Characterizing root response phenotypes by neural network analysis

Crop adaptation to climate change as a consequence of long-term breeding

Major global crops in high-yielding, temperate cropping regions are facing increasing threats from the impact of climate change, particularly from drought and heat at critical developmental timepoints during the crop lifecycle. Research to address this concern is frequently focused on attempts to identify exotic genetic diversity showing pronounced stress tolerance or avoidance, to elucidate and introgress the responsible genetic factors or to discover underlying genes as a basis for targeted genetic modification. Although such approaches are occasionally successful in imparting a positive effect on performance in specific stress environments, for example through modulation of root depth, major-gene modifications of plant architecture or function tend to be highly context-dependent. In contrast, long-term genetic gain through conventional breeding has incrementally increased yields of modern crops through accumulation of beneficial, small-effect variants which also confer yield stability via stress adaptation. Here we reflect on retrospective breeding progress in major crops and the impact of long-term, conventional breeding on climate adaptation and yield stability under abiotic stress constraints. Looking forward, we outline how new approaches might complement conventional breeding to maintain and accelerate breeding progress, despite the challenges of climate change, as a prerequisite to sustainable future crop productivity.

Effects of exogenous lanthanum(III) exposure on the positive interaction between mutually beneficial populations

Rare earth elements (REEs) are widely used in various fields, and their accumulation has been reported to pose environmental risks. Most studies confirmed the damage of excessive REE exposure to individual plants; however, little attention has been given to their effects on plant populations. A positive interaction indicates a mutually beneficial relationship between two populations, which is beneficial to the survival and growth of the populations. However, it remains unknown whether exogenous REEs affect the positive interactions between populations. This study investigated the effects of exogenous lanthanum(III) [La(III)] exposure on the positive interaction between soybean (Glycine max L.) and wheat (Triticum aestivum L.) populations by their modules. At normal nutrient level (½-strength Hoagland), the inhibition of excessive La(III) on population modules decreased with increasing population density. Decreases of 39.26 to 1.05% for soybean and 41.45 to 2.41% for wheat indicated the inhibition of La(III) on the positive interaction of both populations weakened with increasing population density. At low nutrient level (¼-strength Hoagland), the inhibition of excessive La(III) on population modules increased with increasing population density. Decreases of 5.82-57.14% for soybean and 4.22-59.04% for wheat indicated the inhibition of La(III) on the positive interaction of both population was strengthened with increasing population density. In summary, the inhibitory effects of exogenous La(III) exposure on the positive interaction between populations vary with both nutrient level and population density. This is a new factor that needs to be considered when evaluating the safety risks of REEs in the environment.

A Statistical Growth Property of Plant Root Architectures

Numerous types of biological branching networks, with varying shapes and sizes, are used to acquire and distribute resources. Here, we show that plant root and shoot architectures share a fundamental design property. We studied the spatial density function of plant architectures, which specifies the probability of finding a branch at each location in the 3-dimensional volume occupied by the plant. We analyzed 1645 root architectures from four species and discovered that the spatial density functions of all architectures are population-similar. This means that despite their apparent visual diversity, all of the roots studied share the same basic shape, aside from stretching and compression along orthogonal directions. Moreover, the spatial density of all architectures can be described as variations on a single underlying function: a Gaussian density truncated at a boundary of roughly three standard deviations. Thus, the root density of any architecture requires only four parameters to specify: the total mass of the architecture and the standard deviations of the Gaussian in the three (x, y, z) growth directions. Plant shoot architectures also follow this design form, suggesting that two basic plant transport systems may use similar growth strategies.

Effects of nutrient level and planting density on population relationship in soybean and wheat intercropping populations

A positive interaction between plant populations is a type of population relationship formed during long-term evolution. This interaction can alleviate population competition, improve resource utilization in populations, and promote population harmony and community stability. However, cultivated plant populations may have insufficient time to establish a positive interaction, thereby hindering the formation of the positive interaction. As current studies have not fully addressed these issues, our study established soybean/wheat intercropping populations beneficial for growth and explored the effects of nutrient level and planting density on the positive interaction between the two crops. Changes across population modules in both sole cropping and intercropping populations of soybean and wheat were analyzed. Results using nutrient levels of ½- or ¼-strength Hoagland solution indicated that soybean/wheat intercropping population modules significantly increased at low planting densities (D20 and D26) and significantly decreased at high planting densities (D32 and D60). Therefore, as planting density increased, the modules of both intercropping populations initially increased before decreasing. Similarly, positive interaction initially strengthened before weakening. Moreover, at an intermediate planting density, the population modules reached their maxima, and the positive interaction was the strongest. Under the same planting density, ¼-strength Hoagland solution recorded better growth for the soybean/wheat intercropping population modules compared to results using the ½-strength Hoagland solution. These findings indicated that low nutrient level can increase the positive interaction of intercropping populations at a given planting density, and that environmental nutrient level and population planting densities constrain the positive interaction between soybean and wheat populations in the intercropping system. This study highlights issues that need to be addressed when constructing intercropping populations.

