SFGD: a comprehensive platform for mining functional information from soybean transcriptome data and its use in identifying acyl-lipid metabolism pathways
- Juan Yu†1,
- Zhenhai Zhang†1,
- Jiangang Wei1,
- Yi Ling1,
- Wenying Xu1Email author and
- Zhen Su1Email author
© Yu et al.; licensee BioMed Central Ltd. 2014
Received: 3 November 2013
Accepted: 31 March 2014
Published: 8 April 2014
Soybean (Glycine max L.) is one of the world’s most important leguminous crops producing high-quality protein and oil. Increasing the relative oil concentration in soybean seeds is many researchers’ goal, but a complete analysis platform of functional annotation for the genes involved in the soybean acyl-lipid pathway is still lacking. Following the success of soybean whole-genome sequencing, functional annotation has become a major challenge for the scientific community. Whole-genome transcriptome analysis is a powerful way to predict genes with biological functions. It is essential to build a comprehensive analysis platform for integrating soybean whole-genome sequencing data, the available transcriptome data and protein information. This platform could also be used to identify acyl-lipid metabolism pathways.
In this study, we describe our construction of the Soybean Functional Genomics Database (SFGD) using Generic Genome Browser (Gbrowse) as the core platform. We integrated microarray expression profiling with 255 samples from 14 groups’ experiments and mRNA-seq data with 30 samples from four groups’ experiments, including spatial and temporal transcriptome data for different soybean development stages and environmental stresses. The SFGD includes a gene co-expression regulatory network containing 23,267 genes and 1873 miRNA-target pairs, and a group of acyl-lipid pathways containing 221 enzymes and more than 1550 genes. The SFGD also provides some key analysis tools, i.e. BLAST search, expression pattern search and cis-element significance analysis, as well as gene ontology information search and single nucleotide polymorphism display.
The SFGD is a comprehensive database integrating genome and transcriptome data, and also for soybean acyl-lipid metabolism pathways. It provides useful toolboxes for biologists to improve the accuracy and robustness of soybean functional genomics analysis, further improving understanding of gene regulatory networks for effective crop improvement. The SFGD is publically accessible at http://bioinformatics.cau.edu.cn/SFGD/, with all data available for downloading.
Soybean (Glycine max L.) is a major leguminous seed crop providing an important source of oil, and ranks first in oil production among the major oil seed crops . In addition to its usage for human consumption, given its high content of essential fatty acids such as linoleic acid, soybean oil is an important renewable resource for chemical and biofuel production . Increasing the relative oil concentration in soybean seeds is many researchers’ goal, using breeding methods and biotechnological strategies [3–5]. The key governing genes of seed oil biosynthesis in higher plants are those involved in the synthesis pathway of triacylglycerol (TAG), plastid fatty acids, endomembrane lipids and the storage process, which constitute more than 274 genes in soybean . Several functional essays have shown that DGAT1 and DGAT2 have roles in seed oil accumulation [7–9]. Mutant alleles of FAD2-1A and FAD2-1B were combined to create soybeans with the high oleic acid trait . Some important transcription factors (TF) regulating lipid metabolism and seed maturation have been reported, including basic leucine zipper (bZIP) and DNA binding with one finger (DOF) TF families [11, 12]. However, most of these genes’ functions are not clear and the biosynthesis of soybean oil has yet to be elucidated.
With the availability of the soybean whole-genome sequence and large-scale application of high-throughput sequencing technology, research on soybean has made great progress. Numerous high-throughput data including genomics, transcriptomics, proteomics and metabolomics data are available for soybean. These data can provide valuable insights and improve soybeans if integrated and analyzed in a novel and comprehensive way. One of these ways is information mining from transcriptome data, given the overwhelming amount of such transcriptome data. The large amount of microarray expression data and deep sequencing transcriptomic data have allowed increasingly credible methods to be developed for generic networks, such as graphical Gaussian model networks through partial correlation , reverse engineering cellular networks using the ARACNE algorithm , networks based on improved PCC methods  and Bayesian networks . In order to overcome the disadvantage of some functionally related genes with low PCC, a new variable ‘mutual rank’ or MR has been introduced [17, 18], and co-expression networks for Arabidopsis and rice have been generated [19–21].
Summary of published soybean databases
Genomic data, expressed sequence tags and microarray expression experiments, Proteomics of Oilseeds
Soybean physical map and genetic map using Gbrowse as platform
Soybean Full-length cDNA Database 
40,000 full-length sequences of cDNA clones
Soybean transcription factors
Soybean transposable elements
Comprehensive database for curated genetics, genomics, and related data resources developed by USDA-ARS
Comparative genomics and transcriptomics database of model legumes
Whole-genome co-expression networks for seven important plant crop species
Integration of soybean omics data along with annotation of gene function and biological pathway
Microarray expression data and expressed sequence tags 
Soybean genome sequence and gene annotation information
Soybean eFP Browser 
Creates ‘electronic fluorescent pictographic’ representations of genes’ expression pattern
Soybean seed proteins
Soybean genome and gene models
Soybean gene expression resource
http://www.plexdb.org/plex.php?database = Soybean
Driven by this need, we developed a comprehensive database, the Soybean Functional Genomics Database (SFGD), which provides an integration and analysis platform for soybean ‘omics’ data and is a one-stop-shop resource for soybean acyl-lipid metabolism researchers. We hope it will improve the accuracy and robustness of soybean functional genomics analysis, and further speed up research on soybean yield and quality. This database contains 221 enzymes and more than 1550 genes involved in 15 soybean acyl-lipid metabolic pathways by combining data from the PMN  and prediction using Arabidopsis lipid-related genes. It also integrates genome and transcriptome data, e.g. coding genes, full-length cDNA and miRNA sequences, microarray expression experiments, deep sequencing experiments and single nucleotide polymorphisms (SNPs). In addition, a co-expression regulatory network including 23,267 soybean genes represented by 37,593 probe sets (the numbers do not match as one gene can be represented by one or more probe sets) with available microarray expression experiments (255 samples from 14 experiments) and 1873 miRNA–gene pairs in the network is included. There are some other function modules, e.g. a cis-element significance analysis toolbox for gene promoter sequences, an expression pattern search for microarray expression data so users can compare gene expression differences in various growth periods or under diverse stresses. There are also some general functions, such as browse, search and download of data. The platform is freely available at http://bioinformatics.cau.edu.cn/SFGD/.
Construction and content
Data source of SFGD
Coding gene and annotation
66,207 genes, the items of cDNA, CDS and protein are all 75,778, respectively
37,870 (4708 full, 32,063 forward and 27,927 reverse sequences)
Consensus sequence annotation
18,872 (including GO term, EC number and description)
14 experiments, 245 samples
Deep sequencing data
Four experiments, 30 samples
229 (precursor and mature sequences)
17 wild and 14 cultivated soybean species
Microarray expression experiment normalization
Where x is intensity value and n is the number of replications.
High-throughput sequencing data pre-processing
Where N is the number of raw reads mapped on the DNA fragment.
Where C is the number of mappable reads falling into the gene, N is the total number of mappable reads in the experiment and L is the gene length in base-pairs.
