New insights into the genetic basis of natural chilling and cold shock tolerance in rice by genome‐wide association analysis

In order to understand cold adaptability and explore additional genetic resources for the cold tolerance improvement of rice, we investigated the genetic variation of 529 rice accessions under natural chilling and cold shock stress conditions at the seedling stage using genome‐wide association studies; a total of 132 loci were identified. Among them, 12 loci were common for both chilling and cold shock tolerance, suggesting that rice has a distinct and overlapping genetic response and adaptation to the two stresses. Haplotype analysis of a known gene OsMYB2, which is involved in cold tolerance, revealed indica–japonica differentiation and latitude tendency for the haplotypes of this gene. By checking the subpopulation and geographical distribution of accessions with tolerance or sensitivity under these two stress conditions, we found that the chilling tolerance group, which mainly consisted of japonica accessions, has a wider latitudinal distribution than the chilling sensitivity group. We conclude that the genetic basis of natural chilling stress tolerance in rice is distinct from that of cold shock stress frequently used for low‐temperature treatment in the laboratory and the cold adaptability of rice is associated with the subpopulation and latitudinal distribution.     

LcFIN2, a novel chloroplast protein gene from sheepgrass,enhances tolerance to low temperature in Arabidopsis and rice

Adverse environmental stresses affect plant growth and crop yields. Sheepgrass (Leymus chinensis (Trin.) Tzvel), an important forage grass that is widely distributed in the east of Eurasia steppe, has high tolerance to extreme low temperature. Many genes that respond to cold stress were identified in sheepgrass by RNA‐sequencing, but more detailed studies are needed to dissect the function of those genes. Here, we found that LcFIN2, a sheepgrass freezing‐induced protein 2, encoded a chloroplast‐targeted protein. Expression of LcFIN2 was upregulated by freezing, chilling, NaCl and abscisic acid (ABA) treatments. Overexpression of LcFIN2 enhanced the survival rate of transgenic Arabidopsis after freezing stress. Importantly, heterologous expression of LcFIN2 in rice exhibited not only higher survival rate but also accumulated various soluble substances and reduced membrane damage in rice under chilling stress. Furthermore, the chlorophyll content, the quantum photochemistry efficiency of photosystem II (ΦPSII), the non‐photochemical quenching (NPQ), the net photosynthesis rate (Pn) and the expression of some chloroplast ribosomal‐related and photosynthesis‐related genes were higher in the transgenic rice under chilling stress. These findings suggested that the LcFIN2 gene could potentially be used to improve low‐temperature tolerance in crops.     

Low temperature acclimation to chilling tolerance in rice roots

Rice seedlings (Oryza sativa L.) were subjected to low temperature pretreatment (LT-PT; 10°C) for various length of time (1, 2, 4, 6, 12, 18, 24 h) followed by a 48-h chilling temperature stress (2°C). Chilling temperature tolerance of rice roots was improved with increasing duration of LT-PT, but LT-PT longer than 12 h gave no additional improvement. Alcohol dehydrogenase activity and ethanol concentration in the roots were increased with increasing duration of LT-PT up to 12 h. Chilling tolerance was also improved by exogenously applied ethanol. These results suggest that LT-PT may increase chilling tolerance in rice roots owing to ethanol accumulation in the roots and LT-PT acclimation to chilling temperature may occur within 12 h.     

低温对杂交水稻乳熟期剑叶光合作用和光合产物运输的影响

为了解寒露风引起晚稻减产的生理原因,本试验以两个不同抗冷力的杂交水稻组合为材料,研究了低温对水稻乳熟期剑叶光合作用与果糖１,６－二磷酸酯酶（ＦＢＰａｓｅ）活性的影响。结果表明：低温引起离体剑叶光合效率与ＦＢＰａｓｅ 活性下降,不抗冷的“汕优６３”及其亲本的光合效率与ＦＢＰａｓｅ 活性比抗冷的“秀优５７”及其亲本下降幅度较大。乳熟期是籽粒灌浆的高峰期,自然低温（寒露风）造成晚造水稻减产与乳熟期连体剑叶的光合作用下降和ＦＢＰａｓｅ 对低温的适应和调节能力有关     

