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International Journal of Molecular Evolution and Biodiversity
2011, Vol.1, No.1 http://ijmeb.sophiapublisher.com
Research Letter
Open Access
Evolution of the Genes Encoding Starch Synthase in Sorghum and Come Wheat
Xiaoxue Pan 1,3 , Hongbo Yan 2 , Meiru Li 1 , Guojiang Wu 1 , Huawu Jiang 1
1 Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou
510650;
2 Bioscience and Bioengineering School, Hebei University of Economics and Business, Shijiazhuang, 050061;
3 Graduate University of the Chinese Academy of Sciences, Beijing, 100049
Corresponding author email: [email protected];
Author
International Journal of Molecular Evolution and Biodiversity, 2011, Vol.1 No.1 doi: 10.5376/ijmeb.2011.01.0001
Received: 16, Aug., 2011
Accepted: 03, Nov, 2011
Published: 15, Nov., 2011
This article was first published in Molecular Plant Breeding, and here was authorized to redistribute under the terms of Creative Commons Attribution License,
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:
Pan et al., 2011, Evolution of the Genes Encoding Starch Synthase in Sorghum and Come Wheat, Molecular Plant Breeding Vol.2 No.9 (doi:
10.5376/mpb.2011.02.0009)
Abstract Starch synthases (SSs) play important roles in plant starch synthesis. Five enzymetic isoforms of starch synthases have
been found in plant, some of isoforms have further diverged possibly via whole genome duplication events, which might result in two
or three subclasses of the sequences in rice and maize. In this study, we found the retention of GBSS, SSⅡ, and SSⅢ duplicator
except for the SSⅣ duplicator in genomes of sorghum and come wheat. The SSⅣa gene might have been lost in maize and sorghum
genomes based on the synteny relationship among rice maize and sorghum. Expression analyses indicated that the SS duplicators
were also diverged from the duplicators of SbGBSSⅠ, SbSSⅢa in expression pattern, and SbSSⅡa were expressed mainly in
endosperm in sorghum, whereas SbGBSSⅡ, SbSSⅡb, and SbSSⅢb of sorghum, TaSSⅡb and TaSSⅢb of common wheat, were
expressed mainly in leaves. Our observations together with previous studies, indicate that the SSⅣ duplicator should be not
remained in all Gramineae species, while the expression of duplicated SS genes diverged similarly in the studied species.
Keywords Starch synthesis; gene duplication; gene divergence; sorghum; come wheat
Background
Whole genome duplication (WGD) or polyploidy
event is a prominent process in Gramineae plants and
has been significant in the evolution and separation
history (Wendel, 2000). Interdisciplinary approaches
combining phylogenetic and structural genomic data
suggest that the Gramineae genes have undergo a
WGD about 70 million years ago (Mya) before the
divergence of the Gramineae (Paterson et al., 2004).
In addition, it also found that the maize genome is the
product of a genomic allotetraploid event approximately
12 Mya ago (Gaut and Doebley, 1997). Subsequently,
the maize genome ‘diploidized’ by deleting most of
the duplicated centromere regions and deleting or
tolerating the degeneration of one number of most of
its paired genes (Song and Messing, 2003; Brunner et
al., 2005).
Starch is the main storage carbohydrate in plants and
also by far the major carbon source in Gramineae
seeds and is used as a primary store of energy for
metabolism and biosynthesis. Starch is composed of
glucose (Glc) polymer that occurs in two main forms:
amylose and amylopectin. Both type starches are
synthesized inside plastids in higher plants, and are
achieved through the coordinated interactions of
several of starch biosynthetic enzymes, including
ADP glucose pyrophosphorylase (AGPase), starch
synthase (SS), starch branching enzyme (BE), and
starch debranching enzyme (DBE) (Ball and Morell,
2003). The duplicate sets of some genes which
involved in the core pathway of starch biosynthesis
were retained in rice, maize, and wheat following the
ancient WGD event in Gramineae (Harn et al., 1998;
Vrinten and Nakamura, 2000; Hirose and Terao, 2004;
Dian et al., 2005).
The starch synthase (SS, EC 2.4.1.21) catalyzes the
synthesis of the glucan polymers by transfering the
glucosyl moiety from ADP-Glc to the nonreducing
end of a preexisting α-1,4 linked glucan primer.
