Abstract
In the next 20 years, the world population is expected to reach a total of 8.3 billion people. Agriculture will have to produce sufficient food knowing that presently and globally agricultural production nearly matches world consumption. Yet, malnutrition is not only a matter of food amount but also concerns food nutritional quality. In particular, the nutritional value and quality of seeds should be improved to alleviate malnutrition and provide a well-balance diet. Progress in seed biology has considerably benefited from the rise in the last decade of the two model plants Arabidopsis and rice. Along with their genome sequences obtained respectively in 2000 for Arabidopsis and in 2005 for rice, functional genomics became possible because of the rapid development of their mutant libraries, full-length cDNA libraries, stock centers, web-accessible databases, and information portals, such as TAIR (The Arabidopsis Information Resource). Then, the development of high-throughput technological breakthroughs (e.g. DNA and protein array, mass spectrometry) helped to survey the omics state (transcriptome, proteome, and metabolome) of seeds at different developmental and environmental conditions. These approaches fuel candidate genes for seed quality (composition, germination vigor and capacity, good resistance to stress, etc.) that can be confirmed using functional genomics resources. Finally, exploitation of the confirmed candidate genes by plant breeders should improve seed nutritional quality and yield. In this chapter, we discuss how global “omics” technologies can help to find new candidate genes relevant for improvement of seed nutritional quality. Examples of omics application in unraveling the rice seed biology are particularly discussed.
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References
Abe T, Gusti RS, Ono M, Sasahara T (1996) Variations in glutelin and high molecular weight endosperm proteins among subspecies of rice (Oryza sativa L.) detected by two-dimensional electrophoresis. Genes Genet Syst 71:63–68
Agrawal GK, Rakwal R (2006) Rice proteomics: a cornerstone for cereal food crop proteomes. Mass Spectrom Rev 25:1–53
Agrawal GK, Jwa NS, Rakwal R (2009) Rice proteomics: ending phase I and the beginning of phase II. Proteomics 9:935–963
Agrawal GK, Rakwal R (2011) Rice proteomics: a move toward expanded proteome coverage to comparative and functional proteomics uncovers the mysteries of rice and plant biology. Proteomics 11:1630–1649
Agrawal GK, Job D, Zivy M, Agrawal VP, Bradshaw R, Dunn MJ, Haynes PA, van Wijk KJ, Kikuchi S, Renaut J, Weckwerth W, Rakwal R (2011) Time to articulate a vision for the future of plant proteomics—a global perspective. An initiative for establishing the international plant proteomics organization (INPPO). Proteomics 11:1559–1568
Alonso JM, Stepanova AN (2003) T-DNA mutagenesis in Arabidopsis. Methods Mol Biol 236:177–187
Arc E, Galland M, Cueff G, Godin B, Lounifi I, Job D, Rajjou L(2011) Reboot the system thanks to protein post-translational modifications and proteome diversity: how quiescent seeds restart their metabolism to prepare seedling establishment. Proteomics 11:1606–1618
Azevedo RA, Lancien M, Lea PJ (2006) The aspartic acid metabolic pathway, an exciting and essential pathway in plants. Amino acids 30:143–162
Baerenfaller K, Grossmann J, Grobei MA, Hull R, Hirsch-Hoffmann M, Yalovsky S, Zimmermann P, Grossniklaus U, Gruissem W, Baginsky S (2008) Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science 320:938–941
Bailly C, El-Maarouf-Bouteau H, Corbineau F (2008) From intracellular signaling networks to cell death: the dual role of reactive oxygen species in seed physiology. C R Biol 331:806–814
Baroux C, Spillane C, Grossniklaus U (2002) Evolutionary origins of the endosperm in flowering plants. Genome Biol 3:10261–10265
