Movatterモバイル変換

[0]ホーム
URL:

Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
Thehttps:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

NIH NLM Logo
Log inShow account info
Access keysNCBI HomepageMyNCBI HomepageMain ContentMain Navigation
pubmed logo
Advanced Clipboard
User Guide

Full text links

Nature Publishing Group full text link Nature Publishing Group Free PMC article
Full text links

Actions

Share

.2019 Feb 13;9(1):1915.
doi: 10.1038/s41598-019-38532-8.

Taraxacum kok-saghyz (rubber dandelion) genomic microsatellite loci reveal modest genetic diversity and cross-amplify broadly to related species

Affiliations

Taraxacum kok-saghyz (rubber dandelion) genomic microsatellite loci reveal modest genetic diversity and cross-amplify broadly to related species

Marcin Nowicki et al. Sci Rep..

Abstract

Taraxacum kok-saghyz (TKS) carries great potential as alternative natural rubber source. To better inform future breeding efforts with TKS and gain a deeper understanding of its genetic diversity, we utilized de novo sequencing to generate novel genomic simple sequence repeats markers (gSSRs). We utilized 25 gSSRs on a collection of genomic DNA (gDNA) samples from germplasm bank, and two gDNA samples from historical herbarium specimens. PCR coupled with capillary electrophoresis and an array of population genetics tools were employed to analyze the dataset of our study as well as a dataset of the recently published genic SSRs (eSSRs) generated on the same germplasm. Our results using both gSSRs and eSSRs revealed that TKS has low- to- moderate genetic diversity with most of it partitioned to the individuals and individuals within populations, whereas the species lacked population structure. Nineteen of the 25 gSSR markers cross-amplified to other Taraxacum spp. collected from Southeastern United States and identified as T. officinale by ITS sequencing. We used a subset of 14 gSSRs to estimate the genetic diversity of the T. officinale gDNA collection. In contrast to the obligatory outcrossing TKS, T. officinale presented evidence for population structure and clonal reproduction, which agreed with the species biology. We mapped the molecular markers sequences from this study and several others to the well-annotated sunflower genome. Our gSSRs present a functional tool for the biodiversity analyses in Taraxacum, but also in the related genera, as well as in the closely related tribes of the Asteraceae.

