Proteomics 2015, 15, 16711679 DOI 10.1002/pmic.

201400375 1671

REVIEW

Studies on the molecular mechanisms of seed

germination
Chao Han and Pingfang Yang

Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese
Academy of Sciences, Wuhan, P. R. China

Seed germination that begins with imbibition and ends with radicle emergence is the first Received: August 5, 2014
step for plant growth. Successful germination is not only crucial for seedling establishment Revised: December 3, 2014
but also important for crop yield. After being dispersed from mother plant, seed undergoes Accepted: January 14, 2015
continuous desiccation in ecosystem and selects proper environment to trigger germination.
Owing to the contribution of transcriptomic, proteomic, and molecular biological studies,
molecular aspect of seed germination is elucidated well in Arabidopsis. Recently, more and
more proteomic and genetic studies concerning cereal seed germination were performed on
rice (Oryza sativa) and barley (Hordeum vulgare), which possess completely different seed
structure and domestication background with Arabidopsis. In this review, both the common
features and the distinct mechanisms of seed germination are compared among different
plant species including Arabidopsis, rice, and maize. These features include morphological
changes, cell and its related structure recovery, metabolic activation, hormone behavior, and
transcription and translation activation. This review will provide more comprehensive insights
into the molecular mechanisms of seed germination.

Keywords:
Arabidopsis / Molecular mechanism / Plant proteomics / Rice / Seed germination

1 Introduction on regulation of phytohormones, including gibberellic acid

Seed germination, being crucial for next-generation plant
growth, is a prerequisite event for crop yield. Typically, seed
germination begins with dry mature seed imbibition and
ends with radicle protrusion [1, 2]. This process is not an
isolated biological process for the dry seed, but a succes-
sive process combining seed development/desiccation and
seedling establishment [3]. The most important factor for suc-
cessful germination is selection of the proper environmental
condition to initiate this process. Germination depends
Correspondence: Dr. Pingfang Yang, Key Laboratory of Plant
Germplasm Enhancement and Speciality Agriculture, Wuhan
Botanical Garden, Chinese Academy of Sciences, Wuhan 430074,
P. R. China
E-mail: yangpf@wbgcas.cn
Fax: +86-27-87510956
Abbreviations: ABA, abscisic acid; dai, days after imbi-
bition; GA, gibberellic acid; isoAsp, isoaspartyl; OPDA, 12-
oxo-phytodienoic acid; PARP, poly (ADP-ribose) polymerase;
PGIPs, polygalacturonase-inhibiting proteins; PIMT, protein L-
isoaspartyl-O-methyltransferase
(GA), abscisic acid (ABA), ethylene, and auxin. Among them,
ABA and GA are proved to be key regulators, which play an-
tagonistic roles in seed germination [4,5]. Environmental fac-
tors, including light, temperature, and soil water content and
nutrient, influence seed germination mainly through regu-
lating the metabolism and signaling pathways of GA and
ABA [4].
The molecular mechanism of germination has been ex-
tensively studied in Arabidopsis through mutant screening
and related molecular genetic studies. Many specific loci cor-
related with altered seed dormancy and germination have
been identified, including GA and ABA biosynthesis and
signaling-related genes [48]. Based on these mutants, genetic
approach has facilitated in obtaining knowledge regarding
stratification regulating [9,10], lipid reserve mobilization [11],
amino acid metabolism [12], DNA damage recovering [13],
and epigenetic regulating mechanism [14, 15]. Furthermore,
quantitative trait loci studies were performed in Arabidop-
sis and other species, including sunflower, Brassica oleracea,
Colour Online: See the article online to view Fig. 1 in colour.


