Conditional genome-wide associations reveal novel genes

We introduce two novel approaches for gene discovery based on conditional genome-wide associations. Experimental validation of gene targets identified by our top-performing approach uncovers three genes with a previously unknown role in controlling flowering time in Arabidopsis, one of the most well-studied traits in the most well-studied plant genome. This work demonstrates the power of knockoff-based frameworks to uniquely identify novel genes underlying complex traits, a core task across applications in agriculture and human health.