Combinatorial Networks Regulating Seed Development and Seed Filling

Seeds offer plants a unique opportunity to suspend their life cycles in a desiccated state. This enables them to endure adverse environmental conditions and then resume growth by using endogenous storage products when more favorable conditions develop. Seed development is pivotal to the reproductive success of flowering plants (Angiosperms). It is initiated by the process of double fertilization that gives rise to the embryo and the endosperm. The embryo develops following fertilization of the haploid egg cell by one of the sperm cells leading to the formation of a diploid zygote. In contrast, the triploid endosperm results from the fertilization of the maternal homodiploid central cell of the ovule by another sperm cell (Weterings & Russell, 2004). The diploid embryo and the triploid endosperm develop concertedly inside the maternal ovule and are protected by a seed coat constituted of maternally derived inner and outer integuments. The seed coat provides an important interface between the embryo and the external environment (Haughn & Chaudhury, 2005). Thus, different genome combinations contribute to seed ontogeny.


Introduction
Seeds offer plants a unique opportunity to suspend their life cycles in a desiccated state.This enables them to endure adverse environmental conditions and then resume growth by using endogenous storage products when more favorable conditions develop.Seed development is pivotal to the reproductive success of flowering plants (Angiosperms).It is initiated by the process of double fertilization that gives rise to the embryo and the endosperm.The embryo develops following fertilization of the haploid egg cell by one of the sperm cells leading to the formation of a diploid zygote.In contrast, the triploid endosperm results from the fertilization of the maternal homodiploid central cell of the ovule by another sperm cell (Weterings & Russell, 2004).The diploid embryo and the triploid endosperm develop concertedly inside the maternal ovule and are protected by a seed coat constituted of maternally derived inner and outer integuments.The seed coat provides an important interface between the embryo and the external environment (Haughn & Chaudhury, 2005).Thus, different genome combinations contribute to seed ontogeny.Seed formation is an intricate genetically programmed process that is correlated with changes in metabolite levels and is regulated by a complex signaling network mediated by sugar and hormone levels (Wobus & Weber, 1999;Lohe & Chaudhury, 2002;Weber et al., 2005;Holdsworth et al., 2008;Sun et al., 2010).Most of the basic knowledge regarding cellular differentiation, growth regulation, imprinting and signal transduction pertaining to seed development comes from studies with Arabidopsis thaliana (Goldberg et al., 1989;Laux & Jürgens, 1997;Harada, 1999;Smeekens, 2000;Finkelstein et al., 2002;North et al., 2010;Bauer & Fischer, 2011).There is sufficient evidence to state that the fundamental regulatory mechanisms governing seed development and maturation are similar for all plant seeds (Weber et al., 2005).Seed development can be divided into two stages, embryo morphogenesis and maturation, the latter being characterized by storage compound accumulation, acquisition of desiccation tolerance, growth arrest and entry into a dormancy period that is broken upon germination (Harada, 1999).In addition to the diversity of imprinted genes that are maternally expressed in the maize endosperm include the MO17 allele of the dzr1 locus (Chaudhuri & Messing, 1994), one of the -zein alleles (Lund et al., 1995), maize enhancer of Zeste1 gene (Mez1) (Haun et al., 2009) and fertilization independent endosperm1 (Fie1) (Danilevskaya et al., 2003).In Arabidopsis, several imprinted genes involved in early seed development have been identified and include the FIS (FERTILIZATION INDEPENDENT SEED) genes MEDEA (MEA) (Grossniklaus & Schneitz, 1998;Kiyosue et al., 1999), FERTILIZATION INDEPENDENT ENDOSPERM (FIE) (Ohad et al., 1996), FIS2 (Luo et al., 1999), and MULTI-COPY OF IRA1 (MSI1) (Köhler et al., 2003;Ingouff et al., 2007), the MEA homologs CURLY LEAF (CLF) or SWINGER ( SWN) (Makarevich et al., 2006), and other maternally imprinted genes such as MATERNALLY EXPRESSED PAB C-TERMINAL (MPC) (Tiwari et al., 2008) and FLOWERING WAGENINGEN (FWA) (Kinoshita et al., 2004;Köhler & Hennig, 2010) The allele in the MO17 ecotype is maternally imprinted and zein accumulation is regulated Chaudhuri & Messing, 1994 Fertilization independent endosperm 1

