Cold-sensitive Cultivar Research Articles

A Genome-Wide Analysis of the BAM Gene Family and Identification of the Cold-Responsive Genes in Pomegranate (Punica granatum L.).

Beta-amylases (BAMs, EC 3.2.1.2), belonging to a multigene family, play a pivotal role in starch breakdown and are also involved in hormonal and stress responses, notably to cold stress. Pomegranate trees (Punica granatum L.) are adapted to warm climates and are sensitive to cold temperatures. In this study, we analyzed eight PgBAM genes from the pomegranate genome dataset. These members unevenly distributed across chromosomes and were categorized into four groups based on their orthologous members. The motif composition was highly consistent among most members. In contrast, exon numbers and arrangements were conserved within groups or subgroups, whereas significant diversity was observed between different groups. A syntenic analysis revealed that three PgBAM members (PgBAM1/4/5) showed a total of 11 syntenic relationships with the BAM members from Arabidopsis, kiwifruit, and Chinese white pear, respectively. Promoter binding motif prediction suggested potential roles for PgBAMs' genes in light, stress, hormones, and development signaling. Gene expression indicated that PgBAM4 was predominantly expressed in leaves, PgBAM7 in flowers, and PgBAM8 in roots and leaves and during fruit ripening, particularly in pericarp development. A transcriptome analysis identified the starch and sucrose metabolism pathway (map00500) as a key factor in the cold stress response of cold-sensitive cultivar 'Tunisia' seedlings. PgBAM4 exhibited remarkable expression and was closely associated with the cold-responsive BAM genes, characterized by a closer phylogenetic relationship, conserved catalytic residues, and similar secondary and tertiary structures. Moreover, the differences in soluble sugar levels and PgBAM4 expression were closely associated with the varying cold stress resistance observed between 'Tunisia' and 'Sanbai' seedlings. Furthermore, yeast one-hybrid assays confirmed that PgCBF7, a critical transcription factor for enhancing freezing tolerance, binds to the promoter region of PgBAM4. Our findings provide a systematic overview of the PgBAM gene family and shed new light on the regulatory mechanisms underlying cold stress tolerance in pomegranate.

Physiological and transcriptomic comparisons shed light on the cold stress response mechanisms of Dendrobium spp.

Dendrobium spp. comprise a group of tropical orchids with ornamental and medicinal value. Dendrobium spp. are sensitive to low temperature, and the underlying cold response regulatory mechanisms in this group are unclear. To understand how these plants respond to cold stress, we compared the transcriptomic responses of the cold-tolerant cultivar 'Hongxing' (HX) and the cold-sensitive cultivar 'Sonia Hiasakul' (SH) to cold stress. Chemometric results showed that the physiological response of SH in the later stages of cold stress is similar to that of HX throughout the cold treatment. Orthogonal partial least squares discriminant analysis (OPLS-DA) revealed that soluble protein content and peroxidase activity are key physiological parameters for assessing the cold tolerance of these two Dendrobium spp. cultivars. Additionally, weighted gene co-expression network analysis (WGCNA) results showed that many cold response genes and metabolic pathways significantly associated with the physiological indices were enriched in the 12 detected modules. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) enrichment analyses of the 105 hub genes showed that Dendrobium spp. adapt to cold stress by regulating signal transduction, phytohormones, transcription factors, protein translation and modification, functional proteins, biosynthesis and metabolism, cell structure, light, and the circadian clock. Hub genes of the cold stress response network included the remorin gene pp34, the abscisic acid signaling pathway-related genes PROTEIN PHOSPATASE 2C (PP2C), SNF1-RELATED PROTEIN KINASE 2 (SnRK2), ABRE-BINDING FACTOR 1 (ABF1) and SKI-INTERACTING PROTEIN 17 (SKIP17), the Ca2+ signaling-related GTP diphosphokinase gene CRSH1, the carbohydrate-related gene STARCH SYNTHASE 2 (SS2), the cell wall biosynthesis gene CINNAMYL ALCOHOL DEHYDROGENASE (CAD7), and the endocytosis-related gene VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 52A (VPS52A). The cold-responsive genes and metabolic pathways of Dendrobium spp. revealed in this study provide important insight to enable the genetic enhancement of cold tolerance in Dendrobium spp., and to facilitate cold tolerance breeding in related plants.

