Probing the endosperm gene expression landscape in Brassica napus

BMC Genomics

Volumn 10, Issue , 2009, Pages

  Huang, Yi ^a   Chen, Liang ^a,b   Wang, Liping ^a   Vijayan, Kannan ^a   Phan, Sieu ^a   Liu, Ziying ^a   Wan, Lianglu ^a   Ross, Andrew ^a   Xiang, Daoquan ^a   Datla, Raju ^a   Pan, Youlian ^a   Zou, Jitao ^a  

^a NATIONAL RESEARCH COUNCIL CANADA   (Canada)

^b XIAMEN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR; PLANT DNA; VEGETABLE PROTEIN;

AMINO ACID SEQUENCE; ARABIDOPSIS; ARTICLE; COTYLEDON; ENDOSPERM; GENE EXPRESSION; GENE IDENTIFICATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENETICS; PLANT LEAF; PROTEIN ANALYSIS; PROTEIN MICROARRAY; RAPESEED; SEED DEVELOPMENT; DNA MICROARRAY; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; PLANT GENE; PLANT SEED; PRENATAL DEVELOPMENT;

BRASSICA NAPUS;

BRASSICA NAPUS; DNA, PLANT; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENE LIBRARY; GENES, PLANT; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANT PROTEINS; SEEDS; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION FACTORS;

EID: 67649595540     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-256     Document Type: Article

References (71)