Meg1
Cysteine-rich peptide Gutiérrez-Marcos et al., 2004 Table 2. Imprinted genes and their function in maize In plants and animals, homeotic genes encoding the polycomb group (PcG) and trithorax group (trxG) proteins are key players in maintaining repressive and active state of targets, respectively, and are crucial for developmental patterning and growth control (Simon & Tamkun, 2002).PcG and trxG proteins form higher order complexes that have intrinsic histone methyltransferase (HMTase) activity for various types of lysine methylation at the amino-terminus of core histone proteins.This property is conferred by the conserved 130residue SET (Su(var), Enhancer of Zeste, Trithorax) domain (Cao & Zhang, 2004).The FIS proteins MEA, FIE, MSI1 and FIS2 interact and form a protein complex called MEA-FIE complex that is similar to the PRC2 (Polycomb Repressive Complex 2) in animals (Simon & Tamkun, 2002;Köhler & Makarevich, 2006;Baroux et al., 2007).Mutation of any FIS component, such as MEA, leads to the formation of seeds independent of fertilization.Moreover, fis mutants have a prominent maternally determined phenotype after fertilization.Seed that carries a maternally inherited fis allele eventually aborts with an embryo that has arrested at the late heart stage and a multinucleate endosperm that fails to cellularize (Ohad et al., 1996;Grossniklaus & Schneitz, 1998;Kiyosue et al., 1999;Luo et al., 1999;Köhler et al., 2003;Ingouff et al., 2007).This phenotype is in part owing to the derepression of the type I MADS-box gene PHERES1 (PHE1).PHE1 is a direct target gene of the MEA-FIE complex in the embryo at the globular stage and in the central domain of the endosperm (Köhler et al., 2003).Mutation of MEA results in elevated expression of the maternal PHE1 allele through removal of the trimethylation marks from histone 3 lysine 27 (H3K27me3), whereas this has little effect on the activity of the paternal PHE1 allele, suggesting targeting specificity of the MEA-FIE complex to the maternal PHE1 allele (Köhler et al., 2005;Makarevich et al., 2006).In contrast to the action of MEA that is required for PcG target repression during gametophyte and early seed development, MEA homologs CLF/SWN have been demonstrated to repress PHE1 expression by the action of H3K27me3 at later stages of sporophyte development (Makarevich et al., 2006).In maize, genome-wide What are the mechanisms leading to the removal of DNA methylation marks from FIS genes in the central cell?DEMETER (DME) has been identified as a transcriptional activator that regulates MEA, FIS2, FWA and MPC expression in the central cells (Choi et al., 2002;Kinoshita et al., 2004;Gehring et al., 2006;Jullien et al., 2006;Morales-Ruiz et al., 2006;Tiwari et al., 2008;Bauer & Fischer, 2011).DME encodes a DNA glycosylase that removes methylated cytosine through its 5-methylcytosine DNA glycosylase activity at target loci (Choi et al., 2002;Kinoshita et al., 2004;Gehring et al., 2006;Jullien et al., 2006;Morales-Ruiz et al., 2006;Tiwari et al., 2008).DME is expressed predominantly in the central cell before fertilization where it activates target genes such as MEA (Choi et al., 2002).In dem mutant endosperm, the maternal MEA allele is not expressed due to hypermethylation and dem seeds eventually abort (Gehring et al., 2006).This finding suggests that DME removes DNA methylation marks at the maternal MEA allele in the central cell, resulting in hypomethylation and activation of MEA in the early endosperm, whereas the paternal imprinted MEA is methylated and transcriptionally silenced in the endosperm (Baroux et al., 2007;Huh et al., 2007).However, DME is not sufficient to remove all DNA methylation marks from targets such as FIS2 as evidenced by the continued expression of FIS2 and MPC in the dme mutant during female gametogenesis (Choi et al., 2002;Jullien et al., 2006).Recently, an additional mechanism was identified in which the Retinoblastoma pathway is involved in the regulation of maternal imprinting (Jullien et al., 2008).The Arabidopsis homolog RETINOBLASTOMA RELATED (RBR) directly silences MET1 expression via interaction with MSI1 during the late stage of female gametogenesis.When the Retinoblastoma pathway is inactive, expression of FIS2 and FWA in the central cell is completely repressed (Jullien et al., 2008;Berger & Chaudhury, 2009).Partial repression of MET1 by the Retinoblastoma pathway results in DNA hemi-methylation, the preferred substrate for the 5-methylcytosine glycosylase DME (Jullien et al., 2008), and complete demethylation by DME at the promoter regions of target alleles such as FIS2 and FWA leads to activation of these genes in the central cell.
After fertilization, the active maternal allele inherits the demethylation marks, whereas the inactive paternal allele inherits the methylation marks (Berger & Chaudhury, 2009;Gehring et al., 2009) (Fig. 1).Deep sequencing of endosperm or embryo DNA immunoprecipited with antisera against methylcytosine demonstrated a global reduction in DNA methylation on CG sites in the endosperm.The global CG methylation level is reduced by 15-20% in the endosperm in comparison to the levels in vegetative tissues or embryos (Gehring et al., 2009;Hsieh et al., 2009).In maize, a reduction of maternal DNA methylation might also occur in the endosperm (Lauria et al., 2004).Additionally, large amounts of maternally inherited non-coding small RNAs might also affect the genomewide DNA methylation in the endosperm and the embryos via their links to de novo DNA methyltransferases (Mosher et al., 2009).Recent genome-wide deep sequencing of cDNA libraries (Hsieh et al., 2011) or RNA derived from seeds of reciprocal intraspecific crosses (Gehring et al., 2011) has identified many genes that show imprinted gene expression in Arabidopsis endosperm.These genes include transcription factors, proteins involved in hormone signaling and regulators for histone modifications and chromatin remodeling (Gehring et al., 2011;Hsieh et al., 2011).These studies demonstrate that parent-of-origin effect on gene expression is a complex phenomenon and may affect multiple aspects of early seed development.Tamkun, 2002;Köhler & Makarevich, 2006;Baroux et al., 2007).Both maternal and paternal alleles of these imprinted genes are repressed via DNA methylation from the activity of the DNA methyltransferase MET1 in the central cell and sperm (Gehring et al., 2006;Jullien et al., 2006;Huh et al., 2007).During female gametogenesis, MET1 activity is partially repressed by the Retinoblastoma pathway involving RBR1 and its interacting partner MSI1 through DNA hemi-methylation, the preferred substrate for the 5-methylcytosine glycosylase DME (Jullien et al., 2008).The complete demethylation on MET1 in the mature central cell is mediated by DME, resulting in imprinted expression of the FIS-PcG genes (Jullien et al., 2008).During early endosperm development, the inherited paternal FIS-PcG alleles remain silenced by MET1, whereas the imprinted maternal alleles are active leading to the repression of target genes such as the maternal PHE1 through lysine27 on histone H3 (H3K27) methylation.The mechanism underlying PHE1 activation in sperm cell remains unknown.In contrast to the FIS genes MEA and FIS2 that are proposed to play a role for the repression of endosperm proliferation (Kiyosue et al., 1999;Ingouff et al., 2007), paternalspecific expression of PHE1 in the chalazal domain of the endosperm promotes endosperm development (Köhler et al., 2005).
In conjunction with DNA methylation, histone methylation also modulates genomic imprinting.Histone methylation mediated by the SET domain-containing PcG complex represses target genes by modifying the chromatin at or near target gene loci.This suppressive mechanism was proposed to regulate endosperm cell proliferation, as mutation of the target FIS class genes MEA, FIS2 or FIE results in the autonomous central cell divisions (Ohad et al., 1996;Chaudhury et al., 1997;Grossniklaus & Schneitz, 1998;Kiyosue et al., 1999).As described above, the endosperm is the only site where imprinting is known to take place; however, seeds may also form when genomic imprinting mechanisms are bypassed (Nowack et al., 2007).When CDKA;1 mutant pollen was crossed with the FIS gene mutants, mea, fis2 and fie, viable single-fertilized seeds with homodiploid endosperm were produced despite smaller seed size than wild type (Nowack et al., 2007).CDKA;1 encodes a cdc2/cdc28 homolog.Mutation of CDKA;1 leads to the generation of pollen with only one sperm (Iwakawa et al., 2006;Nowack et al., 2006) that preferentially fertilizes the egg cell while the diploid central cell remains unfertilized.Embryos from egg cells pollinated with cdka;1 mutant pollen abort at about 3 days after pollination and only a few divisions of the unfertilized central cell occur (Nowack et al., 2006).Furthermore, when repression exerted by the FIS genes such as MEA in the female gametophyte is disrupted, single-fertilized seeds form (Nowack et al., 2007).This suggests that functional endosperm can arise from the central cell in the female gametophyte without a paternal contribution and that genomic imprinting in the endosperm is not always essential for seed development.This hypothesis is supported by the demonstration that fertilization of the diploid central cell acts as a trigger that initiates proliferation of the multicellular endosperm (Nowack et al., 2007).

Seed maturation and seed filling
According to several models, seed development can be divided into two stages; morphogenesis and maturation.The maturation phase is initiated once the embryo and endosperm have completed the morphogenesis and patterning stages (Wobus & Weber, 1999).While early embryo morphogenesis is mainly maternally controlled, transition to the maturation phase requires a switch from maternal to filial control (Weber et al., 2005).After the switch is initiated, the embryo continues to grow for a short period of time until it matures; the seed then accumulates storage products, develops desiccation tolerance and produces a protective seed coat.Maturation ends with the completion of a desiccation phase after which seed growth arrests and it enters into dormancy, thus, the embryo enters into a quiescent state but retains the capacity to regenerate after imbibition (Harada, 1999).The spatial and temporal regulation of the maturation processes requires the concerted action of several signaling pathways that integrate information from genetic and epigenetic programs, and from both hormonal and metabolic signals (Wobus & Weber, 1999;Weber et al., 2005).Moreover, recent discoveries have led to a better understanding of ABA signaling and metabolic regulation in the maternal to filial switch leading to the maturation phase (Gutierrez et al., 2007;Cutler et al., 2010).

