Identification of anthocyanin biosynthesis genes in rice pericarp using PCAMP

Toward routine basil (Ocimum basilicum L.) callus culture analysis using non-destructive Raman spectroscopy

Here we investigated whether FT-Raman spectroscopy could be used to detect biochemical changes in small-leaved basil (Ocimum basilicum L. var. minimum Alef.) callus culture (CC). To address the effect of culture conditions and elicitor treatments, CC established on 1 mg L-1 2,4-D + 0.5 mg L-1 BAP, or 2.5 mg L-1 NAA + 0.5 mg L-1 KIN was exposed to various spectral light treatments during four weeks and compared to those grown in dark. The composition of CC was analysed both using an FT-Raman spectrometer equipped with laser 1064 nm, and spectrophotometrically. The spectral composition of light had a higher influence on the chemical composition of CC grown on NAA + KIN than on 2,4-D + BAP medium. Spectrophotometrically, no differences in the content of protein or sugar were determined in relation to the plant growth regulators applied. However, significant differences in frequencies and intensities of vibrational bands associated with proteins (S-S disulfide stretching, tyrosine, cystine, and methionine at lower spectral ranges, and amide III stretching in the higher spectral range), and carbohydrates (C-O-C skeletal mode at lower spectral ranges, and C-O-H vibrations at higher spectral ranges) within the Raman spectra were estimated and discussed. The 1525 cm-1 and 1606 cm-1 peaks with high intensities of vibration bands were identified and assigned to carotenoids and phenolics. In all treatments applied the major Raman peaks were detected at 1606, 1629, and 1633 cm-1. PCA analysis showed that CC under blue-red light and blue-red light + UVa (2,4-D + BAP) had higher content of carotenoids and ester groups, while chlorophyll a and phenolics were found in CC grown on NAA + KIN under blue-red light + UVa and blue-red light + far-red. Compared to traditional methods of analysis, which are preceded by the sample destruction before extraction and analysis, it can be concluded that the FT-Raman spectroscopy may serve as a valuable tool for the non-destructive and non-invasive identification of major biochemical changes in basil CC without any sample preparation.

Synergistic effects of Fe3O4-NPs and Enterobacter cloacae in alleviating mercury stress in wheat (Triticum aestivum L.): Insights into morpho-physio-biochemicals attributes

In the current industrial scenario, mercury (Hg) as a metal is of great importance but poses a major threat to the ecosystem because of its toxicity, but fewer studies have been conducted on its effects and alleviation strategies by using nanoparticles (NPs) and plant growth promoting rhizobacteria (PGPR). Taking into consideration the positive effects of iron oxide (Fe3O4)⎯NPs and Enterobacter cloacae rhizobacteria in reducing Hg toxicity in plants, the present study was conducted. A pot experiment was conducted over 60 days using wheat (Triticum aestivum L.) to investigate the effects of varying Hg levels (0, 50 and 100 mg kg⎯1) combined with different concentrations of Fe3O4-NPs (25 and 50 mg L-1) and E. cloacae (10 and 20 ppm) on various morpho-physio-biochemical responses. The research outcomes indicated that elevated levels of Hg stress in the soil significantly (P < 0.05) decreased plant growth and biomass, photosynthetic pigments, nutrients uptake and gas exchange attributes. However, Hg stress also induced oxidative stress in the plants by increasing malondialdehyde (MDA) and hydrogen peroxide (H2O2), which also induced increased compounds of various enzymatic and non-enzymatic antioxidants and also the gene expression and sugar content. Furthermore, a significant (P < 0.05) increase in proline metabolism, the ascorbate-glutathione (AsA-GSH) cycle were observed. Although, the application of Fe3O4-NPs and E. cloacae showed a significant (P < 0.05) increase in plant growth and biomass, nutrients uptake, gas exchange characteristics, enzymatic and non-enzymatic compounds, and their gene expression and also decreased oxidative stress. In addition, the application of Fe3O4-NPs and E. cloacae enhanced cellular fractionation and decreased the proline metabolism and AsA-GSH cycle in T. aestivum seedlings. Research findings, therefore, suggest that the application of Fe3O4-NPs and E. cloacae can ameliorate Hg toxicity in T. aestivum seedlings, resulting in improved plant growth and composition under metal stress, as depicted by balanced antioxidant defense mechanism.

Eco-friendly role of serratia marcescens and pseudomonas fluorescens in enhancing rice growth and mitigating cadmium toxicity via uptake modulation and antioxidant regulation

Plant growth-promoting rhizobacteria (PGPR) offer sustainable means to enhance crop resilience under environmental stress, including heavy metal toxicity. Understanding their role in mitigating such stresses is vital for advancing biotechnological strategies aimed at food security and sustainable agriculture. A pot experiment was conducted to determine the effects of single and/or combined application of different levels [10 and 20 ppm] of Serratia marcescens and Pseudomonas fluorescens on Cd accumulation, morpho-physio-biochemical attributes of rice (Oryza sativa L.) exposed to severe Cd stress [0 (without Cd stress), and 100 µM)]. The research outcomes indicated that elevated levels of Cd stress in the soil significantly (p ≤ 0.05) decreased plant growth and biomass, photosynthetic pigments, and gas exchange attributes. However, Cd stress also induced oxidative stress in the plants by increasing malondialdehyde (MDA) and hydrogen peroxide (H2O2), which also induced increased compounds of various enzymatic and non-enzymatic antioxidants and also the gene expression and sugar content. Furthermore, a significant (p ≤ 0.05) increase in proline metabolism, the ascorbate-glutathione (AsA-GSH) cycle were observed. Although, the application of S. marcescens and P. fluorescens showed a significant (p ≤ 0.05) increase in plant growth and biomass, gas exchange characteristics, enzymatic and non-enzymatic compounds, and their gene expression and also decreased oxidative stress. In addition, the application of S. marcescens and P. fluorescens enhanced cellular fractionation and decreased the proline metabolism and AsA-GSH cycle in O. sativa plants. Research findings, therefore, suggest that the application of S. marcescens and P. fluorescens can ameliorate Cd toxicity in O. sativa, resulting in improved plant growth and composition under metal stress, as depicted by balanced antioxidant defense mechanism.

Impact of amino acid supplementation on hydroponic lettuce (Lactuca sativa L.) growth and nutrient content

Lettuce (Lactuca sativa L.), a widely cultivated leafy green, is valued for its rich content of bioactive compounds, including folates, vitamins, tocopherols, ascorbic acid, and antioxidants. This study aimed to evaluate the effects of amino acid supplementation on the growth and nutrient content of hydroponically grown lettuce. A greenhouse experiment using a completely randomized design (CRD) was conducted, with three replications and three plants per replication. There were 4 treatments (T0 (Control), T1 (Methionine 20 mg/L), T2 (Tryptophan 220 mg/L, T3 (Glycine 200 mg/L) of this experiment Growth parameters, including biomass, leaf length, leaf width, and leaf area, were measured four weeks after transplantation. L-methionine supplementation resulted in a significant improvement in plant growth, with a 23.60% increase in biomass and a 31.41% increase in leaf area. Conversely, L-tryptophan treatment led to substantial reductions in growth, including a 98.78% decrease in biomass. Nutrient analysis revealed that amino acid treatments, especially methionine, enhanced the nitrogen, phosphorus, and potassium content in leaf tissues. These results suggest that L-methionine has a positive effect on both growth and nutrient uptake in hydroponic lettuce, while L-tryptophan and L-glycine negatively affect plant development. The differential responses to amino acid treatments may be attributed to their distinct roles in plant metabolism, with methionine enhancing sulfur-containing compounds and proteins essential for growth, while tryptophan and glycine could disrupt metabolic pathways. Future research should explore the mechanisms underlying these effects and evaluate the optimal amino acid concentrations for maximizing hydroponic lettuce production and nutrient density.

Co-application of potassium and thiourea for mitigating salinity stress in wheat seedlings

Salt stress disrupts ionic homeostasis and induces oxidative damage, leading to reduced plant growth and development. Determining the lethal dose of NaCl is essential for developing effective mitigation strategies. Potassium and other antioxidant regulatory compounds often prove insufficient in addressing salt-induced toxicity, especially in wheat. This laboratory experiment aimed to determine NaCl concentration that reduces plant growth by 50% and to evaluate the effectiveness of different mitigation approaches involving potassium and thiourea supplementation at 0 mM, 10 mM, and 15 mM under the identified NaCl condition. The experiment followed a factorial arrangement with three biological replications. Results showed that NaCl at 198 mM decreased germination and plant growth by 50%. The combined application of potassium and thiourea at 15 mM significantly improved ionic homeostasis, leading to a 14% increase in overall ion balance. This was achieved by reducing sodium ions concentration by 28.55% and increasing potassium ion concentration by 23.92%. Furthermore, the interactive application enhances various growth parameters, including shoot and root length (by 14.20-32.82%), and shoot/root fresh and dry weight (by 18.56/8.89% to 26.60/25.52%, respectively). These improvements were attributed to enhanced physiological processes, including a 10.23% increase in net photosynthetic rate, a 30.20% increase in stomatal conductance, a 6.70% increase in transpiration rate, an 8.12% increase in internal carbon dioxide concentrations and a 10.13% improvement in relative water content. Additionally, oxidative markers, such as hydrogen peroxide and malonaldeahyde, were reduced by 8.43% and 26.20%, respectively. This reduction was associated with increased antioxidant enzyme activity, including a 13.69% increase in superoxide dismutase, an 8.91% increase in catalase, a 20.18% increase in peroxidase, and a 13.11% increase in ascorbate peroxidase. The decrease in oxidative stress contributed to an 8.48% improvement in membrane stability and a 17.06% enhancement in relative water content. Principle component analysis confirmed the efficacy of the K15 + TU15 treatment in improving wheat salt tolerance. The simultaneous application of K and TU at 15 mM effectively mitigated salt-induced toxicity by enhancing ionic homeostasis and reducing oxidative stress through increased antioxidant enzyme activity in wheat.