Baud S, Lepiniec L (2009) Regulation of de novo fatty acid synthesis in maturing oilseeds of Arabidopsis. Plant Physiol Biochem 47:448–455
Baud S, Wuilleme S, To A, Rochat C, Lepiniec L (2009) Role of WRINKLED1 in the transcriptional regulation of glycolytic and fatty acid biosynthetic genes in Arabidopsis. Plant J 60:933–947
Bechtold N, Pelletier G (1998) In planta Agrobacterium-mediated transformation of adult Arabidopsis thaliana plants by vacuum infiltration. Methods Mol Biol 82:259–266
Bennetzen JL (2005) Transposable elements, gene creation and genome rearrangement in flowering plants. Curr Opin Genet Dev 15:621–627
Bennetzen JL, Ma J (2003) The genetic colinearity of rice and other cereals on the basis of genomic sequence analysis. Curr Opin Plant Biol 6:128–133
Bent AF (2000) Arabidopsisin planta transformation. Uses, mechanisms, and prospects for transformation of other species. Plant Physiol 124:1540–1547
Bewley JD (1997) Seed germination and dormancy. Plant Cell 9:1055–1066
Bohn L, Meyer AS, Rasmussen SK (2008) Phytate: impact on environment and human nutrition. A challenge for molecular breeding. J Zhejiang Univ Sci B 9:165–191
Bhat SP, Padayatty JD (1975) Transcriptional events during early phase of germination of rice embryo. Nature 256:227–228
Bolot S, Abrouk M, Masood-Quraishi U, Stein N, Messing J, Feuillet C, Salse J (2009) The ‘inner circle’ of the cereal genomes. Curr Opin Plant Biol 12:119–125
Bourgeois M, Jacquin F, Cassecuelle F, Savois V, Belghazi M, Aubert G, Quillien L, Huart M, Marget P, Burstin J (2011) A PQL (protein quantity loci) analysis of mature pea seed proteins identifies loci determining seed protein composition. Proteomics 11:1581–1594
Bruskiewich R, Metz T, McLaren G (2006) Bioinformatics and crop information systems in rice research. Int Rice Res Notes 31:5–12
Candela H, Hake S (2008) The art and design of genetic screens: maize. Nat Rev Genet 9:192–203
Chai G, Bai Z, Wei F, King GJ, Wang C, Shi L, Dong C, Chen H, Liu S (2010) BrassicaGLABRA2 genes: analysis of function related to seed oil content and development of functional markers. Theor Appl Genet 120:1597–1610
Chantret N, Salse J, Sabot F, Rahman S, Bellec A, Laubin B, Dubois I, Dossat C, Sourdille P, Joudrier P, Gautier MF, Cattolico L, Beckert M, Aubourg S, Weissenbach J, Caboche M, Bernard M, Leroy P, Chalhoub B (2005) Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (Triticum and Aegilops). Plant Cell 17:1033–1045
Charles D (2006) Species conservation. A ‘forever’ seed bank takes root in the Arctic. Science 312:1730–1731
Chen T, Nayak N Majee SM, Lowenson J, Schäfermeyer KR, Eliopoulos AC, Lloyd TD, Dinkins R, Perry SE, Forsthoefel NR, Clarke SG, Vernon DM, Zhou ZS, Rejtar T, Downie AB (2010b) Substrates of the Arabidopsis thaliana protein isoaspartyl methyltransferase 1 identified using phage display and biopanning. J Biol Chem 285:37281–37292
Cordain L (1999) Cereal grains: humanity’s double edged sword. In: Artemis S (ed) Evolutionary aspects of nutrition and health diet, exercise, genetics and chronic disease, vol 84. Karger, Basel, pp 19–73
Dao TH (2003) Polyvalent cation effects on myo-inositol hexakis dihydrogenphosphate enzymatic dephosphorylation in dairy wastewater. J Environ Qual 32:694–701
DellaPenna D, Pogson BJ (2006) Vitamin synthesis in plants: tocopherols and carotenoids. Annu Rev Plant Biol 57:711–738
Devaiah SP, Pan X, Hong Y, Roth M, Welti R, Wang X (2007) Enhancing seed quality and viability by suppressing phospholipase D in Arabidopsis. Plant J 50:950–957
Droc G, Ruiz M, Larmande P, Pereira A, Piffanelli P, Morel JB, Dievart A, Courtois B, Guiderdoni E, Périn C (2006) OryGenesDB: a database for rice reverse genetics. Nucl Acids Res 34:D736–D740
Emami K, Morris NJ, Cockell SJ, Golebiowska G, Shu QY, Gatehouse AM (2010) Changes in protein expression profiles between a low phytic acid rice (Oryza sativa L. Ssp. japonica) line and its parental line: a proteomic and bioinformatic approach. J Agric Food Chem 58:6912–6922