Full-length transcriptome sequencing provides insights into alternative splicing under cold stress in peanut.

Peanut (Arachis hypogaea L.), also called groundnut is an important oil and cash crop grown widely in the world. The annual global production of groundnuts has increased to approximately 50 million tons, which provides a rich source of vegetable oils and proteins for humans. Low temperature (non-freezing) is one of the major factors restricting peanut growth, yield, and geographic distribution. Since the complexity of cold-resistance trait, the molecular mechanism of cold tolerance and related gene networks were largely unknown in peanut. In this study, comparative transcriptomic analysis of two peanut cultivars (SLH vs. ZH12) with differential cold tolerance under low temperature (10°C) was performed using Oxford Nanopore Technology (ONT) platform. As a result, we identified 8,949 novel gene loci and 95,291 new/novel isoforms compared with the reference database. More differentially expressed genes (DEGs) were discovered in cold-sensitive cultivar (ZH12) than cold-tolerant cultivar (SLH), while more alternative splicing events were found in SLH compared to ZH12. Gene Ontology (GO) analyses of the common DEGs showed that the "response to stress", "chloroplast part", and "transcription factor activity" were the most enriched GO terms, indicating that photosynthesis process and transcription factors play crucial roles in cold stress response in peanut. We also detected a total of 708 differential alternative splicing genes (DASGs) under cold stress compared to normal condition. Intron retention (IR) and exon skipping (ES) were the most prevalent alternative splicing (AS) events. In total, 4,993 transcription factors and 292 splicing factors were detected, many of them had differential expression levels and/or underwent AS events in response to cold stress. Overexpression of two candidate genes (encoding trehalose-6-phosphatephosphatases, AhTPPs) in yeast improves cold tolerance. This study not only provides valuable resources for the study of cold resistance in peanut but also lay a foundation for genetic modification of cold regulators to enhance stress tolerance in crops.

Identification of potential metabolites responsible for cold tolerance in buds of Vitis amurensis

Cold tolerance is one of the important traits for grapevine, especially in regions with extremely low temperatures in winter. Vitis amurensis is wild species in the Vitis genus with excellent cold hardiness compared with Vitis vinifera. However, metabolites that contribute to the cold tolerance of V. amurensis remain unknown. Here, the metabolomics of buds from V. amurensis ‘Zuoshan-1’ during cold acclimation (CA) were identified, and cold-sensitive cultivar (V. vinifera ‘Jingzaojing’) was used as the control. The buds were collected in October, November, and December in 2016 and 2018. The cold hardiness of the buds increased during CA in the two grapevines. However, browning was observed only in V. vinifera buds at temperature below −10 °C. Among detected metabolites from buds, 443 metabolites were overlapped between two years. Forty-four and thirty differentially accumulated metabolites (DAMs) were identified in V. amurensis and V. vinifera, respectively. Ten DAMs including monoacylglycerol (MAG, 18: 2) isomer 1, trehalose 6-phosphate, and d-glucose showed identical variations in the two grapevines, indicating conserved CA responses within the Vitis genus. Eighteen DAMs exhibited higher accumulation in V. amurensis than in V. vinifera. Maltotetraose, d-glucoronic acid, l-aspartic acid, azelaic acid, and 4-hydroxybenzoic acid were reported to accumulate during CA in other plants. Enhanced cold tolerance was detected in grapevine leaves with exogenous 5 mmol L−1l-aspartic acid and 1% proanthocyanidins. Potential contributions of other DAMs found in V. amurensis such as Cyanidin 3-O-glucoside need to be further elucidated. Thus, eighteen metabolites accumulated in V. amurensis can be used for practical application in improvement of cold resistance in grapevine. Our findings provide new insights into understanding the cold hardiness of V. amurensis.

Effects of pre-anthesis low-temperature stress on the mineral components in wheat grains.

