LlWRKY39 is involved in thermotolerance by activating LlMBF1c and interacting with LlCaM3 in lily (Lilium longiflorum)

Exploring Agrobacterium-mediated genetic transformation methods and its applications in Lilium

As a typical bulb flower, lily is widely cultivated worldwide because of its high ornamental, medicinal and edible value. Although breeding efforts evolved over the last 10000 years, there are still many problems in the face of increasing consumer demand. The approach of biotechnological methods would help to solve this problem and incorporate traits impossible by conventional breeding. Target traits are dormancy, development, color, floral fragrance and resistances against various biotic and abiotic stresses, so as to improve the quality of bulbs and cut flowers in planting, cultivation, postharvest, plant protection and marketing. Genetic transformation technology is an important method for varietal improvement and has become the foundation and core of plant functional genomics research, greatly assisting various plant improvement programs. However, achieving stable and efficient genetic transformation of lily has been difficult worldwide. Many gene function verification studies depend on the use of model plants, which greatly limits the pace of directed breeding and germplasm improvement in lily. Although significant progress has been made in the development and optimization of genetic transformation systems, shortcomings remain. Agrobacterium-mediated genetic transformation has been widely used in lily. However, severe genotypic dependence is the main bottleneck limiting the genetic transformation of lily. This review will summarizes the research progress in the genetic transformation of lily over the past 30 years to generate the material including a section how genome engineering using stable genetic transformation system, and give an overview about recent and future applications of lily transformation. The information provided in this paper includes ideas for optimizing and improving the efficiency of existing genetic transformation methods and for innovation, provides technical support for mining and identifying regulatory genes for key traits, and lays a foundation for genetic improvement and innovative germplasm development in lily.

SlWRKY55 coordinately acts with SlVQ11 to enhance tomato thermotolerance by activating SlHsfA2

High temperature (HT) severely restricts plant growth, development, and productivity. Plants have evolved a set of mechanisms to cope with HT, including the regulation of heat stress transcription factors (Hsfs) and heat shock proteins (Hsps). However, it is not clear how the transcriptional and translational levels of Hsfs and Hsps are controlled in tomato. Here, we reported that the HT-induced transcription factor SlWRKY55 recruited SlVQ11 to coordinately regulate defense against HT. SlWRKY55 directly bound to the promoter of SlHsfA2 and promoted its expression, which was increased by SlVQ11. Moreover, both SlWRKY55 and SlVQ11 physically interacted with SlHsfA2 to enhance the transcriptional activity of SlHsfA2. Thus, our results revealed a molecular mechanism that the SlWRKY55/SlVQ11-SlHsfA2 cascade enhanced thermotolerance and provided potential target genes for improving the adaptability of crops to HT.

Transcription Cofactor CsMBF1c Enhances Heat Tolerance of Cucumber and Interacts with Heat-Related Proteins CsNFYA1 and CsDREB2

Multiprotein bridging factor 1 (MBF1) is a very important transcription factor (TF) in plants, whose members influence numerous defense responses. Our study found that MBF1c in Cucurbitaceae was highly conserved. CsMBF1c expression was induced by temperature, salt stress, and abscisic acid (ABA) in cucumber. Overexpressed CsMBF1c enhanced the heat resistance of a cucumber, and the Csmbf1c mutant showed decreased resistance to high temperatures (HTs). CsMBF1c played an important role in stabilizing the photosynthetic system of cucumber under HT, and its expression was significantly associated with heat-related TFs and genes related to protein processing in the endoplasmic reticulum (ER). Protein interaction showed that CsMBF1c interacted with dehydration-responsive element binding protein 2 (CsDREB2) and nuclear factor Y A1 (CsNFYA1). Overexpression of CsNFYA1 in Arabidopsis improved the heat resistance. Transcriptional activation of CsNFYA1 was elevated by CsMBF1c. Therefore, CsMBF1c plays an important regulatory role in cucumber's resistance to high temperatures.

BcWRKY1 confers Botrytis cinerea susceptibility via inhibiting JA biosynthesis

WRKYs play important roles in plant stress resistance. However, the role of WRKYs in non-heading Chinese cabbage (Brassica campestris ssp. chinensis) against Botrytis cinerea (B. cinerea) remains poorly understood. Herein, the expression of BcWRKY1 was induced by B. cinerea. Further, the role of BcWRKY1 in B. cinerea infection was identified. Silencing of BcWRKY1 in non-heading Chinese cabbage enhanced plant resistance to B. cinerea. After B. cinerea inoculation, BcWRKY1-silencing plants exhibited lower reactive oxygen species (ROS) content, higher jasmonic acid (JA) content, and the expression level of JA biosynthesis genes, BcOPR3, BcLOX3-1 and BcLOX3-2 were upregulated. Overexpression of BcWRKY1 in Arabidopsis exhibited a complementary phenotype. By directly targeting W-boxes in the promoter of BcLOX3-2, BcWRKY1 inhibited the transcription of this gene. In addition, 13 candidate interacting proteins of BcWRKY1 were identified by yeast two-hybrid (Y2H) screening, and the interaction between BcWRKY1 and BcCaM6 weakened the inhibition of BcLOX3-2. In summary, our findings suggest that BcWRKY1 interacts with BcCaM6 to negatively regulate disease resistance.

