Whirly1 enhances tolerance to chilling stress in tomato via protection of photosystem II and regulation of starch degradation

Light-independent pathway of STN7 kinase activation under low temperature stress in runner bean (Phaseolus coccineus L.)

BACKGROUND

The phosphorylation of the Light-Harvesting Complex of photosystem II (LHCII) driven by STATE TRANSITION 7 (STN7) kinase is a part of one of the crucial regulatory mechanisms of photosynthetic light reactions operating in fluctuating environmental conditions, light in particular. There are evidenced that STN7 can also be activated without light as well as in dark-chilling conditions. However, the biochemical mechanism standing behind this complex metabolic pathway has not been deciphered yet.

RESULTS

In this work, we showed that dark-chilling induces light-independent LHCII phosphorylation in runner bean (Phaseolus coccineus L.). In dark-chilling conditions, we registered an increased reduction of the PQ pool which led to activation of STN7 kinase, subsequent LHCII phosphorylation, and possible LHCII relocation inside the thylakoid membrane. We also presented the formation of a complex composed of phosphorylated LHCII and photosystem I typically formed upon light-induced phosphorylation. Moreover, we indicated that the observed steps were preceded by the activation of the oxidative pentose phosphate pathway (OPPP) enzymes and starch accumulation.

CONCLUSIONS

Our results suggest a direct connection between photosynthetic complexes reorganization and dark-chilling-induced activation of the thioredoxin system. The proposed possible pathway starts from the activation of OPPP enzymes and further NADPH-dependent thioredoxin reductase C (NTRC) activation. In the next steps, NTRC simultaneously activates ADP-glucose pyrophosphorylase and thylakoid membrane-located NAD(P)H dehydrogenase-like complex. These results in starch synthesis and electron transfer to the plastoquinone (PQ) pool, respectively. Reduced PQ pool activates STN7 kinase which phosphorylates LHCII. In this work, we present a new perspective on the mechanisms involving photosynthetic complexes while efficiently operating in the darkness. Although we describe the studied pathway in detail, taking into account also the time course of the following steps, the biological significance of this phenomenon remains puzzling.

Multi-omic dissection of the cold resistance traits of white water lily

The white water lily (Nymphaea candida), exemplifying nature's resilience, thrives in the high-altitude terrains of Xinjiang, China, serving as an ideal model for investigating cold adaptation mechanisms in aquatic plants. This study meticulously elucidates the complex cold adaptation mechanisms of the white water lily through a comprehensive and integrated methodological approach. We discovered that the water lily undergoes ecodormancy in winter, retaining high cellular viability and growth potential. During overwintering, the white water lily demonstrates effective resource reallocation, a process facilitated by morphological adjustments, thereby strengthening its resistance to cold temperatures. This enhancement is achieved particularly through the compartmentalization of large vacuoles, the accumulation of osmoregulatory substances, and an increased antioxidant capacity. We established the first exhaustive full-length transcriptome for the white water lily. A subsequent comprehensive analysis of the transcriptome, phytohormones, and metabolome uncovered a multifaceted regulatory network orchestrating cold adaptation. Our research spotlights phytohormone signaling, amino acid metabolism, and circadian rhythms as key elements in the water lily's defense against cold. The results emphasize the critical role of nitrogen metabolism, especially amino acid-related pathways, during cold stress. Metabolite profiling revealed the importance of compounds like myo-inositol and L-proline in enhancing cold tolerance. Remarkably, our study demonstrates that the white water lily notably diminishes the utilization of unsaturated fatty acids in its temperature regulation strategies. In conclusion, this research substantially enriches our understanding of the white water lily's intricate cold adaptation mechanisms, offering new perspectives on the adaptive strategies of aquatic plants and potential applications in agricultural advancement.

Transcription factor WRKY75 maintains auxin homeostasis to promote tomato defense against Pseudomonas syringae

The hemibiotrophic bacterial pathogen Pseudomonas syringae infects a range of plant species and causes enormous economic losses. Auxin and WRKY transcription factors play crucial roles in plant responses to P. syringae, but their functional relationship in plant immunity remains unclear. Here, we characterized tomato (Solanum lycopersicum) SlWRKY75, which promotes defenses against P. syringae pv. tomato (Pst) DC3000 by regulating plant auxin homeostasis. Overexpressing SlWRKY75 resulted in low free indole-3-acetic acid (IAA) levels, leading to attenuated auxin signaling, decreased expansin transcript levels, upregulated expression of PATHOGENESIS-RELATED GENES (PRs) and NONEXPRESSOR OF PATHOGENESIS-RELATED GENE 1 (NPR1), and enhanced tomato defenses against Pst DC3000. RNA interference-mediated repression of SlWRKY75 increased tomato susceptibility to Pst DC3000. Yeast one-hybrid, electrophoretic mobility shift assays, and luciferase activity assays suggested that SlWRKY75 directly activates the expression of GRETCHEN HAGEN 3.3 (SlGH3.3), which encodes an IAA-amido synthetase. SlGH3.3 enhanced tomato defense against Pst DC3000 by converting free IAA to the aspartic acid (Asp)-conjugated form IAA-Asp. In addition, SlWRKY75 interacted with a tomato valine-glutamine (VQ) motif-containing protein 16 (SlVQ16) in vivo and in vitro. SlVQ16 enhanced SlWRKY75-mediated transcriptional activation of SlGH3.3 and promoted tomato defense responses to Pst DC3000. Our findings illuminate a mechanism in which the SlVQ16-SlWRKY75 complex participates in tomato pathogen defense by positively regulating SlGH3.3-mediated auxin homeostasis.

Exogenous 5-Aminolevulinic acid improved low-temperature tolerance tomato seedling by regulating starch content and phenylalanine metabolism

Tomato is an important horticultural cash crop, and low-temperature stress has seriously affected the yield and quality of tomato. 5-Aminolevulinic acid (ALA) is widely used in agriculture as an efficient and harmless growth regulator. It is currently unclear whether exogenous ALA can cope with low-temperature stress by regulating tomato starch content and phenylalanine metabolism. In this study, exogenous ALA remarkably improved the low-temperature tolerance of tomato seedlings. RNA-sequencing results showed that exogenous ALA affected starch metabolism and phenylalanine metabolism in tomato seedling leaves under low-temperature stress. Subsequently, we used histochemical staining, observation of chloroplast microstructure, substance content determination, and qRT-PCR analysis to demonstrate that exogenous ALA could improve the low-temperature tolerance of tomato seedlings by regulating starch content and phenylalanine metabolism (SlPAL, SlPOD1, and SlPOD2). Simultaneously, we found that exogenous ALA induced the expression of SlMYBs and SlWRKYs under low-temperature stress. In addition, dual luciferase, yeast one hybrid, and electrophoretic mobility shift assays indicate that SlMYB4 and SlMYB88 could regulate the expression of SlPOD2 in phenylalanine metabolism. We demonstrated that exogenous ALA could improve the low-temperature tolerance of tomato seedlings by regulating starch content and phenylalanine metabolism.

Jasmonates Promote β-Amylase-Mediated Starch Degradation to Confer Cold Tolerance in Tomato Plants

Cold stress severely restricts growth and development, reduces yields, and impairs quality in tomatoes (Solanum lycopersicum). Amylase-associated starch degradation and soluble sugar accumulation have been implicated in adaptation and resistance to abiotic stress. Here, we report a β-amylase (BAM) gene, SlBAM3, which plays a central role in tomato cold tolerance. The expression of SlBAM3 was triggered by cold stress. SlBAM3 knockout using the CRISPR/Cas9 system retarded starch degradation and reduced soluble sugar accumulation in tomato plants, eventually attenuating cold tolerance. Expression analysis revealed that the SlBAM3 transcript level was boosted by MeJA. Furthermore, MYC2, an essential component of the JA signaling pathway, could bind to the SlBAM3 promoter and directly activate SlBAM3 transcription, as revealed by yeast one-hybrid and dual LUC assays. In addition, the suppression of MYC2 resulted in increased starch accumulation, decreased soluble sugar content, and reduced tolerance to cold stress in tomato plants. Taken together, these findings demonstrate that JA positively regulates β-amylase-associated starch degradation through the MYC2-SlBAM3 module in tomato during cold stress. The results of the present work expand our understanding of the mechanisms underlying BAM gene activation and starch catabolism under cold stress. The regulatory module of SlBAM3 can be further utilized to breed tomato cultivars with enhanced cold tolerance.

Transcriptome Profiling Reveals Molecular Responses to Salt Stress in Common Vetch (Vicia sativa L.)

Common vetch (Vicia sativa L.) is an important annual diploid leguminous forage. In the present study, transcriptomic profiling in common vetch in response to salt stress was conducted using a salt-tolerant line (460) and a salt-sensitive line (429). The common responses in common vetch and the specific responses associated with salt tolerance in 460 were analyzed. Several KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, including plant hormone and MAPK (mitogen-activated protein kinase) signaling, galactose metabolism, and phenylpropanoid phenylpropane biosynthesis, were enriched in both lines, though some differentially expressed genes (DEGs) showed distinct expression patterns. The roots in 460 showed higher levels of lignin than in 429. α-linolenic acid metabolism, carotenoid biosynthesis, the photosynthesis-antenna pathway, and starch and sucrose metabolism pathways were specifically enriched in salt-tolerant line 460, with higher levels of accumulated soluble sugars in the leaves. In addition, higher transcript levels of genes involved in ion homeostasis and reactive oxygen species (ROS) scavenging were observed in 460 than in 429 in response to salt stress. The transcriptomic analysis in common vetch in response to salt stress provides useful clues for further investigations on salt tolerance mechanism in the future.

