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Abstract Background Dirigent (DIR) genes play a key role in the development of organic products in plants. They confer conformational influence on processes that lack stereoselectivity and regioselectivity through processes that are mostly understood. They are required to produce lignans, which are a unique and widely distributed family of plant secondary metabolites with intriguing pharmacological characteristics and potential role in plant development. DIR genes are implicated in the process of lignification and protect plants from environmental stresses, including biotic and abiotic stresses. Nevertheless, no research has been performed on the DIR gene family in Solanum lycopersicum. This study provides detailed information on the DIR gene family in S. lycopersicum. Methods and results The conserved domain analysis, phylogenetic analysis, evolutionary adaptation, cis-acting elements, proteomic analysis, signal peptide detection, transmembrane potential analysis, sequence identity and similarity analysis, gene assembly, genomic localization, duplication of gene analysis, and evolutionary linkage of 31 potential DIR genes were studied. All these analyses provide a deep understanding of DIR genes in the S. lycopersicum genome that will provide a useful reference for further functional analysis of the DIR genes in S. lycopersicum. Conclusion This research provides an in-depth and comprehensive explanation of the detailed process and structural characterization of DIR genes in the genome of S. lycopersicum, laying the groundwork for future plant genetic engineering and crop development exploration. This work will provide valuable information for identifying DIR genes in higher plants and support future research on the DIR gene family.

Space exploration and interstellar migration are important strategies for long-term human survival. However, extreme environmental conditions, such as space radiation and microgravity, can cause adverse effects, including DNA damage, cerebrovascular disease, osteoporosis, and muscle atrophy, which would require prophylactic and remedial treatment en route. Production of oral drugs in situ is therefore critical for interstellar travel and can be achieved through industrial production utilizing microalgae, which offers high production efficiency, edibility, resource minimization, adaptability, stress tolerance, and genetic manipulation ease. Synthetic biological techniques using microalgae as a chassis offer several advantages in producing natural products, including availability of biosynthetic precursors, potential for synthesizing natural metabolites, superior quality and efficiency, environmental protection, and sustainable development. This article explores the advantages of bioproduction from microalgal chassis using synthetic biological techniques, suitability of microalgal bioreactor-based cell factories for producing value-added natural metabolites, and prospects and applications of microalgae in interstellar travel.

Cottonseed is a by-product of cotton industry, but its broad application in human diets has not been fully elucidated. This study aims to analyse the nutritional composition of cotton sprouts and investigate metabolic and transcriptomic differences under light and darkness. The findings revealed that the glanded ZM41 yellow cotton sprouts were rich in protein (2.8 %), vitamin E (0.443 mg/100 g), and minerals, with < 0.01 % free gossypol. Moreover, protein, aspartic acid (1,026 mg/100 g), and serine (136 mg/100 g) reached their highest levels in nine-day-old sprouts, while no significant differences were observed in the other nutrients on the 7th, 9th, or 11th day. The average quantitative values of 64 cottonseed varieties found gossypol (27.9 mg/kg), protein (3.6 %), potassium (1,487.3 mg/kg), calcium (506.2 mg/kg) and magnesium (330.2 mg/kg). Integrated metabolome and transcriptome analyses revealed that 317 out of 1,880 metabolites were differentially accumulated between light and dark conditions, wherein the downregulation of structural genes encoding CHI, F3H, FLS, DFR, F3′H, ANS, LAR and ANR resulted in decreased flavonoid levels in dark-cultivated sprouts, while the upregulation of HMGR and 2-ODD-1 enhanced the biosynthesis of gossypol. This study provides insights into the nutritional and metabolic aspects of cotton sprouts, offering a reference for potential commercial applications.

Light quality has significant effects on the growth and metabolite accumulation of algal cells. However, the related mechanism has not been fully elucidated. This study reveals that both red and blue light can promote the growth and biomass accumulation of Chlorella pyrenoidosa, with the enhancing effect of blue light being more pronounced. Cultivation under blue light reduced the content of total carbohydrate in Chlorella pyrenoidosa, while increasing the content of protein and lipid. Conversely, red light decreased the content of protein and increased the content of carbohydrate and lipid. Blue light induces a shift in carbon flux from carbohydrate to protein, while red light transfers carbon flux from protein to lipid. Transcriptomic and metabolomic analysis indicated that both red and blue light positively regulate lipid synthesis in Chlorella pyrenoidosa, but they exhibited distinct impacts on the fatty acid compositions. These findings suggest that manipulating light qualities can modulate carbon metabolic pathways, potentially converting protein into lipid in Chlorella pyrenoidosa.

Safflower (Carthamus tinctorius L.), a member of the Asteraceae family, is widely used in traditional herbal medicine. This review summarized agronomic conditions, genetic diversity, clinical application, and phytochemicals and pharmacological properties of safflower. The genetic diversity of the plant is rich. Abundant in secondary metabolites like flavonoids, phenols, alkaloids, polysaccharides, fatty acids, polyacetylene, and other bioactive components, the medicinal plant is effective for treating cardiovascular diseases, neurodegenerative diseases, and respiratory diseases. Especially, Hydroxysafflor yellow A (HYSA) has a variety of pharmacological effects. In terms of treatment and prevention of some space sickness in space travel, safflower could be a potential therapeutic agent. Further studies are still required to support the development of safflower in medicine. Our review indicates that safflower is an important medicinal plant and research prospects regarding safflower are very broad and worthy of further investigation.

HxTx-Hv1h, a neurotoxic peptide derived from spider venom, has been developed for use in commercial biopesticide formulations. Cell Penetrating Peptides (CPPs) are short peptides that facilitate the translocation of various biomolecules across cellular membranes. Here, we evaluated the aphidicidal efficacy of a conjugated peptide, HxTx-Hv1h/CPP-1838, created by fusing HxTx-Hv1h with CPP-1838. Additionally, we aimed to establish a robust recombinant expression system for HxTx-Hv1h/CPP-1838. We successfully achieved the secretory production of HxTx-Hv1h, its fusion with Galanthus nivalis agglutinin (GNA) forming HxTx-Hv1h/GNA and HxTx-Hv1h/CPP-1838 in yeast. Purified HxTx-Hv1h exhibited contact toxicity against Megoura crassicauda, with a 48 h median lethal concentration (LC50) of 860.5 μg/mL. Fusion with GNA or CPP-1838 significantly enhanced its aphidicidal potency, reducing the LC50 to 683.5 μg/mL and 465.2 μg/mL, respectively. The aphidicidal efficacy was further improved with the addition of surfactant, decreasing the LC50 of HxTx-Hv1h/CPP-1838 to 66.7 μg/mL—over four times lower compared to HxTx-Hv1h alone. Furthermore, we engineered HxTx-Hv1h/CPP-1838 multi-copy expression vectors utilizing the BglBrick assembly method and achieved high-level recombinant production in laboratory-scale fermentation. This study is the first to document a CPP fusion strategy that enhances the transdermal aphidicidal activity of a natural toxin like HxTx-Hv1h and opens up the possibility of exploring the recombinant production of HxTx-Hv1h/CPP-1838 for potential applications.

