Genetic diversity and relationships among Chinese Eucommia ulmoides cultivars revealed by sequence-related amplified polymorphism, amplified fragment length polymorphism, and inter-simple sequence repeat markers

Li, Y.; Wang, S.H.; Li, Z.Q.; Jin, Cangfu; Liu, M.H.

doi:10.4238/2014.october.27.11

Cited by 4 publications

(4 citation statements)

References 19 publications

(30 reference statements)

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“…The PCR conditions were: initial denaturation at 94 °C for 4 min, followed by 30 cycles of 1 min at 94 °C, 50 s at 52 to 60 °C (depending on the T m of the primer pair used), and 1 min at 72 °C; then a final extension for 7 min at 72 °C. The resulting PCR products were subjected to electrophoresis on 12% non-denaturing polyacrylamide gels at 250 V for 2–2.5 h and stained using a silver-staining protocol 50 . Cluster analysis was conducted and displayed using the neighbor-joining algorithm and STRUCTURE analysis as implemented in MEGA ver.…”

Section: Methodsmentioning

confidence: 99%

De novo transcriptome assembly of Zanthoxylum bungeanum using Illumina sequencing for evolutionary analysis and simple sequence repeat marker development

Feng

Zhao

Liu

et al. 2017

Sci Rep

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Zanthoxylum, an ancient economic crop in Asia, has a satisfying aromatic taste and immense medicinal values. A lack of genomic information and genetic markers has limited the evolutionary analysis and genetic improvement of Zanthoxylum species and their close relatives. To better understand the evolution, domestication, and divergence of Zanthoxylum, we present a de novo transcriptome analysis of an elite cultivar of Z. bungeanum using Illumina sequencing; we then developed simple sequence repeat markers for identification of Zanthoxylum. In total, we predicted 45,057 unigenes and 22,212 protein coding sequences, approximately 90% of which showed significant similarities to known proteins in databases. Phylogenetic analysis indicated that Zanthoxylum is relatively recent and estimated to have diverged from Citrus ca. 36.5–37.7 million years ago. We also detected a whole-genome duplication event in Zanthoxylum that occurred 14 million years ago. We found no protein coding sequences that were significantly under positive selection by Ka/Ks. Simple sequence repeat analysis divided 31 Zanthoxylum cultivars and landraces into three major groups. This Zanthoxylum reference transcriptome provides crucial information for the evolutionary study of the Zanthoxylum genus and the Rutaceae family, and facilitates the establishment of more effective Zanthoxylum breeding programs.

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Section: Methodsmentioning

confidence: 99%

De novo transcriptome assembly of Zanthoxylum bungeanum using Illumina sequencing for evolutionary analysis and simple sequence repeat marker development

Feng

Zhao

Liu

et al. 2017

Sci Rep

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“…The two selected clones were authorized cultivars; they were selected from 40 clones from all over China (Zhang et al, 2004). The seven hybrid clones were selected from the hybrid offspring of superior varieties (Li et al, 2014b) in China according to secondary metabolite content and growth traits. The nine clones were grafted with the same 1-year-old E. ulmoides clones on the trunk near the root.…”

Section: Materials and Experimental Designmentioning

confidence: 99%

Phenotypic Trait Subdivision Provides New Sight Into the Directional Improvement of Eucommia ulmoides Oliver

Deng

Hu²,

et al. 2022

Front. Plant Sci.

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Eucommia ulmoides Oliver has been used extensively in many fields. To satisfy increasing demand, great efforts must be made to further improve its traits. However, limited information is available on these traits, which is a factor that restricts their improvement. To improve traits directionally, nine clones were assigned to six sites to analyze the effect of different variation sources (the genotype, site, and genotype × environment interaction) on the phenotypic trait. In addition, a mixed linear model was used to assess the contribution of variations. In general, for most traits, the site effect accounted for a larger proportion of the variance, followed by the genotype and genotype × environment interaction effects. All the studied genotypes and sites had a significant effect, indicating that they could be improved by selecting preferable genotypes or cultivation areas, respectively. Interestingly, growth traits or economic traits could be improved simultaneously. Trait performance and stability are necessary when selecting genotypes. Moreover, the discriminating ability of genotypes should be considered in selecting cultivation areas. Annual mean temperature and annual sunshine duration proved to be crucial factors that affected the traits. They were correlated positively with economic traits and leaf yield and correlated negatively with growth traits. These findings contributed to selecting a wider range of cultivation areas. Regarding the genotype × environment interaction effect, there were significant differences only in the gutta-percha content, the total number of leaves, and the chlorogenic acid content. These traits could also be improved by choosing appropriate genotypes for the local environment. The research has provided preliminary data on the main factors that affect the traits of E. ulmoides and offered solutions for trait improvement. This information could be a reference for the trait improvement of other plants.

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“…Among these, 56 AFM trees comprised 15 EUO cultivars and 41 superior individuals. The 15 EUO cultivars were selected from different areas of China [43], and the 41 superior individuals were selected from the F1 generation of cross breeding of the superior cultivars according to the tree height and ground diameter. Forty-four in 56 of AFM trees and "Qinzhong NO.…”

Section: Plant Materialsmentioning

confidence: 99%

Trait Variations and Probability Grading Index System on Leaf-Related Traits of Eucommia ulmoides Oliver Germplasm

Deng

Xie

Long

et al. 2021

Plants

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Eucommia ulmoides Oliver (EUO), an economic tree grown specifically in China, is widely used in various fields. To satisfy the requirements of industrial development, superior varieties need to be selected for different uses. However, there is no unified standard for breeders to reference. In this study, leaf-related traits were classified by a probability grading method. The results indicated there were significant differences between different planting models for the studied traits, and the traits in the Arbor forest model showed more abundant variation. Compared with genotype, the planting model accounted for relatively bigger variance, indicating that the standard should be divided according to planting models. Furthermore, the optimum planting model for different traits would be obtained by analyzing the variation range. Association analyses were conducted among traits to select the crucial evaluation indexes. The indexes were divided into three grades in different planting models. The evaluation system on leaf-related traits of EUO germplasm was established preliminarily, which considered planting models and stability across years for the first time. It can be treated as a reference to identify and evaluate EUO germplasm resources. Additionally, the study served as an example for the classification of quantitative traits in other economically important perennial plants.

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Genetic diversity and relationships among Chinese Eucommia ulmoides cultivars revealed by sequence-related amplified polymorphism, amplified fragment length polymorphism, and inter-simple sequence repeat markers

Cited by 4 publications

References 19 publications

De novo transcriptome assembly of Zanthoxylum bungeanum using Illumina sequencing for evolutionary analysis and simple sequence repeat marker development

De novo transcriptome assembly of Zanthoxylum bungeanum using Illumina sequencing for evolutionary analysis and simple sequence repeat marker development

Phenotypic Trait Subdivision Provides New Sight Into the Directional Improvement of Eucommia ulmoides Oliver

Trait Variations and Probability Grading Index System on Leaf-Related Traits of Eucommia ulmoides Oliver Germplasm

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