Effects of Chilling Temperature on Photosynthesis and Photosynthate Transport in Flag Leaves of Hybrid Rice at Milky Stage

To understand the physiological reasons for poor yield of the second rice crop in southern China challenged by low temperature. The authors investigated the effects of chilling temperature on photosynthesis and the activity of fructose 1, 6-diphosphatase (FBPase) of flag leaves at milky stage using two hybrid rice varieties with different cold tolerance. The results indicated that chilling temperature caused decreases of photosynthetic efficiency and FBPase activity in detached flag leaves. The decline of photosynthetic efficiency and FBPase activity was greater in Shanyou-63 which is as cold sensitive as its parents than in Xiuyou-57 which is cold tolerant like its parents. The milky stage is the period of the fastest grain filling. The decreased the yield of the second rice crop caused by natural low temperature was associated with decline of photosynthesis and the abilities of adaption and adjustment of FBPase in attached flag leaves. The relationship between the effects of chilling temperature on photosynthesis and photosynthate transport and the yield formed by grain was discussed.     

Timing of Photoperiodic Flowering：Light Perception and Circadian Clock

Flowering symbolizes the transition of s plant from vegetative phase to reproductive phase and is controlled by fairly complex and highly coordinated regulatory pathways. Over the last decade, genetic studies in Arabidopsis have aided the discovery of many signaling components involved in these pathways. In this review, we discuss how the timing of flowering is regulated by photoperiod and the involvement of light perception and the circadian clock in this process. The specific regulatory mechanisms on CONSTANS expression and CONSTANS stability by the circadian clock and photoreceptors are described in detail. In addition, the roles of CONSTANS, FLOWERING LOCUS T, and several other light signaling and circadian-dependent components in photoperiodic flowering are also highlighted.     

Timing of Photoperiodic Flowering:Light Perception and Circadian Clock

Flowering symbolizes the transition of a plant from vegetative phase to reproductive phase and is controlled by fairly complex and highly coordinated regulatory pathways. Over the last decade, genetic studies in Arabidopsis have aided the discovery of many signaling components involved in these pathways. In this review, we discuss how the timing of flowering is regulated by photoperiod and the involvement of light perception and the circadian clock in this process. The specific regulatory mechanisms on CONSTANS expression and CONSTANS stability by the circadian clock and photoreceptors are described in detail. In addition, the roles of CONSTANS, FLOWERING LOCUS T, and several other light signaling and circadiandependent components in photoperiodic flowering are also highlighted.     

Plant dual‐specificity tyrosine phosphorylation‐regulated kinase optimizes light‐regulated growth and development in Arabidopsis

Light controls vegetative and reproductive development of plants. For a plant, sensing the light input properly ensures coordination with the ever‐changing environment. Previously, we found that LIGHT‐REGULATED WD1 (LWD1) and LWD2 regulate the circadian clock and photoperiodic flowering. Here, we identified Arabidopsis YET ANOTHER KINASE1 (AtYAK1), an evolutionarily conserved protein and a member of dual‐specificity tyrosine phosphorylation‐regulated kinases (DYRKs), as an interacting protein of LWDs. Our study revealed that AtYAK1 is an important regulator for various light responses, including the circadian clock, photomorphogenesis and reproductive development. AtYAK1 could antagonize the function of LWDs in regulating the circadian clock and photoperiodic flowering. By examining phenotypes of atyak1, we found that AtYAK1 regulated light‐induced period‐length shortening and photomorphogenic development. Moreover, AtYAK1 mediated plant fertility especially under inferior light conditions including low light and short‐day length. This study discloses a new regulator connecting environmental light to plant growth.     