Introduction: During the arms race between plants and pathogens, pathogenesis-related proteins (PR) in host plants play a crucial role in disease resistance, especially PR1. PR1 constitute a secretory peptide family, and their role in plant defense has been widely demonstrated in both hosts and in vitro. However, the mechanisms by which they control host-pathogen interactions and the nature of their targets within the pathogen remain poorly understood. Objectives: The present study was aimed to investigate the anti-oomycete activity of secretory PR1 proteins and elaborate their underlying mechanisms. Methods: This study was conducted in the potato-Phytophthora infestans pathosystem. After being induced by the pathogen infection, the cross-kingdom translocation of secretory PR1 was demonstrated by histochemical assays and western blot, and their targets in P. infestans were identified by yeast-two-hybrid assays, bimolecular fluorescence complementation assays, and co-immunoprecipitation assay. Results: The results showed that the expression of secretory PR1-encoding genes was induced during pathogen infection, and the host could deliver PR1 into P. infestans to inhibit its vegetative growth and pathogenicity. The translocated secretory PR1 targeted the subunits of the AMPK kinase complex in P. infestans, thus affecting the AMPK-driven phosphorylation of downstream target proteins, preventing ROS homeostasis, and down-regulating the expression of RxLR effectors. Conclusion: The results provide novel insights into the molecular function of PR1 in protecting plants against pathogen infection, and uncover a potential target for preventing pre- and post-harvest late blight.

The production of cotton is negatively affected by salinity. For this purpose, 8 parents and their 16 F1 hybrids were evaluated under saline stress (15 dSm−1) in Line × Tester fashion. Mean values of plant height, number of bolls plant−1, boll weight, lint weight, seed cotton yield plant−1, seed index, no. of seeds boll−1, seed mass boll−1, lint mass boll−1, seed volume per 100 seeds, fiber strength, fiber length, lint%, K+, K+/Na+ ratio, CAT, TSP, chlorophyll a, b, and relative water contents decreased under salt stress whilst the values of lint index, seed density, fiber fineness, Na+, H2O2, SOD, POD carotenoids, malondialdehyde, phenolic contents, ascorbic acid, and flavonoids increased under saline conditions. Under saline MS-71× CRS-2007, MS-71× KAHKASHAN, and IUB-65 × FH-312 exhibited performed better than other genotypes for most traits. For fiber quality traits IUB-65× CRS-2007 and IUB-65× FH-312 showed the highest value under salt stress. Improved identified cotton genotypes can enhance our capacity to grow cotton in salt-affected soils and the key morpho-biochemical traits can potentially be exploited to obtain higher and more stable crops yield under stressed environments.

Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has been spreading globally for over 2 years, causing serious contagious disease and incalculable damage. The introduction of vaccines has slowed the spread of SARS‐CoV‐2 to some extent, but there remains a need for specific and effective treatment. The high chemical diversity and safety profiles of natural products make them a potential source of effective anti‐SARS‐CoV‐2 drugs. Cotton plant is one of the most important economic and medical crops and is the source of a large number of antiviral phytochemicals. In this work, we used SARS‐CoV‐2 main protein (Mpro) as the target to identify potential anti‐SARS‐CoV‐2 natural products in cotton. An in vitro assay showed that of all cotton tissues examined, cotton flower extracts (CFs) exhibited optimal inhibitory effects against Mpro. We proceeded to use the CF metabolite database to screen natural Mpro inhibitors by combining virtual screening and biochemical assays. We identified that several CF natural products, including astragalin, myricitrin, and astilbin, significantly inhibited Mpro with half‐maximal inhibitory concentrations (IC50s) of 0.13, 10.73, and 7.92 μm, respectively. These findings may serve as a basis for further studies into the suitability of cotton as a source of potential therapeutics for SARS‐CoV‐2.

Cotton (Gossypium hirsutum L.) productivity is decreasing alarmingly by salinity. For genetic analysis of cotton response to salinity 8 parental genotypes and their 16 F1 crosses were evaluated in Line × Tester fashion under normal and salt stress 15 dSm−1. Data were recorded for plant height, number of bolls plant−1, boll weight, lint weight, seed cotton yield plant−1, lint percentage, seed index, lint index, number of seeds boll−1, seed mass boll−1, lint mass boll−1, lint mass per seed, seed volume 100−1 seeds, seed surface area, ionic ratio, fiber strength, fiber length, fiber fineness, GOT %, SOD, POD, CAT, TSP, and H2O2. The results showed that SCA estimates were higher than the GCA indicating the preponderance of non-additive gene action. Kahkashan, MS-71, and CRS-2007 were found good general combiner whereas FH-114 × FH-312 was found the best specific combiner. FH-114 × KAHKASHAN and FH-114 × FH-312 demonstrated significant heterosis for most traits under normal and salt stress conditions. The present study revealed that salt tolerance ability is controlled by a few dominant genes in the identified genotypes.

Introduction: Biofungicides with low toxicity and high efficiency are a global priority for sustainable agricultural development. Phytohormone salicylic acid (SA) is an ancient medicine against various diseases in humans and activates the immune system in plants, but little is known of its function as a biofungicide. Objectives: Here, Fusarium oxysporum, the causal agent of devastating Fusarium wilt and immunodepressed patients, was used as a model system to explore whether SA can enter the pathogen cells and suppress key targets of the pathogen. Methods: Oxford Nanopore MinION sequencing and high-throughput chromosome conformation capture (Hi-C) sequencing were used to analyzed the genome of F. oxysporum. In addition, RNA-seq, qRT-PCR, and western blotting were conducted to detect gene and protein expression levels. Results: We isolated and sequenced the genome of F. oxysporum from potato dry rot, and the F. oxysporum included 12 chromosomes and 52.3 Mb genomic length. Pharmacological assays showed that exogenous application of SA can efficiently arrest hyphal growth, spore production, and pathogenicity of F. oxysporum, whereas endogenous salicylate hydroxylases significantly detoxify SA. The synergistic growth inhibition of F. oxysporum was observed when SA was combined with rapamycin. Kinase assays showed that SA inhibits FoTOR complex 1 (FoTORC1) by activating FoSNF1 in vivo. Transgenic potato plants with the interference of FoTOR1 and FoSAH1 genes inhibited the invasive growth of hyphae and significantly prevented the occurrence of Fusarium wilt. Conclusion: This study revealed the underlying mechanisms of SA against F. oxysporum and provided insights into SA in controlling various fungal diseases by targeting the SNF1-TORC1 pathway of pathogens.

