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

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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.

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Data availability

The datasets supporting the conclusions of this article have been deposited in the NCBI GEO database under accession numbers GSE151779 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE151779) and GSE151552 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE151552).

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Acknowledgements

This research was funded by Heilongjiang Academy of Agricultural Sciences Innovation Fund of China, grant number 2020FJZX005, 2019YYYF012, and National Characteristic Oil Plants Industry Technology System, grant number CARS-14. We thank Institute of Field and Vegetable Crops (Novi Sad, Serbia) for providing high oleic acid sunflower materials “L-1-OL-1”.

Funding

This research was funded by Heilongjiang Academy of Agricultural Sciences Innovation Fund of China, grant number 2020FJZX005, 2019YYYF012, and National Characteristic Oil Plants Industry Technology System, grant number CARS-14.

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  1. Yan Liu and Fei Zhou contributed equally to this work and should be considered co-first authors.

Authors and Affiliations

  1. College of Life Science, Northeast Forestry University, Harbin, 150040, China

    Yan Liu & Fujuan Feng

  2. Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China

    Yan Liu, Fei Zhou, Xutang Huang, Wenjun Wang & Shuquan Zhang

  3. Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Harbin, 150086, China

    Fei Zhou

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11738_2021_3259_MOESM1_ESM.rar

Supplementary file1 Fig. S1 The length distribution of sRNAs in each sample. Table S1 The mRNAs, lncRNAs and miRNAs found. Table S2 The differentially expressed mRNAs, lncRNAs and miRNAs. Table S3 The GO analysis of mRNAs. Table S4 The KEGG analysis of mRNAs. Table S5 DEGs riched in fatty acid metabolism. Table S6 Transcription factors related to lipid metabolism. Table S7 The GO analysis of lncRNAs and miRNAs. Table S8 The KEGG analysis of lncRNAs and miRNAs. Table S9 The ceRNA network related lncRNAs and mRNAs. Table S10 The lipid metabolism related KEGG network (RAR 50434 kb)

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Liu, Y., Zhou, F., Huang, X. et al. Identification and integrated analysis of mRNAs, lncRNAs, and microRNAs of developing seeds in high oleic acid sunflower (Helianthus annuus L.). Acta Physiol Plant 43, 85 (2021). https://doi.org/10.1007/s11738-021-03259-5

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