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1672 C. Han and P. Yang
and Medicago truncatula, which detected several novel genes
that participate in seed germination regulation [1619]. This
technique is also applied in construction of genetic archi-
tecture of seed germination in response to environmental
stresses [20, 21]. All these almost cover every physiologi-
cal process during germination and form a basic molec-
ular regulation model for seed germination. Meanwhile,
there are drastic morphological changes during seed ger-
mination, a tiny seed transforming into a normal seedling,
which implies the large-scale changes and regulation of gene
expression.
Owing to the development of quantitative -omics tech-
nologies and the completion of Arabidopsis genome annota-
tion, large-scale and high-throughput omics studies, includ-
ing transcriptomic [22], proteomic [23], and metabolomics
studies [24], have been widely used in investigating the mech-
anism of Arabidopsis seed germination. Combining the data
from mutants and omics studies, several key regulators that
are involved in regulation of germination were characterized,
and their functions were elucidated. In spite of all the studies,
there is still much to be done to fully understand its molecular
mechanism [25].
Moreover, molecular mechanism of other crop species is
not explored as much as that in Arabidopsis. Rice, being a typ-
ical monocotyledon plant, is one of the most important crops,
which feeds half of the world population [26]. Understanding
rice seed germination features will provide the guide for rice
production and new hybrid cultivation. Recently, numerous
proteomic studies focusing on rice and other cereal species,
such as barley, seed germination were conducted [27, 28].
Rice seed germination possesses both features common with
Arabidopsis and distinct characters of its own. Generally, seed
germination is separated into three phases based on water-
absorption style and weight changes [1]. In this review, the
series of activities happening during germination were dis-
cussed, which might help to comprehensively understand
this physiological process.
2 Structure and function recovery
After maturation, the orthodox seed is subject to a desiccation
stage, a bridge between maturation and germination [3]. It has
been reported that all the necessary genetic information for
germination are programed in the desiccated seeds [22, 29].
To survive from desiccation, seeds have to obtain certain spe-
cial characters including increase of cellular solutes gradient,
formation of gel-phase membrane system, and changes in
physical structures, which is not suitable for any biological
reactions [30].
Upon imbibition, dry seeds undergo a rapid water uptake
phase, which is defined as phase I of germination [1]. Dur-
ing this phase, absorption of water into cells of dry seed is a
physical process, which is driven by the matrix potential and
can also occur in dead seeds [31]. During seed maturation,

