Overexpression of SrDXS1 and SrKAH enhances steviol glycosides content in transgenic Stevia plants

Bioactivities and biotechnological tools for obtaining bioactive metabolites from Stevia rebaudiana

Several natural compounds have already been isolated from the leaves of the Stevia rebaudiana, the main ones are stevioside and rebaudiosides, which are used commercially in the food and pharmaceutical industries because they are considered a low-calorie alternative for sweetening. Thus, the development of different strategies to increase the production of steviol glycosides, as well as the health benefits of these compounds with a sweet characteristic, are well-documented in the literature. However, there is a limited number of published works on the other bioactive metabolites present in S. rebaudiana. The objective of this review is to report the main basal and specialized metabolites present in the plant, their biological activities, and the different biotechnological tools used to obtain these metabolites from S. rebaudiana. The use of new natural sources of bioactive compounds with functional properties, such as S. rebaudiana, is highly relevant to the food and pharmaceutical industries.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-024-01776-w.

Advances in RNAi-based nanoformulations: revolutionizing crop protection and stress tolerance in agriculture

Nucleic acid-based therapeutics have the ability to tackle a wide range of diseases and stress tolerance that present significant obstacles for conventional approaches in agriculture. RNA-based medicines have become a promising approach, using nanoformulation treatments to specifically target certain diseases. Nanoformulations offer numerous benefits in comparison to alternative treatment methods, such as precise administration, minimal toxicity, and medication loading compatibility due to their bioactivity. There are a variety of nanoformulations available today, such as liposomes, polymeric nanoparticles (NPs), magnetic NPs, nanogels, and solid lipid nanoparticles (SLNs). RNA-based therapy employs intracellular gene nanoparticles containing messenger RNA (mRNA), which play an important role in stress management and pest as well as disease control. The adoption of mRNA-based technology paves the way for future technological progress. This review focuses on elucidating the process underlying the development of RNA interference (RNAi) and the diverse array of nanocarriers employed for the transportation of RNAi. Currently, this technique is being employed in the field of crop protection to combat diseases, pests, and environmental stress. The article highlights the benefits of RNAi mediated nanoformulations and discusses the significant obstacles that must be overcome to improve the viability of this technology for future applications.

Genome-Wide Mapping, Allelic Fingerprinting, and Haplotypes Validation Provide Insights Into the Genetic Control of Phenotypic Plasticity in Rice

Plant density significantly impacts photosynthesis, crop growth, and yield, thereby shaping the [CO2] fertilization effect and intricate physiological interactions in rice. An association panel of 171 rice genotypes was evaluated for physiological and yield-related traits, including the cumulative response index, under both normal planting density (NPD) and low planting density (LPD) conditions. LPD, serving as a proxy for elevated atmospheric [CO2], significantly increased all trait values, except for harvest index, compared to NPD. A genome-wide association study identified 172 QTNs, including 12 associated with multiple traits under NPD or LPD conditions. Candidate gene mining and network analysis within QTN regions identified potential candidates such as OsHAK1, RGA1, OsalphaCA3, OsalphaCA4, OsalphaCA5, OsCYP38, and OsPIN1, influencing various physiological and yield-related traits under LPD conditions. A significant relationship between the percentage of favorable alleles in genotypes and their performance under different conditions was observed. Potential haplotypes were validated using genotypes identified with contrasting [CO2] responses, grown under LPD and Free-Air [CO2] Enrichment facility. These findings can aid in selectively breeding genotypes with favorable alleles or haplotypes to enhance [CO2] responsiveness in rice. Incorporating greater phenotypic plasticity can help develop climate-smart rice varieties that increase grain yield and quality while mitigating losses from warming temperatures.

Integrative analysis of transcriptome and metabolome reveal molecular mechanism of tolerance to salt stress in rice

BACKGROUND

Salt stress is considered to be one of the major abiotic stresses influencing rice growth and productivity. To improve rice crop productivity in saline soils, it is essential to choose a suitable variety for mitigating salt stress and gain a deep understanding of the underlying mechanisms. The current study explored the salt tolerance mechanism of wild rice 'HD96-1 (salt resistive)' and conventional rice 'IR29 (salt sensitive)' by evaluating morph-physiological, transcriptomic, and metabolomic approaches.