Strigolactones alleviate AlCl3 stress by vacuolar compartmentalization and cell wall blocking in apple

Poor management and excess fertilization of apple (Malus domestica Borkh.) orchards are causing increasingly serious soil acidification, resulting in Al toxicity and direct poisoning of roots. Strigolactones (SLs) are reported to be involved in plant responses to abiotic stress, but their role and mechanism under AlCl3 stress remain unknown. Here, we found that applying 1 μm GR24 (an SL analoge) significantly alleviated AlCl3 stress of M26 apple rootstock, mainly by blocking the movement of Al through cell wall and by vacuolar compartmentalization of Al. RNA-seq analysis identified the core transcription factor gene MdWRKY53, and overexpressing MdWRKY53 enhanced AlCl3 tolerance in transgenic apple plants through the same mechanism as GR24. Subsequently, we identified MdPMEI45 (encoding pectin methylesterase inhibitor) and MdALS3 (encoding an Al transporter) as downstream target genes of MdWRKY53 using chromatin immunoprecipitation followed by sequencing (ChIP-seq). GR24 enhanced the interaction between MdWRKY53 and the transcription factor MdTCP15, further increasing the binding of MdWRKY53 to the MdPMEI45 promoter and inducing MdPMEI45 expression to prevent Al from crossing cell wall. MdWRKY53 also bound to the promoter of MdALS3 and enhanced its transcription to compartmentalize Al in vacuoles under AlCl3 stress. We therefore identified two modules involved in alleviating AlCl3 stress in woody plant apple: the SL-WRKY+TCP-PMEI module required for excluding external Al by blocking the entry of Al3+ into cells and the SL-WRKY-ALS module allowing internal detoxification of Al through vacuolar compartmentalization. These findings lay a foundation for the practical application of SLs in agriculture.

Functional validation of AaCaM3 response to high temperature stress in Amorphophallus albus

Amorphophallus is a perennial monocotyledonous herbaceous plant native to the southwestern region of China, widely used in various fields such as food processing, biomedicine and chemical agriculture. However, Amorphophallus is a typical thermolabile plant, and the continuous high temperature in summer have seriously affected the growth, development and economic yield of Amorphophallus in recent years. Calmodulin (CaM), a Ca2+ sensor ubiquitous in eukaryotes, is the most important multifunctional receptor protein in plant cells, which affects plant stress resistance by participating in the activities of a variety of signaling molecules. In this study, the key gene AaCaM3 for the Ca2+-CaM regulatory pathway was obtained from A. albus, the sequence analysis confirmed that it is a typical calmodulin. The qRT-PCR results demonstrated that with the passage of heat treatment time, the expression of AaCaM3 was significantly upregulated in A. albus leaves. Subcellular localization analysis revealed that AaCaM3 localized on the cytoplasm and nucleus. Meanwhile, heterologous transformation experiments have shown that AaCaM3 can significantly improve the heat tolerance of Arabidopsis under heat stress. The promoter region of AaCaM3 was sequenced 1,338 bp by FPNI-PCR and GUS staining assay showed that the promoter of AaCaM3 was a high-temperature inducible promoter. Yeast one-hybrid analysis and Luciferase activity reporting system analysis showed that the AaCaM3 promoter may interact with AaHSFA1, AaHSFA2c, AaHSP70, AaDREB2a and AaDREB2b. In conclusion, this study provides new ideas for further improving the signal transduction network of high-temperature stress in Amorphophallus.

Obtaining and Characterization of an Interspecific Hybrid between Lilium callosum and 'Snow Queen' and Evaluation of the Botrytis Stress Response

To cultivate excellent lily germplasms, an interspecific hybrid (LC×SQ-01) was successfully obtained by using a cut-style pollination method in which the rare wild lily Lilium callosum was used as the female parent and the cut flower L. longiflorum 'Snow Queen' was used as the male parent. The morphological features of LC×SQ-01 included height, leaf length, and width, which were observed to be between those of the parents in the tissue-cultured seedlings. The height and leaf length of LC×SQ-01 were more similar to those of the male parent, and the width was between the widths of the parents for field-generated plants. The epidermal cell length and the guard cell and stoma sizes were between those of both parents in tissue-cultured and field-generated plants. In addition, the shapes of the epidermal cells and anticlinal wall in LC×SQ-01 were more analogous to those in the male parent, while the stoma morphology was different from that of both parents. Fourteen pairs of polymorphic SSR primers were identified in both parents, and the validity of LC×SQ-01 was demonstrated by PCR amplification using five pairs of SSR primers. Flow cytometry and root tip squashing assays revealed that LC×SQ-01 was a diploid plant, similar to its parents. Furthermore, the LC×SQ-01 hybrid was more resistant to B. cinerea than its parents, and it also showed much greater peroxidase (POD) and catalase (CAT) activity than the parents. These results lay a foundation for breeding a new high-resistance and ornamental lily variety.

Identification of WRKY Family Members and Characterization of the Low-Temperature-Stress-Responsive WRKY Genes in Luffa (Luffa cylindrica L.)

The plant-specific WRKY transcription factor family members have diverse regulatory effects on the genes associated with many plant processes. Although the WRKY proteins in Arabidopsis thaliana and other species have been thoroughly investigated, there has been relatively little research on the WRKY family in Luffa cylindrica, which is one of the most widely grown vegetables in China. In this study, we performed a genome-wide analysis to identify L. cylindrica WRKY genes, which were subsequently classified and examined in terms of their gene structures, chromosomal locations, promoter cis-acting elements, and responses to abiotic stress. A total of 62 LcWRKY genes (471-2238 bp) were identified and divided into three phylogenetic groups (I, II, and III), with group II further divided into five subgroups (IIa, IIb, IIc, IId, and IIe) in accordance with the classification in other plants. The LcWRKY genes were unevenly distributed across 13 chromosomes. The gene structure analysis indicated that the LcWRKY genes contained 0-11 introns (average of 4.4). Moreover, 20 motifs were detected in the LcWRKY proteins with conserved motifs among the different phylogenetic groups. Two subgroup IIc members (LcWRKY16 and LcWRKY31) contained the WRKY sequence variant WRKYGKK. Additionally, nine cis-acting elements related to diverse responses to environmental stimuli were identified in the LcWRKY promoters. The subcellular localization analysis indicated that three LcWRKY proteins (LcWRKY43, LcWRKY7, and LcWRKY23) are localized in the nucleus. The tissue-specific LcWRKY expression profiles reflected the diversity in LcWRKY expression. The RNA-seq data revealed the effects of low-temperature stress on LcWRKY expression. The cold-induced changes in expression were verified via a qRT-PCR analysis of 24 differentially expressed WRKY genes. Both LcWRKY7 and LcWRKY12 were highly responsive to the low-temperature treatment (approximately 110-fold increase in expression). Furthermore, the LcWRKY8, LcWRKY12, and LcWRKY59 expression levels increased by more than 25-fold under cold conditions. Our findings will help clarify the evolution of the luffa WRKY family while also providing valuable insights for future studies on WRKY functions.

A LlWRKY33-LlHSFA4-LlCAT2 module confers resistance to Botrytis cinerea in lily

Gray mold caused by Botrytis cinerea is one of the major threats in lily production. However, limited information is available about the underlying defense mechanism against B. cinerea in lily. Here, we characterized a nuclear-localized class A heat stress transcription factor (HSF)-LlHSFA4 from lily (Lilium longiflorum), which positively regulated the response to B. cinerea infection. LlHSFA4 transcript and its promoter activity were increased by B. cinerea infection in lily, indicating its involvement in the response to B. cinerea. Virus-induced gene silencing (VIGS) of LlHSFA4 impaired the resistance of lily to B. cinerea. Consistent with its role in lily, overexpression of LlHSFA4 in Arabidopsis (Arabidopsis thaliana) enhanced the resistance of transgenic Arabidopsis to B. cinerea infection. Further analysis showed that LlWRKY33 directly activated LlHSFA4 expression. We also found that both LlHSFA4 and LlWRKY33 positively regulated plant response to B. cinerea through reducing cell death and H2O2 accumulation and activating the expression of the reactive oxygen species (ROS) scavenging enzyme gene LlCAT2 (Catalase 2) by binding its prompter, which might contribute to reducing H2O2 accumulation in the infected area. Taken together, our data suggested that there may be a LlWRKY33-LlHSFA4-LlCAT2 regulatory module which confers B. cinerea resistance via reducing cell death and the ROS accumulation.

Calcium Signaling and the Response to Heat Shock in Crop Plants

Climate change and the increasing frequency of high temperature (HT) events are significant threats to global crop yields. To address this, a comprehensive understanding of how plants respond to heat shock (HS) is essential. Signaling pathways involving calcium (Ca2+), a versatile second messenger in plants, encode information through temporal and spatial variations in ion concentration. Ca2+ is detected by Ca2+-sensing effectors, including channels and binding proteins, which trigger specific cellular responses. At elevated temperatures, the cytosolic concentration of Ca2+ in plant cells increases rapidly, making Ca2+ signals the earliest response to HS. In this review, we discuss the crucial role of Ca2+ signaling in raising plant thermotolerance, and we explore its multifaceted contributions to various aspects of the plant HS response (HSR).

A wheat WRKY transcription factor TaWRKY17 enhances tolerance to salt stress in transgenic Arabidopsis and wheat plant

WRKY transcription factors are essential to plant growth, development, resistance, and the regulation of metabolic pathways. In this study, we characterized TaWRKY17, a WRKY transcription factor from wheat, which was differentially expressed in various wheat organs and was up-regulated by salt, drought, hydrogen peroxide (H2O2) and abscisic acid (ABA) treatment. To analyze TaWRKY17 function under salt stress, we obtained stable T3 generation transgenic Arabidopsis and wheat TaWRKY17 overexpression plants. TaWRKY17 overexpression in Arabidopsis and wheat caused a significant plant salt-stress tolerance enhancement. Under salt stress, superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) enzyme activities were elevated in transgenic Arabidopsis and wheat plants compared with the wild type (WT), whereas H2O2 and malondialdehyde (MDA) accumulation was reduced in the transgenic lines. Moreover, ABA/reactive oxygen species (ROS)-related, and stress-response genes were regulated in the transgenic wheat plants, increasing tolerance to salt stress. The transgenic wheat plants were highly sensitive to ABA during seed germination and early seedling growth. In addition, TaWRKY17 virus-induced gene silencing (VIGS) decreased salt tolerance. These results showed that TaWRKY17 enhances salt tolerance by regulating ABA/ROS-related, and stress-response genes and increasing anti-oxidative stress capabilities. Therefore, this gene could be a target for the genetic modification of wheat.

Low LdMYB12 expression contributes to petal spot deficiency in Lilium davidii var. unicolor

Petal spots are widespread in plants, they are important for attracting pollinators and as economic traits in crop breeding. However, the genetic and developmental control of petal spots has seldom been investigated. To further clarify the development of petal spots formation, we performed comparative transcriptome analysis of Lilium davidii var. unicolor and Lilium davidii petals at the full-bloom stage. In comparison with the parental species L. davidii, petals of the lily variety L. davidii var. unicolor do not have the distinct anthocyanin spots. We show that among 7846 differentially expressed genes detected, LdMYB12 was identified as a candidate gene contributing to spot formation in lily petals. The expression level of LdMYB12 in the petals of L. davidii was higher than that in L. davidii var. unicolor petals. Moreover, overexpression of LdMYB12 led to the appearance of spots on the petals of L. davidii var. unicolor, accompanied by increased expression of anthocyanin synthesis-related genes. Taken together, these results indicate that abnormal expression of LdMYB12 contributes to petal spot deficiency in L. davidii var. unicolor.

WRKY transcription factors in plant defense

Environmental stressors caused by climate change are fundamental barriers to agricultural sustainability. Enhancing the stress resilience of crops is a key strategy in achieving global food security. Plants perceive adverse environmental conditions and initiate signaling pathways to activate precise responses that contribute to their survival. WRKY transcription factors (TFs) are essential players in several signaling cascades and regulatory networks that have crucial implications for defense responses in plants. This review summarizes advances in research concerning how WRKY TFs mediate various signaling cascades and metabolic adjustments as well as how epigenetic modifications involved in environmental stress responses in plants can modulate WRKYs and/or their downstream genes. Emerging research shows that clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas)-mediated genome editing of WRKYs could be used to improve crop resilience.

