An integrated omics analysis reveals molecular mechanisms that are associated with differences in seed oil content between Glycine max and Brassica napus

Abstract

BackgroundRapeseed (Brassica napus L.) and soybean (Glycine max L.) seeds are rich in both protein and oil, which are major sources of biofuels and nutrition. Although the difference in seed oil content between soybean (~ 20%) and rapeseed (~ 40%) exists, little is known about its underlying molecular mechanism.ResultsAn integrated omics analysis was performed in soybean, rapeseed, Arabidopsis (Arabidopsis thaliana L. Heynh), and sesame (Sesamum indicum L.), based on Arabidopsis acyl-lipid metabolism- and carbon metabolism-related genes. As a result, candidate genes and their transcription factors and microRNAs, along with phylogenetic analysis and co-expression network analysis of the PEPC gene family, were found to be largely associated with the difference between the two species. First, three soybean genes (Glyma.13G148600, Glyma.13G207900 and Glyma.12G122900) co-expressed with GmPEPC1 are specifically enriched during seed storage protein accumulation stages, while the expression of BnPEPC1 is putatively inhibited by bna-miR169, and two genes BnSTKA and BnCKII are co-expressed with BnPEPC1 and are specifically associated with plant circadian rhythm, which are related to seed oil biosynthesis. Then, in de novo fatty acid synthesis there are rapeseed-specific genes encoding subunits β-CT (BnaC05g37990D) and BCCP1 (BnaA03g06000D) of heterogeneous ACCase, which could interfere with synthesis rate, and β-CT is positively regulated by four transcription factors (BnaA01g37250D, BnaA02g26190D, BnaC01g01040D and BnaC07g21470D). In triglyceride synthesis, GmLPAAT2 is putatively inhibited by three miRNAs (gma-miR171, gma-miR1516 and gma-miR5775). Finally, in rapeseed there was evidence for the expansion of gene families, CALO, OBO and STERO, related to lipid storage, and the contraction of gene families, LOX, LAH and HSI2, related to oil degradation.ConclusionsThe molecular mechanisms associated with differences in seed oil content provide the basis for future breeding efforts to improve seed oil content.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1542-8) contains supplementary material, which is available to authorized users.

Drought‐responsive genes, late embryogenesis abundant group3 (LEA3) and vicinal oxygen chelate, function in lipid accumulation in Brassica napus and Arabidopsis mainly via enhancing photosynthetic efficiency and reducing ROS

“…The higher carbon fixation levels and elevated capacity for photosynthesis also contribute to FA accumulation. Previously, an integrated omics analysis of B. napus and Glycine max also showed that some genes involved in photosynthesis were related to lipid metabolism (Zhang et al ., ). Thus, the enhanced photosynthetic efficiency in the LEA‐OE and VOC‐OE lines could confer drought tolerance and contribute to lipid accumulation.…”

Genome-wide identification and expression analysis of Raffinose synthetase family in cotton

“…Conserved functional motifs of RAFS genes were identified using the program Multiple Em for Motif Elicitation (MEME, http://meme-suite.org/tools/meme ) with the following parameters: the width of a motif was between 6 and 50aa, and the number of motifs was no more than 20 [ 36 ]. The website GSDS2.0 ( http://gsds.cbi.pku.edu.cn/ ) was used to draw gene structure diagrams[ 2 ].…”

Identification and analysis of oil candidate genes revealed the molecular basis of oil accumulation in Gossypium hirsutum L. for cottonseed biofuels development

“…Acyl-lipid synthesis, as a complex biological process, includes at least the conversion of sucrose to pyruvate, plastid de novo FA synthesis, endoplasmic TAG synthesis, and oil-body assembly [45]. Moreover, an integrated omics analysis of rapeseed and soybean previously showed that some genes involved in photosynthesis and plant hormone signal transduction were related to lipid metabolism [46], as well as substrate competition between seed oil and protein synthesis exists in oil crops [47]. Therefore, the six pathways, "biosynthesis of amino acids", "valine, leucine and isoleucine biosynthesis", "glycine, serine and threonine metabolism", "biosynthesis of unsaturated fatty acids", "fatty acid metabolism", and "fatty acid biosynthesis", were ultimately selected for subsequent identi cation of candidate oil genes based on the results of KEGG enrichment analysis and network analyses of enriched terms (Fig.…”