Cargando…

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

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 aft...

Descripción completa

Detalles Bibliográficos
Autores principales: Bog, Manuela, Braglia, Luca, Morello, Laura, Noboa Melo, Karen I., Schubert, Ingo, Shchepin, Oleg N., Sree, K. Sowjanya, Xu, Shuqing, Lam, Eric, Appenroth, Klaus J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9696241/
https://www.ncbi.nlm.nih.gov/pubmed/36432762
http://dx.doi.org/10.3390/plants11223033
_version_ 1784838259990331392
author Bog, Manuela
Braglia, Luca
Morello, Laura
Noboa Melo, Karen I.
Schubert, Ingo
Shchepin, Oleg N.
Sree, K. Sowjanya
Xu, Shuqing
Lam, Eric
Appenroth, Klaus J.
author_facet Bog, Manuela
Braglia, Luca
Morello, Laura
Noboa Melo, Karen I.
Schubert, Ingo
Shchepin, Oleg N.
Sree, K. Sowjanya
Xu, Shuqing
Lam, Eric
Appenroth, Klaus J.
author_sort Bog, Manuela
collection PubMed
description 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.
format Online
Article
Text
id pubmed-9696241
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-96962412022-11-26 Strategies for Intraspecific Genotyping of Duckweed: Comparison of Five Orthogonal Methods Applied to the Giant Duckweed Spirodela polyrhiza Bog, Manuela Braglia, Luca Morello, Laura Noboa Melo, Karen I. Schubert, Ingo Shchepin, Oleg N. Sree, K. Sowjanya Xu, Shuqing Lam, Eric Appenroth, Klaus J. Plants (Basel) Article 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. MDPI 2022-11-09 /pmc/articles/PMC9696241/ /pubmed/36432762 http://dx.doi.org/10.3390/plants11223033 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Bog, Manuela
Braglia, Luca
Morello, Laura
Noboa Melo, Karen I.
Schubert, Ingo
Shchepin, Oleg N.
Sree, K. Sowjanya
Xu, Shuqing
Lam, Eric
Appenroth, Klaus J.
Strategies for Intraspecific Genotyping of Duckweed: Comparison of Five Orthogonal Methods Applied to the Giant Duckweed Spirodela polyrhiza
title Strategies for Intraspecific Genotyping of Duckweed: Comparison of Five Orthogonal Methods Applied to the Giant Duckweed Spirodela polyrhiza
title_full Strategies for Intraspecific Genotyping of Duckweed: Comparison of Five Orthogonal Methods Applied to the Giant Duckweed Spirodela polyrhiza
title_fullStr Strategies for Intraspecific Genotyping of Duckweed: Comparison of Five Orthogonal Methods Applied to the Giant Duckweed Spirodela polyrhiza
title_full_unstemmed Strategies for Intraspecific Genotyping of Duckweed: Comparison of Five Orthogonal Methods Applied to the Giant Duckweed Spirodela polyrhiza
title_short Strategies for Intraspecific Genotyping of Duckweed: Comparison of Five Orthogonal Methods Applied to the Giant Duckweed Spirodela polyrhiza
title_sort strategies for intraspecific genotyping of duckweed: comparison of five orthogonal methods applied to the giant duckweed spirodela polyrhiza
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9696241/
https://www.ncbi.nlm.nih.gov/pubmed/36432762
http://dx.doi.org/10.3390/plants11223033
work_keys_str_mv AT bogmanuela strategiesforintraspecificgenotypingofduckweedcomparisonoffiveorthogonalmethodsappliedtothegiantduckweedspirodelapolyrhiza
AT braglialuca strategiesforintraspecificgenotypingofduckweedcomparisonoffiveorthogonalmethodsappliedtothegiantduckweedspirodelapolyrhiza
AT morellolaura strategiesforintraspecificgenotypingofduckweedcomparisonoffiveorthogonalmethodsappliedtothegiantduckweedspirodelapolyrhiza
AT noboamelokareni strategiesforintraspecificgenotypingofduckweedcomparisonoffiveorthogonalmethodsappliedtothegiantduckweedspirodelapolyrhiza
AT schubertingo strategiesforintraspecificgenotypingofduckweedcomparisonoffiveorthogonalmethodsappliedtothegiantduckweedspirodelapolyrhiza
AT shchepinolegn strategiesforintraspecificgenotypingofduckweedcomparisonoffiveorthogonalmethodsappliedtothegiantduckweedspirodelapolyrhiza
AT sreeksowjanya strategiesforintraspecificgenotypingofduckweedcomparisonoffiveorthogonalmethodsappliedtothegiantduckweedspirodelapolyrhiza
AT xushuqing strategiesforintraspecificgenotypingofduckweedcomparisonoffiveorthogonalmethodsappliedtothegiantduckweedspirodelapolyrhiza
AT lameric strategiesforintraspecificgenotypingofduckweedcomparisonoffiveorthogonalmethodsappliedtothegiantduckweedspirodelapolyrhiza
AT appenrothklausj strategiesforintraspecificgenotypingofduckweedcomparisonoffiveorthogonalmethodsappliedtothegiantduckweedspirodelapolyrhiza