Abstract Transgenic technology played a crucial role in developing insect-resistant plants resulting in the reduced application of pesticides. This article reports the expression of two cry proteins (Cry3Bb1 and Cry3) in cotton for enhanced resistance against chewing insect pests. The aforementioned genes were synthetically developed and were cloned under appropriate regulatory sequences followed by transformation into Eagle-2 genotype (Gossypium hirsutum) of cotton through shoot apex-cut Agro-infiltration. The transgene integration was validated by polymerase chain reaction using primers flanking the aforementioned cry genes. Transgene expression was assessed by qRT-PCR using GADPH as a reference gene. The relative fold expression analyses revealed the highest expression of the transgene(s) in M1 plants, which is a 4.5-fold expression (Cry3 + Cry3Bb1) followed by M3 (fold expression, 3.0) (Cry3Bb1) and M2 (fold expression, 2.5) (Cry3) transformants of cotton. The confirmed transgenic plants were exposed to insect pests, pink bollworm (Pectinophora gossypiella), and army bollworm (Helicoverpa armigera). Bioassay results revealed that 60% mortality was observed against pink bollworm, and 75% mortality was observed against army bollworm in transgenic plants containing both Cry3Bb1 and Cry3 genes (M1 transgenic plants). In M2 transgenic plants containing only the Cry3Bb1 gene, the mortality was observed to be 40% in the pink bollworm population, whereas 45% mortality was observed in the army bollworm population. In the case of M3 transgenic plants containing single gene-Cry3, the mortality was 20% in the pink bollworm population, whereas 30% mortality was observed in the army bollworm population. Almost no mortality was observed in non-transgenic Eagle-2 control plants. Hence, the developed cotton transformants have improved resistance against chewing insect pests.

Glycogen synthase kinase 3 (GSK3) family members are evolutionally conserved Ser/Thr protein kinases in mammals and plants. In plants, the GSK3s function as signaling hubs to integrate the perception and transduction of diverse signals required for plant development. Despite their role in the regulation of plant growth and development, emerging research has shed light on their multilayer function in plant stress responses. Here we review recent advances in the regulatory network of GSK3s and the involvement of GSK3s in plant adaptation to various abiotic and biotic stresses. We also discuss the molecular mechanisms underlying how plants cope with environmental stresses through GSK3s-hormones crosstalk, a pivotal biochemical pathway in plant stress responses. We believe that our overview of the versatile physiological functions of GSK3s and underlined molecular mechanism of GSK3s in plant stress response will not only opens further research on this important topic but also provide opportunities for developing stress-resilient crops through the use of genetic engineering technology.

Abstract Background AP2/ERF transcription factors are important in a variety of biological activities, including plant growth, development, and responses to biotic and abiotic stressors. However, little study has been done on cotton’s AP2/ERF genes, although cotton is an essential fibre crop. We were able to examine the tissue and expression patterns of AP2/ERF genes in cotton on a genome-wide basis because of the recently published whole genome sequence of cotton. Genome-wide analysis of ERF gene family within two diploid species (G. arboreum & G. raimondii) and two tetraploid species (G. barbadense, G. hirsutum) was performed. Results A total of 118, 120, 213, 220 genes containing the sequence of single AP2 domain were identified in G. arboreum, G. raimondii, G. barbadense and G. hirsutum respectively. The identified genes were unevenly distributed across 13/26 chromosomes of A and D genomes of cotton. Synteny and collinearity analysis revealed that segmental duplications may have played crucial roles in the expansion of the cotton ERF gene family, as well as tandem duplications played a minor role. Cis-acting elements of the promoter sites of Ghi-ERFs genes predict the involvement in multiple hormone responses and abiotic stresses. Transcriptome and qRT-PCR analysis revealed that Ghi-ERF-2D.6, Ghi-ERF-12D.13, Ghi-ERF-6D.1, Ghi-ERF-7A.6 and Ghi-ERF-11D.5 are candidate genes against salinity tolerance in upland cotton. Conclusion Overwhelmingly, the present study paves the way to better understand the evolution of cotton ERF genes and lays a foundation for future investigation of ERF genes in improving salinity stress tolerance in cotton.

Abstract Outbreaks of coronaviruses (CoVs), especially severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), have posed serious threats to humans and animals, which urgently calls for effective broad‐spectrum antivirals. RNA‐dependent RNA polymerase (RdRp) plays an essential role in viral RNA synthesis and is an ideal pan‐coronaviral therapeutic target. Herein, based on cryo‐electron microscopy and biochemical approaches, gossypol (GOS) is identified from 881 natural products to directly block SARS‐CoV‐2 RdRp, thus inhibiting SARS‐CoV‐2 replication in both cellular and mouse infection models. GOS also acts as a potent inhibitor against the SARS‐CoV‐2 variant of concern (VOC) and exerts same inhibitory effects toward mutated RdRps of VOCs as the RdRp of the original SARS‐CoV‐2. Moreover, that the RdRp inhibitor GOS has broad‐spectrum anti‐coronavirus activity against alphacoronaviruses (porcine epidemic diarrhea virus and swine acute diarrhea syndrome coronavirus), betacoronaviruses (SARS‐CoV‐2), gammacoronaviruses (avian infectious bronchitis virus), and deltacoronaviruses (porcine deltacoronavirus) is showed. The findings demonstrate that GOS may serve as a promising lead compound for combating the ongoing COVID‐19 pandemic and other coronavirus outbreaks.