Topography-mediated light environment regulates intra-specific seasonal and diurnal patterns of photosynthetic plasticity and plant ecophysiological adaptation strategies

Due to substantial topographic variations in the Himalaya, incident solar radiation in the forest canopy is highly unequal. This results in significant environmental differences at finer scales and may lead to considerable differences in photosynthetic productivity in montane forests. Therefore, local-scale ecophysiological investigations, may be more effective and instructive than landscape-level inventories and models. We investigated leaf ecophysiological differences and related adaptations between two Quercus semecarpifolia forests in aspect-mediated, significantly varying light regimes in the same mountain catchment. Seasonal and diurnal rates of photosynthesis (A) were significantly higher in south aspect (S) than the north (N). Although temperature was a key contributor to seasonal fluctuations in photosynthetic physiology, photoperiod significantly determined intraspecific variations in seasonal and diurnal plasticity of leaf ecophysiological traits between the two topography-mediated light environments. The regression model for A as a function of stomatal conductivity (gsw) explained the critical role of gsw in triggering photosynthetic plasticity as an adaptive function against varying environmental stresses due to seasonal solar differences. We also examined, modifications in chlorophyll content between the two light regimes across seasons to determine the chlorophyll adaptation strategy. The N aspect had higher leaf chl a, b, and chl a + b and a lower chl-allocation ratio (a/b) than S, which helped to optimize the required light reception in the photoreaction centers for improved photosynthetic performance. The leaf light response curves for A and gsw were observed against varying incident photosynthetic photon flux densities (0-2000 mol.m2 s-1 PPFD) for both aspects. We found that the same species developed significantly distinct light response strategies and photosynthetic capacities in S than in N for the given magnitudes of PPFD. Such acquired ecophysiological adaptations owing to varying light environments may provide significant clues for understanding the impact of future climate change on Himalayan tree species.

Differential heat-response characteristics of two plastid isoforms of triose phosphate isomerase in tomato

Heat stress causes dysfunction of the carbon-assimilation metabolism. As a member of Calvin-Benson-Bassham (CBB) cycle, the chloroplast triose phosphate isomerases (TPI) catalyse the interconversion of glyceraldehyde 3-phosphate (GAP) and dihydroxyacetone phosphate (DHAP). The tomato (Solanum lycopersicum) genome contains two individual SlTPI genes, Solyc10g054870 and Solyc01g111120, which encode the chloroplast-located proteins SlTPI1 and SlTPI2, respectively. The tpi1 and tpi2 single mutants had no visible phenotypes, but the leaves of their double mutant lines tpi1tpi2 had obviously reduced TPI activity and displayed chlorotic variegation, dysplasic chloroplasts and lower carbon-assimilation efficiency. In addition to altering carbon metabolism, proteomic data showed that the loss of both SlTPI1 and SlTPI2 severely affected photosystem proteins, reducing photosynthetic capacity. None of these phenotypes was evident in the tpi1 or tpi2 single mutants, suggesting that SlTPI1 and SlTPI2 are functionally redundant. However, the two proteins differed in their responses to heat stress; the protein encoded by the heat-induced SlTPI2 showed a higher level of thermotolerance than that encoded by the heat-suppressed SlTPI1. Notably, heat-induced transcription factors, SlWRKY21 and SlHSFA2/7, which negatively regulated SlTPI1 expression and positively regulated SlTPI2 expression, respectively. Our findings thus reveal that SlTPI1 and SlTPI2 have different thermostabilities and expression patterns in response to heat stress, which have the potential to be applied in thermotolerance strategies in crops.

Identification of genetic loci and candidate genes underlying freezing tolerance in wheat seedlings

KEY MESSAGE

Ten stable loci for freezing tolerance (FT) in wheat were detected by genome-wide association analysis. The putative candidate gene TaRPM1-7BL underlying the major locus QFT.ahau-7B.2 was identified and validated. Frost damage restricts wheat growth, development, and geographical distribution. However, the genetic mechanism of freezing tolerance (FT) remains unclear. Here, we evaluated FT phenotypes of 245 wheat varieties and lines, and genotyped them using a Wheat 90 K array. The association analysis showed that ten stable loci were significantly associated with FT (P < 1 × 10-4), and explained 6.45-26.33% of the phenotypic variation. In particular, the major locus QFT.ahau-7B.2 was consistently related to all nine sets of FT phenotypic data. Based on five cleaved amplified polymorphic sequence (CAPS) markers closely linked to QFT.ahau-7B.2, we narrowed down the target region to the 570.67-571.16 Mb interval (0.49 Mb) on chromosome 7B, in which four candidate genes were annotated. Of these, only TaRPM1-7BL exhibited consistent differential expression after low temperature treatment between freezing-tolerant and freezing-sensitive varieties. The results of cloning and whole-exome capture sequencing indicated that there were two main haplotypes for TaRPM1-7BL, including freezing-tolerant Hap1 and freezing-sensitive Hap2. Based on the representative SNP (+1956, A/G), leading to an amino acid change in the NBS domain, a CAPS marker (CAPS-TaRPM1-7BL) was developed and validated in 431 wheat varieties (including the above 245 materials) and 318 F2 lines derived from the cross of 'Annong 9267' (freezing-tolerant) × 'Yumai 9' (freezing-sensitive). Subsequently, the TaRPM1-7BL gene was silenced in 'Yumai 9' by virus-induced gene silencing (VIGS), and these silenced wheat seedlings exhibited enhanced FT phenotypes, suggesting that TaRPM1-7BL negatively regulates FT. These findings are valuable for understanding the complex genetic basis of FT in wheat.

The tuber-specific StbHLH93 gene regulates proplastid-to-amyloplast development during stolon swelling in potato

In potato, stolon swelling is a complex and highly regulated process, and much more work is needed to fully understand the underlying mechanisms. We identified a novel tuber-specific basic helix-loop-helix (bHLH) transcription factor, StbHLH93, based on the high-resolution transcriptome of potato tuber development. StbHLH93 is predominantly expressed in the subapical and perimedullary region of the stolon and developing tubers. Knockdown of StbHLH93 significantly decreased tuber number and size, resulting from suppression of stolon swelling. Furthermore, we found that StbHLH93 directly binds to the plastid protein import system gene TIC56 promoter, activates its expression, and is involved in proplastid-to-amyloplast development during the stolon-to-tuber transition. Knockdown of the target TIC56 gene resulted in similarly problematic amyloplast biogenesis and tuberization. Taken together, StbHLH93 functions in the differentiation of proplastids to regulate stolon swelling. This study highlights the critical role of proplastid-to-amyloplast interconversion during potato tuberization.

Daily fluctuation of colonic microbiome in response to nutrient substrates in a pig model

Studies on rodents indicate the daily oscillations of the gut microbiota have biological implications for host. However, the responses of fluctuating gut microbes to the dynamic nutrient substrates are not fully clear. In the study, we found that the feed intake, nutrient substrates, microbiota and metabolites in the colon underwent asynchronous oscillation within a day. Short-chain fatty acids (SCFAs) including acetate, propionate, butyrate and valerate peaked during T24 ~ T27 (Timepoint 24, 12:00 pm, T27, 03:00 am) whereas branched SCFAs isobutyrate and isovalerate peaked during T09 ~ T12. Further extended local similarity analysis (eLSA) revealed that the fluctuation of feed intake dynamically correlated with the colonic carbon substrates which further influenced the oscillation of sugar metabolites and acetate, propionate, butyrate and valerate with a certain time shift. The relative abundance of primary degrader Ruminococcaceae taxa was highly related to the dynamics of the carbon substrates whereas the fluctuations of secondary degraders Lactobacillaceae and Streptococcaceae taxa were highly correlated with the sugar metabolites. Meanwhile, colonic nitrogen substrates were correlated with branched amino acids and the branched SCFAs. Furthermore, we validated the evolution of gut microbes under different carbohydrate and protein combinations by using an in vitro fermentation experiment. The study pictured the dynamics of the micro-ecological environment within a day which highlights the implications of the temporal dimension in studies related to the gut microbiota. Feed intake, more precisely substrate intake, is highly correlated with microbial evolution, which makes it possible to develop chronotherapies targeting the gut microbiota through nutrition intervention.

SlMYB41 positively regulates tomato thermotolerance by activating the expression of SlHSP90.3

High-temperature stress has become a major abiotic factor that dramatically limits plant growth and crop yield. Plants have evolved complex mechanisms to cope with high-temperature stress, but the factors that regulate plant thermotolerance remain to be discovered. Here, a high temperature-induced MYB transcription factor SlMYB41 was cloned from tomato (Solanum lycopersicum). Two individual SlMYB41-RNA interference (RNAi) lines (MR) and one CRISPR/Cas9 mediated myb41 mutant (MC) were obtained to investigate the function of SlMYB41 in tomato thermotolerance. Under high-temperature stress, we found that the MR and MC lines showed more wilting than the wild type (WT), with more ion leakage, more MDA accumulation, lower contents of osmotic adjustment substances, and more accumulation of reactive oxygen species (ROS) which was resulted from lower antioxidative enzyme activities. In addition, the photosynthetic capacity and complex of MR and MC lines were damaged more seriously than WT plants under high-temperature stress, mainly manifested in lower photosynthetic rate and Fv/Fm. Moreover, heat stress-related genes, such as SlHSP17.6, SlHSP17.7, and SlHSP90.3 were downregulated in MR and MC lines. Importantly, Y1H and LUC analysis indicated that SlMYB41 can directly activate the transcription of SlHSP90.3. Together, our study suggest that SlMYB41 positively regulates tomato thermotolerance by activating the expression of SlHSP90.3.