Consequences of early chilling stress in two Triticum species: plastic responses and adaptive significance

Phenotypic plasticity of two primitive wheat species (Triticum monococcum L. and Triticum dicoccum S.) was studied in response to early chilling stress. Selection pressure differentials, gradients and plasticity costs on plant morphogenesis, growth and reserve carbohydrate consumption were estimated. Regression analysis was applied to investigate differential developmental changes and patterns between treatments. Four‐day‐old seedlings of T. monococcum and T. dicoccum, differing in plant stature and reserve carbohydrates, were given an early chilling temperature (4 °C for 42 day) and compared with control plants grown at 23 °C. Early chilling stress resulted in a significant increase in leaf mass ratio (LMR) and relative growth rate (RGR), a reduction in flag leaf size, total biomass, specific leaf area (SLA) and reserve carbohydrate storage at flowering, together with advanced onset of flowering. Selection pressure within the early chilling environment favoured early flowering, smaller SLA, higher LMR and lower reserve carbohydrates, suggesting the observed responses were adaptive. Furthermore, a regression of daily cumulative plant biomass derived from a crop growth simulation model (CERES‐Wheat) on crop vegetation period revealed a divergent developmental pattern in early‐chilled plants. Using selection pressure gradient analysis, we found similar responses among these traits, except for SLA and sucrose, indicating that these two traits have indirect effects on fitness. Thus, the total effects of SLA and reserve sucrose on relative fitness seem to be buffered via the rapid growth rate in chilled plants. While lower SLA may reduce early chilling stress effects at an individual leaf level, a higher LMR and use of reserve carbohydrates indicated that compensatory growth of chilled plants during the recovery period relied on the concerted action of altered resource allocation and reserve carbohydrate consumption. However, a significant cost of plasticity was evident only for flowering time, LMR and fructan levels in the early chilling environment. Our results demonstrate that morphological and intrinsic developmental (ontogenetic) patterns in two Triticum species respond to early chilling stress.     

Temporal organization of chilling resistance in cotton seedlings: effects of low temperature and relative humidity

The effect of temperature and relative humidity (RH) on the time course of the rhythmic endogenous changes of chilling resistance was studied in cotton (Gossypium hirsutum L. cv. Deltapine 50) seedlings grown under light-dark cycles of 12:12 h. The resistant phase to 5° C, 85% RH lasted during most of the dark period while to 5° C, 100% RH it was longer and extended into the last half of the light period because a transient phase advance occurred when chilling started at the middle of the light period. Seedlings acclimated by low temperature were resistant throughout the light-dark cycle. A treatment with 100% RH before chilling to acclimated seedlings introduced a sensitive phase that corresponded to that of non-acclimated seedlings. In non-acclimated seedlings, this treatment decreased the resistance but the basic pattern of the rhythm was sustained. Changes in chilling resistance were analyzed under fluctuating temperatures and RHs, and explained taking into consideration the functioning of the circadian clock and environmental induction of resistance.Abbreviations CR chilling resistance - LDC light-dark cycle of 24 h - RH relative humidity     

Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures

Circadian clocks exhibit ‘temperature compensation’, meaning that they show only small changes in period over a broad temperature range. Several clock genes have been implicated in the temperature‐dependent control of period in Arabidopsis. We show that blue light is essential for this, suggesting that the effects of light and temperature interact or converge upon common targets in the circadian clock. Our data demonstrate that two cryptochrome photoreceptors differentially control circadian period and sustain rhythmicity across the physiological temperature range. In order to test the hypothesis that the targets of light regulation are sufficient to mediate temperature compensation, we constructed a temperature‐compensated clock model by adding passive temperature effects into only the light‐sensitive processes in the model. Remarkably, this model was not only capable of full temperature compensation and consistent with mRNA profiles across a temperature range, but also predicted the temperature‐dependent change in the level of LATE ELONGATED HYPOCOTYL, a key clock protein. Our analysis provides a systems‐level understanding of period control in the plant circadian oscillator.     

OsMPK4 promotes phosphorylation and degradation of IPA1 in response to salt stress to confer salt tolerance in rice

Salt stress adversely affects plant growth, development, and crop yield. Rice (Oryza sativa L.) is one of the most salt-sensitive cereal crops, especially at the early seedling stage. Mitogen-activated protein kinase (MAPK/MPK) cascades have been shown to play critical roles in salt response in Arabidopsis. However, the roles of the MPK cascade signaling in rice salt response and substrates of OsMPK remain largely unknown. Here, we report that the salt-induced OsMPK4-Ideal Plant Architecture 1 (IPA1) signaling pathway regulates the salt tolerance in rice. Under salt stress, OsMPK4 could interact with IPA1 and phosphorylate IPA1 at Thr180, leading to degradation of IPA1. Genetic evidence shows that IPA1 is a negative regulator of salt tolerance in rice, whereas OsMPK4 promotes salt response in an IPA1-dependent manner. Taken together, our results uncover an OsMPK4-IPA1 signal cascade that modulates the salt stress response in rice and sheds new light on the breeding of salt-tolerant rice varieties.     

