Untargeted Metabolomics Reveals Shared and Cultivar-Associated Metabolic Changes During Somatic Embryo Development in Two Rubber Tree (Hevea brasiliensis) Cultivars

Somatic embryogenesis is important for the clonal propagation of elite rubber tree (Hevea brasiliensis) germplasm, yet metabolic changes during embryo development, particularly in triploid cultivars, remain poorly understood. Here, LC–MS-based untargeted metabolomics was used to compare the diploid cultivar Yunyan73477 and the triploid cultivar Yunyan7346 across four stages: mature callus, heart-shaped somatic embryos, cotyledonary somatic embryos, and mature somatic embryos, with three biological replicates per cultivar-stage group. Differential metabolite accumulation analysis, stage-ordered abundance trend analysis, and KEGG pathway enrichment analysis were performed. The cultivars differed in the numbers and patterns of differentially accumulated metabolites (DAMs) during early transitions. During the cotyledonary-to-mature somatic embryo transition, 90 and 64 DAMs were identified in Yunyan73477 and Yunyan7346, respectively; 86 and 60 decreased in relative abundance, including 44 shared DAMs. In both cultivars, metabolites with overall decreasing trends were significantly enriched for isoflavonoid biosynthesis, whereas those with increasing trends were significantly enriched for linoleic acid and alpha-linolenic acid metabolism. Under the applied statistical thresholds, diterpenoid biosynthesis was significantly enriched only among metabolites assigned to the overall increasing STEM Profile 9 in Yunyan7346, including annotated gibberellin-related compounds, although this statistical enrichment does not by itself indicate enhanced diterpenoid pathway activity. These exploratory findings reveal shared stage-associated metabolic patterns and cultivar-associated differences between the two tested cultivars, Yunyan73477 and Yunyan7346, under the applied culture conditions, and provide candidate metabolites for targeted validation and subsequent functional investigation.