Abstract Background The tricarboxylic acid (TCA) cycle is crucial for energy supply in animal, plant, and microbial cells. It is not only the main pathway of carbohydrate catabolism but also the final pathway of lipid and protein catabolism. Some TCA genes have been found to play important roles in the growth and development of tomato and potato, but no comprehensive study of TCA cycle genes in Solanaceae crops has been reported. Results In this study, we analyzed TCA cycle genes in four important Solanaceae vegetable crops (potato (Solanum tuberosum), tomato (Solanum lycopersicum), eggplant (Solanum melongena), and pepper (Capsicum annuum)) based on comparative genomics. The four Solanaceae crops had a total of 180 TCA cycle genes: 43 in potato, 44 in tomato, 40 in eggplant, and 53 in pepper. Phylogenetic analysis, collinearity analysis, and tissue expression patterns revealed the conservation of and differences in TCA cycle genes between the four Solanaceae crops and found that there were unique subgroup members in Solanaceae crops that were independent of Arabidopsis genes. The expression analysis of potato TCA cycle genes showed that (1) they were widely expressed in various tissues, and some transcripts like Soltu.DM.01G003320.1(SCoAL) and Soltu.DM.04G021520.1 (SDH) mainly accumulate in vegetative organs, and some transcripts such as Soltu.DM.12G005620.3 (SDH) and Soltu.DM.02G007400.4 (MDH) are preferentially expressed in reproductive organs; (2) several transcripts can be significantly induced by hormones, such as Soltu.DM.08G023870.2 (IDH) and Soltu.DM.06G029290.1 (SDH) under ABA treatment, and Soltu.DM.07G021850.2 (CSY) and Soltu.DM.09G026740.1 (MDH) under BAP treatment, and Soltu.DM.02G000940.1 (IDH) and Soltu.DM.01G031350.4 (MDH) under GA treatment; (3) Soltu.DM.11G024650.1 (SDH) can be upregulated by the three disease resistance inducers including Phytophthora infestans, acibenzolar-S-methyl (BTH), and DL-β-amino-n-butyric acid (BABA); and (4) the levels of Soltu.DM.01G045790.1 (MDH), Soltu.DM.01G028520.3 (CSY), and Soltu.DM.12G028700.1 (CSY) can be activated by both NaCl and mannitol. The subcellular localization results of three potato citrate synthases showed that Soltu.DM.01G028520.3 was localized in mitochondria, while Soltu.DM.12G028700.1 and Soltu.DM.07G021850.1 were localized in the cytoplasm. Conclusions This study provides a scientific foundation for the comprehensive understanding and functional studies of TCA cycle genes in Solanaceae crops and reveals their potential roles in potato growth, development, and stress response.

To understand the effect of heat stress on morphology and physiology of the cotton, eight cotton genotypes with their 15F1 hybrids (five lines, three testers) were grown in the field conditions under randomized complete block design (RCBD) with two treatments i.e. normal and high-temperature stresses with two replications followed by split-plot arrangement. Data were collected for biochemical and yield-related parameters. Mean values of all studied traits were reduced significantly under high-temperature stress whilst the mean value of lint%, catalase activity, total soluble proteins, peroxidase, and carotenoids were increased under high-temperature. Under both conditions, the number of bolls, boll weight, seed cotton yield, lint index, seed mass per boll, hydrogen peroxide content, catalase activity, total soluble proteins, carotenoids, and chlorophyll contents had high heritability values along with high genetic advance percent mean which revealed, these traits were controlled by additive gene action. The lint%, seed index, short fiber index, fiber strength, fiber fineness, upper half mean length and peroxidase activity had high heritability with moderate genetic advance under heat stress conditions which showed, these traits were controlled by non-additive gene action. Under both temperature conditions, FH-458, IUB-65, CRS-2, and FH-313 were good general combiners for physicochemical and yield-related traits. The cross combination of IUB-013× CRS-2 and FH-458× FH-313 were good specific combiner for plant height and seed cotton yield whilst for fiber quality and biochemical traits, the best specific combiners were VH-329× FH-313 and IUB-013× CRS-2. These identified parents and cross combinations might be used for improving already present commercial varieties under high-temperature stress.

In the recent past, the production of wastewater from domestic and industrial sources steadily increased through population growth, urbanization, the Industrial Revolution, and economic development. In the world, 80% of wastewater consists of several harmful substances and hazardous chemicals that cause many deadly effects on human beings as well as ecosystems. So, the elimination of this toxic substance before discarding it into landfills is utilized as an alternative source of water which is an emerging need. Using treated wastewater for agricultural purposes is an excellent approach to rendering wastewater beneficial. As the quantity of wastewater grows, it becomes necessity to redistribute the water in a beneficial way. The rapidly increasing world population will undoubtedly increase the food demand, which directly requires more water for irrigation purposes. The rapidly increasing world population rate will undoubtedly demand an increased food production rate, which directly impacts agricultural water usage. In order to achieve sustainability in terms of agricultural water usage, alternative water resources should be explored. In this review, we tried to focus on summarizing all the leading studies in the field of wastewater utilization, the most prominent treatment methods, and a benchmarking of their technical efficiency in agriculture with special emphasis on agriculture in the marginal lands, with special emphasis on the United Arab Emirates.

Abstract Background Cotton (Gossypium hirsutum L.) is grown for fiber and oil purposes in tropical and sub-tropical areas of the world. Pakistan is the 4th largest producer of cotton. It has a significant contribution in the GDP of Pakistan. Therefore, the present study was performed to assess the genetic variations and genetic diversity of yield and fiber quality traits in cotton and to analyze the associations present among them. Results Analysis of variance exhibited significant variation for all studied traits except total number of nodes and the height to node ratio. The phenotypic coefficient of variation was higher than the genotypic coefficient of variation for all studied traits. Plant height, monopodial branches, total number of bolls, lint index, seed index, and seed cotton yield displayed high heritabilities in a broad sense with maximum genetic advance. Correlation analysis revealed that seed cotton yield had a significant positive association with plant height, the number of monopodial branches, the number of sympodial branches, ginning outturn (GOT), the number of bolls, seed per boll, seed index, uniformity index, the number of sympodial branches, reflectance, and seed index at the genotypic level while a significant positive relationship was observed with plant height, the number of sympodial branches, boll number, and GOT. Plant height, monopodial branches, GOT, boll weight, seeds per boll, and short fiber index exerted direct positive effects on seed cotton yield. The first 6 principal component analysis (PCs) out of the total fourteen PCs displayed eigenvalues (> 1) and had maximum share to total variability (82.79%). The attributes that had maximum share to total divergence included plant height, uniformity index, the number of sympodial branches, seed per boll, GOT, seed cotton yield, and short fiber index. Conclusion The genotype AA-802, IUB-13, FH-159, FH-458, and CIM-595 were genetically diverse for most of the yield and fiber quality traits and could be utilized for the selection of better performing genotypes for further improvement.

