TY  - JOUR
A1  - Childs, Liam H.
A1  - Witucka-Wall, Hanna
A1  - Guenther, Torsten
A1  - Sulpice, Ronan
A1  - Korff, Maria V.
A1  - Stitt, Mark
A1  - Walther, Dirk
A1  - Schmid, Karl J.
A1  - Altmann, Thomas
T1  - Single feature polymorphism (SFP)-based selective sweep identification and association mapping of growth- related metabolic traits in Arabidopsis thaliana
N2  - Background: Natural 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. Results: A 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. Conclusions: We 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.
Y1  - 2010
UR  - http://www.biomedcentral.com/1471-2164/
U6  - https://doi.org/10.1186/1471-2164-11-188
SN  - 1471-2164
ER  - 
TY  - JOUR
A1  - Schmid, Karl J.
A1  - Torjek, Otto
A1  - Meyer, Rhonda C.
A1  - Schmuths, Heike
A1  - Hoffmann, Matthias H.
A1  - Altmann, Thomas
T1  - Evidence for a large-scale population structure of Arabidopsis thaliana from genome-wide single nucleotide polymorphism markers
N2  - Population-based methods for the genetic mapping of adaptive traits and the analysis of natural selection require that the population structure and demographic history of a species are taken into account. We characterized geographic patterns of genetic variation in the model plant Arabidopsis thaliana by genotyping 115 genome-wide single nucleotide polymorphism (SNP) markers in 351 accessions from the whole species range using a matrix-assisted laser desorption/ionization time-of-flight assay, and by sequencing of nine unlinked short genomic regions in a subset of 64 accessions. The observed frequency distribution of SNPs is not consistent with a constant-size neutral model of sequence polymorphism due to an excess of rare polymorphisms. There is evidence for a significant population structure as indicated by differences in genetic diversity between geographic regions. Accessions from Central Asia have a low level of polymorphism and an increased level of genome-wide linkage disequilibrium (LD) relative to accessions from the Iberian Peninsula and Central Europe. Cluster analysis with the structure program grouped Eurasian accessions into K=6 clusters. Accessions from the Iberian Peninsula and from Central Asia constitute distinct populations, whereas Central and Eastern European accessions represent admixed populations in which genomes were reshuffled by historical recombination events. These patterns likely result from a rapid postglacial recolonization of Eurasia from glacial refugial populations. Our analyses suggest that mapping populations for association or LD mapping should be chosen from regional rather than a species-wide sample or identified genetically as sets of individuals with similar average genetic distances
Y1  - 2006
UR  - http://www.springerlink.com/content/d1683r7455648841/fulltext.html
U6  - https://doi.org/10.1007/s00122-006-0212-7
ER  -