ArticleBMC genomics2010
Single feature polymorphism (SFP)-based selective sweep identification and association mapping of growth-related metabolic traits in Arabidopsis thaliana.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed, 14 citations in OpenAlex.
- Transcriptome Analysis of Reciprocal Hybrids Between Crassostrea gigas and C. angulata Reveals the Potential Mechanisms Underlying Thermo-Resistant Heterosis.Marine biotechnology (New York, N.Y.) · 2023Article
- Genome-Wide Association Study in Arabidopsis thaliana of Natural Variation in Seed Oil Melting Point: A Widespread Adaptive Trait in Plants.The Journal of heredity · 2016Article
- Genetic variants in root architecture-related genes in a Glycine soja accession, a potential resource to improve cultivated soybean.BMC genomics · 2015Article
- Characterization and identification of cis-regulatory elements in Arabidopsis based on single-nucleotide polymorphism information.Plant physiology · 2014Article
- An improved algorithm for the detection of genomic variation using short oligonucleotide expression microarrays.Molecular ecology resources · 2012Article
- Plant-growth promoting effect of newly isolated rhizobacteria varies between two Arabidopsis ecotypes.Plant signaling & behavior · 2012Article
- Parsimonious higher-order hidden Markov models for improved array-CGH analysis with applications to Arabidopsis thaliana.PLoS computational biology · 2012Article
- Improved haplotype-based detection of ongoing selective sweeps towards an application in Arabidopsis thaliana.BMC research notes · 2011Article
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Authors and funding
9 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNatural accessions of Arabidopsis thaliana are characterized by a high level of phenotypic variation that can be used to investigate the extent and mode of selection on the primary metabolic traits. A collection of 54 A. thaliana natural accession-derived lines were subjected to deep genotyping through Single Feature Polymorphism (SFP) detection via genomic DNA hybridization to Arabidopsis Tiling 1.0 Arrays for the detection of selective sweeps, and identification of associations between sweep regions and growth-related metabolic traits.
resultsA total of 1,072,557 high-quality SFPs were detected and indications for 3,943 deletions and 1,007 duplications were obtained. A significantly lower than expected SFP frequency was observed in protein-, rRNA-, and tRNA-coding regions and in non-repetitive intergenic regions, while pseudogenes, transposons, and non-coding RNA genes are enriched with SFPs. Gene families involved in plant defence or in signalling were identified as highly polymorphic, while several other families including transcription factors are depleted of SFPs. 198 significant associations between metabolic genes and 9 metabolic and growth-related phenotypic traits were detected with annotation hinting at the nature of the relationship. Five significant selective sweep regions were also detected of which one associated significantly with a metabolic trait.
conclusionsWe generated a high density polymorphism map for 54 A. thaliana accessions that highlights the variability of resistance genes across geographic ranges and used it to identify selective sweeps and associations between metabolic genes and metabolic phenotypes. Several associations show a clear biological relationship, while many remain requiring further investigation.
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