RESULTS

Physiological data indicated that HD96-1 had higher chlorophyll content, higher photosynthetic efficiency, more stable Na+/K+, less H₂O₂, and lower electrolyte leakage under salt stress compared with IR29. Transcriptomic and metabolomic data showed that the expression of NHXs in IR29 was significantly down-regulated under salt stress, leading to a large accumulation of Na⁺ in the cytoplasm, and that the expression of CHLH, PORA, and PORB was significantly down-regulated, inhibiting chlorophyll synthesis. HD96-1 maintained the balance of Na⁺ and K⁺ by increasing the expression of NHX4, and there was no significant change in the expression of genes related to chlorophyll synthesis, which made HD96-1 more resistant to salt stress than IR29. In addition, HD96-1 inhibited the excessive synthesis of hydrogen peroxide (H₂O₂) and alleviated oxidative damage by significantly down-regulating the expression of ACX4 under salt stress. HD96-1 promoted the accumulation of isoleucine by up-regulating genes of branched-chain amino acid aminotransferase 2 and branched-chain amino acid aminotransferase 4 and might promote the synthesis of raffinose and stachyose by up-regulating the expression of the gene for galactitol synthase 2, which, in turn, maintained a stable osmotic pressure and relieved osmotic stress. We also found that IR29 and HD96-1 alleviated the inhibition of photosynthesis by salt stress by down-regulating the expression of light-harvesting chromophore protein complex (LHCH II)-related genes and reducing the excessive accumulation of glucose metabolites, respectively. In addition, HD96-1 enhances salt tolerance by regulating C2H2 and bHLH153 transcription factors.

CONCLUSION

Under salt stress, HD96-1 maintained ionic balance and photosynthetic efficiency by up-regulating the expression of NHX4 gene and reducing the overaccumulation of glucose metabolites, respectively, and mitigated osmotic stress and oxidative stress by down-regulating the expression of ACX4 and promoting the accumulation of isoleucine, respectively, thereby enhancing the adaptability to salt stress. IR29 maintained photosynthetic efficiency under salt stress by down-regulating the expression of light-harvesting chromophore protein complex (LHCH II)-related genes, thereby enhancing adaptation to salt stress.

Comparative transcriptomics reveals potential regulators of climate adaptation in Santalum album L. (Indian Sandalwood)

Santalum album L. (Indian Sandalwood), a valued tree species known for its fragrant heartwood and essential oil is facing increasing threat due to severe anthropogenic pressures compounded by climate change which has resulted in depletion of its adaptive gene pool. The present study investigates the transcriptome-level responses of nine sandalwood genotypes sourced from diverse climatic zones to identify adaptive genes in the species. Comparative transcriptomics predicted 727, 1141 and 479 differentially expressed transcripts (DETs) across wet vs. dry; monsoon vs. dry and wet vs. monsoon conditions, respectively, and majority of DETs were up-regulated in samples sourced from high rainfall areas. Transcripts including heat shock proteins, Zinc finger binding protein, ribosomal proteins, transcription factors and protein kinase were identified as probable regulators of climate adaptation in S. album. The expression changes of eight selected transcripts were further validated by real-time quantitative PCR. Protein-protein interaction analysis revealed key hub transcripts involved in climate response, while alternative splicing events in transcripts such as SURP and G-patch domain-containing protein 1-like protein, G-type lectin S-receptor-like serine/threonine protein kinase B120, Tetraspanin-3 and ARM repeat superfamily protein indicated the probable role of alternate splicing in increasing the transcript diversity during adaptation. This study presents the first insight into the molecular mechanisms of climate adaptation in the species and can form the basis for specific interventions such as selective breeding, genetic manipulation, and habitat management for conservation and long-term survival of sandalwood.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-025-04218-4.