Ermolaeva MD, Wu M, Eisen JA, Salzberg SL (2003) The age of the Arabidopsis thaliana genome duplication. Plant Mol Biol 51:859–866
Fait A, Angelovici R, Less H, Ohad I, Urbanczyk-Wochniak E, Fernie AR, Galili G (2006) Arabidopsis seed development and germination is associated with temporally distinct metabolic switches. Plant Physiol 142:839–854
Feschotte C (2008) Transposable elements and the evolution of regulatory networks. Nat Rev Genet 9:397–405
Feschotte C, Jiang N, Wessler SR (2002) Plant transposable elements: where genetics meets genomics. Nat Rev Genet 3:329–341
Feuillet C, Langridge P, Waugh R (2008) Cereal breeding takes a walk on the wild side. Trends Genet 24:24–32
Fincher GB (1989) Molecular and cellular biology associated with endosperm mobilization in geminating cereal grain. Annu Rev Plant Physiol Plant Mol Biol 40:305–346
Finch-Savage WE, Leubner-Metzger G (2006) Seed dormancy and the control of germination. New Phytol 171:501–523
Finnie C, Svensson B (2009) Barley seed proteomics from spots to structures. J Proteomics 72:315–324
Fitzgerald MA, McCouch SR, Hall RD (2009) Not just a grain of rice: the quest for quality. Trends Plant Sci 14:133–139
Focks N, Benning C (1998) Wrinkled 1: a novel, low seed-soil-mutant Arabidopsis with a deficiency in the seed-specific regulation of carbohydrate metabolism. Plant Physiol 118:91–101
Frohlich MW, Chase MW (2007) After a dozen years of progress the origin of angiosperms is still a great mystery. Nature 450:1184–1189
Fukuzawa K, Tokumura A, Ouchi S, Tsukatani H (1982) Antioxidant activities of tocopherols on Fe2+-ascorbate-induced lipid peroxidatoin in lecithin liposomes. Lipids 17:511–513
Gallardo K, Job C, Groot SPC, Puype M, Demol H, Vandekerckhove J, Job D (2001) Proteomic analysis of Arabidopsis seed germination and priming. Plant Physiol 126:835–848
Gallardo K, Firnhaber C, Zuber H, Hericher D, Belghazi M, Henry C, Kuster H, Thompson RD (2007) A combined proteome and transcriptome analysis of developing Medicago truncatula seeds. Mol Cell Proteomics 6:2165–2179
Germain V, Rylott EL, Larson TR, Sherson SM, Bechtold N, Carde JP, Bryce JH, Graham IA, Smith SM (2001) Requirement for 3-ketoacyl-CoA thiolase-2 in peroxisome development, fatty acid beta-oxidation and breakdown of triacylglycerol in lipid bodies of Arabidopsis seedlings. Plant J 28:1–12
Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun WL, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100
Gutierrez L, Van Wuytswinkel O, Castelain M, Bellini C (2007) Combined networks regulating seed maturation. Trends Plant Sci 12:294–300
Hajduch M, Casteel JE, Tang S, Hearne LB, Knapp S, Thelen JJ (2007) Proteomic analysis of near-isogenic sunflower varieties differing in seed oil traits. J Proteome Res 6:3232–3241
Herman EM, Larkins BA (1999) Protein storage bodies and vacuoles. Plant Cell 11: 601–614
Holdsworth MJ, Bentsink L, Soppe WJJ (2008a) Molecular networks regulating Arabidopsis seed maturation, after-ripening, dormancy and germination. New Phytol 179:33–54
Holdsworth MJ, Finch-Savage WE, Grappin P, Job D (2008b) Postgenomics dissection of seed dormancy and germination. Trends Plant Sci 13:7–13
Howell KA, Narsai R, Carroll A, Ivanova A, Lohse M, Usadel B, Millar AH, Whelan J (2009) Mapping metabolic and transcript temporal switches during germination in rice highlights specific transcription factors and the role of RNA instability in the germination process. Plant Physiol 149:961–980
Hsieh TF, Shin J, Uzawa R, Silva P, Cohen S, Bauer MJ, Hashimoto M, Kirkbride RC, Harada JJ, Zilberman D, Fischer RL (2011) Regulation of imprinted gene expression in Arabidopsis endosperm. Proc Natl Acad Sci U S A 108:1755–1762
