Microsatellite marker development in the crop wild relative  Linum bienne  using genome skimming

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Abstract

Premise

Nuclear microsatellite markers were developed for Linum bienne, the sister species of the crop L. usitatissimum, to provide molecular genetic tools for the investigation of L. bienne genetic diversity and structure.

Methods and Results

Fifty microsatellite loci were identified in L. bienne by means of genome skimming, and 44 loci successfully amplified. Of these, 16 loci evenly spread across the L. usitatissimum reference nuclear genome were used for genotyping six L. bienne populations. Excluding one monomorphic locus, the number of alleles per locus ranged from two to 12. Four out of six populations harbored private alleles. The levels of expected and observed heterozygosity were 0.076 to 0.667 and 0.000 to 1.000, respectively. All 16 loci successfully cross‐amplified in L. usitatissimum.

Conclusions

The 16 microsatellite loci developed here can be used for population genetic studies in L. bienne, and 28 additional loci that successfully amplified are available for further testing.

Related collections

Most cited references 11

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msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer design.

Brant C Faircloth (2008)

msatcommander is a platform-independent program designed to search for microsatellite arrays, design primers, and tag primers using an automated routine. msatcommander accepts as input DNA sequence data in single-sequence or concatenated, fasta-formatted files. Search data and locus-specific primers are written to comma-separated value files for subsequent use in spreadsheet or database programs. Binary versions of the graphical interface for msatcommander are available for Apple OS X and Windows XP. Users of other operating systems may run the graphical interface version using the available source code, provided their environment supports at least Python 2.4, Biopython 1.43, and wxPython 2.8. msatcommander is available from http://code.google.com/p/msatcommander/. © 2007 The Author.

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Integrated consensus genetic and physical maps of flax (Linum usitatissimum L.)

Sylvie Cloutier, Raja Ragupathy, Evelyn Miranda … (2012)

Three linkage maps of flax (Linum usitatissimum L.) were constructed from populations CDC Bethune/Macbeth, E1747/Viking and SP2047/UGG5-5 containing between 385 and 469 mapped markers each. The first consensus map of flax was constructed incorporating 770 markers based on 371 shared markers including 114 that were shared by all three populations and 257 shared between any two populations. The 15 linkage group map corresponds to the haploid number of chromosomes of this species. The marker order of the consensus map was largely collinear in all three individual maps but a few local inversions and marker rearrangements spanning short intervals were observed. Segregation distortion was present in all linkage groups which contained 1–52 markers displaying non-Mendelian segregation. The total length of the consensus genetic map is 1,551 cM with a mean marker density of 2.0 cM. A total of 670 markers were anchored to 204 of the 416 fingerprinted contigs of the physical map corresponding to ~274 Mb or 74 % of the estimated flax genome size of 370 Mb. This high resolution consensus map will be a resource for comparative genomics, genome organization, evolution studies and anchoring of the whole genome shotgun sequence. Electronic supplementary material The online version of this article (doi:10.1007/s00122-012-1953-0) contains supplementary material, which is available to authorized users.

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A Target Capture-Based Method to Estimate Ploidy From Herbarium Specimens

Juan Viruel, María Conejero, Oriane Hidalgo … (2019)

Whole genome duplication (WGD) events are common in many plant lineages, but the ploidy status and possible occurrence of intraspecific ploidy variation are unknown for most species. Standard methods for ploidy determination are chromosome counting and flow cytometry approaches. While flow cytometry approaches typically use fresh tissue, an increasing number of studies have shown that recently dried specimens can be used to yield ploidy data. Recent studies have started to explore whether high-throughput sequencing (HTS) data can be used to assess ploidy levels by analyzing allelic frequencies from single copy nuclear genes. Here, we compare different approaches using a range of yam (Dioscorea) tissues of varying ages, drying methods and quality, including herbarium tissue. Our aims were to: (1) explore the limits of flow cytometry in estimating ploidy level from dried samples, including herbarium vouchers collected between 1831 and 2011, and (2) optimize a HTS-based method to estimate ploidy by considering allelic frequencies from nuclear genes obtained using a target-capture method. We show that, although flow cytometry can be used to estimate ploidy levels from herbarium specimens collected up to fifteen years ago, success rate is low (5.9%). We validated our HTS-based estimates of ploidy using 260 genes by benchmarking with dried samples of species of known ploidy (Dioscorea alata, D. communis, and D. sylvatica). Subsequently, we successfully applied the method to the 85 herbarium samples analyzed with flow cytometry, and successfully provided results for 91.7% of them, comprising species across the phylogenetic tree of Dioscorea. We also explored the limits of using this HTS-based approach for identifying high ploidy levels in herbarium material and the effects of heterozygosity and sequence coverage. Overall, we demonstrated that ploidy diversity within and between species may be ascertained from historical collections, allowing the determination of polyploidization events from samples collected up to two centuries ago. This approach has the potential to provide insights into the drivers and dynamics of ploidy level changes during plant evolution and crop domestication.