A regulatory network for seed maturation
Precise spatial and temporal regulation of gene expression is required for proper seed maturation.The expression of genes involved in the regulation of metabolism occurring during seed maturation is highly coordinated (Vicente-Carbajosa et al., 1998;Santos-Mendoza et al., 2005;Gutierrez et al., 2007;Holdsworth et al., 2008;Sun et al., 2010).The maize Opaque2 (O2) was one of the first genes encoding a plant transcription factor to be characterized (Hartings et al., 1989;Schmidt et al., 1990).The O2 orthologs, SPA from wheat (Triticum aestivum) and BLZ2 from barley (Hordeum vulgare), were reported to have the same functions as O2 in their corresponding species (Albani et al., 1997;Oñate et al., 1999).In Arabidopsis, three members of the B3 family of transcription factors, LEAFY COTYLEDON (LEC) 2, ABSCISIC ACID-INSENTITIVE 3 (ABI3) and FUSCA 3 (FUS3) and a fourth regulator, a HAP3 subunit of the CCAAT-box binding transcription factor (CBF) LEC1, are key regulators of seed maturation processes (Fig. 2).A redundant gene regulatory network linking these master regulators was elucidated by examining the expression of ABI3, FUS3 and LEC2 in abi3, fus3, lec1 and lec2 single, double and triple mutants (To et al., 2006).Using Affymetrix GeneChips to profile Arabidopsis genes active in seeds from fertilization to maturation, 289 seed-specific genes have been identified, including 48 transcription factors such as LEC1, LEC2 and FUS3 (Le et al., 2010).In combination with ABA, GA, auxin and sugar signaling, this regulatory network governs most seed-specific traits, such as accumulation of storage compounds, acquisition of desiccation tolerance and entry into quiescence, in a partially redundant manner (Harada, 1999;Brocard-Gifford et al., 2003;Gazzarrini et al., 2004;Kagaya et al., 2005b;To et al., 2006;Stone et al., 2008).LEC1 and LEC2 are expressed early in embryogenesis and ectopic expression of these two regulators is sufficient to confer embryonic traits to vegetative organs (Lotan et al., 1998;Stone et al., 2001;Santos-Mendoza et al., 2005).ABI3 and FUS3 expression occurs later in embryogenesis and their overexpression results in ectopic expression of some seed maturation genes, such as At2S3 and CRC, in vegetative tissues in an ABA-dependent manner, demonstrating that the SSP gene expression is controlled by LEC1 through the regulation of ABI3 and FUS3 (Parcy et al., 1994;Kagaya et al., 2005b).Genetic and molecular studies have shown that ABI3, FUS3 and LEC2 regulate oleosin gene expression and lipid accumulation (Crowe et al., 2000;Santos-Mendoza et al., 2005;Baud et al., 2007).Loss of ABI3 function alters accumulation of seed storage reserves and leads to loss of desiccation tolerance, dormancy, ABA sensitivity upon germination and chlorophyll degradation (Vicente-Carbajosa & Carbonero, 2005).In addition, the APETALA2 (AP2) protein, ABI4, and the bZIP domain factor, ABI5, are involved in many aspects of seed maturation through their interaction with the major regulators LEC2, ABI3 and FUS3 (Carles et al., 2002;Brocard-Gifford et al., 2003;Lara et al., 2003;Acevedo-Hernández et al., 2005).In addition to these complex genetic interactions, ABI3 expression was found to be regulated by both post-transcriptional and post-translational mechanisms.After excision of the long 5'-untranslated region (UTR) of the ABI3 transcript, ABI3-GUS expression level was markedly increased, suggesting that ABI3 expression is negatively regulated by its own 5'-UTR (Ng et al., 2006).Moreover, ABI3 levels are regulated by an ABI3-interacting protein, AIP2 an E3 ligase that targets ABI3 to the 26S proteasome for degradation (Zhang et al., 2005).The ectopic expression of the ABI3 maize ortholog, Viviparous (VP1), in Arabidopsis leads to the expression of a subset of seedspecific genes in vegetative tissues, indicating that VP1 is a key determinant for embryonic traits (Suzuki et al., 2003).This also suggests that ABI3-dependent regulatory mechanisms are conserved in both dicots and cereals.
Seed maturation-related genes, such as those governing SSP and lipid accumulation, are controlled by the interaction of transcriptional regulators with cis-acting elements in their promoters.The best characterized cis-elements include the RY repeat (CATGCA), ACGT-box (CACGTG) and AACA motif, that are recognized by B3, bZIP and MYB domain transcription factors, respectively.Functional analysis and in vitro protein-DNA interaction assays demonstrated binding of the B3 factors (LEC2, ABI3 and FUS3) to RY repeats (Reidt et al., 2000;Kroj et al., 2003;Mönke et al., 2004;Braybrook et al., 2006), and bZIP factors (ABI5, AtbZIP10, AtbZIP25 and bZIP53) to ACGT-boxes (Bensmihen et al., 2002;Lara et al., 2003;Alonso et al., 2009;Reeves et al., 2011 ).Moreover, ABI5 and its homolog EEL play antagonistic roles to influence the expression of the late embryogenesis abundant (LEA) gene, AtEm1, through competition for the same DNA binding site (Bensmihen et al., 2002).In addition to direct binding to DNA elements, the major regulators indirectly regulate the expression of seed maturation genes.Genetic and molecular studies have shown that LEC1 and LEC2 act upstream of ABI3 and FUS3 and control SSP gene expression through the regulation of ABI3 and FUS3 expression (Kagaya et al., 2005b;To et al., 2006).ABI3 functions as a seed-specific transcriptional co-activator that physically interacts with ABI5, AtZIP10 and AtZIP25 (Nakamura et al., 2001;Lara et al., 2003).Recently, another G-box binding group C bZIP factor, bZIP53, was shown to be a key regulator of seed maturation gene expression and enhanced expression by heterodimerization with bZIP10 or bZIP25 (Alonso et al., 2009).FUS3 expression in the protoderm and its negative regulation of TRANSPARENT TESTA GLABRA1 (TTG1) are critical for embryogenesis (Tsuchiya et al., 2004).Moreover, FUS3 was induced by auxin and indirectly influences the seed maturation process by positive and negative regulation of ABA and GA synthesis, respectively (Gazzarrini et al., 2004).The germination potential of seeds and seedling establishment are determined by the afterripening process, hormones (GAs) and multiple embryonic repressors.Adapted from Refs.(Baud et al., 2002;Weber et al., 2005;Braybrook & Harada, 2008).
