QTL across and between microbial treatments
A total of 32 QTL were identified for 12 traits across all environments
(Fig. 3; Table S5, Table S6). The additive effects of each QTL
explained from 2.9 - 22% of trait variation (Table S5). Of these 32
QTL, six QTL occupied unique positions in the genome. The confidence
intervals of all other QTL overlapped or colocalized with at least one
other QTL. Eight traits (shoot biomass, tiller number, SRL, lateral root
length, root diameter, root number, root biomass and total root length)
had 16 QTL with overlapping confidence intervals grouped into two
hotspots on chromosome three (Fig. 3; Table S5). The hotspot located on
3@4.3 (chromosome number @ centimorgan) showed an additive effect in the
direction of parental ecotype divergence, while the other hotspot
located on 3@58 showed an additive effect opposite the direction of
parental divergence. Pleiotropic genes or linked genes with correlated
effects may drive these genomic hotspots of correlated traits. We also
found significant epistatic interaction between these two hotspots.
Individuals possessing the hallii allele for the QTL on 3@58,
masked the effects of their interactive QTL on 3@4.3 (Table S5).
We detected 11 genotype x microbiome QTL for 10 traits that show
location specific QTL (Fig. 4a-k; Table S5, Table S6). Each of these QTL
were analyzed to directly test in which treatment they were present, and
to estimate the direction and magnitude of their effects (Fig. 4a-k;
Table S7, Table S8). In the MI treatment, QTL for shoot biomass, root
biomass and root number were detected with the hallii allele
contributing to a higher trait value (Fig. 4a, i, j). In the CI
treatment, QTL for RMR and SRL were detected with the filipesallele contributing to a higher trait value (Fig. 4b, c). In the AI
treatment, QTL for tiller number, root number, root diameter, lateral
root length, shoot biomass, root biomass, root length and first order
root length had allelic effects with the hallii allele
contributing to a higher value for all traits except root diameter (Fig.
4d-k). Of these QTL, four have overlapping confidence intervals and are
grouped into a hotspot on chromosome seven and three are grouped
together on chromosome nine (Fig. 4e-k; Table S7, Table S8). Two of the
three QTL present on chromosome nine were also detected in the MI
treatment (Fig. 4i, j; Table S7, Table S8). Epistatic interactions
between two QTL for root diameter (chr 1@68 and 2@78.8) were present
only in AI and CI (Fig. 5a-c, Table S7, Table S8) and individuals
possessing genotypes at the two loci from the same parent (recovering
the ecotypic configuration) produced traits with the smaller magnitude
(Fig. 5b, c).