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Proteomics 2015, 15, 16711679
the desiccation could lead to damages on membrane system,
proteins, and DNAs, which will be more severe along with
the fast water absorption upon imbibition [32]. The pertur-
bation of membrane structure will result in the leakage of
solutes and metabolites and speed up water absorption [1],
which facilitates germination by lowering the concentration
of inhibitors [33].
To cope with the damages imposed during desiccation
and rehydration, plant seeds have evolved fine repair mecha-
nisms during imbibitions. The damages on proteins usually
happen on aspartyl residues that are converted into isoas-
partyl (isoAsp). This damage could be reversed by isoAsp
methyltransferase [34]. Protein L-isoAsp-O-methyltransferase
(PIMT) possesses the ability to repair the abnormal isoAsp
to normal Asp and Asn [35]. In Arabidopsis, pimt1 mutant
possessing extremely higher transcript and protein level in
dry seeds exhibited more resistance to aging treatment and
lower level of isoAsp than those of wild-type seeds, which
indicated that PIMT in dry seed is essential for success-
ful germination after long-time storage [34]. In rice and
corn seeds, the PIMT also kept high activity in the early
stage of germination [36]. It seems that higher plants share
the same seed protein repairing mechanism for long-time
storage.
Damages on DNAs include strand breaks and loss of telom-
eric sequences, which seem to be a major factor negatively
influencing seed viability [37, 38]. DNA damages can be re-
paired by DNA ligases. Arabidopsis DNA LIGASE VI contains
the same -caspase motif with DNA double-strand break re-
pair factor Artemis. Upon imbibition, DNA ligase expression
is quickly activated, and de novo DNA synthesis is conducted
at high level in Arabidopsis seed [33]. Loss of function on two
DNA ligase isoforms delayed germination [39]. Poly (ADP-
ribose) polymerases (PARPs) are important components in
DNA damage response in human cell. Arabidopsis homolog
AtPARP3 was highly expressed in germinating seeds. Its re-
lated mutants displayed delayed germination compared to
wild-type seeds [40]. PARPs were also discovered in rice
germinating seed proteome, which implied similar DNA
damage recovery mechanism between rice and Arabidopsis
[29].
Besides the recovery of macromolecules, membrane sys-
tem and organelles are also subjected to a repair process
upon imbibition. Mitochondria exist in mature dry seed but
are poorly differentiated. It is believed that preexisting mito-
chondria are developed and activated in starchy seeds during
germination, while more new mitochondria are produced in
oil-storing seeds [1]. Mitochondria differentiation process in
rice embryo during germination was observed by electron
microscope. This differentiation process coincided with the
transcript abundance increase of mitochondria protein, in-
cluding TCA cycle and respiratory chain related proteins [41].
How repair on the damaged membrane is achieved is still
an open question, and it may be an interesting topic in seed
biology.
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Proteomics 2015, 15, 16711679
3 Reactivation of metabolisms and gene
expression
Following up with phase I, water absorption and changes in
seed size stagnate, and then germination steps into phase
II or the plateau phase. During this phase, reactivation
of metabolisms and regulation of genes expression occur
comprehensively.
3.1 Reserves mobilization and metabolism activation
During seed development, all kinds of nutrients are accu-
mulated, including lipids, proteins, and starch. Upon imbibi-
tions, the cellular structure and enzymes activity are grad-
ually resumed in phases I and II. Once enough water is
absorbed, different kinds of metabolisms are activated. Pro-
teomic analyses have shown that large amount of enzymes
necessary for major metabolisms is accumulated in mature
dry seeds and kept stable or increased during germination
[4245]. For Arabidopsis seeds, lipid is the major reserve stored
in cotyledon. Lipid mobilization is repressed by ABI4 during
seed germination [11], and this process is not associated with
GA signaling [42]. It is believed that the major reserve in seed,
such as lipid for Arabidopsis, is not mobilized during germina-
tion until seedling establishment [1]. However, mobilization
of storage proteins is probably more important for dicotyle-
don plant during germination. In vetch seed germination,
vicilin in radicle, which is not the dormant storage protein,
was almost consumed in the first 23 days after imbibition
(dai). After vascular strands establishment on the third day
after imbibition, globulin mobilization in cotyledons began
[46]. It seems that seed mobilizes the minor storage nutrients
first for germination and major storage nutrients are utilized
for seedling establishment subsequently.
Contrary to Arabidopsis, rice seeds contain large amount of
starch in endosperm for germination and seedling establish-
ment. The -amylase was proved to be the first enzyme to be
attached to starch granule and to help release the soluble glu-
cans that are substrates for further degradation [47]. Although
proteomic studies indicated that rice -amylase was induced
in germinating seeds after 2 days of imbibition [44, 48], it
seems that degradation of starch occurs earlier than that [29].
It was reported that GA synthesized in rice scutellar epithe-
lium induced the -amylase expression in aleurone cells [49].
In response to GA synthesis in scutellar tissues, the tran-
scription factor GAMYB can bind to GA-responsive element
in -amylase promoter and activate its expression in rice and
barley aleurone cells [50]. The activation of -amylase in aleu-
rone cells by GA could be repressed by ABA signaling through
protein kinase PKABA1 [51]. Finally, -amylase was secreted
into rice endosperm and regulated by phosphoinositideCa2+
signaling [52].
Another feature of rice seed reserve mobilization is the
way of nutrients transportation from endosperm to embryo.
As mentioned above, rice seeds contain a large endosperm,

