SELECTED PUBLICATIONS OF PARTICIPATING SCIENTISTS ON RICE

Kathuria, H., Giri, J., Nataraja, K. N., Murata, N., Udayakumar, M. and Tyagi, A. K. 2009. Glycinebetaine-induced water-stress tolerance in codA-expressing transgenic indica rice is associated with up-regulation of several stress responsive genes. Plant Biotechnol. J. (in press).

Vij, S., Giri, J., Dansana, P., Kapoor, S. and Tyagi, A. K. 2008. The Receptor-Like Cytoplasmic Kinase (OsRLCK) Gene Family in Rice: Organization, Phylogenetic Relationship, and Expression during Development and Stress. Molecular Plant 1:732-750.

Vij, S. and Tyagi, A. K. 2008. A20/AN1 zinc-finger domain-containing proteins in plants and animals represent common elements in stress response. Functional & Integrative Genomics 8: 301-307.

Kapoor, M., Arora, R., Lama, T., Nijhawan, A., Khurana, J. P., Tyagi, A. K. and Kapoor, S. 2008. Genome-wide identification, organization and phylogenetic analysis of Dicer-like, Argonaute and RNA-dependent RNA Polymerase gene families and their expression analysis during reproductive development and stress in rice. BMC Genomics 9:451(17 pages).

Jain, M., Tyagi, A. K. and Khurana, J. P. 2008. Genome-wide identification, classification, evolutionary expansion and expression analyses of homeobox genes in rice. FEBS J. 275:2845-2861.

Jain, M., Khurana, P., Tyagi, A. K. and Khurana, J. P. 2008. Genome-wide analysis of intronless genes in rice and Arabidopsis. Functional and Integrative Genomics 8: 69-78.

Jain, M., Tyagi, A. K. and Khurana, J. P. 2008. Constitutive expression of a meiotic recombination protein gene hemolog, OsTOP6A1, from rice confers abiotic stress tolerance in transgenic Arabidopsis plants. Plant Cell Reports 27:767-778.

Jain, M., Tyagi, A. K. and Khurana, J. P. 2008. Differential gene expression of rice two component signaling elements during reproductive development and regulation by abiotic stress. Functional & Integrative Genomics 8:175-180.

Nijhawan, A., Jain, M., Tyagi, A. K. and Khurana, J. P. 2008. A genomic survey and gene expression analysis of basic leucine zipper (bZIP) transcription factor family in rice. Plant Physiol 146:333-350.

Rice Annotation Project 2008. The rice annotation projet database (RAP-DB): 2008 update. Nucl. Acids Res 36:D1028-D1033.

Agarwal, P., Arora, R., Ray, S., Singh, A. K., Singh, V. P., Takatsuji, H., Kapoor, S. and Tyagi, A. K. 2007. Genome-wide identification of C2H2 zinc-finger gene family in rice and their phylogeny and expression analysis. Plant Mol. Biol. 65: 467-485.

Arora, R., Agarwal, P., Ray, S., Singh, A., Singh, V., Tyagi, A. K. and Kapoor, S. 2007. MADS-box gene family in rice: Genome-wide identification, organization and expression profiling during reproductive development and stress. BMC Genomics 8: 242 (21 pages).

Gupta, V., Khurana, R. and Tyagi, A. K. 2007. Promoters of two anther-specific genes confer organ-specific expression in a stage-specific manner in transgenic systems. Plant Cell Reports 26: 1919-1931.

Jain, M., Sharma, P., Tyagi, S. B., Tyagi, A. K. and Khurana, J. P. 2007. Light regulation and differential tissue-specific expression of phototropin homologues from rice (Oryza sativa ssp. indica). Plant Science 172: 164-171.

Jain, M., Nijhawan, A., Arora, R., Agarwal, P., Ray, S., Sharma, P., Kapoor, S., Tyagi, A. K. and Khurana, J. P. 2007. F-box proteins in rice : genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol. 143: 1467-1483.

