Hostname: page-component-78c5997874-v9fdk Total loading time: 0 Render date: 2024-11-19T19:30:20.875Z Has data issue: false hasContentIssue false
  • English
  • Français

Genome-wide analyses of gene activity during seed development

Published online by Cambridge University Press:  05 January 2012

John J. Harada  and
Julie Pelletier
John J. Harada*
Affiliation:
Department of Plant Biology, University of California, One Shields Avenue, Davis, CA 95616, USA
Julie Pelletier
Affiliation:
Department of Plant Biology, University of California, One Shields Avenue, Davis, CA 95616, USA
*
*Correspondence Email: [email protected]
Get access Rights & Permissions [Opens in a new window]

Abstract

The seed consists of three distinct regions, the zygotic embryo and endosperm and the maternal seed coat. Development of the seed requires co-ordinated growth and differentiation within each of these regions. Although the major events that occur during seed development have been studied extensively at the anatomical, physiological and molecular level, a comprehensive understanding of gene activity in each seed region has been lacking. DNA microarrays and extensive sequencing of cDNA libraries permit genome-wide analyses of mRNA populations of biological samples. We review recent studies of genome-wide gene activity that illustrate approaches used to provide new insights into the processes that occur during seed development.

Keywords

ArabidopsisDNA microarrayembryoendospermRNA sequencingseed coat
Type
Review Article
Information
Seed Science Research , Volume 22 , Supplement S1: Seed Science in the 21st Century , February 2012 , pp. S15 - S22
Copyright
Copyright © Cambridge University Press 2012

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle Scholar
Berger, F. and Chaudhury, A. (2009) Parental memories shape seeds. Trends in Plant Science 14, 550–556.CrossRefGoogle ScholarPubMed
Bewley, J.D. and Black, M. (1994) Seeds: physiology of development and germination. New York, Plenum Publishing Corporation.CrossRefGoogle Scholar
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.CrossRefGoogle Scholar
Brown, R.C., Lemmon, B.E., Nguyen, H. and Olsen, O.A. (1999) Development of endosperm in Arabidopsis thaliana. Sexual Plant Reproduction 12, 32–42.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.Google Scholar
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.CrossRefGoogle Scholar
Day, R.C., McNoe, L.A. and Macknight, R.C. (2007) Transcript analysis of laser microdissected plant cells. Physiologia Plantarum 129, 267–282.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Grossniklaus, U. and Vielle-Calzada, J.-P. (1998) … response: Parental conflict and infanticide during embryogenesis. Trends in Plant Science 3, 328.CrossRefGoogle Scholar
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.Google Scholar
Harada, J.J. (1997) Seed maturation and control of germination. pp. 545–592 in Larkins, B.A.; Vasil, I.K. (Eds) Advances in cellular and molecular biology of plants. Dordrecht, Kluwer Academic.Google Scholar
Haughn, G. and Chaudhury, A. (2005) Genetic analysis of seed coat development in Arabidopsis. Trends in Plant Science 10, 472–477.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Huh, J.H., Bauer, M.J., Hsieh, T.F. and Fischer, R.L. (2008) Cellular programming of plant gene imprinting. Cell 132, 735–744.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Jofuku, K.D., Boer, B., Montagu, M.V. and Okamuro, J.K. (1994) Control of Arabidopsis flower and seed development by the homeotic gene APETALA2. Plant Cell 6, 1211–1225.Google ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Lopes, M.A. and Larkins, B.A. (1993) Endosperm origin, development, and function. Plant Cell 5, 1383–1399.Google Scholar
Lucas, M., Laplaze, L. and Bennett, M.J. (2011) Plant systems biology: network matters. Plant Cell & Environment 34, 535–553.CrossRefGoogle ScholarPubMed
Mardis, E.R. (2008) Next-generation DNA sequencing methods. Annual Review of Genomics and Human Genetics 9, 387–402.CrossRefGoogle ScholarPubMed
Meinke, D., Muralla, R., Sweeney, C. and Dickerman, A. (2008) Identifying essential genes in Arabidopsis thaliana. Trends in Plant Science 13, 483–491.CrossRefGoogle ScholarPubMed
Moreno-Risueno, M.A., Busch, W. and Benfey, P.N. (2010) Omics meet networks – using systems approaches to infer regulatory networks in plants. Current Opinion in Plant Biology 13, 126–131.CrossRefGoogle ScholarPubMed
Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. and Wold, B. (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods 5, 621–628.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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 proliferation in angiosperm embryogenesis. Nature Genetics 38, 63–67.CrossRefGoogle ScholarPubMed
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.Google Scholar
Olsen, O.-A. (2004) Nuclear endosperm development in cereals and Arabidopsis thaliana. Plant Cell 16, S214–S227.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Raissig, M.T., Baroux, C. and Grossniklaus, U. (2011) Regulation and flexibility of genomic imprinting during seed development. Plant Cell 23, 16–26.CrossRefGoogle ScholarPubMed
Ruan, Y., Gilmore, J. and Conner, T. (1998) Towards Arabidopsis genome analysis: monitoring expression profiles of 1400 genes using cDNA microarrays. Plant Journal 15, 821–833.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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 regulation of AGAMOUS-LIKE36. PLOS Genetics 7, e1001303.CrossRefGoogle ScholarPubMed
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/.Google Scholar
Western, T.L., Burn, J., Tan, W.L., Skinner, D.J., Martin-McCaffrey, 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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed