Global Gene-Expression Analysis to Identify Differentially Expressed Genes Critical for the Heat Stress Response in Brassica rapa

Construction of heat stress regulation networks based on Illumina and SMRT sequencing data in potato

Potato (Solanum tuberosum L.) is one of the most important tuber food crops in the world; however, the cultivated potatoes are susceptible to high temperature, by which potato production is adversely affected. Understanding the coping mechanism of potato to heat stress is essential to secure yield and expand adaptability under environmental conditions with rising temperature. However, the lack of heat-related information has significantly limited the identification and application of core genes. To gain deeper insights into heat tolerance genes, next-generation sequencing and single-molecule real-time sequencing were used to learn the transcriptional response of potato to heat stress and 13,159 differentially expressed genes (DEGs) were identified in this study. All DEGs were grouped into 12 clusters using the K-means clustering algorithm. Gene Ontology enrichment analysis revealed that they were involved in temperature signaling, phytohormone, and protein modification. Among them, there were 950 differentially expressed transcription factors (DETFs). According to the network analysis of DETFs at the sixth hour under heat stress, we found some genes that were previously reported to be associated with photoperiodic tuberization, StCO (CONSTANS), tuber formation, StBEL11 (BEL1-LIKE 11), and earliness in potato, StCDF1 (CYCLING DOF FACTOR 1) responding to temperature. Furthermore, we verified the relative expression levels using quantitative real-time polymerase chain reaction, and the results were consistent with the inferences from transcriptomes. In addition, there were 22,125 alternative splicing events and 2,048 long non-coding RNAs. The database and network established in this study will extend our understanding of potato response to heat stress. It ultimately provided valuable resources for molecular analysis of heat stress response in potato and cultivation of potato varieties with heat tolerance.

Genome-Wide Identification of BrCAX Genes and Functional Analysis of BrCAX1 Involved in Ca2+ Transport and Ca2+ Deficiency-Induced Tip-Burn in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)

Calcium (Ca2+) plays essential roles in plant growth and development. Ca2+ deficiency causes a physiological disorder of tip-burn in Brassiceae crops and is involved in the regulation of cellular Ca2+ homeostasis. Although the functions of Ca2+/H+ exchanger antiporters (CAXs) in mediating transmembrane transport of Ca2+ have been extensively characterized in multiple plant species, the potential roles of BrCAX genes remain unclear in Chinese cabbage. In this study, eight genes of the BrCAX family were genome-widely identified in Chinese cabbage. These BrCAX proteins contained conserved Na_Ca_ex domain and belonged to five members of the CAX family. Molecular evolutionary analysis and sequence alignment revealed the evolutionary conservation of BrCAX family genes. Expression profiling demonstrated that eight BrCAX genes exhibited differential expression in different tissues and under heat stress. Furthermore, Ca2+ deficiency treatment induced the typical symptoms of tip-burn in Chinese cabbage seedlings and a significant decrease in total Ca2+ content in both roots and leaves. The expression changes in BrCAX genes were related to the response to Ca2+ deficiency-induced tip-burn of Chinese cabbage. Specially, BrCAX1-1 and BrCAX1-2 genes were highly expressed gene members of the BrCAX family in the leaves and were significantly differentially expressed under Ca2+ deficiency stress. Moreover, overexpression of BrCAX1-1 and BrCAX1-2 genes in yeast and Chinese cabbage cotyledons exhibited a higher Ca2+ tolerance, indicating the Ca2+ transport capacity of BrCAX1-1 and BrCAX1-2. In addition, suppression expression of BrCAX1-1 and BrCAX1-2 genes reduced cytosolic Ca2+ levels in the root tips of Chinese cabbage. These results provide references for functional studies of BrCAX genes and to investigate the regulatory mechanisms underlying Ca2+ deficiency disorder in Brassiceae vegetables.

Brassica napus Roots Use Different Strategies to Respond to Warm Temperatures

Elevated growth temperatures are negatively affecting crop productivity by increasing yield losses. The modulation of root traits associated with improved response to rising temperatures is a promising approach to generate new varieties better suited to face the environmental constraints caused by climate change. In this study, we identified several Brassica napus root traits altered in response to warm ambient temperatures. Different combinations of changes in specific root traits result in an extended and deeper root system. This overall root growth expansion facilitates root response by maximizing root-soil surface interaction and increasing roots' ability to explore extended soil areas. We associated these traits with coordinated cellular events, including changes in cell division and elongation rates that drive root growth increases triggered by warm temperatures. Comparative transcriptomic analysis revealed the main genetic determinants of these root system architecture (RSA) changes and uncovered the necessity of a tight regulation of the heat-shock stress response to adjusting root growth to warm temperatures. Our work provides a phenotypic, cellular, and genetic framework of root response to warming temperatures that will help to harness root response mechanisms for crop yield improvement under the future climatic scenario.

Comprehensive transcriptome analysis reveals heat-responsive genes in flowering Chinese cabbage (Brassica campestris L. ssp. chinensis) using RNA sequencing

Flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee, 2n=20, AA) is a vegetable species in southern parts of China that faces high temperatures in the summer and winter seasons. While heat stress adversely impacts plant productivity and survival, the underlying molecular and biochemical causes are poorly understood. This study investigated the gene expression profiles of heat-sensitive (HS) '3T-6' and heat-tolerant (HT) 'Youlu-501' varieties of flowering Chinese cabbage in response to heat stress using RNA sequencing. Among the 37,958 genes expressed in leaves, 20,680 were differentially expressed genes (DEGs) at 1, 6, and 12 h, with 1,078 simultaneously expressed at all time points in both varieties. Hierarchical clustering analysis identified three clusters comprising 1,958, 556, and 591 down-regulated, up-regulated, and up- and/or down-regulated DEGs (3205 DEGs; 8.44%), which were significantly enriched in MAPK signaling, plant-pathogen interactions, plant hormone signal transduction, and brassinosteroid biosynthesis pathways and involved in stimulus, stress, growth, reproductive, and defense responses. Transcription factors, including MYB (12), NAC (13), WRKY (11), ERF (31), HSF (17), bHLH (16), and regulatory proteins such as PAL, CYP450, and photosystem II, played an essential role as effectors of homeostasis, kinases/phosphatases, and photosynthesis. Among 3205 DEGs, many previously reported genes underlying heat stress were also identified, e.g., BraWRKY25, BraHSP70, BraHSPB27, BraCYP71A23, BraPYL9, and BraA05g032350.3C. The genome-wide comparison of HS and HT provides a solid foundation for understanding the molecular mechanisms of heat tolerance in flowering Chinese cabbage.

Mechanisms of Kale (Brassica oleracea var. acephala) Tolerance to Individual and Combined Stresses of Drought and Elevated Temperature

Rising temperatures and pronounced drought are significantly affecting biodiversity worldwide and reducing yields and quality of Brassica crops. To elucidate the mechanisms of tolerance, 33 kale accessions (B. oleracea var. acephala) were evaluated for individual (osmotic and elevated temperature stress) and combined stress (osmotic + temperature). Using root growth, biomass and proline content as reliable markers, accessions were evaluated for stress responses. Four representatives were selected for further investigation (photosynthetic performance, biochemical markers, sugar content, specialized metabolites, transcription level of transcription factors NAC, HSF, DREB and expression of heat shock proteins HSP70 and HSP90): very sensitive (392), moderately sensitive (395), tolerant (404) and most tolerant (411). Accessions more tolerant to stress conditions were characterized by higher basal content of proline, total sugars, glucosinolates and higher transcription of NAC and DREB. Under all stress conditions, 392 was characterized by a significant decrease in biomass, root growth, photosynthesis performance, fructan content, especially under osmotic and combined stress, a significant increase in HSF transcription and HSP accumulation under temperature stress and a significant decrease in NAC transcription under all stresses. The most tolerant accession under all applied stresses, 411 showed the least changes in all analyzed parameters compared with the other accessions.

Insight into melatonin-mediated response and signaling in the regulation of plant defense under biotic stress

Melatonin plays a crucial role in the mitigation of plant biotic stress through induced defense responses and pathogen attenuation. Utilizing the current knowledge of signaling and associated mechanism of this phytoprotectant will be invaluable in sustainable plant disease management. Biotic stress in plants involves complex regulatory networks of various sensory and signaling molecules. In this context, the polyfunctional, ubiquitous-signaling molecule melatonin has shown a regulatory role in biotic stress mitigation in plants. The present review conceptualized the current knowledge concerning the melatonin-mediated activation of the defense signaling network that leads to the resistant or tolerant phenotype of the infected plants. Fundamentals of signaling networks involved in melatonin-induced reactive oxygen species (ROS) or reactive nitrogen species (RNS) scavenging through enzymatic and non-enzymatic antioxidants have also been discussed. Increasing evidence has suggested that melatonin acts upstream of mitogen-activated proteinase kinases in activation of defense-related genes and heat shock proteins that provide immunity against pathogen attack. Besides, the direct application of melatonin on virulent fungi and bacteria showed disrupted spore morphology, destabilization of cell ultrastructure, reduced biofilm formation, and enhanced mortality that led to attenuate disease symptoms on melatonin-treated plants. The transcriptome analysis has revealed the down-regulation of pathogenicity genes, metabolism-related genes, and up-regulation of fungicide susceptibility genes in melatonin-treated pathogens. The activation of melatonin-mediated systemic acquired resistance (SAR) through cross-talk with salicylic acid (SA), jasmonic acid (JA) has been essential for viral disease management. The high endogenous melatonin concentration has also been correlated with the up-regulation of genes involved in pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI). The present review highlights the versatile functions of melatonin towards direct inhibition of pathogen propagule along with active participation in mediating oxidative burst and simulating PTI, ETI and SAR responses. The hormonal cross-talk involving melatonin mediated biotic stress tolerance through defense signaling network suggests its suitability in a sustainable plant protection system.

CabZIP23 Integrates in CabZIP63-CaWRKY40 Cascade and Turns CabZIP63 on Mounting Pepper Immunity against Ralstonia solanacearum via Physical Interaction

CabZIP63 and CaWRKY40 were previously found to be shared in the pepper defense response to high temperature stress (HTS) and to Ralstonia solanacearum inoculation (RSI), forming a transcriptional cascade. However, how they activate the two distinct defense responses is not fully understood. Herein, using a revised genetic approach, we functionally characterized CabZIP23 in the CabZIP63-CaWRKY40 cascade and its context specific pepper immunity activation against RSI by interaction with CabZIP63. CabZIP23 was originally found by immunoprecipitation-mass spectrometry to be an interacting protein of CabZIP63-GFP; it was upregulated by RSI and acted positively in pepper immunity against RSI by virus induced gene silencing in pepper plants, and transient overexpression in Nicotiana benthamiana plants. By chromatin immunoprecipitation (ChIP)-qPCR and electrophoresis mobility shift assay (EMSA), CabZIP23 was found to be directly regulated by CaWRKY40, and CabZIP63 was directly regulated by CabZIP23, forming a positive feedback loop. CabZIP23-CabZIP63 interaction was confirmed by co-immunoprecipitation (CoIP) and bimolecular fluorescent complimentary (BiFC) assays, which promoted CabZIP63 binding immunity related target genes, including CaPR1, CaNPR1 and CaWRKY40, thereby enhancing pepper immunity against RSI, but not affecting the expression of thermotolerance related CaHSP24. All these data appear to show that CabZIP23 integrates in the CabZIP63-CaWRKY40 cascade and the context specifically turns it on mounting pepper immunity against RSI.

Adaptation Strategies to Improve the Resistance of Oilseed Crops to Heat Stress Under a Changing Climate: An Overview

Temperature is one of the decisive environmental factors that is projected to increase by 1. 5°C over the next two decades due to climate change that may affect various agronomic characteristics, such as biomass production, phenology and physiology, and yield-contributing traits in oilseed crops. Oilseed crops such as soybean, sunflower, canola, peanut, cottonseed, coconut, palm oil, sesame, safflower, olive etc., are widely grown. Specific importance is the vulnerability of oil synthesis in these crops against the rise in climatic temperature, threatening the stability of yield and quality. The natural defense system in these crops cannot withstand the harmful impacts of heat stress, thus causing a considerable loss in seed and oil yield. Therefore, a proper understanding of underlying mechanisms of genotype-environment interactions that could affect oil synthesis pathways is a prime requirement in developing stable cultivars. Heat stress tolerance is a complex quantitative trait controlled by many genes and is challenging to study and characterize. However, heat tolerance studies to date have pointed to several sophisticated mechanisms to deal with the stress of high temperatures, including hormonal signaling pathways for sensing heat stimuli and acquiring tolerance to heat stress, maintaining membrane integrity, production of heat shock proteins (HSPs), removal of reactive oxygen species (ROS), assembly of antioxidants, accumulation of compatible solutes, modified gene expression to enable changes, intelligent agricultural technologies, and several other agronomic techniques for thriving and surviving. Manipulation of multiple genes responsible for thermo-tolerance and exploring their high expressions greatly impacts their potential application using CRISPR/Cas genome editing and OMICS technology. This review highlights the latest outcomes on the response and tolerance to heat stress at the cellular, organelle, and whole plant levels describing numerous approaches applied to enhance thermos-tolerance in oilseed crops. We are attempting to critically analyze the scattered existing approaches to temperature tolerance used in oilseeds as a whole, work toward extending studies into the field, and provide researchers and related parties with useful information to streamline their breeding programs so that they can seek new avenues and develop guidelines that will greatly enhance ongoing efforts to establish heat stress tolerance in oilseeds.

Gene co-expression network analysis of the heat-responsive core transcriptome identifies hub genes in Brassica rapa

Gene co-expression network analysis of the heat-responsive core transcriptome in two contrasting Brassica rapa accessions reveals the main metabolic pathways, key modules and hub genes, are involved in long-term heat stress. Brassica rapa is a widely cultivated and economically important vegetable in Asia. High temperature is a common stress that severely impacts leaf head formation in B. rapa, resulting in reduced quality and production. The purpose of this study was thus to identify candidate heat tolerance genes by comparative transcriptome analysis of two contrasting B. rapa accessions in response to long-term heat stress. Two B. rapa accessions, '268' and '334', which showed significant differences in heat tolerance, were used for RNA sequencing analysis. We identified a total of 11,055 and 8921 differentially expressed genes (DEGs) in '268' and '334', respectively. Functional enrichment analyses of all of the identified DEGs, together with the genes identified from weighted gene co-expression network analyses (WGCNA), revealed that the autophagy pathway, glutathione metabolism, and ribosome biogenesis in eukaryotes were significantly up-regulated, whereas photosynthesis was down-regulated, in the heat resistance of B. rapa '268'. Furthermore, when B. rapa '334' was subjected to long-term high-temperature stress, heat stress caused significant changes in the expression of certain functional genes linked to protein processing in the endoplasmic reticulum and plant hormone signal transduction pathways. Autophagy-related genes might have been induced by persistent heat stress and remained high during recovery. Several hub genes like HSP17.6, HSP17.6B, HSP70-8, CLPB1, PAP1, PYR1, ADC2, and GSTF11 were discussed in this study, which may be potential candidates for further analyses of the response to long-term heat stress. These results should help elucidate the molecular mechanisms of heat stress adaptation in B. rapa.

Natural variation in glycine-rich region of Brassica oleracea cold shock domain protein 5 (BoCSDP5) is associated with low temperature tolerance

BACKGROUND

Low temperature (LT) or cold stress is a major environmental stress that seriously affects plant growth and development, limiting crop productivity. Cold shock domain proteins (CSDPs), which are present in most living organism, are involved in RNA metabolisms influencing abiotic stress tolerance.

OBJECTIVE

The aims of this study are to identify target gene for LT-tolerance, like CSDPs, characterize genetics, and develop molecular marker distinguishing LT-tolerance in cabbage (Brassica oleracea var. capitata).

METHODS

Semi-quantitative RT-PCR or qRT-PCR was used in gene expression study. LT-tolerance was determined by electrolyte leakage and PCR with allelic specific primers.

RESULTS

Allelic variation was found in BoCSDP5 coding sequence (CDs) between LT-tolerant (BN106 and BN553) and -susceptible inbred lines (BN107 and BN554). LT-tolerant inbred lines contained variant type of BoCSDP5 (named as BoCSDP5v) which encodes extra CCHC zinc finger domain at C-terminus. Association of LT-tolerance with BoCSDP5v was confirmed by electrolyte leakage and segregation using genetic population derived from BN553 and BN554 cross. Allelic variation in BoCSDP5 gene does not influence the rate of gene expression, but produces different proteins with different number of CCHC zinc finger domains. LT-tolerance marker designed on the basis of polymorphism between BoCSDP5 and BoCSDP5v was confirmed with samples used in previous B. oleracea CIRCADIAN CLOCK ASSOCIATED 1 (BoCCA1) marker validation.

CONCLUSIONS

LT-tolerant allele (BoCSDP5v) is dominant and independent of CBF pathway, and sufficient to generate molecular markers to identify LT-tolerant cabbage when it is used in combination with another marker, like BoCCA1-derived one. Production and analysis of overexpressing plants of BoCSDP1, BoCSDP3, BoCSDP5 and BoCSDP5v will be required for elucidating the function of CCHC zinc finger domains in LT-tolerance.

Molecular Characterization, Expression Pattern and Function Analysis of Glycine-Rich Protein Genes Under Stresses in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)

Plant Glycine-rich proteins (GRP), a superfamily with a glycine-rich domain, play an important role in various stresses such as high or low temperature stress and drought stress. GRP genes have been studied in many plants, but seldom in Chinese cabbage (Brassica rapa L. ssp. pekinensis). In this study, a total of 64 GRP genes were identified in Chinese cabbage by homology comparative analysis. The physical and chemical characteristics predicted by ProtParam tool revealed that 62.5% of BrGRPs were alkaline, 53.1% were stable, and 79.7% were hydrophilic. Conserved domain analysis by MEME and TBtools showed that 64 BrGRPs contained 20 of the same conserved motifs, based on which BrGRPs were classified into five main classes and four subclasses in class IV to clarify their evolutionary relationship. Our results demonstrated that The BrGRP genes were located on ten chromosomes and in three different subgenomes of Chinese cabbage, and 43 pairs of orthologous GRP genes were found between Chinese cabbage and Arabidopsis. According to the transcriptome data, 64 BrGRP genes showed abnormal expression under high temperature stress, 52 under low temperature stress, 39 under drought stress, and 23 responses to soft rot. A large number of stress-related cis-acting elements, such as DRE, MYC, MYB, and ABRE were found in their promoter regions by PlantCare, which corresponded with differential expressions. Two BrGRP genes-w546 (Bra030284) and w1409 (Bra014000), both belonging to the subfamily Subclass IVa RBP-GRP (RNA binding protein-glycine rich protein), were up-regulated under 150 mmol⋅L-1 NaCl stress in Chinese cabbage. However, the overexpressed w546 gene could significantly inhibit seed germination, while w1409 significantly accelerated seed germination under 100 mmol⋅L-1 NaCl or 300 mmol⋅L-1 mannitol stresses. In short, most BrGRP genes showed abnormal expression under adversity stress, and some were involved in multiple stress responses, suggesting a potential capacity to resist multiple biotic and abiotic stresses, which is worthy of further study. Our study provides a systematic investigation of the molecular characteristics and expression patterns of BrGRP genes and promotes for further work on improving stress resistance of Chinese cabbage.

Molecular and genetic bases of heat stress responses in crop plants and breeding for increased resilience and productivity

To ensure the food security of future generations and to address the challenge of the 'no hunger zone' proposed by the FAO (Food and Agriculture Organization), crop production must be doubled by 2050, but environmental stresses are counteracting this goal. Heat stress in particular is affecting agricultural crops more frequently and more severely. Since the discovery of the physiological, molecular, and genetic bases of heat stress responses, cultivated plants have become the subject of intense research on how they may avoid or tolerate heat stress by either using natural genetic variation or creating new variation with DNA technologies, mutational breeding, or genome editing. This review reports current understanding of the genetic and molecular bases of heat stress in crops together with recent approaches to creating heat-tolerant varieties. Research is close to a breakthrough of global relevance, breeding plants fitter to face the biggest challenge of our time.