ZFE (Z-score for expression) and ZFM (Z-score for motif)
Z-score is a statistical measurement of the distance in standard deviations of a sample from the mean. Z-scores allow analysts to convert scores from different data sets into scores that can be accurately compared to each other , since they can act as a normalization method to eliminate the difference caused by background for a series of different experiments. For this reason, Z-score transformation statistics have been used in aspects of biology research, such as comparing gene expression between experimental and control groups in microarray analysis [63–66].
ZFE: we found that ZFE reflected the relationship of transcriptome change more accurately and visually than expression values (Additional file 2: Figure S2). Here we show the method used to generate the ZFE values from the average intensity values.
Where is the average value of all in an experiment, is of the treatment samples and is of the control samples.
Where pnorm() is the distribution function for the normal distribution in the R package, and the P-value cutoff is 0.1, which is decided with reference to the soybean genetic motif related experimental result, as well as the annotation of motifs in PLACE .
For two genes (or probe sets) X and Y, first all microarray expression values are used to respectively calculate all genes’ PCC values for X and Y. Then PCCs are respectively sorted from large to small for X and Y; then ‘a’ (start from 1, with step size of 1) is used to mark the position of Y in X’s list, and similarly, ‘b’ marks the position of X in Y’s list. For the hub gene, the network shows the top 10 co-expressed genes according to the arrangement of MR from small to large in the first level; for the second level, the top five genes that co-expressed with first level genes are selected; and the selection of genes in the third level follows the same rules as for the second level. The threshold of MR is in reference to the already published Arabidopsis co-expression network .
miRNA:target alignment criteria
In plants, miRNAs generally precisely direct their mRNA targets for endonucleolytic cleavage [69–71]. To predict potential targets of the miRNAs in this study, we developed a set of computational ‘criteria’ for soybean miRNA-target interaction based on previous research [69, 72]. The ‘criteria’ as following: (a) The mismatch of miRNA:target must be ≤ 4 and the mismatch in the first half-pair must be ≤ 2.5 (G:U = 0.5); (b) The continuous mismatch must be ≤ 2 and continuous mismatch between 2 and 12 bp must be ≤ 1; (c) The bases 11 and 12 must be a perfect match; and (d) The minimum free energy (MFE) of miRNA:target must be < 75% compared with when the miRNA perfectly matched with its target. With these criteria, we successfully predicted 1873 miRNA-gene pairs.
Utility and results
SFGD uses Generic Genome Browser (Gbrowse) as an integration platform for soybean transcriptome data (Table 2) and generates some data mining tools, such as ‘gene co-expression network’, ‘pathway’ and ‘motif’. The tool ‘gene co-expression network’ aims to display a gene’s co-expressed genes and miRNA:target interaction; ‘pathway’ is a functional tool containing soybean acyl-lipid metabolic data; ‘motif’ is a tool for searching and analyzing significant cis-elements in one or more genes; and ‘pattern’ is a tool for searching tissue/time specific genes based on microarray expression experiments (Additional file 3: Table S1), and some other function modules such as BLAST and general search.
Gbrowse: a repository of the transcriptional information
Gbrowse is a genome viewer. Soybean protein coding genes, full-length cDNAs, miRNA precursors, probe set consensus sequences, microarray expression experiments and deep sequencing data have been integrated into Gbrowse with clickable links to a new webpage. This webpage shows descriptions of each keyword: e.g. ‘gene detail information web page’ shows the co-expression gene network, microarray expression profile, deep sequence evidence and coding sequence; for ‘microarray expression data’, a diagram displays the other probe sets related to it with PCC > 0.7 or PCC < -0.65.
The coding gene’s result page includes gene annotation, the list of co-expressing genes, 14 microarray expression experiments [only if there is a probe set(s) in its context] and deep sequence evidence of it in the 30 deep sequencing samples. Following are the gene’s genome location information and sequences (including promoter, cDNA and protein sequences).
For the microarray expression profile section (e.g. ‘GmaAffx.88235.1.S1_at’), we have integrated 14 experiments in total. Each has horizontal bars according to the experiment’s treatment and control expression level generated using ZFE (red bars represent up-regulated and green bars down-regulated, Additional file 4: Figure S1). For example, if users click horizontal bars below ‘GSE7511’ (‘Expression data from soybean seed compartments with embryos at the heart stage’), it will show gene Glyma15g34770’s (represented by probe set ‘GmaAffx.88235.1.S1_at’) expression profile in different tissues of soybean seed. With ‘GmaAffx.88235.1.S1_at’ is included a diagram generated using expression values and standard errors, values table display and the probe sets most positively and most negatively correlated (PCC > 0.7 and PCC < -0.65, respectively). Users can get all these probe sets’ expression values and line charts produced by expression values and ZFEs (Additional file 2: Figure S2) and send the probe set list to agriGO  for gene ontology (GO) enrichment analysis. Users can also get the promoter sequence of genes that are positively correlated with this gene and scan the cis-elements contained for significance analysis.
miRNAs are ~21-nt-long endogenetic non-coding small RNAs that function as post-transcriptional regulators in eukaryotes . All miRNAs in SFGD came from recently published literature [38–45]. Here, soybean miRNA information is integrated into PMRD (Plant MicroRNA Database) format , which mainly includes four regions: precursor, mature, target and reference regions.
The repository also has 30 RNA-seq samples that cover various tissue types and stress conditions. This can be used for deep sequencing evidence of one gene’s expression in particular tissues or at particular time points.
For other content in Gbrowse–such as full-length cDNA, probe set consensus sequence and SNP information–users can obtain their description and related information by clicking the corresponding icons.
Gene co-expression network
We generated a soybean gene co-expression regulatory network based on 255 samples from 14 microarray expression experiments using PCC and MR . After converting the probe sets to the corresponding genes, we obtained a gene co-expression network including 23,267 genes represented by 37,593 probe sets (one gene may be represented by one or more probe sets).
There are 240,496 edges left after setting the MR threshold ≤ 30, giving 20.7 edges for each gene on average–Additional file 5: Table S2 lists the top 10 genes with the greatest number of edges as well as the genes’ annotations. Cytoscape Web software  is used to display the gene network, and for each gene (central node), all its co-expression genes are sorted according to MR values and several with the top values are displayed. There is a recursive search using this process for the second and third levels. For the first level [genes (subprime nodes) immediately linked with the central gene], the top 10 MR-value genes are displayed. For the second level (genes directly linked with first level genes, linked with central node through subprime nodes) the top 5 MR-value genes for each subprime node are shown. In the third level, although we collected all top 10 MR-value genes of second level genes, only those which have previously displayed in the first and second levels remain, because other genes are not likely to be closely related to the central gene. A table is also generated to show all genes and gene annotations appearing in the Cytoscape Web file–users can use these genes to scan their promoter motifs and analyze their significance using the textbox at the bottom of the web page.
The soybean miRNA: target information was also integrated into the network. Soybean miRNA:target pairs were predicted using in-house programs with all miRNAs and mRNA genes deposited in our database, then we compared our results with psRNATarget . Finally we separated the results into two parts: high credibility miRNA:targets (338 pairs, predicted by both programs) and low credibility miRNA:targets (1535 pairs, predicted by one of the programs).
