Genome-wide association study of 107 phenotypes in a common set of Arabidopsis thaliana inbred lines

By S. Atwell, Yu S. Huang, Bjarni J. Vilhjálmsson, Glenda Willems, Matthew W Horton, Yan Li, Dazhe Meng, Alexander Platt, A. Tarone, T. Hu and 26 more. Nature, 2010

974 citations recorded by the source corpus.

Although pioneered by human geneticists as a potential solution to the challenging problem of finding the genetic basis of common human diseases, genome-wide association (GWA) studies have, owing to advances in genotyping and sequencing technology, become an obvious general approach for studying the genetics of natural variation and traits of agricultural importance. They are particularly useful when inbred lines are available, because once these lines have been genotyped they can be phenotyped multiple times, making it possible (as well as extremely cost effective) to study many different traits in many different environments, while replicating the phenotypic measurements to reduce environmental noise. Here we demonstrate the power of this approach by carrying out a GWA study of 107 phenotypes in Arabidopsis thaliana, a widely distributed, predominantly self-fertilizing model plant known to harbour considerable genetic variation for many adaptively important traits. Our results are dramatically different from those of human GWA studies, in that we identify many common alleles of major effect, but they are also, in many cases, harder to interpret because confounding by complex genetics and population structure make it difficult to distinguish true associations from false. However, a-priori candidates are significantly over-represented among these associations as well, making many of them excellent candidates for follow-up experiments. Our study demonstrates the feasibility of GWA studies in A. thaliana and suggests that the approach will be appropriate for many other organisms.

Subfields: Genetics, Plant Science

View Paper: https://www.semanticscholar.org/paper/3c6ceaf63520f0cb204c8200de75962802400271

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Citations in the corpus

Enumerate Lasso Solutions for Feature Selection (2017, methodology): “Gene Expression Data We used the thaliana gene expression data used in (Atwell et al. 2010).”
Genome‐Wide Association Analysis Identifies Candidate Genes Associated with Iron Deficiency Chlorosis in Soybean (2011, background): “Th e most extensive experiment to date was performed in A. thaliana where 107 traits were mapped using genotype data from a high density array (Atwell et al., 2010).”
Variable Selection in Heterogeneous Datasets: A Truncated-rank Sparse Linear Mixed Model with Applications to Genome-wide Association Studies (2017, methodology): “For Arabidopsis thaliana, we used the validated knowledge of the genetic associations reported in [36].”
Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity (2014, positive): “arabidopsidis in a recent genome-wide association study examining 107 different phenotypes (Atwell et al., 2010).”
BLINK: a package for the next level of genome-wide association studies with both individuals and markers in the millions (2018, neutral): “These datasets covered five species including Arabidopsis thaliana [10], human [5], maize [37], mouse [38], and pig [39].”
Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa (2011, background): “3 Mb around HD1 , corresponding to a 'mountain range' as described by Atwell et al”
Association Mapping for Enhancing Maize (Zea mays L.) Genetic Improvement (2011, methodology): “Nevertheless, there always remains a chance that statistically signifi cant associations are due to chance (Gordon and Finch, 2005) and it is highly diffi cult to distinguish true associations from spurious associations (Atwell et al., 2010).”
Demographic fate of Arabidopsis thaliana cohorts of autumn‐ and spring‐germinated plants along an altitudinal gradient (2012, neutral): “…and molecular basis of such phenotypic variation (Mitchell-Olds 1995; Feder & Mitchell-Olds 2003; Alonso-Blanco, Méndez-Vigo & Koornneef 2005; Tonsor, Alonso-Blanco & Koornneef 2005; Mitchell-Olds & Schmitt 2006; Stinchcombe &Hoekstra 2008; Ungerer, Johnson & Herman 2008; Atwell et al. 2010).”
Whole-genome sequencing of multiple Arabidopsis thaliana populations (2011, methodology): “, and the information from this endeavor has already been successfully used for genome-wide association studies (GWAS”
On the Relevance and Control of Leaf Angle (2010, methodology): “…such as hypocotyl assays provides an excellent platform for (suppressor) mutant screens or for extensive Genome Wide Association mapping (GWA) approaches which in particular requires large sets of accessions to be screened (Nordborg et al., 2005; Nordborg and Weigel, 2008; Atwell et al., 2010).”