Label free quantitative proteomic analysis reveals the physiological and biochemical responses of Arabidopsis thaliana to cinnamon essential oil

The increasing use of synthetic chemical herbicides has resulted in environmental, human and animal health issues. This has also led to the development of herbicide resistance in weed populations. The use of essential oils (EOs) can contribute to the development of effective, eco-friendly and nature-based alternatives to these chemical products due to their phytotoxicity and multisite action. Our study aimed to evaluate the proteomic response of Arabidopsis thaliana (A. thaliana) leaves to the application of a cinnamon essential oil (CEO) emulsion. The results showed that the application of CEO emulsion at a concentration of 6% severely impacted the proteomic profile of A. thaliana, especially for membrane proteins and those involved in the photosynthesis process. Interestingly, 40 proteins were identified and listed as the most differentially accumulated proteins in the leaves of A. thaliana. CEO decreased the expression of all the proteins associated with catabolism and anabolism processes while simultaneously increasing the expression levels of proteins involved in the response to oxidative stress. Overall, these findings allowed us to obtain a global view of the proteome response to CEO, opening promising perspectives for the development of natural herbicides, especially given the low probability of developing resistant weed populations.

Effects of elevated atmospheric ozone concentration on biomass and non-structural carbohydrates allocation of cherry radish

Regional increases in atmospheric O3 have phytotoxicity due to its strong oxidizing properties. Cherry radish (Raphanus sativus L.), with its sensitivity to O3 and rapid growth cycle, serves as an excellent model for investigating the effects of elevated O3 on plant physiological responses. To determine the response of cherry radish to elevated O3 levels, we used nine open-top chambers with three O3 concentrations (Ambient-LO; 70 ppb O3 above ambient-MO; 140 ppb O3 above ambient-HO) in Beijing, China to examine the MDA, chlorophyll contents, biomass, soluble sugar, and starch contents in response to O3 exposure. The results showed that: 1) elevated O3 (EO3) did not affect leaf chlorophyll contents but increased carotenoid contents; (2). The total biomass, hypocotyl biomass and hypocotyl size were significantly decreased by 41% and 49%, 51% and 37%, 53% and 40% by MO and HO, respectively. The above-to-below-ground biomass ratio (A/B) increased by 49% and 61% under MO and HO treatments; (3). HO and MO significantly increased leaf fructose, sucrose, and glucose contents by 192% and 79%, 40% and 37%, 110% and 45%, respectively; (4). leaf soluble sugar biomass proportion increased by 75% and 99% under HO and MO mainly contributed by fructose biomass proportion increase; (5). radish plant allocated more soluble sugar, starch and NSC biomass proportion to leaf but not hypocotyl under EO3. In conclusion, radishes exposed to O3 allocate more nonstructural carbohydrates (NSC) to the leaf at the expense of a great loss of hypocotyl biomass. This is possible mainly due to compensation of O3-induced damage via the sugar transport pathways, where transport is blocked so that the inefficient conversion of soluble sugars into starch can lead to reduced biomass accumulation and ultimately lower crop yields of radish. The role of radish fructose in protecting against or responding to O3 risks may be underestimated as it affects the overall sugar metabolism and transport within the plant.

Advancing vegetable genetics with gene editing: a pathway to food security and nutritional resilience in climate-shifted environments

As global populations grow and climate change increasingly disrupts agricultural systems, ensuring food security and nutritional resilience has become a critical challenge. In addition to grains and legumes, vegetables are very important for both human and animals because they contain vitamins, minerals, and fibre. Enhancing the ability of vegetables to withstand climate change threats is essential; however, traditional breeding methods face challenges due to the complexity of the genomic clonal multiplication process. In the postgenomic era, gene editing (GE) has emerged as a powerful tool for improving vegetables. GE can help to increase traits such as abiotic stress tolerance, herbicide tolerance, and disease resistance; improve agricultural productivity; and improve nutritional content and shelf-life by fine-tuning key genes. GE technologies such as Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 (CRISPR-Cas9) have revolutionized vegetable breeding by enabling specific gene modifications in the genome. This review highlights recent advances in CRISPR-mediated editing across various vegetable species, highlighting successful modifications that increase their resilience to climatic stressors. Additionally, it explores the potential of GE to address malnutrition by increasing the nutrient content of vegetable crops, thereby contributing to public health and food system sustainability. Additionally, it addresses the implementation of GE-guided breeding strategies in agriculture, considering regulatory, ethical, and public acceptance issues. Enhancing vegetable genetics via GE may provide a reliable and nutritious food supply for an expanding global population under more unpredictable environmental circumstances.