Acyl-lipid metabolic pathways
Soybean acyl-lipid metabolism pathway
Lipid metabolism pathway
Fatty acid synthesis
Fatty acid elongation, desaturation and export from plastid
Triacylglycerol and fatty acid degradation
Eukaryotic galactolipid and sulfolipid synthesis
Prokaryotic galactolipid, sulfolipid, phospholipid synthesis
Eukaryotic phospholipid metabolism
Mitochondrial phospholipid metabolism
Sphingolipid synthesis and transport
Mitochondrial lipoic acid synthesis
Wax synthesis and transport
Cutin synthesis and transport
Suberin synthesis and transport
If the user’s input is a fasta format sequence of a promoter, all motifs appearing in the sequence are listed, and these motifs’ occurrence frequencies counted using the in-house program.
Cis-element significance analysis
For each gene’s promoter sequence or a sequence submitted by the user, all the potential motifs are scanned. If a list of gene names is submitted, all motifs appearing in their promoter region will be scanned. The platform also offers the result of significant motifs in promoters of these genes.
In order to find genes’ specific expressions under specific conditions, we selected four experiments with different tissues and stress conditions. GSE7511, which contains 23 samples to identify all genes active in 10 different compartments, was isolated using the Leica AS LMD system from heart-stage seed. GSE7881, includes 18 samples, identified all genes active in cotyledon-stage seed within nine isolated compartments. GSE8112, contains 34 samples obtained from early maturation stage of seed, which was isolated within 17 compartments. GSE8432 contains 27 samples obtained from a soybean plant PI200492 with two treatments: HW94-1 (Phakopsora pachyrhizi isolates, which produces a resistant reaction in the host) or TW72-1 (P. pachyrhizi isolates, which produces a susceptible reaction in the host) at four time points (6, 12, 24 and 48 h post inoculation). Furthermore, we developed two function tools in the corresponding web page: ‘Expression pattern search’ and ‘Tissue/time specific search’.
For the ‘Expression pattern search’ function, selections submitted by users are converted to corresponding values – high (or up-regulated), even and low (or down-regulated) represented by 1, 0 and -1, respectively–then PCC is calculated between users’ selections and ZFE of data in our database, using a PCC threshold of 0.7.
The ‘Tissue/time specific search’ toolbox only returns probe sets that are highly expressed in the specific condition according to the ZFE set up by users. The resulting web pages for both ‘Expression pattern search’ and ‘Tissue/time specific search’ also include links to ‘agriGO’  for GO enrichment analysis and ‘motif scan’ function for cis-element significance analysis as described above.
Soybean lipid biosynthesis related genes (WRI1 network genes)
GmaAffx.50807.1.S1_at, GmaAffx.50807.2.S1_at, GmaAffx.26813.1.A1_at
LACS9 (LONG CHAIN ACYL-COA SYNTHETASE 9); long-chain-fatty-acid-CoA ligase
CAC1 (CHLOROPLASTIC ACETYLCOENZYME A CARBOXYLASE 1); acetyl-CoA carboxylase/biotin binding
LPD1 (LIPOAMIDE DEHYDROGENASE 1); dihydrolipoyl dehydrogenase
Phosphatidic acid phosphatase-related/PAP2-related
Disease resistance-responsive family protein
3-oxoacyl-(acyl-carrier protein) reductase, chloroplast/3-ketoacyl-acyl carrier protein reductase
CAC2; acetyl-CoA carboxylase/ biotin carboxylase
DREB2A; DNA binding/transcription activator/ transcription factor
nodulin family protein
aspartyl protease family protein
AREB3 (ABA-RESPONSIVE ELEMENT BINDING PROTEIN 3); DNA binding/transcription activator/transcription factor
ATCNGC4 (CYCLIC NUCLEOTIDE-GATED CATION CHANNEL 4); calmodulin binding/cation channel/cation transmembrane transporter/cyclic nucleotide binding
GA3 (GA REQUIRING 3); ent-kaurene oxidase/oxygen binding
GmaAffx.93571.1.S1_s_at, GmaAffx.93571.1.S1_at, GmaAffx.73653.1.S1_at
CYP76G1; electron carrier/heme binding/iron ion binding/monooxygenase/oxygen binding
Gma.17374.1.S1_at, GmaAffx.64124.1.S1_at, GmaAffx.87290.1.S1_at
starch synthase, putative
disease resistance-responsive family protein
CAC2; acetyl-CoA carboxylase/ biotin carboxylase
arginosuccinate synthase family
oxidoreductase, 2OG-Fe(II) oxygenase family protein
GT72B1; UDP-glucosyltransferase/UDP-glycosyltransferase/transferase, transferring glycosyl groups
Amino acid transporter family protein
bHLH071 (beta HLH protein 71); DNA binding/transcription factor
GmaAffx.59734.1.A1_at, GmaAffx.86023.1.S1_at, GmaAffx.33541.1.S1_at
GA3 (GA REQUIRING 3); ent-kaurene oxidase/oxygen binding
Nuclear transport factor 2 (NTF2) family protein/RNA recognition motif (RRM)-containing protein
ATCPISCA (chloroplast-localized IscA-like protein); structural molecule
Gma.10258.1.A1_s_at, Gma.10258.2.S1_at, GmaAffx.83788.1.S1_at
emb1879 (embryo defective 1879)
Gma.11469.1.S1_at, GmaAffx.67403.1.S1_at, GmaAffx.67403.1.A1_at
phosphatidic acid phosphatase-related/PAP2-related
KAS III (3-KETOACYL-ACYL CARRIER PROTEIN SYNTHASE III); 3-oxoacyl-[acyl-carrier-protein] synthase/catalytic/transferase, transferring acyl groups other than amino-acyl groups
Motif significance analysis results of soybean triacylglycerol biosynthesis related genes
napA; storage protein; ABRE; napin; seed
poly A signal
ABA; ABRE; EMBP-1; seed
ABA; ABRE; motif A; DRE
G box; rbcS; tomato; G-box; leaf; shoot
Chalcone synthase; CHS; light; Box II; LRE; leaf; shoot
phyA; phytochrome; light
ABA; ABF; bZIP factors
Box II; Box 2; CHS; chs; light regulation
EMBP-1; Em; ABA; ABF; ABRE; bZIP; seed
phyA; phytochrome; light
UPR; unfolded protein response
Aux28; G box; auxin; bZIP; SGBF-1; SGBF-2
CAB; cab; cab-E; CABE; light; leaf; shoot
root; shoot; Fe; iron
Freezing tolerance; seed; shoot; CBF2
Ga; seed; germination
Root; ACGT; G box; G-box; ABRE motif; bZIP binding enhancement
Leucine zipper motif; meristem; OBF1; bZIP; lip19; LIP1
Alpha-Amylase; cotyledon; seed germination; seed
G box; G-box; rbcs; chs; ACGT element; adh; Bz-2; R-motif; STR;GT-1; GBF; elicitor; bZIP; napin; strictosidine synthase; cell
SEF1 factor binding site;seeds
Light responsive element
BoxII; CPRF; bZIP; leaf; shoot; CHS; ACE; light; bZIP
MADS; AGAMOUS; AGL; embryo
ABA; responsive element; ABRE; rd22; RD22; dehydration; shoot
More function modules
Home page: this describes the whole database project and other soybean resources.
General search page: SFGD supports fuzzy queries by one or a list of gene names, flcDNA IDs, probe set IDs or function keywords. Users can convert gene names to corresponding probe set names by input of a list of gene names, and vice-versa.