Kathuria, H., Giri, J., Tyagi, H. and Tyagi, A. K. 2007. Advances in transgenic rice biotechnology. Critical Reviews in Plant Sciences 26: 65-103.

Ray, S., Agarwal, P., Arora, R., Kapoor. S. and Tyagi, A. K. 2007. Expression analysis of calcium-dependent kinase gene family during reproductive development and abiotic stress conditions in rice (Oryza sativa L. ssp. Indica). Mol. Genet. Genomics 278: 493-505.

Rice Annotation Project 2007. Curated genome annotation of Oryza sativa ssp. Japonica and comparative genome analysis with Arabidopsis thaliana. Genome Res. 17: 175-183.

Tyagi, A. K. 2007. Rice genome and beyond. Natl Acad Sci Lett. 30: 191-196.

Vij, S. and Tyagi, A. K. 2007. Emerging trends in functional genomics of abiotic response in crop plants. Plant Biotech. Jour. 5: 361-380.

Jain, M., Nijhawan, A., Tyagi, A. K. and Khurana J. P. 2006. Validation of housekeeping genes as internal control for studying gene expression in rice by quantitative real-time PCR. BBRC 345: 646-651.

Jain, M., Tyagi, A. K. and Khurana J. P. 2006. Overexpression of putative topoisomerase 6 genes from rice confers stress tolerance in transgenic Arabidopsis plants. FEBS J 273: 5245-5260.

Jain, M., Tyagi, A. K. and Khurana, J. P. 2006. Genome-wide analysis, evolutionary expansion, and expression of early auxin-responsive SAUR gene family of rice (Oryza sativa). Genomics 88: 360-371.

Tyagi, A. K. 2006. Rice genomics. Perspectives of Cytology and Genetics 12: 13-24.

Varshney, R. K., Hoisington, D. A. and Tyagi, A. K. 2006. Advances in cereal genomics and applications in crop breeding. Trends in Biotechnology 24: 490-497.

Vij. S. and Tyagi, A. K. 2006. Genome-wide analysis of the stress associated protein (SAP) gene family containing A20/ANI zinc-finger(s) in rice and their phylogenetic relationship with Arabidopsis. MGG 276: 565-171
.

Jain, M., Tyagi, A. K. and Khurana, J. P. 2006. Molecular characterization and differential expression of cytokinin-responsive type-A response regulators in rice (Oryza sativa). BMC Plant Biology 6: 1 (11 pages)

Jain, M., Kaur, N., Garg, R., Thakur, J. K., Tyagi, A. K. and Khurana, J. P. 2006. Structure and expression analysis of early auxin-responsive AUX/IAA gene family in rice(Oryza sativa). Func. Integr. Genomics 6: 47-59.

Jain, M., Kaur, N., Tyagi, A. K. and Khurana, J. P. 2006. Comprehensive analysis of auxin responsive GH3 gene family in rice (Oryza sativa). Func. Integr. Genomics 6: 36-46.

Vij, S., Gupta, V., Kumar, D., Vydianathan, R., Raghuvanshi, S., Khurana, P., Khurana, J. P., Tyagi, A. K. 2006. Decoding the rice genome. Bioessays 28: 421-432.

Thakur, J. K., Jain, M., Tyagi, A. K. and Khurana, J. P. 2005. Exogenous auxin enhances the degradation of a light down-regulated and nuclear-localized OSIIAA1, an AUX/IAA protein from rice, via proteasome. Biochem. Biophys. Acta 1736: 196-205.

Sharma, T. R., Shanker, P., Singh, B. K., Jana, T. K., Madhav, M. S., Gaikwad, K., Singh, N. K., Plaha, P., Rathour, R. 2005. Molecular mapping of rice blast resistance gene PiKh in the rice variety Tetep. J. Plant Biochem. Biotech. 14: 127-133.