MaBEL1 regulates banana fruit ripening by activating cell wall and starch degradation-related genes

Banana is a typical subtropical fruit, sensitive to chilling injuries and prone to softening disorder. However, the underlying regulatory mechanisms of the softening disorder caused by cold stress remain obscure. Herein, we found that BEL1-LIKE HOMEODOMAIN transcription factor 1 (MaBEL1) and its associated proteins regulate the fruit softening and ripening process. The transcript and protein levels of MaBEL1 were up-regulated with fruit ripening but severely repressed by the chilling stress. Moreover, the MaBEL1 protein interacted directly with the promoters of the cell wall and starch degradation-related genes, such as MaAMY3, MaXYL32, and MaEXP-A8. The transient overexpression of MaBEL1 alleviated fruit chilling injury and ripening disorder caused by cold stress and promoted fruit softening and ripening of "Fenjiao" banana by inducing ethylene production and starch and cell wall degradation. The accelerated ripening was also validated by the ectopic overexpression in tomatoes. Conversely, MaBEL1-silencing aggravated the chilling injury and ripening disorder and repressed fruit softening and ripening by inhibiting ethylene production and starch and cell wall degradation. MaABI5-like and MaEBF1, the two positive regulators of the fruit softening process, interacted with MaBEL1 to enhance the promoter activity of the starch and cell wall degradation-related genes. Moreover, the F-box protein MaEBF1 does not modulate the degradation of MaBEL1, which regulates the transcription of MaABI5-like protein. Overall, we report a novel MaBEL1-MaEBF1-MaABI5-like complex system that mediates the fruit softening and ripening disorder in "Fenjiao" bananas caused by cold stress.

Transcriptome Analysis Reveals Brassinolide Signaling Pathway Control of Foxtail Millet Seedling Starch and Sucrose Metabolism under Freezing Stress, with Implications for Growth and Development

Low-temperature stress limits the growth and development of foxtail millet. Freezing stress caused by sudden temperature drops, such as late-spring coldness, often occurs in the seedling stage of foxtail millet. However, the ability and coping strategies of foxtail millet to cope with such stress are not clear. In the present study, we analyzed the self-regulatory mechanisms of freezing stress in foxtail millet. We conducted a physiological study on foxtail millet leaves at -4 °C for seven different durations (0, 2, 4, 6, 8, 10, and 12 h). Longer freezing time increased cell-membrane damage, relative conductance, and malondialdehyde content. This led to osmotic stress in the leaves, which triggered an increase in free proline, soluble sugar, and soluble protein contents. The increases in these substances helped to reduce the damage caused by stress. The activities of superoxide dismutase, peroxidase, and catalase increased reactive oxygen species (ROS) content. The optimal time point for the response to freezing stress was 8 h after exposure. The transcriptome analysis of samples held for 8 h at -4 °C revealed 6862 differentially expressed genes (DEGs), among which the majority are implicated in various pathways, including the starch and sucrose metabolic pathways, antioxidant enzyme pathways, brassinolide (BR) signaling pathway, and transcription factors, according to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. We investigated possible crosstalk between BR signals and other pathways and found that BR signaling molecules were induced in response to freezing stress. The beta-amylase (BAM) starch hydrolase signal was enhanced by the BR signal, resulting in the accelerated degradation of starch and the formation of sugars, which served as emerging ROS scavengers and osmoregulators to resist freezing stress. In conclusion, crosstalk between BR signal transduction, and both starch and sucrose metabolism under freezing stress provides a new perspective for improving freezing resistance in foxtail millet.

ETHYLENE-INSENSITIVE 3-LIKE 2 regulates β-carotene and ascorbic acid accumulation in tomatoes during ripening

ETHYLENE-INSENSITIVE 3/ETHYLENE-INSENSITIVE 3-LIKEs (EIN3/EILs) are important ethylene response factors during fruit ripening. Here, we discovered that EIL2 controls carotenoid metabolism and ascorbic acid (AsA) biosynthesis in tomato (Solanum lycopersicum). In contrast to the red fruits presented in the wild type (WT) 45 d after pollination, the fruits of CRISPR/Cas9 eil2 mutants and SlEIL2 RNA interference lines (ERIs) showed yellow or orange fruits. Correlation analysis of transcriptome and metabolome data for the ERI and WT ripe fruits revealed that SlEIL2 is involved in β-carotene and AsA accumulation. ETHYLENE RESPONSE FACTORs (ERFs) are the typical components downstream of EIN3 in the ethylene response pathway. Through a comprehensive screening of ERF family members, we determined that SlEIL2 directly regulates the expression of 4 SlERFs. Two of these, SlERF.H30 and SlERF.G6, encode proteins that participate in the regulation of LYCOPENE-β-CYCLASE 2 (SlLCYB2), encoding an enzyme that mediates the conversion of lycopene to carotene in fruits. In addition, SlEIL2 transcriptionally repressed L-GALACTOSE 1-PHOSPHATE PHOSPHATASE 3 (SlGPP3) and MYO-INOSITOL OXYGENASE 1 (SlMIOX1) expression, which resulted in a 1.62-fold increase of AsA via both the L-galactose and myoinositol pathways. Overall, we demonstrated that SlEIL2 functions in controlling β-carotene and AsA levels, providing a potential strategy for genetic engineering to improve the nutritional value and quality of tomato fruit.

Chloroplast metalloproteinase SlL2 reduces the thermotolerance of tomato by decreasing the content of SlCDJ1

Chloroplast is one of the most sensitive organelles to heat stress in plants. In chloroplasts, various proteases affect photosynthesis by degrading proteins under stress conditions. Tomato Lutescent2 (SlL2), a chloroplast zinc metalloprotease, was previously reported to alter chloroplast development and delay fruit ripening. However, its enzyme activity and roles in plant response to abiotic stress are still unclear. Here, we confirmed that the SlL2 protein which localized on thylakoid membrane was an ATP-independent hydrolase, and SlL2 gene responded to heat stress. Phenotype analysis showed that SlL2 plays a negative role in the heat-response mechanism. Under heat stress, the transgenic plants overexpressing SlL2 (OE) grew worse than the wild type (WT), as reflected by their decreased membrane stability, osmotic-regulating substance, and antioxidative enzyme activities, as well as increased reactive oxygen species (ROS) accumulation. By contrast, l2 mutant line showed the opposite phenotype and corresponding physiological indices under heat stress. In addition, overexpression of SlL2 decreased the photosynthetic activities, especially photosystem II. Moreover, SlL2 was found to interact with chloroplast-located chaperone protein SlCDJ1, decreasing its content under heat stress. These results indicate that SlL2 reduces the thermotolerance of tomato by reducing the content of SlCDJ1.

Salicylic acid regulates two photosystem II protection pathways in tomato under chilling stress mediated by ETHYLENE INSENSITIVE 3-like proteins

Chilling stress seriously impairs photosynthesis and activates a series of molecular responses in plants. Previous studies have shown that ETHYLENE INSENSITIVE 3 (EIN3) and EIN3-like (SlEIL) proteins mediate ethylene signaling and reduce plant tolerance to freezing in tomato (Solanum lycopersicum). However, the specific molecular mechanisms underlying an EIN3/EILs-mediated photoprotection pathway under chilling stress are unclear. Here, we discovered that salicylic acid (SA) participates in photosystem II (PSII) protection via SlEIL2 and SlEIL7. Under chilling stress, the phenylalanine ammonia-lyase gene SlPAL5 plays an important role in the production of SA, which also induces WHIRLY1 (SlWHY1) transcription. The resulting accumulation of SlWHY1 activates SlEIL7 expression under chilling stress. SlEIL7 then binds to and blocks the repression domain of the heat shock factor SlHSFB-2B, releasing its inhibition of HEAT SHOCK PROTEIN 21 (HSP21) expression to maintain PSII stability. In addition, SlWHY1 indirectly represses SlEIL2 expression, allowing the expression of l-GALACTOSE-1-PHOSPHATE PHOSPHATASE3 (SlGPP3). The ensuing higher SlGPP3 abundance promotes the accumulation of ascorbic acid (AsA), which scavenges reactive oxygen species produced upon chilling stress and thus protects PSII. Our study demonstrates that SlEIL2 and SlEIL7 protect PSII under chilling stress via two different SA response mechanisms: one involving the antioxidant AsA and the other involving the photoprotective chaperone protein HSP21.

Low light intensity elongates period and defers peak time of photosynthesis: a computational approach to circadian-clock-controlled photosynthesis in tomato

Photosynthesis is involved in the essential process of transforming light energy into chemical energy. Although the interaction between photosynthesis and the circadian clock has been confirmed, the mechanism of how light intensity affects photosynthesis through the circadian clock remains unclear. Here, we propose a first computational model for circadian-clock-controlled photosynthesis, which consists of the light-sensitive protein P, the core oscillator, photosynthetic genes, and parameters involved in the process of photosynthesis. The model parameters were determined by minimizing the cost function ( [Formula: see text]), which is defined by the errors of expression levels, periods, and phases of the clock genes (CCA1, PRR9, TOC1, ELF4, GI, and RVE8). The model recapitulates the expression pattern of the core oscillator under moderate light intensity (100 μmol m ^-2 s^-1). Further simulation validated the dynamic behaviors of the circadian clock and photosynthetic outputs under low (62.5 μmol m^-2 s^-1) and normal (187.5 μmol m^-2 s^-1) intensities. When exposed to low light intensity, the peak times of clock and photosynthetic genes were shifted backward by 1-2 hours, the period was elongated by approximately the same length, and the photosynthetic parameters attained low values and showed delayed peak times, which confirmed our model predictions. Our study reveals a potential mechanism underlying the circadian regulation of photosynthesis by the clock under different light intensities in tomato.