BLAST search: a BLAST search toolbox is provided and users can do BLAST searches against soybean cDNA, flcDNA, probe set consensus and protein sequence.
Download: users can download all coding genes’ sequences and their annotations. Full-length cDNA sequences, consensus sequences and annotations appear in the database.
There is no doubt that a novel and comprehensive method of integration and analysis for soybean omics data will provide valuable insights and help to improve soybean. However, a powerful mining tool for omics data is limited. To fill the gap of a platform for acyl-lipid comprehensive analysis and information for high-throughput omics data, we developed SFGD–a comprehensive and integrated database for mining functional information from soybean transcriptome data and identifying acyl-lipid metabolism pathways. This database include a variety of information, for instance, microarray expression data with 255 samples from 14 experiments, 30 mRNA-seq samples belonging to four experiments, other genomic data including coding and non-coding genes (miRNA), as well as a set of SNPs from 17 wild and 14 cultivated soybean sub-species . By integration and analysis of these data, we provide a one-stop-shop resource for acyl-lipid researchers, we also integrated the genome and transcriptome information into Gbrowse, which can provide the tissue and time points for specific expression information. We then built some function toolboxes: e.g. gene co-expression network, cis-element significance analysis tool, expression pattern search module and some other functions.
As an example of TAG biosynthesis in the previous description (Figure 1A), Gbrowse provides gene expression information on various tissue types and stress conditions. From these data, we can infer the main place, time or possible function for a specific enzyme (Figure 1B).
The biosynthesis of TAG occurs at the endoplasmic reticulum and probably also involves reactions at the oil body . The classical pathway of TAG biosynthesis in seeds is the acyl-CoA dependent Kennedy pathway (or the glycerol phosphate pathway)–this pathway consists of sequential acylation and subsequent dephosphorylation of glycerol-3-phosphate (G3P). The first acylation of G3P is catalyzed by glycerol-3-phosphate acyltransferase (GPAT; EC 188.8.131.52). GPAT was first cloned from Saccharomyces cerevisiae; and a member of the Arabidopsis GPAT gene family displayed GPAT activity when expressed in yeast. However, mutations of GPAT gene in Arabidopsis do not appear to affect seed oil level, but play a role in production of cutin and suberin [80–82]. In our search through the transcriptome profiling data, we found few GPAT family genes were highly expressed in seed at the development stage. Of course, this does not suggest that there is no relationship between GPAT family and seed oil level. Genes encoding GPAT9 are most likely to be important in soybean oil synthesis and have significantly higher expression in seeds at different stages. Similar results were also reported in castor .
The second acylation is catalyzed by 1-acylglycerol-3-phosphate acyltransferase (LPAAT; EC 184.108.40.206). A number of LPAAT genes are highly expressed in the dry whole seed, suggesting involvement in the storage rather than the synthesis stage of oil metabolism.
Phospatidate phosphatase (PP; EC 220.127.116.11) catalyzes the dephosphorylation of phosphatidic acid to form sn-1,2-diacylglycerol . A variety of PP types and isoforms exist in plants but their exact role in TAG biosynthesis is unclear. In our analysis results, we found that some PP genes were highly expressed in dry seeds–e.g. PHA1 (Glyma19g35930), PHA2 (Glyma 17 g36130, Glyma06g04230) and LCBCP (Glyma19g39180)–these genes will be candidates for further study.
The final acylation reaction, converting diacylglycerol (DAG) to TAG is catalyzed by enzymes. In Arabidopsis, DGAT1 has been shown to play a role in seed oil accumulation [85–87], and has also been reported as a key enzyme determining oil content and composition in maize . In our database, most DGAT genes were highly expressed in seeds and especially dry whole seeds. Therefore, we predict that DGAT is a crucial enzyme for oil production of soybean–a suggestion also supported by previous study .
In acyl-CoA independent TAG synthesis pathway, lysophosphatidylcholine acyltransferase (LPCAT; EC 18.104.22.168) activity controls the regeneration of phosphocholine (PC) from lyso-PC. In our dataset, two members are highly expressed in floral buds and early-maturation seed, suggesting that the enzyme plays a role in early stages of oil synthesis but not during the storage phase.
DAG can also be acylated using PC as the acyl donor by a phospholipid:diacylglycerol acyltransferase (PDAT; EC 22.214.171.124). PDAT activity has been discovered in yeast and plants’ developing oil seeds . PDAT1 and DGAT1 have overlapping functions in TAG biosynthesis in developing seeds, and the absence of DGAT1 is evidently compensated by PDAT1. However, the degree that each enzyme contributes to TAG biosynthesis in developing seeds is unknown. In our dataset, some PDAT genes are highly expressed in early maturation-stage seed, and others are highly expressed in seedlings and leaves, suggesting that in other tissues, PDAT-acylated TAG synthesis plays an important role.
DAG can also be converted to phosphatidylcholine (PtdC) via the action of phosphatidylcholine:diacylglycerol cholinephosphotransferase (PDCT) or sn-1,2-diacylglycerol:cholinephosphotransferase (CPT). It has been reported in soybean seeds that about 60% of newly synthesized acyl chains directly incorporate into the sn-2 position of PC through an acyl-editing mechanism rather than a pathway for sequential acylation of G3P . PDCT has a clear seed-specific expression, but DAG-CPT does not have a clear tissue-expression–this does not immediately suggest a major role for DAG-CPT in tri-ricinolein synthesis as reported in castor .
In our gene co-expression regulation network, we use PCC and MR  values to mark the relationship between each gene (probe set). Many transcription factors are involved in a complex network to regulate TAG production [90, 91]. The mutants for WRINKLED1 produce wrinkled seeds with severe depletion of TAGs [77, 78], which can also be triggered by other transcription factors, such as LEC2, FUS3 and ABI3 [92, 93]–with our co-expression network tool, their co-expression interaction can also be found. In addition, some other transcription factors were detected in this co-expression network (Table 4), such as AREB3, NF-YB6 and MYB65, suggesting that they may participate in the regulated network for TAG synthesis. We also compared our results with the soybean gene network in PlaNet  (Additional file 6: Table S4). The Glyma15g34770 network in PlaNet lists 37 genes co-expressed with WRI1, and there are 33 genes in our network, and seven of them overlap with results from PlaNet, and form the ‘band 7 family’, ‘LACS9’, ‘DREB2A’, ‘AREB3’, ‘CYP76G1’ and so on. There are some differences between these two web sites, mainly due to the diversity of microarray expression experiments used in these two web services: e.g. PlaNet’s microarray expression experiments are all tissue-specific treatments (Additional file 7: Table S5, these treatments from the top three microarray expression experiments appear in Additional file 3: Table S1), and we included some other experiments, such as time series experiments, gene mutant experiments and plant responses to biotic and abiotic stresses.
Table 5 shows the significance analysis results of motifs for all genes that appeared in Table 4, and some keywords have a close relationship with seed development, such as motif ‘ABREBNNAPA’, which has been reported as conserved in many storage-protein gene promoters of seeds [94–97] and motif ‘ABRETAEM’ play a role in seed gene expression and response to ABA [98, 99]. This information gives some indication of interaction between motif and function.
The advantages of microarray expression experiments are the maturation of this technology, high-throughput and many types of analysis software. There are some disadvantages of microarray experiments in that they do not cover all soybean genes, microarrays cannot identify new genes and there may be errors when expression levels are close to background signals. Thus the next deep sequencing experiments may play important roles in constructing the gene network.