Calcium signaling-mediated transcriptional reprogramming during abiotic stress response in plants

Calcium (Ca2+) is a second messenger in plants growth and development, as well as in stress responses. The transient elevation in cytosolic Ca2+ concentration have been reported to be involved in plants response to abiotic and biotic stresses. In plants, Ca2+-induced transcriptional changes trigger molecular mechanisms by which plants adapt and respond to environment stresses. The mechanism for transcription regulation by Ca2+ could be either rapid in which Ca2+ signals directly cause the related response through the gene transcript and protein activities, or involved amplification of Ca2+ signals by up-regulation the expression of Ca2+ responsive genes, and then increase the transmission of Ca2+ signals. Ca2+ regulates the expression of genes by directly binding to the transcription factors (TFs), or indirectly through its sensors like calmodulin, calcium-dependent protein kinases (CDPK) and calcineurin B-like protein (CBL). In recent years, significant progress has been made in understanding the role of Ca2+-mediated transcriptional regulation in different processes in plants. In this review, we have provided a comprehensive overview of Ca2+-mediated transcriptional regulation in plants in response to abiotic stresses including nutrition deficiency, temperature stresses (like heat and cold), dehydration stress, osmotic stress, hypoxic, salt stress, acid rain, and heavy metal stress.

RsGLK2.1-RsNF-YA9a module positively regulates the chlorophyll biosynthesis by activating RsHEMA2 in green taproot of radish

Radish (Raphanus sativus L.) is an economically important and widely cultivated root vegetable crop. The coloration of the green skin and green flesh is an important trait influencing the nutrition and flavor quality in fruit radish. GOLDEN2-LIKEs (GLKs) play critically important roles in plastid development and chlorophyll biosynthesis in plants. However, the molecular mechanism underlying chlorophyll biosynthesis still remain elusive in green fruit radish taproot. Herein, the RsGLK2.1 gene exhibited higher expression level in taproot with a green skin (GS) and green flesh (GF) than that in taproot of the white or red radish genotypes. RsGLK2.1 is a nuclear transcription factor that has intrinsic transcriptional activation activity. Overexpression of RsGLK2.1 increased the total chlorophyll content of 20.68%-45.84% in radish leaves. Knockout of the RsGLK2.1 gene via CRISPR/Cas9 technology resulted in a significant decrease in the chlorophyll content. Overexpression of the RsGLK2.1 gene could restore the phenotype of the glk1glk2 mutant Arabidopsis. RsGLK2.1 was participated in regulating the chlorophyll biosynthesis by directly binding to the promoter of RsHEMA2 and activating its transcription. The interaction of RsNF-YA9a with RsGLK2.1 increased the transcriptional activity of the downstream gene RsHEMA2 under the light condition rather than the dark condition, indicating that both of them regulate the chlorophyll biosynthesis in a light-dependent manner of radish. Overall, these results provided insights into the molecular framework of the RsGLK2.1-RsNF-YA9a module, and could facilitate dissecting the regulatory mechanism underlying chlorophyll biosynthesis in green taproot of radish, and genetic improvement of quality traits in fruit radish breeding programs.

BcWRKY22 Activates BcCAT2 to Enhance Catalase (CAT) Activity and Reduce Hydrogen Peroxide (H2O2) Accumulation, Promoting Thermotolerance in Non-Heading Chinese Cabbage (Brassica campestris ssp. chinensis)

WRKY transcription factors (TFs) participate in plant defense mechanisms against biological and abiotic stresses. However, their regulatory role in heat resistance is still unclear in non-heading Chinese cabbage. Here, we identified the WRKY-IIe gene BcWRKY22(BraC09g001080.1), which is activated under high temperatures and plays an active role in regulating thermal stability, through transcriptome analysis. We further discovered that the BcWRKY22 protein is located in the nucleus and demonstrates transactivation activity in both the yeast and plant. Additionally, our studies showed that the transient overexpression of BcWRKY22 in non-heading Chinese cabbage activates the expression of catalase 2 (BcCAT2), enhances CAT enzyme activity, and reduces Hydrogen Peroxide (H2O2) accumulation under heat stress conditions. In addition, compared to its wild-type (WT) counterparts, Arabidopsis thaliana heterologously overexpresses BcWRKY22, improving thermotolerance. When the BcWRKY22 transgenic root was obtained, under heat stress, the accumulation of H2O2 was reduced, while the expression of catalase 2 (BcCAT2) was upregulated, thereby enhancing CAT enzyme activity. Further analysis revealed that BcWRKY22 directly activates the expression of BcCAT2 (BraC08g016240.1) by binding to the W-box element distributed within the promoter region of BcCAT2. Collectively, our findings suggest that BcWRKY22 may serve as a novel regulator of the heat stress response in non-heading Chinese cabbage, actively contributing to the establishment of thermal tolerance by upregulating catalase (CAT) activity and downregulating H2O2 accumulation via BcCAT2 expression.

Enhancing heat stress tolerance in Lanzhou lily (Lilium davidii var. unicolor) with Trichokonins isolated from Trichoderma longibrachiatum SMF2

Lanzhou lily (Lilium davidii var. unicolor) is a renowned edible crop produced in China and relatively sensitive to high temperature (HT). Trichokonins (TKs) are antimicrobial peptaibols secreted from Trichoderma longibrachiatum strain SMF2. Here, we report that TKs application improves the thermotolerance of Lanzhou lily. The activity of the antioxidant enzyme system (SOD, CAT, and POD), the level of heat-resistance-associated phytohormones (ABA, SA, and JA), the relative water content (RWC), the content of chlorophyll (Chl), and the net photosynthetic rate (P _n) were promoted by TKs treatment in Lanzhou lily plants subjected to heat stress (HS). TKs treatment also mitigated cell injury as shown by a lower accumulation of malondialdehyde (MDA) and relative electrolyte leakage (REL) under HS conditions. RNA-seq data analysis showed that more than 4.5 times differentially expressed genes (DEGs) responded to TKs treatment under HS compared to non-HS, and TKs treatment reduced protein folding and enhanced cellular repair function under HS conditions. The analyses of DEGs involved in hormone (ABA, SA and JA) synthesis and signaling pathways suggested that TKs might improve Lanzhou lily heat tolerance by promoting ABA synthesis and signal transduction. TKs highly induced DEGs of the HSF-HSP pathway under HS, in which HSFA2 accounted for most of the HSF family. Furthermore, TKs treatment resulted in the upregulation of heat-protective genes LzDREB2B, LzHsfA2a, LzMBF1c, LzHsp90, and LzHsp70 involved in HSF-HSP signal pathway after long-term HS. LzHsfA2a-1 likely plays a key role in acquisition of TKs-induced thermotolerance of Lanzhou lily as evidenced by the sustained response to HS, the enhanced response to TKs treatment under long-term HS, and the high sequence similarity to LlHsfA2a which is a key regulator for the improvement of heat tolerance in Lilium longiflorum. Our results reveal the underlying mechanisms of TKs-mediated thermotolerance in Lanzhou lily and highlight an attractive approach to protecting crop plants from damage caused by HS in a global warming future.

Integrated analysis of transcriptome and microRNAs associated with exogenous calcium-mediated enhancement of hypoxic tolerance in cucumber seedlings (Cucumis sativus L.)

Plants often suffer from hypoxic stress due to flooding caused by extreme weather. Hypoxia usually leads to restricted oxygen supply and alters metabolic patterns from aerobic to anaerobic. Cucumber roots are fragile and highly sensitive to damage from hypoxic stress. The purpose of this study was to investigate the regulatory mechanism of exogenous calcium alleviating hypoxic stress in cucumber through transcriptome and small RNAs analysis. Three treatments were performed in this paper, including untreated-control (CK), hypoxic stress (H), and hypoxic stress + exogenous calcium treatment (H + Ca²⁺). A large number of differentially expressed genes (DEGs) were identified, 1,463 DEGs between CK vs H, 3,399 DEGs between H vs H + Ca²⁺, and 5,072 DEGs between CK vs H + Ca²⁺, respectively. KEGG analysis of DEGs showed that exogenous calcium could activate hormone signaling pathways (ethylene, ABA, IAA and cytokinin), transcription factors (MYB, MYB-related, bHLH, bZIP, and WRKY), calcium signaling and glycolysis pathway to mitigating hypoxic stress in cucumber seedlings. Additionally, miRNA and their target genes were detected and predicted between treatments. The target genes of these miRNAs revealed that auxin, cellulose synthase, and mitochondrial ribosomal related genes (Csa2G315390, Csa6G141390, Csa4G053280, and Csa6G310480) probably play in the improvement of the hypoxic tolerance of cucumber seedlings through exogenous calcium application. In short, our data adds new information to the mechanism of exogenous calcium mitigation of hypoxic stress injury in cucumber seedlings at transcriptional and post-transcriptional levels.

Lily HD-Zip I Transcription Factor LlHB16 Promotes Thermotolerance by Activating LlHSFA2 and LlMBF1c

HD-Zip I transcription factors play important roles in plant development and response to abiotic stresses; however, their roles in thermotolerance are largely unknown. Through transcriptome analysis in lily (Lilium longiflorum), we isolated and identified a HD-Zip I gene differentially expressed at high temperatures, LlHB16, which belongs to the β2 subgroup and positively regulates thermotolerance. The expression of LlHB16 was rapidly and continuously activated by heat stress. LlHB16 protein localized to the nucleus and exhibited transactivation activity in both plant and yeast cells, and its C-terminus contributed to its transcriptional activity. Overexpressing LlHB16 in Arabidopsis and lily improved thermotolerance and activated the expression of heat-related genes in both plants, especially that of HSFA2 and MBF1c. In addition, LlHB16 overexpression in Arabidopsis also caused growth defects, delayed flowering and abscisic acid (ABA) insensitivity. Further analysis revealed that LlHB16 directly binds to the promoters of LlHSFA2 and LlMBF1c and activates their expressions. Similarly, the expression of AtHSFA2 and AtMBF1c was also elevated in LlHB16 transgenic Arabidopsis lines. Together, our findings demonstrate that LlHB16 participates in the establishment of thermotolerance involved in activating LlHSFA2 and LlMBF1c, and LlHB16 overexpression resulted in ABA insensitivity in transgenic plants, suggesting that LlHB16 links the basal heat-responsive pathway and ABA signal to collaboratively regulate thermotolerance.

Natural variations of HSFA2 enhance thermotolerance in grapevine

Heat stress limits growth and development of crops including grapevine which is a popular fruit in the world. Genetic variability in crops thermotolerance is not well understood. We identified and characterized heat stress transcription factor HSFA2 in heat sensitive Vitis vinifera 'Jingxiu' (named as VvHSFA2) and heat tolerant Vitis davidii 'Tangwei' (named as VdHSFA2). The transcriptional activation activities of VdHSFA2 are higher than VvHSFA2, the variation of single amino acid (Thr315Ile) in AHA1 motif leads to the difference of transcription activities between VdHSFA2 and VvHSFA2. Based on 41 Vitis germplasms, we found that HSFA2 is differentiated at coding region among heat sensitive V. vinifera, and heat tolerant Vitis davidii and Vitis quinquangularis. Genetic evidence demonstrates VdHSFA2 and VvHSFA2 are positive regulators in grape thermotolerance, and the former can confer higher thermotolerance than the latter. Moreover, VdHSFA2 can regulate more target genes than VvHSFA2. As a target gene of both VdHSFA2 and VvHSFA2, overexpression of MBF1c enhanced the grape thermotolerance whereas dysfunction of MBF1c resulted in thermosensitive phenotype. Together, our results revealed that VdHSFA2 confers higher thermotolerance than VvHSFA2, and MBF1c acts as their target gene to induce thermotolerance. The VdHSFA2 may be adopted for molecular breeding in grape thermotolerance.