Time-restricted feeding affects colonic nutrient substrates and modulates the diurnal fluctuation of microbiota in pigs

Introduction

Studies demonstrate that time-restricted feeding (TRF) can regulate gut microbiota composition. However, it is unclear whether TRF could affect the gut microbial rhythmicity in growing pigs. Therefore, the present study aimed to explore the effects of TRF on the dynamic fluctuation of the gut microbiota.

Methods

A total of 10 healthy growing pigs equipped with T cannula were employed. Pigs were randomly allotted to the free access (FA) and the TRF groups with 5 replicates (1 pig/replicates). Pigs in the FA group were fed free access during the whole experimental period, whereas pigs in the TRF group were fed free access three times per day within limited times (7:00-8:00, 12:00-13:00, 17:00-18:00). The experiment lasted for 15 days, at 06:00 a.m. of the day 16, colonic digesta were collected at a 6-h interval for consecutive 24 h marked as T06 (06:00), T12 (12:00), T18 (18:00), T24 (24:00), T30 (06:00), respectively.

Results

Results showed that TRF altered the distribution of feed intake without changing the total feed intake within a day (p = 0.870). TRF decreased the overall concentration of colonic cellulose and altered their oscillating patterns. All alpha-diversity indexes of different time points showed significant differences regardless of feeding pattern with a trough at T18 or T24. TRF shifted the trough of the alpha-diversity index Simpson and Invsimpson. TRF lost the rhythmicity of Prevotellaceae, Ruminococcaceae, Bacteroidales_S24-7_group, and Peptococcaceae and gained the rhythmicity of Pasteurellaceae, Clostridiaceae_1, Veillonellaceae, and Peptostreptococcaceae. Also, TRF altered the interaction pattern by increasing the microbes involved in the co-occurrence network and their crosstalk, especially at T24. Interestingly, the microbial variation at T24 could largely explained by colonic substrates starch (R² = 0.369; p = 0.001), cellulose (R² = 0.235; p = 0.009) and NH4-N (R² = 0.489; p = 0.001).

Conclusion

In conclusion, TRF has changed the concentrates of cellulose and the relative abundance of specific microbes and certain microbial metabolites. In addition, TRF has more powerful effects on the fluctuation modes of these nutrient substrates, microbes, and metabolites by shifting their peaks or troughs. This knowledge facilitates the development of precision regulation targeting gut microbial rhythmicity.

Regulation of drought tolerance in Arabidopsis involves the PLATZ4-mediated transcriptional repression of plasma membrane aquaporin PIP2;8

Plant A/T-rich protein and zinc-binding protein (PLATZ) transcription factors play important roles in plant growth, development and abiotic stress responses. However, how PLATZ influences plant drought tolerance remains poorly understood. The present study showed that PLATZ4 increased drought tolerance in Arabidopsis thaliana by causing stomatal closure. Transcriptional profiling analysis revealed that PLATZ4 affected the expression of a set of genes involved in water and ion transport, antioxidant metabolism, small peptides and abscisic acid (ABA) signaling. Among these genes, the direct binding of PLATZ4 to the A/T-rich sequences in the plasma membrane intrinsic protein 2;8 (PIP2;8) promoter was identified. PIP2;8 consistently reduced drought tolerance in Arabidopsis through inhibiting stomatal closure. PIP2;8 was localized in the plasma membrane, exhibited water channel activity in Xenopus laevis oocytes and acted epistatically to PLATZ4 in regulating the drought stress response in Arabidopsis. PLATZ4 increased ABA sensitivity through upregulating the expression of ABSCISIC ACID INSENSITIVE 3 (ABI3), ABI4 and ABI5. The transcripts of PLATZ4 were induced to high levels in vegetative seedlings under drought and ABA treatments within 6 and 3 h, respectively. Collectively, these findings reveal that PLATZ4 positively influences plant drought tolerance through regulating the expression of PIP2;8 and genes involved in ABA signaling.

WHIRLY1 Acts Upstream of ABA-Related Reprogramming of Drought-Induced Gene Expression in Barley and Affects Stress-Related Histone Modifications

WHIRLY1, a small plant-specific ssDNA-binding protein, dually located in chloroplasts and the nucleus, is discussed to act as a retrograde signal transmitting a stress signal from the chloroplast to the nucleus and triggering there a stress-related gene expression. In this work, we investigated the function of WHIRLY1 in the drought stress response of barley, employing two overexpression lines (oeW1-2 and oeW1-15). The overexpression of WHIRLY1 delayed the drought-stress-related onset of senescence in primary leaves. Two abscisic acid (ABA)-dependent marker genes of drought stress, HvNCED1 and HvS40, whose expression in the wild type was induced during drought treatment, were not induced in overexpression lines. In addition, a drought-related increase in ABA concentration in the leaves was suppressed in WHIRLY1 overexpression lines. To analyze the impact of the gain-of-function of WHIRLY1 on the drought-related reprogramming of nuclear gene expression, RNAseq was performed comparing the wild type and an overexpression line. Cluster analyses revealed a set of genes highly up-regulated in response to drought in the wild type but not in the WHIRLY1 overexpression lines. Among these genes were many stress- and abscisic acid (ABA)-related ones. Another cluster comprised genes up-regulated in the oeW1 lines compared to the wild type. These were related to primary metabolism, chloroplast function and growth. Our results indicate that WHIRLY1 acts as a hub, balancing trade-off between stress-related and developmental pathways. To test whether the gain-of-function of WHIRLY1 affects the epigenetic control of stress-related gene expression, we analyzed drought-related histone modifications in different regions of the promoter and at the transcriptional start sites of HvNCED1 and HvS40. Interestingly, the level of euchromatic marks (H3K4me3 and H3K9ac) was clearly decreased in both genes in a WHIRLY1 overexpression line. Our results indicate that WHIRLY1, which is discussed to act as a retrograde signal, affects the ABA-related reprogramming of nuclear gene expression during drought via differential histone modifications.

Proteomic Analysis Comparison on the Ecological Adaptability of Quinclorac-Resistant Echinochloa crus-galli

Barnyardgrass (Echinochloa crus-galli L.) is the most serious weed threatening rice production, and its effects are aggravated by resistance to the quinclorac herbicide in the Chinese rice fields. This study conducted a comparative proteomic characterization of the quinclorac-treated and non-treated resistant and susceptible E. crus-galli using isobaric tags for relative and absolute quantification (iTRAQ). The results indicated that the quinclorac-resistant E. crus-galli had weaker photosynthesis and a weaker capacity to mitigate abiotic stress, which suggested its lower environmental adaptability. Quinclorac treatment significantly increased the number and expression of the photosynthesis-related proteins in the resistant E. crus-galli and elevated its photosynthetic parameters, indicating a higher photosynthetic rate compared to those of the susceptible E. crus-galli. The improved adaptability of the resistant E. crus-galli to quinclorac stress could be attributed to the observed up-regulated expression of eight herbicide resistance-related proteins and the down-regulation of two proteins associated with abscisic acid biosynthesis. In addition, high photosynthetic parameters and low glutathione thiotransferase (GST) activity were observed in the quinclorac-resistant E. crus-galli compared with the susceptible biotype, which was consistent with the proteomic sequencing results. Overall, this study demonstrated that the resistant E. crus-galli enhanced its adaptability to quinclorac by improving the photosynthetic efficiency and GST activity.

RNA 5-Methylcytosine Modification Regulates Vegetative Development Associated with H3K27 Trimethylation in Arabidopsis

Methylating RNA post-transcriptionally is emerging as a significant mechanism of gene regulation in eukaryotes. The crosstalk between RNA methylation and histone modification is critical for chromatin state and gene expression in mammals. However, it is not well understood mechanistically in plants. Here, the authors report a genome-wide correlation between RNA 5-cytosine methylation (m5 C) and histone 3 lysine27 trimethylation (H3K27me3) in Arabidopsis. The plant-specific Polycomb group (PcG) protein EMBRYONIC FLOWER1 (EMF1) plays dual roles as activators or repressors. Transcriptome-wide RNA m5 C profiling revealed that m5 C peaks are mostly enriched in chromatin regions that lacked H3K27me3 in both wild type and emf1 mutants. EMF1 repressed the expression of m5 C methyltransferase tRNA specific methyltransferase 4B (TRM4B) through H3K4me3, independent of PcG-mediated H3K27me3 mechanism. The 5-Cytosine methylation on targets is increased in emf1 mutants, thereby decreased the mRNA transcripts of photosynthesis and chloroplast genes. In addition, impairing EMF1 activity reduced H3K27me3 levels of PcG targets, such as starch genes, which are de-repressed in emf1 mutants. Both EMF1-mediated promotion and repression of gene activities via m5 C and H3K27me3 are required for normal vegetative growth. Collectively, t study reveals a previously undescribed epigenetic mechanism of RNA m5 C modifications and histone modifications to regulate gene expression in eukaryotes.