The nutritional value of wheat is important to human health. Despite minerals being essential nutrients for the human body, they are often neglected in consideration of the nutritional quality of cereal grains. Extreme low-temperature events have become more frequent due to the current environmental unpredictability, and it is yet unknown how the mineral components in grains are affected by low temperature. To provide valuable information for enhancing the nutritional quality of wheat under potential climatic conditions, we treated different cold-sensitive wheat cultivars at four low-temperature levels during the individual and combined stages of jointing and booting in controlled-environment phytotrons. In general, the contents of P, K, Ca, and Zn in the cold-sensitive cultivar (Yangmai16) and K in the cold-tolerant cultivar (Xumai30) were enhanced by low temperature. However, the accumulation of minerals in mature grains was reduced under low-temperature treatment, except for P, Ca, and Zn in Yangmai16. In addition, the mineral content and accumulation in Yangmai16 (except for Fe) were more susceptible to low temperature during the combined stages, while the mineral content and accumulation of K, Fe, and Zn in Xumai30 were more susceptible to low temperature during the booting stage. Moreover, Yangmai16 under extremely low temperatures (T3 and T4) during booting and Xumai30 under all low-temperature treatments during the combined stages had lower comprehensive evaluation values. These findings offer a crucial reference for enhancing the nutritional quality of wheat grains under climate change.

Alterations of phenotype, physiology, and functional substances reveal the chilling-tolerant mechanism in two common Olea Europaea cultivars.

Olive suffers from cold damage when introduced to high-latitude regions from its native warm climes. Therefore, this study aims to improve the adaption of olive to climates in which it is cold for part of the year. The phenotype, physiological performance, nutrient content, and gene expression of olive leaves (from two widely planted cultivars) were examined after cultivation in normal and cold stress conditions. The results showed that the cold-tolerant cultivar possessed stronger photosynthesis efficiency and higher anti-oxidase activity after cold treatment than the cold-sensitive cultivar. Alteration of gene expression and metabolites in the amino acid metabolism, glycerolipid metabolism, diterpenoid biosynthesis, and oleuropein metabolism pathways played an important role in the cold responses of olive. Furthermore, the construction of the network of genes for ubiquitination and metabolites suggested that polyubiquitination contributes most to the stable physiology of olive under cold stress. Altogether, the results of this study can play an important role in helping us to understand the cold hardiness of olive and screen cold-resistant varieties for excellent quality and yield.

Integrative analysis of transcriptome and metabolome provides insights into the underlying mechanism of cold stress response and recovery in two tobacco cultivars

Low temperature is one of major environmental factors limiting the growth, quality and yield of tobacco. However, the molecular mechanism of tobacco cold response remains largely unknown. Here, integrated biochemical, transcriptomic and metabolomic analyses were carried out on tobacco leaves of cold-tolerant cultivar Xiangyan7 and cold-sensitive cultivar Taiyan8 under short- /long-term cold stress and recovery. Physiological and biochemical results showed that Taiyan8 was sensitive while Xiangyan7 was insensitive to cold stress. Integrated transcriptomics and metabolomics analysis revealed several key pathways in tobacco response to cold, including flavonoid biosynthesis, glutathione metabolism, zeatin biosynthesis, phenylpropanoid biosynthesis, starch and sucrose metabolism; two important pathways in the recovery, namely glyoxylate and dicarboxylate metabolism, flavonoid biosynthesis. The two cultivars had similar mechanisms in response to long-term cold stress. Whereas, more enriched pathways were identified in Taiyan8 under short-term stress, and the specifically enriched pathways were mainly involved in amino acid metabolism. By analyzing the metabolites involved in these pathways, a total of 26 key metabolites were screened out. These metabolites contents and biochemical indicator values were used as trait data for correlation analysis with gene expression modules, and 5 highly correlated modules were found. Within these modules, we identified 12 key candidate genes weighted as module hub genes, which involved ATPases, chlorophyll A-B binding protein, S-adenosine methionine decarboxylase, chalcone and stilbene synthases, UDP-glucosyltransferases, alcohol dehydrogenase, abhydrolase, proteins with ankyrin-repeat domains. The expression profiles of these genes further verified their involvement in tobacco cold response and recovery. These findings provide new insights into the regulatory networks of tobacco response to cold stress. • Compared with Taiyan8, Xiangyan7 is relatively insensitive to low temperature stress. • There are some similar mechanisms in the two cultivars response to long-term cold stress. • Amino acid metabolism is specifically enriched in Taiyan8 under short-term cold stress. • Five correlated modules are identified through module-trait relationship analysis. • Twelve key candidate genes are expression validated and discussed.