Gene Networks Involved in Plant Heat Stress Response and Tolerance

Global warming is an environmental problem that cannot be ignored. High temperatures seriously affect the normal growth and development of plants, and threaten the development of agriculture and the distribution and survival of species at risk. Plants have evolved complex but efficient mechanisms for sensing and responding to high temperatures, which involve the activation of numerous functional proteins, regulatory proteins, and non-coding RNAs. These mechanisms consist of large regulatory networks that regulate protein and RNA structure and stability, induce Ca²⁺ and hormone signal transduction, mediate sucrose and water transport, activate antioxidant defense, and maintain other normal metabolic pathways. This article reviews recent research results on the molecular mechanisms of plant response to high temperatures, highlighting future directions or strategies for promoting plant heat tolerance, thereby helping to identify the regulatory mechanisms of heat stress responses in plants.

A calmodulin-like protein (CML10) interacts with cytosolic enzymes GSTU8 and FBA6 to regulate cold tolerance

Calmodulin-like proteins (CMLs) are calcium (Ca2+) sensors involved in plant growth and development as well as adaptation to environmental stresses; however, their roles in plant responses to cold are not well understood. To reveal the role of MsCML10 from alfalfa (Medicago sativa) in regulating cold tolerance, we examined transgenic alfalfa and Medicago truncatula overexpressing MsCML10, MsCML10-RNAi alfalfa, and a M. truncatula cml10-1 mutant and identified MsCML10-interacting proteins. MsCML10 and MtCML10 transcripts were induced by cold treatment. Upregulation or downregulation of MsCML10 resulted in increased or decreased cold tolerance, respectively, while cml10-1 showed decreased cold tolerance that was complemented by expressing MsCML10, suggesting that MsCML10 regulates cold tolerance. MsCML10 interacted with glutathione S-transferase (MsGSTU8) and fructose 1,6-biphosphate aldolase (MsFBA6), and the interaction depended on the presence of Ca2+. The altered activities of Glutathione S-transferase and FBA and levels of ROS and sugars were associated with MsCML10 transcript levels. We propose that MsCML10 decodes the cold-induced Ca2+ signal and regulates cold tolerance through activating MsGSTU8 and MsFBA6, leading to improved maintenance of ROS homeostasis and increased accumulation of sugars for osmoregulation, respectively.

Transcription factor ZmWRKY20 interacts with ZmWRKY115 to repress expression of ZmbZIP111 for salt tolerance in maize

Maize (Zea mays) is an important cereal crop worldwide. However, its yield and quality are adversely affected by salt stress resulting from soil hypersalinity. Exploring the regulatory mechanisms of stress responses is of vital importance to increase maize seed production. In the present study, we screened ethyl methanesulfonate-induced maize mutants and identified a salt-tolerant mutant. A single base was mutated in ZmWRKY20, leading to the formation of a truncated protein variant. A detailed phenotypic analysis revealed that this mutant had significantly higher resistance to wilting and lower reactive oxygen species levels than the inbred line B73. ZmWRKY20 showed transcriptional activity in yeast and specifically bound W-boxes according to the results of our yeast one-hybrid, electrophoretic mobility shift, and dual-luciferase assays. Overexpression of ZmWRKY20 decreased salt tolerance in maize. Transcriptome profiling revealed that ZmWRKY20 overexpression extensively reprogrammed genes involved in regulating defense and oxidation-reduction responses. The results substantiate that ZmWRKY20 is directly targeted to the basic leucine zipper (bZIP) motif in the transcription factor ZmbZIP111. It was also verified that ZmWRKY20 interacts with ZmWRKY115 and both proteins act jointly to enhance ZmbZIP111 repression. The results indicate that the ZmWRKY20 and ZmWRKY115 transcription factors interact in the nucleus, leading to repression of ZmbZIP111 expression by directly binding its promoter, and increase the sensitivity of maize seedlings to salt stress. The current study improves our understanding of the complicated responses of maize to salt stress.

Lily WRKY factor LlWRKY22 promotes thermotolerance through autoactivation and activation of LlDREB2B

Most of WRKY transcription factors play important roles in plant development, protection against disease, and response to abiotic stress; however, their roles in lily are largely unknown. Transcriptome analysis in lily (Lilium longiflorum) led to the identification and isolation of a WRKY-IIe gene, LlWRKY22, which was found to be activated at high temperature and play a positive role in thermotolerance regulation. LlWRKY22 expression was continuously activated by heat stress. We further found that LlWRKY22 protein localized to the nucleus and exhibited transactivation activity in both yeast and plant cells, and that its C terminus contributed to its transactivation activity. Meanwhile, overexpression of LlWRKY22 in lily improved thermotolerance and activated the expression of heat-related LlDREB2B gene; however, silencing of LlWRKY22 exerted the opposite effects. Further analysis revealed that LlWRKY22 directly activated the expression of LlDREB2B by binding to two tandem W-box elements on its promoter. Simultaneously, we also found that LlWRKY22 can directly bind its own promoter, thereby activating its own expression and forming a positive regulatory loop. Combined, our findings demonstrated that LlWRKY22 may be a new regulator of heat stress response and positively participates in the establishment of thermotolerance by activating itself and LlDREB2B.

Physiological and transcriptional responses to heat stress and functional analyses of PsHSPs in tree peony (Paeonia suffruticosa)

Tree peony (Paeonia suffruticosa) is a traditional Chinese flower that is not resistant to high temperatures, and the frequent sunburn during summer limits its normal growth. The lack of understanding of the molecular mechanisms in tree peony has greatly restricted the improvement of novel heat-tolerant varieties. Therefore, we treated tree peony cultivar "Yuhong" (P. suffruticosa "Yuhong") at normal (25°C) and high temperatures (40°C) and sequenced the transcriptomes, to investigate the molecular responsive mechanisms to heat stress. By comparing the transcriptomes, a total of 7,673 differentially expressed genes (DEGs) were detected comprising 4,220 upregulated and 3,453 downregulated genes. Functional annotation showed that the DEGs were mainly related to the metabolic process, cells and binding, carbon metabolism, and endoplasmic reticulum protein processing. qRT-PCR revealed that three sHSP genes (PsHSP17.8, PsHSP21, and PsHSP27.4) were upregulated in the response of tree peony to heat stress. Tissue quantification of the transgenic lines (Arabidopsis thaliana) showed that all three genes were most highly expressed in the leaves. The survival rates of transgenic lines (PsHSP17.8, PsHSP21, and PsHSP27.4) restored to normal growth after high-temperature treatment were 43, 36, and 31%, respectively. In addition, the activity of superoxide dismutase, accumulation of free proline, and chlorophyll level was higher than those of the wild-type lines, while the malondialdehyde content and conductivity were lower, and the membrane lipid peroxidation reaction of the wild-type plant was more intense. Our research found several processes and pathways related to heat resistance in tree peony including metabolic process, single-organism process, phenylpropane biosynthesis pathway, and endoplasmic reticulum protein synthesis pathway. PsHSP17.8, PsHSP21, and PsHSP27.4 improved heat tolerance by increasing SOD activity and proline content. These findings can provide genetic resources for understanding the heat-resistance response of tree peony and benefit future germplasm innovation.

