Unraveling Site-Specific Seed Formation Abnormalities in Picea Neoveitchii Mast. Trees via Widely Metabolomic and Transcriptomic Analysis

Background: Picea neoveitchii Mast. is a rare and threatened species of evergreen coniferous tree in China. Damaged seeds, abnormal seed growth, and empty seed shells are common problems in P. neoveitchii in China. But the intensity of these abnormalities varies at different places; unfortunately, the reasons behind these inconsistencies are completely unknown.Results: In this study, we compared the seeds from two locations: Taibai (Shaanxi province), a 150-year-old tree (TB150), and Zhouqu (Gansu province), a 150-year-old tree (ZQ150). The results showed obvious changes in 43 different metabolites. Among them, the number of damaged seeds and empty seed shells was higher in TB150, and the number of abnormal and normal (viable) seeds was higher in ZQ150 by increasing indole-3-acetic acid (IAA), methyl jasmonate (JA-me), and brassinosteroid (BR) contents and decreasing abscisic acid (ABA) contents. Moreover, to further investigate these inconsistencies, we used high-throughput deep sequencing technology, aiming to perform de novo transcriptomic assembly and functional annotation of unigenes at both sites. Totally, 2355 differentially expressed genes were observed between TB150 and ZQ150, with 1280 upregulated and 1075 downregulated. Hormone signaling and sugar metabolism-related unigenes were further studied for their involvement in these inconsistencies.Summary: ZQ150 increased the number of normal seeds by enhancing endogenous IAA levels and the expression of genes related to the auxin signaling pathway. In contrast, TB150 had the highest percentage of empty seed shells, which can be attributed to higher ABA levels and the activation of genes involved in the ABA signaling pathway. We also hypothesize that the upregulation of genes related to sugar metabolism promotes normal seed development.