4-Coumarate: coenzyme A ligase (4CL) is an important rate-limiting enzyme in phenylpropanoid metabolism that plays an important role in the biosynthesis of phenylpropanoid, flavonoid, lignin and other secondary metabolites in plants. However, the family members and functions have not been identified in Eucommia ulmoides (E. ulmoides). In this study, 35 Eu4CLs were identified in the E. ulmoides genome, and the gene structure, conserved domain, evolutionary relationship and expression pattern were comprehensively analyzed. The results show that 35 Eu4CLs were assembled into three subgroups according to the classification in Arabidopsis, where Eu4CLs in the same subgroup had similar gene structures and conserved protein motifs. Putative cis-element analysis of Eu4CL promoter regions uncovered numerous elements related to the response of stress and plant hormones. Expression patterns showed that Eu4CL4/5/13/34 expression levels were positively related to chlorogenic acid content in different periods, which indicate that the synthesis of chlorogenic acid in E. ulmoides was regulated by multiple genes, and the genes regulating the synthesis of chlorogenic acid in different tissues were different. In addition, nine selected Eu4CL genes showed different expression patterns under cold, WeJA (methyl jasmonate), and ethylene by quantitative reverse transcription-PCR (qRT-PCR) assay, suggesting that Eu4CL genes not only play an important role in the synthesis of chlorogenic acid, but also plays an important role in the process of biotic and abiotic stress. Taken together, these findings provide theoretical reference for further exploring the molecular characteristics and biological functions of Eu4CL genes.

As a primary approach to nutrient propagation for many woody plants, cutting roots is essential for the breeding and production of Eucommia ulmoides Oliver. In this study, hormone level, transcriptomics, and metabolomics analyses were performed on two E. ulmoides varieties with different adventitious root (AR) formation abilities. The higher JA level on the 0th day and the lower JA level on the 18th day promoted superior AR development. Several hub genes executed crucial roles in the crosstalk regulation of JA and other hormones, including F-box protein (EU012075), SAUR-like protein (EU0125382), LOB protein (EU0124232), AP2/ERF transcription factor (EU0128499), and CYP450 protein (EU0127354). Differentially expressed genes (DEGs) and metabolites of AR formation were enriched in phenylpropanoid biosynthesis, flavonoid biosynthesis, and isoflavonoid biosynthesis pathways. The up-regulated expression of PAL, CCR, CAD, DFR, and HIDH genes on the 18th day could contribute to AR formation. The 130 cis-acting lncRNAs had potential regulatory functions on hub genes in the module that significantly correlated with JA and DEGs in three metabolism pathways. These revealed key molecules, and vital pathways provided more comprehensive insight for the AR formation mechanism of E. ulmoides and other plants.

Fruits of 240 Eucommia ulmoides Oliver individuals were collected from 12 different geographical regions across a wide area of China. The seed oil content ranged from 28.54% in Guilin and Lueyang to 31.35% in Chaoyang. Gas chromatography–mass spectrometry analysis of the seed oil revealed that linolenic acid (56.68–60.70%), oleic acid (16.31–17.80%), and linoleic acid (11.02–13.32%) were the major components, and the oil showed good potential for the food and health care industries. Three levels (high, medium, and low) of linolenic acid and oil content were observed among the 12 populations according to principal component analysis. Canonical correspondence analysis showed that environmental factors had a large influence on oil content and fatty acids composition and explained 89.33% of the total variance. Latitude and precipitation were key environmental factors and were significantly correlated with the fatty acid composition of E. ulmoides seeds.