Effect of Chilling on Photosynthesis in Flag Leaves at Primary Heading Stage of F1 Hybrid Rice Cultivars and Their Parental Lines (Three Lines)

With the purpose of selecting and breeding cold stress tolerance of hybrid rice cultivars, the effect of chilling on five hybrid rice combinations was investigated. The results indicated that the cold tolerance of different hybrid rice varieties were different. The order of the cold tolerance as the degrees of inhibition of maximum photosynthetic rate and of apparent quantum yield of flag leaves at primary heading stage by chilling was as follows: The cold tolerance of Japanica type Xiuyou-57 was the highest then lndica type Qing-Youzao followed by Shangyou-63, Shangyou-64 and Weiyou-64. The cold tolerance of Fx hybrid rice was similar to that of the maternal lines and not similar to the paternal lines. The cold tolerance of maintainer lines was similar to that of the male sterile lines. The tests on the survival rate of hybrid rice seedlings after chilling treatment also showed a similar re gular patterns. These indicated that the responses by the chilling temperature in these five hybrid combinations were exactly the same in the Seedling stage as well as in the late growing stage. The results of these experiments on the impact of selecting and breeding cold tolerance in hybrid rice were discussed.     

The cell adhesion molecule EphA4 is involved in circadian clock functions

Circadian (～24 h) rhythms of cellular network plasticity in the central circadian clock, the suprachiasmatic nucleus (SCN), have been described. The neuronal network in the SCN regulates photic resetting of the circadian clock as well as stability of the circadian system during both entrained and constant conditions. EphA4, a cell adhesion molecule regulating synaptic plasticity by controlling connections of neurons and astrocytes, is expressed in the SCN. To address whether EphA4 plays a role in circadian photoreception and influences the neuronal network of the SCN, we have analyzed circadian wheel‐running behavior of EphA4 knockout (EphA4^?/?) mice under different light conditions and upon photic resetting, as well as their light‐induced protein response in the SCN. EphA4^?/? mice exhibited reduced wheel‐running activity, longer endogenous periods under constant darkness and shorter periods under constant light conditions, suggesting an effect of EphA4 on SCN function. Moreover, EphA4^?/? mice exhibited suppressed phase delays of their wheel‐running activity following a light pulse during the beginning of the subjective night (CT15). Accordingly, light‐induced c‐FOS (FBJ murine osteosarcoma viral oncogene homolog) expression was diminished. Our results suggest a circadian role for EphA4 in the SCN neuronal network, affecting the circadian system and contributing to the circadian response to light.     

Overexpression of ethylene response factor <Emphasis Type="Italic">TERF2</Emphasis> confers cold tolerance in rice seedlings

Rice (Oryza sativa L.) is a warm-season plant exposed to various stresses. Low temperature is an important factor limiting extension of rice cultivation areas and productivity. Previously, we have demonstrated that tomato ERF protein TERF2 enhances freezing tolerance of transgenic tobacco and tomato plants. Herein, we report that overexpression of TERF2 enhances transgenic rice tolerance to cold without affecting growth or agronomic traits. Physiological assays revealed that TERF2 could not only increase accumulation of osmotic substances and chlorophyll, but also reduce reactive oxygen species (ROS) and malondialdehyde (MDA) content and decrease electrolyte leakage in rice under cold stress. Further analysis of gene expression showed that TERF2 could activate expression of cold-related genes, including OsMyb, OsICE1, OsCDPK7, OsSODB, OsFer1, OsTrx23, and OsLti6, in transgenic rice plants under natural condition or cold stress. Thus, our findings demonstrated that TERF2 modulated expression of stress-related genes and a series of physiological adjustments under cold stress, indicating that TERF2 might have important regulatory roles in response to abiotic stress in rice and possess potential utility in improving crop cold tolerance.