Abscisic acid represses the transcription of chloroplast genes

Regulation of chloroplast biogenesis, development, and signaling by endogenous and exogenous cues

Chloroplasts are one of the defining features in most plants, primarily known for their unique property to carry out photosynthesis. Besides this, chloroplasts are also associated with hormone and metabolite productions. For this, biogenesis and development of chloroplast are required to be synchronized with the seedling growth to corroborate the maximum rate of photosynthesis following the emergence of seedlings. Chloroplast biogenesis and development are dependent on the signaling to and from the chloroplast, which are in turn regulated by several endogenous and exogenous cues. Light and hormones play a crucial role in chloroplast maturation and development. Chloroplast signaling involves a coordinated two-way connection between the chloroplast and nucleus, termed retrograde and anterograde signaling, respectively. Anterograde and retrograde signaling are involved in regulation at the transcriptional level and downstream modifications and are modulated by several metabolic and external cues. The communication between chloroplast and nucleus is essential for plants to develop strategies to cope with various stresses including high light or high heat. In this review, we have summarized several aspects of chloroplast development and its regulation through the interplay of various external and internal factors. We have also discussed the involvement of chloroplasts as sensors of various external environment stress factors including high light and temperature, and communicate via a series of retrograde signals to the nucleus, thus playing an essential role in plants' abiotic stress response.

SUPPRESSOR OF MAX2 LIKE 6, 7, and 8 Interact with DDB1 BINDING WD REPEAT DOMAIN HYPERSENSITIVE TO ABA DEFICIENT 1 to Regulate the Drought Tolerance and Target SUCROSE NONFERMENTING 1 RELATED PROTEIN KINASE 2.3 to Abscisic Acid Response in Arabidopsis

SUPPRESSOR OF MAX2-LIKE 6, 7, and 8 (SMXL6,7,8) function as repressors and transcription factors of the strigolactone (SL) signaling pathway, playing an important role in the development and stress tolerance in Arabidopsis thaliana. However, the molecular mechanism by which SMXL6,7,8 negatively regulate drought tolerance and ABA response remains largely unexplored. In the present study, the interacting protein and downstream target genes of SMXL6,7,8 were investigated. Our results showed that the substrate receptor for the CUL4-based E3 ligase DDB1-BINDING WD-REPEAT DOMAIN (DWD) HYPERSENSITIVE TO ABA DEFICIENT 1 (ABA1) (DWA1) physically interacted with SMXL6,7,8. The degradation of SMXL6,7,8 proteins were partially dependent on DWA1. Disruption of SMXL6,7,8 resulted in increased drought tolerance and could restore the drought-sensitive phenotype of the dwa1 mutant. In addition, SMXL6,7,8 could directly bind to the promoter of SUCROSE NONFERMENTING 1 (SNF1)-RELATED PROTEIN KINASE 2.3 (SnRK2.3) to repress its transcription. The mutations in SnRK2.2/2.3 significantly suppressed the hypersensitivity of smxl6/7/8 to ABA-mediated inhibition of seed germination. Conclusively, SMXL6,7,8 interact with DWA1 to negatively regulate drought tolerance and target ABA-response genes. These data provide insights into drought tolerance and ABA response in Arabidopsis via the SMXL6,7,8-mediated SL signaling pathway.

Response of waxy maize (Zea mays L. var. ceratina Kulesh) leaf photosynthesis to low temperature during the grain-filling stage

Low temperature (LT) during the grain-filling stage is an important factor that affects the source-sink relationship and leads to yield loss in maize (Zea mays L). In this study, field and pot trials were conducted to investigate the effects of LT during the grain-filling stage on leaf photosynthesis, antioxidant system, hormones, and grain yield of waxy maize cultivars Suyunuo 5 (S5) and Yunuo 7 (Y7). The results showed that LT treatment inhibited the chlorophyll biosynthesis and reduced the photosynthetic pigment levels during grain-filling stage. Ribulose-1,5-bisphosphate carboxylase and phosphoenolpyruvate carboxylase activities, photosynthetic rate, transpiration rate, and stomatal conductance decreased under LT treatment during the grain-filling stage. Furthermore, LT treatment increased the contents of malondialdehyde and reactive oxygen species, and decreased the activities of catalase, superoxide dismutase, peroxidase, and ascorbate peroxidase in the ear leaves, which accelerated the oxidative damage of leaf. The LT treatment also raised abscisic acid content and reduced indole acetic acid content in the ear leaves during grain-filling stage. The results of field and pot trials were verified by each other, but the field effect was greater than that of pot. Overall, LT treatment reduced the waxy maize dry matter accumulation after silking by affecting the physiological and biochemical processes of leaves, and ultimately decreased grain yield.

Dynamic regulation of DNA methylation and histone modifications in response to abiotic stresses in plants

DNA methylation and histone modification are evolutionarily conserved epigenetic modifications that are crucial for the expression regulation of abiotic stress-responsive genes in plants. Dynamic changes in gene expression levels can result from changes in DNA methylation and histone modifications. In the last two decades, how epigenetic machinery regulates abiotic stress responses in plants has been extensively studied. Here, based on recent publications, we review how DNA methylation and histone modifications impact gene expression regulation in response to abiotic stresses such as drought, abscisic acid, high salt, extreme temperature, nutrient deficiency or toxicity, and ultraviolet B exposure. We also review the roles of epigenetic mechanisms in the formation of transgenerational stress memory. We posit that a better understanding of the epigenetic underpinnings of abiotic stress responses in plants may facilitate the design of more stress-resistant or -resilient crops, which is essential for coping with global warming and extreme environments.

Organelles and phytohormones: a network of interactions in plant stress responses

Phytohormones are major signaling components that contribute to nearly all aspects of plant life. They constitute an interconnected communication network to fine-tune growth and development in response to the ever-changing environment. To this end, they have to coordinate with other signaling components, such as reactive oxygen species and calcium signals. On the one hand, the two endosymbiotic organelles, plastids and mitochondria, control various aspects of phytohormone signaling and harbor important steps of hormone precursor biosynthesis. On the other hand, phytohormones have feedback actions on organellar functions. In addition, organelles and phytohormones often act in parallel in a coordinated matter to regulate cellular functions. Therefore, linking organelle functions with increasing knowledge of phytohormone biosynthesis, perception, and signaling will reveal new aspects of plant stress tolerance. In this review, we highlight recent work on organelle-phytohormone interactions focusing on the major stress-related hormones abscisic acid, jasmonates, salicylic acid, and ethylene.

