Differential gene expression in an elite hybrid rice cultivar (Oryza sativa, L) and its parental lines based on SAGE data

BMC Plant Biology

Volumn 7, Issue , 2007, Pages

  Song, Shuhui ^a,b   Qu, Hongzhu ^a,b   Chen, Chen ^a,b   Hu, Songnian ^a   Yu, Jun ^a  

^a Chinese Academy of Sciences and China National Center for Bioinformation   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CARBOHYDRATE;

ABDOMEN; ANIMAL; ANOPHELES GAMBIAE; ARTICLE; BLOOD; DISEASE CARRIER; EATING; EXPRESSED SEQUENCE TAG; FEMALE; GENE; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETICS; METABOLISM; NORTHERN BLOTTING; PARASITOLOGY; PLASMODIUM BERGHEI; RAT; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; CHROMOSOME MAP; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETIC DATABASE; GENOME; HYBRIDIZATION; METHODOLOGY; PLANT LEAF; PLANT ROOT; PLANT STEM; QUANTITATIVE TRAIT LOCUS; RICE; SPECIES DIFFERENCE; STATISTICS;

ABDOMEN; ANIMALS; ANOPHELES GAMBIAE; BLOOD; BLOTTING, NORTHERN; CARBOHYDRATES; EATING; EXPRESSED SEQUENCE TAGS; FEMALE; GENE EXPRESSION REGULATION; GENE LIBRARY; GENES, INSECT; INSECT VECTORS; PLASMODIUM BERGHEI; RATS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; CHROMOSOME MAPPING; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; HYBRIDIZATION, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ORYZA SATIVA; PLANT LEAVES; PLANT ROOTS; PLANT STEMS; QUANTITATIVE TRAIT LOCI; SPECIES SPECIFICITY;

ORYZA SATIVA;

EID: 36248979230     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/1471-2229-7-49     Document Type: Article

References (54)

