Genome-wide analyses of gene activity during seed development

Seed Science Research

Volumn 22, Issue SUPPL. 1, 2012, Pages

  Harada, John J ^a   Pelletier, Julie ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Arabidopsis; DNA microarray; embryo; endosperm; RNA sequencing; seed coat

Indexed keywords

ARABIDOPSIS;

EID: 84855791008     PISSN: 09602585     EISSN: None     Source Type: Journal    
DOI: 10.1017/S0960258511000304     Document Type: Review

References (50)

1. Autran, D., Baroux, C., Raissig, M.T., Lenormand, T., Wittig, M., Grob, S., Steimer, A., Barann, M., Klostermeier, U.C., Leblanc, O., Vielle-Calzada, J.P., Rosenstiel, P., Grimanelli, D. and Grossniklaus, U. (2011) Maternal epigenetic pathways control parental contributions to Arabidopsis early embryogenesis. Cell 145, 707-719.
2. Baroux, C., Autran, D., Gillmor, C.S., Grimanelli, D. and Grossniklaus, U. (2008) The maternal to zygotic transition in animals and plants. Cold Spring Harbor Symposia on Quantitative Biology 73, 89-100.
3. Baud S., Dubreucq B., Miquel M., Rochat C. and Lepiniec L. (2008) Storage reserve accumulation in Arabidopsis: metabolic and developmental control of seed filling. The Arabidopsis Book, e0113. The American Society of Plant Biologists. http://www.bioone.org/loi/arbo.j. doi: 10.1199/tab.0113.
4. Baud, S. and Lepiniec, L. (2009) Regulation of de novo fatty acid synthesis in maturing oilseeds of Arabidopsis. Plant Physiology and Biochemistry 47, 448-455.
5. Beeckman, T., De Rycke, R., Viane, R. and Inzé, D. (2000) Histological study of seed coat development in Arabidopsis thaliana. Journal of Plant Research 113,139-148.
6. Beisson, F., Koo, A.J.K., Ruuska, S., Schwender, J., Pollard, M., Thelen, J.J., Paddock, T., Salas, J.J., Savage, L., Milcamps, A., Mhaske, V.B., Cho, Y. and Ohlrogge, J.B. (2003) Arabidopsis genes involved in acyl lipid metabolism. A 2003 census of the candidates, a study of the distribution of expressed sequence tags in organs, and a web-based database. Plant Physiology 132, 681-697. (Pubitemid 36715066)
7. Berger, F. and Chaudhury, A. (2009) Parental memories shape seeds. Trends in Plant Science 14, 550-556.
8. Bewley, J.D. and Black, M. (1994) Seeds: physiology of development and germination. New York, Plenum Publishing Corporation.
9. Boisnard-Lorig, C., Colon-Carmona, A., Bauch, M., Hodge, S., Doerner, P., Bancharel, E., Dumas, C., Haseloff, J. and Berger, F. (2001) Dynamic analyses of the expression of the HISTONE:YFP fusion protein in Arabidopsis show that syncytial endosperm is divided in mitotic domains. Plant Cell 13,495-509. (Pubitemid 32265371)
10. Brown, R.C., Lemmon, B.E., Nguyen, H. and Olsen, O.A. (1999) Developmentofendosperm in Arabidopsis thaliana. Sexual Plant Reproduction 12, 32-42.
11. Burow, M., Halkier, B.A. and Kliebenstein, D.J. (2010) Regulatory networks of glucosinolates shape Arabidopsis thaliana fitness. Current Opinion in Plant Biology 13, 347-352.
12. Capron, A., Chatfield, S., Provart, N. and Berleth, T. (2009) Embryogenesis: pattern formation from a single cell. The Arabidopsis Book. pp. 1-28, The American Society of Plant Biologists.
13. Da Silva Conceição, A. and Krebbers, E. (1994) A cotyledon regulatory region is responsible for the different spatial expression patterns of Arabidopsis 2S albumin genes. Plant Journal 5,493-505.
14. Day, R.C., Mc Noe, L.A. and Macknight, R.C. (2007) Transcript analysis of laser microdissected plant cells. Physiologia Plantarum 129, 267-282. (Pubitemid 46072483)
15. Day, R.C., Herridge, R.P., Ambrose, B.A. and Macknight, R.C. (2008) Transcriptome analysis of proliferating Arabidopsis endosperm reveals biological implications for the control of syncytial division, cytokinin signaling, and gene expression regulation. Plant Physiology 148, 1964-1984. (Pubitemid 352847474)