Overexpression of a novel heat-inducible ethylene-responsive factor gene LlERF110 from Lilium longiflorum decreases thermotolerance

AP2/ERF (APETALA2/ethylene-responsive factor) family transcription factors are involved in various plant-specific processes, especially in plant development and response to abiotic stress. However, their roles in thermotolerance are still largely unknown. In the current study, we identified a heat-inducible ERF member LlERF110 from Lilium longiflorum that was rapidly induced by high temperature. Its protein was localized in the nucleus, and transcriptional activation activity was observed in yeast and plant cells. In addition, LlERF110 was able to bind to GCC- and CGG-elements, but not to DRE-elements. Overexpression of LlERF110 conferred delayed bolting and bushy phenotype, with decreased thermotolerance accompanied by a disrupted ROS (reactive oxygen species) homeostasis in transgenic plants. The accumulation of LlERF110 may activate certain repressors related to heat stress response (HSR) and indirectly damage the normal expression of heat stress (HS)-protective genes such as AtHSFA2, which consequently leads to reduced thermotolerance. Our results implied that LlERF110 might function as a heat-inducible gene but may hinder the establishment of thermotolerance.

Starch Degradation and Sucrose Accumulation of Lily Bulbs after Cold Storage

Functional lilies are a group of edible lily cultivars with great potential for landscape application. Low-temperature storage can significantly improve their taste, but the knowledge of this process is largely unknown. In this study, we used the functional lilies ‘Fly Shaohua’ and ‘Fly Tiancheng’ as materials. Through physiological observation and transcriptome analysis during the bulbs’ cold storage, it was found that the starch degradation and sucrose accumulation in bulbs contributed to taste improvement. After 60 d of cold storage, the sucrose accumulation was highest and the starch content was lower in the bulbs, suggesting this time-point was optimal for consumption. Accompanying the fluctuation of sucrose content during cold storage, the enzyme activities of sucrose phosphate synthase and sucrose synthase for sucrose synthesis were increased. Transcriptome analysis showed that many differentially expressed genes (DEGs) were involved in the starch and sucrose metabolism pathway, which might promote the conversion of starch to sucrose in bulbs. In addition, the DEGs involved in dormancy and stress response were also determined during cold storage, which might explain the decreased sucrose accumulation with extended storage time over 60 d due to the energy consumption for dormancy release. Taken together, our results indicated sucrose accumulation was a main factor in the taste improvement of lily bulbs after cold storage, which is attributable to the different gene expression of starch and sucrose metabolism pathways in this process.

Combined Analysis of the Metabolome and Transcriptome to Explore Heat Stress Responses and Adaptation Mechanisms in Celery (Apium graveolens L.)

Celery is an important leafy vegetable that can grow during the cool season and does not tolerate high temperatures. Heat stress is widely acknowledged as one of the main abiotic stresses affecting the growth and yield of celery. The morphological and physiological indices of celery were investigated in the present study to explore the physiological mechanisms in response to high temperatures. Results showed that the antioxidant enzyme activity, proline, relative conductivity, and malondialdehyde were increased, while chlorophyll and the water content of leaves decreased under high-temperature conditions. Short-term heat treatment increased the stomatal conductance to cool off the leaves by transpiration; however, long-term heat treatment led to stomatal closure to prevent leaf dehydration. In addition, high temperature caused a disordered arrangement of palisade tissue and a loose arrangement of spongy tissue in celery leaves. Combined metabolomic and transcriptomic analyses were further used to reveal the regulatory mechanisms in response to heat stress at the molecular level in celery. A total of 1003 differential metabolites were identified and significantly enriched in amino acid metabolism and the tricarboxilic acid (TCA) cycle. Transcriptome sequencing detected 24,264 different genes, including multiple transcription factor families such as HSF, WRKY, MYB, AP2, bZIP, and bHLH family members that were significantly upregulated in response to heat stress, suggesting that these genes were involved in the response to heat stress. In addition, transcriptional and metabolic pathway analyses showed that heat stress inhibited the glycolysis pathway and delayed the TCA cycle but increased the expression of most amino acid synthesis pathways such as proline, arginine, and serine, consistent with the results of physiological indicators. qRT-PCR further showed that the expression pattern was similar to the expression abundance in the transcriptome. The important metabolites and genes in celery that significantly contributed to the response to high temperatures were identified in the present study, which provided the theoretical basis for breeding heat-resistant celery.

