Identification of lncRNAs and Their Regulatory Network Involved in Oil Biosynthesis in Developing Seeds of Yellowhorn (<i>Xanthoceras sorbifolium</i>)

Abstract

Yellowhorn (Xanthoceras sorbifolium) seeds can have as high as 67% oil content and are especially rich in oleic acid, linoleic acid, and nervonic acid. Exploration of the lipid biosynthesis regulatory network is essential for increasing the yellowhorn oil content. Long non-coding RNAs (lncRNAs) play important roles in various plant biological processes; however, there is no report on the identification of lncRNAs involved in yellowhorn seed development and lipid biosynthesis affecting oil production. We performed whole transcriptome sequencing of yellowhorn seeds at four developmental stages and identified 16,920 putative lncRNAs. Among them, 325 lncRNAs were revealed to trans-regulate 58 key genes in fatty acid (FA) and triacylglycerol (TAG) biosynthesis pathways. Of these, ECR-2–LNC_009778 was found to be involved in nervonic acid biosynthesis and DGAT-1–LNC_009778 was beneficial to TAG accumulation. sRNA-seq was performed, and 55 microRNAs (miRNAs) were found to target 26 genes involved in FA and TAG biosynthesis; miR396a-4 targets FAD2, affecting linoleic acid biosynthesis, and miR156f-5p targets PDAT-2, contributing to TAG accumulation. Interestingly, 30 lncRNA–miRNA–gene modules involved in FA and TAG biosynthesis were identified, in which the KCS11-1–miR156g-2–LNC_000849 module was found to participate in nervonic acid synthesis, and the DGAT-2–miR172j–LNC_005874 module was assumed to contribute to the accumulation of TAG. Our results constitute the first comprehensive identification of lncRNAs in developing seeds of yellowhorn and serve as a new theoretical reference for improving oil content in the future.

Keywords

• lncRNA
• yellowhorn
• oil synthesis
• lncRNA-gene pairs
• lncRNA–miRNA–gene module