Phenomics for photosynthesis, growth and reflectance in Arabidopsis thaliana reveals circadian and long-term fluctuations in heritability.

BACKGROUND: Recent advances in genome sequencing technologies have shifted the research bottleneck in plant sciences from genotyping to phenotyping. This shift has driven the development of phenomics, high-throughput non-invasive phenotyping technologies. RESULTS: We describe an automated high-throughput phenotyping platform, the Phenovator, capable of screening 1440 Arabidopsis plants multiple times per day for photosynthesis, growth and spectral reflectance at eight wavelengths. Using this unprecedented phenotyping capacity, we have been able to detect significant genetic differences between Arabidopsis accessions for all traits measured, across both temporal and environmental scales. The high frequency of measurement allowed us to observe that heritability was not only trait specific, but for some traits was also time specific. CONCLUSIONS: Such continuous real-time non-destructive phenotyping will allow detailed genetic and physiological investigations of the kinetics of plant homeostasis and development. The success and ultimate outcome of a breeding program will depend greatly on the genetic variance which is sampled. Our observation of temporal fluctuations in trait heritability shows that the moment of measurement can have lasting consequences. Ultimately such phenomic level technologies will provide more dynamic insights into plant physiology, and the necessary data for the omics revolution to reach its full potential.

Altered photosynthetic performance of a natural Arabidopsis accession is associated with atrazine resistance.

Natural variation for photosynthetic traits was studied by determining chlorophyll fluorescence parameters in a collection of Arabidopsis accessions. This screen revealed only one single accession (Ely), exhibiting photosynthetic characteristics markedly different from all others, while a few lines showed small but significant variation. Detailed genetic and physiological analyses showed reduced fitness for Ely compared with the standard laboratory strain Ler for various growth parameters. At low temperature (15 degrees C), Ely had a higher electron transport rate than Ler, indicating increased photosystem II efficiency under this condition, while at high temperature (30 degrees C) the opposite was observed. Ely had a high sensitivity to UV-B radiation compared with Ler and was atrazine resistant. This atrazine-resistance and related chlorophyll fluorescence traits were maternally inherited, pointing towards chloroplast-located gene(s). Definite proof that Ely is atrazine-resistant was obtained by sequencing the psbA gene, encoding the D1 protein of photosystem II, revealing a point mutation causing the same amino acid change as found in other atrazine-resistant species. Additional nuclear encoded genetic variation was also present, as was concluded from the small but significant differences in phenotype between Ely and its reciprocal crosses with Ler. It was concluded that the photosynthetic yield is highly conserved and that only severe selection pressure results in marked variations in photosynthetic performance.