Hurrell RF (2003) Influence of vegetable protein sources on trace element and mineral bioavailability. J Nutr 133:2973S–2977S
International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793–800
International Rice Research Institute, World Rice Statistics (2009) http://ricestat.irri.org:8080/wrs/.Accessed 1 Oct 2012
Inoue H, Higuchi K, Takahashi M, Nakanishi H, Mori S, Nishizawa NK (2003) Three rice nicotianamine synthase genes, OsNAS1, OsNAS2, and OsNAS3 are expressed in cells involved in long-distance transport of iron and differentially regulated by iron. Plant J 36:366–381
Itoh T, Tanaka T, Barrero RA, Yamasaki C, Fujii Y, Hilton PB, Antonio BA, Aono H, Apweiler R, Bruskiewich R, Bureau T, Burr F, Costa de Oliveira A, Fuks G, Habara T, Haberer G, Han B, Harada E, Hiraki AT, Hirochika H, Hoen D, Hokari H, Hosokawa S, Hsing Y, Ikawa H, Ikeo K, Imanishi T, Ito Y, Jaiswal P, Kanno M, Kawahara Y, Kawamura T, Kawashima H, Khurana JP, Kikuchi S, Komatsu S, Koyanagi KO, Kubooka H, Lieberherr D, Lin YC, Lonsdale D, Matsumoto T, Matsuya A, McCombie WR, Messing J, Miyao A, Mulder N, Nagamura Y, Nam J, Namiki N, Numa H, Nurimoto S, O’Donovan C, Ohyanagi H, Okido T, Oota S, Osato N, Palmer LE, Quetier F, Raghuvanshi S, Saichi N, Sakai H, Sakai Y, Sakata K, Sakurai T, Sato F, Sato Y, Schoof H, Seki M, Shibata M, Shimizu Y, Shinozaki K, Shinso Y, Singh NK, Smith-White B, Takeda JI, Tanino M, Tatusova T, Thongjuea S, Todokoro F, Tsugane M, Tyagi AK, Vanavichit A, Wang A, Wing RA, Yamaguchi K, Yamamoto M, Yamamoto N, Yu Y, Zhang H, Zhao Q, Higo K, Burr B, Gojobori T, Sasaki T (2007) Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Res 17:175–183
Izawa T, Shimamoto K (1996) Becoming a model plant: the importance of rice to plant science. Trends Plant Sci 1:95–99
Jain RK, Coffey M, Lai K, Kumar A, MacKenzie SL (2000) Enhancement of seed oil content by expression of glycerol-3-phosphate acyltransferase genes. Biochem Soc Trans 28:958–961
Jaiswal P, Ni J, Yap I, Ware D, Spooner W, Youens-Clark K, Ren L, Liang C, Zhao W, Ratnapu K, Faga B, Canaran P, Fogleman M, Hebbard C, Avraham S, Schmidt S, Casstevens TM, Buckler ES, Stein L, McCouch S (2006) Gramene: a bird’s eye view of cereal genomes. Nucl Acids Res 34:D717–D723
Jako C, Kumar A, Wei Y, Zou J, Barton DL, Giblin EM, Covello PS, Taylor DC (2001) Seed-specific over-expression of an Arabidopsis cDNA encoding a diacylglycerol acyltransferase enhances seed oil content and seed weight. Plant Physiol 126:861–874
Jeon JS, Ryoo N, Hahn TR, Walia H, Nakamura Y (2010) Starch biosynthesis in cereal endosperm. Plant Physiol Biochem 48:383–392
Job C, Rajjou L, Lovigny Y, Belghazi M, Job D (2005) Patterns of protein oxidation in Arabidopsis seeds and during germination. Plant Physiol 138:790–802
Jolliffe NA, Craddock CP, Frigerio L (2005) Pathways for protein transport to seed storage vacuoles. Biochem Soc Trans 33:1016–1018
Jung KH, An G, Ronald PC (2008) Towards a better bowl of rice: assigning function to tens of thousands of rice genes. Nat Rev Genet 9:91–101
Kashkush K, Feldman M, Levy AA (2003) Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nat Genet 33(1):102–106
Kim ST, Kang SY, Wang Y, Kim SG, Hwang du H, Kang KY (2008) Analysis of embryonic proteome modulation by GA and ABA from germinating rice seeds. Proteomics 8:3577–3587
Kondou Y, Higuchi M, Takahashi S, Sakurai T, Ichikawa T, Kuroda H, Yoshizumi T, Tsumoto Y, Horii Y, Kawashima M, Hasegawa Y, Kuriyama T, Matsui K, Kusano M, Albinsky D, Takahashi H, Nakamura Y, Suzuki M, Sakakibara H, Kojima M, Akiyama K, Kurotani A, Seki M, Fujita M, Enju A, Yokotani N, Saitou T, Ashidate K, Fujimoto N, Ishikawa Y, Mori Y, Nanba R, Takata K, Uno K, Sugano S, Natsuki J, Dubouzet JG, Maeda S, Ohtake M, Mori M, Oda K, Takatsuji H, Hirochika H, Matsui M (2009) Systematic approaches to using the FOX hunting system to identify useful rice genes. Plant J 57:883–894
