Gene expression profiles that shape high and low oil content sesames

Abstract

Background: Sesame (Sesamum indicum) can accumulate over 60% oil in its seed. However, low oil content genotypes with an oil content of less than 50% are also observed. To gain insights into how genes shape this variation, we examined 22 seed and carpel transcriptomes from 3 varieties of sesame with high and low oil content.

Results: A total of 34.6~52.2% of the sesame genes were expressed with a RPKM greater than 5 in the 22 tissue samples. The expressed gene numbers tended to decrease in the seed but fluctuated in the carpels from 10 to 30 days post-anthesis (DPA). Compared with that of the low oil content sesames, the high oil content sesame exhibited more positive gene expression during seed development. Typically, genes involved in lipid biosynthesis were enriched and could distinguish the high and low genotypes at 30 DPA, suggesting the pivotal role of seed oil biosynthesis in the later stages. Key homologous lipid genes that function in TAG biosynthesis, including those that encoded glycerol-3-phosphate acyltransferase (GPAT), acyl-CoA:diacylglycerol acyltransferase (DGAT), and phospholipid:diacylglycerol acyltransferase (PDAT), were strengthened asynchronously at different stages, but the lipid transfer protein (LTP)-encoding genes, including SIN_1019175, SIN_1019172 and SIN_1010009, usually were highlighted in the high oil content sesames. Furthermore, a list of 23 candidate genes was identified and predicted to be beneficial for higher oil content accumulation. Despite the different gene expression patterns between the seeds and carpels, the two tissues showed a cooperative relationship during seed development, and biological processes, such as transport, catabolic process and small molecule metabolic process, changed synchronously.

Conclusions: The study elucidated the different expression profiles in high and low oil content sesames and revealed key stages and a list of candidate genes that shaped oil content variation. These findings will accelerate dissection of the genetic mechanism of sesame oil biosynthesis.

Keywords: Carpel; Expression profiling; Gene; Oil content; Seed; Sesamum indicum.

Fig. 1

The development characteristics of the seed and carpel. a The carpels and seeds at 10, 20, 25 and 30 DPA. b The expressed gene numbers in the high and low oil content sesame seeds during development. c The expressed gene numbers in the high and low oil content sesame carpels during development. d The gene expression levels distinguished the seed and carpel after 20 DPA. HOS: Seed of high oil content sesame ZZM4728; LOAS: Seed of low oil content sesame ZZM3495; LOBS: Seed of low oil content sesame ZZM2161; HOS: Carpel of high oil content sesame ZZM4728; LOAS: Carpel of low oil content sesame ZZM3495; LOBS: Carpel of low oil content sesame ZZM2161

Fig. 2

The differentially expressed genes in the high and low oil content sesames during seed development. a Volcano plot illustrating the DEGs between HO and LOA at different stages. The blue, red and green spots indicate the up-, down-, and normally regulated genes, respectively. b Volcano plot illustrating the DEGs between HO and LOB at different stages. c Numbers of the DEGs between the high and low oil content sesames during seed development. d The shared DEGs between HO and LOAS/LOBS

Fig. 3

Expression patterns of the homologous lipid genes in the sesame seed. a Expression profiles of the known rate-limiting homologous lipid genes involved in sesame TAG biosynthesis. b The 11 genes homologous to A. thaliana lipid genes that were upregulated in the high oil content sesame seed

Fig. 4

Shared and special DEGs between the high and low oil content sesames. a Venn diagrams of the shared and special DEGs in the seed at different stages. b Expression profiles of the 805 shared DEGs in the seed between the high and low oil content sesames. A: represents the 13 assembled pseudomolecules of the sesame; B, E, H and K correspond to HO at 10, 20, 25 and 30 DPA, respectively; C, F, I and L correspond to LOA; D, G, J and M correspond to LOB; N: represents the gene density (mRNA, 500-kb window)

Fig. 5

Expression patterns of the core candidate genes for high oil content. a Expression patterns of the 23 common DEGs in the seed between the high and low oil content sesames. b-h Quantitative RT–PCR validation of 7 candidate genes for high oil content, including SIN_1024090, SIN_1014194, SIN_1007513, SIN_1027099, SIN_1027091, SIN_1023684 and SIN_1019175. Pink bars represented the high oil content sesame, and blue bars represented the low oil content sesames

Fig. 6

The relationships between the seed and carpel during development. a The shared and special GO terms of the expressed genes in the two tissues. b Numbers of the shared DEGs between HO and the two low oil content sesames in the carpels at different stages. c The shared and special pathways of the DEGs between the high and low oil content sesames in the two tissues