Optimizing cultivation practices to enhance growth and yield of Indian mustard

Since mustard is a significant oilseed crop in India, improving cultivation practises is essential for enhancing the productivity. The experiment was laid out in randomized block design with three replications at the farm of Department of Agronomy, Lovely Professional University, Phagwara during the rabi season. The work was carried out for two years to analyse the pooled data (2022-2023; 2023-2024) of Indian mustard. A total of 11 treatments were utilized with various sowing techniques, sulphur use, and mulching for enhanced yield on mustard growth and yield traits. With an increase in doses of sulphur, mulching with paddy straw and sowing techniques including flat bed and ridge sowing the growth characteristics such as plant height, number of leaves per plant, number of branches per plant increased and enhanced yield traits. Results from the study revealed that among the various treatments, the application of Treatment T9 = Ridge sowing + recommended NP (100:75 kg/ha) + recommended S (20 kg/ha) + mulching (Paddy straw) had more growth and improved yield as compared to other treatments of Indian mustard. The pooled analysis of data from 2022 to 23 and 2023-24 revealed that treatment T9 achieved the maximum plant heights, measuring 14.8 cm, 80.8 cm, and 131.2 cm at 30, 60, and 90 DAS, number leaves per plant (6.0, 38.8, 83.2) at 30, 60, 90 DAS and number of branches (3.2, 6.7) at 60, 90 DAS. In yield analysis, the greatest number of siliquae per plant (73.6), the longest siliquae length (4.3), seeds per siliquae (23.1), 1000 seed weight peaked at 3.5, seed yield was 1.6 t/ha, stover yield was 4.1 t/ha, and harvest index was 29.6% in 2022-23 analysis. Overall, from pooled analysis the 2022-23 mustard crop had more growth and yield as compared to 2023-24 mustard crop.

Antifungal and antioxidant potential of Ocimum species against Ascochyta rabiei (Pass) Lab

Cicer arietinum L. is a vital source of nutrients that suffers substantial annual losses due to Ascochyta blight, caused by the plant pathogen Ascochyta rabiei. This study aimed to investigate the antifungal potential of Ocimum tenuiflorum L. and O. basilicum L. shoots (leaves and stems) against A. rabiei (Pass) Lab. In vitro bioassays were conducted using methanolic extracts from leaves and stems at six different concentrations: 1%, 1.5%, 2%, 2.5%, 3%, and 3.5%. A total of eight compounds were identified through gas chromatography-mass spectrometry (GC-MS) analysis. The highest inhibition of A. rabiei growth was achieved with a 3.5% methanolic leaf extract of O. basilicum. Methanolic extracts from O. tenuiflorum shoots also reduced fungal growth by 6.18-73%. Additionally, the n-hexane fraction derived from O. basilicum inhibited fungal growth by 71-76% and was subsequently analyzed using GC-MS. This analysis identified eight compounds: (1) cyclopentane, methyl-, (2) cyclohexane, (3) 2,2-dimethylbutane, (4) 2,3-dimethylbutane, pentane, (5) 2,3-dimethyl-, (6) 2-bromoacetonitrile, (7) alpha-cadinol, and (8) phenylpropanolamine. The antioxidant activity of O. tenuiflorum and O. basilicum shoots was also assessed using the 1,1-diphenyl-2-picrylhydrazyl (DPPH) assay. The highest antioxidant activity, 98.58%, was recorded at a 3.5% methanolic stem extract concentration of O. tenuiflorum. The antioxidant activity potential was highest for O. tenuiflorum at 0.729mg/mL, followed by O. basilicum at 0.411mg/mL.

Unraveling the flavor formation process of mellow and thick-type ripened Pu-erh tea through non-targeted metabolomics and metagenomics

Ripened Pu-erh tea (RPT) is renowned for its distinctive flavor and health benefits. However, its complex fermentation process poses challenges in ensuring consistency in production. This study investigated RPT flavor formation through sensory evaluation, multi-omics analysis, and multivariate statistical approaches. By day 24, the tea exhibited a reddish-brown infusion and a mellow, thick taste (MT_RPT), achieving the highest sensory score (94.0, P < 0.05). Sixteen flavor-related chemical components exhibited significant changes (P < 0.05). The contents of free amino acids, L-theanine, tea polyphenols, flavonoids, catechins, and thearubigins decreased. In contrast, the contents of total soluble sugars, caffeine, theobromine, epicatechin, and theabrownins (TBs) increased, reaching 74.1 mg/g, 65.38 mg/g, 3.13 mg/g, 3.33 mg/g, and 134.84 mg/g, respectively. Additionally, 33 nonvolatile metabolites (e.g., pelargonidin 3-O-glucoside, dihydroisorhamnetin, and puerarin) were significantly correlated with MT_RPT flavor (VIP > 1, |r| ≥ 0.8, P < 0.05) and influenced by key functional microbes, including Pantoea, Aspergillus, Brachybacterium, and Staphylococcus. By day 30, the infusion darkened, and sensory scores declined (81.4, P < 0.05), attributed to the dominance of Brevibacterium. This microbial shift reduced water-soluble pectin, free amino acids, and 11 metabolites while increasing TBs and theophylline (219.33 mg/g and 0.09 mg/g, respectively). Therefore, TBs were identified as a crucial indicator of optimal fermentation. Moreover, redundancy analysis indicated that the tea pile's central temperature, moisture content, and pH were essential fermentation parameters (P < 0.05). These findings deepen our understanding of MT_RPT flavor development mechanisms and provide valuable insights into precise fermentation control.

LMFE: A Novel Method for Predicting Plant LncRNA Based on Multi-Feature Fusion and Ensemble Learning

Background/Objectives: Long non-coding RNAs (lncRNAs) play a crucial regulatory role in plant trait expression and disease management, making their accurate prediction a key research focus for guiding biological experiments. While extensive studies have been conducted on animals and humans, plant lncRNA research remains relatively limited due to various challenges, such as data scarcity and genomic complexity. This study aims to bridge this gap by developing an effective computational method for predicting plant lncRNAs, specifically by classifying transcribed RNA sequences as lncRNAs or mRNAs using multi-feature analysis. Methods: We propose the lncRNA multi-feature-fusion ensemble learning (LMFE) approach, a novel method that integrates 100-dimensional features from RNA biological properties-based, sequence-based, and structure-based features, employing the XGBoost ensemble learning algorithm for prediction. To address unbalanced datasets, we implemented the synthetic minority oversampling technique (SMOTE). LMFE was validated across benchmark datasets, cross-species datasets, unbalanced datasets, and independent datasets. Results: LMFE achieved an accuracy of 99.42%, an F1score of 0.99, and an MCC of 0.98 on the benchmark dataset, with robust cross-species performance (accuracy ranging from 89.30% to 99.81%). On unbalanced datasets, LMFE attained an average accuracy of 99.41%, representing a 12.29% improvement over traditional methods without SMOTE (average ACC of 87.12%). Compared to state-of-the-art methods, such as CPC2 and PLEKv2, LMFE consistently outperformed them across multiple metrics on independent datasets (with an accuracy ranging from 97.33% to 99.21%), with redundant features having minimal impact on performance. Conclusions: LMFE provides a highly accurate and generalizable solution for plant lncRNA prediction, outperforming existing methods through multi-feature fusion and ensemble learning while demonstrating robustness to redundant features. Despite its effectiveness, variations in performance across species highlight the necessity for future improvements in managing diverse plant genomes. This method represents a valuable tool for advancing plant lncRNA research and guiding biological experiments.

Mitigating ammonium toxicity in strawberry cultivation: effective fertilization practices for sustainable crop production

Nitrogen is crucial for plant growth, but deficiency and excess can harm plants. Fertilizers like Diammonium Phosphate (DAP), which releases ammonium (NH4+), are common, yet over-application can cause NH4+ toxicity, resulting in stunted roots and leaf damage. This study investigated the impact of NH4+ toxicity on strawberry growth, yield, and fruit quality to inform better fertilization practices. The experiment was conducted at The Islamia University of Bahawalpur, Pakistan. Five treatments with varying DAP rates (0 g, 4 g, 7 g, 10 g, and 13 g per plant) were applied to strawberry plants in a completely randomized design with four replications. Photosynthetic pigments, hydrogen peroxide (H2O2), malondialdehyde (MDA), electrolyte leakage (EL), and yield parameters were measured. The 4 g DAP treatment yielded the highest chlorophyll-a (0.5775 mg/g FW) and total chlorophyll content (0.705 mg/g FW). However, increasing DAP doses led to a decline in chlorophyll-a, chlorophyll-b, and total chlorophyll content, with the 13 g DAP treatment exhibiting the lowest levels. H2O2 content increased with higher DAP doses, with the 13 g DAP treatment showing the highest value (75 µmol/g FW). Higher DAP doses also increased MDA content and EL, indicating oxidative stress and membrane damage. The 4 g DAP treatment showed minimal changes in H2O2 and MDA content. Moderate DAP levels (4 g per plant) enhanced strawberry growth, yield, and photosynthetic activity, while higher doses caused significant stress, leading to reduced growth and yield. Managing NH4+ levels in fertilization is crucial for optimizing strawberry production. Therefore, moderate doses of DAP (ammonium ion) should be used to avoid ammonium toxicity.

Deciphering nutrient stress in plants: integrative insight from metabolomics and proteomics

To comprehend the responses and resilience of plants under unfavorable environmental conditions, it is crucial to study the metabolomics and proteomic insights into nutrient stress. Nutrient stress substantially challenges agriculture, impacting plant growth, development, and productivity due to a lack or imbalance of essential nutrients, which can happen due to poor soil quality, limited nutrient availability, or unfavorable climatic conditions. Although there has been significant progress in the study of plant nutrient stress using metabolomics and proteomics, several challenges and research gaps still need to be addressed, such as the standardized experimental protocols, data integration strategies, and bioinformatic tools are necessary for comparative analysis and interpretation of omics data. Hence, this review explores the theoretical frameworks of metabolomics and proteomics as powerful tools to decode plant responses to nutrient stress, addressing critical knowledge gaps in the field. This review highlights the advantages of integrative analyses, combining metabolomics, proteomics, and transcriptomics, to uncover the molecular networks governing nutrient stress resilience. Key findings underscore the potential of these techniques to enhance breeding strategies and genetic engineering efforts aimed at developing nutrient-efficient crops. Through metabolomics and proteomic analyses, novel molecular components and regulatory networks have been revealed as responsive to nutrient stress, and this breakthrough has the potential to bolster plant resilience and optimize nutrient utilization. Understanding the synergistic roles of metabolites and proteins in nutrient stress resilience has profound implications for crop improvement and agricultural sustainability. Future research should focus on refining integrative methodologies and exploring their applications across diverse plant species and environmental conditions, paving the way for innovative solutions to nutrient stress challenges.

Priming agents combat copper stress in wheat (Triticum aestivum L.) under hydroponic conditions: Insights in impacts on morpho-physio-biochemical traits and health risk assessment

In recent years, the use of priming agents, such as silicon, melatonin, salicylic acid, glycine betaine, and ascorbic acid has gained significant attention for their role in mitigating abiotic stresses across various plant species. While previous research has been conducted on the individual impact of silicon, melatonin, salicylic acid, glycine betaine, and ascorbic acid in metal stress resistance among various crop species, their combined effects in the context of heavy metal stressed conditions remain underexplored. Wheat (Triticum aestivum L.) seedlings was grown under the toxic concentration of copper (Cu) i.e., 100 µM which were applied with silicon, melatonin, salicylic acid, glycine betaine, and ascorbic acid under hydroponic conditions for 21 days. The research outcomes indicated that the toxic concentration of Cu in the nutrient solution notably reduced plant growth and biomass, photosynthetic pigments, and gas exchange attributes. However, Cu stress also induced oxidative stress in the plants by increasing malondialdehyde (MDA), hydrogen peroxide (H2O2) which also induced increased compounds of various enzymatic and non-enzymatic antioxidants, health risk index (HRI) and also the gene expression and sugar content. Furthermore, a significant increase in proline metabolism, the AsA-GSH cycle, and the pigmentation of cellular components was observed. Although, the application of different priming agents, such as silicon, melatonin, salicylic acid, glycine betaine, and ascorbic acid showed a significant increase in plant growth and biomass, gas exchange characteristics, enzymatic and non-enzymatic compounds, and their gene expression and also decreased oxidative stress and HRI. In addition, the application of different priming agents enhanced cellular fractionation and decreased the proline metabolism and AsA-GSH cycle in T. aestivum seedlings. These results open new insights for sustainable agriculture practices and hold immense promise in addressing the pressing challenges of heavy metal contamination in agricultural soils.

Evaluating the potential of Acinetobacter calcoaceticus in alleviation of aluminium stress in Triticum aestivum

Soil contamination with toxic heavy metals [such as aluminum (Al)] is becoming a serious global problem due to the rapid development of the social economy. Although plant growth-promoting rhizo-bacteria (PGPR) are the major protectants to alleviate metal toxicity, the study of these bacteria to ameliorate the toxic effects of Al is limited. Therefore, the present study was conducted to investigate the combined effects of different levels of Acinetobacter calcoaceticus (5 ppm and 10 ppm) of accession number of MT123456 on plant growth and biomass, photosynthetic pigments, gas exchange attributes, oxidative stress and response of antioxidant compounds (enzymatic and nonenzymatic), and their specific gene expression, sugars, nutritional status of the plant, organic acid exudation pattern and Al accumulation from the different parts of the plants, which was spiked with different levels of Al [0 µM (i.e., no Al), 50 µM, and 100 µM] using aluminum sulfate [Al2(SO4)3] in wheat (Triticum aestivum L.). Results from the present study revealed that the Al toxicity induced a substantial decreased in shoot length, root length, number of leaves, leaf area, shoot fresh weight, root fresh weight, shoot dry weight, root dry weight, chlorophyll-a, chlorophyll-b, total chlorophyll, carotenoid content, net photosynthesis, stomatal conductance, transpiration rate, soluble sugar, reducing sugar, non-reducing sugar contents, calcium (Ca2+), magnesium (Mg2+), iron (Fe2+), and phosphorus (P) contents in the roots and shoots of the plants. In contrast, increasing levels of Al in the soil signifcantly (P < 0.05) increased Al concentration in the roots and shoots of the plants, phenolic content, malondialdehyde (MDA), hydrogen peroxide (H2O2), electrolyte leakage (EL), fumaric acid, acetic acid, citric acid, formic acid, malic acid, oxalic acid contents in the roots of the plants. Although, the activities of enzymatic antioxidants such as superoxidase dismutase, peroxidase, catalase, ascorbate peroxidase and their specific gene expression in the roots and shoots of the plants and non-enzymatic such as phenolic, favonoid, ascorbic acid, and anthocyanin contents were initially increased with the exposure of 50 µM Al, but decreased by the increasing the Al concentration 100 µM in the soil. Addition of A. calcoaceticus into the soil signifcantly alleviated Al toxicity effects on T. aestivum by improving photosynthetic capacity and ultimately plant growth. Increased activities of antioxidant enzymes in A. calcoaceticus-treated plants seem to play a role in capturing stress-induced reactive oxygen species as was evident from lower levels of MDA, H2O2, MDA, and EL in A. calcoaceticus-treated plants. Research findings, therefore, suggested that A. calcoaceticus application can ameliorate Al toxicity in T. aestivum seedlings and resulted in improved plant growth and composition under metal stress as depicted by balanced exudation of organic acids.

Arbuscular mycorrhizal fungus and Pseudomonas bacteria affect tomato response to Tuta absoluta (Lepidoptera: Gelechiidae) herbivory

Tuta absoluta (Lepidoptera: Gelechiidae) is one of the most significant invasive and destructive pests worldwide, causing serious economic losses to the tomato industry. Rhizosphere microorganism, such as arbuscular mycorrhizal fungi (AMF) and Pseudomonas bacteria, can interact with plants individually or collectively to improve plant growth and resistance to pests and disease. However, the effects of AMF, Pseudomonas, and their interactions on plant responses to insect herbivores remain unclear. A pot experiment was conducted to investigate the effects of single/dual inoculation with AMF (Funneliformis mosseae, M) and Pseudomonas putida (P) on the growth and defense of tomato variety Dafen (Solanum lycopersicum L.) in response to infestation by T. absoluta, as well as the growth, development, and enzyme activity of insect. The results showed that M, P, and MP promoted tomato growth by increasing nutrient concentrations, with the growth-promoting effect of dual-inoculation significantly surpassing that of single inoculation. M, P, and MP still improved tomato growth in T. absoluta infestation, with biomass increases of 57.34%, 54.46%, and 255.49%. M, P, and MP significantly increased the defense ability of tomato, with jasmonic acid concentrations increasing by 42.15%, 60.87% and 90.02%, and phenylalanine ammonia-lyase activity increasing by 47.40%, 47.68%, and 59.97%. The inoculation treatments inhibited the growth and development of T. absoluta, reduced its feeding, prolonged its growth and development, decreased egg weight, and increased the activity of protective and detoxifying enzymes. Overall, our results indicated that AMF and bacteria can stimulate each other, positively influence tomato growth and enhance resistance to T. absoluta. These findings indicate the feasibility of AMF and bacteria in combinations as potential biocontrol agents for the management of T. absoluta.

Genetic Warfare: The Plant Genome's Role in Fending Off Insect Invaders

The plant defense against insects is multiple layers of interactions. They defend through direct defense and indirect defense. Direct defenses include both physical and chemical barriers that hinder insect growth, development, and reproduction. In contrast, indirect defenses do not affect insects directly but instead suppress them by releasing volatile compounds that attract the natural enemies of herbivores. Insects overcome plant defenses by deactivating biochemical defenses, suppressing defense signaling through effectors, and altering their behavior through chemical regulation. There is always a genetic war between plants and insects. In this genetic war, plant-insect co-evolution act as both weapons and messengers. Because plants always look for new strategies to avoid insects by developing adaptation. There are molecular processes that regulate the interaction between plants and insect. Here, we examine the genes and proteins involved in plant-insect interactions and explore how their discovery has shaped the current model of the plant genome's role. Plants detect damage-associated and herbivore-associated molecular patterns through receptors, which trigger early signaling pathways involving Ca2+, reactive oxygen species, and MAP kinases. The specific defense mechanisms are activated through gene signaling pathways, including phytohormones, secondary metabolites, and transcription factors. Expanding plant genome approaches to unexplored dimensions in fending off insects should be a future priority in order to develop management strategies.

Reverse Mutations in Pigmentation Induced by Sodium Azide in the IR64 Rice Variety

Pigmentation in rice is due mainly to the accumulation of anthocyanins. Five color mutant lines, AZ1701, AZ1702, AZ1711, AZ1714, and AZ1715, derived from the sodium azide mutagenesis on the non-pigmented IR64 variety, were applied to study inheritance modes and genes for pigmentation. The mutant line AZ1711, when crossed with IR64, displays pigmentation in various tissues, exhibiting a 3:1 pigmented to non-pigmented ratio in the F2 progeny, indicating a single dominant locus controlling pigmentation. Eighty-four simple sequence repeat (SSR) markers were applied to map the pigment gene using 92 F2 individuals. RM6773, RM5754, RM253, and RM2615 markers are found to be linked to the color phenotype. RM253 explains 78% of the phenotypic variation, implying linkage to the pigmentation gene(s). Three candidate genes, OsC1 (MYB), bHLH, and 3GT, as anthocyanin biosynthesis-related genes, were identified within a 0.83 Mb region tightly linked to RM253. PCR cloning and sequencing revealed 10 bp and 72 bp insertions in the OsC1 and 3GT genes, respectively, restoring pigmentation as in wild rice. The 72 bp insertion is highly homologous to a sequence of Ty1-Copia retrotransposon and shows a particular secondary structure, suggesting that it was derived from the transposition of Ty1-Copia in the IR64 genome.

A Multi-Omics View of Maize's (Zea mays L.) Response to Low Temperatures During the Seedling Stage

Maize (Zea mays L.) is highly sensitive to temperature during its growth and development stage. A 1 °C drop in temperature can delay maturity by 10 days, resulting in a yield reduction of over 10%. Low-temperature tolerance in maize is a complex quantitative trait, and different germplasms exhibit significant differences in their responses to low-temperature stress. To explore the differences in gene expression and metabolites between B144 (tolerant) and Q319 (susceptible) during germination under low-temperature stress and to identify key genes and metabolites that respond to this stress, high-throughput transcriptome sequencing was performed on the leaves of B144 and Q319 subjected to low-temperature stress for 24 h and their respective controls using Illumina HiSeqTM 4000 high-throughput sequencing technology. Additionally, high-throughput metabolite sequencing was conducted on the samples using widely targeted metabolome sequencing technology. The results indicated that low-temperature stress triggered the accumulation of stress-related metabolites such as amino acids and their derivatives, lipids, phenolic acids, organic acids, flavonoids, lignin, coumarins, and alkaloids, suggesting their significant roles in the response to low temperature. This stress also promoted gene expression and metabolite accumulation involved in the flavonoid biosynthesis pathway. Notably, there were marked differences in gene expression and metabolites related to the glyoxylate and dicarboxylate metabolism pathways between B144 and Q319. This study, through multi-omics integrated analysis, provides valuable insights into the identification of metabolites, elucidation of metabolic pathways, and the biochemical and genetic basis of plant responses to stress, particularly under low-temperature conditions.

Next-generation bulked segregant analysis for Breeding 4.0

Functional cloning and manipulation of genes controlling various agronomic traits are important for boosting crop production. Although bulked segregant analysis (BSA) is an efficient method for functional cloning, its low throughput cannot satisfy the current need for crop breeding and food security. Here, we review the rationale and development of conventional BSA and discuss its strengths and drawbacks. We then propose next-generation BSA (NG-BSA) integrating multiple cutting-edge technologies, including high-throughput phenotyping, biological big data, and the use of machine learning. NG-BSA increases the resolution of genetic mapping and throughput for cloning quantitative trait genes (QTGs) and optimizes candidate gene selection while providing a means to elucidate the interaction network of QTGs. The ability of NG-BSA to efficiently batch-clone QTGs makes it an important tool for dissecting molecular mechanisms underlying various traits, as well as for the improvement of Breeding 4.0 strategy, especially in targeted improvement and population improvement of crops.

Transcriptome analysis reveals important regulatory genes and pathways for tuber color variation in Pinellia ternata (Thunb.) Breit

During the growth of Pinellia ternata (Thunb.) Breit. (P. ternata), the violet-red skin was occasionally produced spontaneously under natural cultivation. However, the specific mechanism leading to the color change is still unclear. This study performed transcriptomes in violet-red and pale-yellow skin and their peeled tubers of P. ternata, and the total flavonoids and anthocyanin contents were also determined. The results showed that the majority of genes involved in anthocyanin production were considerably increased in the violet-red skin of P. ternata tuber compared to the pale-yellow skin. Especially, phenylalanine ammonia-lyase (PAL) and chalcone synthase (CHS) showed a remarkable increase in gene expression levels. Notably, shikimate O-hydroxycinnamoyltransferase (HCT), naringenin 3-dioxygenase (F3H), flavanone 4-reductase (DFR), and anthocyanidin synthase (ANS) were explicitly expressed in violet-red skin of P. ternata tuber, while undetectable in pale-yellow skin. The upregulation of these genes may explain the accumulation of anthocyanins, which forms the violet-red skin of P. ternata tuber. The transcription factors, including C2H2, bZIP, ERF, GATA, bHLH, C3H, NAC, MYB-related, and MYB families, might trigger the skin color change in P. ternata. The entire anthocyanin content in the violet-red skin of P. ternata tuber was 71.10 μg/g, and pale-yellow skin was 7.74 μg/g. According to phenotypic and transcriptome results, the elevated expression levels of genes linked to the synthesis of anthocyanins considerably contributed to the violet-red skin alterations in P. ternata tuber. This study provides a new understanding of the formation of the violet-red skin, lays a theoretical foundation for the cultivation of unique varieties of P. ternata, and provides transcriptome data for further study of the differences between different colors of P. ternata.

An omics strategy increasingly improves the discovery of genetic loci and genes for seed-coat color formation in soybean

The phenotypic color of seeds is a complex agronomic trait and has economic and biological significance. The genetic control and molecular regulation mechanisms have been extensively studied. Here, we used a multi-omics strategy to explore the color formation in soybean seeds at a big data scale. We identified 13 large quantitative trait loci (QTL) for color with bulk segregating analysis in recombinant inbreeding lines. GWAS analysis of colors and decomposed attributes in 763 germplasms revealed associated SNP sites perfectly falling in five major QTL, suggesting inherited regulation on color during natural selection. Further transcriptomics analysis before and after color accumulation revealed 182 differentially expression genes (DEGs) in the five QTL, including known genes CHS, MYB, and F3'H involved in pigment accumulation. More DEGs with consistently upregulation or downregulation were identified as shared regulatory genes for two or more color formations while some DEGs were only for a specific color formation. For example, five upregulated DEGs in QTL qSC-3 were in flavonoid biosynthesis responsible for black and brown seed. The DEG (Glyma.08G085400) was identified in the purple seed only, which encodes gibberellin 2-beta-dioxygenase in the metabolism of colorful terpenoids. The candidate genes are involved in flavonoid biosynthesis, transcription factor regulation, gibberellin and terpenoid metabolism, photosynthesis, ascorbate and aldarate metabolism, and lipid metabolism. Seven differentially expressed transcription factors were also speculated that may regulate color formation, including a known MYB. The finds expand QTL and gene candidates for color formation, which could guide to breed better cultivars with designed colors.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01414-z.

Integrative HPLC profiling and transcriptome analysis revealed insights into anthocyanin accumulation and key genes at three developmental stages of black rice (Oryza sativa. L) caryopsis

Introduction

Anthocyanins are plants' secondary metabolites belonging to the flavonoid class with potential health-promoting properties. They are greatly employed in the food industry as natural alternative food colorants for dairy and ready-to-eat desserts and pH indicators. These tremendous advantages make them economically important with increasing market trends. Black rice is a rich source of anthocyanin that can be used to ensure food and nutritional security around the world. However, research on anthocyanin accumulation and gene expression during rice caryopsis development is lacking.

Methods

In this study, we combined high-performance liquid chromatography (HPLC) and transcriptome analysis to profile the changes in anthocyanin content and gene expression dynamics at three developmental stages (milky, doughy, and mature).

Results

Our results showed that anthocyanin accumulation started to be visible seven days after flowering (DAF), increased rapidly from milky (11 DAF) to dough stage, then started decreasing after the peak was attained at 18 DAF. RNA-seq showed that 519 out of 14889, 477 out of 17914, and 1614 out of 18810 genes were uniquely expressed in the milky, doughy, and mature stages, respectively. We performed three pairwise comparisons: milky vs. dough, milky vs. mature, and dough vs. mature, and identified 6753, 9540, and 2531 DEGs, respectively. The DEGs' abundance was higher in milky vs. mature, with 5527 up-regulated genes and 4013 down-regulated genes, while it was smaller in dough vs. mature, with 1419 up-regulated genes and 1112 down-regulated DEGs. This result was consistent with the changes in anthocyanin profiling, and the expression of structural, regulatory, and transporter genes involved in anthocyanin biosynthesis showed their highest expression at the dough stage. Through the gene expression profile and protein interaction network, we deciphered six main contributors of the anthocyanin peak observed at dough stage, including OsANS, OsDFR, OsGSTU34, OsMYB3, OsbHLH015, and OsWD40-50.

Discussion

This study is the first to report the investigation of anthocyanin and gene expression at three developmental stages of black rice caryopsis. The findings of this study could aid in predicting the best harvesting time to achieve maximum anthocyanin content and the best time to collect samples for various gene expression analysis, laying the groundwork for future research into the molecular mechanisms underlying rice caryopsis coloration.

Simultaneously mapping loci related to two plant architecture traits by phenotypic recombination BSA/BSR in peanut (Arachis hypogaea L.)

KEY MESSAGE

We developed a new method phenotypic recombination BSA/BSR (PR-BSA/BSR), which could simultaneously identify the candidate genomic regions associated with two traits in a segregating population. Bulked segregant analysis sequencing (BSA-seq) has been widely used for identifying the genomic regions affecting a certain trait. In this study, we developed a modified BSA/bulked segregant RNA-sequencing (BSR-seq) method, which we named phenotypic recombination BSA/BSR (PR-BSA/BSR), to simultaneously identify candidate genomic regions associated with two traits in a segregating population. Lateral branch angle (LBA) and flower-branch pattern (FBP) are two important traits associated with the peanut plant architecture because they affect the planting density and light use efficiency. We generated an F₆ population (with two segregating traits) derived from a cross between the inbred lines Pingdu9616 (erect and sequential; ES-type) and Florunner (spreading and alternating; SA-type). The selection of bulks with extreme phenotypes was a key step in this study. Specifically, 30 individuals with recombinant phenotypes [i.e., spreading and sequential (SS-type) and erect and alternating (EA-type)] were selected to generate two bulks. The transcriptomes of individuals were sequenced and then the loci related to LBA and FBP were simultaneously detected via a ΔSNP-index strategy, which involved the direction of positive and negative peaks in the ∆SNP-index plot. The LBA-related locus was mapped to a 6.82 Mb region (101,743,223-108,564,267 bp) on chromosome 15, whereas the FBP-related locus was mapped to a 2.16 Mb region (117,682,534-119,846,824 bp) on chromosome 12. Furthermore, the marker-based classical QTL mapping method was used to analyze the PF-F₆ population, which confirmed our PR-BSA/BSR results. Therefore, the PR-BSA/BSR method produces accurate and reliable data.