The logistical and practical challenges of supplying food for long-term space missions are substantial. In this comment, the authors discuss potential biotechnological approaches that could be used to aid the production of food crops in space.

Abstract The introduction of Bacillus thuringiensis (Bt) cotton has reduced the burden of pests without harming the environment and human health. However, the efficacy of Bt cotton has decreased due to field-evolved resistance in insect pests over time. In this review, we have discussed various factors that facilitate the evolution of resistance in cotton pests. Currently, different strategies like pyramided cotton expressing two or more distinct Bt toxin genes, refuge strategy, releasing of sterile insects, and gene silencing by RNAi are being used to control insect pests. Pyramided cotton has shown resistance against different cotton pests. The multiple genes pyramiding and silencing (MGPS) approach has been proposed for the management of cotton pests. The genome information of cotton pests is necessary for the development of MGPS-based cotton. The expression cassettes against various essential genes involved in defense, detoxification, digestion, and development of cotton pests will successfully obtain favorable agronomic characters for crop protection and production. The MGPS involves the construction of transformable artificial chromosomes, that can express multiple distinct Bt toxins and RNAi to knockdown various essential target genes to control pests. The evolution of resistance in cotton pests will be delayed or blocked by the synergistic action of high dose of Bt toxins and RNAi as well as compliance of refuge requirement.

Paphiopedilum (Orchidaceae) is one of the world’s most popular orchids that is found in tropical and subtropical forests and has an enormous ornamental value. SEPALLATA-like (SEP-like) MADS-box genes are responsible for floral organ specification. In this study, three SEP-like MADS-box genes, PhSEP1, PhSEP2, and PhSEP3, were identified in Paphiopedilum henryanum. These genes were 732–916 bp, with conserved SEPI and SEPII motifs. Phylogenetic analysis revealed that PhSEP genes were evolutionarily closer to the core eudicot SEP3 lineage, whereas none of them belonged to core eudicot SEP1/2/4 clades. PhSEP genes displayed non-ubiquitous expression, which was detectable across all floral organs at all developmental stages of the flower buds. Furthermore, subcellular localization experiments revealed the localization of PhSEP proteins in the nucleus. Yeast two-hybrid assays revealed no self-activation of PhSEPs. The protein–protein interactions revealed that PhSEPs possibly interact with B-class DEFICIENS-like and E-class MADS-box proteins. Our study suggests that the three SEP-like genes may play key roles in flower development in P. henryanum, which will improve our understanding of the roles of the SEP-like MADS-box gene family and provide crucial insights into the mechanisms underlying floral development in orchids.

Lack of precise information about the candidate genes involved in a complex quantitative trait is a major obstacle in the cotton fiber quality improvement, and thus, overall genetic gain in conventional phenotypic selection is low. Recent molecular interventions and advancements in genome sequencing have led to the development of high-throughput molecular markers, quantitative trait locus (QTL) fine mapping, and single nucleotide polymorphisms (SNPs). These advanced tools have resolved the existing bottlenecks in trait-specific breeding. This review demonstrates the significance of chromosomes 3, 7, 9, 11, and 12 of sub-genomes A and D carrying candidate genes for fiber quality. However, chromosome 7 carrying SNPs for stable and potent QTLs related to fiber quality provides great insights for fiber quality-targeted research. This information can be validated by marker-assisted selection (MAS) and transgene in Arabidopsis and subsequently in cotton.

Viruses typically hijack the cellular machinery of their hosts for successful infection and replication, while the hosts protect themselves against viral invasion through a variety of defense responses, including autophagy, an evolutionarily ancient catabolic pathway conserved from plants to animals. Double-membrane vesicles called autophagosomes transport trapped viral cargo to lysosomes or vacuoles for degradation. However, during an ongoing evolutionary arms race, viruses have acquired a strong ability to disrupt or even exploit the autophagy machinery of their hosts for successful invasion. In this review, we analyze the universal role of autophagy in antiviral defenses in animals and plants and summarize how viruses evade host immune responses by disrupting and manipulating host autophagy. The review provides novel insights into the role of autophagy in virus–host interactions and offers potential targets for the prevention and control of viral infection in both plants and animals.

The ever-changing global environment currently includes an increasing ambient temperature that can be a devastating stress for organisms. Plants, being sessile, are adversely affected by heat stress in their physiology, development, growth, and ultimately yield. Since little is known about the response of biochemical traits to high-temperature ambiance, we evaluated eight parental lines (five lines and three testers) and their 15 F1 hybrids under normal and high-temperature stress to assess the impact of these conditions over 2 consecutive years. The research was performed under a triplicate randomized complete block design including a split-plot arrangement. Data were recorded for agronomic, biochemical, and fiber quality traits. Mean values of agronomic traits were significantly reduced under heat stress conditions, while hydrogen peroxide, peroxidase, total soluble protein, superoxide dismutase, catalase (CAT), carotenoids, and fiber strength displayed higher mean values under heat stress conditions. Under both conditions, high genetic advance and high heritability were observed for seed cotton yield (SCY), CAT, micronaire value, plant height, and chlorophyll-a and b content, indicating that an additive type of gene action controls these traits under both the conditions. For more insights into variation, Pearson correlation analysis and principal component analysis (PCA) were performed. Significant positive associations were observed among agronomic, biochemical, and fiber quality-related traits. The multivariate analyses involving hierarchical clustering and PCA classified the 23 experimental genotypes into four groups under normal and high-temperature stress conditions. Under both conditions, the F1 hybrid genotype FB-SHAHEEN × JSQ WHITE GOLD followed by Ghuari-1, CCRI-24, Eagle-2 × FB-Falcon, Ghuari-1 × JSQ White Gold, and Eagle-2 exhibited better performance in response to high-temperature stress regarding the agronomic and fiber quality-related traits. The mentioned genotypes could be utilized in future cotton breeding programs to enhance heat tolerance and improve cotton yield and productivity through resistance to environmental stressors.