Optimized Phosphorus Application Alleviated Adverse Effects of Short-Term Low-Temperature Stress in Winter Wheat by Enhancing Photosynthesis and Improved Accumulation and Partitioning of Dry Matter

Low-temperature stress has become an important abiotic factor affecting high and stable wheat production. Therefore, it is necessary to take appropriate measures to enhance low-temperature tolerance in wheat. A pot experiment was carried out using Yannong19 (YN19, a cold-tolerant cultivar) and Xinmai26 (XM26, a cold-sensitive cultivar). We employed traditional phosphorus application (TPA, i.e., R1) and optimized phosphorus application (OPA, i.e., R2) methods. Plants undertook chilling (T1 at 4 °C) and freezing treatment (T2 at −4 °C) as well as ambient temperature (CK at 11 °C) during the anther differentiation period to investigate the effects of OPA and TPA on photosynthetic parameters and the accumulation and distribution of dry matter. The net photosynthetic rate (Pn), stomatal conductance (Gs) and transpiration rate (Tr) of flag leaves decreased in low-temperature treatments, whereas intercellular carbon dioxide concentration (Ci) increased. Compared with R1CK, Pn in R1T1 and R1T2 treatments was reduced by 26.8% and 42.2% in YN19 and 34.2% and 54.7% in XM26, respectively. In contrast, it increased by 6.5%, 8.9% and 12.7% in YN19 and 7.7%, 15.6% and 22.6% in XM26 for R2CK, R2T1 and R2T2 treatments, respectively, under OPA compared with TPA at the same temperature treatments. Moreover, low-temperature stress reduced dry matter accumulation at the reproductive growth stage. OPA increased dry matter accumulation of vegetative organs after the flowering stage and promoted the transportation of assimilates to grains. Hence, the grain number per spike (GNPS), 1000-grain weight (TGW) and yield per plant (YPP) increased. The low-temperature treatments of T1 and T2 caused yield losses of 24.1~64.1%, and the yield increased by 8.6~20.5% under OPA treatments among the two wheat cultivars. In brief, OPA enhances low-temperature tolerance in wheat, effectively improves wheat architecture and photosynthesis, increases GNPS and TGW and ultimately lessens yield losses.

RNA-seq based analysis of transcriptomic changes associated with ABA-induced postharvest cold tolerance in zucchini fruit

Given that external treatments with ABA had been proved to alleviate chilling injury in the immature zucchini fruit, an RNAseq analysis was conducted to gain insight into the molecular mechanisms that are involved in ABA-induced postharvest cold tolerance. Fruit from the cold sensitive cultivar Sinatra were treated with ABA and then stored for 14 d at 4 ºC. Exocarp samples from control and ABA-treated fruit were taken at 1, 5 and 14 d of cold storage, assessing the transcriptional changes during postharvest storage relative to freshly harvested fruit. The RNAseq analysis produced 229 million high-quality reads from a total of about 23,000 unigenes. Pairwise comparisons of differentially expressed genes (DEGs) in treated and untreated samples at each cold storage time resulted in 852, 793 and 1120 DEGs that were specifically found in the ABA-treated but not in the control fruit at either 1, 5 or 14 d of cold storage. This ABA-specific DEG list was subjected to a GO and KEGG enrichment analysis, as well as to a clusterization of gene expression profiles. This revealed the significance of certain metabolic and signaling pathways participating in ABA-induced postharvest cold tolerance, highlighting the relevance of the Ca2+ signaling pathway, as well as the positive regulation mediated by certain hormones such as ethylene and jasmonate, and the negative regulation mediated by others like auxins and brassinosteroids. A number of DEGs were also found in the ABA-treated fruit that code for transcription factors, as well as for genes involved in oxidative stress response and in membrane and cell wall metabolism. Data indicates that ABA-induced cold tolerance is not mediated by CBF-like genes but involve the up- and down-regulation of several transcription factors in the BZIP, GRAS, MYB, MYC, NAC and ZAT families that are known to participate as positive and negative regulators in the cold defensive response. Moreover, ABA regulates different genes responsible for reducing oxidative stress damage, inducing the biosynthesis of cuticular wax and repressing the biosynthesis of lignin, as well as protecting membrane and cell wall integrity in fruit cells during postharvest cold storage.