In monocots, the starchy endosperm is the prevalent storage domain, where carbohydrates and SSPs accumulate during maturation.Cereal SSP genes were among the first plant genes to be characterized.The AACA motif and the bipartite endosperm box (EB) encompassing the GCN4-like motif (GLM, ATGAGTCAT) and the prolamin box (PB, TGTAAAG) are the best characterized cis-elements affecting SSP gene expression (Forde et al., 1985;Wu et al., 2000).In vitro and in vivo protein-DNA interaction assays have identified direct targeting of the barley R2R3MYB factor HvGAMYB, wheat GAMYB and rice (Oryza sativa) OsMYB5 to the AACA motif.The Dof (DNA binding with one finger) proteins BPBF (prolamin box binding factor) and SAD (scutellum and aleurone-expressed DOF) bind to the PB box, while OPAQUE2 (O2)-like bZIP proteins, SPA (in wheat), BLZ1 and BLZ2 (in barley), bind to the GLM motif (Albani et al., 1997;Mena et al., 1998;Vicente-Carbajosa et al., 1998;Wu et al., 1998;Oñate et al., 1999;Díaz et al., 2002;Yanagisawa, 2002;Diaz et al., 2005).GAMYB was reported to activate expression of the endosperm-specific genes, such as Itr1 which encodes the trypsin inhibitor BTI-CMe (Díaz et al., 2002).Dof proteins, BPBF and SAD, and the O2like bZIP proteins, BLZ1 and BLZ2, activated expression of the B-hordein storage protein gene Hor2 in barley (Mena et al., 1998;Vicente-Carbajosa et al., 1998;Oñate et al., 1999;Diaz et al., 2005).The maize Dof protein PBF was demonstrated to trans-activate the -zein gene ( Z) through the PB box (Marzábal et al., 2008).In addition, the R1MYB-SHA-QYF family proteins, HvMCB1 and HvMYBS3, were shown to regulate endosperm-specific gene expression through binding to the GATA motif (Rubio-Somoza et al., 2006a;2006b).Recently, the barley FUSCA3 (HvFUS3) was demonstrated to bind to the RY-box present in the promoters of many endosperm genes (Moreno-Risueno et al., 2008).HvFUS3 encodes a B3 domain protein that is expressed in the endosperm and embryo of developing seeds.
HvFUS3 expression peaks during the mid maturation phase and it participates in the transcriptional activation of the endosperm-specific genes Hor2 and Itr1 (Moreno-Risueno et al., 2008).Moreover, HvFUS3 was determined to trans-activate seed-specific genes in planta through interaction with the O2-like bZIP factor BLZ2 (Moreno-Risueno et al., 2008), indicating the involvement of both a B3 domain protein and a bZIP factor in the combinatorial regulation of endosperm-specific gene expression.In maize, O2 affects grain size and composition and is important in carbon allocation and amino acid biosynthesis during seed development (Hunter et al., 2002;Manicacci et al., 2009).In addition, two R1MYB transcription factor family proteins from wheat, MCB1 (MYBrelated CAB promoter-binding protein) and MYBS3, were shown to interact with GARC (GA response complex) and to be involved in the regulation of SSP gene expression (Rubio-Somoza et al., 2006a;2006b).Recent deep sequencing analysis of the transcriptome in developing rice seeds identified many differentially expressed novel transcripts and genes that are involved in the biosynthesis of starch and storage proteins.Hundreds of novel conserved patterns of cis-elements were found in the upregulated genes in the rice cultivars with high milling yield and good eating quality (Venu et al., 2011).Similar to the studies in Arabidopsis as described above, these discoveries indicate that complex combinatorial interactions of different transcription factors are pivotal for the regulation of the seed maturation program in cereals.
With the exception of those directly targeting SSP genes for which the regulatory elements in their promoters are well defined, little progress has been made in understanding the interactions between the master regulators and other target proteins, called secondary transcription factors (STF), that are also essential for the regulation of seed maturation processes.Nonetheless, part of the seed maturation program is regulated by indirect means mediated by STF.In rice, mutual interactions have been demonstrated between two transcriptional activators, a DOF-related rice prolamin box binding protein (RPBF) and a RISBZ1 bZIP factor (Yamamoto et al., 2006).In barley, the formation of binary or ternary complexes with PBF and DOF regulatory proteins are important for controlling SSP gene expression (Rubio-Somoza et al., 2006a;2006b;Yamamoto et al., 2006).In Arabidopsis, mutation of LEC-type regulators (LEC1, LEC2 and FUS3) led to reduced accumulation of SSPs and major seed lipid TAGs, while ectopic expression in seedlings caused SSPs and TAGs to accumulate in vegetative tissues (Kagaya et al., 2005b;Santos-Mendoza et al., 2005;Braybrook et al., 2006;Wang et al., 2007).The master regulator LEC2 was also shown to control seed oil accumulation through regulation of WRINKLED1 (WRI1) (Baud et al., 2007) that directly targets fatty acid synthetic genes (Baud et al., 2009;Maeo et al., 2009).WRI1 is an AP2-type transcription factor with two AP2-binding domains (Cernac & Benning, 2004) and functions downstream of LEC1 ad LEC2.Ectopic expression of WRI1 leads to the upregulation of fatty acid synthetic and glycolytic genes in seedlings (Baud et al., 2007;Mu et al., 2008).In vitro and in vivo analyses demonstrated that WRI1 was able to bind to the AW-box [CnTnG](n) 7 [CG] of BCCP2 (acetyl-CoA carboxylase) and PI-PK 1 (a subunit of pyruvate kinase) (Baud et al., 2009;Maeo et al., 2009).These studies provide insight into the understanding of the role of WRI1 in the regulation of oil synthesis during seed maturation.Some other downstream regulatory complexes have also been identified.For instance, biosynthesis of flavonoids, which are found in most seeds and grains and are major metabolites in the embryo and seed coat (Lepiniec et al., 2006), is regulated by a complex with six components including TRANSPARENT TESTA GLABRA1 (TTG1), the expression of which is repressed by FUS3 in the protoderm (Tsuchiya et al., 2004).Discovery of additional STFs and their interactions with the upstream master regulators will allow better exploration of the molecular mechanisms that control seed filling.

