Identifying Causal Genes from Genome Wide Association Studies of Shade Avoidance in Plants

As sessile organisms, plants are unable to move to more favorable environments and must instead adjust to the conditions in which they are growing. In response to changes in light quantity and quality, plants can initiate a shade avoidance response that includes elongated hypocotyls, increased leaf angle, elongated internodes and petioles, and early flowering. While potentially advantageous for the individual plant, this response can divert resources from agronomically relevant tissues, leading to undesirable outcomes in crowded agricultural settings. To reveal genes underlying this shade avoidance response, we can take advantage of the great amount of genome sequence data available for Arabidopsis, a close relative of a number of crop plants including canola and broccoli.  We previously conducted a genome-wide association study that identified regions of the genome associated with shade avoidance in seedlings, and our current work seeks to identify the gene(s) underlying these associations.  In this study, we use a reverse genetics approach to study genes in linkage disequilibrium with single nucleotide polymorphisms (SNPs) found to be associated with altered hypocotyl elongation. Preliminary results indicate a number of novel genes as well as genes known to play a role in light signaling. Future work on these genes will not only enhance our understanding of the shade avoidance response in plants, but can also serve as a model for how to move from a SNP to the underlying causal gene.