Effects of humidity-cold combined stress at the seedling stage in direct-seeded indica rice

Low temperature (LT) and extreme humidity constantly threaten direct-seeded early indica rice production during the seedling stage. However, the physiological mechanism and damage induced by LT combined with high/low humidity are still unclear. A pot experiment was conducted to study seedling growth performance and physiological traits of two indica rice cultivars (i.e., the cold-sensitive cultivar Zhongjiazao17 and the cold-tolerant cultivar Xiangzaoxian6) under LT plus low humidity treatment (LL, 8°C; relative humidity, 25 %), LT plus high humidity treatment (LH, 8°C; relative humidity, 95 %) and a control treatment (CK, 25 °C; relative humidity, 75 %). The results showed that seedling height, rubisco concentration, and APX, PDH and α-KGDH activity significantly decreased under LL and LH compared to CK, and large decreases were found under LH, especially for the cold-sensitive cultivar Zhongjiazao17. However, LH significantly increased the reactive oxygen species O2− and the soluble protein, GSH and ABA concentrations. Moreover, the APX, PDH and α-KGDH activities, rubisco and chlorophyll concentrations, and GA3 induced by LH also significantly decreased after treatment. The differences in physiological traits of Zhongjiazao17 after LL and LH were significant. During three days of recovery, the physiological activity of the two cultivars under LL tended to recover to the level of CK, and the cold-tolerant cultivar showed reduced damage caused by humidity-cold combined stress. The results suggested that the double stress of low temperature plus high humidity rather than low temperature plus low humidity could decrease the growth performance by hampering photosynthetic and respiratory systems and altering the endogenous hormonal regulation of direct-seeded early indica rice, whereas it could significantly enhance the antioxidant protective system derived from the osmotic damage of leaves.

Revision of the relationship between anther morphology and pollen sterility by cold stress at the booting stage in rice.

Cold stress in rice (Oryza sativa) plants at the reproductive stage prevents normal anther development and causes pollen sterility. Tapetum hypertrophy in anthers has been associated with pollen sterility in response to cold at the booting stage. Here, we re-examined whether the relationships between anther abnormality and pollen sterility caused by cold stress at the booting stage in rice can be explained by a monovalent factor such as tapetum hypertrophy. After exposing plants to a 4-d cold treatment at the booting stage, we collected and processed anthers for transverse sectioning immediately and at the flowering stage. We anatomically evaluated the effect of cold treatment on anther internal morphologies, pollen fertilities and pollen numbers in the 13 cultivars with various cold sensitivities. We observed four types of morphological anther abnormalities at each stage. Pollen sterility was positively correlated with the frequency of undeveloped locules, but not with tapetum hypertrophy as commonly believed. In cold-sensitive cultivars grown at low temperatures, pollen sterility was more frequent than anther morphological abnormalities, and some lines showed remarkably high pollen sterility without any anther morphological alterations. Most morphological anomalies occurred only in specific areas within large and small locules. Anther length tended to shorten in response to cold treatment and was positively correlated with pollen number. One cultivar showed a considerably reduced pollen number, but fertile pollen grains under cold stress. We propose three possible relationships to explain anther structure and pollen sterility and reduction due to cold stress. The pollen sterility caused by cold stress at the booting stage was correlated with the frequency of entire locule-related abnormalities, which might represent a phenotypic consequence, but not a direct cause of pollen abortion. Multivalent factors might underlie the complicated relationships between anther abnormality and pollen sterility in rice.

Fatty acid composition in relation to chilling susceptibility of blood orange cultivars at different storage temperatures

Fatty acid composition in the peel of four blood orange cultivars (‘Moro’, ‘Tarocco’, ‘Sanguinello’, and ‘Sanguine’) was identified and quantified by gas chromatography-mass spectrometry (GC-MS), in order to find its correlation with chilling susceptibility at harvest time and after 180 days of storage at 2 and 5 °C (2 days at 20 °C for shelf life). Twelve fatty acids were detected including 6 saturated (SFA) and 6 unsaturated (UFA), from which 4 monounsaturated (MUFA) and 2 polyunsaturated (PUFA) fatty acids occurred. The major fatty acids were palmitic, linoleic, and linolenic acids. The chilling injury (CI) index was significantly higher at 2 than 5 °C for all cultivars, with ‘Sanguinello’ being the more tolerant cultivar. The multivariate statistical analyses showed that ‘Sanguinello’ had the highest UFA, UFA/SFA ratio, and the lowest SFA, while ‘Moro’ as a cold sensitive cultivar had the highest SFA, the lowest UFA, and UFA/SFA ratio. Our findings revealed that the higher level of PUFAs (linoleic and linolenic acids) and enhancement of the UFA/SFA ratio are considered the most main adaptive mechanism under low temperatures of storage.

