Integrated transcriptomics and lipidomics reveal mechanisms regulating lipids formation and accumulation in oil body during walnut seed development.

Abstract

Background: Through combined analysis of the transcriptomics and lipidomics of walnut, the possible molecular mechanism of lipid formation and accumulation in oil bodies was revealed.

Conclusion: The formation and accumulation of lipids are critical determinants of nut quality, with walnut storing lipids primarily in oil bodies (OBs). Currently, there is still a lack of systematic research on the formation and accumulation of lipids in walnut OBs (WOBs). Therefore, this study integrated lipidomics and transcriptomics to comprehensively identify the changes in WOBs and walnut kernels at 60, 74, 88, 102, 116, and 130 days after pollination (DAP). The results showed that fatty acid content in walnut kernels and WOBs had opposite trends, especially oleic, linoleic, and linolenic. Principal component analysis of the samples and cluster analysis of differentially expressed genes (DEGs) showed that the total samples were divided into three main groups: 60-74, 88-102, and 116-130 DAP. RNA sequencing generated 33,918 unigenes (14,995 DEGs), including 228 DEGs highly related to lipid metabolism, in 18 cDNA libraries prepared from walnut kernel. These genes were mainly involved in metabolic pathways such as pyruvate metabolism, glycerophospholipid metabolism, glycerolipid metabolism, and fatty acid biosynthesis during lipid synthesis. On the other hand, the expression levels of ACC, KASII, SAD, FAD2, FAD3, and PDAT genes were downregulated at 88-130 DAP compared with 60-74 DAP, which might be the key genes regulating the reduction of free fatty acid content in WOBs. In addition, 21 FAD genes were identified, including seven SAD genes, three FAD2 genes, five FAD3 genes, one FAD5 gene, one FAD6 gene, and four FAD7/8 genes. These genes were closely related to the synthesis of unsaturated fatty acids in WOBs, especially FAD2 and FAD3. The findings offered valuable insights into the dynamic changes in lipids and genetic resources and provided a foundation for walnut quality improvement.