The threshold between life and death in Cistus albidus L. seedlings: mechanisms underlying drought tolerance and resilience

Drought can lead to important shifts in population dynamics if it occurs during seedling establishment. With the aim of elucidating the underlying mechanisms of drought tolerance and resilience, here we monitored the survival of seedlings of the Mediterranean shrub Cistus albidus L. throughout a year growing in the natural Park of the Montserrat Mountains (Spain) and, additionally, we studied the response to severe drought and subsequent recovery after rewatering of seedlings grown in growth chambers. To find possible mechanisms explaining how seedlings respond to drought, growth and survival together with physiological-related parameters such as chlorophyll contents, vitamin E and stress-related phytohormones were measured. We found that survival decreased by 30% at the end of summer and that the main proxy of seedling survival was total chlorophyll. This proxy was further confirmed in the growth chambers, where we found that seedlings that recovered from drought had higher levels of total chlorophyll compared with the seedlings that did not recover. Furthermore, modulation of vitamin E and jasmonates contents appeared to be crucial in the drought response of C. albidus seedlings. We propose a prediction model of survival that includes total chlorophyll height, leaf mass area and maximum photosystem II efficiency with chlorophyll contents being a good long-term predictor of C. albidus seedling survival under severe stress, which, in turn, could help to better foresee population fluctuations in the field.

Ferredoxin 1 is downregulated by the accumulation of abscisic acid in an ABI5-dependent manner to facilitate rice stripe virus infection in Nicotiana benthamiana and rice

Ferredoxin 1 (FD1) accepts and distributes electrons in the electron transfer chain of plants. Its expression is universally downregulated by viruses and its roles in plant immunity have been brought into focus over the past decade. However, the mechanism by which viruses regulate FD1 remains to be defined. In a previous report, we found that the expression of Nicotiana benthamiana FD1 (NbFD1) was downregulated following infection with potato virus X (PVX) and that NbFD1 regulates callose deposition at plasmodesmata to play a role in defense against PVX infection. We now report that NbFD1 is downregulated by rice stripe virus (RSV) infection and that silencing of NbFD1 also facilitates RSV infection, while viral infection was inhibited in a transgenic line overexpressing NbFD1, indicating that NbFD1 also functions in defense against RSV infection. Next, a RSV-derived small interfering RNA was identified that contributes to the downregulation of FD1 transcripts. Further analysis showed that the abscisic acid (ABA) which accumulates in RSV-infected plants also represses NbFD1 transcription. It does this by stimulating expression of ABA insensitive 5 (ABI5), which binds the ABA response element motifs in the NbFD1 promoter, resulting in negative regulation. Regulation of FD1 by ABA was also confirmed in RSV-infected plants of the natural host rice. The results therefore suggest a mechanism by which virus regulates chloroplast-related genes to suppress their defense roles.

Exogenous abscisic acid and jasmonic acid restrain polyethylene glycol-induced drought by improving the growth and antioxidative enzyme activities in pearl millet

Drought stress is one of the most immense and permanent constraints in agriculture, which leads to a massive loss of crop productivity. However, little is known about the mitigation role of exogenously applied abscisic acid (ABA) and jasmonic acid (JA) in pearl millet (Pennisetum glaucum L.) under PEG-induced drought stress. Therefore, the current study investigated the putative role of exogenous ABA and JA in improving drought stress tolerance in pearl millet. Thirteen-day-old seedlings were exposed to six different treatments as follow; control (ck), PEG-600 (20%), JA (100 μM), ABA (100 μM), PEG+JA, and PEG+ABA, and data were collected at 7 and 14 days after treatment (DAT). Results showed that PEG decreased plant growth while the oxidative damage increased due to over production of H₂ O₂ and MDA content as a result of decreased activities of the antioxidative enzymes including APX, CAT, and SOD in the leaves. However, exogenous ABA and JA positively enhanced the growth profile of seedlings by improving chlorophyll and relative water content under PEG treatment. A significant improvement was observed in the plant defense system resulting from increased activities of antioxidative enzymes due to exogenous ABA and JA under PEG. Overall, the performance of JA was found better than ABA under PEG-induced drought stress, and future investigations are needed to explore the potential effects of these phytohormones on the long-term crop management and productivity under drought stress.

Hormonal impact on photosynthesis and photoprotection in plants

Photosynthesis is not only essential for plants, but it also sustains life on Earth. Phytohormones play crucial roles in developmental processes, from organ initiation to senescence, due to their role as growth and developmental regulators, as well as their central role in the regulation of photosynthesis. Furthermore, phytohormones play a major role in photoprotection of the photosynthetic apparatus under stress conditions. Here, in addition to discussing our current knowledge on the role of the phytohormones auxin, cytokinins, gibberellins, and strigolactones in promoting photosynthesis, we will also highlight the role of abscisic acid beyond stomatal closure in modulating photosynthesis and photoprotection under various stress conditions through crosstalk with ethylene, salicylates, jasmonates, and brassinosteroids. Furthermore, the role of phytohormones in controlling the production and scavenging of photosynthesis-derived reactive oxygen species, the duration and extent of photo-oxidative stress and redox signaling under stress conditions will be discussed in detail. Hormones have a significant impact on the regulation of photosynthetic processes in plants under both optimal and stress conditions, with hormonal interactions, complementation, and crosstalk being important in the spatiotemporal and integrative regulation of photosynthetic processes during organ development at the whole-plant level.

From Spaceflight to Mars g-Levels: Adaptive Response of A. Thaliana Seedlings in a Reduced Gravity Environment Is Enhanced by Red-Light Photostimulation

The response of plants to the spaceflight environment and microgravity is still not well understood, although research has increased in this area. Even less is known about plants' response to partial or reduced gravity levels. In the absence of the directional cues provided by the gravity vector, the plant is especially perceptive to other cues such as light. Here, we investigate the response of Arabidopsis thaliana 6-day-old seedlings to microgravity and the Mars partial gravity level during spaceflight, as well as the effects of red-light photostimulation by determining meristematic cell growth and proliferation. These experiments involve microscopic techniques together with transcriptomic studies. We demonstrate that microgravity and partial gravity trigger differential responses. The microgravity environment activates hormonal routes responsible for proliferation/growth and upregulates plastid/mitochondrial-encoded transcripts, even in the dark. In contrast, the Mars gravity level inhibits these routes and activates responses to stress factors to restore cell growth parameters only when red photostimulation is provided. This response is accompanied by upregulation of numerous transcription factors such as the environmental acclimation-related WRKY-domain family. In the long term, these discoveries can be applied in the design of bioregenerative life support systems and space farming.