Selective Iodination Enables Anthocyanin Synthesis to Be More General

The current synthesis routes of anthocyanins are relatively complicated, which significantly hinders their development. We optimized the method by introducing a selective iodination reaction and also established a general scheme for preparing anthocyanin diglycosides. This method allows anthocyanin synthesis to require fewer steps and costs. Based on this, we prepared four common anthocyanins and two anthocyanin diglucosides and measured their antioxidant and anti-insulin resistance activities.

Grain and Leaf Anthocyanin Concentration Varies among Purple Rice Varieties and Growing Condition in Aerated and Flooded Soil

Anthocyanins are a group of pigments responsible for the red-blue color in plant parts, and have potential for health benefits and pharmaceutical ingredients. To evaluate whether anthocyanin concentrations in five purple rice varieties could be varied by water condition, plants were grown in waterlogged and aerobic (well-drained) soil. Grain anthocyanin concentration and grain yield were measured at maturity, while leaf anthocyanin concentrations were measured at booting and flowering stages. Four varieties grown under the waterlogged condition had 2.0−5.5 times higher grain anthocyanin than in the aerobic condition. There was a positive relationship between grain and leaf anthocyanin at booting in the waterlogged condition (r = 0.90, p < 0.05), while grain and leaf anthocyanin were positively correlated at flowering in both the waterlogged (r = 0.88, p < 0.05) and aerobic (r = 0.97, p < 0.01) conditions. The results suggest that water management should be adopted as a practical agronomic tool for improving the anthocyanin concentration of purple rice for specialist markets, but the specific responses between rice varieties to water management should be carefully considered.

DeepBSA: A deep-learning algorithm improves bulked segregant analysis for dissecting complex traits

Bulked segregant analysis (BSA) is a rapid, cost-effective method for mapping mutations and quantitative trait loci (QTLs) in animals and plants based on high-throughput sequencing. However, the algorithms currently used for BSA have not been systematically evaluated and are complex and fallible to operate. We developed a BSA method driven by deep learning, DeepBSA, for QTL mapping and functional gene cloning. DeepBSA is compatible with a variable number of bulked pools and performed well with various simulated and real datasets in both animals and plants. DeepBSA outperformed all other algorithms when comparing absolute bias and signal-to-noise ratio. Moreover, we applied DeepBSA to an F₂ segregating maize population of 7160 individuals and uncovered five candidate QTLs, including three well-known plant-height genes. Finally, we developed a user-friendly graphical user interface for DeepBSA, by integrating five widely used BSA algorithms and our two newly developed algorithms, that is easy to operate and can quickly map QTLs and functional genes. The DeepBSA software is freely available to non-commercial users at http://zeasystemsbio.hzau.edu.cn/tools.html and https://github.com/lizhao007/DeepBSA.

AAQSP increases mapping resolution of stable QTLs through applying NGS-BSA in multiple genetic backgrounds

In this study, we present AAQSP as an extension of existing NGS-BSA applications for identifying stable QTLs at high resolution. GhPAP16 and GhIQD14 fine mapped on chromosome D09 of upland cotton are identified as important candidate genes for lint percentage (LP). Bulked segregant analysis combined with next generation sequencing (NGS-BSA) allows rapid identification of genome sequence differences responsible for phenotypic variation. The NGS-BSA approach applied to crops mainly depends on comparing two bulked DNA samples of individuals from an F₂ population. Since some F₂ individuals still maintain high heterozygosity, heterosis will exert complications in pursuing NGS-BSA in such populations. In addition, the genetic background influences the stability of gene expression in crops, so some QTLs mapped in one segregating population may not be widely applied in crop improvement. The AAQSP (Association Analysis of QTL-seq on Semi-homologous Populations) reported in our study combines the optimized scheme of constructing BSA bulks with NGS-BSA analysis in two (or more) different parental genetic backgrounds for isolating the stable QTLs. With application of AAQSP strategy and construction of a high-density linkage map, we have successfully identified a QTL significantly related to lint percentage (LP) in cultivated upland cotton, followed by map-based cloning to dissect two candidate genes, GhPAP16 and GhIQD14. This study demonstrated that AAQSP can efficiently identify stable QTLs for complex traits of interest, and thus accelerate the genetic improvement of upland cotton and other crop plants.

Identification of candidate genes and clarification of the maintenance of the green pericarp of weedy rice grains

The weedy rice (Oryza sativa f. spontanea) pericarp has diverse colors (e.g., purple, red, light-red, and white). However, research on pericarp colors has focused on red and purple, but not green. Unlike many other common weedy rice resources, LM8 has a green pericarp at maturity. In this study, the coloration of the LM8 pericarp was evaluated at the cellular and genetic levels. First, an examination of their ultrastructure indicated that LM8 chloroplasts were normal regarding plastid development and they contained many plastoglobules from the early immature stage to maturity. Analyses of transcriptome profiles and differentially expressed genes revealed that most chlorophyll (Chl) degradation-related genes in LM8 were expressed at lower levels than Chl a/b cycle-related genes in mature pericarps, suggesting that the green LM8 pericarp was associated with inhibited Chl degradation in intact chloroplasts. Second, the F₂ generation derived from a cross between LM8 (green pericarp) and SLG (white pericarp) had a pericarp color segregation ratio of 9:3:4 (green:brown:white). The bulked segregant analysis of the F₂ populations resulted in the identification of 12 known genes in the chromosome 3 and 4 hotspot regions as candidate genes related to Chl metabolism in the rice pericarp. The RNA-seq and sqRT-PCR assays indicated that the expression of the Chl a/b cycle-related structural gene DVR (encoding divinyl reductase) was sharply up-regulated. Moreover, genes encoding magnesium-chelatase subunit D and the light-harvesting Chl a/b-binding protein were transcriptionally active in the fully ripened dry pericarp. Regarding the ethylene signal transduction pathway, the CTR (encoding an ethylene-responsive protein kinase) and ERF (encoding an ethylene-responsive factor) genes expression profiles were determined. The findings of this study highlight the regulatory roles of Chl biosynthesis- and degradation-related genes influencing Chl accumulation during the maturation of the LM8 pericarp.

Genomic Analysis Provides Insights Into the Plant Architecture Variations in in situ Conserved Chinese Wild Rice (Oryza rufipogon Griff.)

In situ conserved wild rice (Oryza rufipogon Griff.) is a promising source of alleles for improving rice production worldwide. In this study, we conducted a genomic analysis of an in situ conserved wild rice population (Guiping wild rice) growing at the center of wild rice genetic diversity in South China. Differences in the plant architecture in this population were investigated. An analysis using molecular markers revealed the substantial genetic diversity in this population, which was divided into subgroups according to the plant architecture. After resequencing representative individuals, the Guiping wild rice population was compared with other O. rufipogon and Oryza sativa populations. The results indicated that this in situ conserved wild rice population has a unique genetic structure, with genes that were introgressed from aromatic and O. sativa ssp. indica and japonica populations. The QTLs associated with plant architecture in this population were detected via a pair-wise comparison analysis of the sequencing data for multiple DNA pools. The results suggested that a heading date-related gene (DHD1) might be associated with variations in plant architecture and may have originated in cultivated rice. Our findings provide researchers with useful insights for future genomic analyses of in situ conserved wild rice populations.

Transcriptome and metabolome profiling in different stages of infestation of Eucalyptus urophylla clones by Ralstonia solanacearum

Eucalyptus urophylla is an economically important tree species that widely planted in tropical and sub-tropical areas around the world, which suffers significant losses due to Ralstonia solanacearum. However, little is known about the molecular mechanism of pathogen-response of Eucalyptus. We collected the vascular tissues of a E. urophylla clone infected by R. solanacearum in the laboratory, and combined transcriptome and metabolome analysis to investigate the defense responses of Eucalyptus. A total of 11 flavonoids that differentially accumulated at the first stage or a later stage after infection. The phenylpropanoid of p-coumaraldehyde, the two alkaloids trigonelline and DL-ephedrine, two types of traditional Chinese medicine with patchouli alcohol and 3-dihydrocadambine, and the amino acid phenylalanine were differentially accumulated after infection, which could be biomarkers indicating a response to R. solanacearum. Differentially expressed genes involved in plant hormone signal transduction, phenylpropanoids, flavonoids, mitogen-activated protein kinase (MAPK) signaling, and amino acid metabolism were activated at the first stage of infection or a later stage, indicating that they may participate in the defense against infection. This study is expected to deliver several insights into the molecular mechanism in response to pathogens in E. urophylla, and the findings have far-reaching implications in the control of E. urophylla pathogens.

Genome-wide association mapping and genomic prediction for kernel color traits in intermediate wheatgrass (Thinopyrum intermedium)

BACKGROUND

Intermediate wheatgrass (IWG) is a novel perennial grain crop currently undergoing domestication. It offers important ecosystem benefits while producing grain suitable for human consumption. Several aspects of plant biology and genetic control are yet to be studied in this new crop. To understand trait behavior and genetic characterization of kernel color in IWG breeding germplasm from the University of Minnesota was evaluated for the CIELAB components (L*, a*, b*) and visual differences. Trait values were used in a genome-wide association scan to reveal genomic regions controlling IWG's kernel color. The usability of genomic prediction in predicting kernel color traits was also evaluated using a four-fold cross validation method.

