Functional genomics of rice pollen and seed development by genome-wide transcript profiling and Ds insertion mutagenesis

International Journal of Biological Sciences

Volumn 7, Issue 1, 2011, Pages 28-40

  Jiang, Shu Ye ^a   Ramachandran, Srinivasan ^a  

^a TEMASEK LIFE SCIENCES LABORATORY   (Singapore)

Author keywords

Activator Dissociation (Ac Ds); Flanking sequence tags; Gene trap; Germplasm; Grain yield; Pollen and seed development

Indexed keywords

ZEA MAYS;

EID: 79952477174     PISSN: 14492288     EISSN: None     Source Type: Journal    
DOI: 10.7150/ijbs.7.28     Document Type: Article

References (49)

1. Khush GS. What it will take to feed 5.0 billion rice consumers in 2030. Plant Mol Biol. 2005; 59: 1-6.
2. Tzafrir I, Dickerman A, Brazhnik O, Nguyen Q, McElver J, Frye C, Patton D, Meinke D. The Arabidopsis Seed Genes Project. Nucleic Acids Res. 2003; 31: 90-93.
3. Tzafrir I, Pena-Muralla R, Dickerman A, Berg M, Rogers R, Hutchens S, Sweeney TC, McElver J, Aux G, Patton D, Meinke D. Identification of genes required for embryo development in Arabidopsis. Plant Physiol. 2004; 135: 1206-1220.
4. Itoh J, Nonomura K, Ikeda K, Yamaki S, Inukai Y, Yamagishi H, Kitano H, Nagato Y. Rice plant development: from zygote to spikelet. Plant Cell Physiol. 2005; 46: 23-47.
5. Kurata N, Miyoshi K, Nonomura K, Yamazaki Y, Ito Y. Rice mutants and genes related to organ development, morphogenesis and physiological traits. Plant Cell Physiol. 2005; 46: 48-62.
6. Borg M, Brownfield L, Twell D. Male gametophyte development: a molecular perspective. J Exp Bot. 2009; 60: 1465-1478.
7. Wilson ZA, Zhang DB. From Arabidopsis to rice: pathways in pollen development. J Exp Bot. 2009; 60: 1479-1492.
8. International Rice Research Institute. Annual Report for 1966. Los Banos, Philippines: International Rice Research Institute. 1967: 59-82.
9. Virmani SS, Sun ZX, Mou TM, Jauhar Ali A, Mao CX. Two-line hybrid rice breeding manual. Los Banos, Philippines: International Rice Research Institute. 2003.
10. Yuan L. Hybrid rice technology for food security in the world. Rome, Italy: FAO Rice Conference. 2004.
11. Brock RD. Quantitatively inherited variation in Arabidopsis thaliana induced by chemical mutagens. Environ. Exp. Bot. 1976; 16: 241-253.
12. Ahloowalia BS, Maluszynski M, Nichterlein K. Global impact of mutation-derived varieties. Euphytica 2004; 135: 187-204.
13. Jain SM. Tissue culture-derived variation in crop improvement. Euphytica. 2001; 118: 153-166.
14. Larkin PJ, Scowcroft WR. Somaclonal variation-a novel source of variability from cell cultures for plant improvement. Theor Appl Genet. 1981; 60: 197-214.
15. Bajaj S, Mohanty A. Recent advances in rice biotechnology-towards genetically superior transgenic rice. Plant Biotechnol J. 2005; 3: 275-307.
16. International Rice Genome Sequencing Project. The map-based sequence of the rice genome. Nature. 2005; 436: 793-800.
17. Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P, Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Tao M, Wang J, Zhu L, Yuan L, Yang H. A draft sequence of the rice genome (Oryza sativa L. ssp. Indica). Science. 2002; 296: 79-92.
18. Upadhyaya NM, Wing R, Yu SM. Rice Functional Genomics---Challenges, Progress and Prospects. New York: Springer. 2007:181-271.