Abstract Background The tricarboxylic acid (TCA) cycle is crucial for cellular energy metabolism and carbon skeleton supply. However, the detailed functions of the maize TCA cycle genes remain unclear. Results In this study, 91 TCA genes were identified in maize by a homology search, and they were distributed on 10 chromosomes and 1 contig. Phylogenetic results showed that almost all maize TCA genes could be classified into eight major clades according to their enzyme families. Sequence alignment revealed that several genes in the same subunit shared high protein sequence similarity. The results of cis-acting element analysis suggested that several TCA genes might be involved in signal transduction and plant growth. Expression profile analysis showed that many maize TCA cycle genes were expressed in specific tissues, and replicate genes always shared similar expression patterns. Moreover, qPCR analysis revealed that some TCA genes were highly expressed in the anthers at the microspore meiosis phase. In addition, we predicted the potential interaction networks among the maize TCA genes. Next, we cloned five TCA genes located on different TCA enzyme complexes, Zm00001d008244 (isocitrate dehydrogenase, IDH), Zm00001d017258 (succinyl-CoA synthetase, SCoAL), Zm00001d025258 (α-ketoglutarate dehydrogenase, αKGDH), Zm00001d027558 (aconitase, ACO) and Zm00001d044042 (malate dehydrogenase, MDH). Confocal observation showed that their protein products were mainly localized to the mitochondria; however, Zm00001d025258 and Zm00001d027558 were also distributed in the nucleus, and Zm00001d017258 and Zm00001d044042 were also located in other unknown positions in the cytoplasm. Through the bimolecular fluorescent complimentary (BiFC) method, it was determined that Zm00001d027558 and Zm00001d044042 could form homologous dimers, and both homologous dimers were mainly distributed in the mitochondria. However, no heterodimers were detected between these five genes. Finally, Arabidopsis lines overexpressing the above five genes were constructed, and those transgenic lines exhibited altered primary root length, salt tolerance, and fertility. Conclusion Sequence compositions, duplication patterns, phylogenetic relationships, cis-elements, expression patterns, and interaction networks were investigated for all maize TCA cycle genes. Five maize TCA genes were overexpressed in Arabidopsis, and they could alter primary root length, salt tolerance, and fertility. In conclusion, our findings may help to reveal the molecular function of the TCA genes in maize.

Molecular interventions have helped to explore the genes involved in fiber length, fiber strength, and other quality parameters with improved characteristics, particularly in cotton. The current study is an extension and functional validation of previous findings that Gh_A07G1537 influences fiber length in cotton using a chromosomal segment substitution line MBI7747 through RNA-seq data. The recombinant Gh_A07G1537 derived from the MBI7747 line was over-expressed in CCRI24, a genotype with a low profile of fiber quality parameters. Putative transformants were selected on MS medium containing hygromycin (25mg/ml), acclimatized, and shifted to a greenhouse for further growth and proliferation. Transgene integration was validated through PCR and Southern Blot analysis. Stable integration of the transgene (ΔGh_A07G1537) was validated by tracking its expression in different generations (T0, T1, and T2) of transformed cotton plants. It was found to be 2.97-, 2.86-, and 2.92-folds higher expression in T0, T1, and T2 plants, respectively, of transgenic compared with non-transgenic cotton plants. Fiber quality parameters were also observed to be improved in the engineered cotton line. Genetic modifications of Gh_A07G1537 support the improvement in fiber quality parameters and should be appreciated for the textile industry.

Phytophthora infestans, one of most famous pathogenic oomycetes, triggered the Great Irish Famine from 1845 to 1852. The target of rapamycin (TOR) is well known as a key gene in eukaryotes that controls cell growth, survival and development. However, it is unclear about its function in controlling the mycelial growth, sporulation capacity, spore germination and virulence of Phytophthora infestans. In this study, key components of the TOR signaling pathway are analyzed in detail. TOR inhibitors, including rapamycin (RAP), AZD8055 (AZD), KU-0063794 (KU), and Torin1, inhibit the mycelial growth, sporulation capacity, spore germination, and virulence of Phytophthora infestans with AZD showing the best inhibitory effects on Phytophthora infestans. Importantly, compared with a combination of RAP + KU or RAP + Torin1, the co-application of RAP and AZD show the best synergistic inhibitory effects on P. infestans, resulting in the reduced dosage and increased efficacy of drugs. Transcriptome analysis supports the synergistic effects of the combination of RAP and AZD on gene expression, functions and pathways related to the TOR signaling pathway. Thus, TOR is an important target for controlling Phytophthora infestans, and synergism based on the application of TOR inhibitors exhibit the potential for controlling the growth of Phytophthora infestans.

ABSCISIC ACID INSENSITIVE5 (ABI5) is an important regulator of abscisic acid (ABA) signaling pathway involved in regulating seed germination and postgerminative growth in Arabidopsis, which integrates various phytohormone pathways to balance plant growth and stress responses. However, the transcriptional regulatory mechanisms underlying ABI5 and its interacting proteins remain largely unknown. Here, we found that inhibition of AtTOR could increase ABA content by up-regulating the expression levels of ABA biosynthesis-related genes, and thus activated the expression of ABA-responsive genes. Pharmacological assay showed that abi5-1 mutant was insensitive to TOR inhibitor AZD8055, whereas AtABI5 overexpression lines were hypersensitive to AZD8055 in Arabidopsis. Biochemical interaction assays demonstrated that ABI5 physically interacted with the RIBOSOMAL S6 KINASE2 (S6K2) protein in plant cell. S6K2 positively regulated ABA responses during seedling growth and upregulated ABA-responsive genes expression. Furthermore, genetic and physiological analysis indicated that AtS6K2 overexpression lines enhanced resistance to drought treatment while AtS6K2 interference lines were sensitive to drought. These results indicated that AtABI5 interacted with AtS6K2 to positively modulate ABA responses during seedling growth and shed light on a underlying mechanism of the crosstalk between TOR and ABA signaling pathways in modulating seedling growth in Arabidopsis.

Heat tolerance is a physiologically and genetically complex trait regulated by multiple genes. To investigate the genetic basis of heat tolerance, eight parents (five lines and three testers) and their fifteen F1 hybrids were evaluated under normal and high-temperature stress conditions for two consecutive years. Data were recorded for plant height, number of bolls, boll weight, seed cotton yield, ginning out turn (GOT%), H2O2, catalase, peroxidase, super-oxidase dismutase, total soluble proteins, carotenoids, chlorophyll a & b contents, short fiber index, fiber strength, UHML, micronaire value, reflectance, and uniformity index. Line × tester analysis suggested that the contribution of lines was higher than testers. Non-additive gene action was observed for all studied traits. The variances of SCA were greater than GCA variances for all studied traits revealed that these traits were governed by a few largely dominant genes. Fb-Shaheen, Eagle-2 and JSQ White Gold were found good general combiner whereas the cross Fb-Shaheen × JSQ White Gold was a good specific combiner and revealed significant better parent heterosis for most of the traits during two years under normal and high temperature stress conditions. The information obtained could be utilized in a breeding program for the development of new synthetic varieties of heat tolerance.