Hormonal signaling during seed maturation
The phytohormone ABA, an endogenous messenger derived from epoxycarotenoid, has a wide rage of functions in plant development, and in responses to biotic and abiotic stresses through its interaction with the Mg-chelatase H subunit (CHLH) and PYR1/RCAR1 (Shen et al., 2006;Ma et al., 2009;Park et al., 2009;Cutler et al., 2010).Many factors involved in ABA signaling have been characterized (Finkelstein, 2006;Razem et al., 2006;Adie et al., 2007;Hirayama & Shinozaki, 2007).ABA is the key hormone regulating several seed maturation processes including the initiation of the maturation phase, filling of seed reserves and entrance into dormancy (Nambara & Marion-Poll, 2003;Finch-Savage & Leubner-Metzger, 2006).ABA is initially synthesized in the maternal tissues and subsequently in the embryo (Nambara & Marion-Poll, 2003;Frey et al., 2004).Many genes for seed ABA biosynthesis have been identified including ABA1 (ABA DEFICIENT1) encoding a zeaxanthin epoxidase that functions in first step of the ABA biosynthesis, NCEDs encoding 9-cis-epoxycarotenoid dioxygenases and ABA2/GIN1 (GLUCOSE INSENSITIVE1)/SDR1 ( SHORT-CHAIN DEHYDROGENASE REDUCTASE1)/SIS4 ( SUGAR-INSENSITIVE4) encoding a cytosolic short-chain dehydrogenase/reductase involved in the conversion of xanthoxin to ABAaldehyde during ABA biosynthesis (Nambara & Marion-Poll, 2003).A subset of ABA response mutants have been isolated and served as tools for dissecting the ABA singaling pathway (Kucera et al., 2005).For example, mutant analyses reveal that the ABA-activated protein kinases, PP2Cs (serine-threonine phosphatase type 2C) ABI1 and ABI2, and the transcriptional regulators ABI3, ABI4 and ABI5, are involved in the ABA signaling pathway and associated with seed dormancy (Finkelstein et al., 2002;Himmelbach et al., 2003).In Arabidopsis, ABA level is dynamically modulated and increases concurrent with the initiation of seed maturation phase, remains high throughout the maturation phase, declines at late maturation and is very low during germination and seedling establishment (Fig. 2) (Nambara & Marion-Poll, 2003;Seo et al., 2009).During seed maturation, ABA signaling is intimately associated with the actions of the master regulators LEC1, LEC2, ABI3 and FUS3 (Finkelstein et al., 2002;Gutierrez et al., 2007;Braybrook & Harada, 2008).For instance, FUS3 expression leads to the elevation of ABA levels (Gazzarrini et al., 2004) and exogenous application of ABA enhances FUS3 expression (Kagaya et al., 2005a;2005b).As well, activation of embryonic gene (e.g.storage protein, LEA and oleosin genes) expression by LEC1, FUS3 and ABI3 is enhanced by ABA application (Parcy et al., 1994;Kagaya et al., 2005a;2005b).A number of genes have been characterized that regulate ABA homeostasis.
In Arabidopsis, CYP707A1 and CYP707A2 are major regulators for ABA degradation in the embryo at mid maturation and in both the embryo and the endosperm during late maturation (Okamoto et al., 2006).In barley and bean (Phaseolus vulgaris), the expression of CYP707A genes is the major mechanism controlling ABA catabolism in seeds (Millar et al., 2006;Yang et al., 2006).Moreover, HvNCED2 was shown to upregulate ABA biosynthesis during grain development, whereas HvCYP707A1 downregulated ABA levels during the subsequent seed maturation phase (Chono et al., 2006).
GA is also important in controlling seed maturation, germination and seedling growth (Seo et al., 2009).As shown in Fig. 2, GA levels are suppressed throughout the seed maturation phase until germination at which time GA levels elevate significantly.It was demonstrated that ABA interacts with GA during the maturation process (Seo et al., 2006).GA biosynthesis is suppressed by ABA in developing seeds through activation of AtGA2ox6.Seed maturation and germination are not determined by ABA alone, but instead by the ABA/GA ratio (Karssen et al., 1983;Giraudat et al., 1994;Dubreucq et al., 1996;Debeaujon & Koornneef, 2000;Finkelstein et al., 2002;Koornneef et al., 2002;Ogawa et al., 2003).At the beginning of the maturation phase, ABA levels increases in seeds and the resulting elevated ABA/GA ratio promotes maturation, induces dormancy and inhibits germination.Consistent with the lower ABA/GA ratio in the seeds of lec2 and fus3 mutants, and with the precocious cell differentiation and growth of mutant embryos, FUS3 and LEC2 were found to inhibit GA biosynthesis through the repression of GA biosynthetic genes (Curaba et al., 2004;Gazzarrini et al., 2004).However, reduced GA levels alone are not sufficient to confer desiccation tolerance during late maturation phase and SSP accumulation was defective in the fus3 mutant in spite of the GA status (Gazzarrini et al., 2004).Additionally, ABI3 and FUS3 were shown to be regulated by ABA and/or GA at the post-translational level.AIP2 (ABI3-interacting protein 2), an E3 ligase controlled by ABA, can trigger the degradation of ABI3 (Zhang et al., 2005).Besides the importance of ABA/GA ratio for the regulation of seed maturation, the balance between ABA and other hormones is also important.For example, grain-filling rate in wheat was correlated with increases in the ABA/ethylene ratio (Yang et al., 2006).
Genetic and molecular studies have shown that auxin plays an essential role in embryogenesis and post-embryonic organ formation through its dynamic directional distribution (Tanaka et al., 2006).During embryogenesis, auxin accumulation is directed by PIN-FORMED (PIN)-mediated polar transportation from the apical cells to the hypophysis, the founder cell of the root stem-cell system (Tanaka et al., 2006).It has been suggested that auxin is required for the embryonic regulators FUS3, LEC1 and LEC2 to potentiate embryogenesis and seed maturation processes (Gazzarrini et al., 2004;Casson & Lindsey, 2006;Stone et al., 2008).ABI3 has been shown to be involved auxin signaling and lateral root development (Brady & McCourt, 2003).Auxin-responsive genes can be activated by the ectopic expression of LEC2 (Braybrook & Harada, 2008) and FUS3 expression was induced by auxin (Gazzarrini et al., 2004).ASIL1 (for Arabidopsis 6b-interacting protein 1-like 1), a trihelix transcriptional repressor of seed maturation genes in Arabidopsis, is not responsive to ABA, but is moderately induced by auxin (Gao et al., 2009).In dry or imbibed wild-type seeds, LEC1 and LEC2 transcripts were not observed, whereas expression was elevated in asil1 mutants at 1 h after imbibition with this increase being enhanced by the application of auxin (Gao et al., 2009).Given the fact that somatic embryogenesis is induced by the synthetic auxin 2,4-D (2,4-dichlorophenoxyacetic acid) (Mordhorst et al., 1998) and that derepression of LEC1 and LEC2 in imbibed asil1 mutant seeds was enhanced by auxin, similar to ABA, it was suggested to function as a signal for the activation of embryonic genes.Auxin accumulation is also dynamically changed during germination and vegetative growth.For example, auxin activity was highly localized in the radical tips of germinating and germinated seeds (Liu et al., 2007) and the initiation sites of organ primordia in roots and shoots correspond to regions with increased auxin levels (Tanaka et al., 2006).ASIL1 expression also exhibited a modest response to auxin and the level of ASIL1 transcript is elevated at 1h post-imbibition, therefore the rise in ASIL1 transcript levels may correspond to the distribution of auxin in cells of germinating seeds (Gao et al., 2009).LEC1 and LEC2 function upstream of other embryonic and seed maturation genes (To et al., 2006) and their ectopic expression is sufficient to provoke the embryonic program in vegetative tissues (Lotan et al., 1998;Stone et al., 2001;Santos-Mendoza et al., 2005).Therefore, expression of these two major regulators of embryonic programming should be strictly prevented during germination and seedling development.Given the up-regulation of ASIL1 by auxin and the derepression of embryonic genes in germinating asil1 seeds as well as in 2-week-old asil1 seedlings, ASIL1 may prevent ectopic expression of LEC1 and LEC2 in cells that encounter elevated auxin levels during germination and vegetative growth (Gao et al., 2009).Although significant progress has been made in understanding the connection between seed maturation and auxin signaling, the precise roles that auxin plays and its mode of action during the maturation phase remain to be established.Only minor auxin-related traits have been detected in lec mutants during early embryogenesis (Lotan et al., 1998;Stone et al., 2001).The lec1 and lec2 mutants have strongly reduced ability to generate somatic embryos (Gaj et al., 2005), whereas ectopic expression of LEC1 and LEC2 in seedlings induced the formation of embryonic traits (Lotan et al., 1998;Stone et al., 2001).Therefore, it has been proposed that LEC transcription factors seem to build an environment in somatic cells that prime them to respond to auxin and undergo somatic embryogenesis; this competence might be affected by the repression of GA synthesis by LEC regulators or influenced by ABA signaling alone or by the ABA/GA balance (Braybrook & Harada, 2008).