Currently we have integrated soybean genome data, full-length cDNA, microarray expression experiments, deep sequencing data, miRNA precursor and SNP information into our database (Table 2). We have also developed a soybean gene co-expression regulatory network web service, a graphical display of acyl-lipid metabolic pathways, a cis-element significance analysis toolbox, an expression pattern for positive/negative search function modules and other general tools in the database. We hope this will improve the accuracy and robustness of soybean functional genomics analysis, and further hasten understanding of the gene regulatory networks for effective crop improvement. SFGD is freely available at http://bioinformatics.cau.edu.cn/SFGD/, and it will be updated every 3-6 months with the development of soybean research; however, the update must be performed by the administrator.
Availability and requirements
This research was supported by grants from the Ministry of Science and Technology of China (31371291 and 2012CB215301) and the Ministry of Education of China (NCET-09-0735).
- Singh RJ, Hymowitz T: Soybean genetic resources and crop improvement. Genome. 1999, 42 (4): 605-616. 10.1139/g99-039.View ArticleGoogle Scholar
- Clemente TE, Cahoon EB: Soybean oil: genetic approaches for modification of functionality and total content. Plant Physiol. 2009, 151 (3): 1030-1040. 10.1104/pp.109.146282.PubMed CentralPubMedView ArticleGoogle Scholar
- Eskandari M, Cober ER, Rajcan I: Genetic control of soybean seed oil: II: QTL and genes that increase oil concentration without decreasing protein or with increased seed yield. Theor Appl Genet. 2013, 126 (6): 1677-1687. 10.1007/s00122-013-2083-z.PubMedView ArticleGoogle Scholar
- Li R, Hatanaka T, Yu K, Wu Y, Fukushige H, Hildebrand D: Soybean oil biosynthesis: role of diacylglycerol acyltransferases. Funct Integr Genomics. 2013, 13 (1): 99-113. 10.1007/s10142-012-0306-z.PubMedView ArticleGoogle Scholar
- Hwang EY, Song Q, Jia G, Specht JE, Hyten DL, Costa J, Cregan PB: A genome-wide association study of seed protein and oil content in soybean. BMC Genomics. 2014, 15 (1): 1-10.1186/1471-2164-15-1.PubMed CentralPubMedView ArticleGoogle Scholar
- Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L: Genome sequence of the palaeopolyploid soybean. Nature. 2010, 463 (7278): 178-183. 10.1038/nature08670.PubMedView ArticleGoogle Scholar
- Lardizabal K, Effertz R, Levering C, Mai J, Pedroso MC, Jury T, Aasen E, Gruys K, Bennett K: Expression of umbelopsis ramanniana DGAT2A in seed increases oil in soybean. Plant Physiol. 2008, 148 (1): 89-96. 10.1104/pp.108.123042.PubMed CentralPubMedView ArticleGoogle Scholar
- Li R, Yu K, Hildebrand DF: DGAT1, DGAT2 and PDAT expression in seeds and other tissues of epoxy and hydroxy fatty acid accumulating plants. Lipids. 2010, 45 (2): 145-157. 10.1007/s11745-010-3385-4.PubMedView ArticleGoogle Scholar
- Li R, Yu K, Hatanaka T, Hildebrand DF: Vernonia DGATs increase accumulation of epoxy fatty acids in oil. Plant Biotechnol J. 2010, 8 (2): 184-195. 10.1111/j.1467-7652.2009.00476.x.PubMedView ArticleGoogle Scholar
- Pham AT, Lee JD, Shannon JG, Bilyeu KD: Mutant alleles of FAD2-1A and FAD2-1B combine to produce soybeans with the high oleic acid seed oil trait. BMC Plant Biol. 2010, 10: 195-10.1186/1471-2229-10-195.PubMed CentralPubMedView ArticleGoogle Scholar
- Song QX, Li QT, Liu YF, Zhang FX, Ma B, Zhang WK, Man WQ, Du WG, Wang GD, Chen SY, Zhang JS: Soybean GmbZIP123 gene enhances lipid content in the seeds of transgenic Arabidopsis plants. J Exp Bot. 2013, 64: 4329-4341. 10.1093/jxb/ert238.PubMed CentralPubMedView ArticleGoogle Scholar
- Wang HW, Zhang B, Hao YJ, Huang J, Tian AG, Liao Y, Zhang JS, Chen SY: The soybean Dof-type transcription factor genes, GmDof4 and GmDof11, enhance lipid content in the seeds of transgenic Arabidopsis plants. Plant J. 2007, 52 (4): 716-729. 10.1111/j.1365-313X.2007.03268.x.PubMedView ArticleGoogle Scholar
- Ma S, Gong Q, Bohnert HJ: An Arabidopsis gene network based on the graphical Gaussian model. Genome Res. 2007, 17 (11): 1614-1625. 10.1101/gr.6911207.PubMed CentralPubMedView ArticleGoogle Scholar
- Margolin AA, Wang K, Lim WK, Kustagi M, Nemenman I, Califano A: Reverse engineering cellular networks. Nat Protocols. 2006, 1 (2): 662-671. 10.1038/nprot.2006.106.View ArticleGoogle Scholar
- Atias O, Chor B, Chamovitz DA: Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network. BMC Syst Biol. 2009, 3: 86-10.1186/1752-0509-3-86.PubMed CentralPubMedView ArticleGoogle Scholar
- Pe'er D: Bayesian network analysis of signaling networks: a primer. Sci STKE. 2005, 2005 (281): l4-Google Scholar
- Edgar R, Domrachev M, Lash AE: Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002, 30 (1): 207-210. 10.1093/nar/30.1.207.PubMed CentralPubMedView ArticleGoogle Scholar
- Obayashi T, Kinoshita K: Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression. DNA Res. 2009, 16 (5): 249-260. 10.1093/dnares/dsp016.PubMed CentralPubMedView ArticleGoogle Scholar
- Obayashi T, Kinoshita K, Nakai K, Shibaoka M, Hayashi S, Saeki M, Shibata D, Saito K, Ohta H: ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Res. 2007, 35 (Database issue): D863-D869.PubMed CentralPubMedView ArticleGoogle Scholar
- Obayashi T, Hayashi S, Saeki M, Ohta H, Kinoshita K: ATTED-II provides coexpressed gene networks for Arabidopsis. Nucleic Acids Res. 2009, 37 (Database issue): D987-D991.PubMed CentralPubMedView ArticleGoogle Scholar
- Obayashi T, Nishida K, Kasahara K, Kinoshita K: ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants. Plant Cell Physiol. 2011, 52 (2): 213-219. 10.1093/pcp/pcq203.PubMed CentralPubMedView ArticleGoogle Scholar
- Grant D, Nelson RT, Cannon SB, Shoemaker RC: SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Res. 2010, 38 (Database issue): D843-D846.PubMed CentralPubMedView ArticleGoogle Scholar