Koornneef M, Meinke D (2010) The development of Arabidopsis as a model plant. Plant J 61:909–291
Koornneef M, Hanhart CJ, Hilhorst HWM, Karssen CM (1989) In vivo inhibition of seed development and reserve protein accumulation in recombinants of abscisic acid biosynthesis and responsiveness mutants in Arabidopsis thaliana. Plant Physiol 90:463–469
Krishnan HB, Natarajan SS (2009) A rapid method for depletion of rubisco from soybean (Glycine max) leaf for proteomic analysis of lower abundance proteins.Phytochemistry 70:1958–1964
Laibach F. (1943) Arabidopsis thaliana (L.) Heynh. als object fur genetische und entwicklungsphysiologische untersuchungen. Bot Archiv 44:439–455
Le BH, Cheng C, Bui AQ, Wagmaister JA, Henry KF, Pelletier J, Kwong L, Belmonte M, Kirkbride R, Horvath S, Drews GN, Fischer RL, Okamuro JK, Harada JJ, Goldberg RB (2010) Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors. Proc Natl Acad Sci U S A 107:8063–8070
Linkies A, Graeber K, Knight C, Leubner-Metzger G (2010) The evolution of seeds. New Phytol 186: 817–831
Martínez-Barajas E, Delatte T, Schluepmann H, de Jong GJ, Somsen GW, Nunes C, Primavesi LF, Coello P, Mitchell RA, Paul MJ (2011) Wheat grain development is characterized by remarkable trehalose 6-phosphate accumulation pregrain filling: tissue distribution and relationship to SNF1-related protein kinase1 activity. Plant Physiol 156: 373–381
McCourt P, Benning C (2010) Arabidopsis: A rich harvest 10 years after completion of the genome sequence. Plant J 61: 905–908
Mène-Saffrané L, DellaPenna D (2010) Biosynthesis, regulation and functions of tocochromanols in plants. Plant Physiol Biochem 48:301–309
Messing J, Dooner HK (2006) Organization and variability of the maize genome. Curr Opin Plant Biol 9:157–163
Meurs C, Basra AS, Karssen CM, van Loon LC (1992) Role of abscisic acid in the induction of desiccation tolerance in developing seeds of Arabidopsis thaliana. Plant Physiol 98:1484–1493
Miernyk JA, Hajduch M (2011) Seed proteomics. J Proteomics 74:389–400
Miller A., Engel KH (2006) Content of gamma-oryzanol and composition of steryl ferulates in brown rice (Oryza sativa L.) of European origin. J Agric Food Chem 54:8127–8133
Molvig L, Tabe LM, Eggum BO, Moore AE, Craig S, Spencer D, Higgins TJV (1997) Enhanced methionine levels and increased nutritive value of seeds of transgenic lupins (Lupinus angustifolius L.) expressing a sunflower seed albumin gene. Proc Natl Acad Sci U S A 94:8393–8398
Moore G, Devos KM, Wang Z, Gale MD (1995) Cereal genome evolution. Grasses, line up and form a circle. Curr Biol 5:737–739
Muller-Landau HC (2003) Seeds of understanding of plant diversity. Proc Natl Acad Sci U S A 100:1469–1471
Murthy UM, Sun WQ (2000) Protein modification by Amadori and Maillard reactions during seed storage: roles of sugar hydrolysis and lipid peroxidation. J Exp Bot 51(348):1221–1228
Müntz K (1998) Deposition of storage proteins. Plant Mol Biol 38:77–99
Nambara E, Akazawa T, McCourt P (1991) Effects of the gibberellin biosynthetic inhibitor uniconazol on mutants of Arabidopsis. Plant Physiol 97:736–738
North H, Baud S, Debeaujon I, Dubos C, Dubreucq B, Grappin P, Jullien M, Lepiniec L, Marion-Poll A, Miquel M, Rajjou L, Routaboul JM, Caboche M (2010) Arabidopsis seed secrets unravelled after a decade of genetic and omics-driven research. Plant J 61:971–981
Nozoye T, Inoue H, Takahashi M, Ishimaru Y, Nakanishi H, Mori S, Nishizawa NK (2007) The expression of iron homeostasis-related genes during rice germination. Plant Mol Biol 64:35–47
Ogé L, Bourdais G, Bove J, Collet B, Godin B, Granier F, Boutin JP, Job D, Jullien M, Grappin P (2008) Protein repair L-isoaspartyl methyltransferase 1 is involved in both seed longevity and germination vigor in Arabidopsis. Plant Cell 20:3022–3037