Multiple isoforms of SSs are found in plants (Smith et
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2011, Vol.1, No.1 http://ijmeb.sophiapublisher.com
al., 1997; Ball et al., 1998; Hirose and Terao, 2004).
The granule-bound starch synthase family (GBSS) is
responsible for amylose synthesis and is exclusively
bound to the starch granule. The SSⅠ-Ⅲ isoforms
are involved in amylopectin biosynthesis, while the
SSⅣ isoform in the control of granule numbers (Ball
and Morell, 2003; Roldán et al., 2007).
SS isoforms have been identified in several Gramineae
genomes through amino acid homology analysis. In
rice (Oryza sativa L.), there are 10 SS isoforms
separated into five types, including two GBSS genes
(GBSSⅠ/WX and GBSSⅡ), one SSⅠ gene, three SS
Ⅱ genes (SSⅡa, SSⅡb, and SSⅡc), two SSⅢ genes
(SSⅢa and SSⅢb), and two SSⅣgenes (SSⅣa and SS
Ⅳb) (Hirose and Terao, 2004). Compared to the rice
genome through the current data, Maize (Zea mays L.)
genome contains two SSⅡb and two SSⅢb genes, but
only one SSⅣ gene (Yan et al., 2009). In wheat,
seven SS genes, GBSSⅠ/WX, GBSSⅡ, SSⅠ, SSⅡa,
SSⅡc, SSⅢa, and SSⅣb, had been cloned (Clark et
al., 1991; Li et al., 1999a, 1999b, 2000; Leterrier et al.,
2008; Yan et al., 2009).
In this study, we reported the cloning and
characterization of the genes encoding GBSS, SSⅠ,
SSⅡ, SSⅢ and SSⅣ in sorghum, and the SSⅡb and
SSⅢb genes in wheat. We found that the duplicator of
SSⅣ gene was lost in the sorghum, maize and wheat
genomes. The expression patterns of the detected SS
genes were analyzed and the evolution of the SS gene
family in Gramineae was discussed.
1 Results and Discussion
1.1 Identification of the SS genes in sorghum and
wheat
The previous studies reported the cloning of the genes
encoding GBSSⅠ, GBSSⅡ (Clark et al., 1991), SSⅠ
(Li et al., 1999b), SSⅡa (Li et al., 999a), SSⅡc (Yan
et al., 2009), SSⅢa (Li et al., 2000), SSⅣ (Leterrier et
al., 2008) in wheat, and GBSSⅠ/WX (EF089858), SSⅠ
(AF168786) in sorghum. In this study, we determined
the complete coding domain sequences of the other six
SS genes in sorghum and two in wheat. The
designated gene names and GenBank accession
numbers were SbGBSS Ⅱ (EF472254), SbSS Ⅱ a
(EU620718), SbSS Ⅱ b (EU620719), SbSS Ⅱ c
(EU307275), SbSS Ⅲ a (EU620720), SbSS Ⅲ b
(EU620721), TaSS Ⅱ b (EU333947) and TaSS Ⅲ b
(EU333946). Only one SSⅣ gene (XM_002440083)
was detected in the public sorghum genomic
sequences and EST database. No SSⅣ a gene was
detected in wheat genomic sequences and EST
database in NCBI and the raw Chinese spring
genomic sequence reads using BLAST (http://www.
cerealsdb.uk.net/search_reads.htm). The domain organization of SS proteins in Gramineae was listed in
Table 1.
1.2 Phylogenetic relationships among the duplicated
SS genes
In order to characterize the identified SS genes in
sorghum and wheat, a phylogenetic tree was built with
58 SS amino acid sequences from some monocots and
dicots (Figure 1, a bacterium glycogen synthase,
EcGS, was as out group for the phylogenetic analysis).
The phylogenetic tree indicated that the SS proteins
are grouped into five clades of GBSS, SSⅠ, SSⅡ, SS
Ⅲ , and SSⅣ. In Gramineae, GBSS proteins were
further divided into two subisoforms of GBSSⅠ and
GBSSⅡ, SSⅡ proteins into SSⅡa, SSⅡb and SSⅡ
c, SSⅢ proteins into SSⅢa and SSⅢb, SSⅣ proteins
into SSⅣa and SSⅣb, respectively (Figure 1). The
present determined wheat SSⅡ and SSⅢ fall into the
SSⅡb and SSⅢb subisoforms, respectively (Figure 1).
The previous study found the WGD event occurred
approximately 70 million years ago (Mya) prior to the
divergence of the Gramineae (Paterson et al., 2004).