Enrichment of rice endosperm with anthocyanins by endosperm-specific expression of rice endogenous genes

A diet rich in anthocyanins can benefit human health against a broad spectrum of human diseases due to the high antioxidant activities of anthocyanins. Enrichment of anthocyanins in the starchy endosperm of rice is an effective solution to provide nutritional food in human diets. However, previous attempts failed to engineer anthocyanin biosynthesis in the rice endosperm by transgenic expression of rice endogenous genes. In this study, four rice endogenous genes, OsDFR (encoding dihydroflavonol 4-reductase), OsRb (encoding a bHLH family transcription factor), OsC1 (encoding an R2R3-MYB-type transcription factor) and OsPAC1 (encoding a WD40 class protein), were employed to rebuild the anthocyanin biosynthesis pathway in the rice endosperm. Endosperm-specific expression of OsDFR-OsRb-OsC1 (DRC) or OsDFR-OsPAC1-OsRb-OsC1 (DPRC) resulted in transgenic rice germplasm with dark purple grains. The expression of endogenous anthocyanin biosynthesis-related genes was significantly upregulated in the transgenic lines. Metabolomics analysis revealed a substantial increase in flavonoids flux, including 12 anthocyanins, in the polished grains of these transgenic lines. Our findings demonstrated that ectopic expressing a minimal set of three rice endogenous genes enabled de novo anthocyanin biosynthesis in the rice endosperm. This study contributes valuable insights into the molecular mechanisms underlying rice organ coloration and provides valuable guidance for future anthocyanin biofortification in crops.

Enhancing salt stress tolerance in Carthamus tinctorius L. through selenium soil treatment: anatomical, biochemical, and physiological insights

Selenium (Se) plays a crucial role in ameliorating the negative impact of abiotic stress. The present study was performed to elucidate the efficacy of soil treatment of Se in reducing salt-induced stress in Carthamus tinctorius L. In this study, three different levels of Na2SeO4 (0, 0.01, and 0.02 g kg- 1) and four levels of NaCl (0, 0.5, 1.5, and 2.5 g kg- 1) were applied. The findings revealed that while NaCl decreased seed germination parameters, growth characteristics, K+ content, relative water content (RWC), and photosynthetic pigments, it increased Na+ content, soluble carbohydrates, H2O2 content, and malondialdehyde (MDA) level. The application of Se showed a positive effect on seed germination and growth characteristics under salinity conditions, which is linked to alterations in anatomical, biochemical, and physiological factors. Anatomical studies showed that treatment with Se led to increased stem diameter, cortical parenchyma thickness, and pith diameter under salinity stress. However, variations in the thickness of the xylem and phloem did not reach statistical significance. The application of Se (0.02 g kg- 1) raised Na+ content (7.65%), K+ content (29.24%), RWC (15%), Chl a (17%), Chl b (21.73%), Chl a + b (16.9%), Car (4.22%), and soluble carbohydrates (11%) in plants subjected to NaCl (2.5 g kg- 1) stress. Furthermore, it decreased H2O2 (25.65%) and MDA (11.9%) in the shoots. The findings of the current study advocate the application of the Se-soil treating technique as an approach for salt stress mitigation in crops grown in saline conditions.

Enhanced Production of Rebaudioside D and Rebaudioside M through V155T Substitution in the Glycosyltransferase UGT91D2 from Stevia rebaudiana

Steviol glycosides (SGs) are noncaloric natural sweeteners found in the leaves of stevia (Stevia rebaudiana). These diterpene glycosides are biosynthesized by attaching varying numbers of monosaccharides, primarily glucose, to steviol aglycone. Rebaudioside (Reb) D and Reb M are highly glucosylated SGs that are valued for their superior sweetness and organoleptic properties, yet they are present in limited quantities in stevia leaves. This study aims to improve the substrate preference and catalytic efficiency of UDP-sugar-dependent glycosyltransferase UGT91D2 from stevia, which acts as a bottleneck in the biosynthesis of Reb D and Reb M. We modeled the structure of UGT91D2 and substituted two amino acid residues, Y134 and V155, which are located near the glycosyl acceptor and donor, respectively. Expression of the UGT91D2V155T in budding yeast significantly enhanced the production of Reb D and Reb M. Furthermore, transient expression in Nicotiana benthamiana revealed that the V155T substitution improved the glucosylation activity of UGT91D2, suggesting that this substitution enhances UDP-glucose binding and reduces side reactions involving nonglucose donors. By coexpressing multiple stevia UGT genes in N. benthamiana, we successfully produced highly glucosylated SGs from steviol. Our results provide insights into the substrate specificity of UGT91D2 and contribute to the engineering of SG biosynthesis.

