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.