Ohyanagi H, Tanaka T, Sakai H, Shigemoto Y, Yamaguchi K, Habara T, Fujii Y, Antonio BA, Nagamura Y, Imanishi T, Ikeo K, Itoh T, Gojobori T, Sasaki T (2006) The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information. Nucl Acids Res 34:D741–D744
O’Neill CM, Gill S, Hobbs D, Morgan C, Bancroft I (2003) Natural variation for seed oil composition in Arabidopsis thaliana. Phytochemistry 64:1077–1090
Ooms JJJ, Léon-Kloosterziel KM, Bartels D, Koornneef M, Karssen CM (1993) Acquisition of desiccation tolerance and longevity in seeds of Arabidopsis thaliana (A comparative study using abscisic acid-intensive abi3 mutants). Plant Physiol 102:1185–1191
Opanowicz M, Vain P, Draper J, Parker D, Doonan JH (2008) Brachypodium distachyon: making hay with a wild grass. Trends Plant Sci 13:172–177
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 (2007) The TIGR rice genome annotation resource: improvements and new features. Nucl Acids Res 35:D883–D887
Pinfield-Wells H, Rylott EL, Gilday AD, Graham S, Job K, Larson TR, Graham IA (2005) Sucrose rescues seedling establishment but not germination of Arabidopsis mutants disrupted in peroxisomal fatty acid catabolism. Plant J 43:861–872
Prieto-Dapena P, Castaño R, Almoguera C, Jordano J (2006) Improved resistance to controlled deterioration in transgenic seeds. Plant Physiol 142:1102–1112
Rabinowicz PD, Bennetzen JL (2006) The maize genome as a model for efficient sequence analysis of large plant genomes. Curr Opin Plant Biol 9:149–156
Rajjou L, Debeaujon I (2008) Seed longevity: survival and maintenance of high germination ability of dry seeds. C R Biologies 331:796–805
Rajjou L, Belghazi M, Huguet R, Robin C, Moreau A, Job C, Job D (2006) Proteomic investigation of the effect of salicylic acid on Arabidopsis seed germination and establishment of early defense mechanisms. Plant Physiol 141:910–923
Rajjou L, Lovigny Y, Groot SPC, Belghazi M, Job C, Job D (2008) Proteome-wide characterization of seed aging in Arabidopsis: a comparison between artificial and natural aging protocols. Plant Physiol 148:620–641
Rakwal R, Agrawal GK (2003) Rice proteomics: current status and future perspectives. Electrophoresis 24:3378–3389
Reissner KJ, Aswad DW (2003) Deamidation and isoaspartate formation in proteins: unwanted alterations or surreptitious signals? Cell Mol Life Sci 60:1281–1295
Rensink WA, Buell CR (2004) Arabidopsis to rice. Applying knowledge from a weed to enhance our understanding of a crop species. Plant Physiol 135:622–629
Sasaki T, Burr B (2000) International Rice Genome Sequencing Project: the effort to completely sequence the rice genome. Curr Opin Plant Biol 3:138–141
Sattler SE, Gilliland LU, Magallanes-Lundback M, Pollard M, DellaPenna D (2004) Vitamin E is essential for seed longevity and for preventing lipid peroxidation during germination. Plant Cell 16:1419–1432
Sattler SE, Mène-Saffrané L, Farmer EE, Krischke M, Mueller MJ, DellaPenna D (2006) Nonenzymatic lipid peroxidation reprograms gene expression and activates defense markers in Arabidopsis tocopherol-deficient mutants. Plant Cell 18:3706–3720
Schneider C (2005) Chemistry and biology of vitamin E. Mol Nutr Food Res 49:7–30
Shen B, Sinkevicius KW, Selinger DA, Tarczynski MC (2006) The homeobox gene GLABRA2 affects seed oil content in Arabidopsis. Plant Mol Biol 60:377–387
Shimamoto K, Kyozuka J (2002) Rice as a model for comparative genomics of plants. Annu Rev Plant Biol 53:399–419
Shin JH, Kim SR, An G (2009) Rice aldehyde dehydrogenase 7 is needed for seed maturation and viability. Plant Physiol 149:905–915
Somerville C, Koornneef M (2002) A fortunate choice: the history of Arabidopsis as a model plant. Nat Rev Genet 3:883–889
Sreenivasulu N, Graner A, Wobus U (2008a) Barley genomics: an overview. Int J Plant Genomics 2008: 486258
Sreenivasulu N, Usadel B, Winter A, Radchuk V, Scholz U, Stein N, Weschke W, Strickert M, Close TJ, Stitt M, Graner A, Wobus U (2008b) Barley grain maturation and germination: metabolic pathway and regulatory network commonalities and differences highlighted by new MapMan/PageMan profiling tools. Plant Physiol 146:1738–1758
