Phenotypic spectrum: uncovering root architecture diversity in common
bean (Phaseolus vulgaris)
Abstract
Plant roots exhibit distinct architectural organization and overall
shape. Current concepts to quantify architectural variation assume a
homogeneous phenotype for a given genotype. However, this assumption
neglects the observable variation in root architecture for two reasons:
(i) sampling strategies are designed to capture architectural variation
only for the most common phenotype, and (ii) traits are often measured
locally within a root system and ignore the architectural organization.
Here, we introduce a new concept: the phenotypic spectrum of crop roots
to quantify architectural variation as the number of architecture types
for one genotype in a specific environment. We use the shape descriptor
DS-curve to characterize the whole root system architecture. Using DS
curves as a core, we developed a computing pipeline that combines
Kmeans++ clustering, outlier filtering and the Fréchet distance as a
similarity metric to classify types of root architectures. Subsequently,
we applied this pipeline to analyze a field dataset including three
common bean (Phaseolus vulgaris) genotypes DOR364 (n=797), L88_57
(n=1772), and SEQ7 (n=768) under non-limiting and water-stressed
conditions in 2015 and 2016. We found DOR364 showed five different root
architecture types across environments, while L88_57 and SEQ7 showed
four. The total variation within classified root architecture types of
DOR364, L88_57, and SEQ reduced by 58.59%, 50.19% and 53.01%,
compared to the variation of the complete data sets. DOR364 had stable
fractions of root architecture types across environments. In contrast,
L88_57 and SEQ7 showed more variation in their fractions. There was no
significant biomass difference among root architecture types for all
studied genotypes within each environment. As such, we hypothesize that
the phenotypic spectrum might buffer the impact of environmental
stresses as an acclimatization strategy by changing the composition of
root architecture types at the population level.