Identification and integrated analysis of mRNAs, lncRNAs, and microRNAs of developing seeds in high oleic acid sunflower (Helianthus annuus L.)

Abstract

High unsaturated fatty acid content of sunflower seed is desirable for human-healthy high oleic acid oil production. Knowledge of lipid metabolic regulatory mechanisms is key to improving oil content and quality. This study is expected to explore regulatory mechanisms of lipid metabolism in high oleic acid seeds. First, we analyzed the oil contents and detected the fatty acid compositions in developing sunflower seeds with high oleic acid content. Next, high-throughput sequencing (HTS) of seed RNA samples from three key seed developmental stages relevant to oil content and quality was performed. Pairwise comparisons of differentially expressed mRNAs, long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) yielded respective differentially expressed transcripts as follows: 52293, 120625, 95 (L7d vs L22d); 57398, 123485, 127 (L7 vs L37d); 15417, 9554, 77 (L22d vs L37d). 15652 novel mRNAs, 123888 novel lncRNAs, and 98 novel miRNAs were identified, which enriched the RNA library of sunflower. Furthermore, gene functions were predicted using GO and KEGG analyses. These prediction analysis revealed that differentially expressed ncRNAs and mRNAs were mainly included in fatty acid metabolism and oil accumulation. Moreover, 9072 pairs of competing endogenous RNA (ceRNA) relationships comprised of interacting lncRNAs, miRNAs, and mRNAs. Pathway network analysis of differentially expressed lipid metabolism-associated ceRNAs revealed several important enzymes including glycerol-3-phosphate O-acyltransferase, linoleate 9S-lipoxygenase, acyl-CoA oxidase, and others that were enriched in fatty acid synthesis and oil accumulation, which highlighted competitive interactions in lipid metabolism. This study will elucidate potential regulatory mechanisms of lipid metabolism in sunflower seeds.