Cytokinin-Regulated Expression of Arabidopsis thaliana PAP Genes and Its Implication for the Expression of Chloroplast-Encoded Genes

Cytokinins (CKs) are known to regulate the biogenesis of chloroplasts under changing environmental conditions and at different stages of plant ontogenesis. However, the underlying mechanisms are still poorly understood. Apparently, the mechanisms can be duplicated in several ways, including the influence of nuclear genes that determine the expression of plastome through the two-component CK regulatory circuit. In this study, we evaluated the role of cytokinins and CK signaling pathway on the expression of nuclear genes for plastid RNA polymerase-associated proteins (PAPs). Cytokinin induced the expression of all twelve Arabidopsis thalianaPAP genes irrespective of their functions via canonical CK signaling pathway but this regulation might be indirect taking into consideration their different functions and versatile structure of promoter regions. The disruption of PAP genes contributed to the abolishment of positive CK effect on the accumulation of the chloroplast gene transcripts and transcripts of the nuclear genes for plastid transcription machinery as can be judged from the analysis of pap1 and pap6 mutants. However, the CK regulatory circuit in the mutants remained practically unperturbed. Knock-out of PAP genes resulted in cytokinin overproduction as a consequence of the strong up-regulation of the genes for CK synthesis.

Effect of exogenously-applied abscisic acid, putrescine and hydrogen peroxide on drought tolerance of barley

The objective of this study was to identify the effect of abscisic acid (ABA), putrescine (Put) and hydrogen peroxide (H2O2) foliar pre-treatment on drought tolerance of barley. Despite water limitation, ABA-sprayed plants preserved increased water content, photosynthetic efficiency of PSII (ΦPSII) and CO2 assimilation rate (Pn) compared to untreated stressed plants. The ABA-treated plants presented also the lowest rate of lipid peroxidation (MDA), lowered the rate of PSII primary acceptor reduction (1 – qP) and increased the yield of regulated energy dissipation (NPQ) with higher accumulation of PGRL1 (PROTON GRADIENT REGULATION LIKE1) protein. These plants preserved a similar level of photochemical efficiency and the rate of electron transport of PSII (ETRII) to the well-watered samples. The significantly less pronounced response was observed in Put-sprayed samples under drought. Additionally, the combined effects of drought and H2O2 application increased the 1 – qP and quantum yield of non-regulated energy dissipation in PSII (ΦNO) and reduced the accumulation of Rubisco activase (RCA). In conclusion, ABA foliar application allowed to balance water retention and preserve antioxidant capacity resulting in efficient photosynthesis and the restricted risk of oxidative damage under drought. Neither hydrogen peroxide nor putrescine has been able to ameliorate drought stress as effectively as ABA.

Metabolic and physiological responses to progressive drought stress in bread wheat

Wheat (Tritium aestivum) is vulnerable to future climate change because it is predominantly grown under rain-fed conditions in drought-prone areas. Thus, in-depth understanding of drought effect on wheat metabolism is essential for developing drought-tolerant wheat varieties. Here, we exposed wheat 'Norin 61' plants to progressive drought stress [0 (before drought), 2, 4, 6, 8, and 10 days after withholding water] during the flowering stage to investigate physiological and metabolomic responses. Transcriptional analyses of key abscisic acid-responsive genes indicated that abscisic acid signalling played a major role in the adaptation of wheat to water deficit. Carbon isotope composition had a higher value than the control while canopy temperature (CT) increased under drought stress. The CT depression was tightly correlated with soil water potential (SWP). Additionally, SWP at - 517 kPa was identified as the critical point for increasing CT and inducing reactive oxygen species. Metabolome analysis identified four potential drought-responsive biomarkers, the enhancement of nitrogen recycling through purine and pyrimidine metabolism, drought-induced senescence based on 1-aminocyclopropane-1-carboxylic acid and Asn accumulation, and an anti-senescence response through serotonin accumulation under severe drought stress. Our findings provide in-depth insight into molecular, physiological and metabolite changes involved in drought response which are useful for wheat breeding programs to develop drought-tolerant wheat varieties.

Expression of a carotenogenic gene allows faster biomass production by redesigning plant architecture and improving photosynthetic efficiency in tobacco

Because carotenoids act as accessory pigments in photosynthesis, play a key photoprotective role and are of major nutritional importance, carotenogenesis has been a target for crop improvement. Although carotenoids are important precursors of phytohormones, previous genetic manipulations reported little if any effects on biomass production and plant development, but resulted in specific modifications in carotenoid content. Unexpectedly, the expression of the carrot lycopene β-cyclase (DcLCYB1) in Nicotiana tabacum cv. Xanthi not only resulted in increased carotenoid accumulation, but also in altered plant architecture characterized by longer internodes, faster plant growth, early flowering and increased biomass. Here, we have challenged these transformants with a range of growth conditions to determine the robustness of their phenotype and analyze the underlying mechanisms. Transgenic DcLCYB1 lines showed increased transcript levels of key genes involved in carotenoid, chlorophyll, gibberellin (GA) and abscisic acid (ABA) biosynthesis, but also in photosynthesis-related genes. Accordingly, their carotenoid, chlorophyll, ABA and GA contents were increased. Hormone application and inhibitor experiments confirmed the key role of altered GA/ABA contents in the growth phenotype. Because the longer internodes reduce shading of mature leaves, induction of leaf senescence was delayed, and mature leaves maintained a high photosynthetic capacity. This increased total plant assimilation, as reflected in higher plant yields under both fully controlled constant and fluctuating light, and in non-controlled conditions. Furthermore, our data are a warning that engineering of isoprenoid metabolism can cause complex changes in phytohormone homeostasis and therefore plant development, which have not been sufficiently considered in previous studies.

