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.

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.

Ammopiptanthus mongolicus is an ancient remnant species from the Mediterranean displaying characteristics such as high-temperature tolerance, drought resistance, cold resistance, and adaptability to impoverished soil. In the case of high-temperature tolerance, heat shock transcription factors (HSFs) are integral transcriptional regulatory proteins exerting a critical role in cellular processes. Despite extensive research on the HSF family across various species, there has been no analysis specifically focused on A. mongolicus. In this study, we identified 24 members of the AmHSF gene family based on the genome database of A. mongolicus, which were unevenly distributed over 9 chromosomes. Phylogenetic analysis showed that these 24 members can be categorized into 5 primary classes consisting of a total of 13 subgroups. Analysis of the physical and chemical properties revealed significant diversity among these proteins. With the exception of the AmHSFB3 protein, which is localized in the cytoplasm, all other AmHSF proteins were found to be situated in the nucleus. Comparison of amino acid sequences revealed that all AmHSF proteins contain a conserved DNA-binding domains structure, and the DNA-binding domains and oligomerization domains of the AmHSF gene exhibit conservation with counterparts across diverse species; we investigated the collinearity of AmHSF genes in relation to those of three other representative species. Through GO enrichment analysis, evidence emerged that AmHSF genes are involved in heat stress responses and may be involved in multiple transcriptional regulatory pathways that coordinate plant growth and stress responses. Finally, through a comprehensive analysis using transcriptome data, we examined the expression levels of 24 AmHSFs under 45 °C. The results revealed significant differences in the expression profiles of AmHSFs at different time intervals during exposure to high temperatures, highlighting their crucial role in responding to heat stress. In summary, these results provide a better understanding of the role and regulatory mechanisms of HSF in the heat stress response of A. mongolicus, meanwhile also establishing a foundation for further exploration of the biological functions of AmHSF in the adversity response of A. mongolicus.

Based on the single nucleotide polymorphism (SNP) markers developed by whole genome resequencing (WGRS), the relationship and population genetic structure of 53 common apricot (P. armeniaca) varieties were analyzed to provide a theoretical basis for revealing the phylogenetic relationship and classification of the common apricot. WGRS was performed on 53 common apricot varieties, and high-quality SNP sites were obtained after alignment with the “Yinxiangbai” apricot genome as a reference. Phylogenetic analysis, G matrix analysis, principal component analysis, and population structure analysis were performed using Genome-wide Complex Trait Analysis (GCTA), FastTree, Admixture, and other software. The average comparison ratio between the sequencing results and the reference genome was 97.66%. After strict screening, 88,332,238 high-quality SNP sites were finally obtained. Based on the statistical SNP variation type, it was found that LNLJX had the largest number of variations (3,951,322) and the lowest base transition/base transversion ratio (ts/tv = 1.77), indicating that its gene exchange events occurred less frequently. Based on the SNP point estimation of the relationship and genetic distance between samples, the relationship between species was 1.41–0.01, among which PLDJX and BK1 had the closest relationship of 1.41, and YZH and LGWSX had the farthest relationship of 0.01. The genetic distance between species was 0.00367–0.264344, the genetic distance between HMX and JM was the closest, and the genetic distance between WYX and YX was the farthest, which was the largest. Phylogenetic tree, PCA, and genetic structure analysis results all divided 53 common apricot varieties into four groups, and the classification results were consistent. The SNP markers mined using WGRS technology are useful not only to analyze the variation of common apricots, but also to effectively identify their kinship and genetic structure, which plays a critical role in the classification and utilization of common apricot germplasm resources.

MicroRNAs (miRNAs) play essential roles in regulating various development processes in plants. However, their role in regulating rubber biosynthesis in Eucommia ulmoides is largely unknown. Rubber is mainly distributed in the tissue covering the seed (GZ) rather than the periphery (GB) of the pericarp of E. ulmoides during accumulation in May. To investigate the roles of miRNAs in rubber biosynthesis, we conducted high-throughput small RNA sequencing using GZ and GB collected on 11 May (rapid accumulation) and 11 June (reduced accumulation). In total, 12 and 25 miRNAs were either up- or downregulated in GZ in May (GZ511) compared to GB (GB511) in May, while 27 and 38 miRNAs were either up- or downregulated in GZ in May compared to GZ in June (GZ611), respectively. Functional analyses of differentially expressed (DE−) genes targeted by DE-miRNAs revealed that miRNAs may regulate genes involved in rubber biosynthesis. For instance, when Eu-miR45 expression declined, the expression of its predicted target, small rubber particle protein 1 (EuSRPP1), increased in GZ511 vs. GB511 and GZ511 vs. GZ611, possibly resulting in higher rubber accumulation in GZ511. Additionally, we identified potential lncRNA−miRNA−mRNA networks in rubber biosynthesis. Overall, these results indicate that miRNAs play pivotal roles in regulating rubber biosynthesis via miRNA-target gene pairs and lncRNA−miRNA−mRNA networks in E. ulmoides. Our findings will enhance research on the mechanisms of rubber biosynthesis in plants.