Fig. 2

Circular Manhattan plot representing marker significance counts on 50 random \(80\%\) sub-samples of top: the Maize dataset and \(\alpha T\) trait; bottom: the Sorghum dataset and Plant Height trait. The X-axis depicts the physical position of markers on the reference genome, the Y-axis depicts the maximum proportion of times each marker was detected for a single trait linear mixed model with single marker testing (stLMM-sm), b multitrait linear mixed model with single marker testing (mtLMM-sm), c multitrait linear model with L1 penalty (mtLM-L1), d multitrait linear model with L1 + trait-wise clustering penalty (mtLM-clust), e multitrait linear mixed model with L1 penalty (mtLMM-L1), and f multitrait linear mixed model with L1 + trait-wise clustering penalty (mtLMM-clust)