1. Hill LM Morley-Smith ER Rawsthorne S Metabolism of Sugars in the Endosperm of Developing Seeds of Oilseed Rape Plant Physiol 2003, 131(1):228-236. 166802 12529530 10.1104/pp.010868
2. Scott RJ Spielman M Bailey J Dickinson HG Parent-of-origin effects on seed development in Arabidopsis thaliana Development 1998, 125(17):3329-3341. 9693137
3. Penfield S Rylott EL Gilday AD Graham S Larson TR Graham IA Reserve mobilization in the Arabidopsis endosperm fuels hypocotyl elongation in the dark, is independent of abscisic acid, and requires PHOSPHOENOLPYRUVATE CARBOXYKINASE1 Plant Cell 2004, 16(10):2705-2718. 520966 15367715 10.1105/tpc.104.024711
4. Ohad N Margossian L Hsu YC Williams C Repetti P Fischer RL A mutation that allows endosperm development without fertilization Proceedings of the National Academy of Sciences of the United States of America 1996, 93(11):5319-5324. 39243 11607683 10.1073/pnas.93.11.5319
5. Chaudhury AM Ming L Miller C Craig S Dennis ES Peacock WJ Fertilization-independent seed development in Arabidopsis thaliana Proceedings of the National Academy of Sciences of the United States of America 1997, 94(8):4223-4228. 20611 9108133 10.1073/pnas.94.8.4223
6. Garcia D Saingery V Chambrier P Mayer U Jurgens G Berger F Arabidopsis haiku mutants reveal new controls of seed size by endosperm Plant physiology 2003, 131(4):1661-1670. 166922 12692325 10.1104/pp.102.018762
7. Lai J Dey N Kim CS Bharti AK Rudd S Mayer KF Larkins BA Becraft P Messing J Characterization of the maize endosperm transcriptome and its comparison to the rice genome Genome research 2004, 14(10A):1932-1937. 524417 15466291 10.1101/gr.2780504
8. Laudencia-Chingcuanco DL Stamova BS Lazo GR Cui X Anderson OD Analysis of the wheat endosperm transcriptome Journal of applied genetics 2006, 47(4):287-302. 17132893
9. Lu C Wallis J Browse J An analysis of expressed sequence tags of developing castor endosperm using a full-length cDNA library BMC Plant Biology 2007, 7(1):42. 1950504 17672910 10.1186/1471-2229-7-42
10. Tiwari S Spielman M Day RC Scott RJ Proliferative phase endosperm promoters from Arabidopsis thaliana Plant Biotechnology Journal 2006, 4(4):393-407. 10.1111/j.1467-7652.2006.00189.x 17177805
11. Prakash S Hinata K Taxonomy, cytogenetics and origin of crop Brassicas, a review Opera Botanica 1980, 55:1-57.
12. Bowman J ed Arabidopsis: An Atlas of Morphology and Development Berlin: Springer-Verlag 1, 1994.
13. Brown RC Lemmon BE Nguyen H Olsen O-A Development of endosperm in Arabidopsis thaliana Sexual Plant Reproduction 1999, 12(1):32-42. 10.1007/s004970050169
14. Abernathy JW Xu P Li P Xu DH Kucuktas H Klesius P Arias C Liu Z Generation and analysis of expressed sequence tags from the ciliate protozoan parasite Ichthyophthirius multifiliis BMC Genomics 2007, 8:176. 1906770 17577414 10.1186/1471-2164-8-176
15. Gene Ontology (GO) Consortium http://www.geneontology.org
16. Brassica endosperm EST database http://bioinfo.pbi.nrc.ca/home/ service_est.html
17. White JA Todd J Newman T Focks N Girke T de Ilarduya OM Jaworski JG Ohlrogge JB Benning C A new set of Arabidopsis expressed sequence tags from developing seeds. The metabolic pathway from carbohydrates to seed oil Plant physiology 2000, 124(4):1582-1594. 59857 11115876 10.1104/ pp.124.4.1582
18. Borner GH Lilley KS Stevens TJ Dupree P Identification of glycosylphosphatidylinositol-anchored proteins in Arabidopsis. A proteomic and genomic analysis Plant physiology 2003, 132(2):568-577. 166998 12805588 10.1104/pp.103.021170
19. Park SY Jauh GY Mollet JC Eckard KJ Nothnagel EA Walling LL Lord EM A lipid transfer-like protein is necessary for lily pollen tube adhesion to an in vitro stylar matrix Plant Cell 2000, 12(1):151-164. 140221 10634914 10.1105/tpc.12.1.151
20. Arabidopsis e-FP browser http://www.bar.utoronto.ca/efp/cgi-bin/ efpWeb.cgi
21. Kumari S Mayor S ARF1 is directly involved in dynamin-independent endocytosis Nat Cell Biol 2008, 10(1):30-41. 10.1038/ncb1666 18084285
22. Horiguchi G Kim GT Tsukaya H The transcription factor AtGRF5 and the transcription coactivator AN3 regulate cell proliferation in leaf primordia of Arabidopsis thaliana Plant J 2005, 43(1):68-78. 10.1111/ j.1365-313X.2005.02429.x 15960617
23. PRoteomics IDEntifications database http://www.ebi.ac.uk/pride/
24. Feiler HS Desprez T Santoni V Kronenberger J Caboche M Traas J The higher plant Arabidopsis thaliana encodes a functional CDC48 homologue which is highly expressed in dividing and expanding cells EMBO J 1995, 14(22):5626-5637. 394678 8521820
