ryan PR and Upadhyaya NM (2006) Over-expression of the rice OsAMT1-1 gene increases ammonium uptake and content, but impairs growth and development of plants under high ammonium nutrition. Functional Plant Biology 33:153-163.
9. Islam N, Upadhyaya NM, Lonsdale M,  Higgins TJ, Campbell PM and Akhurst R (2005)  Decreased accumulation of glutelin types in rice grains constitutively expressing a sunflower seed albumin gene. Phytochemistry 66: 2534-2539.

10. Margis M, Zhou X-R, Zhu Q-H, Dennis ES and Upadhyaya NM (2005) Isolation and characterization of a Ds-tagged rice (Oryza sativa L.) GA responsive dwarf mutant defective in an early step of the gibberellin biosynthesis pathway. Plant Cell Reports 23:819-833.

11. Zhu  Q-H, Ramm K, Shivakkumar R, Dennis ES and Upadhyaya NM (2004) The ANTHER INDEHISCENCE1 gene encoding a single MYB domain protein is involved in anther development in rice (Oryza sativa L.). Plant Physiology 135:1514-1525.

12. Eamens AL, Blanchard CL, Dennis ES, and Upadhyaya NM (2004) A bidirectional gene trap construct for T-DNA and Ds mediated insertional mutagenesis in rice (Oryza sativa L.) Plant Biotechnology Journal 2:367-380.
13. Hirochika H, Guiderdoni E, An G, Hsing Y-I, Eun MY, Upadhyaya NM, Ramachandran S, Zhang Q, Pereira A, Sundaresan V and Leung  H (2004)  Rice mutant resources for gene discovery. Plant Molecular Biology 54:325-334.
14. Zhu Q-H, Hoque MS, Dennis ES and Upadhyaya NM (2003) Ds tagging of BRANCHED FLORETLESS 1 (BFL1) that mediates the transition from spikelet to floret meristem in rice (Oryza sativa L.). BMC Plant Biology online 3:6.
15. Upadhyaya NM, Zhou X-R, Ramm K, Zhu Q-H, L.Wu, Eamens A, Sivakumar R, Kato T, Yun D-W, Kumar S, Narayanan KK, Thomas G, Peacock WJ and Dennis ES (2002).  An iAc/Ds gene and enhancer trapping system for insertional mutagenesis in rice. Functional Plant Biology 29: 547-559. 
16. Upadhyaya NM, Zhou X-R, Wu L, Ramm K, Dennis ES (2000) The tms2 gene works as a negative selection marker in rice. Plant Molecular Biology Reporter 18:227-233.
17. Upadhyaya NM, Surin B, Schünmann P, Ramm K, Gaudron J, Taylor WC,Waterhouse PM  (2000) Agrobacterium-mediated transformation of Australian rice cultivars Jarrah and Amaroo with modified promoters and selectable markers. Australian Journal of Plant Physiology 27:201-210.

Other articles

1. Upadhyaya NM, Zhu Q-H, Bhat RS (2011) Transposon insertional mutagenesis in rice In: A. Pereira (ed) Plant Reverse Genetics Humana Press Inc pp 147-177

2. Upadhyaya NM, Dennis ES (2010) Rice Genomics- gateway for future cereal improvement In: Jain SM and Brar DS (eds) Molecular Techniques in Crop Improvement 2^nd edition  Springer, Dordrecht pp 257-279

3. Upadhyaya NM, Watson JM, Pereira A (2010) Biotech crops in functional genomics. In: Kole C, Michler CH, Abbott AG, Hall TC (eds) Deployment of Transgenic Plants.  Springer-Verlag  pp 359-390

4. Bhat RS, Upadhyaya NM, Chaudhury A, Raghavan C, Qiu F, Wang H, Wu J, McNally K, Leung H, Till B, Henikoff S and Comai L (2007) Chemical and irradiation induced mutants and TILLING. In: Upadhyaya NM (ed) Rice Functional Genomics- Challenges, Progress and Prospects. Springer, NY pp 149-180

5. Zhu Q-H, Eun MY, Han C-D, Kumar CS, Pereira A, Ramachandran S, Sundaresan V, Eamens AL, Upadhyaya NM and  Wu R (2007) Transposon insertional mutants: a resource for rice functional genomics. In: Upadhyaya NM (ed) Rice Functional Genomics- Challenges, Progress and Prospects. Springer, NY pp 223-271

6. Upadhyaya NM, Zhu Q-H and Dennis ES (2006) A gene machine for functional genomics of rice. A Report for Rural Industries Research and Development Corporation, Australia. RIRDC Publication No. W05/194 (downloadable from http://www.rirdc.gov.au/fullreports/rice.html )

7. Upadhyaya NM and Dennis ES (2005) New lines on offer at rice mutant gene library. IREC Farmers’Newsletter, 168, Rice R&D Edition: 48-49

8. Islam N, Lonsdale M, Upadhyaya NM, Higgins TJ, Hirano H, and Akhurst R (2004) Protein extraction from mature rice leaves for two-dimensional gel electrophoresis and its application in proteome analysis. Proteomics 4:1903-1908.

