Genotype-Phenotype association analysis
We used the SNPs identified in the 42 mother trees for the GPA association analysis, focusing on the traits significantly associated with drought treatments. For the wet treatment traits, we use the average trait value across all members of each family in the wet treatment to run GPA analysis. For the drought response traits, we deduct the average trait value for a given family in the wet treatment from the value for each family’s offspring in the drought treatment and then use the mean difference as the input for GPA. We used LFMM 2 (Caye et al. 2019) to run the GPA association analysis and then identified associations based on p (<10-5) value.