Thus, it is likely that the duplicators of GBSS, SSⅡ,
and SSⅢb, but not SSⅣ, were retained in genomes of
the observed Gramineae species.
1.3 Alignments of syntenic regions that contain the
SS Ⅳ gene among rice, maize, and sorghum
genome
The two SS Ⅳ genes in rice were located on
chromosome 1 and chromosome 5, respectively. In
order to determine whether the SSⅣa gene is lost in
sorghum and maize genomes, we compared the gene
cluster on syntenic region containing the SSⅣ genes
among rice, sorghum, and maize, based on the
rice-maize-sorghum synteny (http://www.gramene. org/).
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2011, Vol.1, No.1 http://ijmeb.sophiapublisher.com
Table 1 Domain organization of the SS proteins in Gramineae
Gene name
Protein domains
Sorghum
Rice
Maize
Wheat
GBSSI
TP
VR
77
4
76
5
72
4
71
6
CD
526
526
530
528
TP
76
77
76
67
VR
4
3
4
4
CD
527
528
530
528
TP
61
70
62
16
VR
190
248
178
291
CD
492
492
486
492
TP
28
64
29
63
VR
184
138
177
119
CD
492
492
492
492
TP
64
44
69
64
VR
209
193
214
186
CD
492
492
492
492
TP
68
49
69
67
VR
668
558
657
611
SBD
490
488
492
490
CD
448
444
448
458
TP
81
47
47
45
VR
181
222
200
308
SBD
471
489
486
460
CD
448
448
448
444
GBSSII
SSIIa
SSIIb
SSIIc
SSIIIa
SSIIIb
SSIVa
TP
78
VR
399
CD
SSIVb
485
TP
54
33
54
45
VR
361
388
361
375
CD
484
484
485
486
Note: TP: The putative transit peptide, which was identified using the ChloroP neural network analysis of the 100 amino acids at the
N-terminus of each sequence; CD: The putative catalytic domain, which was identified by GenBank conserved domain database
search service, v2.13; VR: The variable region; SBD: The starch binding domain
The selected genomic fragment containing the SSⅣa
gene (GFa) was 544 Kb on rice chromosome 1 (rC1)
which contains 63 putative protein-coding genes
(from Os01g0714900, a Ras-related gene, to Os01g0726100, an Ole e Ⅰ family gene). The genomic
fragment containing the SSⅣb gene (GFb) was 296 Kb
on rice chromosome 5 (rC5) which contains 34
putative protein-coding genes (from Os05g0531200,
an Ole e I family gene, to Os05g0536900, a Rasrelated gene) (http://rapdb.dna.affrc.go.jp/viewer/gbr-
owse/build4/) (supplement and Figure 2). There are 16
paralogous between GFa and GFb. The OsSSⅣa gene
is located between a chlorophyll a-b binding protein
gene and a serine acetyltransferase gene, while the
OsSSⅣb gene located between a serine acetyltransferase gene and a NADH-ubiquinone oxidoreductase
20 kD subunit gene (supplement and Figure 2).
Based on the rice-sorghum synteny (http://www.gramene.org/), the syntenic region of rice GFa in sorghum
is 436 kb on sorghum chromosome 3 (sC3), while the
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2011, Vol.1, No.1 http://ijmeb.sophiapublisher.com
Figure 1 Phylogenetic tree derived from the full amino acid
sequences of starch synthesis proteins
Note: The tree was drawn according to the results generated by
PhyML Online analysis (http://mobyle.pasteur.fr/cgibin/Mobyle
Portal/portal.py?form=phyml) with the JTT model. Bootstrap
values calculated for 100 replicates are indicated at
corresponding nodes. The scale bar represents the branch
length corresponding to the indicated substitutions per site. The
GenBank accession numbers are shown in brackets
syntenic region of rice GFb in sorghum is 248 kb on
sorghum chromosome 9 (sC9). In sorghum, the GFa
contains 58 putative protein-coding genes (from
Sb03g032810, a Ras-related gene, to Sb03g033370,
an Ole e I family gene), while the GFb contains 36
putative protein-coding genes (from Sb09g026510, an
Ole e I family gene, to Sb09g026820, a Ras-related
gene) (http://rapdb.dna.affrc.go.jp/viewer/ gbrowse/
Figure 2 Comparison of the starch synthesis genes on the rice/
sorghum/maize synteny physical map
note: rC=Rice chromosome, sC=sorghum chromosome, mC=
maize chromosome. Arrows indicate the loci of SSⅣ genes
build4/) (supplement and Figure 2). GFa and GFb
have 12 paralogous genes in sorghum. There are 44
orthologous genes in GFa, while 29 orthologous genes
in GFb between in the rice genome and sorghum
genome. Like the OsSSⅣb in rice, the SbSSⅣb gene
was also located between a serine acetyltransferase 1
and a NADH-ubiquinone oxidoreductase 20 kD
subunit in sorghum. However, the SSⅣa gene which
located between the chlorophyll a-b binding protein
gene and serine acetyltransferase gene in GFa in rice
was lost in GFa in sorghum (supplement and Figure 2).