- Shultz JL, Kurunam D, Shopinski K, Iqbal MJ, Kazi S, Zobrist K, Bashir R, Yaegashi S, Lavu N, Afzal AJ, Yesudas CR, Kassem MA, Wu C, Zhang HB, Town CD, Meksem K, Lightfoot DA: The Soybean Genome Database (SoyGD): a browser for display of duplicated, polyploid, regions and sequence tagged sites on the integrated physical and genetic maps of Glycine max. Nucleic Acids Res. 2006, 34 (Database issue): D758-D765.PubMed CentralPubMedView ArticleGoogle Scholar
- Alkharouf NW, Matthews BF: SGMD: the Soybean Genomics and Microarray Database. Nucleic acids research. 2004, 32 (Database issue): D398-400.PubMed CentralPubMedView ArticleGoogle Scholar
- Cheng KC, Stromvik MV: SoyXpress: a database for exploring the soybean transcriptome. BMC Genomics. 2008, 9: 368-10.1186/1471-2164-9-368.PubMed CentralPubMedView ArticleGoogle Scholar
- Joshi T, Fitzpatrick MR, Chen S, Liu Y, Zhang H, Endacott RZ, Gaudiello EC, Stacey G, Nguyen HT, Xu D: Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding. Nucleic Acids Res. 2013, 42 (1): D1245-D1252.PubMed CentralPubMedGoogle Scholar
- Mutwil M, Klie S, Tohge T, Giorgi FM, Wilkins O, Campbell MM, Fernie AR, Usadel B, Nikoloski Z, Persson S: PlaNet: combined sequence and expression comparisons across plant networks derived from seven species. The Plant cell. 2011, 23 (3): 895-910. 10.1105/tpc.111.083667.PubMed CentralPubMedView ArticleGoogle Scholar
- Plant Metabolic Network (PMN). [http://www.plantcyc.org/]
- Umezawa T, Sakurai T, Totoki Y, Toyoda A, Seki M, Ishiwata A, Akiyama K, Kurotani A, Yoshida T, Mochida K, Kasuga M, Todaka D, Maruyama K, Nakashima K, Enju A, Mizukado S, Ahmed S, Yoshiwara K, Harada K, Tsubokura Y, Hayashi M, Sato S, Anai T, Ishimoto M, Funatsuki H, Teraishi M, Osaki M, Shinano T, Akashi R, Sakaki Y, et al: Sequencing and analysis of approximately 40,000 soybean cDNA clones from a full-length-enriched cDNA library. DNA Res. 2008, 15 (6): 333-346. 10.1093/dnares/dsn024.PubMed CentralPubMedView ArticleGoogle Scholar
- Wang Z, Libault M, Joshi T, Valliyodan B, Nguyen HT, Xu D, Stacey G, Cheng J: SoyDB: a knowledge database of soybean transcription factors. BMC Plant Biol. 2010, 10: 14-10.1186/1471-2229-10-14.PubMed CentralPubMedView ArticleGoogle Scholar
- Du J, Grant D, Tian Z, Nelson RT, Zhu L, Shoemaker RC, Ma J: SoyTEdb: a comprehensive database of transposable elements in the soybean genome. BMC Genomics. 2010, 11: 113-10.1186/1471-2164-11-113.PubMed CentralPubMedView ArticleGoogle Scholar
- Li J, Dai X, Liu T, Zhao PX: LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes. Nucleic Acids Res. 2011, 40 (Database issue): D1221-D1229.PubMed CentralPubMedGoogle Scholar
- Phytozome. [http://www.phytozome.net/soybean]
- Soybean eFP Browser. [http://soykb.org/cgi-bin_new/efpWeb.cgi]
- Tavakolan M, Alkharouf NW, Khan FH, Natarajan S: SoyProDB: a database for the identification of soybean seed proteins. Bioinformation. 2013, 9 (3): 165-167. 10.6026/97320630009165.PubMed CentralPubMedView ArticleGoogle Scholar
- GmGDB. [http://www.plantgdb.org/GmGDB/]
- SoyPLEX. [http://www.plexdb.org/plex.php?database=Soybean]
- Dezulian T, Palatnik J, Huson D, Weigel D: Conservation and divergence of microRNA families in plants. Genome Biol. 2005, 6: P13-10.1186/gb-2005-6-11-p13.View ArticleGoogle Scholar
- Zhang BH, Pan XP, Wang QL, Cobb GP, Anderson TA: Identification and characterization of new plant microRNAs using EST analysis. Cell Res. 2005, 15 (5): 336-360. 10.1038/sj.cr.7290302.PubMedView ArticleGoogle Scholar
- Zhang B, Pan X, Cannon CH, Cobb GP, Anderson TA: Conservation and divergence of plant microRNA genes. Plant J. 2006, 46 (2): 243-259. 10.1111/j.1365-313X.2006.02697.x.PubMedView ArticleGoogle Scholar
- Subramanian S, Fu Y, Sunkar R, Barbazuk WB, Zhu JK, Yu O: Novel and nodulation-regulated microRNAs in soybean roots. BMC Genomics. 2008, 9: 160-10.1186/1471-2164-9-160.PubMed CentralPubMedView ArticleGoogle Scholar
- Zhang B, Pan X, Stellwag EJ: Identification of soybean microRNAs and their targets. Planta. 2008, 229 (1): 161-182. 10.1007/s00425-008-0818-x.PubMedView ArticleGoogle Scholar
- Jagadeeswaran G, Zheng Y, Li YF, Shukla LI, Matts J, Hoyt P, Macmil SL, Wiley GB, Roe BA, Zhang W, Sunkar R: Cloning and characterization of small RNAs from Medicago truncatula reveals four novel legume-specific microRNA families. New Phytol. 2009, 184 (1): 85-98. 10.1111/j.1469-8137.2009.02915.x.PubMedView ArticleGoogle Scholar
- Wang Y, Li P, Cao X, Wang X, Zhang A, Li X: Identification and expression analysis of miRNAs from nitrogen-fixing soybean nodules. Biochem Biophys Res Commun. 2009, 378 (4): 799-803. 10.1016/j.bbrc.2008.11.140.PubMedView ArticleGoogle Scholar
- Joshi T, Yan Z, Libault M, Jeong DH, Park S, Green PJ, Sherrier DJ, Farmer A, May G, Meyers BC, Xu D, Stacey G: Prediction of novel miRNAs and associated target genes in Glycine max. BMC Bioinformatics. 2010, 11 (Suppl 1): S14-10.1186/1471-2105-11-S1-S14.PubMed CentralPubMedView ArticleGoogle Scholar
- affymetrix. [http://www.affymetrix.com/estore/index.jsp]
- Gotz S, Garcia-Gomez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talon M, Dopazo J, Conesa A: High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res. 2008, 36 (10): 3420-3435. 10.1093/nar/gkn176.PubMed CentralPubMedView ArticleGoogle Scholar
- Libault M, Farmer A, Brechenmacher L, Drnevich J, Langley RJ, Bilgin DD, Radwan O, Neece DJ, Clough SJ, May GD, Stacey G: Complete transcriptome of the soybean root hair cell, a single-cell model, and its alteration in response to Bradyrhizobium japonicum infection. Plant Physiol. 2009, 152 (2): 541-552.PubMedView ArticleGoogle Scholar
- Libault M, Farmer A, Joshi T, Takahashi K, Langley RJ, Franklin LD, He J, Xu D, May G, Stacey G: An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants. Plant J. 2010, 63 (1): 86-99.PubMedGoogle Scholar