19. Izawa T, Ohnishi T, Nakano T, Ishida N, Enoki H, Hashimoto H, Itoh K, Terada R, Wu C, Miyazaki C, Endo T, Iida S, Shimamoto K. Transposon tagging in rice. Plant Mol Biol. 1997; 35: 219-229.
20. Hirochika H, Guiderdoni E, An G, Hsing YI, Eun MY, Han CD, Upadhyaya N, Ramachandran S, Zhang Q, Pereira A, Sundaresan V, Leung H. Rice mutant resources for gene discovery. Plant Mol Biol. 2004; 54: 325-334.
21. Kim CM, Piao HL, Park SJ, Chon NS, Je BI, Sun B, Park SH, Park JY, Lee EJ, Kim MJ, Chung WS, Lee KH, Lee YS, Lee JJ, Won YJ, Yi G, Nam MH, Cha YS, Yun DW, Eun MY, Han CD. Rapid, large-scale generation of Ds transposant lines and analysis of the Ds insertion sites in rice. Plant J. 2004; 39: 252-263.
22. Kumar CS, Wing RA, Sundaresan V. Efficient insertional mutagenesis in rice using the maize En/Spm elements. Plant J. 2005; 44: 879-897.
23. Jeong DH, An S, Park S, Kang HG, Park GG, Kim SR, Sim J, Kim YO, Kim MK, Ki m SR, Kim J, Shi n M, Jung M, An G. Generation of a flanking sequence-tag database for activation-tagging lines in japonica rice. Plant J. 2006; 45: 123-132.
24. Hsing YI, Chern CG, Fan MJ, Lu PC, Chen KT, Lo SF, Sun PK, Ho SL, Lee KW, Wang YC, Huang WL, Ko SS, Chen S, Chen JL, Chung CI, Lin YC, Hour AL, Wang YW, Chang YC, Tsai MW, Lin YS, Chen YC, Yen HM, Li CP, Wey CK, Tseng CS, Lai MH, Huang SC, Chen LJ, Yu SM. A rice gene activation/knockout mutant resource for high throughput functional genomics. Plant Mol Biol. 2007; 63: 351-364.
25. Miyao A, Iwasaki Y, Kitano H, Itoh J, Maekawa M, Murata K, Yatou O, Nagato Y, Hirochika H. Large-scale collection of phenotypic data describing an insertional mutant population to facilitate functional analysis of rice genes. Plant Mol Biol. 2007; 63: 625-635.
26. Park SH, Jun NS, Kim CM, Oh TY, Huang J, Xuan YH, Park SJ, Je BI, Piao HL, Park SH, Cha YS, Ahn BO, Ji HS, Lee MC, Suh SC, Nam MH, Eun MY, Yi G, Yun DW, Han CD. Analysis of gene-trap Ds rice populations in Korea. Plant Mol Biol. 2007; 65: 373-384.
27. Kolesnik T, Szeverenyi I, Bachmann D, Kumar CS, Jiang SY, Ramamoorthy R, Cai M, Ma ZG, Sundaresan V, Ramachandran S. Establishing an efficient Ac/Ds tagging system in rice: large-scale analysis of Ds flanking sequences. Plant J. 2004; 37: 301-314.
28. Jiang SY, Bachmann D, La H, Ma Z, Venkatesh PN, Ramamoorthy R, Ramachandran S. Ds insertion mutagenesis as an efficient tool to produce diverse variations for rice breeding. Plant Mol Biol. 2007; 65: 385-402.
29. Song ZP, Lu BR, Chen JK. A study of pollen viability and longevity in Oryza rufipogon, O sativa, and their hybrids. International Rice Research Newsletter. 2001; 26: 31-32.
30. Liu YG, Whittier RF. Thermal asymmetric interlaced PCR: automatable amplification and sequencing of insert end fragments from P1 and YAC clones for chromosome walking. Genomics. 1995; 25: 674-681.
31. Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, Johnson D, Luo S, McCurdy S, Foy M, Ewan M, Roth R, George D, Eletr S, Albrecht G, Vermaas E, Williams SR, Moon K, Burcham T, Pallas M, DuBridge RB, Kirchner J, Fearon K, Mao J, Corcoran K. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol. 2000; 18: 630-634.
32. Nobuta K, Venu RC, Lu C, Beló A, Vemaraju K, Kulkarni K, Wang W, Pillay M, Green PJ, Wang GL, Meyers BC. An expression atlas of rice mRNAs and small RNAs. Nat Biotechnol. 2007; 25: 473-477.