Based on the sorghum-maize synteny (http://www.gra
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2011, Vol.1, No.1 http://ijmeb.sophiapublisher.com
mene.org/), the syntenic region of sorghum GFa in
maize is a 313 kb on maize chromosome 3 (zC3),
while the syntenic region of sorghum GFb in sorghum
is a 64 kb and 131 kb on maize chromosome 6 (zC6)
and chromosome 8 (zC8), respectively. In maize, the
GFa contains 11 putative protein-coding genes (from
GRMZM2G099166_T02, a DUF581 family protein,
to GRMZM2G116282_T02, a RNA-binding protein),
while the GFb on zC6 contains 6 putative proteincoding genes (from GRMZM2G033971_T01, a
DUF212 family protein, to GRMZM2G043035_T02,
an Ole eⅠ family protein), and on zC8 contains 6
putative protein-coding genes (from GRMZM2G044866_T01, a DUF616 family protein, to GRMZM2G121117_T02, a hypothetical protein) (http://rapdb.dna.
affrc.go.jp/viewer/gbrowse/build4/) (supplement and
Figure 2). There are 11 orthologous genes in GFa
between in the rice and sorghum genome. There are 6
orthologous genes respectively in GFb on maize
chromosome 6 and 8 between in the maize and
sorghum genome. The ZmSSⅣb was located between
a hypothetical protein and a DUF212 family protein
(supplement and Figure 2). Moreover, we can not
found the SSⅣa gene on chromosomr 3 regions in
maize, and the chlorophyll a-b binding protein and the
Serine acetyltransferase 3 also lost. These results
strongly suggested that the SSⅣa gene was lost in
sorghum and maize genomes during their evolution.
1.4 Organ expression profile of the SS genes in
sorghum and wheat
Expression divergence was often the first step in the
functional divergence between duplicate genes, thus
increasing the chance of retention of duplicated genes
in a genome (Force et al., 1999). To define the
function of the deteced SS genes, we investigated their
expression in root, leaf and developing endosperm
using RT-PCR in sorghum and wheat. The results
indicated that the SbGBSSⅠ, SbSSⅡa and SbSSⅢa
genes were expressed mainly in endosperms, while the
SbGBSSⅡ, SbSSⅡb, and SbSSⅢb genes mainly in
leaf in sorghum. The SbSSⅠ, SbSSⅡc and SbSSⅣ
genes were constitutively expressed in sorghum. In
addition, the SbGBSSⅡ and SbSSⅢb genes were also
highly expressed in roots (Figure 3A). TaSSⅡb and
TaSS Ⅲ b were mainly expressed in leaves, and
moderately in roots and the early stage endosperms
(Figure 3B).
Figure 3 The organ expression analysis of SS genes in sorghum
and wheat
Note: A: RT-PCR analysis of the expression of SS genes in
sorghum; B: RT-PCR analysis of the expression of SSⅡb and
SSⅢb genes in wheat; Thermocycling time and temperature are
as follows: 95℃ for 5 min, followed by indicated cycles of
95℃ for 30 s, respective annealing temperature (Table 2; Table
3) for 30 s, 72℃ for 40 s, and a final extension period 72℃ for
7 min; Lower panel shows the loading control of an Actin
(X79378 of sorghum and AY663392 of wheat) transcripts in
each sample. DAF, days after flowering
The mRNA for the TaSSⅡa was expressed in leaves
and endosperms under the conditions used (Li et al.,
1999a), but the SGP-B1 (TaSSⅡa) protein was not
detected in leaf using monoclonal antibodies
(Shimbata et al., 2005). This result is similar to the
findings of OsSSⅡa in rice that the transcripts could
be tested at a lower level in leaf, but its proteins could
not be detected in leaf soluble or starch granule
extracts using polyclonal antibodies (Jiang et al.,
2004). The expression of TaSSⅡb and TaSSⅢb was
mainly in leaves and roots, but lower in filling stage
endosperms, suggests that TaSSⅡ b and TaSS Ⅲ b
mainly function in leaves and roots, while TaSSⅡa
and TaSSⅢa in endosperms as those in maize and rice
(Jiang et al., 2004; Yan et al., 2009). These results
indicated SS duplicators were also diverged in
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2011, Vol.1, No.1 http://ijmeb.sophiapublisher.com
expression in wheat and sorghum as in rice and maize
(Dian et al., 2003; Jiang et al., 2004; Yan et al., 2009).