Identification of Heat-Responsive Genes in Guar [Cyamopsis tetragonoloba (L.) Taub]

The threat of heat stress on crop production increased dramatically due to global warming leading to the rise on the demand of heat-tolerant crops and understanding their tolerance. The leguminous forage crop Guar [Cyamopsis tetragonoloba (L.) Taub] is a high-temperature tolerant plant with numerous works on its tolerance at morph-physiological levels but lack on molecular thermotolerance level. In the current study, the differential gene expression and the underlying metabolic pathways induced by heat treatment were investigated. An RNA-Seq study on Guar leaves was carried out to estimate gene abundance and identify genes involved in heat tolerance to better understand the response mechanisms to heat stress. The results uncovered 1551 up- and 1466 downregulated genes, from which 200 and 72 genes with unknown function could be considered as new genes specific to guar. The upregulated unigenes were associated with 158 enzymes and 102 KEGG pathways. Blast2GO, InterProScan, and Kyoto Encyclopaedia of Genes and Genomes packages were utilized to search the functional annotation, protein analysis, enzymes, and metabolic pathways and revealed hormone signal transduction were enriched during heat stress tolerance. A total of 301 protein families, 551 domains, 15 repeats, and 3 sites were upregulated and matched to those unigenes. A batch of heat-regulated transcription factor transcripts were identified using the PlantTFDB database, which may play roles in heat response in Guar. Interestingly, several heat shock protein families were expressed in response to exposure to stressful conditions for instance small HSP20, heat shock transcription factor family, heat shock protein Hsp90 family, and heat shock protein 70 family. Our results revealed the expressional changes associated with heat tolerance and identified potential key genes in the regulation of this process. These results will provide a good start to dissect the molecular behaviour of plants induced by heat stress and could identify the key genes in stress response for marker-assisted selection in Guar and reveal their roles in stress adaptation in plants.

A potential seedling-stage evaluation method for heat tolerance in Indian mustard (Brassica juncea L. Czern and Coss)

Heat stress is one of the major limitations to crop productivity. In the present study, an efficient method of screening was adopted for identification of heat tolerant Indian Mustard genotypes by applying 4-day cycle of heat stress to seedlings. Thirty-four genotypes were screened based upon lipid peroxidation and survival percentage and classified them into five different classes according to membership function value (MFV) for response against high temperature. The maximum and minimum value of mean MFV were 0.89 (highly heat tolerant, TPM1) and 0.12 (highly heat sensitive, JM2), respectively. The coefficient of determination (R ²) between the mean MFV and the heat tolerance index (HTI) of MDA content, survival percentage was 0.914 and 0.808 suggesting that these parameters are reliable traits to evaluate the heat tolerance of Brassica juncea genotypes. The evaluation method was further validated using identified contrasting genotypes and assessment of heat stress associated biochemical parameters. Results showed efficient recovery of tolerant genotype as compared to sensitive genotype. Expression profiling of heat stress-related genes (HSP21 and HSFA7A) showed significant upregulation in the tolerant genotype (TPM1) (9.73- and 4.87-fold, respectively) as compared to the sensitive genotype (JM2) (4.18- and 1.73-fold, respectively) under heat stress condition. The results imply development of an efficient screening method which is useful for evaluation and breeding of thermo-tolerant B. juncea.

Dynamic Transcriptome Analysis of Anther Response to Heat Stress during Anthesis in Thermotolerant Rice (Oryza sativa L.)

High temperature at anthesis is one of the most serious stress factors for rice (Oryza sativa L.) production, causing irreversible yield losses and reduces grain quality. Illustration of thermotolerance mechanism is of great importance to accelerate rice breeding aimed at thermotolerance improvement. Here, we identified a new thermotolerant germplasm, SDWG005. Microscopical analysis found that stable anther structure of SDWG005 under stress may contribute to its thermotolerance. Dynamic transcriptomic analysis totally identified 3559 differentially expressed genes (DEGs) in SDWG005 anthers at anthesis under heat treatments, including 477, 869, 2335, and 2210 for 1, 2, 6, and 12 h, respectively; however, only 131 were regulated across all four-time-points. The DEGs were divided into nine clusters according to their expressions in these heat treatments. Further analysis indicated that some main gene categories involved in heat-response of SDWG005 anthers, such as transcription factors, nucleic acid and protein metabolisms related genes, etc. Comparison with previous studies indicates that a core gene-set may exist for thermotolerance mechanism. Expression and polymorphic analysis of agmatine-coumarin-acyltransferase gene OsACT in different accessions suggested that it may involve in SDWG005 thermotolerance. This study improves our understanding of thermotolerance mechanisms in rice anthers during anthesis, and also lays foundation for breeding thermotolerant varieties via molecular breeding.

