Genetic diversity and population structure of Eucommia ulmoides Oliver, an endangered medicinal plant in China

Yu, Jing; Wang, Y; Peng, Liang; Ru, Mei; Liang-gang, Zong

doi:10.4238/2015.march.30.5

Cited by 7 publications

(5 citation statements)

References 29 publications

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“…The genetic markers of SSR, AFLP and SRAP have been developed and used for the population genetics studies of E. ulmoides [ 18 , 20 , 21 ]. However, the above fingerprinting markers [ 23 , 24 ] may provide insufficient genetic information to resolve the population structure and history of E. ulmoides . The relationships among natural and cultivated populations of E. ulmoides are elusive at present [ 18 , 24 ].…”

Section: Discussionmentioning

confidence: 99%

“…However, the above fingerprinting markers [ 23 , 24 ] may provide insufficient genetic information to resolve the population structure and history of E. ulmoides . The relationships among natural and cultivated populations of E. ulmoides are elusive at present [ 18 , 24 ]. SNP markers are ample in plant cp genomes, making them useful candidates for population genetics studies.…”

Section: Discussionmentioning

confidence: 99%

“…Amplified fragment length polymorphism (AFLP) and sequence-related amplified polymorphism (SRAP) have been used to construct genetic maps of E. ulmoides [ 20 , 21 ]. The genetic markers of random amplified polymorphic DNA (RAPD), chloroplast microsatellite (cpSSR) and inter-simple sequence repeat (ISSR) have also been uncovered [ 22 , 23 , 24 ]. Nevertheless, the variability of these developed fingerprinting markers in E. ulmoides is relatively low, with limited population genetics information.…”

Section: Introductionmentioning

confidence: 99%

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Whole-Genome Comparison Reveals Heterogeneous Divergence and Mutation Hotspots in Chloroplast Genome of Eucommia ulmoides Oliver

Wang

Chen

Zhang

2018

IJMS

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Eucommia ulmoides (E. ulmoides), the sole species of Eucommiaceae with high importance of medicinal and industrial values, is a Tertiary relic plant that is endemic to China. However, the population genetics study of E. ulmoides lags far behind largely due to the scarcity of genomic data. In this study, one complete chloroplast (cp) genome of E. ulmoides was generated via the genome skimming approach and compared to another available E. ulmoides cp genome comprehensively at the genome scale. We found that the structure of the cp genome in E. ulmoides was highly consistent with genome size variation which might result from DNA repeat variations in the two E. ulmoides cp genomes. Heterogeneous sequence divergence patterns were revealed in different regions of the E. ulmoides cp genomes, with most (59 out of 75) of the detected SNPs (single nucleotide polymorphisms) located in the gene regions, whereas most (50 out of 80) of the indels (insertions/deletions) were distributed in the intergenic spacers. In addition, we also found that all the 40 putative coding-region-located SNPs were synonymous mutations. A total of 71 polymorphic cpDNA fragments were further identified, among which 20 loci were selected as potential molecular markers for subsequent population genetics studies of E. ulmoides. Moreover, eight polymorphic cpSSR loci were also developed. The sister relationship between E. ulmoides and Aucuba japonica in Garryales was also confirmed based on the cp phylogenomic analyses. Overall, this study will shed new light on the conservation genomics of this endangered plant in the future.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Whole-Genome Comparison Reveals Heterogeneous Divergence and Mutation Hotspots in Chloroplast Genome of Eucommia ulmoides Oliver

Wang

Chen

Zhang

2018

IJMS

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“…In total 119,411 putative SNPs were detected in the gene regions with an average of one SNP per 980 bp, showing more than five folds higher of density than in the rubber tree ( H. brasiliensis ) gene regions (one SNP per 5.2 kb) [ 74 ]. The dioecious sexual system of E. ulmoides may be one of the factors contributing to the high level of its genetic diversity [ 73 , 75 ]. Furthermore, the plentiful SNP markers detected here could use to construct finer genetic maps of E. ulmoides compared to the previously published ones [ 76 , 77 ] to improve the molecular breeding process of E. ulmoides .…”

Section: Discussionmentioning

confidence: 99%

Identification of the Sex-Biased Gene Expression and Putative Sex-Associated Genes in Eucommia ulmoides Oliver Using Comparative Transcriptome Analyses