Arabidopsis Plastid-RNA Polymerase RPOTp Is Involved in Abiotic Stress Tolerance

Plastid gene expression (PGE) must adequately respond to changes in both development and environmental cues. The transcriptional machinery of plastids in land plants is far more complex than that of prokaryotes. Two types of DNA-dependent RNA polymerases transcribe the plastid genome: a multimeric plastid-encoded polymerase (PEP), and a monomeric nuclear-encoded polymerase (NEP). A single NEP in monocots (RPOTp, RNA polymerase of the T3/T7 phage-type) and two NEPs in dicots (plastid-targeted RPOTp, and plastid- and mitochondrial-targeted RPOTmp) have been hitherto identified. To unravel the role of PGE in plant responses to abiotic stress, we investigated if Arabidopsis RPOTp could function in plant salt tolerance. To this end, we studied the sensitivity of T-DNA mutants scabra3-2 (sca3-2) and sca3-3, defective in the RPOTp gene, to salinity, osmotic stress and the phytohormone abscisic acid (ABA) required for plants to adapt to abiotic stress. sca3 mutants were hypersensitive to NaCl, mannitol and ABA during germination and seedling establishment. Later in development, sca3 plants displayed reduced sensitivity to salt stress. A gene ontology (GO) analysis of the nuclear genes differentially expressed in the sca3-2 mutant (301) revealed that many significantly enriched GO terms were related to chloroplast function, and also to the response to several abiotic stresses. By quantitative RT-PCR (qRT-PCR), we found that genes LHCB1 (LIGHT-HARVESTING CHLOROPHYLL a/b-BINDING1) and AOX1A (ALTERNATIVE OXIDASE 1A) were respectively down- and up-regulated in the Columbia-0 (Col-0) salt-stressed plants, which suggests the activation of plastid and mitochondria-to-nucleus retrograde signaling. The transcript levels of genes RPOTp, RPOTmp and RPOTm significantly increased in these salt-stressed seedlings, but this enhanced expression did not lead to the up-regulation of the plastid genes solely transcribed by NEP. Similar to salinity, carotenoid inhibitor norflurazon (NF) also enhanced the RPOTp transcript levels in Col-0 seedlings. This shows that besides salinity, inhibition of chloroplast biogenesis also induces RPOTp expression. Unlike salt and NF, the NEP genes were significantly down-regulated in the Col-0 seedlings grown in ABA-supplemented media. Together, our findings demonstrate that RPOTp functions in abiotic stress tolerance, and RPOTp is likely regulated positively by plastid-to-nucleus retrograde signaling, which is triggered when chloroplast functionality is perturbed by environmental stresses, e.g., salinity or NF. This suggests the existence of a compensatory mechanism, elicited by impaired chloroplast function. To our knowledge, this is the first study to suggest the role of a nuclear-encoded plastid-RNA polymerase in salt stress tolerance in plants.

Abscisic Acid-Enemy or Savior in the Response of Cereals to Abiotic and Biotic Stresses?

Abscisic acid (ABA) is well-known phytohormone involved in the control of plant natural developmental processes, as well as the stress response. Although in wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) its role in mechanism of the tolerance to most common abiotic stresses, such as drought, salinity, or extreme temperatures seems to be fairly well recognized, not many authors considered that changes in ABA content may also influence the sensitivity of cereals to adverse environmental factors, e.g., by accelerating senescence, lowering pollen fertility, and inducing seed dormancy. Moreover, recently, ABA has also been regarded as an element of the biotic stress response; however, its role is still highly unclear. Many studies connect the susceptibility to various diseases with increased concentration of this phytohormone. Therefore, in contrast to the original assumptions, the role of ABA in response to biotic and abiotic stress does not always have to be associated with survival mechanisms; on the contrary, in some cases, abscisic acid can be one of the factors that increases the susceptibility of plants to adverse biotic and abiotic environmental factors.

A Chloroplast COR413 Protein From Physcomitrella patens Is Required for Growth Regulation Under High Light and ABA Responses

COR413 genes belong to a poorly characterized group of plant-specific cold-regulated genes initially identified as part of the transcriptional activation machinery of plants during cold acclimation. They encode multispanning transmembrane proteins predicted to target the plasma membrane or the chloroplast inner membrane. Despite being ubiquitous throughout the plant kingdom, little is known about their biological function. In this study, we used reverse genetics to investigate the relevance of a predicted chloroplast localized COR413 protein (PpCOR413im) from the moss Physcomitrella patens in developmental and abiotic stress responses. Expression of PpCOR413im was strongly induced by abscisic acid (ABA) and by various environmental stimuli, including low temperature, hyperosmosis, salinity and high light. In vivo subcellular localization of PpCOR413im-GFP fusion protein revealed that this protein is localized in chloroplasts, confirming the in silico predictions. Loss-of-function mutants of PpCOR413im exhibited growth and developmental alterations such as growth retardation, reduced caulonema formation and hypersensitivity to ABA. Mutants also displayed altered photochemistry under various abiotic stresses, including dehydration and low temperature, and exhibited a dramatic growth inhibition upon exposure to high light. Disruption of PpCOR413im also caused altered chloroplast ultrastructure, increased ROS accumulation, and enhanced starch and sucrose levels under high light or after ABA treatment. In addition, loss of PpCOR413im affected both nuclear and chloroplast gene expression in response to ABA and high light, suggesting a role for this gene downstream of ABA in the regulation of growth and environmental stress responses. Developmental alterations exhibited by PpCOR413im knockout mutants had remarkable similarities to those exhibited by hxk1, a mutant lacking a major chloroplastic hexokinase, an enzyme involved in energy homeostasis. Based on these findings, we propose that PpCOR413im is involved in coordinating energy metabolism with ABA-mediated growth and developmental responses.

Cellulose defects in the Arabidopsis secondary cell wall promote early chloroplast development

Lincomycin (LIN)-mediated inhibition of protein synthesis in chloroplasts prevents the greening of seedlings, represses the activity of photosynthesis-related genes in the nucleus, including LHCB1.2, and induces the phenylpropanoid pathway, resulting in the production of anthocyanins. In genomes uncoupled (gun) mutants, LHCB1.2 expression is maintained in the presence of LIN or other inhibitors of early chloroplast development. In a screen using concentrations of LIN lower than those employed to isolate gun mutants, we have identified happy on lincomycin (holi) mutants. Several holi mutants show an increased tolerance to LIN, exhibiting de-repressed LHCB1.2 expression and chlorophyll synthesis in seedlings. The mutations responsible were identified by whole-genome single-nucleotide polymorphism (SNP) mapping, and most were found to affect the phenylpropanoid pathway; however, LHCB1.2 expression does not appear to be directly regulated by phenylpropanoids, as indicated by the metabolic profiling of mutants. The most potent holi mutant is defective in a subunit of cellulose synthase encoded by IRREGULAR XYLEM 3, and comparative analysis of this and other cell-wall mutants establishes a link between secondary cell-wall integrity and early chloroplast development, possibly involving altered ABA metabolism or sensing.