Acclimation to cold stress reduces injury from low temperature and bispyribac-sodium on rice.

In subtropical areas, early planting exposes rice seedlings to cold stress, impairing seedling growth and making them more vulnerable to other stresses including herbicide injury. The objectives of this work were: to evaluate the effect of cold stress on bispyribac-sodium selectivity in rice; to determine the mechanisms of cold tolerance in sensitive ('Epagri 109') and tolerant ('IRGA 424') rice cultivars; and to ascertain that cold acclimatization influences bispyribac-sodium selectivity in rice. Prolonged cold stress caused high lipid peroxidation, increased rice injury, and stunted growth. Short-term acclimation with cold stress reduced rice injury with bispyribac-sodium. Total phenols were upregulated in rice exposed to cold stress. Prolonged cold stress increased the superoxide dismutase and catalase activity in IRGA 424. Antioxidant activity was higher in the cold-tolerant than in the cold-sensitive cultivar. Only catalase activity was responsive to bispyribac-sodium. OsRAN2, OsGSTL2, and CYP72A21 were upregulated by cold and herbicide stress in both cultivars. OsGSTL2 was upregulated more in IRGA 424 than in Epagri 109. OsFAD8 was upregulated in cold-sensitive rice exposed to short-duration cold stress but was not responsive to bispyribac-sodium. Cold stress reduces bispyribac-sodium selectivity in rice. Short-term acclimation to cold stress reduces the effect of cold stress and enhances bispyribac-sodium selectivity. The tolerance of rice (IRGA 424) to cold stress is due to differential induction of protection genes CYP72A21 and OsGSTL2 associated with herbicide metabolism, together with the accumulation of total phenols and higher activity of antioxidant enzymes.

Balance between oxidative stress and the antioxidant system is associated with the level of cold tolerance in sweet potato roots

Abstract The balance between oxidative stress and antioxidant defense system was investigated in roots of the cold-sensitive (cvs. BRS Rubissol and BRS Cuia) and cold-tolerant (cv. Beauregard) sweet potato stored at 6 or 13 °C for 60 d. We hypothesized that the absence of chilling injury symptoms on cv. Beauregard stored at 6 °C depends on the induction capacity of enzymatic and non-enzymatic antioxidant systems. The manifestation of chilling injury symptoms on cvs. BRS Rubissol and BRS Cuia were associated with the loss of membrane integrity, increased lipid peroxidation, accumulation of hydrogen peroxide (H2O2), and low catalase (CAT) and ascorbate peroxidase (APX) activities. In these cold-sensitive cultivars, proline and total phenolics increased with the progression of chilling injury, acting as markers for cold sensitivity, and parallel increased activity of phenylalanine ammonia-lyase. In contrast, constitutive levels of enzymatic and non-enzymatic antioxidants, as well as stress-induced increased CAT and APX activity played an important role in the detoxification of H2O2 in the tolerant cv. Beauregard. Our results suggest that the balance between oxidative stress and antioxidant system is involved in the tolerance of cv. Beauregard to chilling injury.

Transcriptome Sequencing and iTRAQ of Different Rice Cultivars Provide Insight into Molecular Mechanisms of Cold-Tolerance Response in Japonica Rice

