Effect of microbiome inoculation on parental traits
Trait differences among parents were driven by plant genotype,
environment and genotype by environment interactions (GxE). Parents
differed in shoot and root traits across all treatments. For example,
FIL2 produced 1.64-fold more shoot biomass (P <0.0001),
1.98-fold more root biomass (P <0.0001), 1.80-fold lower
specific root length (SRL) (P <0.0001) and 1.46-fold
higher RTD (P <0.0001) relative to HAL2 (Fig. 2a, d, e;
Table S2; Table S3). These results mirrored earlier descriptive studies
of P. hallii ecotypes (Palacio-Meija et al. , 2021; Lowryet al. , 2014), including studies of the shoot and root traits
studied in current work. (Khasanova et al. 2019). Treatment also
had a significant effect on plant traits (Fig. 2a-c, e, f; Table S2,
Table S3). For example, inoculated plants had greater shoot biomass
(1.35-fold more biomass in CI and 1.17-fold more in AI treatments
relative to the MI treatment (P =0.027)), lower lateral root
length (1.2-fold less in CI and 1.53-fold less in AI relative to MI
(P =0.046)), and showed changes in specific leaf area (SLA)
dependent upon treatment (1.05-fold increase in AI and 1.06-decrease in
CI relative to MI (P =0.039)). Importantly, we also identified
several ecotype x microbiome interactions (Fig. 2d-f; Table S2, Table
S3). For example, SRL of FIL2 decreased 1.17-fold under AI and 1.33-fold
under CI relative to MI soil, while HAL2 showed 1.1-fold increase in SRL
under AI and no change under CI relative to MI (P =0.039; Fig. 2d;
Table S2, Table S3). Root tissue density (RTD) of FIL2 increased
1.1-fold under AI and 1.36-fold under CI relative to MI, while HAL2
showed 1.1-fold decrease under AI and 1.1-fold increase under CI
relative to MI (P=0.046; Fig. 2e; Table S2, Table S3). In total, seven
traits showed ecotype differences between parents, five traits were
affected by microbial treatment and three traits had significant ecotype
x microbiome interaction (Fig. 2; Table S2, Table S3).
The impact of the microbiome on the quantitative genetic architecture of
our measured traits was evaluated by comparing “base” and “GxE”
linear mixed models. In 11 out of 12 cases, the GxE models were favored
by AIC and log likelihood ratio tests (Table S4). Broad-sense
heritability was low for most traits (ranging from 0.01 to 0.18; Table
S2). Overall, we document considerable evidence that the microbiome
modifies the expression of quantitative genetic variation in P.
hallii .