- Schmidt MA, Barbazuk WB, Sandford M, May G, Song Z, Zhou W, Nikolau BJ, Herman EM: Silencing of soybean seed storage proteins results in a rebalanced protein composition preserving seed protein content without major collateral changes in the metabolome and transcriptome. Plant Physiol. 2011, 156 (1): 330-345. 10.1104/pp.111.173807.PubMed CentralPubMedView ArticleGoogle Scholar
- Tuteja JH, Zabala G, Varala K, Hudson M, Vodkin LO: Endogenous, tissue-specific short interfering RNAs silence the chalcone synthase gene family in glycine max seed coats. Plant cell. 2009, 21 (10): 3063-3077. 10.1105/tpc.109.069856.PubMed CentralPubMedView ArticleGoogle Scholar
- Lam HM, Xu X, Liu X, Chen W, Yang G, Wong FL, Li MW, He W, Qin N, Wang B, Li J, Jian M, Wang J, Shao G, Wang J, Sun SS, Zhang G: Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genetics. 2010, 42 (12): 1053-1059. 10.1038/ng.715.View ArticleGoogle Scholar
- Li-Beisson Y, Shorrosh B, Beisson F, Andersson MX, Arondel V, Bates PD, Baud S, Bird D, Debono A, Durrett TP, Franke RB, Graham IA, Katayama K, Kelly AA, Larson T, Markham JE, Miquel M, Molina I, Nishida I, Rowland O, Samuels L, Schmid KM, Wada H, Welti R, Xu C, Zallot R, Ohlrogge J: Acyl-lipid metabolism. Arabidopsis Book. 2013, 11: e0161-PubMed CentralPubMedView ArticleGoogle Scholar
- Higo K, Ugawa Y, Iwamoto M, Korenaga T: Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res. 1999, 27 (1): 297-300. 10.1093/nar/27.1.297.PubMed CentralPubMedView ArticleGoogle Scholar
- Lescot M, Dehais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouze P, Rombauts S: PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 2002, 30 (1): 325-327. 10.1093/nar/30.1.325.PubMed CentralPubMedView ArticleGoogle Scholar
- Steffens NO, Galuschka C, Schindler M, Bulow L, Hehl R: AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome. Nucleic Acids Res. 2004, 32 (Database issue): D368-D372.PubMed CentralPubMedView ArticleGoogle Scholar
- Zhang W, Zhang T, Wu Y, Jiang J: Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis. Plant cell. 2012, 24 (7): 2719-2731. 10.1105/tpc.112.098061.PubMed CentralPubMedView ArticleGoogle Scholar
- Zhang Z, Yu J, Li D, Zhang Z, Liu F, Zhou X, Wang T, Ling Y, Su Z: PMRD: plant microRNA database. Nucleic Acids Res. 2010, 38 (Database issue): D806-D813.PubMed CentralPubMedView ArticleGoogle Scholar
- FASTX-Toolkit. [http://hannonlab.cshl.edu/fastx_toolkit/index.html]
- Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009, 10 (3): R25-10.1186/gb-2009-10-3-r25.PubMed CentralPubMedView ArticleGoogle Scholar
- Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B: Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008, 5 (7): 621-628. 10.1038/nmeth.1226.PubMedView ArticleGoogle Scholar
- INVESTOPEDTA. [http://www.investopedia.com]
- Lemkin PF, Thornwall GC, Walton KD, Hennighausen L: The microarray explorer tool for data mining of cDNA microarrays: application for the mammary gland. Nucleic Acids Res. 2000, 28 (22): 4452-4459. 10.1093/nar/28.22.4452.PubMed CentralPubMedView ArticleGoogle Scholar
- Vawter MP, Barrett T, Cheadle C, Sokolov BP, Wood WH, Donovan DM, Webster M, Freed WJ, Becker KG: Application of cDNA microarrays to examine gene expression differences in schizophrenia. Brain Res Bull. 2001, 55 (5): 641-650. 10.1016/S0361-9230(01)00522-6.PubMedView ArticleGoogle Scholar
- Virtaneva K, Wright FA, Tanner SM, Yuan B, Lemon WJ, Caligiuri MA, Bloomfield CD, de La Chapelle A, Krahe R: Expression profiling reveals fundamental biological differences in acute myeloid leukemia with isolated trisomy 8 and normal cytogenetics. Proc Natl Acad Sci U S A. 2001, 98 (3): 1124-1129. 10.1073/pnas.98.3.1124.PubMed CentralPubMedView ArticleGoogle Scholar
- Cheadle C, Vawter MP, Freed WJ, Becker KG: Analysis of microarray data using Z score transformation. J Mol Diagn. 2003, 5 (2): 73-81. 10.1016/S1525-1578(10)60455-2.PubMed CentralPubMedView ArticleGoogle Scholar
- Quackenbush J: Microarray data normalization and transformation. Nat Genet. 2002, 32 (Suppl): 496-501.PubMedView ArticleGoogle Scholar
- Nemhauser JL, Mockler TC, Chory J: Interdependency of brassinosteroid and auxin signaling in Arabidopsis. PLoS Biol. 2004, 2 (9): E258-10.1371/journal.pbio.0020258.PubMed CentralPubMedView ArticleGoogle Scholar
- Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP: Prediction of plant microRNA targets. Cell. 2002, 110 (4): 513-520. 10.1016/S0092-8674(02)00863-2.PubMedView ArticleGoogle Scholar
- Zhu JK: Reconstituting plant miRNA biogenesis. Proc Natl Acad Sci U S A. 2008, 105 (29): 9851-9852. 10.1073/pnas.0805207105.PubMed CentralPubMedView ArticleGoogle Scholar
- Voinnet O: Origin, biogenesis, and activity of plant microRNAs. Cell. 2009, 136 (4): 669-687. 10.1016/j.cell.2009.01.046.PubMedView ArticleGoogle Scholar
- Allen E, Xie Z, Gustafson AM, Carrington JC: microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell. 2005, 121 (2): 207-221. 10.1016/j.cell.2005.04.004.PubMedView ArticleGoogle Scholar
- Du Z, Zhou X, Ling Y, Zhang Z, Su Z: agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 2010, 38 (Suppl): W64-W70.PubMed CentralPubMedView ArticleGoogle Scholar
- Bartel DP: MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004, 116 (2): 281-297. 10.1016/S0092-8674(04)00045-5.PubMedView ArticleGoogle Scholar
- Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, Bader GD: Cytoscape Web: an interactive web-based network browser. Bioinformatics. 2010, 26 (18): 2347-2348. 10.1093/bioinformatics/btq430.PubMed CentralPubMedView ArticleGoogle Scholar
- Dai X, Zhao PX: psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res. 2011, 39 (Web Server issue): W155-W159.PubMed CentralPubMedView ArticleGoogle Scholar
- Cernac A, Benning C: WRINKLED1 encodes an AP2/EREB domain protein involved in the control of storage compound biosynthesis in Arabidopsis. Plant J. 2004, 40 (4): 575-585. 10.1111/j.1365-313X.2004.02235.x.PubMedView ArticleGoogle Scholar