33. Yuan Q, Ouyang S, Wang A, Zhu W, Maiti R, Lin H, Hamilton J, Haas B, Sultana R, Cheung F, Wortman J, Buell CR. The institute for genomic research Osa1 rice genome annotation database. Plant Physiol. 2005; 138: 18-26.
34. Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L, Orvis J, Haas B, Wortman J, Buell CR. The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res. 2007; 35 (Database Issue): D846-D851.
35. Berardini TZ, Mundodi S, Reiser L, Huala E, Garcia-Hernandez M, Zhang P, Mueller LA, Yoon J, Doyle A, Lander G, Moseyko N, Yoo D, Xu I, Zoeckler B, Montoya M, Miller N, Weems D, Rhee SY. Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol. 2004; 135: 745-755.
36. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat Genetics. 2000; 25: 25-29.
37. Jiang SY, Cai M, Ramachandran S. ORYZA SATIVA MYOSIN XI B controls pollen development by photoperiod-sensitive protein localizations. Dev Biol. 2007; 304: 579-592.
38. Fujita M, Horiuchi Y, Ueda Y, Mizuta Y, Kubo T, Yano K, Yamaki S, Tsuda K, Nagata T, Niihama M, Kato H, Kikuchi S, Hamada K, Mochizuki T, Ishimizu T, Iwai H, Tsutsumi N, Kurata N. Rice expression atlas in reproductive development. Plant Cell Physiol. 2010; 51: 2060-2081.
39. Wei LQ, Xu WY, Deng ZY, Su Z, Xue Y, Wang T. Genome-scale analysis and comparison of gene expression profiles in developing and germinated pollen in Oryza sativa. BMC Genomics. 2010; 11: 338.
40. Akama K, Kanetou J, Shimosaki S, Kawakami K, Tsuchikura S, Takaiwa F. Seed-specific expression of truncated OsGAD2 produces GABA-enriched rice grains that influence a decrease in blood pressure in spontaneously hypertensive rats. Transgenic Res. 2009; 18: 865-876.
41. Yang L, Suzuki K, Hirose S, Wakasa Y, Takaiwa F. Development of transgenic rice seed accumulating a major Japanese cedar pollen allergen (Cry j 1) structurally disrupted for oral immunotherapy. Plant Biotechnol J. 2007; 5: 815-826.
42. Xing Y, Zhang Q. Genetic and molecular bases of rice yield. Annu Rev Plant Biol. 2010; 61: 421-442.
43. Deshmukh R, Singh A, Jain N, Anand S, Gacche R, Singh A, Gaikwad K, Sharma T, Mohapatra T, Singh N. Identification of candidate genes for grain number in rice (Oryza sativa L.). Funct Integr Genomics. 2010; 10: 339-347.
44. Li X, Qian Q, Fu Z, Wang Y, Xiong G, Zeng D, Wang X, Liu X, Teng S, Hiroshi F, Yuan M, Luo D, Han B, Li J. Control of tillering in rice. Nature. 2003; 422: 618-621.
45. Ashikari M, Sakakibara H, Lin S, Yamamoto T, Takashi T, Nishimura A, Angeles ER, Qian Q, Kitano H, Matsuoka M. Cytokinin oxidase regulates rice grain production. Science. 2005; 309: 741-745.
46. Song XJ, Huang W, Shi M, Zhu MZ, Lin HX. A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet. 2007; 39: 623-630.
47. Xue W, Xing Y, Weng X, Zhao Y, Tang W, Wang L, Zhou H, Yu S, Xu C, Li X, Zhang Q. Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet. 2008; 40: 761-767.
48. Shomura A, Izawa T, Ebana K, Ebitani T, Kanegae H, Konishi S, Yano M. 2008. Deletion in a gene associated with grain size increased yields during rice domestication. Nat Genet. 2008; 40: 1023-1028.
49. Huang X, Qian Q, Liu Z, Sun H, He S, Luo D, Xia G, Chu C, Li J, Fu X. Natural variation at the DEP1 locus enhances grain yield in rice. Nat Genet. 2009; 41: 494-497.