Integration of Transcriptomics and Metabolomics for Pepper (Capsicum annuum L.) in Response to Heat Stress

Heat stress (HS), caused by extremely high temperatures, is one of the most severe forms of abiotic stress in pepper. In the present study, we studied the transcriptome and metabolome of a heat-tolerant cultivar (17CL30) and a heat-sensitive cultivar (05S180) under HS. Briefly, we identified 5754 and 5756 differentially expressed genes (DEGs) in 17CL30 and 05S180, respectively. Moreover, we also identified 94 and 108 differentially accumulated metabolites (DAMs) in 17CL30 and 05S180, respectively. Interestingly, there were many common HS-responsive genes (approximately 30%) in both pepper cultivars, despite the expression patterns of these HS-responsive genes being different in both cultivars. Notably, the expression changes of the most common HS-responsive genes were typically much more significant in 17CL30, which might explain why 17CL30 was more heat tolerant. Similar results were also obtained from metabolome data, especially amino acids, organic acids, flavonoids, and sugars. The changes in numerous genes and metabolites emphasized the complex response mechanisms involved in HS in pepper. Collectively, our study suggested that the glutathione metabolic pathway played a critical role in pepper response to HS and the higher accumulation ability of related genes and metabolites might be one of the primary reasons contributing to the heat resistance.

High ambient temperature leads to reduced FT expression and delayed flowering in Brassica rapa via a mechanism associated with H2A.Z dynamics

Flowering time is a relevant agronomic trait because is crucial for the optimal formation of seeds and fruits. The genetic pathways controlling this developmental phase transition have been studied extensively in Arabidopsis thaliana. These pathways converge in a small number of genes including FT, the so-called florigen, which integrates environmental cues like ambient temperature. Nevertheless, detailed and functional studies about flowering time in Brassica crops are scarce. Here we study the role of the FT Brassica rapa homologues and the effect of high ambient temperature on flowering time in this crop. Phenotypic characterization and gene-expression analyses suggest that BraA.FT.a (BraA02g016700.3C) is decisive for initiating floral transition; consequently, braA.ft.a loss-of-function and hypomorphic mutations result in late flowering phenotypes. We also show that high ambient temperature delays B. rapa floral transition by reducing BraA.FT.a expression. Strikingly, these expression changes are associated with increased histone H2A.Z levels and less accessible chromatin configuration of the BraA.FT.a locus at high ambient temperature. Interestingly, increased H2A.Z levels at high ambient temperature were also observed for other B. rapa temperature-responsive genes. Previous reports delimited that Arabidopsis flowers earlier at high ambient temperature due to reduced H2A.Z incorporation in the FT locus. Our data reveal a conserved chromatin-mediated mechanism in B. rapa and Arabidopsis in which the incorporation of H2A.Z at FT chromatin in response to warm ambient temperature results in different flowering time responses. This work will help to develop improved Brassica crop varieties with flowering time requirements to cope with global warming. OPEN RESEARCH BADGES: This article has earned an Open Materials Badge for making publicly available the components of the research methodology needed to reproduce the reported procedure and analysis. Methods are available at protocols.iodx.doi.org/10.17504/protocols.io.zmff43n.

bHLH92 from sheepgrass acts as a negative regulator of anthocyanin/proanthocyandin accumulation and influences seed dormancy

LcbHLH92, a pleiotropic gene from sheepgrass, negatively regulates anthocyanins/proanthocyandins and reduces seed dormancy in transgenic Arabidopsis.

Enhanced Tolerance of Chinese Cabbage Seedlings Mediated by Bacillus aryabhattai H26-2 and B. siamensis H30-3 against High Temperature Stress and Fungal Infections

Two rhizobacteria Bacillus aryabhattai H26-2 and B. siamensis H30-3 were evaluated whether they are involved in stress tolerance against drought and high temperature as well as fungal infections in Chinese cabbage plants. Chinese cabbage seedlings cv. Ryeokgwang (spring cultivar) has shown better growth compared to cv. Buram-3-ho (autumn cultivar) under high temperature conditions in a greenhouse, whilst there was no difference in drought stress tolerance of the two cultivars. In vitro growth of B. aryabhattai H26-2 and B. siamensis H30-3 were differentially regulated under PEG 6000-induced drought stress at different growing temperatures (30, 40 and 50°C). Pretreatment with B. aryabhattai H26-2 and B. siamensis H30-3 enhanced the tolerance of Chinese cabbage seedlings to high temperature, but not to drought stress. It turns out that only B. siamensis H30-3 showed in vitro antifungal activities and in planta crop protection against two fungal pathogens Alternaria brassicicola and Colletotrichum higginsianum causing black spots and anthracnose on Chinese cabbage plants cv. Ryeokgwang, respectively. B. siamensis H30-3 brings several genes involved in production of cyclic lipopeptides in its genome and secreted hydrolytic enzymes like chitinase, protease and cellulase. B. siamensis H30-3 was found to produce siderophore, a high affinity iron-chelating compound. Expressions of BrChi1 and BrGST1 genes were up-regulated in Chinese cabbage leaves by B. siamensis H30-3. These findings suggest that integration of B. aryabhattai H26-2 and B. siamensis H30-3 in Chinese cabbage production system may increase productivity through improved plant growth under high temperature and crop protection against fungal pathogens.

