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

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

Research output: Contribution to journalArticlepeer-review

4 Scopus citations

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.

Original languageEnglish (US)
Article number3033
JournalPlants
Volume11
Issue number22
DOIs
StatePublished - Nov 2022
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Ecology
  • Plant Science

Keywords

  • Lemnaceae
  • Spirodela polyrhiza
  • duckweed
  • genotyping
  • intraspecific variation

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