Wang

Zhang

2017

Molecules

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Eucommia ulmoides is a model representative of the dioecious plants with sex differentiation at initiation. Nevertheless, the genetic mechanisms of sexual dimorphism and sex determination in E. ulmoides remain poorly understood. In this study de novo transcriptome sequencing on Illumina platform generated >45 billion high-quality bases from fresh leaves of six male and female individuals of E. ulmoides. A total of 148,595 unigenes with an average length of 801 base-pairs (bp) were assembled. Through comparative transcriptome analyses, 116 differentially expressed genes (DEGs) between the males and the females were detected, including 73 male-biased genes and 43 female-biased genes. Of these DEGs, three female-biased genes were annotated to be related with the sexually dimorphic gutta content in E. ulmoides. One male-biased DEG was identified as putative MADS box gene APETALA3, a B class floral organ identity gene in the flowering plants. SNPs calling analyses further confirmed that the APETALA3-like gene was probably involved in the sex determination in E. ulmoides. Four other male-biased DEGs were potential sex-associated genes as well with segregated SNPs in accord with sex type. In addition, the SNPs density was 1.02 per kilobase (kb) in the expressed genes of E. ulmoides, implying a relatively high genetic diversity.

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“…E. ulmoides was a monotypic species of Eucommiaceae. Germplasm genetic diversity of E. ulmoides had been evaluated by morphological traits, major active metabolites, and a number of molecular markers from RAPD to SNP ( Wu et al., 2011 ; Yao et al., 2012 ; Yu et al., 2015 ; Du et al., 2017 ; Liu et al., 2022 ). Most results tended to believe that the genetic diversity of E. ulmoides at the intra-population level was higher than at the inter-population level, and its genetic distance was not evidently correlated to geographical distribution.…”

Section: Introductionmentioning

confidence: 99%

Analysis of chemotypes and their markers in leaves of core collections of Eucommia ulmoides using metabolomics

Meng

Du²,

Du³

et al. 2023

Front. Plant Sci.

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The leaves of Eucommia ulmoides contain various active compunds and nutritional components, and have successively been included as raw materials in the Chinese Pharmacopoeia, the Health Food Raw Material Catalogue, and the Feed Raw Material Catalogue. Core collections of E. ulmoides had been constructed from the conserved germplasm resources basing on molecular markers and morphological traits, however, the metabolite diversity and variation in this core population were little understood. Metabolite profiles of E. ulmoides leaves of 193 core collections were comprehensively characterized by GC-MS and LC-MS/MS based non-targeted metabolomics in present study. Totally 1,100 metabolites were identified and that belonged to 18 categories, and contained 120 active ingredients for traditional Chinese medicine (TCM) and 85 disease-resistant metabolites. Four leaf chemotypes of the core collections were established by integrated uses of unsupervised self-organizing map (SOM), supervised orthogonal partial least squares discriminant analysis (OPLS-DA) and random forest (RF) statistical methods, 30, 23, 43, and 23 chemomarkers were screened corresponding to the four chemotypes, respectively. The morphological markers for the chemotypes were obtained by weighted gene co-expression network analysis (WGCNA) between the chenomarkers and the morphological traits, with leaf length (LL), chlorophyll reference value (CRV), leaf dentate height (LDH), and leaf thickness (LT) corresponding to chemotypes I, II, III, and IV, respectively. Contents of quercetin-3-O-pentosidine, isoquercitrin were closely correlated to LL, leaf area (LA), and leaf perimeter (LP), suggesting the quercetin derivatives might influence the growth and development of E. ulmoides leaf shape.

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Genetic diversity and population structure of Eucommia ulmoides Oliver, an endangered medicinal plant in China

Cited by 7 publications

References 29 publications

Whole-Genome Comparison Reveals Heterogeneous Divergence and Mutation Hotspots in Chloroplast Genome of Eucommia ulmoides Oliver

Whole-Genome Comparison Reveals Heterogeneous Divergence and Mutation Hotspots in Chloroplast Genome of Eucommia ulmoides Oliver

Identification of the Sex-Biased Gene Expression and Putative Sex-Associated Genes in Eucommia ulmoides Oliver Using Comparative Transcriptome Analyses

Analysis of chemotypes and their markers in leaves of core collections of Eucommia ulmoides using metabolomics

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