ArticlePlant molecular biology2018
Sequence-guided approach to genotyping plant clones and species using polymorphic NB-ARC-related genes.
Article in Plant molecular biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed, 8 citations in OpenAlex.
- Strategies for Intraspecific Genotyping of Duckweed: Comparison of Five Orthogonal Methods Applied to the Giant DuckweedPlants (Basel, Switzerland) · 2022Article
- Intraspecific Diversity in Aquatic Ecosystems: Comparison betweenPlants (Basel, Switzerland) · 2022Article
- Return of the Lemnaceae: duckweed as a model plant system in the genomics and postgenomics era.The Plant cell · 2021Article
- Duckweed Species Genotyping and Interspecific Hybrid Discovery by Tubulin-Based Polymorphism Fingerprinting.Frontiers in plant science · 2021Article
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
key messageLeveraging the heightened levels of polymorphism in NB-ARC-related protein encoding genes in higher plants, a bioinformatic pipeline was created to identify regions in this gene family from sequenced plant genomes that exhibit fragment length or single nucleotide differences in different accessions of the same species. Testing this approach with the aquatic plant Spirodela polyrhiza demonstrated its superior performance in comparison with currently available genotyping technologies based on PCR amplification. Rapid and economical genotyping tools that can reliably distinguish species and intraspecific variations in plants can be powerful tools for biogeographical and ecological studies. Clones of the cosmopolitan duckweed species, Spirodela polyrhiza, are difficult to distinguish morphologically due to their highly abbreviated architecture and inherently low levels of sequence variation. The use of plastidic markers and generic Amplification Fragment Length Polymorphism approaches have met with limited success in resolving clones of S. polyrhiza from diverse geographical locales. Using whole genome sequencing data from nine S. polyrhiza clones as a training set, we created an informatic pipeline to identify and rank polymorphic regions from nuclear-encoded NB-ARC-related genes to design markers for PCR, Sanger sequencing (barcoding), and fragment length analysis. With seven primer sets, we found 21 unique fingerprints from a set of 23 S. polyrhiza clones. However, three of these clones share the same fingerprint and are indistinguishable by these markers. These primer sets can also be used as interspecific barcoding tools to rapidly resolve S. polyrhiza from the closely related S. intermedia species without the need for DNA sequencing. Our work demonstrates a general approach of using hyper-polymorphic loci within genomes as a resource to produce facile tools that can have high resolving power for genotyping applications.
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