In addition, those SS duplication and expression
divergence were similar to the starch legumes (mung
bean and cowpea) genomes (Pan et al., 2009). In
summary, the present study and previous reports
indicate that duplicators of GBSSⅠ, SSⅡ, and SSⅢ,
but not SS Ⅳ , were remained in the genome and
diverged in expression in all observed Gramineae
species.
2 Materials and methods
2.1 Plant materials and growth conditions
The sorghum (Sorghum bicolor L.) and common
wheat (Triticum aestivum L.) variety Shi4185 were
planted in trail field in South China Botanical Garden,
Chinese Academy of Sciences, Guangzhou, and P. R.
China. The seeds were harvested four times after
flowering, while the roots were got from the fifth day
after germinate (DAG) seeding and full expanded
leaves were taken from seedling at one day after
flowering. Samples were frozen under liquid nitrogen
and stored at -72℃ until use. All samples were
collected in a time period between 9:00 am to 10:00 am.
2.2 cDNA cloning of GBSS, SSⅡ, and SSⅢ genes
in sorghum and wheat
Total RNA was isolated from sampled leaves with
Plant RNAout kit (Tiandz Company, http://www.tiandz.com). First-strand cDNA synthesis using M-MLV
reverse transcriptase (Promega, http://www.promega.
com) following manufacture's protocol. A specific
fragment of sorghum and wheat GBSS, SSⅡ, and SSⅢ
genes were amplified with the primer pair (Table 2),
designed based on the conserved regions of the
corresponding genes from other higher plants. The
purified fragments were cloned into a pMD18-T
vector (TaKaRa, http://www.takara.com.cn) and
confirmed by sequencing in the Invitrogen Company
(http://www.invitrogen.com.cn). The 5'- and 3'-ends
of sorghum GBSS, SS Ⅱ , and SS Ⅲ genes were
obtained with a 5' full RACE cDNA Amplification kit
(Clontech) according to the user's instructions. Based
on these sequences, 5’-end of the TaSSⅡb and TaSSⅢb
cDNAs was determined by using the BD SMART™
RACE cDNA Amplification Kit (Invitrogen, Carlsbad,
CA, USA). Putative transit peptide were identified
using the ChloroP neural network analysis of the 100
amino acids at the N terminus of each sequence
(http:// www.cbs.dtu.dk/ services/ChloroP).
2.3 Semi-quantitative RT-PCR analysis
Total RNA was extracted from roots, leaves and
developing endosperms using the Plant RNAout kit.
PCR amplifications were performed on the first cDNA
strand using their specific primer sets (Table 2; Table 3).
Primers (Table 2; Table 3) that amplify sorghum Actin
(X79378) and wheat Actin (AY663392) were used as
a control. PCR products were analyzed by 1% agarose
gels, with ethidium bromide staining and take photo
through Fluorescence Chemiluminescence & Visible
Imaging System. Afterwards the purified fragments
were cloned into the pMD18-T vector and the
sequence were determined.
2.4 Data analysis
Phylogenetic analysis was carried out using the
conserved domains sequences of SS genes.
Alignments of the SS sequences were aligned using
the ClustalW program on EBI Web server. Phylogenetic trees were calculated using PhyML Online
analysis (Guindon et al., 2005) (http://mobyle.
pasteur.fr/cgi-bin/MobylePortal/portal.py?form=phyml)
based on the JTT model with a constant rate of site
variation (Guindon and Gascuel, 2003). Bootstrap
values were calculated from 100 replicate analyses.