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Author and article information

Contributors

Beatrice Landoni:

ORCID: https://orcid.org/0000-0002-3815-5011

beatrice.landoni@myport.ac.uk

Journal

Journal ID (nlm-ta): Appl Plant Sci

Journal ID (iso-abbrev): Appl Plant Sci

Journal ID (doi): 10.1002/(ISSN)2168-0450

Journal ID (publisher-id): APS3

Title: Applications in Plant Sciences

Publisher: John Wiley and Sons Inc. (Hoboken )

ISSN (Electronic): 2168-0450

Publication date (Electronic): 26 May 2020

Publication date Collection: May 2020

Volume: 8

Issue: 5 ( doiID: 10.1002/aps3.v8.5 )

Electronic Location Identifier: e11349

Affiliations

[ ¹ ] School of Biological Sciences University of Portsmouth PO1 2DY Portsmouth United Kingdom

[ ² ] Royal Botanic Gardens, Kew TW9 3AE Richmond, London United Kingdom

[ ³ ] Departamento de Ecología Integrativa Estación Biológica de Doñana (EBD) Consejo Superior de Investigaciones Científicas (CSIC) 41092 Seville Spain

[ ⁴ ] School of Life Sciences University of Warwick CV4 7AL Warwick United Kingdom

[ ⁵ ] Department of Biosciences Durham University Stockton Road DH1 3LE Durham United Kingdom

Author notes

[*] [* ]Author for correspondence: beatrice.landoni@ 123456myport.ac.uk

Author information

Beatrice Landoni https://orcid.org/0000-0002-3815-5011

Juan Viruel https://orcid.org/0000-0001-5658-8411

Robin G. Allaby https://orcid.org/0000-0001-5046-002X

Adrian C. Brennan https://orcid.org/0000-0002-8171-769X

F. Xavier Picó https://orcid.org/0000-0003-2849-4922

Rocio Pérez‐Barrales https://orcid.org/0000-0002-2472-2214

Article

Publisher ID: APS311349

DOI: 10.1002/aps3.11349

PMC ID: 7249271

PubMed ID: 32477845

SO-VID: 1d5e5d04-a94d-40f8-a43a-1014718a47e0

License:

This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

History

Date received : 27 November 2019

Date accepted : 26 January 2020

Page count

Figures: 0, Tables: 2, Pages: 6, Words: 6436

Funding

Funded by: Institute of Biological and Biomedical Science Research and Innovation

Funded by: Agencia Estatal de Investigación/Fondo Europeo de Desarrollo Regional (AEI/FEDER)

Award ID: CGL2016‐77720‐P

Custom metadata

source-schema-version-number 2.0

cover-date May 2020

details-of-publishers-convertor Converter:WILEY_ML3GV2_TO_JATSPMC version:5.8.2 mode:remove_FC converted:26.05.2020

Keywords: crop wild relative,linaceae,linum bienne,pale flax,population genetics,simple sequence repeat (ssr)

Data availability:

Keywords: crop wild relative, linaceae, linum bienne, pale flax, population genetics, simple sequence repeat (ssr)

Microsatellite marker development in the crop wild relative Linum bienne using genome skimming

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Abstract

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Methods and Results

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Related collections

Genome Engineering using CRISPR

Most cited references 11

msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer design.

Integrated consensus genetic and physical maps of flax (Linum usitatissimum L.)

A Target Capture-Based Method to Estimate Ploidy From Herbarium Specimens

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