Plasticity screening using Arabidopsis thalianaaccessions in response to N availability
We screened 190 Arabidopsis accessions (Table S1), grown on soil
supplemented with three different concentrations of N (Methods), for
plasticity of focal traits (i.e. phenotypes) including early
rosette diameter (ERD), final rosette diameter (FRD), flowering time
(FT) and yield (YIE) (Table S2). A pilot experiment with a subset of
accessions, following an established protocol (Pandey et al., 2019), was
used to determine the N conditions considered as limiting, intermediate
and optimal for growth (Methods). Accessions with missing data in at
least one N condition were removed from further analysis, resulting in
142 (ERD), 109 (FRD), 127 (FT) and 102 (YIE) accessions to characterize
plasticity of the four phenotypes. On average, the accessions were
larger, flowered earlier and produced more seeds when grown under
optimal N in comparison to intermediate and limiting N (Figure 1a).
Clustering of the accessions according to their reactions norms,
representing the phenotype mean as a function of different environments,
partitioned the accessions into three groups for ERD and two groups for
each of the other complex traits (FRD, FT, and YIE) (k-means clustering,
k determined by silhouette index analysis, Figure 1b, Table S2). The
differences in response of the studied phenotypes between the clusters
of accessions indicated that there is a genetic variation in plasticity
of these phenotypes to N availability.
To quantify plasticity of the phenotypes, we calculated the coefficient
of variation (CV) for each accession using the mean values in the three
N conditions (Methods, Table S3). The average CVs for all traits were
smaller than 1, implying a generally low degree of plasticity (Figure
2a). ERD showed higher median plasticity (0.46) than the other
phenotypes (Figure 2a). In contrast, FT, measured as the number of days
from pricking of the seedlings to the first open flower, had the lowest
median CV (0.11) in response to the three N conditions (Figure 2a). We
also asked if the accessions differed with respect to the pattern of
plasticities for the four phenotypes. To this end, we clustered the 77
accessions for which the CV of all four phenotypes were measured, and
found that they can be partitioned into three groups (Figure 2b; Table
S3). The accessions in cluster 1 showed lower plasticity in the ERD than
those in clusters 2 and 3, while the accessions in cluster 2 showed
higher plasticity in the ERD and FRD than those in clusters 1 and 3
(Figure 2b, Table S3). These findings demonstrated that accessions
differed with respect to the plasticities of the four investigated
phenotypes. Next, using the CVs of the 77 accessions, we tested if the
plasticities of the four phenotypes correlated. We found that the CV of
the ERD showed significant positive Spearman correlation with the CV of
the FRD (0.42, p-value = 4.7x10-5) and FT (0.37,
p-value = 5.7x10-5), indicating that plasticity of the
size in the beginning of vegetative growth is moderately associated with
plasticity in flowering time (Figure 2c).
To investigate whether the plasticity in the flowering time was due to
change in the developmental timing or the growth pattern, we scored the
number of rosette leaves until bolting for six accessions with varying
plasticities of FT. We noted that under the same N condition, the total
number of leaves differed between the selected accessions, but all of
them produced approximately twice the number of leaves under optimal N
in comparison to the limiting N (Figure S1). This suggests that the
earlier flowering under optimal N was due to a faster developmental
transition to the reproductive phase.