Genome-Wide Analysis of Multiple Organellar RNA Editing Factor Family in Poplar Reveals Evolution and Roles in Drought Stress

Poplar (Populus) is one of the most important woody plants worldwide. Drought, a primary abiotic stress, seriously affects poplar growth and development. Multiple organellar RNA editing factor (MORF) genes-pivotal factors in the RNA editosome in Arabidopsis thaliana-are indispensable for the regulation of various physiological processes, including organelle C-to-U RNA editing and plasmid development, as well as in the response to stresses. Although the poplar genome sequence has been released, little is known about MORF genes in poplar, especially those involved in the response to drought stress at the genome-wide level. In this study, we identified nine MORF genes in the Populus genome. Based on the structural features of MORF proteins and the topology of the phylogenetic tree, the P. trichocarpa (Ptr) MORF family members were classified into six groups (Groups I⁻VI). A microsynteny analysis indicated that two (22.2%) PtrMORF genes were tandemly duplicated and seven genes (77.8%) were segmentally duplicated. Based on the d_N/d_S ratios, purifying selection likely played a major role in the evolution of this family and contributed to functional divergence among PtrMORF genes. Moreover, analysis of qRT-PCR data revealed that PtrMORFs exhibited tissue- and treatment-specific expression patterns. PtrMORF genes in all group were involved in the stress response. These results provide a solid foundation for further analyses of the functions and molecular evolution of MORF genes in poplar, and, in particular, for improving the drought resistance of poplar by genetics manipulation.

Green magic: regulation of the chloroplast stress response by (p)ppGpp in plants and algae

The hyperphosphorylated nucleotides guanosine pentaphosphate and tetraphosphate [together referred to as (p)ppGpp, or 'magic spot'] orchestrate a signalling cascade in bacteria that controls growth under optimal conditions and in response to environmental stress. (p)ppGpp is also found in the chloroplasts of plants and algae where it has also been shown to accumulate in response to abiotic stress. Recent studies suggest that (p)ppGpp is a potent inhibitor of chloroplast gene expression in vivo, and is a significant regulator of chloroplast function that can influence both the growth and the development of plants. However, little is currently known about how (p)ppGpp is wired into eukaryotic signalling pathways, or how it may act to enhance fitness when plants or algae are exposed to environmental stress. This review discusses our current understanding of (p)ppGpp metabolism and its extent in plants and algae, and how (p)ppGpp signalling may be an important factor that is capable of influencing growth and stress acclimation in this major group of organisms.

Stress-induced senescence and plant tolerance to abiotic stress

Senescence is an age-dependent process, ultimately leading to plant death, that in annual crop plants overlaps with the reproductive stage of development. Research on the molecular and biochemical mechanisms of leaf senescence has revealed a multi-layered regulatory network operating to control age-dependent processes. Abiotic stress-induced senescence challenges source-sink relationships and results in significant reduction in crop yields. Although processes associated with plant senescence are well studied, the mechanisms regulating stress-induced senescence are not well known. Here, we discuss the effects of abiotic stress on crop productivity, mechanisms associated with stress-induced senescence, and the possible use of these mechanisms for the generation of plant stress tolerance. We emphasize the involvement of source strength and stability of the photosynthetic apparatus in this process, and suggest a possible role of a perennial plant life strategy for the amelioration of stress-induced senescence.

Proteomic Investigations of Proteases Involved in Cotyledon Senescence: A Model to Explore the Genotypic Variability of Proteolysis Machinery Associated with Nitrogen Remobilization Efficiency during the Leaf Senescence of Oilseed Rape

Oilseed rape is characterized by a low nitrogen remobilization efficiency during leaf senescence, mainly due to a lack of proteolysis. Because cotyledons are subjected to senescence, it was hypothesized that contrasting protease activities between genotypes may be distinguishable early in the senescence of cotyledons. To verify this assumption, our goals were to (i) characterize protease activities in cotyledons between two genotypes with contrasting nitrogen remobilization efficiency (Ténor and Samouraï) under limiting or ample nitrate supply; and (ii) test the role of salicylic acid (SA) and abscisic acid (ABA) in proteolysis regulation. Protease activities were measured and identified by a proteomics approach combining activity-based protein profiling with LC-MS/MS. As in senescing leaves, chlorophyll and protein contents decrease in senescing cotyledons and are correlated with an increase in serine and cysteine protease activities. Two RD21-like and SAG-12 proteases previously associated with an efficient proteolysis in senescing leaves of Ténor are also detected in senescing cotyledons. The infiltration of ABA and SA provokes the induction of senescence and several cysteine and serine protease activities. The study of protease activities during the senescence of cotyledons seems to be a promising experimental model to investigate the regulation and genotypic variability of proteolysis associated with efficient N remobilization.

Salt stress affects mRNA editing in soybean chloroplasts

Soybean, a crop known by its economic and nutritional importance, has been the subject of several studies that assess the impact and the effective plant responses to abiotic stresses. Salt stress is one of the main environmental stresses and negatively impacts crop growth and yield. In this work, the RNA editing process in the chloroplast of soybean plants was evaluated in response to a salt stress. Bioinformatics approach using sRNA and mRNA libraries were employed to detect specific sites showing differences in editing efficiency. RT-qPCR was used to measure editing efficiency at selected sites. We observed that transcripts of NDHA, NDHB, RPS14 and RPS16 genes presented differences in coverage and editing rates between control and salt-treated libraries. RT-qPCR assays demonstrated an increase in editing efficiency of selected genes. The salt stress enhanced the RNA editing process in transcripts, indicating responses to components of the electron transfer chain, photosystem and translation complexes. These increases can be a response to keep the homeostasis of chloroplast protein functions in response to salt stress.

Chloroplast proteome response to drought stress and recovery in tomato (Solanum lycopersicum L.)

BACKGROUND

Drought is a major constraint for plant growth and crop productivity that is receiving an increased attention due to global climate changes. Chloroplasts act as environmental sensors, however, only partial information is available on stress-induced mechanisms within plastids. Here, we investigated the chloroplast response to a severe drought treatment and a subsequent recovery cycle in tomato through physiological, metabolite and proteomic analyses.