9. Eamens AL, Zhu Q-H, Dennis ES, Upadhyaya NM (2004) Designer constructs for T-DNA and Dissociation (Ds) mediated insertional mutagenesis in plants. ISB News Report November, 2004 http://www.isb.vt.edu/news/2004/news04.Nov.html

10. Upadhyaya NM, Zhou X-R, Zhu Q-H, Eamens A, Ramm K, Wu L, Sivakumar R, Kumar S, Narayanan KK, Thomas G, Kato T, Yun D-W, Peacock WJ, Dennis ES (2003). A gene machine for rice. In Khush GS, Brar DS, Hardy B (eds), Proceedings of the  4^th International Rice Genetics Symposium, 22-27 October 2000, Los Baños, Philippines: International Rice Research Institute. 352 p

11. Zhou X-R, Ramm K, Wu L, Sivakumar R, Dennis ES Upadhyaya NM (2003). New Ac/Ds-based constructs for efficient gene and enhancer trapping in rice. In Khush GS, Brar DS, Hardy B (eds), Proceedings of the  4^th International Rice Genetics Symposium, 22-27 October 2000, Los Baños, Philippines: International Rice Research Institute. 362 p.

12. Upadhyaya NM, Zhu Q-H, Eamens A and Dennis ES (2002) Rice gene machine: a vehicle for finding functions of cereal genes. Asia Pacific Biotech News 6:936-942.  

13. Upadhyaya NM, Zhou X-R, Zhu Q-H, Eamens A, Wang M-B, Waterhouse PM and Dennis ES (2000) Transgenic Rice. In Transgenic Cereals, eds O'Brien L , Henry RJ, AACC, Minnesota pp 28-87.  

Invited/selected Presentations 

1. Abreu-Neto JB, Richter S, Bevitori R, Zanettini MH, Upadhyaya N, Margis-Pinheiro M (2009) Functional characterization of the gene OsGMBP1 of rice (Oryza sativa L.). Paper to be presented at the “II Simpósio Brasileiro de Genética Molecular de Plantas" (http://www.sbg.org.br/Eventos/IISBGMP/pt-br/index.html ).

2. Upadhyaya NM, Ramm K, Spriggs A (2008) Natural antisense transcripts (NATs), small RNAs and drought stress responsive gene control in rice. Proceedings 6^th International Symposium of Rice Functional Genomics (Jeju, Korea, 10-12 November, 2008

3. Upadhyaya NM, Ramm K, Spriggs A (2008) Naturally occurring antisense transcripts (NATs) of rice in stress responsive gene control. Poster presented at  COMBIO2008 (Canberra, Australia, 21-25 September 2008

4. Upadhyaya NM, Ramm K, Spriggs A (2007) Naturally occurring antisense transcripts (NATS) in stress responsive gene control in rice. Proceedings 5^th International Symposium of Rice Functional Genomics (Tsukaba, Japan, 15-17 October, 2007)

5. Upadhyaya NM, Zhu Q-H, Bhat RS, Hoque MS, Ramm K, Shivakkumar R, Dennis ES (2006) CSIRO launch pads for chromosomal region directed localized gene tagging in rice. Paper presented at the 4th International Symposium on Rice Functional Genomics, 9-11 October, 2006, Montpellier, France

6. Upadhyaya NM, Zhu Q-H, Bhat RS, Hoque MS, Ramm K, Shivakkumar R, Li S, Liu J, Dennis ES (2005) Mining Seedling Vigour Genes using the Rice Gene Machine. Poster presented at the 5 International Rice Genetics Congress 20-24 November 2005, Manila, Philippines.

7. Zhu Q-H, Dennis Es and Upadhyaya NM (2005) COMPACT SHOOT AND LEAFY HEAD1 (CSL1), a heterochronic gene  regulates leaf initiation and developmental transition in rice. Poster presented at the 5 International Rice Genetics Congress 20-24 November 2005, Manila, Philippines.

8. Henry L, Ramm K, Zhu Q-H and Upadhyaya NM (2005) Rice Gene Machine Information Management System (RGMIMS). Poster presented at the 5 International Rice Genetics Congress 20-24 November 2005, Manila, Philippines.

9. Bhat RS Zhu Q-H, Hoque MS, Ramm K, Shivakkumar R, Li S, Liu J, Dennis ES And Upadhyaya NM, 2005, Mining Seedling Vigour Genes using the Rice Gene Machine. Poster presented in COMBIO-2005 at Adelaide, Australia, 25-29, Sept, 2005.

10. Upadhyaya NM, Zhu Q-H, Hoque MS, Ramm K, Shivakkumar S, Smith K, Pan
    S-T, Li S, Peng K, Dennis ES (2004) Dissociation (Ds) insertional mutagenesis using the transiently expressed transposase: Improved constructs and their suitability for targeted saturation mutagenesis. Invited paper presented at the 2nd International Symposium on Rice Functional Genomics held in Tucson, Arizona, USA (15-17 Nov. 2004).

11. Upadhyaya NM, Zhu Q-H, Eamens A, Margis M, Ramm K, Hoque MS, Shivakkumar R and Dennis ES (2003) Ac/Ds for insertional mutagenesis in rice Invited paper presented at the First International Symposium on Rice Functional Genomics held in Shanghai, China (19-21 Nov. 2003). Abstract    

12. Upadhyaya NM,  Zhu Q-H, Eamens A, Dennis E (2003) Rice Gene Machine – A key to finding functions of cereal genes. Symposium paper presented at the XIX International Congress of Genetics, Melbourne, Australia (6-11 August 2003) (Abstract)

13. Upadhyaya NM, Zhou X-R, Zhu Q-H, Eamens A, Peacock J and Dennis ES (2001). Rice gene machine. Invited presentation at the "Functional Genomics workshop" held as a part of "International Rice Genome Meeting 2001, Tsukuba, Ibaraki (7-9 Feb. 2001).

14. Upadhyaya NM, Kumar S, Ramm K, Wu L,  Zhou X-R Narayanan K, Thomas G, Waterhouse PM, Chaudhury A, Peacock J, Dennis E. Functional genomics in rice by transposon tagging (1999)  Paper presented at the General Meeting of the International Program on Rice Biotechnology, held at Phuket, Thailand, 20-24 Sept 1999.