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Schematic map ofTaraxacum kok-saghyz (TKS) markers on theHelianthus annuus genome. Sequences of the markers were retrieved by searching the TKS genome contigs, and ~1 kb sequences containing the markers of Ariaset al., McAsseyet al. and ourde novo gSSRs were used to search the sunflower genome using their BLAST algorithm. Physical positions of the best hits, occasionally located to several positions of the sunflower genome with comparable reliability, are shown. Markers used to generate the TKS linkage map are black on white plates with their original linkage groups (LG) markings; eSSRs of McAsseyet al. are black on red plates; ourde novo gSSRs are gray on orange plates. TheH.annuus chromosomes are numbered on top with their respective sizes [Mbp] indicated. Scale on the left ticks every 20 Mbp.
Figure 2
Figure 2
Taraxacum spp. genetic diversity. Neighbor-joining tree of genetic distances, between theT.kok-saghyz (TKS) populations used in this study captured with gSSRs (left panel), TKS eSSRs dataset of McAsseyet al. (middle panel), and UST.officinale using chosen gSSRs of this study (right panel). Neighbor-joining trees were generated using the Prevosti algorithm with 1,000 permuted randomizations. Bootstrap support exceeding 70% is indicated. The computed genetic distance scales are placed on top of each respective tree.
Figure 3
Figure 3
Mantel test of the correlation of geographic distance and genetic distance matrices for theTaraxacum kok-saghyz (TKS) gSSR dataset (left panel; two Herbarium samples removed), TKS eSSR dataset of McAsseyet al. (2016; middle panel), and UST.officinale using 14 gSSRs (right panel) were analyzed using 1,000 permutations. Mantel’s R indices and their corresponding statistical support are indicated, respectively.
Figure 4
Figure 4
Minimum spanning networks for theTaraxacum kok-saghyz (TKS) gSSR dataset (left panel), TKS eSSR dataset of McAsseyet al. (middle panel), and UST.officinale dataset using 14 gSSRs selected for this study (right panel). Bruvo’s distance (considering the motifs lengths) was used to reticulate the datasets. Color legends for the populations and Bruvo distance scales/shading are indicated, respectively, on each graph.
Figure 5
Figure 5
Discriminant Analysis of Principal Components (DAPC) for theTaraxacum kok-saghyz (TKS) gSSR dataset (left panel), TKS eSSR dataset of McAsseyet al. (middle panel), and UST.officinale using 14 gSSRs selected for this study (right panel). Optimized and cross-checked PCA eigenvalues were used to generate each graph, respectively (gSSR: 5 PCAs retained; eSSR: 39;T.officinale gSSR: 11). Color legends for the populations and DA/PCA eigenvalues used are shown, respectively, on each graph. Alleles contributing the most to explaining the variance for each dataset are indicated on either axis, respectively (with percentages of the variance explained in the parentheses, respectively).
Figure 6
Figure 6
Phylogenetic relationships between dandelions used in the study. The ITS sequences ofTaraxacum kok-saghyz (TKS), otherTaraxacum species of interest, US dandelions, and outgroup specimens from Southeastern US were aligned using MAFFT,, trimmed with SeaView-Gblocks to remove the uninformative characters, and used for thorough-bootstrap RAxML analysis (100 runs with 10,000 repeats, rapid hill-climbing mode, GTR substitutions, multiple outgroup), over 451 distinct alignment patterns. The Gblocks regions alignment was 660 bp long. Proportion of gaps and completely undetermined characters in this alignment: 3.39%. The resultant tree was built using FigTree, and the branches are colored as per the bootstrap support (indicated on the color legend). Arrows indicate positions of sequences pulled from NCBI (T.ceratophorum: consensus of three ITS sequences deposited;T.erythrospermum: consensus of 12 ITS sequences;T.officinale: consensus of 49 sequences; Supplementary Table S2), of the historicalT.officinale specimen (TofficinaleW413345: WTU 413345; picture published with permission of the Burke Museum, University of Washington) and the historical specimens of TKS (TKSherbKent: KE 650; TKSherbMontana: MONT 51683), or other species (for TKS,Ceratoidea). No ITS sequences forT.brevicorniculatum were found at NCBI. The sample origin (population names) orTaraxacum species names are indicated. Dotted grey box delimits the out-group for RAxML (non-Taraxacum species by ITS BLAST of sequences); orange box indicates the TKS. Sample ESKUSA E55/12 was used forde novo sequencing and development of the gSSRs used in this study. Pictures of exemplary specimens show TKS,T.brevicorniculatum (BRE), andT.officinalis (OFF; the dashed lines are indicating which specimens are shown). Samples of TKS,T.officinale, andT.brevicorniculatum marked with S were grown for another study.
Figure 7
Figure 7
Phylogenetic relationships among the USTaraxacum officinale using 14 gSSRs selected for this study. Bruvo’s distances among the specimens were calculated to generate the FastME tree (1,000 permutations; bootstrap support of 70% and more is indicated). The dandelion individuals were color-coded as per the Bayesian Information Criterion in R packagepoppr, (K-means hierarchical clustering; Kmin = 7).
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. van Beilen JB, Poirier Y. Guayule and Russian dandelion as alternative sources of natural rubber. Critical Reviews in Biotechnology. 2007;27:217–231. doi: 10.1080/07388550701775927. - DOI - PubMed
    1. Cornish K. Alternative natural rubber crops: Why should we care? Technology & Innovation. 2017;18:244–255. doi: 10.21300/18.4.2017.245. - DOI
    1. van Beilen JB, Poirier Y. Establishment of new crops for the production of natural rubber. Trends in Biotechnology. 2007;25:522–529. doi: 10.1016/j.tibtech.2007.08.009. - DOI - PubMed
    1. Lin, T. et al. Genome analysis of Taraxacum kok-saghyz Rodin provides new insights into rubber biosynthesis. National Science Review 5, 78–87 (2017).
    1. Bowers, J. E. Natural rubber-producing plants for the United States. (National Agricultural Library, Beltsville, Maryland, USA, 1990).

Publication types

MeSH terms

Substances

Related information

LinkOut - more resources

Full text links
Nature Publishing Group full text link Nature Publishing Group Free PMC article
Cite
Send To

NCBI Literature Resources

MeSHPMCBookshelfDisclaimer

The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). Unauthorized use of these marks is strictly prohibited.

[8]ページ先頭
©2009-2025 Movatter.jp