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Combinatorial Networks Regulating Seed Development and Seed Filling 203

Sugar signaling and metabolic regulation
Sugars generated by photosynthesis play a key role in plant development as structural components, storage molecules, energy sources and as intermediates for the synthesis of other organic molecules.In addition, sugars may act as signaling molecules that regulate the expression of genes involved in photosynthesis and metabolism.High sugar levels lead to a negative feedback on photosynthesis while promoting starch biosynthesis.Conversely, low sugar levels increase photosynthetic gene expression and promote storage reserve mobilization while limiting the use of carbohydrates to metabolic processes (Wobus & Weber, 1999;Rook et al., 2006).For instance, many plant developmental processes, such as seed germination, seedling establishment, flowering and senescence, are influenced by glucose (Gibson, 2000;Smeekens, 2000;Gibson, 2005;Rolland et al., 2006).Gene expression can be regulated by sugar-induced signal transduction through diverse mechanisms at the transcriptional, post-transcriptional, translational and post-translational levels (Rolland et al., 2006).Many studies have determined that the initiation of seed maturation processes is triggered by sugar signaling, notably the sucrose/hexose ratio in the embryos (Fig. 2) (Weber et al., 2005).During endosperm or cotyledon differentiation, gradients in metabolite concentrations emerge and provide signals for the transition into the maturation phase (Weber et al., 2005).Glucose concentration is directly correlated with cell division.This is supported by the observation of higher levels of glucose in nondifferentiated premature regions and low levels in mature starch-accumulating regions (Borisjuk et al., 2003).
Conversely, young embryos contain moderately low levels of sucrose and the highest concentration of sucrose occurs in the actively elongating and starch-accumulating cells during maturation, which is consistent with the expression of genes involved in the storage compound synthesis (Borisjuk et al., 2002).This alteration in sugar balance is correlated with the establishment of an epidermis-localized sucrose uptake system via the formation of transfer cells (Offler et al., 2003).A strong and transient increase in sucrose uptake occurs while free hexose levels decrease markedly in the embryo.Sucrose signaling subsequently controls storage filling and differentiation processes in seeds through the regulation of gene expression and metabolic enzyme activities (Gibson, 2005;Rolland et al., 2006).In Arabidopsis, mutation of the gene encoding sugar transporter SUC5 delayed the conversion of sugar to lipids and AtSUC5 plays a major role in the progression into maturation phase (Baud et al., 2005).More interestingly, seed mass was increased in an ap2 (apetala2) mutant, which is characterized by an increase in embryo cell size and number.This phenotype is the consequence of a prolonged period of cell division regulated by elevation of hexose/sucrose ratio (Ohto et al., 2005).In tps1 ( TREHALOSE-6-PHOSPHATE SYNTHASE1) mutant embryos, starch instead of lipids accumulated due to the downregulation of genes involved in the starch-sucrose breakdown and the upregulation of genes responsible for the lipid mobilization for gluconeogenesis, demonstrating the importance of trehalose in the sugar signaling pathway regulating the maturation phase (Gómez et al., 2006).As such, sugar signaling was suggested to be a ubiquitous regulatory system involved in seed maturation (Gutierrez et al., 2007).
Seed storage metabolism involves the movement of intermediates between several distinct subcellular compartments including mitochondria, plastids and cytosol (Fait et al., 2006).In cells of heterotrophic embryos, ATP is mainly generated in bioenergetic organelles, the mitochondria, by respiration and is imported into plastids through ATP/ADP translocators in a rate-limiting manner (Tjaden et al., 1998;Rawsthorne, 2002).Studies in legumes, barley and maize have shown that ATP levels are associated with seed maturation processes.ATP levels are low in young cotyledons and increase toward maturation starting from the abaxial region.The active storage-accumulating regions contain high levels of ATP during maturation (Borisjuk et al., 2003;Rolletschek et al., 2004).The photoheterotrophic plastids in seed embryos are different from leaf chloroplasts with regard to morphology and physiology.These differences include elevated cyclic electron transport via photosystem II, but a low capacity for photosynthetic CO 2 fixation (Asokanthan et al., 1997).Seed photosynthesis plays a role in controlling biosynthetic fluxes through the production of ATP and O 2 by preventing hypoxic conditions inside the seed (Rolletschek et al., 2005a;Weber et al., 2005).The low O 2 levels in developing seeds affect enzymatic activity, gene expression patterns, mitochondrial ATP production, and metabolite fluxes.Hypoxia leads to energy depletion so that embryo cells are stressed and storage reserve accumulation is constrained (Borisjuk et al., 2003;Rolletschek et al., 2004;Rolletschek et al., 2005a;Weber et al., 2005;Borisjuk & Rolletschek, 2009).Therefore, photosynthesis in developing seeds is important for storage reserve synthesis and accumulation (Borisjuk et al., 2005;Rolletschek et al., 2005a;Fait et al., 2006).The energy status is also important for controlling the flux of substrates into different storage products (Rolletschek et al., 2005b).In general, energy demand is highest for lipids, followed by storage proteins, and lowest for starch (Weber et al., 2005).For instance, in Brassica napus, the developmental transfer from starch to lipid storage at mid maturation is accompanied by increased ATP/ADP ratios.Starch synthesis is saturated at lower ATP levels than is lipid synthesis (Vigeolas et al., 2003).Moreover, during seed maturation in oilseeds B. napus and soybean (Glycine max), the biosynthetic switch from starch to lipids is linked to the import of specific metabolites, suggesting that the relative fluxes into different storage products are not only energy dependant but also developmentally controlled (Eastmond & Rawsthorne, 2000;Weber et al., 2005).
Seed maturation is also influenced by nitrogen metabolism because storage protein accumulation depends on nitrogen uptake and availability (Golombek et al., 2001;Miranda et al., 2001;Rolletschek et al., 2005c).Asparagine is acquired from the phloem, metabolized and reconstructed in the seed coat and unloaded at later stages.In soybean, the level of asparagine in developing cotyledons plays a rate-limiting role in protein biosynthesis (Hernandez-Sebastia et al., 2005).Moreover, amino acid biosynthesis controls storage protein synthesis.For example, in soybean, pea (Pisum sativum), Fava bean (Vicia faba) and wheat, phosphoenolpyruvate carboxylase (PEPC), a ubiquitous and highly regulated enzyme, is as a determinant of SSP biosynthesis.Therefore, PEPC has become a promising target for increasing protein content of crop seeds.For example, overexpression of PEPC in bean seeds resulted in the accumulation of up to 20% more protein per gram seed dry weight due to the shift of metabolic fluxes from sugars/starch into organic acids and free amino acids during maturation; seed dry weight was higher by 20% -30% possibly owing to elevated carbon fixation (Fait et al., 2006).A major metabolic switch has been identified that is associated with the transition from seed filling to the desiccation phase.Seed metabolism is fundamentally changed during this switch.Seed storage accumulation during maturation is associated with the reduction of most sugars, amino acids and organic acids.However, desiccation tolerance is associated with increases in the content of distinct sugars, organic acids, nitrogen-rich amino acids and shikimate-derived metabolites (Fait et al., 2006).Similarly, studies using gene profiling in Medicago truncatula seeds have demonstrated that www.intechopen.com Combinatorial Networks Regulating Seed Development and Seed Filling 205 lipids, starch and oligosaccharides are mobilized, consistent with the elevation in sucrose level during the early desiccation stage (Buitink et al., 2006).Protein phosphorylation was shown to be involved in the metabolic regulation during seed maturation as the storageassociated enzyme PEPC is activated by phosphorylation (Goldberg & Fischer, 1999).In legume seeds, SPS (sucrose-phosphate synthase) activity is inhibited by phosphorylation during the switch from high hexose to high sucrose levels (Weber et al., 2005).In rice seeds, a calcium-dependent protein kinase (CDPK) isoform was found to control storage reserve accumulation by phosphorylation of sucrose synthase (Asano et al., 2002).Overexpression of CDPK2 in rice arrests seed development at an early stage (Morello et al., 2000).A large number of functionally diverse phosphoproteins were expressed during seed filling in B. napus (Agrawal & Thelen, 2006).OsCPK23 is markedly upregulated in developing seeds in comparison to mature leaves (Ray et al., 2007).The 12S globulin cruciferin was found to be the major phosphorylated storage protein in Arabidopsis seeds (Wan et al., 2007) and protein tyrosine kinases and protein tyrosine phosphatases were shown to be involved in the storage protein accumulation and lipid reserve mobilization processes (Ghelis et al., 2008).
Recently, the leucine-rich repeat receptor kinase encoded by IKU2 (HAIKU2) was shown to directly target the positive seed regulator SHB1 (Zhou et al., 2009).Mutation of IKU2 reduced seed size and affected embryo and endosperm development (Luo et al., 2005).