Apple russeting-causes, physiology and control measures: A review

MAIN CONCLUSION

This review serves as a critical framework for guiding future research into the causes of russeting and the development of effective control strategies to enhance fruit quality. Russeting is a condition characterized by the formation of brown, corky patches on fruit skin which significantly impairs both the quality and market value of apples. This phenomenon arises from a complex interplay of various biotic and abiotic factors. Among the abiotic factors, environmental conditions, such as light, temperature, and relative humidity, as well as nutrient imbalances and the application of agrochemicals are important, whereas biotic factors include the influence of yeasts, fungi, viruses, and bacteria. The susceptibility of apple cultivars to russeting varies with yellow-fleshed varieties generally exhibiting higher incidences compared to red-fleshed ones. While russeting is partly determined by varietal and genetic factors, it can be mitigated through the implementation of effective cultural practices, nutrient management, plant growth regulators, biological agents, and pesticides. Understanding these dynamics provides valuable insights for developing future research strategies aimed at improving fruit quality and production.

Multi-locus genome wide association study uncovers genetics of fresh seed dormancy in groundnut

Pre-harvest sprouting (PHS) in groundnut leads to substantial yield losses and reduced seed quality, resulting in reduced market value of groundnuts. Breeding cultivars with 14-21 days of fresh seed dormancy (FSD) holds promise for precisely mitigating the yield and quality deterioration. In view of this, six multi-locus genome-wide association study (ML-GWAS) models alongside a single-locus GWAS (SL-GWAS) model were employed on a groundnut mini-core collection using multi season phenotyping and 58 K "Axiom_Arachis" array genotyping data. A total of 9 significant SNP-trait associations (STAs) for FSD were detected on A01, A04, A08, A09, B02, B04, B05, B07 and B09 chromosomes using six ML-GWAS models. Additionally, the SL-GWAS model identified 38 STAs across 14 chromosomes of groundnut. A single STA on chromosome B02 (qFSD-B02-1) was consistently identified in both ML-GWAS and SL-GWAS models. Furthermore, candidate gene mining identified nine high confidence genes viz., Cytochrome P450 705 A, Dormancy/auxin associated family protein, WRKY family transcription factor, Protein kinase superfamily protein, serine/threonine protein phosphatase, myb transcription factor, transcriptional regulator STERILE APETALA-like, ethylene-responsive transcription factor 7-like and F-box protein interaction domain protein as prime regulators involved in Abscisic acid/Gibberellic acid signaling pathways regulating dormancy/germination. In addition, three of the allele-specific markers developed from the identified STAs were validated across a diverse panel. These markers hold potential for increasing dormancy in groundnut through marker-assisted selection (MAS). Thus, this research offers insights into genetic and molecular mechanisms underlying groundnut seed dormancy in addition to providing markers and donors for breeding future varieties with 2-3 weeks of FSD.

Integrated metabolomic and transcriptomic analysis reveals the role of root phenylpropanoid biosynthesis pathway in the salt tolerance of perennial ryegrass

Perennial ryegrass (Lolium perenne) is a widely cultivated forage and turf grass species. Salt stress can severely damage the growth of grass plants. The genome-wide molecular mechanisms of salt tolerance have not been well understood in perennial grass species. In this study, the salt sensitive genotype P1 (PI265351, Chile) and the salt tolerant genotype P2 (PI368892, Algeria) of perennial ryegrass were subjected to 200 mM NaCl, and transcriptomics and metabolomics analyses were performed. A total of 5,728 differentially expressed genes (DEGs) were identified through pairwise comparisons. Antioxidant enzyme encoding genes (LpSOD1, LpCAT1), ion channel gene LpCaC1 and transcription factors (LpERFs, LpHSF1 and LpMYB1) were significantly upregulated in P2, suggesting their involvement in regulating expression of salt-responsive genes for salt tolerance. Functional analysis of DEGs revealed that biosynthesis of secondary metabolites, carbohydrate metabolism and signal transduction were the main pathways in response to salt stress. Weighted gene co-expression network analysis (WGCNA) based on RNA-Seq data showed that membrane transport and ABC transporters were significantly correlated with salt tolerance-related traits. The combined transcriptomics and metabolomics analysis demonstrated that the phenylpropanoid biosynthesis pathway was a major secondary metabolic pathway in the salt response of perennial ryegrass. Especially, the tolerant genotype P2 had greater amounts of upregulated phenylpropanoids, flavonoids and anthocyanins and higher expressions of relevant genes in the pathway than the sensitive genotype P1, indicating a role of phenylpropanoid biosynthesis for perennial ryegrass to adapt to salt stress. The results provided insights into the molecular mechanisms of perennial ryegrass adaptation to salinity and laid a base for genetic improvement of salt tolerance in perennial grass species.