RESULTS

A wide phenotypic variation was observed for all four kernel color traits with pairwise trait correlations ranging from - 0.85 to 0.27. Medium to high estimates of broad sense trait heritabilities were observed and ranged from 0.41 to 0.78. A genome-wide association scan with single SNP markers detected 20 significant marker-trait associations in 9 chromosomes and 23 associations in 10 chromosomes using multi-allelic haplotype blocks. Four of the 20 significant SNP markers and six of the 23 significant haplotype blocks were common between two or more traits. Evaluation of genomic prediction of kernel color traits revealed the visual score to have highest mean predictive ability (r² = 0.53); r² for the CIELAB traits ranged from 0.29-0.33. A search for candidate genes led to detection of seven IWG genes in strong alignment with MYB36 transcription factors from other cereal crops of the Triticeae tribe. Three of these seven IWG genes had moderate similarities with R-A1, R-B1, and R-D1, the three genes that control grain color in wheat.

CONCLUSIONS

We characterized the distribution of kernel color in IWG for the first time, which revealed a broad phenotypic diversity in an elite breeding germplasm. Identification of genetic loci controlling the trait and a proof-of-concept that genomic selection might be useful in selecting genotypes of interest could help accelerate the breeding of this novel crop towards specific end-use.

Anthocyanin and Flavonol Glycoside Metabolic Pathways Underpin Floral Color Mimicry and Contrast in a Sexually Deceptive Orchid

Sexually deceptive plants secure pollination by luring specific male insects as pollinators using a combination of olfactory, visual, and morphological mimicry. Flower color is a key component to this attraction, but its chemical and genetic basis remains poorly understood. Chiloglottis trapeziformis is a sexually deceptive orchid which has predominantly dull green-red flowers except for the central black callus projecting from the labellum lamina. The callus mimics the female of the pollinator and the stark color contrast between the black callus and dull green or red lamina is thought to enhance the visibility of the mimic. The goal of this study was to investigate the chemical composition and genetic regulation of temporal and spatial color patterns leading to visual mimicry, by integrating targeted metabolite profiling and transcriptomic analysis. Even at the very young bud stage, high levels of anthocyanins were detected in the dark callus, with peak accumulation by the mature bud stage. In contrast, anthocyanin levels in the lamina peaked as the buds opened and became reddish-green. Coordinated upregulation of multiple genes, including dihydroflavonol reductase and leucoanthocyanidin dioxygenase, and the downregulation of flavonol synthase genes (FLS) in the callus at the very young bud stage underpins the initial high anthocyanin levels. Conversely, within the lamina, upregulated FLS genes promote flavonol glycoside over anthocyanin production, with the downstream upregulation of flavonoid O-methyltransferase genes further contributing to the accumulation of methylated flavonol glycosides, whose levels peaked in the mature bud stage. Finally, the peak anthocyanin content of the reddish-green lamina of the open flower is underpinned by small increases in gene expression levels and/or differential upregulation in the lamina in select anthocyanin genes while FLS patterns showed little change. Differential expression of candidate genes involved in specific transport, vacuolar acidification, and photosynthetic pathways may also assist in maintaining the distinct callus and contrasting lamina color from the earliest bud stage through to the mature flower. Our findings highlight that flower color in this sexually deceptive orchid is achieved by complex tissue-specific coordinated regulation of genes and biochemical pathways across multiple developmental stages.

Quality Improvement in Vegetable Greenhouse by Cadmium Pollution Remediation

Greenhouse vegetable production (GVP) has grown in importance as a source of public vegetable consumption as well as income for farmers. Due to the high cropping index, substantial agricultural input, and confined environment, numerous contaminants can accumulate in GVP. Polluted soil is treated with metal cadmium pollution remediation technology in order to improve the quality of vegetable greenhouse soil and increase crop yields. The heavy metal cadmium-contaminated soil in vegetable greenhouses is rectified utilizing three methods: chemical remediation, bioremediation, and physical remediation. Soil restoration with broom sedge planting might result in a 9.78 percent reduction in cadmium pollution. Planting broom sedge has a root > stem > leaf effect on pollution remediation. The elimination of cadmium from the soil around the anode can be as high as 75.1 percent. The clearance rate of the soil near the anode was 75.1 percent and 77.9 percent, respectively, when the anode cadmium mass fraction dropped fast. Hence this paper focuses on the reduction of cadmium pollution to improve the quality of GVP crop to yield more benefit. Chemical leaching is faster, more efficient, and less dangerous, with a higher application value. The approach of bioremediation is of low cost and creates no secondary contaminants. Physical electrodynamics is easy to understand and has a distinct effect.

Bulk segregation analysis in the NGS era: a review of its teenage years

Bulk segregation analysis (BSA) utilizes a strategy of pooling individuals with extreme phenotypes to conduct economical and rapidly linked marker screening or quantitative trait locus (QTL) mapping. With the development of next-generation sequencing (NGS) technology in the past 10 years, BSA methods and technical systems have been gradually developed and improved. At the same time, the ever-decreasing costs of sequencing accelerate NGS-based BSA application in different species, including eukaryotic yeast, grain crops, economic crops, horticultural crops, trees, aquatic animals, and insects. This paper provides a landscape of BSA methods and reviews the BSA development process in the past decade, including the sequencing method for BSA, different populations, different mapping algorithms, associated region threshold determination, and factors affecting BSA mapping. Finally, we summarize related strategies in QTL fine mapping combining BSA.

Metabolic Insight into Cold Stress Response in Two Contrasting Maize Lines

Maize (Zea mays L.) is sensitive to a minor decrease in temperature at early growth stages, resulting in deteriorated growth at later stages. Although there are significant variations in maize germplasm in response to cold stress, the metabolic responses as stress tolerance mechanisms are largely unknown. Therefore, this study aimed at providing insight into the metabolic responses under cold stress at the early growth stages of maize. Two inbred lines, tolerant (B144) and susceptible (Q319), were subjected to cold stress at the seedling stage, and their corresponding metabolic profiles were explored. The study identified differentially accumulated metabolites in both cultivars in response to induced cold stress with nine core conserved cold-responsive metabolites. Guanosine 3′,5′-cyclic monophosphate was detected as a potential biomarker metabolite to differentiate cold tolerant and sensitive maize genotypes. Furthermore, Quercetin-3-O-(2″′-p-coumaroyl)sophoroside-7-O-glucoside, Phloretin, Phloretin-2′-O-glucoside, Naringenin-7-O-Rutinoside, L-Lysine, L-phenylalanine, L-Glutamine, Sinapyl alcohol, and Feruloyltartaric acid were regulated explicitly in B144 and could be important cold-tolerance metabolites. These results increase our understanding of cold-mediated metabolic responses in maize that can be further utilized to enhance cold tolerance in this significant crop.

Combined Transcriptome and Metabolome Analysis of Musa nana Laur. Peel Treated With UV-C Reveals the Involvement of Key Metabolic Pathways

An increasing attention is being given to treat fruits with ultraviolet C (UV-C) irradiation to extend shelf-life, senescence, and protection from different diseases during storage. However, the detailed understanding of the pathways and key changes in gene expression and metabolite accumulation related to UV-C treatments are yet to be explored. This study is a first attempt to understand such changes in banana peel irradiated with UV-C. We treated Musa nana Laur. with 0.02 KJ/m2 UV-C irradiation for 0, 4, 8, 12, 15, and 18 days and studied the physiological and quality indicators. We found that UV-C treatment reduces weight loss and decay rate, while increased the accumulation of total phenols and flavonoids. Similarly, our results demonstrated that UV-C treatment increases the activity of defense and antioxidant system related enzymes. We observed that UV-C treatment for 8 days is beneficial for M. nana peels. The peels of M. nana treated with UV-C for 8 days were then subjected to combined transcriptome and metabolome analysis. In total, there were 425 and 38 differentially expressed genes and accumulated metabolites, respectively. We found that UV-C treatment increased the expression of genes in secondary metabolite biosynthesis related pathways. Concomitant changes in the metabolite accumulation were observed. Key pathways that were responsive to UV-C irradiation include flavonoid biosynthesis, phenylpropanoid bios6ynthesis, plant-pathogen interaction, MAPK signaling (plant), and plant hormone signal transduction pathway. We concluded that UV-C treatment imparts beneficial effects on banana peels by triggering defense responses against disease, inducing expression of flavonoid and alkaloid biosynthesis genes, and activating phytohormone and MAPK signaling pathways.

Broadening the horizon of crop research: a decade of advancements in plant molecular genetics to divulge phenotype governing genes

Advancements in sequencing, genotyping, and computational technologies during the last decade (2011-2020) enabled new forward-genetic approaches, which subdue the impediments of precise gene mapping in varied crops. The modern crop improvement programs rely heavily on two major steps-trait-associated QTL/gene/marker's identification and molecular breeding. Thus, it is vital for basic and translational crop research to identify genomic regions that govern the phenotype of interest. Until the advent of next-generation sequencing, the forward-genetic techniques were laborious and time-consuming. Over the last 10 years, advancements in the area of genome assembly, genotyping, large-scale data analysis, and statistical algorithms have led faster identification of genomic variations regulating the complex agronomic traits and pathogen resistance. In this review, we describe the latest developments in genome sequencing and genotyping along with a comprehensive evaluation of the last 10-year headways in forward-genetic techniques that have shifted the focus of plant research from model plants to diverse crops. We have classified the available molecular genetic methods under bulk-segregant analysis-based (QTL-seq, GradedPool-Seq, QTG-Seq, Exome QTL-seq, and RapMap), target sequence enrichment-based (RenSeq, AgRenSeq, and TACCA), and mutation-based groups (MutMap, NIKS algorithm, MutRenSeq, MutChromSeq), alongside improvements in classical mapping and genome-wide association analyses. Newer methods for outcrossing, heterozygous, and polyploid plant genetics have also been discussed. The use of k-mers has enriched the nature of genetic variants which can be utilized to identify the phenotype-causing genes, independent of reference genomes. We envisage that the recent methods discussed herein will expand the repertoire of useful alleles and help in developing high-yielding and climate-resilient crops.