2.5 Gene loci comparison
To confirm their physical location, the gene loci on
rice and sorghum were obtained by the alignment of
the cDNA sequences from the NCBI database (http://
www.ncbi.nlm.nih.gov/blast) to the corresponding
chromosome-based pseudomolecules using PHYTOZOME blast (http://www.phytozome.net/search.php?
show=blast). The location of the maize genes on the
chromosome pseudomolecules was traced though the
anchored corresponding BAC genome sequences or
related markers (http://www. maizegdb.org). Finally,
the loci of anchored rice, maize and sorghum starch
synthesis genes were compared on the rice/maize/
sorghum synteny physical maps available at Gramene
(http://www.gramene.org/).
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2011, Vol.1, No.1 http://ijmeb.sophiapublisher.com
Table 2 Primers used for sorghum in this study
Primer name
cDNA cloning
sGBSSIIF
sGBSSIIR
sSSIIaF
sSSIIaR
sSSIIbF
sSSIIbR
sSSIIcF
sSSIIcR
sSSIIIaF1
sSSIIIaR1
sSSIIIaF2
sSSIIIaR2
sSSIIIbF1
sSSIIIbR1
sSSIIIbF2
sSSIIIbR2
Semi-RT-PCR
SbGBSSIF
SbGBSSIR
SbGBSSIIF
SbGBSSIIR
SbSSIF
SbSSIR
SbSSIIaF
SbSSIIaR
SbSSIIbF
SbSSIIbR
SbSSIIcF
SbSSIIcR
SbSSIIIaF
SbSSIIIaR
SbSSIIIbF
SbSSIIIbR
SbSSIVF
SbSSIVR
ActF
ActR
Sequence (5′→3′)
Annealing temperature (℃)
AGCACTAGCAGCCGCGAGGTCATC
AACTGGTGGTTTTGCCGGTGTCTG
ATGTCGTCGGCGGCCGTGTCGTCC
CCTCTGTCAACGCACCAACCCCCAGC
AAGCAGCAGCAGCAGTAGCGT
AGGCATCACCGTAGCTCACATACA
CTCCAATGGCGGCTTCTACTTTC
CCTCCTGTACCAAAAGCGTCTAA
TCTATAAATGGAGATGGCCCTACG
AGCAAGCTCTTGAAGCATCCTCTG
GGAGTCACCTAATGATAACGTGGA
CTAACTGAAGACAAGGAGAGGCTG
GGGCTGAGGGGGGAGGTTTTGC
CTTCCCATAGACACATCCAACCCA
TGGGTTGGATGTGTCTATGGGAAG
AGAACTGGTCCGAACTCCGAAGTC
60
TGACCACCCGCTGTTCCTTGAG
ACGGCGATGTACTTGTCCTTGC
CAACAACGGCACCTGAAGCAAG
CTCAACATCTCGCCAGCCACC
GATGGGTTGGATTTAGTGTTC
CACGTGAAGTCTTTTGACATG
ACCCAAGGCTTTAGCGAGAAG
CAGGAGTGCAGTGTGCCAATC
AGAAGCCCGAGATTTAGGTGTG
CACGACCCTGATGAGCAATG
GACACCACTTACGGAGAATC
GATGTCAGTTCGGTTCCCAC
TTATTTGAGGATTTCTTGGCTG
ATGTTATTCGGAAGGGTAGC
CTACATTCCCAAGCAGGCATAC
TTTCAGCACCCTCCCTTTCTC
CAAGATATGGACTGGGACTGT
GCCACAATATGCTAAATCCTG
GGAACCGGTATGGTCAAGGC
AGTCTCGTGAATGCCAGCAG
56
65
63
60
60
60
60
60
58
52
56
56
58
58
56
52
60
Table 3 Primers used for wheat in this study
Primer name
Sequence (5′→3′)
cDNA cloning
tSSIIbR1
tSSIIbR2
tSSIIbF1
tSSIIbF2
tSSIIIbR1
tSSIIIbR2
tSSIIIbF1
tSSIIIbF2
TAGTTCCAGTACGTGTTGAGGCAG
AAGGCTCGAACAGCGACGGCATGA
GGCCGTTCAAAGAGCATATC
CATCCCATTCTGCGGTTCCA
TTCATCCCCGTCACCTTCTATATGC
AGAACACAAAGTCTAATCTGTATGC
TTGGGTTGGATGTGTCTATG
TCTCCCTGCCAGCTTAAAGTCT
Annealing temperature (℃)
56
55
52
50
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Continuing table 2
Primer name
Semi-RT-PCT
TaSSIIbF
TaSSIIbR
TaSSIIIbF
TaSSIIIbR
ActF
ActR
Sequence (5′→3′)
Annealing temperature (℃)
GGCGGGCTTGGAGATGTCGT
GAAGGGCGGGGCCTCTAAGAATAC
TGCAGGGACCACAGTTGATG
TCCCACCTTCTTCCGACTCA
GCCGTGCTTTCCCTCTATGC
CCTCTCTGCGCCAATCGTGA
Acknowledgements
This research was supported by funds received from the National Natural
Science Foundation of China (No. 31070227) and the CAS/SAFEA
International Partnership Program for Creative Research Teams.