Sugar and ABA signal interaction
As described above, transition of embryo morphogenesis into the maturation phase is governed by sugars and ABA signaling and their coordinated interaction (Brocard-Gifford et al., 2003;Gibson, 2004).Genetic and molecular studies demonstrated that sugar signaling in higher plants is intimately associated with hormone signaling, in particular with ABA (Leon & Sheen, 2003;Rook et al., 2006;Dekkers et al., 2008).Four independent screens have been conducted to identify sugar response mutants: sun (sucrose uncoupled), isi (impaired sucrose induction), gin and sis.All four screens identified the ABA deficient mutants (aba2/isi4/gin1/sis4 and aba3/gin5) and ABA insensitive4 (i.e.abi4/sun6/isi3/gin6/sis5) (Arenas-Huertero et al., 2000;Huijser et al., 2000;Laby et al., 2000;Rook et al., 2001) suggesting genetic interactions between sugar and ABA signaling pathways.Furthermore, ABA biosynthetic and signaling genes were found to be regulated by glucose.Several sugar signaling mutants, such as gin1, gin5, isi4 and sis4, exhibit lower endogenous ABA levels (Arenas-Huertero et al., 2000;Laby et al., 2000;Rook et al., 2001), which is consistent with the previously identified ABA deficient mutants aba1, aba2 and aba3 that show a gin phenotype (Arenas-Huertero et al., 2000;Huijser et al., 2000;Laby et al., 2000).Transcripts of several ABA biosynthetic genes, such as ABA1, AAO3 and ABA3, are increased by low concentrations of glucose (2%) (Cheng et al., 2002), as well as by ABA itself (Xiong et al., 2001;Cheng et al., 2002;Seo & Koshiba, 2002).These observations suggest that ABA biosynthetic genes and ABA accumulation are directly regulated by glucose.ABI4 and ABI5 were shown to be involved in ABA signaling and play important roles during seed development (Finkelstein, 1994;Brocard et al., 2002).As indicated above, sugar response mutants, such as sun6, isi3, gin6 and sis5, are allelic to abi4.The abi4 mutant was isolated based on its ability to germinate in the presence of high levels of ABA (3 µM) (Finkelstein, 1994).Expression of ABI4 was activated by 6% glucose in an ABA-dependent fashion, but had a limited response to ABA alone (Arenas-Huertero et al., 2000;Cheng et al., 2002).These investigations indicate that ABA biosynthetic and signaling genes can be regulated by both glucose and ABA.Besides abi4 and abi5, abi8 mutants also displayed a glucose insensitive phenotype, although this phenotype was not as obvious as that of the abi4 mutant (Arenas-Huertero et al., 2000;Huijser et al., 2000;Laby et al., 2000;Brocard-Gifford et al., 2003).Similar to ABI4, ABI5 expression is also induced by glucose in an ABA-dependent manner (Cheng et al., 2002) and overexpression of ABI5 increased sensitivity to glucose (Brocard et al., 2002).Additionally, ABI3 expression was also found to be induced by glucose in an ABA-dependent manner, although not as significant as ABI4 and ABI5 (Cheng et al., 2002).
Overexpression of ABI3 confers hypersensitivity to sugars (Finkelstein et al., 2002;Zeng & Kermode, 2004) and abi3 mutants were insensitive to glucose in combination with ABA (Nambara & Marion-Poll, 2003).A similar sugar-ABA interaction was shown for the regulation of ApL3 (ADP pyrophosphorylase large subunit) in starch biosynthesis in rice (Akihiro et al., 2005).These findings clearly connect sugar to ABA signaling; however, a number of genes are coregulated by sugar and ABA (Li et al., 2006).Additionally, ABI1, ABI2 and ABI3 appear not to have a major role in sugar signaling (Arenas-Huertero et al., 2000;Huijser et al., 2000;Laby et al., 2000).Taken together, genetic and molecular analyses of sugar signaling have uncovered complex and extensive interactions between sugar and ABA signaling pathways.Whether a direct molecular link exists between sugar and ABA signaling pathways remains unresolved, and more efforts might be devoted to the establishment of their connections in a more direct and specific way.

