Phenotypic Trait Identification Using a Multimodel Bayesian Method: A Case Study Using Photosynthesis in Brassica rapa Genotypes

The genome sequence of Hirschfeldia incana, a new Brassicaceae model to improve photosynthetic light-use efficiency

Photosynthesis is a key process in sustaining plant and human life. Improving the photosynthetic capacity of agricultural crops is an attractive means to increase their yields. While the core mechanisms of photosynthesis are highly conserved in C₃ plants, these mechanisms are very flexible, allowing considerable diversity in photosynthetic properties. Among this diversity is the maintenance of high photosynthetic light-use efficiency at high irradiance as identified in a small number of exceptional C₃ species. Hirschfeldia incana, a member of the Brassicaceae family, is such an exceptional species, and because it is easy to grow, it is an excellent model for studying the genetic and physiological basis of this trait. Here, we present a reference genome of H. incana and confirm its high photosynthetic light-use efficiency. While H. incana has the highest photosynthetic rates found so far in the Brassicaceae, the light-saturated assimilation rates of closely related Brassica rapa and Brassica nigra are also high. The H. incana genome has extensively diversified from that of B. rapa and B. nigra through large chromosomal rearrangements, species-specific transposon activity, and differential retention of duplicated genes. Duplicated genes in H. incana, B. rapa, and B. nigra that are involved in photosynthesis and/or photoprotection show a positive correlation between copy number and gene expression, providing leads into the mechanisms underlying the high photosynthetic efficiency of these species. Our work demonstrates that the H. incana genome serves as a valuable resource for studying the evolution of high photosynthetic light-use efficiency and enhancing photosynthetic rates in crop species.

The use of R in photosynthesis research

R is one of the most commonly used analytical tools in the plant sciences. To identify key trends in general reported R use and patterns in photosynthesis research, we explored the frequency of R use in 2966 articles published in the 377 journals with 'photosynthesis' in the title from 2010 to 2019 using the Web of Science search. Solutions provided by each R package cited in the articles or online sources was recorded and classified. The percentage of research articles reporting R use increased linearly from 3.6% in 2010 to 12.5% in 2019. The three main categories of R package solutions were 'general statistical calculations and graph packages' (G); 'photosynthesis special-purpose packages' (S); and 'genetic and evolutionary packages' (E). The top five R packages cited were nlme (G), lme4 (G), multcomp (G), plantecophys (S), and ape (E). The increasing popularity of R use in photosynthesis research is due to its user-friendly and abundant open-source codes online for handling specific issues, particularly in fitting photosynthesis models. These findings are limited by the number of articles and online sources, but they reveal a significant increase in usage in photosynthesis research over the past decade and have a bright prospect in the future.

Cellular interactions between social experience, alcohol sensitivity, and GABAergic inhibition in a crayfish neural circuit

We report here that prior social experience modified the behavioral responses of adult crayfish to acute alcohol exposure. Animals housed individually for 1 wk before alcohol exposure were less sensitive to the intoxicating effects of alcohol than animals housed in groups, and these differences are based on changes in the nervous system rather than differences in alcohol uptake. To elucidate the underlying neural mechanisms, we investigated the neurophysiological responses of the lateral giant (LG) interneurons after alcohol exposure. Specifically, we measured the interactions between alcohol and different GABA_A-receptor antagonists and agonists in reduced crayfish preparations devoid of brain-derived tonic GABAergic inhibition. We found that alcohol significantly increased the postsynaptic potential of the LG neurons, but contrary to our behavioral observations, the results were similar for isolated and communal animals. The GABA_A-receptor antagonist picrotoxin, however, facilitated LG postsynaptic potentials more strongly in communal crayfish, which altered the neurocellular interactions with alcohol, whereas TPMPA [(1,2,5,6-tetrahydropyridin-4-yl)methylphosphinic acid], an antagonist directed against GABA_A-receptors with ρ subunits, did not produce any effects. Muscimol, an agonist for GABA_A-receptors, blocked the stimulating effects of alcohol, but this was independent of prior social history. THIP [4,5,6,7-tetrahydroisoxazolo(5,4-c)pyridin-3-ol], an agonist directed against GABA_A-receptors with δ subunits, which were not previously known to exist in the LG circuit, replicated the suppressing effects of muscimol. Together, our findings provide strong evidence that alcohol interacts with the crayfish GABAergic system, and the interplay between prior social experience and acute alcohol intoxication might be linked to changes in the expression and function of specific GABA_A-receptor subtypes.NEW & NOTEWORTHY The complex interactions between alcohol and prior social experience are still poorly understood. Our work demonstrates that socially isolated crayfish exhibit lower neurobehavioral sensitivity to acute ethanol compared with communally housed animals, and this socially mediated effect is based on changes in the nervous systems rather than on differences in uptake or metabolism. By combining intracellular neurophysiology and neuropharmacology, we investigated the role of the main inhibitory neurotransmitter GABA, and its receptor subtypes, in shaping this process.

Rapid Chlorophyll a Fluorescence Light Response Curves Mechanistically Inform Photosynthesis Modeling

Crop improvement is crucial to ensuring global food security under climate change, and hence there is a pressing need for phenotypic observations that are both high throughput and improve mechanistic understanding of plant responses to environmental cues and limitations. In this study, chlorophyll a fluorescence light response curves and gas-exchange observations are combined to test the photosynthetic response to moderate drought in four genotypes of Brassica rapa The quantum yield of PSII (ϕ PSII ) is here analyzed as an exponential decline under changing light intensity and soil moisture. Both the maximum ϕ PSII and the rate of ϕ PSII decline across a large range of light intensities (0-1,000 μmol photons m-2 s-1; β PSII ) are negatively affected by drought. We introduce an alternative photosynthesis model (β PSII model) incorporating parameters from rapid fluorescence response curves. Specifically, the model uses β PSII as an input for estimating the photosynthetic electron transport rate, which agrees well with two existing photosynthesis models (Farquhar-von Caemmerer-Berry and Yin). The β PSII model represents a major improvement in photosynthesis modeling through the integration of high-throughput fluorescence phenotyping data, resulting in gained parameters of high mechanistic value.

Genetic variation for photosynthetic capacity and efficiency in spring wheat

One way to increase yield potential in wheat is screening for natural variation in photosynthesis. This study uses measured and modelled physiological parameters to explore genotypic diversity in photosynthetic capacity (Pc, Rubisco carboxylation capacity per unit leaf area at 25 °C) and efficiency (Peff, Pc per unit of leaf nitrogen) in wheat in relation to fertilizer, plant stage, and environment. Four experiments (Aus1, Aus2, Aus3, and Mex1) were carried out with diverse wheat collections to investigate genetic variation for Rubisco capacity (Vcmax25), electron transport rate (J), CO2 assimilation rate, stomatal conductance, and complementary plant functional traits: leaf nitrogen, leaf dry mass per unit area, and SPAD. Genotypes for Aus1 and Aus2 were grown in the glasshouse with two fertilizer levels. Genotypes for Aus3 and Mex1 experiments were grown in the field in Australia and Mexico, respectively. Results showed that Vcmax25 derived from gas exchange measurements is a robust parameter that does not depend on stomatal conductance and was positively correlated with Rubisco content measured in vitro. There was significant genotypic variation in most of the experiments for Pc and Peff. Heritability of Pc reached 0.7 and 0.9 for SPAD. Genotypic variation and heritability of traits show that there is scope for these traits to be used in pre-breeding programmes to improve photosynthesis with the ultimate objective of raising yield potential.