Sreenivasulu N, Borisjuk L, Junker BH, Mock HP, Rolletschek H, Seiffert U, Weschke W, Wobus U (2010) Barley grain development: toward an integrative view. Int Rev Cell Mol Biol 281:49–89
Sung HG, Shin HT, Ha JK, Lai HL, Cheng KJ, Lee JH (2005) Effect of germination temperature on characteristics of phytase production from barley. Bioresour Technol 96:1297–1303
Takahashi M, Terada Y, Nakai I, Nakanishi H, Yoshimura E, Mori S, Nishizawa NK (2003) Role of nicotianamine in the intracellular delivery of metals and plant reproductive development. Plant Cell 15:1263–1280
Talon M, Koornneef M, Zeevaart JA (1990) Endogenous gibberellins in Arabidopsis thaliana and possible steps blocked in the biosynthetic pathways of the semidwarf ga4 and ga5 mutants. Proc Natl Acad Sci U S A 87:7983–7987
Tanaka T, Antonio BA, Kikuchi S, Matsumoto T, Nagamura Y, Numa H, Sakai H, Wu J, Itoh T, Sasaki T, Aono R, Fujii Y, Habara T, Harada E, Kanno M, Kawahara Y, Kawashima H, Kubooka H, Matsuya A, Nakaoka H, Saichi N, Sanbonmatsu R, Sato Y, Shinso Y, Suzuki M, Takeda JI, Tanino M, Todokoro F, Yamaguchi K, Yamamoto N, Yamasaki C, Imanishi T, Okido T, Tada M, Ikeo K, Tateno Y, Gojobori T, Lin YC, Wei FJ, Hsing YI, Zhao Q, Han B, Kramer MR, McCombie RW, Lonsdale D, O’Donovan CC, Whitfield EJ, Apweiler R, Koyanagi KO, Khurana JP, Raghuvanshi S, Singh NK, Tyagi AK, Haberer G, Fujisawa M, Hosokawa S, Ito Y, Ikawa H, Shibata M, Yamamoto M, Bruskiewich RM, Hoen DR, Bureau TE, Namiki N, Ohyanagi H, Sakai Y, Nobushima S, Sakata K, Barrero RA, Sato Y, Souvorov A, Smith-White B, Tatusova T, An S, An G, OOta S, Fuks G, Messing J, Christie KR, Lieberherr D, Kim H, Zuccolo A, Wing RA, Nobuta K, Green PJ, Lu C, Meyers BC, Chaparro C, Piegu B, Panaud O, Echeverria M (2008) The rice annotation project database (RAP-DB): 2008 update. Nucl Acids Res. 36:D1028–D1033
The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815
The International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463:763–768
Tranbarger TJ, Dussert S, Joët T, Argout X, Summo M, Champion A, Cros D, Omore A, Nouy B, Morcillo F (2011) Regulatory mechanisms underlying oil palm fruit mesocarp maturation, ripening, and functional specialization in lipid and carotenoid metabolism. Plant Physiol 156:564–584
Tresset A, Vigne JD (2011) Last hunter-gatherers and first farmers of Europe. C R Biol 334:182–189
Trisiriroj A, Jeyachok N, Chen ST (2004) Proteomics characterization of different bran proteins between aromatic and nonaromatic rice (Oryza sativa L. ssp. indica). Proteomics 4:2047–2057
Troncoso-Ponce MA, Kruger NJ, Ratcliffe G, Garcés R, Martínez-Force E (2009) Characterization of glycolytic initial metabolites and enzyme activities in developing sunflower (Helianthus annuus L.) seeds. Phytochemistry 70:1117–1122
Valentine L (2003) Agrobacterium tumefaciens and the plant: the David and Goliath of modern genetics. Plant Physiol 133:948–955
Vensel WH, Tanaka CK, Cai N, Wong JH, Buchanan BB, Hurkman WJ (2005) Developmental changes in the metabolic protein profiles of wheat endosperm. Proteomics 5:1594–1611
Venu RC, Sreerekha MV, Nobuta K, Belo A, Ning Y, An G, Meyers BC, Wang GL (2011) Deep sequencing reveals the complex and coordinated transcriptional regulation of genes related to grain quality in rice cultivars. BMC Genomics 12:190
Vigeolas H, Waldeck P, Zank T, Geigenberger P (2007) Increasing seed oil content in oil-seed rape (Brassica napus L.) by over-expression of a yeast glycerol-3-phosphate dehydrogenase under the control of a seed-specific promoter. Plant Biotechnol J 5:431–441
Waddell J (1958) Supplementation of plant proteins with amino acids. In: Altschul AM (ed) Processed plant protein foodstuffs. Academic, New York, pp 307–351