Sharma,T. R., Madhav, M. S., Singh, B. K., Shanker, P., Jana, T. K., Dalal, V. , Pandit, A., Singh, A. , Gaikwad, K ., Upreti, H. C. and Singh N. K. 2005. High resolution mapping, cloning and molecular characterization of the PiKh gene of rice, which confers resistance to M. grisea. Mol. Genet. & Genomics : 274: 569-578.

The Rice Chromosomes 11 and 12 Sequencing Consortia 2005. The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplication. BMC Biology 3: 20 (18 pages).

The International Rice Genome Sequencing Project. 2005. The map-based sequence of the rice genome. Nature 436: 793-800.

Singh, R. K., Sharma, R. K., Singh, A. K., Singh, V. P., Singh, N. K., Tiwari, S. P. and Mohapatra, T. 2004. Suitability of mapped sequence tagged microsatellite site markers for establishing distinctness, uniformity and stability in aromatic rice. Euphytica 135:135-143.

Kohli, S., Mohapatra, T., Das, S. R., Singh, A. K., Tandon, V. and Sharma, R. P. 2004. Composite genetic structure of rice land races revealed by STMS markers. Curr. Sci. 86: 850-854.

Joseph, M., Gopalakrishnan, S., Sharma, R. K., Singh, V. P., Singh, A. K., Singh, N. K. and Mohapatra, T. 2004. Combining bacterial blight resistance and Basmati quality characteristics by phenotypic and molecular marker-assisted selection in rice. Molecular Breeding 13: 377-387.

Singh, N. K, Raghuvanshi, S., Srivastava, S. K., Gaur, A., Pal, A. K., Dalal, V., Singh, A., Ghazi, I.A., Bhargav, A., Yadav, M., Dixit, A., Batra, K., Gaikwad, K., Sharma, T. R., Mohapatra, T., Mohanty, A., Bharti. A. K., Kapur, A., Gupta, V., Kumar, D., Vij, S., Ravi, V., Parul Khurana, Sharma, S., McCombie, D., Messing, J., Wing, R., Sasaki, T., Paramjit Khurana, Khurana, J. P. and Tyagi, A. K. 2004. Sequence analysis of the long arm of rice chromosome 11 for rice-wheat synteny. Func. Integr. Genomics 4: 102-117.

Mukhopadhyay, A., Vij, S. and Tyagi, A. K. 2004. Overexpression of a zinc-finger protein gene from rice confers tolerance to cold, dehydration, and salt stress in transgenic tobacco. Proc. Natl. Acad. Sci. USA 101: 6309-6314.

Dhingra, A., Khurana, J. P. and Tyagi, A. K. 2004. Involvement of G-proteins, calmodulin and tagetitoxin-sensitive RNA polymerase in light-regulated expression of plastid genes (psbA, psaA and rbcL) in rice (Oryza sativa L.). Plant Science 166: 163-168.

Jain, M., Tyagi, S. B., Thakur, J. K., Tyagi, A. K. and Khurana, J. P. 2004. Molecular characterization of a light-responsive gene, breast basic conserved protein 1(OsiBBC1), encoding nuclear-localized protein homologous to ribosomal protein L13 from Oryza sativa indica. Biochimica et Biophysica Acta 1676: 182– 192.

Thakur, J. K., Malik, M. R., Bhatt, V., Reddy, M. K., Sopory, S. K., Tyagi, A. K. and Khurana, J. P. 2003. A POLYCOMB group gene of rice (Oryza sativa L. subspecies indica), OsiEZ1, codes for a nuclear-localized protein expressed preferentially in young seedlings and during reproductive development. Gene 314: 1-13.

Kathuria, H., Mohanty, A. and Tyagi, A. K. 2003. Analysis of inheritability and expression profile of a single and multi-copy transgene(s) in rice over generations. J. Plant Biochem. Biotechnol.  12: 103-107.

