Comparative transcriptomes analysis at different developmental stages of seed embryo in maize by RNA-sequencing

we used two contrasting maize genotypes with differential oil accumulation percentage. High oil content (HOC) maize had 11% oil content while low oil content (LOC) maize had significantly lower oil content (5.4%). Transmission electron microscopy revealed a higher accumulation of oil bodies in the HOC maize embryo as compared to LOC maize. Comparative RNA-sequencing analysis at different developmental stages of seed embryo identified 739 genes that are constantly differentially expressed (DEGs) at all the six developmental stages from 15 days after pollination (DAP) to 40 DAP. KEGG enrichment analysis identified fatty acid metabolism and fatty acid biosynthesis as the most enriched biological pathways contributed by these DEGs. Notably, transcriptional changes are more intense at the early stages of embryo development as compared to later stages. In addition, pathways related to oil biosynthesis and their corresponding genes were more enriched at 30 DAP, which seems to be the key stage for oil accumulation. The study also identified 33 key DEGs involved in fatty acid and triacylglycerols biosynthesis, most of them were up-regulated in HOC, which may shape the differential oil contents in the two contrasting maize. Notably, we uncovered that both acyl-CoA-dependent and acyl-CoA-independent processes are essential for the high oil accumulation in maize embryo. Thirty six libraries representing the embryos from the two genotypes collected at six developmental stages and in three replicates were constructed for transcriptome sequencing