Strategies for Intraspecific Genotyping of Duckweed: Comparison of Five Orthogonal Methods Applied to the Giant Duckweed Spirodela polyrhiza

Publication type:
Journal article
Metadata:
Autoren
  • Manuela Bog
  • Luca Braglia
  • Laura Morello
  • Karen I Noboa Melo
  • Ingo Schubert
  • Oleg N Shchepin
  • K Sowjanya Sree
  • Shuqing Xu
  • Eric Lam
  • Klaus J Appenroth
Autoren-URL
https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000887848600001&DestLinkType=FullRecord&DestApp=WOS_CPL
DOI
10.3390/plants11223033
eISSN
2223-7747
Externe Identifier
  • Clarivate Analytics Document Solution ID: 6K9YV
  • PubMed Identifier: 36432762
Ausgabe der Veröffentlichung
22
Zeitschrift
PLANTS-BASEL
Schlüsselwörter
  • Spirodela polyrhiza
  • Lemnaceae
  • duckweed
  • genotyping
  • intraspecific variation
Artikelnummer
ARTN 3033
Datum der Veröffentlichung
2022
Status
Published
Titel
Strategies for Intraspecific Genotyping of Duckweed: Comparison of Five Orthogonal Methods Applied to the Giant Duckweed <i>Spirodela polyrhiza</i>
Sub types
  • Article
Ausgabe der Zeitschrift
11

Data source: Web of Science (Lite)

Other metadata sources:
Abstract
<jats:p>The predominantly vegetative propagating duckweeds are of growing commercial interest. Since clonal accessions within a respective species can vary considerably with respect to their physiological as well as biochemical traits, it is critical to be able to track the clones of species of interest after their characterization. Here, we compared the efficacy of five different genotyping methods for Spirodela polyrhiza, a species with very low intraspecific sequence variations, including polymorphic NB-ARC-related loci, tubulin-gene-based polymorphism (TBP), simple sequence repeat variations (SSR), multiplexed ISSR genotyping by sequencing (MIG-seq), and low-coverage, reduced-representation genome sequencing (GBS). Four of the five approaches could distinguish 20 to 22 genotypes out of the 23 investigated clones, while TBP resolved just seven genotypes. The choice for a particular method for intraspecific genotyping can depend on the research question and the project budget, while the combination of orthogonal methods may increase the confidence and resolution for the results obtained.</jats:p>
Autoren
  • Manuela Bog
  • Luca Braglia
  • Laura Morello
  • Karen I Noboa Melo
  • Ingo Schubert
  • Oleg N Shchepin
  • K Sowjanya Sree
  • Shuqing Xu
  • Eric Lam
  • Klaus J Appenroth
DOI
10.3390/plants11223033
eISSN
2223-7747
Ausgabe der Veröffentlichung
22
Zeitschrift
Plants
Sprache
en
Online publication date
2022
Paginierung
3033 - 3033
Status
Published online
Herausgeber
MDPI AG
Herausgeber URL
http://dx.doi.org/10.3390/plants11223033
Datum der Datenerfassung
2022
Titel
Strategies for Intraspecific Genotyping of Duckweed: Comparison of Five Orthogonal Methods Applied to the Giant Duckweed Spirodela polyrhiza
Ausgabe der Zeitschrift
11

Data source: Crossref

Abstract
The predominantly vegetative propagating duckweeds are of growing commercial interest. Since clonal accessions within a respective species can vary considerably with respect to their physiological as well as biochemical traits, it is critical to be able to track the clones of species of interest after their characterization. Here, we compared the efficacy of five different genotyping methods for <i>Spirodela polyrhiza</i>, a species with very low intraspecific sequence variations, including polymorphic NB-ARC-related loci, tubulin-gene-based polymorphism (TBP), simple sequence repeat variations (SSR), multiplexed ISSR genotyping by sequencing (MIG-seq), and low-coverage, reduced-representation genome sequencing (GBS). Four of the five approaches could distinguish 20 to 22 genotypes out of the 23 investigated clones, while TBP resolved just seven genotypes. The choice for a particular method for intraspecific genotyping can depend on the research question and the project budget, while the combination of orthogonal methods may increase the confidence and resolution for the results obtained.
Addresses
  • Institute of Botany and Landscape Ecology, University of Greifswald, 17489 Greifswald, Germany.
Autoren
  • Manuela Bog
  • Luca Braglia
  • Laura Morello
  • Karen I Noboa Melo
  • Ingo Schubert
  • Oleg N Shchepin
  • K Sowjanya Sree
  • Shuqing Xu
  • Eric Lam
  • Klaus J Appenroth
DOI
10.3390/plants11223033
eISSN
2223-7747
Externe Identifier
  • PubMed Identifier: 36432762
  • PubMed Central ID: PMC9696241
Open access
true
ISSN
2223-7747
Ausgabe der Veröffentlichung
22
Zeitschrift
Plants (Basel, Switzerland)
Sprache
eng
Medium
Electronic
Online publication date
2022
Open access status
Open Access
Paginierung
3033
Datum der Veröffentlichung
2022
Status
Published
Publisher licence
CC BY
Datum der Datenerfassung
2022
Titel
Strategies for Intraspecific Genotyping of Duckweed: Comparison of Five Orthogonal Methods Applied to the Giant Duckweed <i>Spirodela polyrhiza</i>.
Sub types
  • research-article
  • Journal Article
Ausgabe der Zeitschrift
11