OsWHY1 Interacts with OsTRX z and is Essential for Early Chloroplast Development in Rice

WHIRLY (WHY) family proteins, a small family of single-stranded DNA (ssDNA) binding proteins, are widely found in plants and have multiple functions to regulate plant growth and development. However, WHY in rice has received less attention. In this study, we continued our previous study on OsTRX z that is important for chloroplast development. OsTRX z was discovered to interact with OsWHY1, which was confirmed using yeast two-hybrid, pull-down, and BiFC assays. Subsequently, the oswhy1 mutants were obtained by CRISPR/Cas9, which exhibited an albino phenotype and died after the three-leaf stage. Consistent with this albino phenotype, low amounts of Chl a, Chl b, and Car were detected in the oswhy1-1 mutant. Moreover, the oswhy1-1 mutant had chloroplasts with disrupted architecture and no stacked grana and thylakoid membranes. Subcellular localization showed that the OsWHY1-GFP fusion protein was targeted to the chloroplast. What's more, OsWHY1 was found to be preferentially expressed in young leaves and was involved in chloroplast RNA editing and splicing. Mutation of OsWHY1 significantly affected the expression of chloroplast and ribosome development-related and chlorophyll synthesis-related genes. In conclusion, OsWHY1 contributes to early chloroplast development and normal seedling survival in rice. These results will further elucidate the molecular mechanism of chloroplast development and expand our understanding of WHY1 functions.

Identification of AP2/ERF transcription factors in Tetrastigma hemsleyanum revealed the specific roles of ERF46 under cold stress

Tetrastigma hemsleyanum (T. hemsleyanum) is a traditional medicinal plant that is widely used in China. Cultivated T. hemsleyanum usually encounters cold stress, limiting its growth and quality at key developmental stages. APETALA2 (AP2)/ethylene-responsive factor (ERF) transcription factors (TFs) comprise one of the largest gene superfamilies in plants and are widely involved in biotic and abiotic stresses. To reveal the roles of AP2/ERF TFs during T. hemsleyanum development, 70 AP2/ERF TFs were identified in T. hemsleyanum. Among them, 18 and 2 TFs were classified into the AP2 and RAV families, respectively. The other 50 TFs belonged to the ERF family and were further divided into the ERF and (dehydration reaction element binding factor) DREB subfamilies. The ERF subfamily contained 46 TFs, while the DREB subfamily contained 4 TFs. Phylogenetic analysis indicated that AP2/ERF TFs could be classified into five groups, in which 10 conserved motifs were confirmed. Several motifs were group- or subgroup-specific, implying that they were significant for the functions of the AP2/ERF TFs of these clades. In addition, 70 AP2/ERF TFs from the five groups were used for an expression pattern analysis under three low-temperature levels, namely, -4, 0, and 4°C. The majority of these AP2/ERF TFs exhibited a positive response to cold stress conditions. Specifically, ThERF5, ThERF31, ThERF46, and ThERF55 demonstrated a more sensitive response to cold stress. Moreover, AP2/ERF TFs exhibited specific expression patterns under cold stress. Transient overexpression and RNA interference indicated that ThERF46 has a specific tolerance to cold stress. These new insights provide the basis for further studies on the roles of AP2/ERF TFs in cold stress tolerance in T. hemsleyanum.

The Single-Stranded DNA-Binding Gene Whirly (Why1) with a Strong Pathogen-Induced Promoter from Vitis pseudoreticulata Enhances Resistance to Phytophthora capsici

Vitis vinifera plants are disease-susceptible while Vitis pseudoreticulata plants are disease-resistant; however, the molecular mechanism remains unclear. In this study, the single-stranded DNA- and RNA-binding protein gene Whirly (VvWhy1 and VpWhy1) were cloned from V. vinifera "Cabernet Sauvignon" and V. pseudoreticulata "HD1". VvWhy1 and VpWhy1 promoter sequences (pVv and pVp) were also isolated; however, the identity of the promoter sequences was far lower than that between the Why1 coding sequences (CDSs). Both Why1 gene sequences had seven exons and six introns, and they had a C-terminal Whirly conserved domain and N-terminal chloroplast transit peptide, which was then verified to be chloroplast localization. Transcriptional expression showed that VpWhy1 was strongly induced by Plasmopara viticola, while VvWhy1 showed a low expression level. Further, the GUS activity indicated pVp had high activity involved in response to Phytophthora capsici infection. In addition, Nicotiana benthamiana transiently expressing pVp::VvWhy1 and pVp::VpWhy1 enhanced the P. capsici resistance. Moreover, Why1, PR1 and PR10 were upregulated in pVp transgenic N. benthamiana leaves. This research presented a novel insight into disease resistance mechanism that pVp promoted the transcription of Why1, which subsequently regulated the expression of PR1 and PR10, further enhancing the resistance to P. capsici.

WHIRLY1 recruits the histone deacetylase HDA15 repressing leaf senescence and flowering in Arabidopsis

Leaf senescence is controlled by a complex regulatory network in which robustness is ensured by the activity of transcription factors and epigenetic regulators. However, how these coordinate the process of leaf senescence remains poorly understood. We found that WHIRLY1 interacts with Histone Deacetylase (HDA)15, a Reduced Potassium Dependence3 (RPD3)/HDA1-type HDA, by using green fluorescent protein-nanotrap-mass spectrum assays. The development-dependent interaction between WHIRLY1 and HDA15 was further confirmed by bimolecular fluorescence complementation assays and co-immunoprecipitation assays in Arabidopsis. Multi-omics genome-wide transcriptome and H3K9 acetylome enrichment analysis showed that HDA15 delays leaf senescence and flowering by repressing the expression of the positive regulators of leaf senescence and flowering, such as LOX2 and LARP1C, and reducing H3K9ac levels at these loci; WHIRLY1 and HDA15 co-target to the region near the transcription start site of a subset of nutrient recycling-related genes (e.g., Glutathione S-transferases 10, non-coding RNA, and photosystem II protein D1 synthesizer attenuator PDIL1-2), as well as WRKY53 and ELF4, and co-repress their expression by removing H3K9 acetylation. Our study revealed a key transcription regulatory node of nutrient recycling and senescence-associated genes involved in leaf senescence and flowering via the recruitment of HDA15 by the single-stranded DNA/RNA-binding protein WHIRLY1.

Prunus persica transcription factor PpNAC56 enhances heat resistance in transgenic tomatoes

Members of the NAC (NAM, ATAF1,2 and CUC2) transcription factor family are involved in numerous processes of plant growth and development and play an important role in the response to abiotic stresses such as salinity, drought and heat, but little research on this topic has been done in peach. In this study, we analyzed the expression patterns of PpNAC56 under abiotic stress and found that PpNAC56 responded to high-temperature stress. To verify the function of PpNAC56, we overexpressed this gene in tomato plants and found that, compared with WT plants, the transgenic tomato plants could accumulate more osmoregulatory substances after high-temperature treatment and thus were more heat resistance. Then, using Y2H, BIFC, and pull-down assays, we found that PpNAC56 could interact with PpMIEL1. In addition, Y1H and dual-luciferase assays verified that PpNAC56 could activate the expression of PpHSP17.4 and PpSnRK2D. The above experimental results demonstrate that PpNAC56 plays an important role in the plant response to heat stress.

Exogenous Melatonin Enhances Photosynthetic Capacity and Related Gene Expression in A Dose-Dependent Manner in the Tea Plant (Camellia sinensis (L.) Kuntze)

The enhancement of photosynthesis of tea leaves can increase tea yield. In order to explore the regulation mechanism of exogenous melatonin (MT) on the photosynthetic characteristics of tea plants, tea variety 'Zhongcha 108' was used as the experimental material in this study. The effects of different concentrations (0, 0.2, 0.3, 0.4 mM) of melatonin on the chlorophyll (Chl) content, stomatal opening, photosynthetic and fluorescence parameters, antioxidant enzyme activity, and related gene expression of tea plants were detected and analyzed. The results showed that under 0.2-mM MT treatment, chlorophyll (Chl) content, photosynthetic rate (P_n), stomatal conductance (G_s), intercellular CO₂ concentration (C_i), and transpiration rate (T_r) improved, accompanied by a decrease in stomata density and increase in stomata area. Zero point two millimolar MT increased Chl fluorescence level and superoxide dismutase (SOD) activity, and reduced hydrogen peroxide (H₂O₂) and malondialdehyde (MDA) contents, indicating that MT alleviated PSII inhibition and improved photochemical efficiency. At the same time, 0.2 mM MT induced the expression of genes involved in photosynthesis and chlorophyll metabolism to varying degrees. The study demonstrated that MT can effectively enhance the photosynthetic capacity of tea plants in a dose-dependent manner. These results may promote a comprehensive understanding of the potential regulatory mechanism of exogenous MT on photosynthesis in tea plants.

Genome-wide identification and characterization of the Prunus persica ferredoxin gene family and its role in improving heat tolerance

Ferredoxin is involved in many biological processes, such as carbon fixation, nitrogen assimilation, chlorophyll metabolism, and fatty acid synthesis, and it plays a role in plant resistance to stress. However, the functions of Fds in peach during stress are unclear. In this study, 11 members of the peach Fd gene family were identified and divided into six groups (I- VI). We carried out bioinformatics analysis on these sequences, analyzed the physical and chemical properties of PpFd protein and the cis-elements in its promoter region, and predicted and compared the differences in gene structure and conserved protein motifs among groups. The results showed that the PpFd protein was highly conserved in plant species. In addition, overexpression of PpFd08 significantly increased the tolerance of transgenic tomato to high-temperature stress. The transcriptome analysis and qRT-PCR results of PpFd08 transgenic apple calli showed that PpFd08 might enhance heat resistance by modulating the expression of heat tolerance related genes. The results of this study provide a new understanding for the further study of the function of PpFd protein in peach and a candidate gene for improving the heat resistance of peach.

