{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T11:09:54Z","timestamp":1790248194186,"version":"4.1.0"},"reference-count":58,"publisher":"MDPI AG","issue":"19","license":[{"start":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T00:00:00Z","timestamp":1790208000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Hainan Provincial Natural Science Foundation of China","award":["326QN0765"],"award-info":[{"award-number":["326QN0765"]}]},{"name":"State Key Laboratory of Tropical Crop Breeding","award":["SKLTCBGJ202502"],"award-info":[{"award-number":["SKLTCBGJ202502"]}]},{"name":"Central Public-interest Scientific Institution Basal Research Fund","award":["1630022024028"],"award-info":[{"award-number":["1630022024028"]}]},{"name":"Innovational Fund for Scientific and Technological Personnel of Hainan Province","award":["KJRC2025A04-02"],"award-info":[{"award-number":["KJRC2025A04-02"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Plants"],"abstract":"<jats:p>The rubber tree (Hevea brasiliensis (Willd. ex A. Juss.) M\u00fcll. 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.<\/jats:p>","DOI":"10.3390\/plants15192924","type":"journal-article","created":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T10:16:28Z","timestamp":1790244988000},"page":"2924","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Optimized Callus Subculture and Multi-Omics Analysis Reveal Somatic Embryogenesis Bottlenecks in the Cold-Resistant Rubber Tree Clone GT1"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1694-3869","authenticated-orcid":false,"given":"Chenrui","family":"Gu","sequence":"first","affiliation":[{"name":"State Key Laboratory of Tropical Crop Breeding, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Key Laboratory for Cultivation & Physiology of Tropical Crops of Hainan Province, State Key Laboratory Incubation Base for Cultivation & Physiology of Tropical Crops, Haikou Innovative Key Laboratory for Tropical Crop Seedlings, Haikou 571101, China"},{"name":"Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"}]},{"given":"Xinran","family":"Ou","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Tropical Crop Breeding, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Key Laboratory for Cultivation & Physiology of Tropical Crops of Hainan Province, State Key Laboratory Incubation Base for Cultivation & Physiology of Tropical Crops, Haikou Innovative Key Laboratory for Tropical Crop Seedlings, Haikou 571101, China"},{"name":"Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China"},{"name":"School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1526-3607","authenticated-orcid":false,"given":"Xianfeng","family":"Yang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Tropical Crop Breeding, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Key Laboratory for Cultivation & Physiology of Tropical Crops of Hainan Province, State Key Laboratory Incubation Base for Cultivation & Physiology of Tropical Crops, Haikou Innovative Key Laboratory for Tropical Crop Seedlings, Haikou 571101, China"},{"name":"Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"investigation","vocabulary":"credit"}]},{"given":"Xiaochuan","family":"Gu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Tropical Crop Breeding, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Key Laboratory for Cultivation & Physiology of Tropical Crops of Hainan Province, State Key Laboratory Incubation Base for Cultivation & Physiology of Tropical Crops, Haikou Innovative Key Laboratory for Tropical Crop Seedlings, Haikou 571101, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"validation","vocabulary":"credit"}]},{"given":"Quannan","family":"Zhou","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Tropical Crop Breeding, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Key Laboratory for Cultivation & Physiology of Tropical Crops of Hainan Province, State Key Laboratory Incubation Base for Cultivation & Physiology of Tropical Crops, Haikou Innovative Key Laboratory for Tropical Crop Seedlings, Haikou 571101, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"validation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-7121-605X","authenticated-orcid":false,"given":"Jing","family":"Cheng","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Tropical Crop Breeding, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Key Laboratory for Cultivation & Physiology of Tropical Crops of Hainan Province, State Key Laboratory Incubation Base for Cultivation & Physiology of Tropical Crops, Haikou Innovative Key Laboratory for Tropical Crop Seedlings, Haikou 571101, China"},{"name":"Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China"},{"name":"School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"project-administration","vocabulary":"credit"}]},{"given":"Shichao","family":"Xin","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Tropical Crop Breeding, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Key Laboratory for Cultivation & Physiology of Tropical Crops of Hainan Province, State Key Laboratory Incubation Base for Cultivation & Physiology of Tropical Crops, Haikou Innovative Key Laboratory for Tropical Crop Seedlings, Haikou 571101, China"},{"name":"Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Ji","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Tropical Crop Breeding, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Key Laboratory for Cultivation & Physiology of Tropical Crops of Hainan Province, State Key Laboratory Incubation Base for Cultivation & Physiology of Tropical Crops, Haikou Innovative Key Laboratory for Tropical Crop Seedlings, Haikou 571101, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"investigation","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-0754-4841","authenticated-orcid":false,"given":"Tiandai","family":"Huang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Tropical Crop Breeding, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Key Laboratory for Cultivation & Physiology of Tropical Crops of Hainan Province, State Key Laboratory Incubation Base for Cultivation & Physiology of Tropical Crops, Haikou Innovative Key Laboratory for Tropical Crop Seedlings, Haikou 571101, China"},{"name":"Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,24]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1016\/j.molp.2019.10.017","article-title":"The Chromosome-Based Rubber Tree Genome Provides New Insights into Spurge Genome Evolution and Rubber Biosynthesis","volume":"13","author":"Liu","year":"2020","journal-title":"Mol. 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