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1673
which is separated from embryo, and store all kinds of nutri-
ents for germination as well as seedling establishment. The
product of starch mobilization is transported through scutel-
lum parenchyma to the sutellum vasculature connecting to
phloem for embryonic axis growth when starch degradation
begins in endosperm [53]. It seems that the carbohydrate
transported into embryo is sucrose. In wheat seed, sucrose
transporter TaSUT1 was localized in scutellum epidermal cell
of 7-dai germinating seeds [54]. However, in rice 7-dai ger-
minating seeds, OsSUT1 was localized in scutellum vascular
cells [55]. The carbohydrates that are transported into embryo
are not fully degraded but are repolymerized into starch gran-
ule again, which is localized in scutellum and embryonic axis
vascular tissues [29, 56]. Phosphoproteomic study reported
that cytosolic pyruvate orthophosphate dikinase and glucose-
1-phosphate adenylyltransferase were phosphorylated during
germination, which exhibited the same mechanism of starch
synthesis in amyloplast during seed development [56, 57].
Starch synthesis again in embryo during germination might
be an effective mechanism for carbohydrate usage and energy
provision.
Coinciding with seed reserve mobilization, the basic
metabolisms in cell are activated during germination. In
Arabidopsis seed development, the contents of basic metabo-
lites, including amino acids, sugars, organic acids, were de-
creased. During seed desiccation, amino acids and parts of
sugars were accumulated in mature dry seeds, which will
be used at the beginning of germination. After seed imbi-
bition, amino acids and related organic acids contents were
increased continuously, and the phosphorylated sugars, in-
cluding fructose-6-phosphate and glucose-6-phosphate, were
extremely increased, which indicates activation of catabolism.
Phosphorylated sugars are an essential means by which
sugar enters into glycolysis pathway and for energy provi-
sion [24]. As for rice seed germination, fructose-6-phosphate
and glucose-6-phosphate were activated extremely after 1-h
imbibition. However, differing with Arabidopsis germination,
soluble sugars were also increased after 12-h imbibition, in-
cluding glucose and fructose [58].
Aspartate amino acids family seems to be vital for Ara-
bidopsis seed germination. During Arabidopsis germination,
aspartate was increased the most among all kinds of amino
acids [24]. Lysine, as an aspartate metabolism product, was
proved to provide substrate for TCA cycle, resulting in suffi-
cient energy for germination and seedling establishment [12].
Another aspartate metabolism product, cysteine, is a central
metabolite for Arabidopsis germination. The main reason is
that cysteine does not only act as a block for protein syn-
thesis but also as the precursor of S-adenosylmethionine
(AdoMet), which is the precursor for the biosynthesis of
ployamines, vitamin biotin, and ethylene. It provides the ba-
sic metabolite for DNA synthesis, methylation regulation,
and hormone regulation [59]. However, in rice germinat-
ing seeds, glutamate was the most abundant amino acid
[60]. Proteomic analysis constructed amino acid metabolism
pathway in rice embryo during germination (Fig. 1) [61].
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1674 C. Han and P. Yang Proteomics 2015, 15, 16711679

Figure 1. Amino acid metabolism pathway in embryo during the early stage (from late phase I to early phase II) of rice seed germination
and the protein abundance pattern of the significantly changed protein involved in amino acid metabolism. Metabolites are written in the
box. Arrows indicates the reaction direction. Enzymes catalyzing the reactions are written directly on the arrows. The enzymes written
with red font are decreased proteins. Enzymes written with green font are increased proteins. The heat map in the bottom right corner
reflects the protein abundance pattern of related enzymes. The enzymes abbreviations are as follows. ALT, alanine aminotransferase;
CysS, cysteine synthase; DPT, diaminopimelate aminotransferase; GAD, glutamate decarboxylase; GOT1, aspartate aminotransferase;
HGD, homogentisate 1,2-dixoygenase; ilvC, ketol acid reductoisomerase; leuA, 2-isopropylealate synthase; leuB, 2-isopropylmalate de-
hydrogenase; LysA, diaminopimelate decarboxylase; MetK, S-adenosylmethionine synthase; MetS, methionine synthase; OTC, ornithine
carbamoyltransferase; PSAT, phosphoserine aminotransferase; PGD, phosphoglycerate dehydrogenase; POP, 4-aminobutyrate-pyruvate
transaminase; rocD, ornithine-oxo-acid transaminase. The results in this figure were analyzed based on proteomic data in [61].