References
Ball S.G., and Morel M.K., 2003, From bacterial glycogen to starch: understanding the biogenesis of the plant starch granule, Ann Rev Plant Biol., 54:
207-233 doi:10.1146/annurev.arplant.54.031902.134927 PMid: 14502990
Ball S.G., van de Wal M.H.B.J., and Visser R.G.F., 1998, Progress in
understanding the biosynthesis of amylose, Trends Plant Sci., 3(12):
462-467 doi:10.1016/S1360-1385(98)01342-9
Brunner S., Fengler K., Morgante M., Tingey S., and Rafalsk A., 2005,
Evolution of DNA sequence nonhomologies among maize inbreds, The
Plant Cell, 17: 343-360 doi:10.1105/tpc.104.025627 PMid:15659640
PMCid:548811
Clark J.R., Robertson M., and Ainsworth C.C., 1991, Nucleotide sequence of a
wheat (Triticum aestivum L.) cDNA clone encoding the waxy protein, Plant
Mol. Biol., 16(6): 1099-1101 doi:10.1007/BF00016086 PMid:186 3765
Dian W.M., Jiang H.W., Chen Q.S., Liu F.Y., and Wu P., 2003, Cloning and
characteriza- tion of the granule-bound starch synthase II gene in rice: Gene
expression is regulated by the nitrogen level, sugar and circadian rhythm,
Planta, 218(2): 261-268 doi:10.1007/s00425-003-1101-9 PMid: 12955512
Dian W.M., Jiang H.W., and Wu P., 2005, Evolution and expression analysis of
starch synthase III and IV in rice, J. Exp. Bot., 56(412): 623-632 doi:10.
1093/jxb/eri065 PMid:15642712
Force A., Lynch M., Pickett F.B., Amores A., Yan Y.L., and Postlethwait J.,
1999, Preservation of duplicate genes by complementary, degenerative
mutations, Genetics, 151: 1531-1545 PMid:10101175 PMCid:1460548
Gaut B.S., and Doebley J.F., 1997, DNA sequence evidence for the segmental
allotetraploid origin of maize, Proc Natl Acad Sci USA, 94(13): 6809-6814
doi:10.1073/pnas.94.13.6809
Guindon S., and Gascuel O., 2003, A simple, fast and accurate algorithm to
estimate large phylogenies by maximum likelihood, Syst Biol., 52(5):
696-704 doi:10.1080/10635150390235520 PMid:14530136
Guindon S., Lethiec F., Duroux P., and Gascuel O., 2005, PHYML Online a
web server for fast maximum likelihood-based phylogenetic inference,
Nucleic Acids Res., 33: 557-559 doi:10.1093/nar/gki352 PMid:15980534
PMCid:1160113
Harn C., Knight M., Ramakrishnan A., Guan H., Keeling P.L., and Wasserman
B.P., 1998, Isolation and characterization of the zSSIIa and zSSIIb starch
synthase cDNA clones from maize endosperm, Plant Mol Biol., 37(4):
639-649 doi:10.1023/A:1006079009072 PMid:9687068
Hirose T., and Terao T., 2004, A comprehensive expression analysis of the
starch synthase gene family in rice (Oryza sativa L.), Planta, 220(1): 9-16
doi:10.1007/s00425-004-1314-6 PMid:15232694
Jiang H.W., Dian W.M., Liu F.V., and Wu P., 2004, Molecular cloning and
expression analysis of three genes encoding starch synthase II in rice,
Planta, 218(6): 1062-1070 doi:10.1007/s00425-003-1189-y PMid:14740212
Leterrier M., Holappa L.D., Broglie K.E., and Beckles D.M., 2008, Cloning,
characterisa- tion and comparative analysis of a starch synthase IV gene in
56
56
60
wheat: functional and evolutionary implications, BMC Plant Biol., 8: 98
doi:10.1186/1471-2229-8-98 PMid:18826586 PMCid:2576272
Li Z.Y., Chu X.S., Mouille G., Yan L.L., Kosar-Hashemi B., Hey S., Napier J.,