1. Budak H: Understanding of Heterosis. KSUJ Science and Engineering 2002, 5(2):69-75.
2. Xiao J, Li J, Yuan L, Tanksley SD: Dominance is the major genetic basis of heterosis in rice as revealed by QTL analysis using molecular markers. Genetics 1995, 140:745-754.
3. Yu SB, LiJX, Xu GC, Tan YF, Gao YJ, Li XH, Zhang QF, Maroof MAS: Importance of epistasis as the genetic basis of heterosis in an elite rice hybrid. Proc Nati Acad Sci USA 1997, 94:9226-9231.
4. Birchler JA, Auger DL, Riddle NC: In search of the molecular basis of heterosis. Plant Cell 2003, 15(10):2236-2239.
5. Sun Q, Wu L, Ni Z, Meng F, Wang Z, Lin Z: Differential gene expression patterns in leaves between hybrids and their parental inbreds are correlated with heterosis in a wheat diallel cross. Plant Science (Oxford) 2004, 166(3):651-657.
6. Yao Y, Ni Z, Zhang Y, Chen Y, Ding Y, Han Z, Liu Z, Sun Q: Identification of differentially expressed genes in leaf and root between wheat hybrid and its parental inbreds using PCRbased cDNA subtraction. Plant Mol Biol 2005, 58(3):367-384.
7. Wu LM, Ni ZF, Meng FR, Lin Z, Sun QX: Cloning and characterization of leaf cDNAs that are differentially expressed between wheat hybrids and their parents. MGG Molecular Genetics and Genomics 2003, 270(3):281-286.
8. Yao Y, Ni Z, Du J, Wang X, Wu H, Sun Q: Isolation and characterization of 15 genes encoding ribosomal proteins in wheat (Triticum aestivum L.). Plant Science (Oxford) 2006, 170(3):579-586.
9. Xiong LZ, Xu CG, Saghai Maroof MA, Zhang Q: Patterns of cytosine methylation in an elite rice hybrid and its parental lines, detected by a methylation-sensitive amplification polymorphism technique. Mol Gen Genet 1999, 261 (3):439-446.
10. Ni Z, Sun Q, Liu Z, Wu L, Wang X: Identification of a hybrid-specific expressed gene encoding novel RNA-binding protein in wheat seedling leaves using differential display of mRNA. Mol Gen Genet 2000, 263(6):934-938.
11. Huang Y, Zhang L, Zhang J, Yuan D, Xu C, Li X, Zhou D, Wang S, Zhang Q: Heterosis and polymorphisms of gene expression in an elite rice hybrid as revealed by a microarray analysis of 9198 unique ESTs. Plant Mol Biol 2006, 62(4-5):579-591.
12. Khattra J, Delaney AD, Zhao Y, Siddiqui A, AsanoJ, McDonald H, Pandoh P, Dhalla N, Prabhu AL, Ma K, Lee S, Ally A, Tam A, Sa D, Rogers S, Charest D, Stott J, Zuyderduyn S, Varhol R, Eaves C, Jones S, Holt R, Hirst M, Hoodless PA, Marra MA: Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines. Genome Res 2007, 17(1): 108-116.
13. Wang SM: Understanding SAGE data. Trends Genet 2007, 23(1):42-50.
14. Chen J, Sun M, Lee S, Zhou G, Rowley JD, Wang SM: Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags. Proc Natl Acad Sci USA 2002, 99(19): 12257-12262.
15. Boon K, Osorio EC, Greenhut SF, Schaefer CF, Shoemaker J, Polyak K, Morin PJ, Buetow KH, Strausberg RL, De Souza SJ, Riggins GJ: An anatomy of normal and malignant gene expression. Proc Natl Acad Sci USA 2002, 99( 17): I 1287-11292.
16. Lee JY, Lee DH: Use of serial analysis of gene expression technology to reveal changes in gene expression in Arabidopsis pollen undergoing cold stress. Plant Physiol 2003, 132(2):517-529.
17. Fizames C, Munos S, Cazettes C, Nacry P, Boucherez J, Gaymard F, Piquemal D, Delorme V, Commes T, Doumas P, Cooke R, Marti J, Sentenac H, Gojon A: The Arabidopsis root transcripto me by serial analysis of gene expression. Gene identification using the genome sequence. Plant Physiol 2004, 134(1):67-80.
18. Matsumura H, Nirasawa S, Terauchi R: Technical advance: transcript profiling in rice (Oryza sativa L.) seedlings using serial analysis of gene expression (SAGE). Plant J 1999, 20(6):719-726.
19. Gibbings JG, Cook BP, Oufault MR, Madden SL, Khurie S, Tumbull CJ, Dunwell JM: Globle transcript analysis of rice leaf and seed using SAGE technology. Plant Biotechnology Journal 2003, 1:271-285.
20. Wang Q, Zhang QD, Jiang GM, Lu CM, Kuang TY, Wu S, Li CQ, Jiao DM: Photosynthetic Characteristics of Two Superhigh-yield Hybrid Rice. Acta Botanica Sinica 2000, 42( 12): 1285-1288.
21. Bao J, Lee S, Chen C, Zhang X, Zhang Y, Liu S, Clark T, Wang J, Cao M, Yang H, Wang SM, Yu J: Serial analysis of gene expression study of a hybrid rice strain (LYP9) and its parental cultivars. Plant Physiol 2005, 138(3): 1216-1231.
22. 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, et al.: A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 2002, 296(5565):79-92.
23. Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C, Zhang J, Zhang Y, Li R, Xu Z, Li S, Li X, Zheng H, Cong L, Lin L, Yin J, Geng J, Li G, Shi J, Liu J, Lv H, Li J, Wang J, Deng Y, Ran L, Shi X, et al.; The Genomes of Oryza sativa: a history of duplications. PLoS Biol 2005, 3(2):e38.
24. Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N, Yazaki J, Ishikawa M, Yamada H, Ooka H, Hotta I, Kojima K, Namiki T, Ohneda E, Yahagi W, Suzuki K, Li CJ, Ohtsuki K, Shishiki T, Otomo Y, Murakami K, lida Y, Sugano S, Fujimura T, Suzuki Y, Tsunoda Y, Kurosaki T, Kodama T, Masuda H, Kobayashi M, et al.: Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 2003, 301 (5631):376-379.
25. Wu J, Maehara T, Shimokawa T, Yamamoto S, Harada C, Takazaki Y, Ono N, Mukai Y, Koike K, Yazaki J, Fujii F, Shomura A, Ando T, Kono I, Waki K, Yamamoto K, Yano M, Matsumoto T, Sasaki T: A compre-hensive rice transcript map containing 6591 expressed sequence tag sites. Plant Cell 2002, 14(3):525-535.
26. Tang J, Xia H, Li D, Cao M, Tao Y, Tong W, Zhang X, Hu S, Wang J, Yu J, Yang H, Zhu L: Gene expression profiling in rice young panicle and vegetative organs and identification of paniclespecific genes through known gene functions. Mol Genet Genomics 2005, 274(5):467-476.
27. Gene Expression Omnibus [http://www.ncbi.nlm.nih.gov/geo/]
28. Audic S, Claverie JM: The significance of digital gene expression profiles. Genome Res 1997, 7(10):986-995.
29. Kyoto Encyclopedia of Genes and Genomes [http://www.genome.jp/ kegg/]
30. InterPro [http://www.ebi.acuk/interpro/]
31. Gramene [http://www.gramene.org]
32. Pleasance ED, Marra MA, Jones SJ: Assessment of SAGE in transcript identification. Genome Res 2003, 13(6A):1203-1215.
33. Graber JH, Cantor CR, Mohr SC, Smith TF: In silico detection of control signals: mRNA 3-end-processing sequences in diverse species. Proc Natl Acad Sci USA 1999, 96(24): 14055-14060.
34. Tsaftaris SA: Molecular aspects of heterosis in plants. Plant Physiol 1995, 94:362-370.
35. Swanson-Wagner RA, Jia Y, DeCook R, Borsuk LA, Nettleton D. Schnable PS: All possible modes of gene action are observed in a global comparison of gene expression in a maize Fl hybrid and its inbred parents. Proc Notl Acad Sci USA 2006, 103(18):6805-6810.
36. Meng F, Ni Z, Wu L, Sun Q: Differential gene expression between cross-fertilized and self-fertilized kernels during the early stages of seed development in maize. Plant Science 2005, 168:23-28.
37. Stupar RM, Springer NM: Cis-transcriptional variation in maize inbred lines B73 and Mo 17 leads to additive expression patterns in the Fl hybrid. Genetics 2006, 173(4):2199-2210.
38. Song LQ, Fu TD, Tu JX, Ma CZ, Yang GS: Molecular validation of multiple allele inheritance for dominant genie male sterility gene in Brassica napus L. Theor Appl Genet 2006, 113(1 ):55-62.
39. Nagasawa N, Miyoshi M, Sano Y, Satoh H, Hirano H, Sakai H, Nagato Y: SUPERWOMANI and DROOPING LEAF genes control floral organ identity in rice. Development 2003, 130(4):705-718.
40. Kang HG, Jeon JS, Lee S, An G: Identification of class B and class C floral organ identity genes from rice plants. Plant Mol Biol 1998, 38(6): 1021-1029.
41. Haruta M, Constabel CP: Rapid alkalinization factors in poplar cell cultures. Peptide isolation, cDNA cloning, and differential expression in leaves and methyl jasmonate-treated cells. Plant Physiol 2003, 131 (2):814-823.
42. Dai Y, Ni Z, Dai J, Zhao T, Sun Q: Isolation and expression analysis of genes encoding DNA methyltransferase in wheat (Triticum aestivum L.). Biochimica et Biophysica Acta 2005, 1729(2): 118-125.
43. Hollick JB, Patterson GI, Asmundsson IM, Chandler VL: Paramutation alters regulatory control of the maize pi locus. Genetics 2000, 154(4): 1827-1838.
44. Maxon ME, Goodrich JA, Tjian R: Transcription factor IIE binds preferentially to RNA polymerase IIa and recruits TFIIH: a model for promoter clearance. Genes Dev 1994, 8(5):515-524.
45. Okamoto T, Yamamoto S, Watanabe Y, Ohta T, Hanaoka F, Roeder RG, Ohkuma Y: Analysis of the role of TFIIE in transcriptional regulation through structure-function studies of the TFIIE-beta subunit. J Biol Chem 1998, 273(31): 19866-19876.
46. Zhang Z, Gu J, Gu X: How much expression divergence after yeast gene duplication could be explained by regulatory motif evolution? Trends Genet 2004, 20(9):403-407.
47. Adams KL, Wendel JF: Novel patterns of gene expression in polyploid plants. Trends Genet 2005, 21(10):539-543.
48. Rice Information System [http://rise.genomics.org.cn/rice/ index2.jsp]
49. Knowledge-based Oryza Molecular biological Encyclopedia [http://cdna01.dna.affrc.go.jp/cDNA/]
50. National Center for Biotechnology Information [http://www.ncbi. nih.gov/]
51. Kent WJ: BLAT - the BLAST-like alignment tool. Genome Res 2002, 12(4):656-664.
52. McDermott J, Bumgarner R, Samudrala R: Functional annotation from predicted protein interaction networks, Bioinformatics 2005, 21(15):3217-3226.
53. IDEG6 [http://telethon.bio.unipd.it/bioinfo/IDEG6/]
54. Romualdi C, Bortoluzzi S, Danieli GA: Detecting differentially expressed genes in multiple tag sampling experiments: comparative evaluation of statistical tests. Hum Mol Genet 2001, 10(19):2133-2141.