An Integrative Approach to Analyze Seed Germination in Brassica napus

Seed germination is a complex trait determined by the interaction of hormonal, metabolic, genetic, and environmental components. Variability of this trait in crops has a big impact on seedling establishment and yield in the field. Classical studies of this trait in crops have focused mainly on the analyses of one level of regulation in the cascade of events leading to seed germination. We have carried out an integrative and extensive approach to deepen our understanding of seed germination in Brassica napus by generating transcriptomic, metabolic, and hormonal data at different stages upon seed imbibition. Deep phenotyping of different seed germination-associated traits in six winter-type B. napus accessions has revealed that seed germination kinetics, in particular seed germination speed, are major contributors to the variability of this trait. Metabolic profiling of these accessions has allowed us to describe a common pattern of metabolic change and to identify the levels of malate and aspartate metabolites as putative metabolic markers to estimate germination performance. Additionally, analysis of seed content of different hormones suggests that hormonal balance between ABA, GA, and IAA at crucial time points during this process might underlie seed germination differences in these accessions. In this study, we have also defined the major transcriptome changes accompanying the germination process in B. napus. Furthermore, we have observed that earlier activation of key germination regulatory genes seems to generate the differences in germination speed observed between accessions in B. napus. Finally, we have found that protein-protein interactions between some of these key regulator are conserved in B. napus, suggesting a shared regulatory network with other plant species. Altogether, our results provide a comprehensive and detailed picture of seed germination dynamics in oilseed rape. This new framework will be extremely valuable not only to evaluate germination performance of B. napus accessions but also to identify key targets for crop improvement in this important process.

A novel evaluation of the effect of lanthanum exposure on plant populations

The accumulation of rare earth elements (REEs) in the environment has recently become a new environmental problem. There have been many studies about the effects of REEs on plant at the individual, organ, cellular and genetic levels. Plants exist in populations under natural conditions, but little is known about the effects of REEs on plant populations. In this study, the effects of lanthanum (III) [La(III)] on the root module growth of soybean (Glycine max L) populations at different densities were investigated by simulating La(III) pollution. Results showed that at La(III) concentrations of 0.40 and 1.20 mM, both the root module growth parameters and leaf photosynthesis parameters were decreased, with 1.20 mM of La(III) causing a more significant decrease. In addition, the above parameters in low-density soybean populations decreased more significantly than those in high-density soybean populations. The above results show that the inhibitory effects of 0.40 and 1.20 mM of La(III) on the growth of root modules are closely related to the inhibition of photosynthesis in soybean population. Moreover, the inhibitory effect of La(III) on the growth of root modules of soybean population is enhanced as the La(III) concentration increases, while is weakened as plant population density increases. This study would provide a reference for the further research on the ecotoxicology of REEs, and show a new perspective and basis for the objective assessment of the environmental risks of REEs.

ONE SENTENCE SUMMARY

La(III) pollution affects the root module growth and photosynthesis in soybean populations, and the effects vary depending on soybean population densities.

A new method for the rapid characterization of root growth and distribution using digital image correlation

Rapidly determining root growth patterns is biologically important and technically challenging. Current methods focus on direct observation of roots and require destructive excavations or time-consuming root tracing. We developed a novel methodology based on analyzing soil particle displacement, rather than direct observation of roots. This inferred root growth method uses digital image correlation (DIC) analysis, an established and high-throughput method used in many engineering and science disciplines. By applying DIC analyses to repeated images of plants grown in clear window boxes, we produced visually intuitive and quantifiable strain maps, indicating the magnitude and direction of soil movement. From this, we could infer root growth and rapidly quantify root system metrics. Strain measures were closely associated with the spatial distribution of roots and correlated with root length measured using conventional approaches. The method also allowed for the detection of root proliferation in nutrient-enriched soil patches, indicating its suitability for quantifying biological patterns. This novel application of DIC in root biology is effective, scalable, low cost, flexible and complementary to existing technologies. This method offers a new tool for answering questions in plant biology and will be particularly useful in studies involving temporal dynamics of root processes.

Primary Postnatal Dorsal Root Ganglion Culture from Conventionally Slaughtered Calves

Neurological disorders in ruminants have an important impact on veterinary health, but very few host-specific in vitro models have been established to study diseases affecting the nervous system. Here we describe a primary neuronal dorsal root ganglia (DRG) culture derived from calves after being conventionally slaughtered for food consumption. The study focuses on the in vitro characterization of bovine DRG cell populations by immunofluorescence analysis. The effects of various growth factors on neuron viability, neurite outgrowth and arborisation were evaluated by morphological analysis. Bovine DRG neurons are able to survive for more than 4 weeks in culture. GF supplementation is not required for neuronal survival and neurite outgrowth. However, exogenously added growth factors promote neurite outgrowth. DRG cultures from regularly slaughtered calves represent a promising and sustainable host specific model for the investigation of pain and neurological diseases in bovines.

Molecular and systems approaches towards drought-tolerant canola crops

1169 I. 1170 II. 1170 III. 1172 IV. 1176 V. 1181 VI. 1182 1183 References 1183 SUMMARY: Modern agriculture is facing multiple challenges including the necessity for a substantial increase in production to meet the needs of a burgeoning human population. Water shortage is a deleterious consequence of both population growth and climate change and is one of the most severe factors limiting global crop productivity. Brassica species, particularly canola varieties, are cultivated worldwide for edible oil, animal feed, and biodiesel, and suffer dramatic yield loss upon drought stress. The recent release of the Brassica napus genome supplies essential genetic information to facilitate identification of drought-related genes and provides new information for agricultural improvement in this species. Here we summarize current knowledge regarding drought responses of canola, including physiological and -omics effects of drought. We further discuss knowledge gained through translational biology based on discoveries in the closely related reference species Arabidopsis thaliana and through genetic strategies such as genome-wide association studies and analysis of natural variation. Knowledge of drought tolerance/resistance responses in canola together with research outcomes arising from new technologies and methodologies will inform novel strategies for improvement of drought tolerance and yield in this and other important crop species.