A research team has uncovered a possible epigenetic mechanism that enables the elite 'Shuxinyou' (SXY) cultivar of Aquilaria sinensis to produce agarwood more efficiently than ordinary 'Baimu' (BM). Following controlled wounding, SXY accumulated almost four times as much alcohol-soluble resin extract as BM and showed stronger activation of terpenoid biosynthesis. The findings suggest that pre-existing chromatin accessibility may prepare important metabolic genes for rapid activation after injury. This insight could support molecular screening for high-yielding cultivars and contribute to more efficient, quality-conscious agarwood production.
Agarwood is a valuable aromatic resin formed by Aquilaria trees in response to physical injury, microbial infection, or other stresses. Artificial induction methods and high-yielding cultivars have been developed to meet increasing commercial demand, but many productive cultivars generate resin that differs chemically from traditional medicinal agarwood and may lack agarotetrol, an important diagnostic compound. SXY is unusual because it combines high resin production with an agarotetrol-containing chemical profile resembling traditional agarwood. However, SXY and ordinary cultivars display little genetic differentiation, leaving the molecular basis of its superior performance unclear and raising the possibility that regulatory mechanisms beyond DNA sequence determine its productivity.
A study (DOI: 10.48130/tp-0026-0028 ) published in Tropical Plants on 19 June 2026 by Yinglang Wan's team, Hainan University, reports that broader baseline chromatin accessibility in SXY is associated with stronger injury-induced activation of terpenoid genes and substantially greater resin accumulation.
To control environmental and developmental variation, the researchers grafted SXY scions onto one-year-old BM rootstocks and maintained the plants under identical nursery conditions for six months. Comparable BM and SXY branches were wounded using four mechanically drilled holes without chemical injection. Samples were collected before treatment and at 15 and 30 days after injury. After 30 days, SXY branches displayed darker resinous zones and contained 13.2% alcohol-soluble extractives, compared with 3.6% in BM. Chemical analysis also confirmed the agarotetrol-associated profile of traditional agarwood in SXY extracts. The team then combined an assay for transposase-accessible chromatin using sequencing (ATAC-seq) with RNA sequencing (RNA-seq). ATAC-seq characterized chromatin accessibility before wounding, while RNA-seq measured gene-expression responses after injury. SXY contained 71,680 accessible chromatin peaks, substantially more than the 51,489 detected in BM. Its accessible regions were also more concentrated around gene promoters, accounting for 31.4% of peaks versus 26.8% in BM. Researchers identified 5,355 genes associated with SXY-specific accessibility, compared with 1,523 in BM. Transcriptome analysis revealed that BM mounted a broad response involving 2,653 differentially expressed genes, whereas SXY showed a narrower response of 1,779 genes that was more strongly directed toward sesquiterpenoid biosynthesis and secondary metabolism. Integrating the two datasets showed that SXY-specific accessible regions were frequently linked to genes that became more active after injury. Key terpenoid-pathway genes, including DXS, IDI, HMGS, and AsTPS1, exhibited cultivar-biased activation. In particular, an accessible peak at the AsTPS1 promoter was prominent in SXY but largely absent in BM and accompanied a more positive transcriptional response. Motif enrichment and regulatory-network analyses further identified BHLH137 and HYH as candidate transcription factors potentially connecting accessible promoters with terpenoid production.
Overall, the study presents a candidate epigenetic-priming model in which SXY's more open chromatin landscape may place resin-producing genes in a state of heightened readiness before injury occurs. Once wounded, the cultivar can therefore direct its transcriptional response more efficiently toward terpenoid biosynthesis and agarwood formation. The proposed regulators and chromatin signatures could eventually serve as markers for cultivar selection or targets for crop improvement. However, because baseline ATAC-seq used only one library per cultivar, the accessibility differences remain descriptive rather than definitive proof of causality. Replicated, time-resolved chromatin studies and functional validation of BHLH137, HYH, and their predicted targets will be needed to confirm the mechanism.