RESULTS

Under stress conditions, tomato plants showed stunted growth, and elevated levels of proline, abscisic acid (ABA) and late embryogenesis abundant gene transcript. Proteomics revealed that water deficit deeply affects chloroplast protein repertoire (31 differentially represented components), mainly involving energy-related functional species. Following the rewatering cycle, physiological parameters and metabolite levels indicated a recovery of tomato plant functions, while proteomics revealed a still ongoing adjustment of the chloroplast protein repertoire, which was even wider than during the drought phase (54 components differentially represented). Changes in gene expression of candidate genes and accumulation of ABA suggested the activation under stress of a specific chloroplast-to-nucleus (retrograde) signaling pathway and interconnection with the ABA-dependent network.

CONCLUSIONS

Our results give an original overview on the role of chloroplast as enviromental sensor by both coordinating the expression of nuclear-encoded plastid-localised proteins and mediating plant stress response. Although our data suggest the activation of a specific retrograde signaling pathway and interconnection with ABA signaling network in tomato, the involvement and fine regulation of such pathway need to be further investigated through the development and characterization of ad hoc designed plant mutants.

The Plant Immunity Regulating F-Box Protein CPR1 Supports Plastid Function in Absence of Pathogens

The redox imbalanced 6 mutant (rimb6) of Arabidopsis thaliana was isolated in a genetic screening approach for mutants with defects in chloroplast-to-nucleus redox signaling. It has an atypically low activation status of the 2-Cys peroxiredoxin-A promoter in the seedling stage. rimb6 shows wildtype-like germination, seedling development and greening, but slower growth and reduced biomass in the rosette stage. Mapping of the casual mutation revealed that rimb6 carries a single nucleotide polymorphism in the gene encoding CONSTITUTIVE EXPRESSER OF PATHOGENESIS RELATED (PR) GENES 1, CPR1 (At4g12560), leading to a premature stop codon. CPR1 is known as a repressor of pathogen signaling and regulator of microtubule organization. Allelism of rimb6 and cpr1 revealed a function of CPR1 in chloroplast stress protection. Expression studies in pathogen signaling mutants demonstrated that CPR1-mediated activation of genes for photosynthesis and chloroplast antioxidant protection is, in contrast to activation of pathogen responses, regulated independently from PAD4-controlled salicylic acid (SA) accumulation. We conclude that the support of plastid function is a basic, SA-independent function of CPR1.

Organellar Gene Expression and Acclimation of Plants to Environmental Stress

Organelles produce ATP and a variety of vital metabolites, and are indispensable for plant development. While most of their original gene complements have been transferred to the nucleus in the course of evolution, they retain their own genomes and gene-expression machineries. Hence, organellar function requires tight coordination between organellar gene expression (OGE) and nuclear gene expression (NGE). OGE requires various nucleus-encoded proteins that regulate transcription, splicing, trimming, editing, and translation of organellar RNAs, which necessitates nucleus-to-organelle (anterograde) communication. Conversely, changes in OGE trigger retrograde signaling that modulates NGE in accordance with the current status of the organelle. Changes in OGE occur naturally in response to developmental and environmental changes, and can be artificially induced by inhibitors such as lincomycin or mutations that perturb OGE. Focusing on the model plant Arabidopsis thaliana and its plastids, we review here recent findings which suggest that perturbations of OGE homeostasis regularly result in the activation of acclimation and tolerance responses, presumably via retrograde signaling.

ABI5 Is a Regulator of Seed Maturation and Longevity in Legumes

The preservation of our genetic resources and production of high-quality seeds depends on their ability to remain viable and vigorous during storage. In a quantitative trait locus analysis on seed longevity in Medicago truncatula, we identified the bZIP transcription factor ABSCISIC ACID INSENSITIVE5 (ABI5). Characterization of Mt-abi5 insertion mutant seeds revealed that both the acquisition of longevity and dormancy were severely impaired. Using transcriptomes of developing Mt-abi5 seeds, we created a gene coexpression network and revealed ABI5 as a regulator of gene modules with functions related to raffinose family oligosaccharide (RFO) metabolism, late embryogenesis abundant (LEA) proteins, and photosynthesis-associated nuclear genes (PhANGs). Lower RFO contents in Mt-abi5 seeds were linked to the regulation of SEED IMBIBITION PROTEIN1 Proteomic analysis confirmed that a set of LEA polypeptides was reduced in mature Mt-abi5 seeds, whereas the absence of repression of PhANG in mature Mt-abi5 seeds was accompanied by chlorophyll and carotenoid retention. This resulted in a stress response in Mt-abi5 seeds, evident from an increase in α-tocopherol and upregulation of genes related to programmed cell death and protein folding. Characterization of abi5 mutants in a second legume species, pea (Pisum sativum), confirmed a role for ABI5 in the regulation of longevity, seed degreening, and RFO accumulation, identifying ABI5 as a prominent regulator of late seed maturation in legumes.

Genome-Wide Analysis of MicroRNA Responses to the Phytohormone Abscisic Acid in Populus euphratica

MicroRNA (miRNA) is a type of non-coding small RNA with a regulatory function at the posttranscriptional level in plant growth development and in response to abiotic stress. Previous studies have not reported on miRNAs responses to the phytohormone abscisic acid (ABA) at a genome-wide level in Populus euphratica, a model tree for studying abiotic stress responses in woody plants. Here we analyzed the miRNA response to ABA at a genome-wide level in P. euphratica utilizing high-throughput sequencing. To systematically perform a genome-wide analysis of ABA-responsive miRNAs in P. euphratica, nine sRNA libraries derived from three groups (control, treated with ABA for 1 day and treated with ABA for 4 days) were constructed. Each group included three libraries from three individual plantlets as biological replicate. In total, 151 unique mature sequences belonging to 75 conserved miRNA families were identified, and 94 unique sequences were determined to be novel miRNAs, including 56 miRNAs with miRNA(*) sequences. In all, 31 conserved miRNAs and 31 novel miRNAs response to ABA significantly differed among the groups. In addition, 4132 target genes were predicted for the conserved and novel miRNAs. Confirmed by real-time qPCR, expression changes of miRNAs were inversely correlated with the expression profiles of their putative targets. The Populus special or novel miRNA-target interactions were predicted might be involved in some biological process related stress tolerance. Our analysis provides a comprehensive view of how P. euphratica miRNA respond to ABA, and moreover, different temporal dynamics were observed in different ABA-treated libraries.