Files

https://www.mdpi.com/2223-7747/11/22/3033/pdf?version=1668584751 https://europepmc.org/articles/PMC9696241?pdf=render

Data source: Europe PubMed Central

Abstract
The predominantly vegetative propagating duckweeds are of growing commercial interest. Since clonal accessions within a respective species can vary considerably with respect to their physiological as well as biochemical traits, it is critical to be able to track the clones of species of interest after their characterization. Here, we compared the efficacy of five different genotyping methods for Spirodela polyrhiza, a species with very low intraspecific sequence variations, including polymorphic NB-ARC-related loci, tubulin-gene-based polymorphism (TBP), simple sequence repeat variations (SSR), multiplexed ISSR genotyping by sequencing (MIG-seq), and low-coverage, reduced-representation genome sequencing (GBS). Four of the five approaches could distinguish 20 to 22 genotypes out of the 23 investigated clones, while TBP resolved just seven genotypes. The choice for a particular method for intraspecific genotyping can depend on the research question and the project budget, while the combination of orthogonal methods may increase the confidence and resolution for the results obtained.
Date of acceptance
2022
Autoren
  • Manuela Bog
  • Luca Braglia
  • Laura Morello
  • Karen I Noboa Melo
  • Ingo Schubert
  • Oleg N Shchepin
  • K Sowjanya Sree
  • Shuqing Xu
  • Eric Lam
  • Klaus J Appenroth
Autoren-URL
https://www.ncbi.nlm.nih.gov/pubmed/36432762
DOI
10.3390/plants11223033
Externe Identifier
  • PubMed Central ID: PMC9696241
ISSN
2223-7747
Ausgabe der Veröffentlichung
22
Zeitschrift
Plants (Basel)
Schlüsselwörter
  • Lemnaceae
  • Spirodela polyrhiza
  • duckweed
  • genotyping
  • intraspecific variation
Sprache
eng
Country
Switzerland
PII
plants11223033
Datum der Veröffentlichung
2022
Status
Published online
Titel
Strategies for Intraspecific Genotyping of Duckweed: Comparison of Five Orthogonal Methods Applied to the Giant Duckweed Spirodela polyrhiza.
Sub types
  • Journal Article
Ausgabe der Zeitschrift
11

Data source: PubMed

Autoren
  • Manuela Bog
  • Luca Braglia
  • Laura Morello
  • Karen I Noboa Melo
  • Ingo Schubert
  • Oleg N Shchepin
  • K Sowjanya Sree
  • Shuqing Xu
  • Eric Lam
  • Klaus J Appenroth
Autoren-URL
https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000887848600001&DestLinkType=FullRecord&DestApp=WOS
DOI
10.3390/plants11223033
eISSN
2223-7747
Ausgabe der Veröffentlichung
22
Zeitschrift
PLANTS-BASEL
Schlüsselwörter
  • duckweed
  • genotyping
  • intraspecific variation
  • Lemnaceae
  • Spirodela polyrhiza
Artikelnummer
ARTN 3033
Datum der Veröffentlichung
2022
Status
Published
Datum der Datenerfassung
2023
Titel
Strategies for Intraspecific Genotyping of Duckweed: Comparison of Five Orthogonal Methods Applied to the Giant Duckweed Spirodela polyrhiza
Sub types
  • Article
Ausgabe der Zeitschrift
11

Data source: Manual

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