WHIRLIES Are Multifunctional DNA-Binding Proteins With Impact on Plant Development and Stress Resistance

WHIRLIES are plant-specific proteins binding to DNA in plastids, mitochondria, and nucleus. They have been identified as significant components of nucleoids in the organelles where they regulate the structure of the nucleoids and diverse DNA-associated processes. WHIRLIES also fulfil roles in the nucleus by interacting with telomers and various transcription factors, among them members of the WRKY family. While most plants have two WHIRLY proteins, additional WHIRLY proteins evolved by gene duplication in some dicot families. All WHIRLY proteins share a conserved WHIRLY domain responsible for ssDNA binding. Structural analyses revealed that WHIRLY proteins form tetramers and higher-order complexes upon binding to DNA. An outstanding feature is the parallel localization of WHIRLY proteins in two or three cell compartments. Because they translocate from organelles to the nucleus, WHIRLY proteins are excellent candidates for transducing signals between organelles and nucleus to allow for coordinated activities of the different genomes. Developmental cues and environmental factors control the expression of WHIRLY genes. Mutants and plants with a reduced abundance of WHIRLY proteins gave insight into their multiple functionalities. In chloroplasts, a reduction of the WHIRLY level leads to changes in replication, transcription, RNA processing, and DNA repair. Furthermore, chloroplast development, ribosome formation, and photosynthesis are impaired in monocots. In mitochondria, a low level of WHIRLIES coincides with a reduced number of cristae and a low rate of respiration. The WHIRLY proteins are involved in the plants' resistance toward abiotic and biotic stress. Plants with low levels of WHIRLIES show reduced responsiveness toward diverse environmental factors, such as light and drought. Consequently, because such plants are impaired in acclimation, they accumulate reactive oxygen species under stress conditions. In contrast, several plant species overexpressing WHIRLIES were shown to have a higher resistance toward stress and pathogen attacks. By their multiple interactions with organelle proteins and nuclear transcription factors maybe a comma can be inserted here? and their participation in organelle-nucleus communication, WHIRLY proteins are proposed to serve plant development and stress resistance by coordinating processes at different levels. It is proposed that the multifunctionality of WHIRLY proteins is linked to the plasticity of land plants that develop and function in a continuously changing environment.

Plant Response to Cold Stress: Cold Stress Changes Antioxidant Metabolism in Heading Type Kimchi Cabbage (Brassica rapa L. ssp. Pekinensis)

Cold stress is known as the important yield-limiting factor of heading type Kimchi cabbage (HtKc, Brassica rapa L. ssp. pekinensis), which is an economically important crop worldwide. However, the biochemical and molecular responses to cold stress in HtKc are largely unknown. In this study, we conducted transcriptome analyses on HtKc grown under normal versus cold conditions to investigate the molecular mechanism underlying HtKc responses to cold stress. A total of 2131 genes (936 up-regulated and 1195 down-regulated) were identified as differentially expressed genes and were significantly annotated in the category of “response to stimulus”. In addition, cold stress caused the accumulation of polyphenolic compounds, including p-coumaric, ferulic, and sinapic acids, in HtKc by inducing the phenylpropanoid pathway. The results of the chemical-based antioxidant assay indicated that the cold-induced polyphenolic compounds improved the free-radical scavenging activity and antioxidant capacity, suggesting that the phenylpropanoid pathway induced by cold stress contributes to resistance to cold-induced reactive oxygen species in HtKc. Taken together, our results will serve as an important base to improve the cold tolerance in plants via enhancing the antioxidant machinery.

WHIRLY1 functions in the nucleus to regulate barley leaf development and associated metabolite profiles

The WHIRLY (WHY) DNA/RNA binding proteins fulfil multiple but poorly characterised functions in leaf development. Here, we show that WHY1 transcript levels were highest in the bases of 7-day old barley leaves. Immunogold labelling revealed that the WHY1 protein was more abundant in the nuclei than the proplastids of the leaf bases. To identify transcripts associated with leaf development we conducted hierarchical clustering of differentially abundant transcripts along the developmental gradient of wild-type leaves. Similarly, metabolite profiling was employed to identify metabolites exhibiting a developmental gradient. A comparative analysis of transcripts and metabolites in barley lines (W1–1 and W1–7) lacking WHY1, which show delayed greening compared with the wild type revealed that the transcript profile of leaf development was largely unchanged in W1–1 and W1–7 leaves. However, there were differences in levels of several transcripts encoding transcription factors associated with chloroplast development. These include a barley homologue of the Arabidopsis GATA transcription factor that regulates stomatal development, greening and chloroplast development, NAC1; two transcripts with similarity to Arabidopsis GLK1 and two transcripts encoding ARF transcriptions factors with functions in leaf morphogenesis and development. Chloroplast proteins were less abundant in the W1–1 and W1–7 leaves than the wild type. The levels of tricarboxylic acid cycle metabolites and GABA were significantly lower in WHY1 knockdown leaves than the wild type. This study provides evidence that WHY1 is localised in the nuclei of leaf bases, contributing the regulation of nuclear-encoded transcripts that regulate chloroplast development.

Prunus persica Terpene Synthase PpTPS1 Interacts with PpABI5 to Enhance Salt Resistance in Transgenic Tomatoes

Terpene synthase (TPS) is related to the production of aromatic substances, but there are few studies on the impact of abiotic stress on TPS and its molecular mechanism, especially in peaches. This study found that salt resistance and abscisic acid (ABA) sensitivity of transgenic tomatoes were enhanced by overexpression of PpTPS1. Moreover, it was found that PpTPS1 interacted with and antagonized the expression of the bZIP transcription factor ABA INSENSITIVE 5 (PpABI5), which is thought to play an important role in salt suitability. In addition, PpTCP1, PpTCP13, and PpTCP15 were found to activate the expression of PpTPS1 by yeast one-hybrid (Y1H) and dual-luciferase assays, and they could also be induced by ABA. In summary, PpTPS1 may be involved in the ABA signaling regulatory pathway and play an important role in salt acclimation, providing a new reference gene for the improvement of salt resistance in peaches.

Multilocation proteins in organelle communication: Based on protein-protein interactions

Protein-protein interaction (PPI) plays a crucial role in most biological processes, including signal transduction and cell apoptosis. Importantly, the knowledge of PPIs can be useful for identification of multimeric protein complexes and elucidation of uncharacterized protein functions. Arabidopsis thaliana, the best-characterized dicotyledonous plant, the steadily increasing amount of information on the levels of its proteome and signaling pathways is progressively enabling more researchers to construct models for cellular processes for the plant, which in turn encourages more experimental data to be generated. In this study, we performed an overview analysis of the 10 major organelles and their associated proteins of the dicotyledonous model plant Arabidopsis thaliana via PPI network, and found that PPI may play an important role in organelle communication. Further, multilocation proteins, especially phosphorylation-related multilocation proteins, can function as a "needle and thread" via PPIs and play an important role in organelle communication. Similar results were obtained in a monocotyledonous model crop, rice. Furthermore, we provide a research strategy for multilocation proteins by LOPIT technique, proteomics, and bioinformatics analysis and also describe their potential role in the field of plant science. The results provide a new view that the phosphorylation-related multilocation proteins play an important role in organelle communication and provide new insight into PPIs and novel directions for proteomic research. The research of phosphorylation-related multilocation proteins may promote the development of organelle communication and provide an important theoretical basis for plant responses to external stress.

Function of Chloroplasts in Plant Stress Responses

The chloroplast has a central position in oxygenic photosynthesis and primary metabolism. In addition to these functions, the chloroplast has recently emerged as a pivotal regulator of plant responses to abiotic and biotic stress conditions. Chloroplasts have their own independent genomes and gene-expression machinery and synthesize phytohormones and a diverse range of secondary metabolites, a significant portion of which contribute the plant response to adverse conditions. Furthermore, chloroplasts communicate with the nucleus through retrograde signaling, for instance, reactive oxygen signaling. All of the above facilitate the chloroplast’s exquisite flexibility in responding to environmental stresses. In this review, we summarize recent findings on the involvement of chloroplasts in plant regulatory responses to various abiotic and biotic stresses including heat, chilling, salinity, drought, high light environmental stress conditions, and pathogen invasions. This review will enrich the better understanding of interactions between chloroplast and environmental stresses, and will lay the foundation for genetically enhancing plant-stress acclimatization.