Eucommia ulmoides Oliv. (2n = 34), native to China and of a monotypic family and genus, is a multipurpose tree species with high economic, ecological, and social benefits. In this study, an F₁ population of 109 progenies and tow parents were used to construct the first high-density genetic map of E. ulmoides via genotyping-by-sequencing (GBS) with single-nucleotide polymorphism (SNP) markers. A total of 191,095 SNPs were obtained, among which the available markers in F₁ population were types “hkxhk,” “nnxnp,” and “lmxll” and the three polymorphic markers 35,699, 65,800, and 68,022, respectively. Finally, the map comprised 10,103 SNP markers distributed on 17 linkage groups (LGs) that were consisted with the chromosome haploid number in E. ulmoides (n = 17). The interval genetic map covered 90% of the E. ulmoides genomes, with total genetic distance of 4051.11 cM and average distance between markers of 0.45 cM. The length of LGs varied from 70.42 to 495.49 cM, with the mean size of 238.3 cM. On the other hand, 44 QTLs associated with growth traits were detected on LG02, LG06, LG07, LG08, and LG10, with phenotypical variance ranging from 10.0% to 14.2%. A total of 33 candidate genes were identified, and most of them were related to energy storage, signal transmission, hormones, and metabolic pathways. This study could provide a solid foundation for chromosome assembly and refinement, and the localization of growth-trait QTLs will advance the investigation of forestry breeding efforts in E. ulmoides.

Eucommia ulmoides (E. ulmoides) is a significant national strategic resource in China. It is a natural high quality rubber resource, with great development potential. We found large differences in rooting ability during adventitious root (AR) formation in two E. ulmoides improved varieties. Therefore, we used two improved varieties of E. ulmoides, ‘Huazhong 6’ (H6, with rooting rate 85.3%) and ‘Huazhong 8’ (H8, with rooting rate 22.5%) to explore the cutting rooting mechanism. In this study, we mainly determined the morphological development process of E. ulmoides cutting rooting, and compared the rooting-related indexes of the two improved varieties, and the changes in physiological indexes closely related to rooting, which include endogenous hormones, oxidases and nutrients in the phloem of the basal stem. The results showed that indole–3–acetic acid (IAA), zeatin riboside (ZR), IAA/ZR and indoleacetic acid oxidase (IAAO) were the key factors that caused big differences in rooting ability between the two E. ulmoides improved varieties. The increase in endogenous hormone IAA content and IAA/ZR value were necessary for the formation of AR. The increase in IAA content was beneficial to AR formation. The activity of IAAO was significantly negatively correlated with the rooting ability of the E. ulmoides cuttings. The high IAAO activity of the H8 cuttings led to the consumption of IAA. Although the content of IAA increased, the rooting conditions were not reached. The accumulation of nutrients before rooting also has an important effect on rooting; it is easy for cuttings to root when the carbon–nitrogen ratio (C/N) value is high. This research provides an improved understanding of the cellular and physiological underpinnings of the AR process in woody plants. In addition, it provides a theoretical basis and foundation for subsequent research on E. ulmoides cuttage technology.

Studies in multiple species have shown that phospholipid:diacylglycerol acyltransferase (PDAT) and oil bodies are important factors affecting plant oil accumulation. However, little information is available about the PDAT genes and oil bodies in Eucommia ulmoides Oliv. a high-quality oil tree. In this study, the oil bodies in Eucommia ulmoides seeds at different developmental stages were observed by frozen section technology combined with Nile red staining. It was found that there was a significant positive correlation between oil content and oil body number. In addition, seven Eucommia ulmoides PDAT (EuPDAT) genes were cloned from Eucommia ulmoides seeds based on genome data. They were assembled into three subgroups according to their classifications in Arabidopsis. EuPDAT genes in the same subgroup had similar gene structures and conserved motifs. Putative cis-element analysis of EuPDAT gene promoter regions uncovered numerous elements related to stress and plant hormones response. The expression patterns showed that EuPDAT2 and EuPDAT7 expression levels were positively related to oil content in different periods, and the correlation coefficients were 0.78 and 0.91, respectively. Our results suggest that oil body number and EuPDAT genes are important factors affecting oil accumulation in E. ulmoides seeds, and this work provides a theoretical reference for the directional cultivation of new high-oil-content E. ulmoides varieties.