BackgroundRice (Oryza sativa L.) is one of the most important crops cultivated in both tropical and temperate regions. However, it has a high sensitivity to cold stress and chilling stress limits its nitrogen uptake and metabolism. To identify the genes and pathways involved in cold tolerance, specifically within nitrogen metabolism pathways, we compared gene and protein expression differences between a cold-tolerant cultivar, Dongnong428 (DN), and a cold-sensitive cultivar, Songjing10 (SJ).ResultsUsing isobaric tags for relative or absolute quantification (iTRAQ) with high-throughput mRNA sequencing (RNA-seq) techniques, we identified 5549 genes and 450 proteins in DN and 6145 genes and 790 proteins in SJ, which were differentially expressed during low water temperature (Tw) treatments. There were 354 transcription factor (TF) genes (212 downregulated, 142 upregulated) and 366 TF genes (220 downregulated, 146 upregulated), including 47 gene families, differentially expressed in DN under control (CKDN) vs. DN under low-Tw (D15DN) and SJ under control (CKSJ) vs. SJ under low-Tw D15SJ, respectively. Genes associated with rice cold-related biosynthesis pathways, particularly the mitogen-activated protein kinase (MAPK) signaling, zeatin biosynthesis, and plant hormone signal transduction pathways, were significantly differentially expressed in both rice cultivars. Differentially expressed proteins (DEPs) associated with rice cold-related biosynthesis pathways, and particularly glutathione metabolism, were significantly differentially expressed in both rice cultivars. Transcriptome and proteome analysis of the nitrogen metabolism pathways showed that major genes and proteins that participated in γ-aminobutyric acid (GABA) and glutamine synthesis were downregulated under cold stress.ConclusionCold stress conditions during reproductive growth, resulted in genes and proteins related to cold stress biosynthesis pathways being significantly differentially expressed in DN and SJ. The present study confirmed the known cold stress-associated genes and identified new putative cold-responsive genes. We also found that translational regulation under cold stress plays an important role in cold-tolerant DN. Low-Tw treatments affected N uptake and N metabolism in rice, as well as promoted Glu metabolism and the synthesis of ornithine and proline in cold-sensitive SJ.

ITRAQ-based quantitative proteomics analysis of cantaloupe (Cucumis melo var. saccharinus) after cold storage

BackgroundCantaloupe is susceptible to cold stress when it is stored at low temperatures, resulting in the loss of edible and commercial quality. To ascertain the molecular mechanisms of low temperatures resistance in cantaloupe, a cold-sensitive cultivar, Golden Empress-308 (GE) and a cold-tolerant cultivar, Jia Shi-310 (JS), were selected in parallel for iTRAQ quantitative proteomic analysis.ResultsThe two kinds of commercial cultivars were exposed to a temperature of 0.5 °C for 0, 12 and 24 days. We found that the cold-sensitive cultivar (GE) suffered more severe damage as the length of the cold treatment increased. Proteomic analysis of both cultivars indicated that the number of differentially expressed proteins (DEPs) changed remarkably during the chilly treatment. JS expressed cold-responsive proteins more rapidly and mobilized more groups of proteins than GE. Furthermore, metabolic analysis revealed that more amino acids were up-regulated in JS during the early phases of low temperatures stress. The DEPs we found were mainly related to carbohydrate and energy metabolism, structural proteins, reactive oxygen species scavenging, amino acids metabolism and signal transduction. The consequences of phenotype assays, metabolic analysis and q-PCR validation confirm the findings of the iTRAQ analysis.ConclusionWe found that the prompt response and mobilization of proteins in JS allowed it to maintain a higher level of cold tolerance than GE, and that the slower cold responses in GE may be a vital reason for the severe chilling injury commonly found in this cultivar. The candidate proteins we identified will form the basis of future studies and may improve our understanding of the mechanisms of cold tolerance in cantaloupe.

Gene Expression and K+ Uptake of Two Tomato Cultivars in Response to Sub-Optimal Temperature

Sub-optimal temperatures can adversely affect tomato (Solanum lycopersicum) growth, and K+ plays an important role in the cold tolerance of plants. However, gene expression and K+ uptake in tomato in response to sub-optimal temperatures are still not very clear. To address these questions, one cold-tolerant tomato cultivar, Dongnong 722 (T722), and one cold-sensitive cultivar, Dongnong 708 (S708), were exposed to sub-optimal (15/10 °C) and normal temperatures (25/18 °C), and the differences in growth, K+ uptake characteristics and global gene expressions were investigated. The results showed that compared to S708, T722 exhibited lower reduction in plant growth rate, the whole plant K+ amount and K+ net uptake rate, and T722 also had higher peroxidase activity and lower K+ efflux rate under sub-optimal temperature conditions. RNA-seq analysis showed that a total of 1476 and 2188 differentially expressed genes (DEGs) responding to sub-optimal temperature were identified in S708 and T722 roots, respectively. Functional classification revealed that most DEGs were involved in “plant hormone signal transduction”, “phenylpropanoid biosynthesis”, “sulfur metabolism” and “cytochrome P450”. The genes that were significantly up-regulated only in T722 were involved in the “phenylpropanoid biosynthesis” and “plant hormone signal transduction” pathways. Moreover, we also found that sub-optimal temperature inhibited the expression of gene coding for K+ transporter SIHAK5 in both cultivars, but decreased the expression of gene coding for K+ channel AKT1 only in S708. Overall, our results revealed the cold response genes in tomato roots, and provided a foundation for further investigation of mechanism involved in K+ uptake in tomato under sub-optimal temperatures.