25. Chen Q Steinhauer L Hammerlindl J Keller W Zou J Biosynthesis of Phytosterol Esters: Identification of a Sterol O-acyltransferase in Arabidopsis Plant Physiol 2007, 107.106278.
26. Rautengarten C Steinhauser D Bussis D Stintzi A Schaller A Kopka J Altmann T Inferring hypotheses on functional relationships of genes: Analysis of the Arabidopsis thaliana subtilase gene family PLoS Comput Biol 2005, 1(4):e40. 1236819 16193095 10.1371/journal.pcbi.0010040
27. Tanaka H Onouchi H Kondo M Hara-Nishimura I Nishimura M Machida C Machida Y A subtilisin-like serine protease is required for epidermal surface formation in Arabidopsis embryos and juvenile plants Development 2001, 128(23):4681-4689. 11731449
28. Xiang D Datla R Li F Cutler A Malik MR Krochko JE Sharma N Fobert P Georges F Selvaraj G et al Development of a Brassica seed cDNA microarray Genome/National Research Council Canada = Genome/Conseil national de recherches Canada 2008, 51(3):236-242. 18356959
29. Series record (GSE14766) in GEO http://www.ncbi.nlm.nih.gov/geo/info/ linking.html
30. Breitling R Armengaud P Amtmann A Herzyk P Rank products: A simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments FEBS letters 2004, 573(1-3):83-92. 10.1016/j.febslet.2004.07.055 15327980
31. Phan S Famili F Tang Z Pan Y Liu Z Ouyang J Lenferink A O'connor MM-C A novel pattern based clustering methodology for time-series microarray data International Journal of Computer Mathematics 2007, 84(5):585-597. 10.1080/00207160701203419
32. KEGG enzyme database ftp://ftp.genome.jp/pub/kegg/genes/organisms/ath/
33. TAIR pathway database ftp://ftp.arabidopsis.org/home/tair/Pathways/
34. Morley-Smith ER Pike MJ Findlay K Kockenberger W Hill LM Smith AM Rawsthorne S The Transport of Sugars to Developing Embryos Is Not via the Bulk Endosperm in Oilseed Rape Seeds Plant physiology 2008, 147(4):2121-2130. 2492605 18562765 10.1104/pp.108.124644
35. King SP Lunn JE Furbank RT Carbohydrate Content and Enzyme Metabolism in Developing Canola Siliques Plant physiology 1997, 114(1):153-160. 158289 12223695
36. Fallahi H Scofield GN Badger MR Chow WS Furbank RT Ruan YL Localization of sucrose synthase in developing seed and siliques of Arabidopsis thaliana reveals diverse roles for SUS during development J Exp Bot 2008, 59(12):3283-3295. 2529237 18635527 10.1093/jxb/ern180
37. Ruuska SA Girke T Benning C Ohlrogge JB Contrapuntal Networks of Gene Expression during Arabidopsis Seed Filling Plant Cell 2002, 14(6):1191-1206. 150774 12084821 10.1105/tpc.000877
38. Hrabak EM Chan CW Gribskov M Harper JF Choi JH Halford N Kudla J Luan S Nimmo HG Sussman MR et al The Arabidopsis CDPK-SnRK superfamily of protein kinases Plant physiology 2003, 132(2):666-680. 167006 12805596 10.1104/pp.102.011999
39. Raboy V myo-Inositol-1,2,3,4,5,6-hexakisphosphate Phytochemistry 2003, 64(6):1033-1043. 10.1016/S0031-9422(03)00446-1 14568069
40. Otegui MS Capp R Staehelin LA Developing seeds of Arabidopsis store different minerals in two types of vacuoles and in the endoplasmic reticulum Plant Cell 2002, 14(6):1311-1327. 150782 12084829 10.1105/ tpc.010486
41. Shi J Wang H Hazebroek J Ertl DS Harp T The maize low-phytic acid 3 encodes a myo-inositol kinase that plays a role in phytic acid biosynthesis in developing seeds The Plant Journal 2005, 42(5):708-719. 10.1111/j.1365-313X.2005.02412.x 15918884
42. Shukla S VanToai TT Pratt RC Expression and Nucleotide Sequence of an INS (3) P1 Synthase Gene Associated with Low-Phytate Kernels in Maize (Zea mays L.) J Agric Food Chem 2004 52 14 4565 4570 10.1021/jf049976b 15237968
43. Mitsuhashi N Kondo M Nakaune S Ohnishi M Hayashi M Hara-Nishimura I Richardson A Fukaki H Nishimura M Mimura T Localization of myo-inositol-1-phosphate synthase to the endosperm in developing seeds of Arabidopsis J Exp Bot 2008, 59(11):3069-3076. 2504351 18603618 10.1093/jxb/ern161
44. Loenen WA S-adenosylmethionine: Jack of all trades and master of everything? Biochem Soc Trans 2006, 34(Pt 2):330-333. 16545107
45. Radchuk VV Sreenivasulu N Radchuk RI Wobus U Weschke W The methylation cycle and its possible functions in barley endosperm development Plant Mol Biol 2005, 59(2):289-307. 10.1007/s11103-005-8881-1 16247558
46. Pereira LA Todorova M Cai X Makaroff CA Emery RJ Moffatt BA Methyl recycling activities are co-ordinately regulated during plant development J Exp Bot 2007, 58(5):1083-1098. 10.1093/jxb/erl275 17272833