Genome-Wide Identification and Characterization of Warming-Related Genes in Brassica rapa ssp. pekinensis

For sustainable crop cultivation in the face of global warming, it is important to unravel the genetic mechanisms underlying plant adaptation to a warming climate and apply this information to breeding. Thermomorphogenesis and ambient temperature signaling pathways have been well studied in model plants, but little information is available for vegetable crops. Here, we investigated genes responsive to warming conditions from two Brassica rapa inbred lines with different geographic origins: subtropical (Kenshin) and temperate (Chiifu). Genes in Gene Ontology categories “response to heat”, “heat acclimation”, “response to light intensity”, “response to oxidative stress”, and “response to temperature stimulus” were upregulated under warming treatment in both lines, but genes involved in “response to auxin stimulus” were upregulated only in Kenshin under both warming and minor-warming conditions. We identified 16 putative high temperature (HT) adaptation-related genes, including 10 heat-shock response genes, 2 transcription factor genes, 1 splicing factor gene, and 3 others. BrPIF4, BrROF2, and BrMPSR1 are candidate genes that might function in HT adaptation. Auxin response, alternative splicing of BrHSFA2, and heat shock memory appear to be indispensable for HT adaptation in B. rapa. These results lay the foundation for molecular breeding and marker development to improve warming tolerance in B. rapa.

Genome-wide identification and expression analysis of calmodulin-like (CML) genes in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

BACKGROUND

Calmodulin-like (CML) proteins are a primary family of plant-specific Ca2+ sensors that specifically bind to Ca2+ and deliver a Ca2+ signal. CML proteins have been identified and characterized in many plant species, such as the model plant Arabidopsis and rice. Based on considerable evidence, the roles of CML proteins are crucial in plant growth and development and in the response to various external stimuli. Nevertheless, the characterization and expression profiling of CML genes in Chinese cabbage (Brassica rapa L. ssp. pekinensis) remain limited.

RESULTS

In this study, a genome-wide search and comprehensive analysis were performed, and a total of 79 BrCML genes were identified in Chinese cabbage. Gene structure analysis revealed that these BrCML genes contained two to four conserved EF-hand motifs. Phylogenetic analysis showed that CML homologs between Chinese cabbage and Arabidopsis shared close relationships. The identified BrCML genes were located across ten chromosomes and three different subgenomes of Chinese cabbage. Moreover, 126 pairs of orthologous CML genes were found among Chinese cabbage, Arabidopsis and Brassica oleracea. Expression analysis revealed that the expression of some BrCML genes was tissue-specific and that of some was susceptible to temperature stress. A putative interaction network of BrCML proteins was proposed, which suggested that BrCML2, BrCML6, BrCML15 and BrCML25 were co-expressed and might play roles in flower development and other relevant biological processes of Chinese cabbage.

CONCLUSIONS

The results of this study increased the understanding and characterization of BrCML genes in Chinese cabbage, and will be a rich resource for further studies to investigate BrCML protein function in various developmental processes of Chinese cabbage.

Salt tolerance response revealed by RNA-Seq in a diploid halophytic wild relative of sweet potato

Crop wild relatives harbor exotic and novel genetic resources, which hold great potential for crop improvement. Ipomoea imperati is a wild diploid relative of sweet potato with the capability of high salinity tolerance. We compared the transcriptomes of I. imperati under salt stress vs. control to identify candidate genes and pathways involved in salt response. De novo assembly produced 67,911 transcripts with a high depth of coverage. A total of 39,902 putative genes were assigned annotations, and 936 and 220 genes involved in salt response in roots and leaves, respectively. Functional analysis indicated a whole system response during salt stress in I. imperati, which included four metabolic processes: sensory initiation, transcriptional reprogramming, cellular protein component change, and cellular homeostasis regulation. We identified a number of candidate genes involved in the ABA signaling pathway, as well as transcription factors, transporters, antioxidant enzymes, and enzymes associated with metabolism of synthesis and catalysis. Furthermore, two membrane transporter genes, including vacuole cation/proton exchanger and inositol transporter, were considered to play important roles in salt tolerance. This study provided valuable information not only for understanding the genetic basis of ecological adaptation but also for future application in sweet potato and other crop improvements.