The CBL-interacting protein kinase CaCIPK13 positively regulates defence mechanisms against cold stress in pepper

Cold stress is one of the main factors limiting growth and development in pepper. Calcineurin B-like proteins (CBLs) are specific calcium sensors with non-canonical EF-hands to capture calcium signals, and interact with CBL-interacting protein kinases (CIPKs) in the regulation of various stresses. In this study, we isolated a cold-induced CIPK gene from pepper named CaCIPK13, which encodes a protein of 487 amino acids. In silico analyses indicated that CaCIPK13 is a typical CIPK family member with a conserved NAF motif, which consists of the amino acids asparagine, alanine, and phenylalanine. The CaCIPK13 protein was located in the nucleus and plasma membrane. Knock down of CaCIPK13 resulted in enhanced sensitivity to cold stress in pepper, with increased malondialdehyde content, H2O2 accumulation, and electrolyte leakage, while the catalase, peroxidase, superoxide dismutase activities and anthocyanin content were decreased. The transcript level of cold and anthocyanin-related genes was substantially decreased in CaCIPK13-silenced pepper leaves relative to the empty vector control. On the contrary, overexpression of CaCIPK13 in tomato improved cold tolerance via increasing anthocyanin content and activities of reactive oxygen species scavenging enzymes. Furthermore, the interaction of CaCIPK13 with CaCBL1/6/7/8 was Ca2+-dependent. These results indicate that CaCIPK13 plays a positive role in cold tolerance mechanism via CBL-CIPK signalling.

The CaCIPK3 gene positively regulates drought tolerance in pepper

Drought stress is a major agricultural problem restricting the growth, development, and productivity of plants. Calcineurin B-like proteins (CBLs) and CBL-interacting protein kinases (CIPKs) significantly influence the plant response to different stresses. However, the molecular mechanisms of CBL-CIPK in the drought stress response of pepper are still unknown. Here, the function of CaCIPK3 in the regulation of drought stress in pepper (Capsicum annuum L.) was explored. Transcriptomic data and quantitative real-time PCR (qRT-PCR) analysis revealed that CaCIPK3 participates in the response to multiple stresses. Knockdown of CaCIPK3 in pepper increased the sensitivity to mannitol and methyl jasmonate (MeJA). Transient overexpression of CaCIPK3 improved drought tolerance by enhancing the activities of the antioxidant system and positively regulating jasmonate (JA)-related genes. Ectopic expression of CaCIPK3 in tomato also improved drought and MeJA resistance. As the CaCIPK3-interacting partner, CaCBL2 positively influenced drought resistance. Additionally, CaWRKY1 and CaWRKY41 directly bound the CaCIPK3 promoter to influence its expression. This study shows that CaCIPK3 acts as a positive regulator in drought stress resistance via the CBL-CIPK network to regulate MeJA signaling and the antioxidant defense system.

A Novel R2R3-MYB Gene LoMYB33 From Lily Is Specifically Expressed in Anthers and Plays a Role in Pollen Development

Lily (Lilium spp.) is an important commercial flower crop, but its market popularity and applications are adversely affected by severe pollen pollution. Many studies have examined pollen development in model plants, but few studies have been conducted on flower crops such as lily. GAMYBs are a class of R2R3-MYB transcription factors and play important roles in plant development and biotic resistance; their functions vary in different pathways, and many of them are involved in anther development. However, their function and regulatory role in lily remain unclear. Here, the GAMYB homolog LoMYB33 was isolated and identified from lily. The open reading frame of LoMYB33 was 1620 bp and encoded a protein with 539 amino acids localized in the nucleus and cytoplasm. Protein sequence alignment showed that LoMYB33 contained a conserved R2R3 domain and three BOX motifs (BOX1, BOX2, and BOX3), which were unique to the GAMYB family. LoMYB33 had transcriptional activation activity, and its transactivation domain was located within 90 amino acids of the C-terminal. LoMYB33 was highly expressed during the late stages of anther development, especially in pollen. Analysis of the promoter activity of LoMYB33 in transgenic Arabidopsis revealed that the LoMYB33 promoter was highly activated in the pollen of stage 12 to 13 flowers. Overexpression of LoMYB33 in Arabidopsis significantly retarded growth; the excess accumulation of LoMYB33 also negatively affected normal anther development, which generated fewer pollen grains and resulted in partial male sterility in transgenic plants. Silencing of LoMYB33 in lily also greatly decreased the amount of pollen. Overall, our results suggested that LoMYB33 might play an important role in the anther development and pollen formation of lily.

Prediction of temperature tolerance in Lilium based on distribution and climate data

There are plenty publications providing guidance for resistant taxa selection by experimental researches while the number of experimental taxa is often restricted. In this study, we presented a concise method to predict the temperature tolerance of wild Lilium in China based on open access botanical and associated environmental datasets. We divided all taxa into five groups to present an overview of Lilium's adaptability to temperature stress. Furthermore, according to the environmental conditions, the prediction of heat and cold tolerance in Lilium was made based on the combined multi-sources data at taxon level. Thirteen taxa with potential temperature tolerance were predicted of 42 taxa. The results showed that not only is tolerance prediction created by large-scale data analysis possible, but that it may supplement traditional laboratory researches with a comprehensive list of taxa.

Genome-Wide Transcriptomic Identification and Functional Insight of Lily WRKY Genes Responding to Botrytis Fungal Disease

Genome-wide transcriptome analysis using RNA-Seq of Lilium longiflorum revealed valuable genes responding to biotic stresses. WRKY transcription factors are regulatory proteins playing essential roles in defense processes under environmental stresses, causing considerable losses in flower quality and production. Thirty-eight WRKY genes were identified from the transcriptomic profile from lily genotypes, exhibiting leaf blight caused by Botrytis elliptica. Lily WRKYs have a highly conserved motif, WRKYGQK, with a common variant, WRKYGKK. Phylogeny of LlWRKYs with homologous genes from other representative plant species classified them into three groups- I, II, and III consisting of seven, 22, and nine genes, respectively. Base on functional annotation, 22 LlWRKY genes were associated with biotic stress, nine with abiotic stress, and seven with others. Sixteen unique LlWRKY were studied to investigate responses to stress conditions using gene expression under biotic and abiotic stress treatments. Five genes-LlWRKY3, LlWRKY4, LlWRKY5, LlWRKY10, and LlWRKY12-were substantially upregulated, proving to be biotic stress-responsive genes in vivo and in vitro conditions. Moreover, the expression patterns of LlWRKY genes varied in response to drought, heat, cold, and different developmental stages or tissues. Overall, our study provides structural and molecular insights into LlWRKY genes for use in the genetic engineering in Lilium against Botrytis disease.