Melatonin Promotes the Chilling Tolerance of Cucumber Seedlings by Regulating Antioxidant System and Relieving Photoinhibition

Chilling adversely affects the photosynthesis of thermophilic plants, which further leads to a decline in growth and yield. The role of melatonin (MT) in the stress response of plants has been investigated, while the mechanisms by which MT regulates the chilling tolerance of chilling-sensitive cucumber remain unclear. This study demonstrated that MT positively regulated the chilling tolerance of cucumber seedlings and that 1.0 μmol⋅L-1 was the optimum concentration, of which the chilling injury index, electrolyte leakage (EL), and malondialdehyde (MDA) were the lowest, while growth was the highest among all treatments. MT triggered the activity and expression of antioxidant enzymes, which in turn decreased hydrogen peroxide (H2O2) and superoxide anion (O2 ⋅-) accumulation caused by chilling stress. Meanwhile, MT attenuated the chilling-induced decrease, in the net photosynthetic rate (Pn) and promoted photoprotection for both photosystem II (PSII) and photosystem I (PSI), regarding the higher maximum quantum efficiency of PSII (Fv/Fm), actual photochemical efficiency (ΦPSII), the content of active P700 (ΔI/I0), and photosynthetic electron transport. The proteome analysis and western blot data revealed that MT upregulated the protein levels of PSI reaction center subunits (PsaD, PsaE, PsaF, PsaH, and PsaN), PSII-associated protein PsbA (D1), and ribulose-1,5-bisphosphate carboxylase or oxygenase large subunit (RBCL) and Rubisco activase (RCA). These results suggest that MT enhances the chilling tolerance of cucumber through the activation of antioxidant enzymes and the induction of key PSI-, PSII-related and carbon assimilation genes, which finally alleviates damage to the photosynthetic apparatus and decreases oxidative damage to cucumber seedlings under chilling stress.

Wheat TaPUB1 protein mediates ABA response and seed development through ubiquitination

Abscisic acid (ABA) is an important regulator of plant growth, development, and biotic and abiotic stress responses. Ubiquitination plays important roles in regulating ABA signaling. E3 ligase, a key member in ubiquitination, actively participates in the regulation of biosynthesis, de-repression, and activation of ABA response and degradation of signaling components. In this study, we found that that overexpression of wheat E3 ligase TaPUB1 decreased the sensitivity of wheat seedlings to ABA, whereas TaPUB1-RNA interference (TaPUB1-RNAi) lines increased wheat sensitivity to ABA during germination, root growth, and stomatal opening. TaPUB1 influenced the expression of several ABA-responsive genes, and also interacted with TaPYL4 and TaABI5, which are involved in ABA signal transduction, and promoted their degradation. Additionally, we observed that TaPUB1-OE lines resulted in lower single-split grain numbers, larger seed size, and higher thousand kernel weight, when compared with the WT lines. Contrasting results were obtained for TaPUB1-RNAi lines. It suggests that TaPUB1 acts as a negative regulator in the ABA signaling pathway by interacting with TaPYL4 and TaABI5, subsequently affecting seed development in wheat. In addition, the enhanced abiotic tolerance of overexpression lines due to enhanced photosynthesis and root development may be related to the degradation of TaABI5 by TaPUB1.

Interactions between ShPP2-1, an F-box family gene, and ACR11A regulate cold tolerance of tomato

There is a critical need to identify germplasm resources and genes that promote cold tolerance of tomato because global tomato production is threatened by cold stress. We found that the expression of an F-box gene family member named ShPP2-1 from Solanum habrochaites is cold inducible and studied its contribution to cold tolerance. Overexpression of ShPP2-1 in cultivated tomato (AC) reduced cold tolerance by intensifying damage to cell membranes. To explore the underlying molecular mechanism, we conducted a yeast two-hybrid library screen and found that a protein containing ACT domain repeats named ACR11A interacts with PP2-1. Overexpression of SlACR11A in AC enhanced the cold tolerance of seedlings and germinating seeds. Cold tolerance decreased in tomato plants that overexpressed both of these genes. Additionally, we performed seed germination experiments in the cold with 177 tomato accessions and identified two alleles of SlACR11A that differ in one single-nucleotide polymorphism. We found that one of these alleles, SlACR11A^G, is significantly enriched in cold-tolerant tomato plants. Taken together, our findings indicate that the combination of low expression levels of PP2-1 and high expression levels of ACR11A can promote cold tolerance. These genes may therefore serve as direct targets for both genetic engineering and improvement projects that aim to enhance the cold tolerance of tomato.

ELONGATED HYPOCOTYL 5 mediates blue light-induced starch degradation in tomato

Starch is the major storage carbohydrate in plants, and its metabolism in chloroplasts depends mainly on light. However, the mechanism through which photoreceptors regulate starch metabolism in chloroplasts is unclear. In this study, we found that the cryptochrome 1a (CRY1a)-mediated blue light signal is critical for regulating starch accumulation by inducing starch degradation through the transcription factor HY5 in chloroplasts in tomato. cry1a mutants and HY5-RNAi plants accumulated more starch and presented lower transcript levels of starch degradation-related genes in their leaves than wild-type plants. Blue light significantly induced the transcription of starch degradation-related genes in wild-type and CRY1a- or HY5-overexpressing plants but had little effect in cry1a and HY5-RNAi plants. Dual-luciferase assays, electrophoretic mobility shift assays, and chromatin immunoprecipitation-qPCR revealed that HY5 could activate the starch degradation-related genes PWD, BAM1, BAM3, BAM8, MEX1, and DPE1 by directly binding to their promoters. Silencing of HY5 and these starch degradation-related genes in CRY1a-overexpressing plants led to increased accumulation of starch and decreased accumulation of soluble sugars. The findings presented here not only deepen our understanding of how light controls starch degradation and sugar accumulation but also allow us to explore potential targets for improving crop quality.

Fine Mapping and Identification of BnaC06.FtsH1, a Lethal Gene That Regulates the PSII Repair Cycle in Brassica napus

Photosystem II (PSII) is an important component of the chloroplast. The PSII repair cycle is crucial for the relief of photoinhibition and may be advantageous when improving stress resistance and photosynthetic efficiency. Lethal genes are widely used in the efficiency detection and method improvement of gene editing. In the present study, we identified the naturally occurring lethal mutant 7-521Y with etiolated cotyledons in Brassica napus, controlled by double-recessive genes (named cyd1 and cyd2). By combining whole-genome resequencing and map-based cloning, CYD1 was fine-mapped to a 29 kb genomic region using 15,167 etiolated individuals. Through cosegregation analysis and functional verification of the transgene, BnaC06.FtsH1 was determined to be the target gene; it encodes an filamentation temperature sensitive protein H 1 (FtsH1) hydrolase that degrades damaged PSII D1 in Arabidopsis thaliana. The expression of BnaC06.FtsH1 was high in the cotyledons, leaves, and flowers of B. napus, and localized in the chloroplasts. In addition, the expression of EngA (upstream regulation gene of FtsH) increased and D1 decreased in 7-521Y. Double mutants of FtsH1 and FtsH5 were lethal in A. thaliana. Through phylogenetic analysis, the loss of FtsH5 was identified in Brassica, and the remaining FtsH1 was required for PSII repair cycle. CYD2 may be a homologous gene of FtsH1 on chromosome A07 of B. napus. Our study provides new insights into lethal mutants, the findings may help improve the efficiency of the PSII repair cycle and biomass accumulation in oilseed rape.

Cytokinins as central regulators during plant growth and stress response

Cytokinins are a class of phytohormone that participate in the regulation of the plant growth, development, and stress response. In this review, the potential regulating mechanism during plant growth and stress response are discussed. Cytokinins are a class of phytohormone that participate in the regulation of plant growth, physiological activities, and yield. Cytokinins also play a key role in response to abiotic stresses, such as drought, salt and high or low temperature. Through the signal transduction pathway, cytokinins interact with various transcription factors via a series of phosphorylation cascades to regulate cytokinin-target gene expression. In this review, we systematically summarize the biosynthesis and metabolism of cytokinins, cytokinin signaling, and associated gene regulation, and highlight the function of cytokinins during plant development and resistance to abiotic stress. We also focus on the importance of crosstalk between cytokinins and other classes of phytohormones, including auxin, ethylene, strigolactone, and gibberellin. Our aim is to provide a comprehensive overview of recent findings on the mechanisms by which cytokinins act as central regulators of plant development and stress reactions, and highlight topics for future research.

Application of Genome Editing in Tomato Breeding: Mechanisms, Advances, and Prospects

Plants regularly face the changing climatic conditions that cause biotic and abiotic stress responses. The abiotic stresses are the primary constraints affecting crop yield and nutritional quality in many crop plants. The advances in genome sequencing and high-throughput approaches have enabled the researchers to use genome editing tools for the functional characterization of many genes useful for crop improvement. The present review focuses on the genome editing tools for improving many traits such as disease resistance, abiotic stress tolerance, yield, quality, and nutritional aspects of tomato. Many candidate genes conferring tolerance to abiotic stresses such as heat, cold, drought, and salinity stress have been successfully manipulated by gene modification and editing techniques such as RNA interference, insertional mutagenesis, and clustered regularly interspaced short palindromic repeat (CRISPR/Cas9). In this regard, the genome editing tools such as CRISPR/Cas9, which is a fast and efficient technology that can be exploited to explore the genetic resources for the improvement of tomato and other crop plants in terms of stress tolerance and nutritional quality. The review presents examples of gene editing responsible for conferring both biotic and abiotic stresses in tomato simultaneously. The literature on using this powerful technology to improve fruit quality, yield, and nutritional aspects in tomato is highlighted. Finally, the prospects and challenges of genome editing, public and political acceptance in tomato are discussed.