Mishra, G. P., Singh, R. K., Mohapatra, T., Singh, A. K., Prabhu, K. V., Zaman, F. U. and Sharma, R. K. 2003. Molecular mapping of a gene for fertility restoration of wild abortive (WA) cytoplasmic male sterility using a basmati rice restorer line.  J. Plant Biochem. Biotechnol.  12: 37-42.

Mohanty, A., Kathuria, H., Ferjani, A., Sakamoto, A., Mohanty, P., Murata, N. and Tyagi, A. K. 2002. Transgenics of an elite indica rice variety Pusa Basmati 1 harbouring the codA gene are highly tolerant to salt stress. Theor. App. Genet. 106: 51-57.

Mingsheng Chen, Gernot Presting, W. Brad Barbazuk, Jose Luis Goicoechea, Barbara Blackmon, Guangchen Fang, Hyeran Kim, David Frisch, Yeisoo Yu, Shouhong Sun, Stephanie Higingbottom, John Phimphilai, Dao Phimphilai, Scheen Thurmond, Brian Gaudette, Ping Li, Jingdong Liu, Jamie Hatfield, Dorrie Main, Kasey Farrar, Caroline Henderson, Laura Barnett, Ravi Costa, Brian Williams, Suzanne Walser, Michael Atkins, Caroline Hall, Muhammad A. Budiman, Jeffery P. Tomkins, Meizhong Luo, Ian Bancroft, Jerome Salse, Farid Regad, Trilochan Mohapatra, Nagendra K. Singh, Akhilesh K. Tyagi, Carol Soderlund, Ralph A. Dean, and Rod A. Wing. 2002. An Integrated Physical and Genetic Map of the Rice Genome. Plant Cell 14: 537-545.

Mukhopadhyay, A., Sharma, S. and Tyagi, A. K.  2001.   Isolation and characterization of  a novel S-adenosyl-L-methionine synthase cDNA from rice (Orzya sativa L. var. Pusa Basmati 1).   J. Plant Biochem. Biotechnol.  10:  25-29.

Raghuvanshi, S., Kelkar, A., Khurana, J. P. and Tyagi, A. K. 2001. Isolation and molecular characterization of the COP1 gene homolog from rice, Oryza sativa L. subsp. indica var. Pusa Basmati 1.   DNA Research   8:  73-79.  

Thakur, J. K., Tyagi, A. K. and Khurana, J. P. 2001. OsIAA1, an Aux/IAA cDNA from rice, and changes in its expression as influenced by auxin and light. DNA Research 8: 193-203.

Ray Choudhury,  P.,  Kohli,  S., Srinivasan,  K., Mohapatra, T. and Sharma, R. P. 2000.  Identification and classification of aromatic rices based on DNA fingerprinting. Euphytica 118: 243-251.

Gupta, P., Raghuvanshi, S. and Tyagi, A. K.  2000.  PCR amplification and cloning of the coding region of a cDNA for a reversibly glycosylated polypeptide from rice with possible involvement in the biosynthesis of glucans.   J. Plant Biochem. &  Biotechnol. 9:   99-102.  

Mohanty, A., Grover, M., Chaudhury, A., Rizwan-ul-Haq, Q., Sharma, A., Maheshwari, S. C. and Tyagi, A. K.   2000.  Analysis of the activity of promoters from two photosynthesis-related genes psaF and petH of spinach in a monocot plant, rice.  Ind. J. Biochem. Biophys.  37: 447-452.   

Raghunathchari, P., Khanna, V. K., Singh, U. S. and Singh, N. K. 2000. RAPD analysis of genetic variability in Indian scented rice germplasm (Oryza sativa L.). Current Science 79: 994-998.

Santhy, V., Mohapatra, T., Dadlani, M., Sharma, S. P. and Sharma, R. P.  2000.  DNA markers for testing distinctness of rice (Oryza sativa L.) varieties. Plant Varieties Seeds (UK) 13: 141-148.