Glutamate decarboxylase was downregulated during germi-
nation, which repressed glutamate transforming into TCA
cycle. On the other hand, increase of OTC and rocD proteins
abundance led glutamate to enter into urea cycle, which was
beneficial to nucleotide and vitamin synthesis. Several key en-
zymes catalyzing amino acid synthesis, including LysA, MetS,
CysS, LeuA, and LeuB, were upregulated during germination.
Similar to Arabidopsis, activation of MetK translation dur-
ing rice seed germination, leading to AdoMet synthesis, was
proved by several proteomic studies [44, 48, 61, 62]. This indi-
cated that ethylene regulation plays similar roles in rice and
Arabidopsis germination. Above all, amino acid metabolism
activation can mediate transformation of basic metabo-
lites from starch/carbohydrate metabolism to nitrogen-
containing metabolite synthesis, which is vital for rice seed
germination.
3.2 Transcription and translation activation
Upon imbibition, dramatic changes of gene expression were
observed at both transcriptomic and proteomic levels [4, 32],
which indicate that the changes in gene expression are asso-
ciated with germination. It is believed that all the essential


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Proteomics 2015, 15, 16711679
mRNAs have been stored in the desiccated seeds and tran-
scription is not required for germination [22, 29, 58]. Dry ma-
ture seed contains a large number of stored mRNA species.
In Arabidopsis mature dry seeds, more than 12 000 stored
mRNAs were discovered [22], and there were about 17 000
stored mRNAs in rice embryo [58]. However, although
transcription inhibitor -amanitin did not block germina-
tion, it delayed germination in both Arabidopsis and rice
seeds [29, 43]. It seems transcription inhibitor influences the
seedling establishment more than germination [29]. These
results supported that de novo transcription normally allows
the synthesis of factors to ascertain germination speed. A
great transcript increase occurred from 3 to 12 h after imbi-
bition in rice embryo, which led to an increase in secondary
metabolites, including those involved in carbohydrate, amino
acids, and cell-wall metabolism [58].
In contrast to transcription, translation in early stage
of germination is a prerequisite for germination, because
translation inhibitor impaired germination in both Arabidop-
sis and rice seeds [29, 43]. The de novo protein synthesis
began after 8 h of imbibition in Arabidopsis [63]. Hence,
it is believed that stored mRNA is used at this moment.
Stored mRNA translation was important for reserve mobi-
lization and metabolites activation in both Arabidopsis and
rice seeds [59, 64]. In vitro incubation experiment proved
that maize dry seed stored mRNA translation particularly
requires the involvement of eIF(iso)4E [65]. The eIFiso4G1
and eIFiso4G2 knock-out double-mutant i4g1/14g2 in Ara-
bidopsis showed reduced germination rates and long-term
seed viability, which was inferred to be responsible for stored
mRNA translation [13]. It seemed that Arabidopsis and ce-
real seeds possess the same mechanism for stored mRNA
translation.
3.3 The role of ABA and GA in regulation of
germination
Besides these basic metabolisms, stimulants, such as phy-
tohormones, are key regulators for activating germination.
Among them, GA and ABA are the two most important hor-
mones that play central and antagonistic roles in the regu-
lation of seed germination with GA promoting and ABA in-
hibiting germination [4, 5]. The endogenous contents of GA
and ABA have extensive effect on germination. GA biosyn-
thetic upstream gene ent-kaurene oxidase (AtKO1) mRNA
level was increased after 8 h of imbibition in Arabidopsis
seeds. GA 2-oxidases AtGA2ox1 and AtGA2ox2, which cat-
alyzed the reaction at the last step of GA biosynthesis and
produced bioactive GA4, achieved their most abundant tran-
script levels after 8 and 32 h of imbibition, respectively [63].
Increase of GA content is always accompanied by a decrease
of ABA content during germination [4, 5]. The expression
of gene encoding ABA 8 -hydroxylase that catalyzes ABA to
inactive form and releases dormancy was increased from
0 to 6 h after imbibition in both Arabidopsis and barley

