ArticleJournal of experimental botany2012
A collection of INDEL markers for map-based cloning in seven Arabidopsis accessions.
Article in Journal of experimental botany, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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44 citing papers in PubMed.
- A curated list of InDel markers for rapid genetic mapping inPlant biotechnology (Tokyo, Japan) · 2026Article
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- Development of Omni InDel and supporting database for maize.Frontiers in plant science · 2023Article
- Discovery of DNA polymorphisms via genome-resequencing and development of molecular markers between two barley cultivars.Plant cell reports · 2022Article
- TEB/POLQ plays dual roles in protecting Arabidopsis from NO-induced DNA damage.Nucleic acids research · 2022Article
- A Predominant Role of AtEDEM1 in Catalyzing a Rate-Limiting Demannosylation Step of an Arabidopsis Endoplasmic Reticulum-Associated Degradation Process.Frontiers in plant science · 2022Article
- Identification of hybridization and introgression between Cinnamomum kanehirae Hayata and C. camphora (L.) Presl using genotyping-by-sequencing.Scientific reports · 2020Article
- Genome-Wide Discovery of InDel Markers in Sesame (Plants (Basel, Switzerland) · 2020Article
- Identification of SNPs and InDels associated with berry size in table grapes integrating genetic and transcriptomic approaches.BMC plant biology · 2020Article
- Involvement of Arabidopsis BIG protein in cell death mediated by Myo-inositol homeostasis.Scientific reports · 2020Article
- Easy-to-Use InDel Markers for Genetic Mapping between Col-0 and LPlants (Basel, Switzerland) · 2020Article
- Indel marker analysis of putative stress-related genes reveals genetic diversity and differentiation of rice landraces in peninsular Thailand.Physiology and molecular biology of plants : an international journal of functional plant biology · 2020Article
- The Striking Flower-in-Flower Phenotype ofPlants (Basel, Switzerland) · 2019Article
- A novel quantitative trait locus on chromosome A9 controlling oleic acid content in Brassica napus.Plant biotechnology journal · 2019Article
- InDel Marker Based Estimation of Multi-Gene Allele Contribution and Genetic Variations for Grain Size and Weight in Rice (International journal of molecular sciences · 2019Article
- Detection of dominant QTLs for stigma exsertion ratio in rice derived fromBreeding science · 2019Article
- Article
- The Arabidopsis Cop9 signalosome subunit 4 (CNS4) is involved in adventitious root formation.Scientific reports · 2017Article
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7 authors.
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Abstract
The availability of a comprehensive set of resources including an entire annotated reference genome, sequenced alternative accessions, and a multitude of marker systems makes Arabidopsis thaliana an ideal platform for genetic mapping. PCR markers based on INsertions/DELetions (INDELs) are currently the most frequently used polymorphisms. For the most commonly used mapping combination, Columbia×Landsberg erecta (Col-0×Ler-0), the Cereon polymorphism database is a valuable resource for the generation of polymorphic markers. However, because the number of markers available in public databases for accessions other than Col-0 and Ler-0 is extremely low, mapping using other accessions is far from straightforward. This issue arose while cloning mutations in the Wassilewskija (Ws-4) background. In this work, approaches are described for marker generation in Ws-4 x Col-0. Complementary strategies were employed to generate 229 INDEL markers. Firstly, existing Col-0/Ler-0 Cereon predicted polymorphisms were mined for transferability to Ws-4. Secondly, Ws-0 ecotype Illumina sequence data were analyzed to identify INDELs that could be used for the development of PCR-based markers for Col-0 and Ws-4. Finally, shotgun sequencing allowed the identification of INDELs directly between Col-0 and Ws-4. The polymorphism of the 229 markers was assessed in seven widely used Arabidopsis accessions, and PCR markers that allow a clear distinction between the diverged Ws-0 and Ws-4 accessions are detailed. The utility of the markers was demonstrated by mapping more than 35 mutations in a Col-0×Ws-4 combination, an example of which is presented here. The potential contribution of next generation sequencing technologies to more traditional map-based cloning is discussed.
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