Epigenetic regulation of seed maturation
Accumulation of seed reserves is a major process during the seed maturation phase.The main storage products accumulated during seed filling are storage proteins, oil (often TAG) and carbohydrates (often starch).Recently, advances have been made toward understanding the regulatory, metabolic and developmental control of seed filling (Baud et al., 2008;Gallardo et al., 2008;Santos-Mendoza et al., 2008;North et al., 2010).The regulatory networks governing seed maturation in Arabidopsis are repressed prior to germination so that seed storage reserves are not accumulated during vegetative development (Fig. 2).Therefore, studies on the expression of seed maturation genes in nonseed tissues would facilitate understanding of the regulatory mechanisms underlying seed filling.Chromatin modification has been implicated in the repression of these regulatory networks.Phaseolin is the major SSP of bean.Phaseolin (phas) gene expression is temporally and spatially regulated and is completely inactive during the vegetative phase of plant development (Bustos et al., 1989;van Der Geest et al., 1995).Silencing of the phas gene in vegetative tissues was associated with the presence of a nucleosome positioned over the three phased TATA boxes present in the phas promoter (Kadosh & Struhl, 1998).Ectopic expression of the ABI3-like factor ALF potentiated the chromatin structure over the TATA region of the phas promoter and caused phas expression in vegetative tissues in an ABAdependent manner (Goldberg & Fischer, 1999).In developing seeds, this repressive structure is remodeled concomitant with gene activation, leading to the disruption of condensed chromatin configuration and allowing transcription factors to access the phas promoter (Li & Hall, 1999).Chromatin immunoprecipitation assays demonstrated that histone acetylation and methylation-directed chromatin remodeling contributed to the regulation of phas expression (Ng et al., 2006).Acetylation and deacetylation of lysine residue in the amino-terminal tail were shown to be involved in the reversible modification of chromatin structure and had the opposite effect on transcriptional regulation (Berger, www.intechopen.comCombinatorial Networks Regulating Seed Development and Seed Filling 207 2002).Acetylation is catalyzed by histone acetyltransferase (HAT) and results in transcriptional activation (Brownell & Allis, 1996;Kuo & Allis, 1998;Kuo et al., 2000).Deacetylation is catalyzed by histone decaetylase (HDAC) and is linked to transcriptional repression (Kadosh & Struhl, 1998;Rundlett et al., 1998).Inhibition of HDAC activity with trichostatin A during germination led to elevated expression of embryogenesis-related genes (Tanaka et al., 2008).
Several proteins have been identified that act as negative regulators of seed maturation gene expression (Table 3 and Fig. 2).PICKLE (PKL), a CHD3 chromatin remodeling factor belonging to the SWI/SNF class, acts in concert with GA to ensure that embryonic traits are not expressed after germination (Ogas et al., 1997;Ogas et al., 1999).pkl mutants expressed seed maturation genes in primary roots (Ogas et al., 1997;Ogas et al., 1999;Rider et al., 2003;Henderson et al., 2004;Li et al., 2005).The VP1/ABI3-LIKE (VAL) B3 proteins VAL1 and VAL2, also referred to as HSI2 and HSL1, respectively (Tsukagoshi et al., 2007), act together with sugar signaling to repress ectopic expression of seed maturation genes in seedlings and were necessary for the transition from seed maturation to active vegetative growth (Suzuki et al., 2007;Tsukagoshi et al., 2007).VAL1 and VAL2 encode B3 domain proteins with an ERF-associated amphiphilic repression (EAR) motif.Interestingly, a CW domain of unknown function and a putative plant homeodomain (PHD)-like zinc (Zn)-finger domain are frequently present in chromatin remodeling factors and were present in the VAL1 and VAL2 (Suzuki et al., 2007).It was revealed that VAL1/HSI2 functions as a repressor of a sugar-inducible reporter gene (Tsukagoshi et al., 2005).Most of the embryonic and seed maturation genes including LEC1, ABI3, FUS3 and genes for seed storage compounds were derepressed in seedlings of a double mutant of VAL1 and VAL2 (Suzuki et al., 2007;Tsukagoshi et al., 2007).As noted above, PcG group proteins establish epigenetic inheritance of repressed gene expression states through histone methylation of H3K27 (Köhler & Grossniklaus, 2002).Genetic and molecular studies demonstrated that FUS3 is regulated by the PcG proteins, for example, FUS3 expression is derepressed in leaves of a double mutant of CLF and SWN and chromatin immunoprecipitation corroborated the direct targeting of FUS3 by the PcG protein MEA (Makarevich et al., 2006).A member of BRAHMA (BRM)containing SNF2 chromatin remodeling ATPase was also found to be involved in repression of some seed maturation genes in leaves.Mutation of BRM led to the accumulation of transcripts from 2S, FUS3 and some other embryogenesis-related genes in leaf tissues (Tang et al., 2008).Recently, a new embryonic repressor ASIL1 was isolated by its interaction with the Arabidopsis 2S albumin At2S3 promoter (Gao et al., 2009).ASIL1 has domains conserved in the plant-specific trihelix family of DNA binding proteins and belongs to a subfamily of 6b-interacting protein 1-like factors.It is interesting that the trihelix domain of ASIL1 is highly similar to the SANT (Switching-defective protein 3 (Swi3), Adaptor 2 (Ada2), Nuclear receptor co-repressor (N-CoR), Transcription factor (TF)IIIB) domain that functions as a unique histone-interaction module in chromatin remodeling (Boyer et al., 2004).This structural feature suggests that ASIL1 may function as a gene-specific DNA-binding factor to regulate seed maturation genes by recruiting a chromatin remodeling complex.Identification of proteins that interact with ASIL1 will provide further insight into this possible regulatory mechanism.asil1 seedlings exhibit a global shift in gene expression to a profile resembling late embryogenesis.LEC1 and LEC2 were markedly derepressed during early germination, as was a large subset of seed maturation genes, such as those encoding SSPs and oleosins, in seedlings of asil1 mutants.Consistent with this, asil1 seedlings accumulated 2S albumin and oil with a fatty acid composition similar to that of seed-derived lipid.Moreover, ASIL1 specifically binds to a GT element that overlaps the G-box and is in close proximity to the RY repeats of the At2S promoters.It was suggested that ASIL1 targets GT-box-containing embryonic genes by competing with the binding of transcriptional activators to this promoter region.Thus, ASIL1 represents a novel component of the regulatory framework that negatively controls expression of seed maturation genes during post-embroyonic growth (Gao et al., 2009).This finding supports the notion that embryonic traits are actively repressed during and after germination and are directly or indirectly regulated by epigenetic means (Fig. 2).

Conclusion
Seeds are the key link between two sporophytic generations in the life cycle of flowering plants.Seed development is an intricate genetically programmed process that is correlated with changes in metabolite levels and regulated by a complex signaling network mediated by sugars and hormones.The coordinated expression of embryo and endosperm tissues is required for proper early seed development, which is primarily maternally controlled through epigenetic mechanisms such as histone-and DNA-methylation.The transition to the maturation phase requires a switch to filial control which is denoted by a distinct hormone and metabolite profile.Genetic, physiological and cytological approaches have been employed to dissect the molecular mechanisms underlying seed development.Such studies have elucidated the elaborate regulatory and metabolic pathways governing the onset of seed maturation, seed filling, acquisition of desiccation tolerance and after-ripening phases.Considering the importance of seeds for human food, animal feed and sustainable feedstocks for biofuel production, much effort has been devoted to the genetic and metabolic control of starch, protein and lipid deposition in cereal grains and oilseeds.Molecular, physiological and genetic approaches are being used in combination to identify the individual steps in the pathways leading to storage compound synthesis and the factors that regulate these processes.Currently, these tools and knowledge are being applied to engineer crop plants with altered seed compositions and metabolite profiles to improve seed yield, quality and utility.

Fig. 1 .
Fig. 1.A proposed model for the epigenetic control of early seed development.The FIS-PcG complex includes proteins encoded by FIS class genes such as MEA and FIS2(Simon & Tamkun, 2002; Köhler & Makarevich, 2006;Baroux et al., 2007).Both maternal and paternal alleles of these imprinted genes are repressed via DNA methylation from the activity of the DNA methyltransferase MET1 in the central cell and sperm(Gehring et al., 2006;Jullien et al., 2006;Huh et al., 2007).During female gametogenesis, MET1 activity is partially repressed by the Retinoblastoma pathway involving RBR1 and its interacting partner MSI1 through DNA hemi-methylation, the preferred substrate for the 5-methylcytosine glycosylase DME(Jullien et al., 2008).The complete demethylation on MET1 in the mature central cell is mediated by DME, resulting in imprinted expression of the FIS-PcG genes(Jullien et al., 2008).During early endosperm development, the inherited paternal FIS-PcG alleles remain silenced by MET1, whereas the imprinted maternal alleles are active leading to the repression of target genes such as the maternal PHE1 through lysine27 on histone H3 (H3K27) methylation.The mechanism underlying PHE1 activation in sperm cell remains unknown.In contrast to the FIS genes MEA and FIS2 that are proposed to play a role for the repression of endosperm proliferation(Kiyosue et al., 1999;Ingouff et al., 2007), paternalspecific expression of PHE1 in the chalazal domain of the endosperm promotes endosperm development(Köhler et al., 2005).

Fig. 2 .
Fig. 2. Schematic representation of seed development in Arabidopsis.Embryogenesis after double fertilization in angiosperms involves two phases, morphogenesis and maturation.During the morphogenesis phase (approximately the first one third of the time of embryogenesis), the basic body plan is established and generates the different morphological domains of the embryo, the embryonic tissue and organ systems.After transition to the maturation phase, the embryo undergoes typical seed filling, growth arrest, acquisition of desiccation tolerance and entry into quiescence.Major reserves synthesized and accumulated during maturation phase include starch, storage proteins and lipids.Transition into the maturation phase is coordinated by the interactions of stage-specific developmental regulators such as the LEC regulators and the competing effects of sugars (sucrose-hexose ratio), hormones (ABA-GAs balance) and their synchronized interactions.The germination potential of seeds and seedling establishment are determined by the afterripening process, hormones (GAs) and multiple embryonic repressors.Adapted from Refs.(Baud et al., 2002;Weber et al., 2005; Braybrook & Harada, 2008).

Table 1 .
. PcG proteins required for early seed development in Arabidopsis

Table 3 .
Genes involved in seed repression in Arabidopsis seedlings