16. Dean, G., Cao, Y., Xiang, D., Provart, N.J., Ramsay, L., Ahad, A., White, R., Selvaraj, G., Datla, R. and Haughn, G. (2011) Analysis of gene expression patterns during seed coat development in Arabidopsis. Mol. Plant 4, 1074-1091.
17. Debeaujon, I., Nesi, N., Perez, P., Devic, M., Grandjean, O., Caboche, M. and Lepiniec, L. (2003) Proanthocyanidin-accumulating cells in Arabidopsis testa: regulation of differentiation and role in seed development. Plant Cell 15, 2514-2531. (Pubitemid 37470655)
18. Garcia, D., Fitz Gerald, J.N. and Berger, F. (2005) Maternal control of integument cell elongation and zygotic control of endosperm growth are coordinated to determine seed size in Arabidopsis. Plant Cell 17, 52-60. (Pubitemid 41672987)
19. Grossniklaus, U. and Vielle-Calzada, J.-P. (1998) ... response: Parental conflict and infanticide during embryogenesis. Trends in Plant Science 3, 328. (Pubitemid 28422232)
20. Haig, D. and Westoby, M. (1991) Genomic imprinting in the endosperm: its effect on seed development in crosses between species, and between different ploidies of the same species, and its implications for the evolution of apomixis. Philosophical Transactions of the Royal Society London 333,1-13.
21. Harada, J.J. (1997) Seed maturation and control of germina-tion. pp. 545-592 in Larkins, BA.; Vasil, I.K. (Eds) Advances in cellular and molecular biology of plants. Dordrecht, Kluwer Academic.
22. Haughn, G. and Chaudhury, A. (2005) Genetic analysis of seed coat development in Arabidopsis. Trends in Plant Science 10, 472-477. (Pubitemid 41395268)
23. Hsieh, T.F., Shin, J.Y., Uzawa, R., Silva, P., Cohen, S., Bauer, M.J., Hashimoto, M., Kirkbride, R.C., Harada, J.J., Zilberman, D. and Fischer, R.L. (2011) Regulation of imprinted gene expression in Arabidopsis endosperm. Proceedings of the National Academy of Sciences USA 108, 1755-1762.
24. Huh, J.H., Bauer, M.J., Hsieh, T.F. and Fischer, R.L. (2008) Cellular programming of plant gene imprinting. Cell 132, 735-744. (Pubitemid 351312806)
25. Jenik, P.D., Gillmor, C.S. and Lukowitz, W. (2007) Embryonic patterning in Arabidopsis thaliana. Annual Review of Cellular and Developmental Biology 23, 207-236.
26. Jofuku, K.D., Boer, B., Montagu, M.V. and Okamuro, J.K. (1994) Control of Arabidopsis flower and seed develop-ment by the homeotic gene APETALA2. Plant Cell 6, 1211-1225.
27. Kiyosue, T., Ohad, N., Yadegari, R., Hannon, M., Dinneny, J., Wells, D., Katz, A., Margossian, L., Harada, J.J., Goldberg, R.B. and Fischer, R.L. (1999) Control of fertilization-independent endosperm development by the MEDEA polycomb gene in Arabidopsis. Proceedings of the National Academy of Sciences USA 96, 4186-4191. (Pubitemid 29169058)
28. Le, B.H., Cheng, C., Bui, A.Q., Wagmaister, J.A., Henry, K.F., Pelletier, J., Kwong, L., Belmonte, M., Kirkbride, R., Horvath, S., Drews, G.N., Fischer, R.L., Okamuro, J.K., Harada, J.J. and Goldberg, R.B. (2010) Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors. Proceedings of the National Academy of Sciences USA 107, 8063-8070.
29. Li, C. and Wong, W.H. (2001) Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection. Proceedings of the National Academy of Sciences USA 98, 31-36. (Pubitemid 32095858)
30. Lopes, M.A. and Larkins, B.A. (1993) Endosperm origin, development, and function. Plant Cell 5,1383-1399. (Pubitemid 2001816)
31. Lucas, M., Laplaze, L. and Bennett, M.J. (2011) Plant systems biology: network matters. Plant Cell & Environment 34, 535-553.
32. Mardis, E.R. (2008) Next-generation DNA sequencing methods. Annual Review of Genomics and Human Genetics 9, 387-402.
33. Meinke, D., Muralla, R., Sweeney, C. and Dickerman, A. (2008) Identifying essential genes in Arabidopsis thaliana. Trends in Plant Science 13, 483-491.
