Many traits of individuals are controlled by genetic basis, as well as by the environment. Despite intense research over the last several decades, genotype-phenotype relationships remain largely unclear. However, with the accumulation of large numbers of individual genome sequences due to the rapid development of sequencing technology, this is beginning to change. A Genome-Wide Association Study (GWAS) is a method for identifying the genetic basis of quantitative traits by exploring associations between SNPs and phenotypic variations within a population. Extension of GWAS models makes it possible to flexibly estimate the effects of genetics, the environment, and their interaction. Using these extended GWAS models and natural populations of the model plant Arabidopsis thaliana, we are exploring the genetic architectures underlying complex quantitative traits. In this seminar, I will introduce two examples of GWAS applications from our previous studies. The first example concerns the genetic and environmental interactions (G x E) that control a life-history trait, flowering time (Sasaki et al., 2015). Although the environmental response is a major factor of adaptation, the genetic basis of this response is largely unknown. Using GWAS, we screened for environment-dependent genetic effects on flowering time phenotypes and identified small fractions of the genome that explained almost all the flowering time variation. The second example concerns the genetic control of an epigenetic mark, DNA methylation variation (Kawakatsu et al., 2016). DNA methylation plays an important role in various biological systems, including silencing of transposons and imprinting, and large natural variation in methylation has been reported. In this study, we identified major alleles controlling this phenotypic variation in two key DNA methylation pathways and found the geographic cline.

References
Sasaki, E. et al., "Missing" G x E Variation Controls Flowering Time in Arabidopsis thaliana. PLoS Genet., 11(10):e1005597 (2015)
Kawakatsu T., et al., Epigenetic Diversity in a Global Collection of Arabidopsis thaliana Accessions. Cell, 166:492-505 (2016)