A chloroplast-localized S1 domain-containing protein SRRP1 plays a role in Arabidopsis seedling growth in the presence of ABA

Although the roles of S1 domain-containing proteins have been characterized in diverse cellular processes in the cytoplasm, the functional roles of a majority of S1 domain-containing proteins targeted to the chloroplast are largely unknown. Here, we characterized the function of a nuclear-encoded chloroplast-targeted protein harboring two S1 domains, designated SRRP1 (for S1 RNA-binding ribosomal protein 1), in Arabidopsis thaliana. Subcellular localization analysis of SRRP1-GFP fusion proteins revealed that SRRP1 is localized to the chloroplast. The T-DNA tagged loss-of-function srrp1 mutants displayed poorer seedling growth and less cotyledon greening than the wild-type plants on MS medium supplemented with abscisic acid (ABA), suggesting that SRRP1 plays a role in seedling growth in the presence of ABA. Splicing of the trnL intron and processing of 5S rRNA in chloroplasts were altered in the mutant plants. Importantly, SRRP1 complemented the growth-defective phenotypes of an RNA chaperone-deficient Escherichia coli mutant at low temperatures and had nucleic acid-melting ability, indicating that SRRP1 possesses RNA chaperone activity. Taken together, these results suggest that SRRP1, the chloroplast-localized S1 domain-containing protein, harboring RNA chaperone activity affects the splicing and processing of chloroplast transcripts and plays a role in Arabidopsis seedling growth in the presence of ABA.

Current Understanding of the Interplay between Phytohormones and Photosynthesis under Environmental Stress

Abiotic stress accounts for huge crop losses every year across the globe. In plants, the photosynthetic machinery gets severely damaged at various levels due to adverse environmental conditions. Moreover, the reactive oxygen species (ROS) generated as a result of stress further promote the photosynthetic damage by inhibiting the repair system of photosystem II. Earlier studies have suggested that phytohormones are not only required for plant growth and development, but they also play a pivotal role in regulating plants’ responses to different abiotic stress conditions. Although, phytohormones have been studied in great detail in the past, their influence on the photosynthetic machinery under abiotic stress has not been studied. One of the major factors that limits researchers fromelucidating the precise roles of phytohormones is the highly complex nature of hormonal crosstalk in plants. Another factor that needs to be elucidated is the method used for assessing photosynthetic damage in plants that are subjected to abiotic stress. Here, we review the current understanding on the role of phytohormones in the photosynthetic machinery under various abiotic stress conditions and discuss the potential areas for further research.

Abscisic acid affects transcription of chloroplast genes via protein phosphatase 2C-dependent activation of nuclear genes: repression by guanosine-3'-5'-bisdiphosphate and activation by sigma factor 5

Abscisic acid (ABA) represses the transcriptional activity of chloroplast genes (determined by run-on assays), with the exception of psbD and a few other genes in wild-type Arabidopsis seedlings and mature rosette leaves. Abscisic acid does not influence chloroplast transcription in the mutant lines abi1-1 and abi2-1 with constitutive protein phosphatase 2C (PP2C) activity, suggesting that ABA affects chloroplast gene activity by binding to the pyrabactin resistance (PYR)/PYR1-like or regulatory component of ABA receptor protein family (PYR/PYL/RCAR) and signaling via PP2Cs and sucrose non-fermenting protein-related kinases 2 (SnRK2s). Further we show by quantitative PCR that ABA enhances the transcript levels of RSH2, RSH3, PTF1 and SIG5. RelA/SpoT homolog 2 (RSH2) and RSH3 are known to synthesize guanosine-3'-5'-bisdiphosphate (ppGpp), an inhibitor of the plastid-gene-encoded chloroplast RNA polymerase. We propose, therefore, that ABA leads to an inhibition of chloroplast gene expression via stimulation of ppGpp synthesis. On the other hand, sigma factor 5 (SIG5) and plastid transcription factor 1 (PTF1) are known to be necessary for the transcription of psbD from a specific light- and stress-induced promoter (the blue light responsive promoter, BLRP). We demonstrate that ABA activates the psbD gene by stimulation of transcription initiation at BLRP. Taken together, our data suggest that ABA affects the transcription of chloroplast genes by a PP2C-dependent activation of nuclear genes encoding proteins involved in chloroplast transcription.

Efficient high light acclimation involves rapid processes at multiple mechanistic levels

Like no other chemical or physical parameter, the natural light environment of plants changes with high speed and jumps of enormous intensity. To cope with this variability, photosynthetic organisms have evolved sensing and response mechanisms that allow efficient acclimation. Most signals originate from the chloroplast itself. In addition to very fast photochemical regulation, intensive molecular communication is realized within the photosynthesizing cell, optimizing the acclimation process. Current research has opened up new perspectives on plausible but mostly unexpected complexity in signalling events, crosstalk, and process adjustments. Within seconds and minutes, redox states, levels of reactive oxygen species, metabolites, and hormones change and transmit information to the cytosol, modifying metabolic activity, gene expression, translation activity, and alternative splicing events. Signalling pathways on an intermediate time scale of several minutes to a few hours pave the way for long-term acclimation. Thereby, a new steady state of the transcriptome, proteome, and metabolism is realized within rather short time periods irrespective of the previous acclimation history to shade or sun conditions. This review provides a time line of events during six hours in the 'stressful' life of a plant.

Endogenous abscisic acid promotes hypocotyl growth and affects endoreduplication during dark-induced growth in tomato (Solanum lycopersicum L.)

Dark-induced growth (skotomorphogenesis) is primarily characterized by rapid elongation of the hypocotyl. We have studied the role of abscisic acid (ABA) during the development of young tomato (Solanum lycopersicum L.) seedlings. We observed that ABA deficiency caused a reduction in hypocotyl growth at the level of cell elongation and that the growth in ABA-deficient plants could be improved by treatment with exogenous ABA, through which the plants show a concentration dependent response. In addition, ABA accumulated in dark-grown tomato seedlings that grew rapidly, whereas seedlings grown under blue light exhibited low growth rates and accumulated less ABA. We demonstrated that ABA promotes DNA endoreduplication by enhancing the expression of the genes encoding inhibitors of cyclin-dependent kinases SlKRP1 and SlKRP3 and by reducing cytokinin levels. These data were supported by the expression analysis of the genes which encode enzymes involved in ABA and CK metabolism. Our results show that ABA is essential for the process of hypocotyl elongation and that appropriate control of the endogenous level of ABA is required in order to drive the growth of etiolated seedlings.