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1675
nondormant seeds [66]. The environmental factors control
seed germination through either affecting the contents or
integrating the signaling pathways of GA or ABA [67, 68].
The transcription factors PIL5 and HFR1 are proved to
be very important in mediating the integration between
different signaling pathways [69, 70]. Gene encoding 1-
aminocyclopropane-1-carboxylic acid oxidase, which is re-
sponsible for the critical step of ethylene synthesis, was also
activated in mRNA level during early stage of Arabidopsis seed
germination [71]. All these examples proved that transcrip-
tional activation during early stage of germination accelerates
germination.
4 Radicle protrusion
For the triphasic seed germination, another rapid increase
of water uptake occurs after the completion of phase II be-
cause of the elongation of embryonic axes. Without dormancy
release, dormant seed could not enter into phase III [1]; in
nondormant seeds, ABA could inhibit the transition from
phase II to III, but did not affect the transition from phase I
to II [72, 73].
In the two-step germination seeds including Arabidopsis,
cress, and tobacco, testa rupture occurred at the end of phase
II, and endosperm rupture and radicle protrusion happened
in phase III, which is named as the completion of germina-
tion sensu stricto [72,73]. The radicle protrusion is the symbol
of germination, which is also the most important morpholog-
ical change. This process is completed through two steps and
expands from phase I to phase III in dicotyledonous plants,
such as Arabidopsis thaliana and Lepidium sativum, whose em-
bryo is covered by inner endosperm layer and outer testa layer
[73]. Endosperm contains just one layer of cells that is tightly
associated with the testa, while testa contains several cell lay-
ers, including three cell layers inner integument being full
of proanthocyanidins and two cell layers outer integument
filled with mucilage [7476]. Testa is the part of seed that
comes into contact with the environmental conditions. Its
permeability determines the rate of water uptake during ger-
mination [77]. In Brassica, seeds with different morphologi-
cal structures showed different germination features [33, 78].
Proanthocyanidins are accumulated in testa during seed de-
velopment, and oxidized during desiccation, which helps to
form the brown pigment of seed testa and is crucial for phyto-
hormone sensitivity and dormancy maintenance [74, 79, 80].
The mucilage, whose major component is pectin, makes up
a thickened wall in outer layer of testa and forms a boundary
for gas exchange and radicle protrusion [80].
During Arabidopsis seed germination, the first step of radi-
cle protrusion is testa rupture and radicle with endosperm
layer emerging [73]. The pectin degradation in testa is reg-
ulated by ABA and 12-oxo-phytodienoic acid (OPDA) signal
synergistically. The transcriptome analysis of a single-copy
gene encoding an ATP-binding cassette transporter ped3 mu-
tant and transcriptional factor in ABA signal abi5 mutant
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1676 C. Han and P. Yang
proved that two genes coincidently induced the expression
of polygalacturonase-inhibiting proteins (PGIPs) during ger-
mination, while the ped3 abi5 double mutant showed the
equal PGIPs expression pattern with abi5 mutant, which
implied that ABI5 functions downstream of PED3 and in-
duced PGIPs expression. PGIPs inhibit polygalacturonase
activity and degradation of pectin in testa, which impaired
Arabidopsis germination [81]. The mutation of ATP-binding
cassette transporter, which is involved in transporting sub-
strates for -oxidation into peroxisome, led to the OPDA
accumulation in germinating seed. And OPDA treatment
caused ABI5 protein accumulation in Arabidopsis germinat-
ing seeds result in the delay of germination [82, 83]. It seems
that ABI5 is the key regulator for testa rupture to control
germination process. Contrarily, osmotic stress caused ABI5
protein accumulation in seed, which arrests the germinating
seed development until the stress is removed. This is called
ABA-dependent checkpoint of germination, which increases
the survival ratio of seeds under potential water stress [84].
Germinating seed can go back to a certain extent of dor-
mancy before completion of testa rupture in control of ABA
signal.
The second step for Arabidopsis seed germination is
that radicle breaks through the endosperm and emerges
completely [73]. Proteomic study on Arabidopsis seed ger-
mination proved that S-adenosyl-methionine (Ado-Met)
synthase and -glucosidase expression in germinating
GA-deficient ga1 mutant seed was strictly dependent on
exogenous GA [42]. Induced -glucosidase expression was
beneficial for cell-wall loosening and radicle extension.
Numerous cell-wall remodeling proteins, including endo-
-1,4-mannanase, endo--1,3-glucanase, and expansins, are
specifically expressed in micropylar endosperm and involved
in endosperm tissue weakening for different species during
germination [8587]. In tomato seed germination, it was
proved that expansins were induced by GA in GA-deficient
(gib-1) mutant seeds. However, the expression of expansin
protein in micropylar endosperm induced by GA could be
repressed by ABA treatment [85]. Meanwhile, endosperm
weakening is regulated by GA/ABA ratio in both Lepidium
sativa and Arabidopsis thaliana seeds [73].
Differing with Arabidopsis, cereal seeds, such as rice and
barley, contain large endosperms for nutrient accumulation
and tiny embryos for seedling establishment. During ger-
mination, rice endosperm underwent quick water uptake
and weight increase without obvious changes in size during
phase I, while the size of embryo expanded along with the
increase in fresh weight [88]. The most important morpho-
logical change of cereal seeds is the elongation of embryonic
axis, including radicle and shoot that are covered by coleorhiza
and coleoptile, respectively. During the early stage of cereal
seed germination, radicle and shoot elongation begin. As a
result, embryo tissue expands. In barley seed germination,
radicle elongation, including coleorhiza, began rapidly and
elongated more as compared to shoot [64]. It is proved that
ABA content decreased during early stage of germination in

