Integrated Analysis of Transcriptome and Lipid Metabolome Reveals the Differences in α-Linolenic Acid Synthesis Regulation in Different Perilla frutescens

doi:10.13560/j.cnki.biotech.bull.1985.2025-1008

Abstract

Abstract:

Objective This study aims to analyze the differences in α-linolenic acid (ALA) content between QO10 and QS5 seeds of Perilla frutescens, and find out genes related to ALA synthesis and regulation. The results will provide genetic resources for the further creation of new perilla varieties with high ALA content. Method Using morphological index determination, transcriptomics, and lipid metabolomics techniques, a systematic analysis was performed on the seed morphology, differentially expressed genes (DEGs), and lipid metabolite profiles of perilla QO10 and QS5. Result The 1 000-seed weight of QS5 seeds was significantly higher than that of QO10. Seed coat color difference analysis indicated that the seed coat color of QS5 was brighter than that of QO10, and the two were easily distinguishable in terms of seed coat color. Results of lipid metabolomics analysis demonstrated that there were significant differences in the types and relative contents of lipid metabolites between QO10 and QS5 seeds; the contents of stearic acid (SA) and ALA in QS5 seeds were higher than those in QO10. Transcriptomic analysis results showed that 188 differentially expressed genes (DEGs) were enriched in 6 GO terms and 5 KEGG pathways related to fatty acid (FA) metabolism. Based on the results of transcriptome-lipid metabolome integrated analysis, 15 key enzyme and protein-coding genes were finally screened out. These included ACSL, FABP, FAD2, ENR, KAR, and KAS as well as lipase (lipase)-coding gene, LCAT3, FAR, SCL, and HMGCR. Furthermore, transcriptomic analysis revealed that 38 WRKY transcription factors (TFs) and 26 MYB TFs were differentially expressed; 2 WRKY TFs and 2 MYB TFs with the largest fold changes in differential expression were selected as candidate TFs. Finally, 10 candidate genes related to the regulation of ALA biosynthesis were verified by RT-qPCR, and the quantitative results were consistent with those of transcriptome sequencing. Conclusion There were significant morphological differences between the seeds of QO10 and QS5, and QS5 contained higher levels of SA and ALA. Nineteen genes related to the regulation of ALA biosynthesis were screened out, whose differential expression in QO10 and QS5 seeds is a potential cause of the difference in ALA content.

Key words: Perilla frutescens, seeds, α-linolenic acid, metabolome, transcriptome, lipid, integrated analysis

WANG Yu-kun, YUAN Yuan, WANG Bin, ZHU Yun-na, REN Xiao-qiang, REN Fei, YE Hong. Integrated Analysis of Transcriptome and Lipid Metabolome Reveals the Differences in α-Linolenic Acid Synthesis Regulation in Different Perilla frutescens[J]. Biotechnology Bulletin, 2026, 42(4): 129-140.

Figures/Tables 10

Fig. 1 Morphological observation of perilla (Perilla frutescens) QO10 and QS5 seedsA: Morphology of QO10 and QS5 seeds; B: 1 000-seed weight of QO10 and QS5 seeds; C‒F: determination of color difference parameters of seed coats of QO10 and QS5 seeds. The L* value indicates the lightness of a color. The a* value indicates the color’s bias on the “red-green” axis. The b* value indicates the color’s bias on the “yellow-blue” axis. The ΔE value indicates the total color difference value calculated by integrating the differences in the three dimensions of L*, a*, and b*. ** P<0.01; n.s..: no significant difference. Scale bar=1 cm

Fig. 2 Types, quantities, and accumulation patterns of differential lipid metabolites in perilla QO10 and QS5 seeds

Fig. 3 Top20 differential lipid metabolites and their relative contents in perilla QO10 and QS5 seeds

Table 2 Transcriptome sequencing data statistics

样本 Samples	总读数 Total reads	干净读数 Clean reads	干净碱基 Clean bases	GC含量 GC content （%）	Q30百分比Q30 percentage （%）	比对读数 Mapped reads	特异比对读数 Unique mapped reads
Q010-1	43 192 794	21 596 397	6 460 553 535	47.69	94.72	41 275 128 （95.56%）	38 960 150 （90.20%）
Q010-2	49 973 860	24 986 930	7 472 777 948	47.50	94.35	47 022 281 （94.09%）	44 202 523 （88.45%）
Q010-3	41 845 218	20 922 609	6 256 919 302	47.65	94.85	39 954 021 （95.48%）	37 653 099 （89.98%）
QS5-1	38 146 772	19 073 386	5 698 842 059	49.37	94.56	34 751 710 （91.10%）	30 637 108 （88.16%）
QS5-2	36 792 684	18 396 342	5 494 890 960	49.46	94.45	34 287 102 （93.19%）	30 669 813 （89.45%）
QS5-3	36 323 210	18 161 605	5 424 955 610	49.49	94.73	34 314 537 （94.47%）	30 502 192 （88.89%）

Fig. 4 Volcano plot of DEGs

Fig. 5 GO (A) and KEGG (B) enrichment analysis of DEGs

Fig. 6 Functional annotation and expression patterns of candidate DEGs

Fig. 7 Joint analysis of transcriptome and metabolome of ALA anabolism in perilla seedsRed font indicates upregulation and blue font indicates downregulation. The transcriptome heatmap represents the expression levels (FPKM) of genes in different samples, and the metabolome heatmap indicates the accumulation of metabolites in different samples. R1‒R3 indicates biological replications

Fig. 8 Expression patterns of differentially expressed WRKY (A) and MYB (B) TFs

Fig. 9 RT-qPCR validation of the expression patterns of DEGs

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