- Baud S, Mendoza MS, To A, Harscoet E, Lepiniec L, Dubreucq B: WRINKLED1 specifies the regulatory action of LEAFY COTYLEDON2 towards fatty acid metabolism during seed maturation in Arabidopsis. Plant J. 2007, 50 (5): 825-838. 10.1111/j.1365-313X.2007.03092.x.PubMedView ArticleGoogle Scholar
- Huang AH: Oleosins and oil bodies in seeds and other organs. Plant Physiol. 1996, 110 (4): 1055-1061. 10.1104/pp.110.4.1055.PubMed CentralPubMedView ArticleGoogle Scholar
- Beisson F, Li Y, Bonaventure G, Pollard M, Ohlrogge JB: The acyltransferase GPAT5 is required for the synthesis of suberin in seed coat and root of Arabidopsis. Plant cell. 2007, 19 (1): 351-368. 10.1105/tpc.106.048033.PubMed CentralPubMedView ArticleGoogle Scholar
- Li Y, Beisson F, Koo AJ, Molina I, Pollard M, Ohlrogge J: Identification of acyltransferases required for cutin biosynthesis and production of cutin with suberin-like monomers. Proc Natl Acad Sci U S A. 2007, 104 (46): 18339-18344. 10.1073/pnas.0706984104.PubMed CentralPubMedView ArticleGoogle Scholar
- Li-Beisson Y, Pollard M, Sauveplane V, Pinot F, Ohlrogge J, Beisson F: Nanoridges that characterize the surface morphology of flowers require the synthesis of cutin polyester. Proc Natl Acad Sci U S A. 2009, 106 (51): 22008-22013. 10.1073/pnas.0909090106.PubMed CentralPubMedView ArticleGoogle Scholar
- Brown AP, Kroon JT, Swarbreck D, Febrer M, Larson TR, Graham IA, Caccamo M, Slabas AR: Tissue-specific whole transcriptome sequencing in castor, directed at understanding triacylglycerol lipid biosynthetic pathways. PLoS One. 2012, 7 (2): e30100-10.1371/journal.pone.0030100.PubMed CentralPubMedView ArticleGoogle Scholar
- Dahlqvist A, Stahl U, Lenman M, Banas A, Lee M, Sandager L, Ronne H, Stymne S: Phospholipid:diacylglycerol acyltransferase: an enzyme that catalyzes the acyl-CoA-independent formation of triacylglycerol in yeast and plants. Proc Natl Acad Sci U S A. 2000, 97 (12): 6487-6492. 10.1073/pnas.120067297.PubMed CentralPubMedView ArticleGoogle Scholar
- Katavic V, Reed DW, Taylor DC, Giblin EM, Barton DL, Zou J, Mackenzie SL, Covello PS, Kunst L: Alteration of seed fatty acid composition by an ethyl methanesulfonate-induced mutation in Arabidopsis thaliana affecting diacylglycerol acyltransferase activity. Plant Physiol. 1995, 108 (1): 399-409. 10.1104/pp.108.1.399.PubMed CentralPubMedView ArticleGoogle Scholar
- Routaboul JM, Benning C, Bechtold N, Caboche M, Lepiniec L: The TAG1 locus of Arabidopsis encodes for a diacylglycerol acyltransferase. Plant Physiol Biochem. 1999, 37 (11): 831-840. 10.1016/S0981-9428(99)00115-1.PubMedView ArticleGoogle Scholar
- Zou J, Wei Y, Jako C, Kumar A, Selvaraj G, Taylor DC: The Arabidopsis thaliana TAG1 mutant has a mutation in a diacylglycerol acyltransferase gene. Plant J. 1999, 19 (6): 645-653. 10.1046/j.1365-313x.1999.00555.x.PubMedView ArticleGoogle Scholar
- Zheng P, Allen WB, Roesler K, Williams ME, Zhang S, Li J, Glassman K, Ranch J, Nubel D, Solawetz W, Bhattramakki D, Llaca V, Deschamps S, Zhong GY, Tarczynski MC, Shen B: A phenylalanine in DGAT is a key determinant of oil content and composition in maize. Nat Genet. 2008, 40 (3): 367-372. 10.1038/ng.85.PubMedView ArticleGoogle Scholar
- Bates PD, Durrett TP, Ohlrogge JB, Pollard M: Analysis of acyl fluxes through multiple pathways of triacylglycerol synthesis in developing soybean embryos. Plant Physiol. 2009, 150 (1): 55-72. 10.1104/pp.109.137737.PubMed CentralPubMedView ArticleGoogle Scholar
- Santos-Mendoza M, Dubreucq B, Baud S, Parcy F, Caboche M, Lepiniec L: Deciphering gene regulatory networks that control seed development and maturation in Arabidopsis. Plant J. 2008, 54 (4): 608-620. 10.1111/j.1365-313X.2008.03461.x.PubMedView ArticleGoogle Scholar
- Suzuki M, McCarty DR: Functional symmetry of the B3 network controlling seed development. Curr Opin Plant Biol. 2008, 11 (5): 548-553. 10.1016/j.pbi.2008.06.015.PubMedView ArticleGoogle Scholar
- Nag R, Maity MK, Dasgupta M: Dual DNA binding property of ABA insensitive 3 like factors targeted to promoters responsive to ABA and auxin. Plant Mol Biol. 2005, 59 (5): 821-838. 10.1007/s11103-005-1387-z.PubMedView ArticleGoogle Scholar
- Tsukagoshi H, Morikami A, Nakamura K: Two B3 domain transcriptional repressors prevent sugar-inducible expression of seed maturation genes in Arabidopsis seedlings. Proc Natl Acad Sci U S A. 2007, 104 (7): 2543-2547. 10.1073/pnas.0607940104.PubMed CentralPubMedView ArticleGoogle Scholar
- Stalberg K, Ellerstom M, Ezcurra I, Ablov S, Rask L: Disruption of an overlapping E-box/ABRE motif abolished high transcription of the napA storage-protein promoter in transgenic Brassica napus seeds. Planta. 1996, 199 (4): 515-519.PubMedView ArticleGoogle Scholar
- Busk PK, Pages M: Regulation of abscisic acid-induced transcription. Plant Mol Biol. 1998, 37 (3): 425-435. 10.1023/A:1006058700720.PubMedView ArticleGoogle Scholar
- Ezcurra I, Ellerstrom M, Wycliffe P, Stalberg K, Rask L: Interaction between composite elements in the napA promoter: both the B-box ABA-responsive complex and the RY/G complex are necessary for seed-specific expression. Plant Mol Biol. 1999, 40 (4): 699-709. 10.1023/A:1006206124512.PubMedView ArticleGoogle Scholar
- Ezcurra I, Wycliffe P, Nehlin L, Ellerstrom M, Rask L: Transactivation of the Brassica napus napin promoter by ABI3 requires interaction of the conserved B2 and B3 domains of ABI3 with different cis-elements: B2 mediates activation through an ABRE, whereas B3 interacts with an RY/G-box. Plant J. 2000, 24 (1): 57-66. 10.1046/j.1365-313x.2000.00857.x.PubMedView ArticleGoogle Scholar
- Lam E, Chua NH: Tetramer of a 21-base pair synthetic element confers seed expression and transcriptional enhancement in response to water stress and abscisic acid. J Biol Chem. 1991, 266 (26): 17131-17135.PubMedGoogle Scholar
- Thomas TL: Gene expression during plant embryogenesis and germination: an overview. Plant Cell. 1993, 5 (10): 1401-1410.PubMed CentralPubMedView ArticleGoogle Scholar
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