title: "Missing" G x E Variation Controls Flowering Time in Arabidopsis thaliana.
abstract: Understanding how genetic variation interacts with the environment is essential for understanding adaptation. In particular, the life cycle of plants is tightly coordinated with local environmental signals through complex interactions with the genetic variation (G x E). The mechanistic basis for G x E is almost completely unknown. We collected flowering time data for 173 natural inbred lines of Arabidopsis thaliana from Sweden under two growth temperatures (10°C and 16°C), and observed massive G x E variation. To identify the genetic polymorphisms underlying this variation, we conducted genome-wide scans using both SNPs and local variance components. The SNP-based scan identified several variants that had common effects in both environments, but found no trace of G x E effects, whereas the scan using local variance components found both. Furthermore, the G x E effects appears to be concentrated in a small fraction of the genome (0.5%). Our conclusion is that G x E effects in this study are mostly due to large numbers of allele or haplotypes at a small number of loci, many of which correspond to previously identified flowering time genes.
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.
authors.forename: Eriko
authors.initials: E
authors.lastname: Sasaki
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria; Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America.
authors.forename: Pei
authors.initials: P
authors.lastname: Zhang
authors.affiliation: Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America.
authors.forename: Susanna
authors.initials: S
authors.lastname: Atwell
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria; Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America.
authors.forename: Dazhe
authors.initials: D
authors.lastname: Meng
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.
authors.forename: Magnus
authors.initials: M
authors.lastname: Nordborg
mesh_terms: D000064:Acclimatization / Q000235:genetics*; D000222:Adaptation, Physiological / Q000235:genetics*; D000483:Alleles; D017360:Arabidopsis / Q000235:genetics / Q000254:growth & development; D035264:Flowers / Q000235:genetics* / Q000254:growth & development; D059647:Gene-Environment Interaction; D014644:Genetic Variation; D005838:Genotype; D006239:Haplotypes; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics