The environment has constantly shaped plant genomes, but the genetic bases underlying how plants adapt to environmental influences remain largely unknown. We constructed a high-density genomic variation map of 263 geographically representative peach landraces and wild relatives. A combination of whole-genome selection scans and genome-wide environmental association studies (GWEAS) was performed to reveal the genomic bases of peach adaptation to diverse climates. A total of 2092 selective sweeps that underlie local adaptation to both mild and extreme climates were identified, including 339 sweeps conferring genomic pattern of adaptation to high altitudes. Using genome-wide environmental association studies (GWEAS), a total of 2755 genomic loci strongly associated with 51 specific environmental variables were detected. The molecular mechanism underlying adaptive evolution of high drought, strong UVB, cold hardiness, sugar content, flesh color, and bloom date were revealed. Finally, based on 30 yr of observation, a candidate gene associated with bloom date advance, representing peach responses to global warming, was identified. Collectively, our study provides insights into molecular bases of how environments have shaped peach genomes by natural selection and adds candidate genes for future studies on evolutionary genetics, adaptation to climate changes, and breeding.
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A balancing act: how plants integrate nitrogen and water signals
Abstract Nitrogen (N) and water (W) are crucial inputs for plant survival as well as costly resources for agriculture. Given their importance, the molecular mechanisms that plants rely on to signal changes in either N or W status have been under intense scrutiny. However, how plants sense and respond to the combination of N and W signals at the molecular level has received scant attention. The purpose of this review is to shed light on what is currently known about how plant responses to N are impacted by W status. We review classic studies which detail how N and W combinations have both synergistic and antagonistic effects on key plant traits, such as root architecture and stomatal aperture. Recent molecular studies of N and W interactions show that mutations in genes involved in N metabolism affect drought responses, and vice versa. Specifically, perturbing key N signaling genes may lead to changes in drought-responsive gene expression programs, which is supported by a meta-analysis we conduct on available transcriptomic data. Additionally, we cite studies that show how combinatorial transcriptional responses to N and W status might drive crop phenotypes. Through these insights, we suggest research strategies that could help to develop crops adapted to marginal soils depleted in both N and W, an important task in the face of climate change.
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- Award ID(s):
- 1840761
- NSF-PAR ID:
- 10231630
- Editor(s):
- Xu, Guohua
- Date Published:
- Journal Name:
- Journal of Experimental Botany
- Volume:
- 71
- Issue:
- 15
- ISSN:
- 0022-0957
- Page Range / eLocation ID:
- 4442 to 4451
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Water availability influences all aspects of plant growth and development; however, most studies of plant responses to drought have focused on vegetative organs, notably roots and leaves. Far less is known about the molecular bases of drought acclimation responses in fruits, which are complex organs with distinct tissue types. To obtain a more comprehensive picture of the molecular mechanisms governing fruit development under drought, we profiled the transcriptomes of a spectrum of fruit tissues from tomato (Solanum lycopersicum), spanning early growth through ripening and collected from plants grown under varying intensities of water stress. In addition, we compared transcriptional changes in fruit with those in leaves to highlight different and conserved transcriptome signatures in vegetative and reproductive organs. We observed extensive and diverse genetic reprogramming in different fruit tissues and leaves, each associated with a unique response to drought acclimation. These included major transcriptional shifts in the placenta of growing fruit and in the seeds of ripe fruit related to cell growth and epigenetic regulation, respectively. Changes in metabolic and hormonal pathways, such as those related to starch, carotenoids, jasmonic acid, and ethylene metabolism, were associated with distinct fruit tissues and developmental stages. Gene coexpression network analysis provided further insights into the tissue-specific regulation of distinct responses to water stress. Our data highlight the spatiotemporal specificity of drought responses in tomato fruit and indicate known and unrevealed molecular regulatory mechanisms involved in drought acclimation, during both vegetative and reproductive stages of development.
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BACKGROUND The availability of nitrogen (N) to plants and microbes has a major influence on the structure and function of ecosystems. Because N is an essential component of plant proteins, low N availability constrains the growth of plants and herbivores. To increase N availability, humans apply large amounts of fertilizer to agricultural systems. Losses from these systems, combined with atmospheric deposition of fossil fuel combustion products, introduce copious quantities of reactive N into ecosystems. The negative consequences of these anthropogenic N inputs—such as ecosystem eutrophication and reductions in terrestrial and aquatic biodiversity—are well documented. Yet although N availability is increasing in many locations, reactive N inputs are not evenly distributed globally. Furthermore, experiments and theory also suggest that global change factors such as elevated atmospheric CO 2 , rising temperatures, and altered precipitation and disturbance regimes can reduce the availability of N to plants and microbes in many terrestrial ecosystems. This can occur through increases in biotic demand for N or reductions in its supply to organisms. Reductions in N availability can be observed via several metrics, including lowered nitrogen concentrations ([N]) and isotope ratios (δ 15 N) in plant tissue, reduced rates of N mineralization, and reduced terrestrial N export to aquatic systems. However, a comprehensive synthesis of N availability metrics, outside of experimental settings and capable of revealing large-scale trends, has not yet been carried out. ADVANCES A growing body of observations confirms that N availability is declining in many nonagricultural ecosystems worldwide. Studies have demonstrated declining wood δ 15 N in forests across the continental US, declining foliar [N] in European forests, declining foliar [N] and δ 15 N in North American grasslands, and declining [N] in pollen from the US and southern Canada. This evidence is consistent with observed global-scale declines in foliar δ 15 N and [N] since 1980. Long-term monitoring of soil-based N availability indicators in unmanipulated systems is rare. However, forest studies in the northeast US have demonstrated decades-long decreases in soil N cycling and N exports to air and water, even in the face of elevated atmospheric N deposition. Collectively, these studies suggest a sustained decline in N availability across a range of terrestrial ecosystems, dating at least as far back as the early 20th century. Elevated atmospheric CO 2 levels are likely a main driver of declines in N availability. Terrestrial plants are now uniformly exposed to ~50% more of this essential resource than they were just 150 years ago, and experimentally exposing plants to elevated CO 2 often reduces foliar [N] as well as plant-available soil N. In addition, globally-rising temperatures may raise soil N supply in some systems but may also increase N losses and lead to lower foliar [N]. Changes in other ecosystem drivers—such as local climate patterns, N deposition rates, and disturbance regimes—individually affect smaller areas but may have important cumulative effects on global N availability. OUTLOOK Given the importance of N to ecosystem functioning, a decline in available N is likely to have far-reaching consequences. Reduced N availability likely constrains the response of plants to elevated CO 2 and the ability of ecosystems to sequester carbon. Because herbivore growth and reproduction scale with protein intake, declining foliar [N] may be contributing to widely reported declines in insect populations and may be negatively affecting the growth of grazing livestock and herbivorous wild mammals. Spatial and temporal patterns in N availability are not yet fully understood, particularly outside of Europe and North America. Developments in remote sensing, accompanied by additional historical reconstructions of N availability from tree rings, herbarium specimens, and sediments, will show how N availability trajectories vary among ecosystems. Such assessment and monitoring efforts need to be complemented by further experimental and theoretical investigations into the causes of declining N availability, its implications for global carbon sequestration, and how its effects propagate through food webs. Responses will need to involve reducing N demand via lowering atmospheric CO 2 concentrations, and/or increasing N supply. Successfully mitigating and adapting to declining N availability will require a broader understanding that this phenomenon is occurring alongside the more widely recognized issue of anthropogenic eutrophication. Intercalibration of isotopic records from leaves, tree rings, and lake sediments suggests that N availability in many terrestrial ecosystems has steadily declined since the beginning of the industrial era. Reductions in N availability may affect many aspects of ecosystem functioning, including carbon sequestration and herbivore nutrition. Shaded areas indicate 80% prediction intervals; marker size is proportional to the number of measurements in each annual mean. Isotope data: (tree ring) K. K. McLauchlan et al. , Sci. Rep. 7 , 7856 (2017); (lake sediment) G. W. Holtgrieve et al. , Science 334 , 1545–1548 (2011); (foliar) J. M. Craine et al. , Nat. Ecol. Evol. 2 , 1735–1744 (2018)more » « less
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Abstract Classifying the diverse ways that plants respond to hydrologic stress into generalizable ‘water‐use strategies’ has long been an eco‐physiological research goal. While many schemes for describing water‐use strategies have proven to be quite useful, they are also associated with uncertainties regarding their theoretical basis and their connection to plant carbon and water relations. In this review, we discuss the factors that shape plant water stress responses and assess the approaches used to classify a plant's water‐use strategy, paying particular attention to the popular but controversial concept of a continuum from isohydry to anisohydry.
A generalizable and predictive framework for assessing plant water‐use strategies has been historically elusive, yet recent advances in plant physiology and hydraulics provide the field with a way past these obstacles. Specifically, we promote the idea that many metrics that quantify water‐use strategies are highly dynamic and emergent from the interaction between plant traits and environmental conditions, and that this complexity has historically hindered the development of a generalizable water‐use strategy framework.
This idea is explored using a plant hydraulics model to identify: (a) distinct temporal phases in plant hydraulic regulation during drought that underpin dynamic water‐use responses, and (b) how variation in both traits and environmental forcings can significantly alter common metrics used to characterize plant water‐use strategies. This modelling exercise can bridge the divide between various conceptualizations of water‐use strategies and provide targeted hypotheses to advance the understanding and quantification of plant water status regulation across spatial and temporal scales.
Finally, we describe research frontiers that are necessary to improve the predictive capacity of the plant water‐use strategy concept, including further investigation into the below‐ground determinants of plant water relations, targeted data collection efforts and the potential to scale these concepts from individuals to whole regions.
A free
Plain Language Summary can be found within the Supporting Information of this article. -
null (Ed.)Like animals, plants have internal biological clocks that allow them to adapt to daily and yearly changes, such as day-night cycles or seasons turning. Unlike animals, however, plants cannot move when their environment becomes different, so they need to be able to weather these changes by adjusting which genes they switch on and off. To do this, plants keep track of how long days are using external cues such as light or temperature. One of the effects of climate change is that these cues become less reliable, making it harder for plants to adapt to their environment and survive. This is a potential problem for crop species, like Brassica rapa . This plant has many edible forms, including Chinese cabbage, oilseed, pak choi, and turnip. It is also a close relative of the well-studied model plant, Arabidopsis . Since evolving away from Arabidopsis , the genome of B. rapa tripled, meaning it has one, two, or three copies of each gene. This has allowed the extra gene copies to mutate and adapt to different purposes. The question is, what impact has this genome expansion had on the plant's biological clock? One way to find out is to perform RNA-sequencing experiments, which record the genes a plant is using at any one time. Here, Greenham, Sartor et al. report the results of a series of RNA-sequencing experiments performed every two hours across two days. Plants were first exposed to light-dark or temperature cycles and then samples were taken when the plants were in constant light and temperature. This revealed which genes B. rapa turned on and off in response to signals from the internal biological clock. It turns out that the biological clock of B. rapa controls close to three quarters of its genes. These genes showed distinct phases, increasing or decreasing in regular patterns. But the different copies of duplicated and triplicated genes did not necessarily all behave in the same way. Many of the copies had different rhythms, and some increased and decreased in patterns totally opposite to their counterparts. Not only did the daily patterns differ, but responses to stressors like drought were also altered. Comparing these patterns to the patterns seen in Arabidopsis revealed that often, one B. rapa gene behaved just like its Arabidopsis equivalent, while its copies had evolved new behaviors. The different behaviors of the copies of each gene in B. rapa relative to its biological clock allow this plant to grow in different environments with varying temperatures and day lengths. Understanding how these adaptations work opens new avenues of research into how plants detect and respond to environmental signals. This could help to guide future work into targeting genes to improve crop growth and stress resilience.more » « less
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1093/jxb/eraa054