Shewry P., Clarke B., Appels R., Morell M.K., and Rahman S., 1999a, The
localization and expression of the class II starch synthases of wheat, Plant
Physiol., 120: 1147-1156 doi:10.1104/pp.120.4.1147 PMid:10444098
Li Z.Y., Mouille G., Kosar-Hashemi B., Rahman S., Clarke B., Gale K.R.,
Appels R., and Morell M.K., 2000, The structure and expression of the
wheat starch synthase III gene: motifs in the expressed gene define the
lineage of the starch synthase III gene family, Plant Physiol., 123(2):
613-624 doi:10.1104/pp.123.2.613 PMid:10859191 PMCid:59029
Li Z.Y., Rahman S., Kosar-Hashemi B., Mouille G., Appels R., and Morell
M.K., 1999b, Cloning and characterization of a gene encoding wheat
starch synthase I, Theor Appl Genet., 98(8): 1208-1216 doi:10.1007/s00
1220051186
Pan X.X., Tang Y.Y., Li M.R., Wu G.J., and Jiang H.W., 2009, Isoforms of
GBSSI and SSII in four legumes and their phylogenetic relationship to
their orthologs from other angiosperms, J Mol Evol., 69(6): 625-634
doi:10.1007/s00239-009-9300-z PMid:19888543
Paterson A.H., Bowers J.E., and Chapman B.A., 2004, Ancient polyploidization
predating divergence of the cereals, and its consequences for comparative
genomics, Proc Natl Acad Sci USA, 101(26): 9903-9908 doi:10.1073/pnas.
0307901101 PMid:15161969 PMCid:470771
Roldán I., Wattebled F., Mercedes L.M., Delvallé D., Planchot V., Jiménez S.,
Pérez R., Ball S., D'Hulst C., and Mérida A., 2007, The phenotype of
soluble starch synthase IV defective mutants of Arabidopsis thaliana
suggests a novel function of elongation enzymes in the control of starch
granule formation, Plant J., 49(3): 492-504 doi:10.1111/j.1365-313X.2006.
02968.x PMid:17217470
Shimbata T., Nakamura T., Vrinten P., Saito M., Yonemaru J., Seto Y., and
Yasuda H., 2005, Mutations in wheat starch synthase II genes and
PCR-based selection of a SGP-1 null line, Theor Appl Genet., 111(6):
1072-1079 doi:10.1007/s00122-005-0032-1 PMid:16172895
Smith A.M., Denyer K., and Martin C., 1997, The synthesis of the starch
granule, Annu Rev Plant Physiol Plant Mol Biol., 48: 67-87 doi:10.1146/
annurev.arplant.48.1.67 PMid:15012257
Song R., and Messing J., 2003, Gene expression of a gene family in maize
based on noncollinear haplotypes, Proc Natl Acad Sci USA, 100(15):
9055-9060 doi:10.1073/pnas.1032999100 PMid:12853580 PMCid:166437
Vrinten P.L., and Nakamura T., 2000, Wheat granule-bound starch synthase I
and II are encoded by separate genes that are expressed in different tissues,
Plant Physiol., 122(1): 255-264 doi:10.1104/pp.122.1.255 PMid:10631269
Wendel J.F., 2000, Genome evolution in polyploids, Plant Mol Biol., 42(1):
225-249 doi:10.1023/A:1006392424384 PMid:10688139
Yan H.B., Jiang H.W., Pan X.X., Li M.R., Chen Y.P., and Wu G.J., 2009, The
gene encoding starch synthase IIc exists in maize and wheat, Plant Science,
176(1): 51-57 doi:10.1016/j.plantsci.2008.09.003
Yan H.B., Pan X.X., Jiang H.W., and Wu G.J., 2009, Comparison of the starch
synthesis genes between maize and rice: Copies, chromosome location and
expression divergence, Theor. Appl. Genet., 119(5): 815-825 doi:10.1007/
s00122-009-1091-5 PMid:19593540
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