Comparative Transcriptome Analysis Identifies Key Regulatory Genes Involved in Anthocyanin Metabolism During Flower Development in Lycoris radiata

Lycoris is used as a garden flower due to the colorful and its special flowers. Floral coloration of Lycoris is a vital trait that is mainly regulated via the anthocyanin biosynthetic pathway. In this study, we performed a comparative transcriptome analysis of Lycoris radiata petals at four different flower development stages. A total of 38,798 differentially expressed genes (DEGs) were identified by RNA sequencing, and the correlation between the expression level of the DEGs and the anthocyanin content was explored. The identified DEGs are significantly categorized into 'flavonoid biosynthesis,' 'phenylpropanoid biosynthesis,' 'Tropane, piperidine and pyridine alkaloid biosynthesis,' 'terpenoid backbone biosynthesis' and 'plant hormone signal transduction' by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. The candidate genes involved in anthocyanin accumulation in L. radiata petals during flower development stages were also identified, which included 56 structural genes (especially LrDFR1 and LrFLS) as well as 27 key transcription factor DEGs (such as C3H, GATA, MYB, and NAC). In addition, a key structural gene namely LrDFR1 of anthocyanin biosynthesis pathway was identified as a hub gene in anthocyanin metabolism network. During flower development stages, the expression level of LrDFR1 was positively correlated with the anthocyanin content. Subcellular localization revealed that LrDFR1 is majorly localized in the nucleus, cytoplasm and cell membrane. Overexpression of LrDFR1 increased the anthocyanin accumulation in tobacco leaves and Lycoris petals, suggesting that LrDFR1 acts as a positively regulator of anthocyanin biosynthesis. Our results provide new insights for elucidating the function of anthocyanins in L. radiata petal coloring during flower development.

Comparative transcriptome analysis identified important genes and regulatory pathways for flower color variation in Paphiopedilum hirsutissimum

BACKGROUND

Paphiopedilum hirsutissimum is a member of Orchidaceae family that is famous for its ornamental value around the globe, it is vulnerable due to over-exploitation and was listed in Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora, which prevents its trade across borders. Variation in flower color that gives rise to different flower patterns is a major trait contributing to its high ornamental value. However, the molecular mechanism underlying color formation in P. hirsutissimum still remains unexplored. In the present study, we exploited natural variation in petal and labellum color of Paphiopedilum plants and used comparative transcriptome analysis as well as pigment measurements to explore the important genes, metabolites and regulatory pathways linked to flower color variation in P. hirsutissimum.

RESULT

We observed that reduced anthocyanin and flavonoid contents along with slightly higher carotenoids are responsible for albino flower phenotype. Comparative transcriptome analysis identified 3287 differentially expressed genes (DEGs) among normal and albino labellum, and 3634 DEGs between normal and albino petals. Two genes encoding for flavanone 3-hydroxylase (F3H) and one gene encoding for chalcone synthase (CHS) were strongly downregulated in albino labellum and petals compared to normal flowers. As both F3H and CHS catalyze essentially important steps in anthocyanin biosynthesis pathway, downregulation of these genes is probably leading to albino flower phenotype via down-accumulation of anthocyanins. However, we observed the downregulation of major carotenoid biosynthesis genes including VDE, NCED and ABA2 which was inconsistent with the increased carotenoid accumulation in albino flowers, suggesting that carotenoid accumulation was probably controlled at post-transcriptional or translational level. In addition, we identified several key transcription factors (MYB73, MYB61, bHLH14, bHLH106, MADS-SOC1, AP2/ERF1, ERF26 and ERF87) that may regulate structural genes involved in flower color formation in P. hirsutissimum. Importantly, over-expression of some of these candidate TFs increased anthocyanin accumulation in tobacco leaves which provided important evidence for the role of these TFs in flower color formation probably via regulating key structural genes of the anthocyanin pathway.

CONCLUSION

The genes identified here could be potential targets for breeding P. hirsutissimum with different flower color patterns by manipulating the anthocyanin and carotenoid biosynthesis pathways.

De novo genome assembly of the potent medicinal plant Rehmannia glutinosa using nanopore technology

Rehmannia glutinosa is a potent medicinal plant with a significant importance in traditional Chinese medicine. Its root is enriched with various bioactive molecules mainly iridoids, possessing important pharmaceutical properties. However, the molecular biology and evolution of R. glutinosa have been largely unexplored. Here, we report a reference genome of R. glutinosa using Nanopore technology, Illumina and Hi-C sequencing. The assembly genome is 2.49 Gb long with a scaffold N50 length of 70 Mb and high heterozygosity (2%). Since R. glutinosa is an autotetraploid (4n = 56), the difference between each set of chromosomes is very small, and it is difficult to distinguish the two sets of chromosomes using Hi-C. Hence, only one set of the genome size was mounted to the chromosome level. Scaffolds covering 52.61% of the assembled genome were anchored on 14 pseudochromosomes. Over 67% of the genome consists of repetitive sequences dominated by Copia long terminal repeats and 48,475 protein-coding genes were predicted. Phylogenetic analysis corroborates the placement of R. glutinosa in the Orobanchaceae family. Our results indicated an independent and very recent whole genome duplication event that occurred 3.64 million year ago in the R. glutinosa lineage. Comparative genomics analysis demonstrated expansion of the UDP-dependent glycosyltransferases and terpene synthase gene families, known to be involved in terpenoid biosynthesis and diversification. Furthermore, the molecular biosynthetic pathway of iridoids has been clarified in this work. Collectively, the generated reference genome of R. glutinosa will facilitate discovery and development of important pharmacological compounds.

OsTTG1, a WD40 repeat gene, regulates anthocyanin biosynthesis in rice

Anthocyanins play an important role in the growth of plants, and are beneficial to human health. In plants, the MYB-bHLH-WD40 (MBW) complex activates the genes for anthocyanin biosynthesis. However, in rice, the WD40 regulators remain to be conclusively identified. Here, a crucial anthocyanin biosynthesis gene was fine mapped to a 43.4-kb genomic region on chromosome 2, and a WD40 gene OsTTG1 (Oryza sativa TRANSPARENT TESTA GLABRA1) was identified as ideal candidate gene. Subsequently, a homozygous mutant (osttg1) generated by CRISPR/Cas9 showed significantly decreased anthocyanin accumulation in various rice organs. OsTTG1 was highly expressed in various rice tissues after germination, and it was affected by light and temperature. OsTTG1 protein was localized to the nucleus, and can physically interact with Kala4, OsC1, OsDFR and Rc. Furthermore, a total of 59 hub transcription factor genes might affect rice anthocyanin biosynthesis, and LOC_Os01g28680 and LOC_Os02g32430 could have functional redundancy with OsTTG1. Phylogenetic analysis indicated that directional selection has driven the evolutionary divergence of the indica and japonica OsTTG1 alleles. Our results suggest that OsTTG1 is a vital regulator of anthocyanin biosynthesis, and an important gene resource for the genetic engineering of anthocyanin biosynthesis in rice and other plants.

Integrated metabolome and transcriptome analysis of the anthocyanin biosynthetic pathway in relation to color mutation in miniature roses

BACKGROUND

Roses are famous ornamental plants worldwide. Floral coloration is one of the most prominent traits in roses and is mainly regulated through the anthocyanin biosynthetic pathway. In this study, we investigated the key genes and metabolites of the anthocyanin biosynthetic pathway involved in color mutation in miniature roses. A comparative metabolome and transcriptome analysis was carried out on the Neptune King rose and its color mutant, Queen rose, at the blooming stage. Neptune King rose has light pink colored petals while Queen rose has deep pink colored petals.

RESULT

A total of 190 flavonoid-related metabolites and 38,551 unique genes were identified. The contents of 45 flavonoid-related metabolites, and the expression of 15 genes participating in the flavonoid pathway, varied significantly between the two cultivars. Seven anthocyanins (cyanidin 3-O-glucosyl-malonylglucoside, cyanidin O-syringic acid, cyanidin 3-O-rutinoside, cyanidin 3-O-galactoside, cyanidin 3-O-glucoside, peonidin 3-O-glucoside chloride, and pelargonidin 3-O-glucoside) were found to be the major metabolites, with higher abundance in the Queen rose. Thirteen anthocyanin biosynthetic related genes showed an upregulation trend in the mutant flower, which may favor the higher levels of anthocyanins in the mutant. Besides, eight TRANSPARENT TESTA 12 genes were found upregulated in Queen rose, probably contributing to a high vacuolar sequestration of anthocyanins. Thirty transcription factors, including two MYB and one bHLH, were differentially expressed between the two cultivars.

CONCLUSIONS

This study provides important insights into major genes and metabolites of the anthocyanin biosynthetic pathway modulating flower coloration in miniature rose. The results will be conducive for manipulating the anthocyanin pathways in order to engineer novel miniature rose cultivars with specific colors.

Proteome characterization of two contrasting soybean genotypes in response to different phosphorus treatments

Phosphorus (P) is an essential element for the growth and development of plants. Soybean (Glycine max) is an important food crop that is grown worldwide. Soybean yield is significantly affected by P deficiency in the soil. To investigate the molecular factors that determine the response and tolerance at low-P in soybean, we conducted a comparative proteomics study of a genotype with low-P tolerance (Liaodou 13, L13) and a genotype with low-P sensitivity (Tiefeng 3, T3) in a paper culture experiment with three P treatments, i.e. P-free (0 mmol·L-1), low-P (0.05 mmol·L-1) and normal-P (0.5 mmol·L-1). A total of 4126 proteins were identified in roots of the two genotypes. Increased numbers of differentially expressed proteins (DEPs) were obtained from low-P to P-free conditions compared to the normal-P treatment. All DEPs obtained in L13 (660) were upregulated in response to P deficiency, while most DEPs detected in T3 (133) were downregulated under P deficiency. Important metabolic pathways such as oxidative phosphorylation, glutathione metabolism and carbon metabolism were suppressed in T3, which could have affected the survival of the plants in P-limited soil. In contrast, L13 increased the metabolic activity in the 2-oxocarboxylic acid metabolism, carbon metabolism, glycolysis, biosynthesis of amino acids, pentose phosphatase, oxidative phosphorylation, other types of O-glycan biosynthesis and riboflavin metabolic pathways in order to maintain normal plant growth under P deficiency. Three key proteins I1KW20 (prohibitins), I1K3U8 (alpha-amylase inhibitors) and C6SZ93 (alpha-amylase inhibitors) were suggested as potential biomarkers for screening soybean genotypes with low-P tolerance. Overall, this study provides new insights into the response and tolerance to P deficiency in soybean.

