For most traits, phenotypic variance explained by genome-wide relatedness (“PVE LMM”) was greater than the phenotypic variance explained by just the top variants

TraitPVE top variantsaPVE LMMb
Gentamicin resistance0.140.49
Spectinomycin resistance0.430.50
Streptomycin resistance0.340.58
Annual mean temperature0.090.12
Annual precipitation0.100.23
Formic acid0.080.30
Desiccation tolerance0.190.31
A17 biomass0.330.74
R108 biomass0.190.53
R108 nodule number0.060.19
  • a Maximum cumulative PVE among 1 to 25 variants chosen by model selection after subtracting the median of the empirical null distribution obtained from random permutations.

  • b After subtracting median of the null distribution.