Tyagi, A. K. and Mohanty, A.  2000.  Rice  transformation for crop improvement and functional genomics.   Plant Sci.  158: 1-18.

Gandhi, R. and Khurana, P.  1999.  Stress-mediated regeneration of mature embryo derived calli and Agrobacterium-mediated gene transfer in indica rice.  Ind. J. Exp. Biol.  37: 332-339.  

Grover, M., Dhingra, A., Sharma, A., Maheshwari, S. C. and Tyagi, A. K.  1999.  Involvement of phytochrome(s), Ca++ and phosphorylation in light-dependent control of transcript levels for plastid genes (psbA, psaA and rbcL) in rice (Oryza sativa).  Physiol. Plant.  105: 701-707.

Mohanty, A., Sharma, N. P. and Tyagi, A. K.  1999.  Agrobacterium-mediated high frequency transformation of an elite indica rice variety Pusa Basmati and transmission of the transgene to R2 progeny.   Plant Sci.  147: 125-135. 

Tyagi, A. K., Mohanty, A., Bajaj, S., Choudhary, A., and Maheshwari, S. C. 1999. Transgenic rice:  A valuable monocot system for crop improvement and gene research. Crit. Rev. Biotechnol. 19: 41-79.

Verma, S. K., Khanna, V. K. and Singh, N. K. 1999. Random amplified polymorphic DNA analysis of Indian scented 'Basmati' rice germplasm for identification of variability and duplicate accessions, if any. Electrophoresis 20: 1786-1789.

Grover, M., Sharma, A., Dhingra, A., Maheshwari, S. C. and Tyagi, A. K.  1998.  Regulation of plastid gene expression in rice involves calcium and protein phosphotases/kinases for signal transduction.  Plant Sci.  137: 185-190. 

Chowdhry, C. N., Sood, N., Maheshwari, N. and Tyagi, A. K. 1996. Heat-inducible expression of gus gene under control of soy bean heat shock gene ( Gmhsp 17.5-E ) promoter in transient expression system of rice. Proc. Nat. Acad. Sci., India 66: 1-6.

Grover, M., Maheshwari, S. C. and Tyagi, A. K.1996. Diurnal  fluctuation in steady-state mRNAs of certain chloroplast-encoded photosynthesis-related genes in rice.  J. Plant Biochem & Biotechnol.  5: 105-107.  

Chaudhury, A., Maheshwari, S. C. and  Tyagi, A. K. 1995. Transient expression of gus gene in intact seed embryos of indica rice after electroporation mediated gene delivery. Plant Cell Rep.  14: 215-220.  

Chaudhury, A., Chowdhary, C. N., Maheshwari, N., Maheshwari, S. C. and Tyagi, A. K. 1994. Growth behavior of suspension cultures of rice and transient expression of electroporated gene in intact cells.   J. Plant  Biochem. & Biotechnol.   3:  9-13.

Kapoor, S., Maheshwari, S. C. and Tyagi, A. K.  1994. Developmental and light-dependent cues interact to establish steady state levels of transcripts for photosynthesis related genes (psbA, psbD, psaA and rbcL) in rice (Oryza sativa). Curr. Genet.  25: 362-366.

Chaudhury, A., Maheshwari, S. C. and Tyagi, A. K. 1993. Transient expression of electroporated gene in leaf protoplasts of indica rice and influence of template topology and vector sequences.   Physiol. Plant.   89: 842-846.  

Chowdhry, C. N., Tyagi, A. K., Maheshwari, N. and Maheshwari, S. C.  1993.  Effect of L-proline and L-tryptophan on rice (Oryza sativa L. cv. Pusa 169).  Plant Cell, Tissue and Organ Culture   32: 357-361. 

Kapoor, S., Maheshwari, S. C. and Tyagi, A. K. 1993. Organ specific expression of plastid–encoded genes in rice involves both quantitative and qualitative changes in mRNAs.   Plant Cell Physiol.   34: 943-947.