Sucrose degradation pathways in cold-induced sweetening and its impact on the non-enzymatic darkening in sweet potato root

This study investigated sucrose catabolism during cold-induced sweetening (CIS) and its impact on the quality of sweet potato chips of cultivars with varied levels of tolerance to cold during storage at 6 and 13 °C. In contrast to cultivar Beauregard, cultivar BRS Rubissol and BRS Cuia were cold-sensitive exhibiting intense symptoms of chilling injury at 6 °C. CIS in the sensitive cultivars BRS Rubissol and BRS Cuia was characterized by low accumulation of reducing sugar (RS), high non-reducing sugars content, low invertase activity and high sucrose synthase (SuSy) activity. In the tolerant cultivar Beauregard, the high content of RS was due to high invertases activity. In the three cultivars, the darkening of chips was more influenced by the non-reducing sugars, instead of RS. Our results suggest that SuSy was induced by cold stress in cold-sensitive cultivar, but did not contribute to the CIS in sweet potato.

Physiological and genome-wide gene expression analyses of cold-induced leaf rolling at the seedling stage in rice (Oryza sativa L.)

Leaf rolling and discoloration are two chilling-injury symptoms that are widely used as indicators for the evaluation of cold tolerance at the seedling stage in rice. However, the difference in cold-response mechanisms underlying these two traits remains unknown. In the present study, a cold-tolerant rice cultivar, Lijiangxintuanheigu, and a cold-sensitive cultivar, Sanhuangzhan-2, were subjected to low-temperature treatments and physiological and genome-wide gene expression analyses were conducted. Leaf rolling occurred at temperatures lower than 11 °C, whereas discoloration appeared at moderately low temperatures such as 13 °C. Chlorophyll contents in both cultivars were significantly decreased at 13 °C, but not altered at 11 °C. In contrast, the relative water content and relative electrolyte leakage of both cultivars decreased significantly at 11 °C, but did not change at 13 °C. Expression of genes associated with calcium signaling and abscisic acid (ABA) degradation was significantly altered at 11 °C in comparison with 25 °C and 13 °C. Numerous genes in the DREB, MYB, bZIP, NAC, Zinc finger, bHLH, and WRKY gene families were differentially expressed. Many aquaporin genes and the key genes in trehalose and starch synthesis were down regulated at 11 °C in comparison with 25 °C and 13 °C. These results suggest that the two chilling injury symptoms are temperature-specific and are controlled by different mechanisms. Cold-induced leaf rolling is associated with calcium and ABA signaling pathways and is regulated by multiple transcriptional regulators. The suppression of aquaporin genes and reduced accumulation of soluble sugars under cold stress results in a reduction in cellular water potential and consequently leaf rolling.

Detection of QTLs for cold tolerance at the booting stage in near-isogenic lines derived from rice landrace Lijiangxintuanheigu

Chilling damage significantly reduces grain yield in rice, while exploring major quantitative trait loci (QTLs) has the potential to improve rice production. Mapping of QTLs for 5 cold tolerance-related traits at the booting stage was conducted with SSR markers and inclusive composite interval mapping (ICIM) approach, based on 105 near-isogenic lines derived from a backcross between Lijiangxintuanheigu (LTH, cold-tolerant landrace) and Towada (cold-sensitive cultivar). Phenotype values were investigated under five cold-stress environments and analysed by the best linear unbiased prediction (BLUP). Twenty-one QTLs were identified on chromosomes 1, 2, 3, 4, 6, 7, 10 and 11, and the amount of variation (R<sup>2</sup>) explained by each QTL ranged from 7.71 to 29.66%, with five co-located QTL regions. Eight novel major loci (qSF-2, qSF-6a, qSF-7, qGW-6, qDGWP-4, qDSWPP-4, qDWPP-1 and qDWPP-4b) were detected in several environments and BLUP, and their alleles were contributed by LTH with R<sup>2 </sup>variance from 12.24 to 29.66%. These favourable QTLs would facilitate elucidation of the genetic mechanism of cold tolerance and provide strategies for breeding high-productive rice.