34. Moreno-Risueno, M.A., Busch, W. and Benfey, PN. (2010) Omics meet networks - using systems approaches to infer regulatory networks in plants. Current Opinion in Plant Biology 13, 126-131.
35. Mortazavi, A., Williams, B.A., Mc Cue, K., Schaeffer, L. and Wold, B. (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods 5, 621-628. (Pubitemid 351911867)
36. Nesi, N., Debeaujon, I., Jond, C., Stewart, A.J., Jenkins, G.I., Caboche, M. and Lepiniec, L. (2002) The TRANSPARENT TESTA16 locus encodes the ARABIDOPSIS BSISTER MADS domain protein and is required for proper development and pigmentation of the seed coat. Plant Cell 14, 2463-2479. (Pubitemid 35224843)
37. Nowack, M.K., Grini, P.E., Jakoby, M.J., Lafos, M., Koncz, C. and Schnittger, A. (2006) A positive signal from the fertilization of the egg cell sets off endosperm prolifer-ation in angiosperm embryogenesis. Nature Genetics 38, 63-67. (Pubitemid 43011883)
38. Ohto, M., Stone, S.L. and Harada, J.J. (2008) Genetic control of seed development and seed mass. pp. 1-24 in Bradford, K.J.; Nonogaki, H. (Eds) Seed development, dormancy, and germination. Oxford, Blackwell Publishing.
39. Olsen, O.-A. (2004) Nuclear endosperm development in cereals and Arabidopsis thaliana. Plant Cell 16, S214-S227. (Pubitemid 38774230)
40. Pang, P.P., Pruitt, R.E. and Meyerowitz, E.M. (1988) Molecular cloning, genomic organization, expression and evolution of 12S seed storage protein genes of Arabidopsis thaliana. Plant Molecular Biology 11, 805-820.
41. Raissig, M.T., Baroux, C. and Grossniklaus, U. (2011) Regulation and flexibility of genomic imprinting during seed development. Plant Cell 23, 16-26.
42. Ruan, Y., Gilmore, J. and Conner, T. (1998) Towards Arabidopsis genome analysis: monitoring expression profiles of 1400 genes using c DNA microarrays. Plant Journal 15, 821-833.
43. Schena, M., Shalon, D., Davis, R.W. and Brown, P.O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray Science 270, 467-470.
44. Scott, R.J., Spielman, M., Bailey, J. and Dickinson, H.G. (1998) Parent-of-origin effects on seed development in Arabidopsis thaliana. Development 125, 3329-3341. (Pubitemid 28458333)
45. Shirzadi, R., Andersen, E.D., Bjerkan, K.N., Gloeckle, B.M., Heese, M., Ungru, A., Winge, P., Koncz, C., Aalen, R.B., Schnittger, A. and Grini, P.E. (2011) Genome-wide transcript profiling of endosperm without paternal contribution identifies parent-of-origin-dependent regu-lation of AGAMOUS-LIKE36. PLOS Genetics 7, e1001303.
46. Tiwari, S., Spielman, M., Schulz, R., Oakey, R.J., Kelsey, G., Salazar, A., Zhang, K., Pennell, R. and Scott, R.J. (2010) Transcriptional profiles underlying parent-of-origin effects in seeds of Arabidopsis thaliana. BMC Plant Biology 10:72 http://www.biomedcentral.com/bmcplantbiol/.
47. Western, T.L., Burn, J., Tan, W.L., Skinner, D.J., Martin-Mc Caffrey, L., Moffatt, B.A. and Haughn, G.W. (2001 Isolation and characterization of mutants defective in seed coat mucilage secretory cell development in Arabidopsis. Plant Physiology 127, 998-1011. (Pubitemid 33112160)
48. White, J.A., Todd, J., Newman, T., Focks, N., Girke, T., de Ilárduya, O.M.n., Jaworski, J.G., Ohlrogge, J.B. and Benning, C. (2000) A new set of Arabidopsis expressed sequence tags from developing seeds: the metabolic pathway from carbohydrates to seed oil. Plant Physiology 124, 1582-1594. (Pubitemid 32053494)
49. Xiang, D.Q., Venglat, P., Tibiche, C., Yang, H., Risseeuw, E., Cao, Y.G., Babic, V., Cloutier, M., Keller, W., Wang, E., Selvaraj, G. and Datla, R. (2011) Genome-wide analysis reveals gene expression and metabolic network dynamics during embryo development in Arabidopsis. Plant Physiology 156, 346-356.
50. Yuan, J.S., Galbraith, D.W., Dai, S.Y., Griffin, P. and Stewart, C.N. Jr (2008) Plant systems biology comes of age. Trends in Plant Science 13, 165-171.