Genome-Wide Analysis of the bZIP Gene Family Identifies Two ABI5-Like bZIP Transcription Factors, BrABI5a and BrABI5b, as Positive Modulators of ABA Signalling in Chinese Cabbage

bZIP (basic leucine zipper) transcription factors coordinate plant growth and development and control responses to environmental stimuli. The genome of Chinese cabbage (Brassica rapa) encodes 136 putative bZIP transcription factors. The bZIP transcription factors in Brassica rapa (BrbZIP) are classified into 10 subfamilies. Phylogenetic relationship analysis reveals that subfamily A consists of 23 BrbZIPs. Two BrbZIPs within subfamily A, Bra005287 and Bra017251, display high similarity to ABI5 (ABA Insensitive 5). Expression of subfamily A BrbZIPs, like BrABI5a (Bra005287/BrbZIP14) and BrABI5b (Bra017251/BrbZIP13), are significantly induced by the plant hormone ABA. Subcellular localization assay reveal that both BrABI5a and BrABI5b have a nuclear localization. BrABI5a and BrABI5b could directly stimulate ABA Responsive Element-driven HIS (a HIS3 reporter gene, which confers His prototrophy) or LUC (LUCIFERASE) expression in yeast and Arabidopsis protoplast. Deletion of the bZIP motif abolished BrABI5a and BrABI5b transcriptional activity. The ABA insensitive phenotype of Arabidopsis abi5-1 is completely suppressed in transgenic lines expressing BrABI5a or BrABI5b. Overall, these results suggest that ABI5 orthologs, BrABI5a and BrABI5b, have key roles in ABA signalling in Chinese cabbage.

Breeding for plant heat tolerance at vegetative and reproductive stages

KEY MESSAGE

Thermotolerant crop research. Global warming has become a serious worldwide threat. High temperature is a major environmental factor limiting crop productivity. Current adaptations to high temperature via alterations to technical and management systems are insufficient to sustain yield. For this reason, breeding for heat-tolerant crops is in high demand. This review provides an overview of the effects of high temperature on plant physiology, fertility and crop yield and discusses the strategies for breeding heat-tolerant cultivars. Generating thermotolerant crops seems to be a challenging task as heat sensitivity is highly variable across developmental stages and processes. In response to heat, plants trigger a cascade of events, switching on numerous genes. Although breeding has made substantial advances in developing heat-tolerant lines, the genetic basis and diversity of heat tolerance in plants remain largely unknown. The development of new varieties is expensive and time-consuming, and knowledge of heat tolerance mechanisms would aid the design of strategies to screen germplasm for heat tolerance traits. However, gains in heat tolerance are limited by the often narrow genetic diversity. Exploration and use of wild relatives and landraces in breeding can increase useful genetic diversity in current crops. Due to the complex nature of plant heat tolerance and its immediate global concern, it is essential to face this breeding challenge in a multidisciplinary holistic approach involving governmental agencies, private companies and academic institutions.

Comparative Transcriptome Analysis Reveals Heat-Responsive Genes in Chinese Cabbage (Brassica rapa ssp. chinensis)

Chinese cabbage (Brassica rapa ssp. chinensis) is an economically and agriculturally significant vegetable crop and is extensively cultivated throughout the world. Heat stress disturbs cellular homeostasis and causes visible growth inhibition of shoots and roots, severe retardation in growth and development, and even death. However, there are few studies on the transcriptome profiling of heat stress in non-heading Chinese cabbage. In this study, we investigated the transcript profiles of non-heading Chinese cabbage from heat-sensitive and heat-tolerant varieties "GHA" and "XK," respectively, in response to high temperature using RNA sequencing (RNA seq). Approximately 625 genes were differentially expressed between the two varieties. The responsive genes can be divided into three phases along with the time of heat treatment: response to stimulus, programmed cell death and ribosome biogenesis. Differentially expressed genes (DEGs) were identified in the two varieties, including transcription factors (TFs), kinases/phosphatases, genes related to photosynthesis and effectors of homeostasis. Many TFs were involved in the heat stress response of Chinese cabbage, including NAC069 TF which was up-regulated at all the heat treatment stages. And their expression levels were also validated by quantitative real-time-PCR (qRT-PCR). These candidate genes will provide genetic resources for further improving the heat-tolerant characteristics in non-heading Chinese cabbage.

Multi-Level Interactions Between Heat Shock Factors, Heat Shock Proteins, and the Redox System Regulate Acclimation to Heat

High temperature has become a global concern because it seriously affects the growth and reproduction of plants. Exposure of plant cells to high temperatures result in cellular damage and can even lead to cell death. Part of the damage can be ascribed to the action of reactive oxygen species (ROS), which accumulate during abiotic stresses such as heat stress. ROS are toxic and can modify other biomacromolecules including membrane lipids, DNA, and proteins. In order to protect the cells, ROS scavenging is essential. In contrast with their inherent harms, ROS also function as signaling molecules, inducing stress tolerance mechanisms. This review examines the evidence for crosstalk between the classical heat stress response, which consists of heat shock factors (HSFs) and heat shock proteins (HSPs), with the ROS network at multiple levels in the heat response process. Heat stimulates HSF activity directly, but also indirectly via ROS. HSFs in turn stimulate the expression of HSP chaperones and also affect ROS scavenger gene expression. In the short term, HSFs repress expression of superoxide dismutase scavenger genes via induction of miRNA398, while they also activate scavenger gene expression and stabilize scavenger protein activity via HSP induction. We propose that these contrasting effects allow for the boosting of the heat stress response at the very onset of the stress, while preventing subsequent oxidative damage. The described model on HSFs, HSPs, ROS, and ROS scavenger interactions seems applicable to responses to stresses other than heat and may explain the phenomenon of crossacclimation.