The rubber tree (Hevea brasiliensis) is the most important commercial plant for producing natural rubber. Immature seed inner integument and anther-derived somatic embryogenesis techniques play a crucial role in the in vitro large-scale propagation and genetic transformation of the rubber tree. However, somatic embryogenesis is highly genotype-dependent, that is, only a limited number of H. brasiliensis genotypes, such as CATAS73397, CATAS917, and PB260, can be efficiently induced by somatic embryogenesis and used for large-scale propagation or transformation. The genotype dependence of the somatic embryogenesis technique is a conundrum for the application of Hevea biotechnology in most commercially important cultivars, such as Reken628 and CATAS879. Previous studies have shown that several somatic embryogenesis regulators can overcome genotype dependence and enhance the transformation and regeneration efficiency of recalcitrant plants and cultivars. In this review, we first describe the relevant successful applications of somatic embryogenesis technology in seedling production and genetic modification of H. brasiliensis. Second, we discuss the genotype dependence of somatic embryogenesis as the major challenge currently. Third, we summarize the recent significant advances in the understanding of the molecular mechanisms underlying somatic embryogenesis in other plants. Finally, we suggest a roadmap for using somatic embryogenesis regulatory genes to facilitate genotype-dependent somatic embryogenesis technology in H. brasiliensis.

The rubber tree (Hevea brasiliensis (Willd. ex A. Juss.) Müll. Arg.) is the predominant global source of natural rubber; however, its cultivation is largely confined to tropical regions due to chilling sensitivity. Although the chilling-tolerant clone GT1 holds considerable promise for expanding cultivation latitudes and serving as a genetic transformation recipient, its utility is severely compromised by a recalcitrant somatic embryogenesis (SE) capacity relative to the elite clone Reyan 7-33-97 (R73397). Despite prior media optimization efforts, an efficient callus subculture system for GT1 remains elusive, and the molecular basis of its SE recalcitrance is poorly characterized. Here, we establish a repeated GT1 callus subculture system using a pulsed plant growth regulators regimen and integrated comparative transcriptomics, whole-genome bisulfite sequencing (WGBS), and Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) with Tn5 footprinting to elucidate the regulatory bottlenecks distinguishing GT1 from R73397. Our results suggest that, although the GT1 callus has not completely lost the expression of genes that characterize the tendency to develop into embryos, it does not complete the morphogenetic transition into globular embryos, possibly due to the reduced levels of transcription factors critical for embryo patterning. The epigenetic analyses indicate that the differential expression of these regulators is not tightly coupled with DNA methylation or chromatin accessibility, but reveal distinct transposable element silencing mechanisms between the two genotypes. Furthermore, construction of a hierarchical TF-DNA binding network predicts the positions of several transcription factors, which have previously been reported to positively regulate somatic embryogenesis within the gene regulatory network. Collectively, this work overcomes the technical bottleneck associated with multiple subcultures of GT1 callus tissue and provides a multi-omics framework for identifying the precise genetic targets to facilitate SE in chilling-tolerant rubber tree breeding.