Systems genetics of plant adaptation to environmental stresses

Evolutionary systems biology reveals patterns of rice adaptation to drought-prone agro-ecosystems

Rice (Oryza sativa) was domesticated around 10,000 years ago and has developed into a staple for half of humanity. The crop evolved and is currently grown in stably wet and intermittently dry agro-ecosystems, but patterns of adaptation to differences in water availability remain poorly understood. While previous field studies have evaluated plant developmental adaptations to water deficit, adaptive variation in functional and hydraulic components, particularly in relation to gene expression, has received less attention. Here, we take an evolutionary systems biology approach to characterize adaptive drought resistance traits across roots and shoots. We find that rice harbors heritable variation in molecular, physiological, and morphological traits that is linked to higher fitness under drought. We identify modules of co-expressed genes that are associated with adaptive drought avoidance and tolerance mechanisms. These expression modules showed evidence of polygenic adaptation in rice subgroups harboring accessions that evolved in drought-prone agro-ecosystems. Fitness-linked expression patterns allowed us to identify the drought-adaptive nature of optimizing photosynthesis and interactions with arbuscular mycorrhizal fungi. Taken together, our study provides an unprecedented, integrative view of rice adaptation to water-limited field conditions.

Review: Plant eco-evolutionary responses to climate change: Emerging directions

Contemporary climate change is exposing plant populations to novel combinations of temperatures, drought stress, [CO₂] and other abiotic and biotic conditions. These changes are rapidly disrupting the evolutionary dynamics of plants. Despite the multifactorial nature of climate change, most studies typically manipulate only one climatic factor. In this opinion piece, we explore how climate change factors interact with each other and with biotic pressures to alter evolutionary processes. We evaluate the ramifications of climate change across life history stages,and examine how mating system variation influences population persistence under rapid environmental change. Furthermore, we discuss how spatial and temporal mismatches between plants and their mutualists and antagonists could affect adaptive responses to climate change. For example, plant-virus interactions vary from highly pathogenic to mildly facilitative, and are partly mediated by temperature, moisture availability and [CO₂]. Will host plants exposed to novel, stressful abiotic conditions be more susceptible to viral pathogens? Finally, we propose novel experimental approaches that could illuminate how plants will cope with unprecedented global change, such as resurrection studies combined with experimental evolution, genomics or epigenetics.

From Petri Dishes to Model Ecosystems

Model ecosystems could provide significant insight into the evolution and behavior of real ecosystems. We discuss the advantages and limitations of common approaches like mesocosms. In this context, we highlight recent breakthroughs that allow for the creation of networks of organisms with independently controlled environments and rates of chemical exchange.

Conceptualizing plant systems evolution

Organisms inhabiting extreme environments are emerging models in systems evolution, enabling us to identify the molecular alterations effecting major phenotypic divergence through comparative approaches. Here I discuss possible physiological mechanisms underlying evolutionary adaptations to extreme environments both theoretically and in relation to experimental observations. Reasoning leads me to the 'conserved steady-state' hypothesis of evolutionary adaptation: Between closely related plants adapted to differently composed soils, the homeostatically controlled steady-state set point cytosolic (buffered) concentrations of mineral ions are conserved. Subsequently, I compare molecular alterations expected to contribute to physiological adaptations with our present knowledge. Key roles of enhanced gene product dosage in plant evolutionary adaptations question the widespread stimulus response-centric paradigm. As a broader implication, co-regulation networks can lack decisive functional network elements. With this article, I hope to stimulate a discussion across research fields and provide an initial conceptual framework for future experimental testing and for quantitative modelling.

Preferential Geographic Distribution Pattern of Abiotic Stress Tolerant Rice

Crop productivity and stability of the food system are threatened by climate change, mainly through the effects of predicted abiotic stresses. Despite extensive research on abiotic stress tolerance in the past decades, the successful translation of these research to fields/farmers is scarce. The impelling demand of climate resilient varieties, and the poor translation of research into the field despite the availability of high throughput technologies lead us to critically analyse a neglected aspect of current abiotic stress tolerance research. Although environmental factors play the most important role in the development of adaptive traits of plants, most abiotic stress tolerance research ignores eco-geographic aspects of highly stress tolerant accessions. In this review, we critically examined the geographic distribution pattern of highly tolerant rice accessions of all major abiotic stresses along with one micronutrient deficiency. Remarkably, we identified a shared geographic distribution pattern of highly tolerant accessions for all abiotic stresses including zinc deficiency despite the sparseness of highly tolerant accessions. The majority of these tolerant accessions predominately originated from Bangladesh centred narrow geographic region. We therefore analysed the climatic and agro-ecological features of Bangladesh. Considering the threat of climate change on global food security and poverty, urgent concerted research efforts are necessary for the development of climate resilient rice varieties utilizing the technological advancement, know-hows, and the preferential distribution pattern of abiotic stress tolerant rice.