DNA methylation is an indispensable epigenetic modification that dynamically regulates gene expression and genome stability during cell growth and development processes. The target of rapamycin (TOR) has emerged as a central regulator to regulate many fundamental cellular metabolic processes from protein synthesis to autophagy in all eukaryotic species. However, little is known about the functions of TOR in DNA methylation. In this study, the synergistic growth inhibition of Arabidopsis seedlings can be observed when DNA methylation inhibitor azacitidine was combined with TOR inhibitors. Global DNA methylation level was evaluated using whole-genome bisulfite sequencing (WGBS) under TOR inhibition. Hypomethylation level of whole genome DNA was observed in AZD-8055 (AZD), rapamycin (RAP) and AZD + RAP treated Arabidopsis seedlings. Based on functional annotation and KEGG pathway analysis of differentially methylated genes (DMGs), most of DMGs were enriched in carbon metabolism, biosynthesis of amino acids and other metabolic processes. Importantly, the suppression of TOR caused the change in DNA methylation of the genes associated with plant hormone signal transduction, indicating that TOR played an important role in modulating phytohormone signals in Arabidopsis. These observations are expected to shed light on the novel functions of TOR in DNA methylation and provide some new insights into how TOR regulates genome DNA methylation to control plant growth.

Producing food via vertical farming (VF) is an efficient method since it requires less space with increased yield per unit area. Such a system can assist in solving major food-shortage problems since it presents a higher crop yield per unit area compared to conventional farming. Thus, VF can be seen as a production method that can cope with the challenge of the constantly growing population, making it also possible to cultivate crops in regions with adverse climate conditions. However, the public might be concerned about the sustainability of VF systems since plants are produced in an unconventional setting. Therefore, there is a need to consider and evaluate the consumers’ acceptance of VF. The particular study attempts to both analyse consumer acceptance of VF in the Nordic areas and offer insights into VF acceptance among young customers in a comparative analysis. The results indicated that VF is not widely accepted by young Nordic consumers. The concept of sustainability is one of the principles driving forces behind consumer acceptance of vertical farms. The more cases of vertical farms in European cities, the better seems to be the level of acceptance among young customers and their willingness to purchase their products.

The development of high-yielding heat-tolerant cotton cultivars harboring plastic phenotypes across warming climatic regions is prime objectives of today’s cotton breeding programs. We evaluated eight parents and 15 F1 hybrids under normal and heat stress conditions. Agronomic and biochemical characters were analyzed using standard least square, correlation, principal component analysis (PCA), and hierarchical clustering. The results explained a significant reduction in all traits except hydrogen peroxide contents, catalase, and peroxidase activities with a prominent increase under heat stress. A significant positive correlation was observed among all agronomic and biochemical traits. POD was found to have a maximum positive correlation with CAT (0.947) and minimum with boll weight (0.050). PCA showed first two components accounting for 78.64% of the total variation, with 55.83% and 22.80% of the total variation, respectively. Based on multivariate analyses methods 23 genotypes have been placed in 3 groups: tolerant (cluster-3), moderately tolerant (cluster-2), and susceptible (cluster-1). In a general perspective hybrids have better performance across normal and heat stress supports the idea of hybrid adaptability across stress environments. In specific FH-458 × FH-313 cross performed best across both conditions for yield and physiological traits. Hence, the generated information from the present study would support breeders in developing heat-resilient cultivars to endure the prevailing extreme environmental conditions.

Melatonin functions as a plant hormone/regulator in the regulation of growth and development. However, the underlying mechanisms are still unclear. In this study, we found that a high dose of melatonin inhibited hypocotyl elongation in a dose-dependent manner in Arabidopsis. An expression profile analysis showed that hypocotyl growth inhibition by melatonin was involved in reprograming the expression of cell elongation genes and brassinosteroid (BRs) biosynthetic genes. Furthermore, similar to BR biosynthetic inhibitor brassinazole (BRZ), a high concentration of melatonin upregulated BR-biosynthetic genes and downregulated BR-induced genes involved in cell elongation, while melatonin was inefficient in brassinazole-resistant mutants like the bzr1-1D and bes1-D in hypocotyl inhibition. The comparative expression profile analysis showed an opposite expression mode in the co-regulated genes between melatonin and BZR1 or melatonin and brassinolide (BL). Additionally, exogenous BL rescued the repressive phenotype of BR biosynthesis-deficient mutant like det2-1 even in the presence of high-dose melatonin, but not BR receptor mutant bri1-5 or signal transduction mutant bin2-1. A biochemical analysis further confirmed that melatonin reduced endogenous BR levels in a dose-dependent manner in Arabidopsis. Taken together, these results indicate that melatonin inhibits BR biosynthesis but does not block BR signaling in the inhibition of hypocotyl elongation and extends insights on the role of melatonin in cross-talking with plant hormone signaling.

More than 200 plants have been suffering from Verticillium wilt caused by Verticillium dahliae (V. dahliae) across the world. The target of rapamycin (TOR) is a lethal gene and controls cell growth and development in various eukaryotes, but little is known about TOR signaling in V. dahliae. Here, we found that V. dahliae strain is hypersensitive to rapamycin in the presence of rapamycin binding protein VdFKBP12 while the deletion mutant aaavdfkbp12 is insensitive to rapamycin. Heterologous expressing VdFKBP12 in Arabidopsis conferred rapamycin sensitivity, indicating that VdFKBP12 can bridge the interaction between rapamycin and TOR across species. The key across species of TOR complex 1 (TORC1) and TORC2 have been identified in V. dahliae, suggesting that TOR signaling pathway is evolutionarily conserved in eukaryotic species. Furthermore, the RNA-seq analysis showed that ribosomal biogenesis, RNA polymerase II transcription factors and many metabolic processes were significantly suppressed in rapamycin treated cells of V. dahliae. Importantly, transcript levels of genes associated with cell wall degrading enzymes (CWEDs) were dramatically down-regulated in TOR-inhibited cells. Further infection assay showed that the pathogenicity of V. dahliae and occurrence of Verticillium wilt can be blocked in the presence of rapamycin. These observations suggested that VdTOR is a key target of V. dahliae for controlling and preventing Verticillium wilt in plants.