Chloroplast RNA polymerases: Role in chloroplast biogenesis

Plastid genes are transcribed by two types of RNA polymerase in angiosperms: the bacterial type plastid-encoded RNA polymerase (PEP) and one (RPOTp in monocots) or two (RPOTp and RPOTmp in dicots) nuclear-encoded RNA polymerase(s) (NEP). PEP is a bacterial-type multisubunit enzyme composed of core subunits (coded for by the plastid rpoA, rpoB, rpoC1 and rpoC2 genes) and additional protein factors (sigma factors and polymerase associated protein, PAPs) encoded in the nuclear genome. Sigma factors are required by PEP for promoter recognition. Six different sigma factors are used by PEP in Arabidopsis plastids. NEP activity is represented by phage-type RNA polymerases. Only one NEP subunit has been identified, which bears the catalytic activity. NEP and PEP use different promoters. Many plastid genes have both PEP and NEP promoters. PEP dominates in the transcription of photosynthesis genes. Intriguingly, rpoB belongs to the few genes transcribed exclusively by NEP. Both NEP and PEP are active in non-green plastids and in chloroplasts at all stages of development. The transcriptional activity of NEP and PEP is affected by endogenous and exogenous factors. This article is part of a Special Issue entitled: Chloroplast Biogenesis.

Insights into chloroplast biogenesis and development

In recent years many advances have been made to obtain insight into chloroplast biogenesis and development. In plants several plastids types exist such as the proplastid (which is the progenitor of all plastids), leucoplasts (group of colourless plastids important for storage including elaioplasts (lipids), amyloplasts (starch) or proteinoplasts (proteins)), chromoplasts (yellow to orange-coloured due to carotenoids, in flowers or in old leaves as gerontoplasts), and the green chloroplasts. Chloroplasts are indispensable for plant development; not only by performing photosynthesis and thus rendering the plant photoautotrophic, but also for biochemical processes (which in some instances can also take place in other plastids types), such as the synthesis of pigments, lipids, and plant hormones and sensing environmental stimuli. Although we understand many aspects of these processes there are gaps in our understanding of the establishment of functional chloroplasts and their regulation. Why is that so? Even though chloroplast function is comparable in all plants and most of the algae, ferns and moss, detailed analyses have revealed many differences, specifically with respect to its biogenesis. As an update to our prior review on the genetic analysis of chloroplast biogenesis and development [1] herein we will focus on recent advances in Angiosperms (monocotyledonous and dicotyledonous plants) that provide novel insights and highlight the challenges and prospects for unravelling the regulation of chloroplast biogenesis specifically during the establishment of the young plants. This article is part of a Special Issue entitled: Chloroplast Biogenesis.

Identification, cloning and characterization of an ultrapetala transcription factor CsULT1 from Crocus: a novel regulator of apocarotenoid biosynthesis

BACKGROUND

Crocus sativus is a triploid sterile plant with long red stigmas which form commercial saffron. Saffron is the site for synthesis and accumulation of apocarotenoids like crocin, picrocrin and safranal which are responsible for its color, flavour and aroma making it world's most expensive spice. These compounds are formed by oxidative cleavage of zeaxanthin by carotenoid cleavage dioxygenases. Although the biosynthetic pathway of apocarotenoids is known to a considerable extent, the mechanism that regulates its tissue and developmental stage specific expression is not known.

RESULTS

In the present work, we identified, cloned and characterized ultrapetala transcription factor called CsULT1 from Crocus. The gene contains an 80 amino acid long conserved SAND domain. The CsULT1 transcript was more abundant in stigma and showed increase in expression from pre anthesis stage till anthesis and decreased in post anthesis stage which corroborated with the accumulation pattern of crocin indicating its possible role in regulation of apocarotenoid biosynthesis. CsULT1 was found to be transcriptionally active and localized in nucleus. Its expression is induced in response to phytohormones like auxin, methyljasmonate and salicylic acid. Overexpression of CsULT1 in Crocus calli resulted in enhanced expression of key pathway genes like phytoene synthase (PSY), phytoene desaturase (PDS), beta carotene hydroxylase (BCH) and carotenoid cleavage dioxygenases (CCDs) indicating its role in regulation of apocarotenoid biosynthesis.

CONCLUSION

This work presents first report on isolation and characterization of ultrapetala gene from Crocus. Our results suggest that CsULT1 is a novel regulator of Crocus apocarotenoid biosynthesis. We show for the first time involvement of plant SAND domain proteins in regulating secondary metabolic pathways.

Emerging roles of protein kinase CK2 in abscisic acid signaling

The phytohormone abscisic acid (ABA) regulates many aspects of plant growth and development as well as responses to multiple stresses. Post-translational modifications such as phosphorylation or ubiquitination have pivotal roles in the regulation of ABA signaling. In addition to the positive regulator sucrose non-fermenting-1 related protein kinase 2 (SnRK2), the relevance of the role of other protein kinases, such as CK2, has been recently highlighted. We have recently established that CK2 phosphorylates the maize ortholog of open stomata 1 OST1, ZmOST1, suggesting a role of CK2 phosphorylation in the control of ZmOST1 protein degradation (Vilela et al., 2015). CK2 is a pleiotropic enzyme involved in multiple developmental and stress-responsive pathways. This review summarizes recent advances that taken together suggest a prominent role of protein kinase CK2 in ABA signaling and related processes.

Inhibition of the electron transport strongly affects transcription and transcript levels in Arabidopsis mitochondria

Mitochondrial transcription rate and RNA steady-state levels were examined in shoots of Arabidopsis seedlings. The shoots were treated with inhibitors of complex III and IV of the cytochrome pathway (CP) and with an inhibitor of the alternative oxidase (AOX) of the mitochondrial electron transport chain. The inhibition of AOX and CP complexes III and IV affected transcription and transcript levels in different ways. CP and AOX inhibitors had opposite effects. Our data support the idea that the redox state of the electron transport chain is involved in the regulation of mitochondrial gene expression at transcriptional and post-transcriptional levels.

Rice and cold stress: methods for its evaluation and summary of cold tolerance-related quantitative trait loci

Cold stress adversely affects rice (Oryza sativa L.) growth and productivity, and has so far determined its geographical distribution. Dissecting cold stress-mediated physiological changes and understanding their genetic causes will facilitate the breeding of rice for cold tolerance. Here, we review recent progress in research on cold stress-mediated physiological traits and metabolites, and indicate their roles in the cold-response network and cold-tolerance evaluation. We also discuss criteria for evaluating cold tolerance and evaluate the scope and shortcomings of each application. Moreover, we summarize research on quantitative trait loci (QTL) related to cold stress at the germination, seedling, and reproductive stages that should provide useful information to accelerate progress in breeding cold-tolerant rice.