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Proteomics 2015, 15, 16711679
coleorhiza tissues of barley seed. And this is catalyzed by ABA
8-hydroxylase, which is specifically expressed in coleorhiza of
nondormancy seeds [89]. Transcriptomic studies showed that
not only ABA metabolic genes ABA 8-hydroxylase but also
ABA signaling protein lipid phosphate phosphatase (HvLPP)
were upregulated by after-ripening in barley coleorhiza tissue.
To coincide with these results, ABA sensitivity and content
were reduced in after-ripening seeds compared with dormant
seeds [64]. Coleorhiza tissue seems to be a tissue similar to
micropylar endosperm and testa that also cover the radicle
and is the barrier for radicle emergence. In transcriptomic
data, there were high expression levels of cell wall modifica-
tion genes, including endo-1,3--glucosidases and expansins,
in after-ripening coleorhiza. Scanning electron microscope
observation found air space had emerged in coleorhiza tis-
sue after 24-h imbibition [64]. It is implied that decrease of
ABA content and effect leads to coleorhiza tissue loosening
through cell wall modification proteins. This mechanism in
barley coleorhiza tissue is quite similar to that in Arabidopsis
micropylar endosperm tissue.
5 Conclusion and perspectives
Seed biology is as important as any other aspects of plant
science, which attracts more and more attention from the
plant biologists. Based on previous studies, we have known
that seed germination is regulated by very complicated net-
work of signaling and gene expression regulation. Different
plants may share similar molecular mechanisms including
phytohormone behavior, transcription and translation activa-
tion, radicle protrusion process, and so on. However, there
are certain distinct mechanisms for different plant species,
especially for reserves mobilization and metabolism activa-
tion. These differences are probably based on the different
seed reserves. Moreover, crosstalk between phytohormones
and environmental factors signaling pathways during germi-
nation was still delusive. With the advent of different omics
technologies, the molecular mechanisms underlying germi-
nation are becoming increasingly understood, for example,
the proteomic and phosphoproteomic studies in Arabidop-
sis and rice have already identified some particular signal
components and functional proteins involved in germina-
tion. However, there is still a long way to fully understand
this physiological process. In the near future, integration of
new technologies, such as imaging, ChIP-sequencing, tran-
scriptomic and proteomic techniques, will undoubtedly make
significant contribution to our understanding on the mecha-
nisms of how different signals mediate seed germination.
The authors are grateful to Ms. Rebecca Njeri Damaris for her
help in proofreading the manuscript. This work is supported by the
National Natural Science Foundation of China (no. 31271805)
and 100 Talents Program of the Chinese Academy of Sciences.
The authors have declared no conflict of interest.
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Proteomics 2015, 15, 16711679
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