Characterization of full-length transcriptome in Saccharum officinarum and molecular insights into tiller development

BACKGROUND

Although extensive breeding efforts are ongoing in sugarcane (Saccharum officinarum L.), the average yield is far below the theoretical potential. Tillering is an important component of sugarcane yield, however, the molecular mechanism underlying tiller development is still elusive. The limited genomic data in sugarcane, particularly due to its complex and large genome, has hindered in-depth molecular studies.

RESULTS

Herein, we generated full-length (FL) transcriptome from developing leaf and tiller bud samples based on PacBio Iso-Seq. In addition, we performed RNA-seq from tiller bud samples at three developmental stages (T0, T1 and T2) to uncover key genes and biological pathways involved in sugarcane tiller development. In total, 30,360 and 20,088 high-quality non-redundant isoforms were identified in leaf and tiller bud samples, respectively, representing 41,109 unique isoforms in sugarcane. Likewise, we identified 1063 and 1037 alternative splicing events identified in leaf and tiller bud samples, respectively. We predicted the presence of coding sequence for 40,343 isoforms, 98% of which was successfully annotated. Comparison with previous FL transcriptomes in sugarcane revealed 2963 unreported isoforms. In addition, we characterized 14,946 SSRs from 11,700 transcripts and 310 lncRNAs. By integrating RNA-seq with the FL transcriptome, 468 and 57 differentially expressed genes (DEG) were identified in T1vsT0 and T2vsT0, respectively. Strong up-regulation of several pyruvate phosphate dikinase and phosphoenolpyruvate carboxylase genes suggests enhanced carbon fixation and protein synthesis to facilitate tiller growth. Similarly, up-regulation of linoleate 9S-lipoxygenase and lipoxygenase genes in the linoleic acid metabolism pathway suggests high synthesis of key oxylipins involved in tiller growth and development.

CONCLUSIONS

Collectively, we have enriched the genomic data available in sugarcane and provided candidate genes for manipulating tiller formation and development, towards productivity enhancement in sugarcane.

Integrated transcriptome and metabolome analyses of biochar-induced pathways in response to Fusarium wilt infestation in pepper

The present study used soils contaminated with Fusarium oxysporum f. sp. capsici (CCS) and CCS amended with bamboo biochar (CCS + BC) to grow the pepper variety Qujiao No.1. The physiological performance, and transcriptome and metabolome profiling in leaf (L) and fruit (F) of Qujiao No.1 were conducted. Application of biochar improved soil properties, pepper plant nutrition and increased activities of enzymes related to pest/disease resistance, leading to superior physiological performance and lesser F. wilt disease incidence than plants from CCS. Most of the differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were involved in protein processing in endoplasmic reticulum (fruit), plant pathogen interaction (fruit), photosynthesis (leaf), phenylpropanoid biosynthesis (both tissues) and metabolic pathways (both tissues). Biochar improved plant photosynthesis, enhanced the immune system, energy production and increased stress signaling pathways. Overall, our results provide evidence of a number of pathways induced by biochar in pepper regulating its response to F. wilt disease.

Transcriptome and metabolome profiling in naturally infested Casuarina equisetifolia clones by Ralstonia solanacearum

Casuarina equisetifolia is an important pioneer tree and suffers from bacterial wilt caused by Ralstonia solanacearum. We collected resistant (R) and susceptible (S) C. equisetifolia clones naturally infected by R. solanacearum and compared their transcriptome and metabolome with a clone (CK) from a non-infested forest, in order to study their response and resistance to bacterial wilt. We identified 18 flavonoids differentially accumulated among the three clonal groups as potential selection biomarkers against R. solanacearum. Flavonoid synthesis-related genes were up-regulated in the resistant clones, probably enhancing accumulation of flavonoids and boosting resistance against bacterial wilt. The down-regulation of auxin/indoleacetic acid-related genes and up-regulation of brassinosteroid, salicylic acid and jasmonic acid-related differentially expressed genes in the R vs CK and R vs S clonal groups may have triggered defense signals and increased expression of defense-related genes against R. solanacearum. Overall, this study provides an important insight into pathogen-response and resistance to bacterial wilt in C. equisetifolia.

Genetic variation and gene expression of anthocyanin synthesis and transport related enzymes in Oryza sativa against thiocyanate

Plants exposed to environmental contaminants often synthesize anthocyanins (ATHs) as an approach to safeguard themselves from adverse impact. However, the overload of ATHs in plant cells can threaten their growth and development through proteins oxidization and intercalating with DNAs inside cells. In the present study, a microcosm hydroponic experiment was conducted using rice seedlings to investigate the molecular signaling pathways involved in regulating and controlling ATHs synthesis and transport exposed to thiocyanate (SCN^-). Our results indicated that SCN^- exposure significantly (p < 0.05) increased the expression of ATHs synthesis related genes (i.e., PAL, CHS, ANS, UFGT genes) in rice tissues, altered the activities of these ATHs synthesis related enzymes, and consequently elevated the ATHs content. However, SCN^- exposure significantly decreased the expression of ATHs transport related genes (i.e., GST, ABC, MATE genes) in rice seedlings, suggesting that SCN^- exposure have restrained ATHs transport from cytosol to vacuole in cells, eventually posing a significant adverse effect on cells survival. Our findings highlight on one of the plant aspects in managing the toxicity triggered by secondary metabolites under stress conditions.

Transcriptome and metabolome profiling provide insights into molecular mechanism of pseudostem elongation in banana

BACKGROUND

Banana plant height is an important trait for horticultural practices and semi-dwarf cultivars show better resistance to damages by wind and rain. However, the molecular mechanisms controlling the pseudostem height remain poorly understood. Herein, we studied the molecular changes in the pseudostem of a semi-dwarf banana mutant Aifen No. 1 (Musa spp. Pisang Awak sub-group ABB) as compared to its wild-type dwarf cultivar using a combined transcriptome and metabolome approach.

RESULTS

A total of 127 differentially expressed genes and 48 differentially accumulated metabolites were detected between the mutant and its wild type. Metabolites belonging to amino acid and its derivatives, flavonoids, lignans, coumarins, organic acids, and phenolic acids were up-regulated in the mutant. The transcriptome analysis showed the differential regulation of genes related to the gibberellin pathway, auxin transport, cell elongation, and cell wall modification. Based on the regulation of gibberellin and associated pathway-related genes, we discussed the involvement of gibberellins in pseudostem elongation in the mutant banana. Genes and metabolites associated with cell wall were explored and their involvement in cell extension is discussed.

CONCLUSIONS

The results suggest that gibberellins and associated pathways are possibly developing the observed semi-dwarf pseudostem phenotype together with cell elongation and cell wall modification. The findings increase the understanding of the mechanisms underlying banana stem height and provide new clues for further dissection of specific gene functions.

Proteomic Insight into the Symbiotic Relationship of Pinus massoniana Lamb and Suillus luteus towards Developing Al-Stress Resistance

Global warming significantly impacts forest range areas by increasing soil acidification or aluminum toxicity. Aluminum (Al) toxicity retards plant growth by inhibiting the root development process, hindering water uptake, and limiting the bioavailability of other essential micronutrients. Pinus massoniana (masson pine), globally recognized as a reforestation plant, is resistant to stress conditions including biotic and abiotic stresses. This resistance is linked to the symbiotic relationship with diverse ectomycorrhizal fungal species. In the present study, we investigated the genetic regulators as expressed proteins, conferring a symbiotic relationship between Al-stress resistance and Suillus luteus in masson pine. Multi-treatment trials resulted in the identification of 12 core Al-stress responsive proteins conserved between Al stress conditions with or without S. luteus inoculation. These proteins are involved in chaperonin CPN60-2, protein refolding and ATP-binding, Cu-Zn-superoxide dismutase precursor, oxidation-reduction process, and metal ion binding, phosphoglycerate kinase 1, glycolytic process, and metabolic process. Furthermore, 198 Al responsive proteins were identified specifically under S. luteus-inoculation and are involved in gene regulation, metabolic process, oxidation-reduction process, hydrolase activity, and peptide activity. Chlorophyll a-b binding protein, endoglucanase, putative spermidine synthase, NADH dehydrogenase, and glutathione-S-transferase were found with a significant positive expression under a combined Al and S. luteus treatment, further supported by the up-regulation of their corresponding genes. This study provides a theoretical foundation for exploiting the regulatory role of ectomycorrhizal inoculation and associated genetic changes in resistance against Al stress in masson pine.

Exogenous phytohormone application and transcriptome analysis of Mikania micrantha provides insights for a potential control strategy

Effective and complete control of the invasive weed Mikania micrantha is required to avoid increasing damages. We exogenously applied indole 3-acetic acid (IAA), gibberellin (GA), and N-(2-Chloro-4-pyridyl)-N'-phenylurea (CPPU), and their combinations i.e. IAA + CPPU (IC), GA + CPPU (GC), and GA + IAA + CPPU (GIC), at 5, 10, 25, 50, and 75 ppm against distilled water as a control (CK), to examine their effects on the weed. The increasing concentrations of these hormones when applied alone or in combination were fatal to M. micrantha and led towards the death of inflorescences and/or florets. CPPU and GIC were found as the most effective phytohormones. Transcriptome analysis revealed differential regulation of genes in auxin, cytokinin, gibberellin and abscisic acid signaling pathways, suggesting their role in the prohibition of axillary bud differentiation. Collectively, CPPU and GIC at a high concentration (75 ppm) could be used as a control measure to protect forests and other lands from the invasion of M. micrantha.