Protective Effect of γ-Aminobutyric Acid Against Chilling Stress During Reproductive Stage in Tomato Plants Through Modulation of Sugar Metabolism, Chloroplast Integrity, and Antioxidative Defense Systems

Despite the role of γ-aminobutyric acid (GABA) in plant tolerance to chilling stress having been widely discussed in the seedling stage, very little information is clear regarding its implication in chilling tolerance during the reproductive stage of the plant. Here, we investigated the influence of GABA (1 and 2mM) as a foliar application on tomato plants (Solanum lycopersicum L. cv. Super Marmande) subjected to chilling stress (5°C for 6h/day) for 5 successive days during the flowering stage. The results indicated that applied GABA differentially influenced leaf pigment composition by decreasing the chlorophyll a/b ratio and increasing the anthocyanin relative to total chlorophyll. However, carotenoids were not affected in both GABA-treated and non-treated stressed plants. Root tissues significantly exhibited an increase in thermo-tolerance in GABA-treated plants. Furthermore, applied GABA substantially alleviated the chilling-induced oxidative damage by protecting cell membrane integrity and reducing malondialdehyde (MDA) and H₂O₂. This positive effect of GABA was associated with enhancing the activity of phenylalanine ammonia-lyase (PAL), catalase (CAT), superoxide dismutase (SOD), and ascorbate peroxidase (APX). Conversely, a downregulation of peroxidase (POX) and polyphenol oxidase (PPO) was observed under chilling stress which indicates its relevance in phenol metabolism. Interesting correlations were obtained between GABA-induced upregulation of sugar metabolism coinciding with altering secondary metabolism, activities of antioxidant enzymes, and maintaining the integrity of plastids' ultrastructure Eventually, applied GABA especially at 2mM improved the fruit yield and could be recommended to mitigate the damage of chilling stress in tomato plants.

SlWHY2 interacts with SlRECA2 to maintain mitochondrial function under drought stress in tomato

Drought stress in plants leads to inhibition of photosynthesis and respiration, accumulation of reactive oxygen species (ROS), and reprogramming of gene expression. Here, we established that the tomato (Solanum lycopersicum) WHIRLY2 (SlWHY2) gene, which encodes a mitochondrial single-stranded DNA-binding protein, was significantly induced by drought stress. Under drought conditions, SlWHY2 RNAi plants showed more wilting and lower fresh weight, chlorophyll content, quantum yield of photosystem I (PSI; YI), and maximal photochemical efficiency of PSII (Fv/Fm) than the wild type (WT). Drought treatment also caused the SlWHY2 RNAi lines to accumulate more ROS than the WT, and the silenced lines had lower AOX (alternative oxidase) activity. As expected, the mitochondrial membrane potential (MMP) was less stable in the SlWHY2 RNAi lines. The expression levels of seven genes in the mitochondrial genome (SYCF15, NAD7, NAD4, COS2, COX1, COX2, and COX3) were decreased even more in the SlWHY2 RNAi lines than they were in the WT under drought stress. SlWHY2 interacted directly in vivo and in vitro with SlRECA2, a mitochondrial recombinase A that is important for mitochondrial DNA recombination and repair. These results suggest that SlWHY2 plays an essential role in maintaining mitochondrial function and enhancing drought tolerance in tomato.

Pentatricopeptide repeat protein PHOTOSYSTEM I BIOGENESIS FACTOR2 is required for splicing of ycf3

To gain a better understanding of the molecular mechanisms of photosystem I (PSI) biogenesis, we characterized the Arabidopsis thaliana photosystem I biogenesis factor 2 (pbf2) mutant, which lacks PSI complex. PBF2 encodes a P-class pentatricopeptide repeat (PPR) protein. In the pbf2 mutants, we observed a striking decrease in the transcript level of only one gene, the chloroplast gene ycf3, which is essential for PSI assembly. Further analysis of ycf3 transcripts showed that PBF2 is specifically required for the splicing of ycf3 intron 1. Computational prediction of binding sequences and electrophoretic mobility shift assays reveal that PBF2 specifically binds to a sequence in ycf3 intron 1. Moreover, we found that PBF2 interacted with two general factors for group II intron splicing CHLOROPLAST RNA SPLICING2-ASSOCIATED FACTOR1 (CAF1) and CAF2, and facilitated the association of these two factors with ycf3 intron 1. Our results suggest that PBF2 is specifically required for the splicing of ycf3 intron 1 through cooperating with CAF1 and CAF2. Our results also suggest that additional proteins are required to contribute to the specificity of CAF-dependent group II intron splicing.

Expansin gene TaEXPA2 positively regulates drought tolerance in transgenic wheat (Triticum aestivum L.)

Expansins loosen plant cell walls and are involved in cell enlargement and various abiotic stresses. In previous studies, we cloned the expansin gene TaEXPA2 from the wheat cultivar HF9703. Here, we studied its function and regulation in wheat drought stress tolerance. The results indicated that TaEXPA2-overexpressing wheat plants (OE) exhibited drought tolerant phenotypes, whereas down-regulation of TaEXPA2 by RNA interference (RNAi) resulted in elevated drought sensitivity, as measured by survival rate, photosynthetic rate and water containing ability under drought stress. Overexpression of TaEXPA2 enhanced the antioxidant capacity in wheat plants, via elevation of antioxidant enzyme activity and the increase of the transcripts of some ROS scavenging enzyme-related genes. Further investigation revealed that TaEXPA2 positively influenced lateral root formation under drought conditions. A MYB transcription factor of wheat named TaMPS activates TaEXPA2 expression directly by binding to its promoter. Overexpression of TaMPS in Arabidopsis conferred drought tolerance associated with improved lateral root number, and the close homolog genes of TaEXPA2 were up-regulated in Arabidopsis roots overexpressing TaMPS, which suggest that TaMPS may function as one of the regulator of TaEXPA2 gene expression in the root lateral development under drought stress. These findings suggest that TaEXPA2 positively regulates drought stress tolerance in wheat.

The Role of Chloroplast Gene Expression in Plant Responses to Environmental Stress

Chloroplasts are plant organelles that carry out photosynthesis, produce various metabolites, and sense changes in the external environment. Given their endosymbiotic origin, chloroplasts have retained independent genomes and gene-expression machinery. Most genes from the prokaryotic ancestors of chloroplasts were transferred into the nucleus over the course of evolution. However, the importance of chloroplast gene expression in environmental stress responses have recently become more apparent. Here, we discuss the emerging roles of the distinct chloroplast gene expression processes in plant responses to environmental stresses. For example, the transcription and translation of psbA play an important role in high-light stress responses. A better understanding of the connection between chloroplast gene expression and environmental stress responses is crucial for breeding stress-tolerant crops better able to cope with the rapidly changing environment.

Dynamic light caused less photosynthetic suppression, rather than more, under nitrogen deficit conditions than under sufficient nitrogen supply conditions in soybean

BACKGROUND

Plants are always exposed to dynamic light. The photosynthetic light use efficiency of leaves is lower in dynamic light than in uniform irradiance. Research on the influence of environmental factors on dynamic photosynthesis is very limited. Nitrogen is critical for plants, especially for photosynthesis. Low nitrogen (LN) decreases ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and thus limits photosynthesis. The decrease in Rubisco also delays photosynthetic induction in LN leaves; therefore, we hypothesized that the difference of photosynthetic CO2 fixation between uniform and dynamic light will be greater in LN leaves compared to leaves with sufficient nitrogen supply.

RESULTS

To test this hypothesis, soybean plants were grown under low or high nitrogen (HN), and the photosynthetic gas exchange, enzyme activity and protein amount in leaves were measured under uniform and dynamic light. Unexpectedly, dynamic light caused less photosynthetic suppression, rather than more, in LN leaves than in HN leaves. The underlying mechanism was also clarified. Short low-light (LL) intervals did not affect Rubisco activity but clearly deactivated fructose-1,6-bisphosphatase (FBPase) and sedoheptulose-1,7-bisphosphatase (SBPase), indicating that photosynthetic induction after a LL interval depends on the reactivation of FBPase and SBPase rather than Rubisco. In LN leaves, the amount of Rubisco decreased more than FBPase and SBPase, so FBPase and SBPase were present in relative excess. A lower fraction of FBPase and SBPase needs to be activated in LN leaves for photosynthesis recovery during the high-light phase of dynamic light. Therefore, photosynthetic recovery is faster in LN leaves than in HN leaves, which relieves the photosynthetic suppression caused by dynamic light in LN leaves.

CONCLUSIONS

Contrary to our expectations, dynamic light caused less photosynthetic suppression, rather than more, in LN leaves than in HN leaves of soybean. This is the first report of a stress condition alleviating the photosynthetic suppression caused by dynamic light.

WHIRLY1 maintains leaf photosynthetic capacity in tomato by regulating the expression of RbcS1 under chilling stress

Rubisco, which consists of eight large subunits (RBCLs) and eight small subunits (RBCSs), is a major photosynthetic enzyme that is sensitive to chilling stress. However, it is largely unclear how plants maintain high Rubisco content under low temperature conditions. Here, we report that tomato WHIRLY1 (SlWHY1) positively regulates the Rubisco level under chilling stress by directly binding to the promoter region of SlRbcS1, resulting in the activation of SlRbcS1 expression. SlRbcS1-overexpressing lines had higher Rubisco contents and were more resistant to chilling stress compared with the wild type. Quantitative real-time PCR analyses showed that, among the five RbcS genes, only SlRbcS1 expression is up-regulated by chilling treatment. These results indicate that SlWHIRLY1 specifically enhances the levels of SlRbcS1 and confers tolerance to chilling stress. The amino acid sequence of SlRBCS1 shows 92.67% identity with those of another two RBCS proteins and three residues are specifically found in SlRBCS1. However, mutation of these residues to alanine in SlRBCS1 does not influence its function during cold adaptation. Thus, we conclude that high levels of Rubisco, but not the specific residues in SlRBCS1, play important roles in tolerance to chilling stress in tomato.