TOR (Target of Rapamycin) kinase is an evolutionarily conserved protein kinase, which integrates stress-related cues with growth and metabolic outputs. Long non-coding RNAs (lncRNAs) play a vital role in the regulation of eukaryotic genes. However, little is known about TOR's function in regulating the expression of lncRNAs in plants. In this study, four putative homologous genes encoding the TOR protein were identified by utilizing the recently completed cotton genome. Pharmacological experiments with TOR inhibitor AZD8055 and on silencing GhTOR genes resulted in obvious cotton growth retardation, indicating the conserved role of TOR in plant growth. The expression pattern analyses in different tissues reveal that TOR may play a role in root development, and the transcript levels of TOR genes were changed under different stress conditions. Importantly, we found TOR may be a key player in regulating the expression of long non-coding RNAs (lncRNAs). A total of 10,315 lncRNAs were discovered in cotton seedlings, 90.7% of which were long intergenic ncRNAs. Moreover, we identified the differentially expressed lncRNAs, of which 296 were significantly upregulated and 105 were downregulated in TOR inactivated plants. GO and KEGG analyses of differentially expressed lncRNA neighboring genes reveal that these differentially expressed lncRNA-targeted genes are involved in many life processes, including stress response, glutathione, and ribosomes in cotton. A series of differentially expressed lncRNAs potentially involved in plant stress response was identified under TOR inhibition. Collectively, these results suggest that cotton TOR proteins may directly modulate the expression of putative stress-related lncRNAs and eventually play a potential role in the cotton stress response.

Phytophthora infestans, the causal agent of potato late blight, triggered the devastating Great Irish Famine that lasted from 1845 to 1852. Today, it is still the greatest threat to the potato yield. Ethylicin is a broad-spectrum biomimetic-fungicide. However, its application in the control of Phytophthora infestans is still unknown. In this study, we investigated the effects of ethylicin on Phytophthora infestans. We found that ethylicin inhibited the mycelial growth, sporulation capacity, spore germination and virulence of Phytophthora infestans. Furthermore, the integrated analysis of proteomics and metabolomics indicates that ethylicin may inhibit peptide or protein biosynthesis by suppressing both the ribosomal function and amino acid metabolism, causing an inhibitory effect on Phytophthora infestans. These observations indicate that ethylicin may be an anti-oomycete agent that can be used to control Phytophthora infestans.

Phytophthora infestans (P. infestans) is the causal agent of potato late blight, which caused the devastating Irish Potato Famine during 1845-1852. Until now, potato late blight is still the most serious threat to potato growth and has caused significant economic losses worldwide. Melatonin can induce plant innate immunity against pathogen infection, but the direct effects of melatonin on plant pathogens are poorly understood. In this study, we investigated the direct effects of melatonin on P. infestans. Exogenous melatonin significantly attenuated the potato late blight by inhibiting mycelial growth, changing cell ultrastructure, and reducing stress tolerance of P. infestans. Notably, synergistic anti-fungal effects of melatonin with fungicides on P. infestans suggest that melatonin could reduce the dose levels and enhance the efficacy of fungicide against potato late blight. A transcriptome analysis was carried out to mine downstream genes whose expression levels were affected by melatonin. The analysis of the transcriptome suggests that 66 differentially expressed genes involved in amino acid metabolic processes were significantly affected by melatonin. Moreover, the differentially expressed genes associated with stress tolerance, fungicide resistance, and virulence were also affected. These findings contribute to a new understanding of the direct functions of the melatonin on P. infestans and provide a potential ecofriendly biocontrol approach using a melatonin-based paradigm and application to prevent potato late blight.

In the agriculture industry, adventitious root formation is a core issue of plants asexual propagation. However, the underlying molecular mechanism of adventitious root formation is far beyond understanding. In present study we found that target of rapamycin (TOR) signaling plays a key role in adventitious root formation in potato and Arabidopsis. The core components of TOR complex including TOR, RAPTOR, and LST8 are highly conserved in potato, but the seedlings of potato are insensitive to rapamycin, implying FK506 Binding Protein 12 KD (FKBP12) lost the function to bridge the interaction of rapamycin and TOR in potato. To dissect TOR signaling in potato, the rapamycin hypersensitive potato plants (BP12-OE) were engineered by introducing yeast FKBP12 (ScFKBP12) into potato. We found that rapamycin can significantly attenuate the capability of adventitious root formation in BP12-OE potatoes. KU63794 (KU, an active-site TOR inhibitor) combined with rapamycin can more significantly suppress adventitious root formation of BP12-OE potato than the single treatments, such as KU63794 or rapamycin, indicating its synergistic inhibitory effects on potato adventitious root formation. Furthermore, RNA-seq data showed that many genes associated with auxin signaling pathway were altered when BP12-OE potato seedlings were treated with rapamycin + KU, suggesting that TOR may play a major role in adventitious root formation via auxin signaling. The auxin receptor mutant tir1 was sensitive to TOR inhibitors and the double and quadruple mutants including tir1afb2, tir1afb3, and tir1afb1afb2afb3 displayed more sensitive to asTORis than single mutant tir1. Consistently, overexpression of AtTIR1 in Arabidopsis and potato can partially overcome the inhibitory effect of asTORis and promote adventitious root formation under asTORis treatments. These observations suggest that TOR signaling regulates adventitious root formation by mediating auxin signaling in Arabidopsis and potato.

Target of Rapamycin (TOR) signaling is an important regulator in multiple organisms including yeast, plants and animals. However, the TOR signaling in plants is much less understood as compared to that in yeast and animals. TOR kinase can be efficiently suppressed by rapamycin in the presence of functional FK506 Binding Protein 12KD (FKBP12) in yeast and animals. In most examined higher plants rapamycin fails to inhibit TOR kinase due to the non-functional FKBP12. Here we find that tomato plants showed obvious growth inhibition when treated with rapamycin and the inhibitory phenotype is similar to suppression of TOR causing by active-site TOR inhibitors (asTORis) such as KU63794, AZD8055 and Torin1. The chemical genetic assays using TOR inhibitors and heterologous expressing SlFKBP12 in Arabidopsis indicated that the TOR signaling is functional in tomato. The protein gel shifting and TOR inhibitors combination assays showed that SlFKBP12 can mediate the interaction between rapamycin and TOR. Furthermore, comparative expression profiling analysis between treatments with rapamycin and KU63794 identified highly overlapped Differentially Expressed Genes (DEGs) which are involved in many anabolic and catabolic processes, such as photosynthesis, cell wall restructuring, and senescence in tomato. These observations suggest that SlFFBP12 is functional in tomato. The results provided basic information of TOR signaling in tomato, and also some new insights into how TOR controls plant growth and development through reprogramming the transcription profiles