47. Florchinger M Zimmermann M Traub M Neuhaus HE Mohlmann T Adenosine stimulates anabolic metabolism in developing castor bean (Ricinus communis L.) cotyledons Planta 2006:223(2):340-348. 10.1007/ s00425-005-0091-1 16133207
48. Database of Arabidopsis Transcription Factors(DATF) http://datf.cbi.pku.edu.cn/
49. Cernac A Benning C WRINKLED1 encodes an AP2/EREB domain protein involved in the control of storage compound biosynthesis in Arabidopsis Plant J 2004, 40(4):575-585. 10.1111/j.1365-313X.2004.02235.x 15500472
50. Kwong RW Bui AQ Lee H Kwong LW Fischer RL Goldberg RB Harada JJ LEAFY COTYLEDON1-LIKE defines a class of regulators essential for embryo development Plant Cell 2003, 15(1):5-18. 143447 12509518 10.1105/ tpc.006973
51. Gaj MD Zhang S Harada JJ Lemaux PG Leafy cotyledon genes are essential for induction of somatic embryogenesis of Arabidopsis Planta 2005, 222(6):977-988. 10.1007/s00425-005-0041-y 16034595
52. Lotan T Ohto M Yee KM West MA Lo R Kwong RW Yamagishi K Fischer RL Goldberg RB Harada JJ Arabidopsis LEAFY COTYLEDON1 is sufficient to induce embryo development in vegetative cells Cell 1998, 93(7):1195-1205. 10.1016/S0092-8674(00)81463-4 9657152
53. Meinke DW Franzmann LH Nickle TC Yeung EC Leafy Cotyledon Mutants of Arabidopsis Plant Cell 1994, 6(8):1049-1064. 160500 12244265 10.1105/ tpc.6.8.1049
54. Fambrini M Durante C Cionini G Geri C Giorgetti L Michelotti V Salvini M Pugliesi C Characterization of LEAFY COTYLEDON1-LIKE gene in Helianthus annuus and its relationship with zygotic and somatic embryogenesis Dev Genes Evol 2006, 216(5):253-264. 10.1007/s00427-005-0050-7 16450129
55. Santos-Mendoza MDubreucq B Baud S Parcy F Caboche M Lepiniec L Deciphering gene regulatory networks that control seed development and maturation in Arabidopsis Plant J 2008, 54(4):608-620. 10.1111/ j.1365-313X.2008.03461.x 18476867
56. Kagaya Y Toyoshima R Okuda R Usui H Yamamoto A Hattori T LEAFY COTYLEDON1 controls seed storage protein genes through its regulation of FUSCA3 and ABSCISIC ACID INSENSITIVE3 Plant Cell Physiol 2005, 46(3):399-406. 10.1093/pcp/pci048 15695450
57. Li Y Beisson F Pollard M Ohlrogge J Oil content of Arabidopsis seeds: the influence of seed anatomy, light and plant-to-plant variation Phytochemistry 2006, 67(9):904-915. 10.1016/j.phytochem.2006.02.015 16600316
58. Fei H Tsang E Cutler AJ Gene expression during seed maturation in Brassica napus in relation to the induction of secondary dormancy Genomics 2007, 89(3):419-428. 10.1016/j.ygeno.2006.11.008 17207603
59. Vieira J Messing J The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers Gene 1982, 19(3):259-268. 10.1016/0378-1119(82)90015-4 6295879
60. Chou H-H Holmes MH DNA sequence quality trimming and vector removal Bioinformatics 2001, 17(12):1093-1104. 10.1093/bioinformatics/17.12.1093 11751217
61. Trimpoly software http://www.tigr.org/tdb/tgi/software
62. TGICL software http://www.tigr.org/tdb/tgi/software
63. Brassica EST database http://bioinfo.pbi.nrc.ca/newest.beta2/
64. TAIR database http://www.arabidopsis.org/
65. 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. 10.1007/s11103-006-9040-z 16941221
66. Smyth GK Michaud J Scott HS Use of within-array replicate spots for assessing differential expression in microarray experiments Bioinformatics 2005, 21(9):2067-2075. 10.1093/bioinformatics/bti270 15657102
67. Pan Y Pylatuik JD Ouyang J Famili AF Fobert PR Discovery of functional genes for systemic acquired resistance in Arabidopsis thaliana through integrated data mining Journal of bioinformatics and computational biology 2004, 2(4):639-655. 10.1142/S0219720004000776
68. Altschul SF Madden TL Schaffer AA Zhang J Zhang Z Miller W Lipman DJ Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic acids research 1997, 25(17):3389-3402. 146917 9254694 10.1093/nar/25.17.3389
69. ImageJ software http://rsbweb.nih.gov/ij/index.html
70. Teerawanichpan P Hoffman T Ashe P Datla R Selvaraj G Investigations of combinations of mutations in the jellyfish green fluorescent protein (GFP) that afford brighter fluorescence, and use of a version (VisGreen) in plant, bacterial, and animal cells Biochim Biophys Acta 2007, 1770(9):1360-1368. 17658219
71. Jefferson R Assaying chimeric genes in plants: The GUS gene fusion system Plant Molecular Biology Reporter 1987, 5(4):387-405. 10.1007/ BF02667740