Adapting to change: Rice surviving drought conditions in the field

Rice (Oryza sativa) is a staple food that feeds over half of the world (Wang et al., 2018). Therefore, it can be daunting to think what would happen if this crop was eliminated by environmental stressors. Plant populations survive in changing environments by evolving key mechanisms that allow continued growth and reproduction. Domesticated rice, for example, shows adaptive variation in molecular mechanisms that promote growth in drought-prone field conditions. Years of research in rice shoots and roots have revealed the function of genes involved in drought resistance. However, one limitation with these studies is that they are normally performed in controlled laboratory environments. While these settings are appropriate for studying an individual gene under a certain condition, they do not reflect the fluctuating conditions that plants experience while growing in fields. Therefore, more drought-related field studies need to be conducted to close this lab-to-field knowledge gap and understand the genetic strategies plants use to respond to drought. In this issue, Simon C. “Niels” Groen and colleagues (Groen et al., 2022) used an evolutionary systems biology approach to characterize adaptive traits of shoots and roots in order to understand how rice varieties maintain fitness in drought-prone fields.

One interesting aspect of this study is that the authors acquired and analyzed their data from field-grown rice plants. This approach allowed Groen and colleagues to observe the changing interactions with the environment that may take place when a plant is responding to drought. The author first used a panel of diverse rice accessions that have evolved to grow in wet or drought-prone agro-ecosystems to identify traits that have genetic variation and could potentially be used for breeding drought-resistant rice. This analysis was followed up by examining which traits were genetically associated with plant fitness. Despite these experiments being performed in the field, the authors measured traits that were less affected by within-field micro-environmental variations (i.e. xylem sap exudation and plasticity in root density) and observed these to be important for fitness under drought. Obtaining these measurements from field-grown rice roots is a strength of this study, as it is normally difficult to acquire these data because of the combination of the depth of roots and soil heterogeneity in fields.

The authors then performed transcriptome analyses to determine if gene expression was associated with fitness-linked root traits. Indeed, the authors observed gene expression patterns in roots and shoots associated with these traits. Further analyses of these data revealed key co-expression modules that positively correlated with adaptive drought resistance traits and plant growth. Interestingly, the authors identified a root co-expression module associated with root-arbuscular mycorrhizal fungi interactions. This unexpected observation demonstrated an advantage of conducting this analysis with field-grown rice. Another interesting finding was the presence of polygenic selection on fitness-linked transcripts in rice varieties that commonly experience drought stress. This observation may explain why the authors identified a correlation between gene expression patterns from more drought-tolerant varieties and plasticity in root density in dry conditions (see Figure). Finally, the authors validated their transcriptome analysis of enriched biological processes that associated with plant fitness by measuring adaptive root and shoot traits in a second field season.

Figure.

Gene expression patterns are linked to heritable root traits that are critical for rice fitness in drought-prone fields. Crown root samples grown in wet and dry conditions (left panel). This difference in crown root density in dry conditions is likely the result of higher levels of plasticity, a trait that was demonstrated to be linked by gene expression in response to drought (right panel). From Groen et al. (2022), Figures 4 and 7.

To summarize, this evolutionary systems biology approach allowed Groen and colleagues to acquire unique insight into the traits rice show adaptive variation for in response to drought. These traits appear to be heritable, and the author employed techniques to obtain high-quality measurements in rice fields. Importantly, the authors used their transcriptomic data to link gene expression to shoot and root traits related to fitness during drought stress in rice fields. Ultimately, this work provides a valuable resource that can guide the recognition of genetic combinations that underlie adaptive drought responses. It will be interesting to see if future studies will use this work as a blueprint to close the lab-to-field knowledge gap for other biological questions in different crop systems.