Wan Y, Underwood C, Toole G, Skeggs P, Zhu T, Leverington M, Griffiths S, Wheeler T, Gooding M, Poole R, Edwards KJ, Gezan S, Welham S, Snape J, Mills EN, Mitchell RA, Shewry PR (2009) A novel transcriptomic approach to identify candidate genes for grain quality traits in wheat. Plant Biotechnol J 7:401–410
Ware DH, Jaiswal P, Ni J, Yap IV, Pan X, Clark KY, Teytelman L, Schmidt SC, Zhao W, Chang K, Cartinhour S, Stein LD, McCouch SR (2002) Gramene, a tool for grass genomics. Plant Physiol 130:1606–1613
Waterworth WM, Masnavi G, Bhardwaj RM, Jiang Q, Bray CM, West CE (2010) A plant DNA ligase is an important determinant of seed longevity. Plant J 63:848–860
Weitbrecht K, Müller K, Leubner-Metzger G (2011) First off the mark: early seed germination. J Exp Bot 62:3289–3309
Xu XH, Zhao HJ, Liu QL, Frank T, Engel KH, An G, Shu QY (2009) Mutations of the multi-drug resistance-associated protein ABC transporter gene 5 result in reduction of phytic acid in rice seeds. Theor Appl Genet 119:75–83
Yamada C, Izumi H, Hirano J, Mizukuchi A, Kise M, Matsuda T, Kato Y (2005) Degradation of soluble proteins including some allergens in brown rice grains by endogenous proteolytic activity during germination and heat-processing. Biosci Biotechnol Biochem 69:1877–1883
Yamaguchi S, Kamiya Y, Sun T (2001) Distinct cell-specific expression patterns of early and late gibberellin biosynthetic genes during Arabidopsis seed germination. Plant J 28:443–453
Yamakawa H, Hirose T, Kuroda M, Yamaguchi T (2007) Comprehensive expression profiling of rice grain filling-related genes under high temperature using DNA microarray. Plant Physiol 144:258–277
Yang P, Li X, Wang X, Chen H, Chen F, Shen S (2007) Proteomic analysis of rice (Oryza sativa) seeds during germination. Proteomics 7:3358–3368
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, Wang X, Wu Q, Li C, Ren X, Wang J, Wang X, Li D, Liu D, Zhang X, Ji Z, Zhao W, Sun Y, Zhang Z, Bao J, Han Y, Dong L, Ji J, Chen P, Wu S, Liu J, Xiao Y, Bu D, Tan J, Yang L, Ye C, Zhang J, Xu J, Zhou Y, Yu Y, Zhang B, Zhuang S, Wei H, Liu B, Lei M, Yu H, Li Y, Xu H, Wei S, He X, Fang L, Zhang Z, Zhang Y, Huang X, Su Z, Tong W, Li J, Tong Z, Li S, Ye J, Wang L, Fang L, Lei T, Chen C, Chen H, Xu Z, Li H, Huang H, Zhang F, Xu H, Li N, Zhao C, Li S, Dong L, Huang Y, Li L, Xi Y, Qi Q, Li W, Zhang B, Hu W, Zhang Y, Tian X, Jiao Y, Liang X, Jin J, Gao L, Zheng W, Hao B, Liu S, Wang W, Yuan L, Cao M, McDermott J, Samudrala R, Wang J, Wong GKS, Yang H (2005) The Genomes of Oryza sativa: a history of duplications. PLoS Biol 3:e38
Yuan Q, Ouyang S, Liu J, Suh B, Cheung F, Sultana R, Lee D, Quackenbush J, Buell CR (2003) The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists. Nucl Acids Res 31:229–233
Zhang J, Li C, Wu C, Xiong L, Chen G, Zhang Q, Wang S (2006) RMD: a rice mutant database for functional analysis of the rice genome. Nucl Acids Res 34:D745–D748
Zou J, Katavic V, Giblin EM, Barton DL, MacKenzi SL, Keller WA, Hu X, Taylor DC (1997) Modification of seed oil content and acyl composition in the brassicaceae by expression of a yeast sn-2 acyltransferase gene. Plant Cell 9:909–923
Zupan JR, Zambryski P (1995) Transfer of T-DNA from Agrobacterium to the plant cell. Plant Physiol 107:1041–1047
Acknowledgements
This work was supported by the French Ministry for the Economy, Industry, and Employment (Ph.D. thesis support to ImenLounifi and post-doctoral position support to Dr. Marc Galland) in the frame of the Nutrice project.
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Galland, M. et al. (2012). A Role for “Omics” Technologies in Exploration of the Seed Nutritional Quality. In: Agrawal, G., Rakwal, R. (eds) Seed Development: OMICS Technologies toward Improvement of Seed Quality and Crop Yield. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-4749-4_23
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