Functional and biotechnological cues of potassium homeostasis for stress tolerance and plant development

Potassium (K+) is indispensable for the regulation of a plethora of functions like plant metabolism, growth, development, and abiotic stress responses. K+ is associated with protein synthesis and entangled in the activation of scores of enzymes, stomatal regulation, and photosynthesis. It has multiple transporters and channels that assist in the uptake, efflux, transport within the cell as well as from soil to different tissues, and the grain filling sites. While it is implicated in ion homeostasis during salt stress, it acts as a modulator of stomatal movements during water deficit conditions. K+ is reported to abate the effects of chilling and photooxidative stresses. K+ has been found to ameliorate effectively the co-occurrence of drought and high-temperature stresses. Nutrient deficiency of K+ makes leaves necrotic, leads to diminished photosynthesis, and decreased assimilate utilization highlighting the role it plays in photosynthesis. Notably, K+ is associated with the detoxification of reactive oxygen species (ROS) when plants are exposed to diverse abiotic stress conditions. It is irrefutable now that K+ reduces the activity of NADPH oxidases and at the same time maintains electron transport activity, which helps in mitigating the oxidative stress. K+ as a macronutrient in plant growth, the role of K+ during abiotic stress and the protein phosphatases involved in K+ transport have been reviewed. This review presents a holistic view of the biological functions of K+, its uptake, translocation, signaling, and the critical roles it plays under abiotic stress conditions, plant growth, and development that are being unraveled in recent times.

The landscape of sequence variations between resistant and susceptible hot peppers to predict functional candidate genes against bacterial wilt disease

BACKGROUND

Bacterial wilt (BW), caused by Ralstonia solanacearum (Ral), results in substantial yield losses in pepper crops. Developing resistant pepper varieties through breeding is the most effective strategy for managing BW. To achieve this, a thorough understanding of the genetic information connected with resistance traits is essential. Despite identifying three major QTLs for bacterial wilt resistance in pepper, Bw1 on chromosome 8, qRRs-10.1 on chromosome 10, and pBWR-1 on chromosome 1, the genetic information of related BW pepper varieties has not been sufficiently studied. Here, we resequenced two pepper inbred lines, C. annuum 'MC4' (resistant) and C. annuum 'Subicho' (susceptible), and analyzed genomic variations through SNPs and Indels to identify candidate genes for BW resistance.

RESULTS

An average of 139.5 Gb was generated among the two cultivars, with coverage ranging from 44.94X to 46.13X. A total of 8,815,889 SNPs was obtained between 'MC4' and 'Subicho'. Among them, 31,190 (0.35%) were non-synonymous SNPs (nsSNPs) corresponding to 10,926 genes, and these genes were assigned to 142 Gene Ontology (GO) terms across the two cultivars. We focused on three known BW QTL regions by identifying genes with sequence variants through gene set enrichment analysis and securing those belonging to high significant GO terms. Additionally, we found 310 NLR genes with nsSNP variants between 'MC4' (R) and 'Subicho' (S) within these regions. Also, we performed an Indel analysis on these genes. By integrating all this data, we identified eight candidate BW resistance genes, including two NLR genes with nsSNPs variations in qRRs-10.1 on chromosome 10.

CONCLUSION

We identified genomic variations in the form of SNPs and Indels by re-sequencing two pepper cultivars with contrasting traits for bacterial wilt. Specifically, the four genes associated with pBWR-1 and Bw1 that exhibit both nsSNP and Indel variations simultaneously in 'Subicho', along with the two NLR genes linked to qRRs-10.1, which are known for their direct involvement in immune responses, are identified as most likely BW resistance genes. These variants in leading candidate genes associated with BW resistance can be used as important markers for breeding pepper varieties.

Plant membrane transporters function under abiotic stresses: a review

MAIN CONCLUSION

In the present review, we discussed the detailed signaling cascades via membrane transporters that confer plant tolerance to abiotic stresses and possible significant use in plant development for climate-resilient crops. Plant transporters play significant roles in nutrient uptake, cellular balance, and stress responses. They facilitate the exchange of chemicals and signals across the plant's membrane by signal transduction, osmotic adjustment, and ion homeostasis. Therefore, research into plant transporters is crucial for understanding the mechanics of plant stress tolerance. Transporters have potential applications in crop breeding for increased stress resistance. We discuss new results about various transporter families (ABC, MATE, NRAMP, NRT, PHT, ZIP), including their functions in abiotic stress tolerance and plant development. Furthermore, we emphasize the importance of transporters in plant responses to abiotic stresses such as drought, cold, salt, and heavy metal toxicity, low light, flooding, and nutrient deficiencies. We discuss the transporter pathways and processes involved in diverse plant stress responses. This review discusses recent advances in the role of membrane transporters in abiotic stress tolerance in Arabidopsis and other crops. The review contains the genes discovered in recent years and associated molecular mechanisms that improve plants' ability to survive abiotic stress and their possible future applications by integrating membrane transporters with other technologies.

Enhancing salt tolerance in rice genotypes through exogenous melatonin application by modulating growth patterns and antistress agents

Melatonin is a bioactive molecule with an important role in plants responding to various abiotic and biotic stresses. This study aims to determine the role of melatonin in rice under salt stress. This study used a factorial completely randomized design. The first factor was local rice varieties (IR64 and Silaun), and the second factor was plant treatments (control, 1 µM melatonin, 150 mM NaCl, 150 mM NaCl + 1µM melatonin). This study shows that exogenous melatonin can increase plant growth, such as plant height, root length, stem length, leaf length, leaf area, and plant biomass under salt stress compared to treatment without melatonin. Exogenous melatonin can increase the total chlorophyll content, relative water content, and proline content, reduce the total sodium content, and increase potassium absorption under conditions of salinity stress. Melatonin is also able to scavenge ROS in plants, resulted the decrease in ROS and MDA content. In terms of gene expression, OsAPX1 and cytosolic APX exhibited the highest expression in IR64 under combined salt and melatonin treatment, while GPOD, Mn-SOD, and Cu/Zn-SOD were upregulated under various conditions in both varieties. Additionally, OsLEA showed high expression in both varieties under control conditions, and CAT was significantly upregulated under salt stress. Our findings indicate that exogenous melatonin has the potential to enhance various factors under salt stress and helping in the recovery of rice plants from sodium (Na+) damage.

Exploration on cold adaptation of Antarctic lichen via detection of positive selection genes

Lichen as mutualistic symbiosis is the dominant organism in various extreme terrestrial environment on Earth, however, the mechanisms of their adaptation to extreme habitats have not been fully elucidated. In this study, we chose the Antarctic dominant lichen species Usnea aurantiacoatra to generate a high-quality genome, carried out phylogenetic analysis using maximum likelihood and identify genes under positive selection. We performed functional enrichment analysis on the positively selected genes (PSGs) and found that most of the PSGs focused on transmembrane transporter activity and vacuole components. This suggest that the genes related to energy storage and transport in Antarctic U. aurantiacoatra were affected by environmental pressure. Inside of the 86 PSGs screened, two protein interaction networks were identified, which were RNA helicase related proteins and regulator of G-protein signaling related proteins. The regulator of the G-protein signaling gene (UaRGS1) was chosen to perform further verification by the lichen genetic manipulation system Umbilicaria muhlenbergii. Given that the absence of UmRgs1 resulted in elevated lethality to cold shock, the role for UaRgs1 in Antarctic U. aurantiacoatra resistance to cold can be inferred. The investigation of lichen adaptation to extreme environments at the molecular level will be opened up.

Revolutionizing soybean genomics: How CRISPR and advanced sequencing are unlocking new potential

Soybean Glycine max L., paleopolyploid genome, poses challenges to its genetic improvement. However, the development of reference genome assemblies and genome sequencing has completely changed the field of soybean genomics, allowing for more accurate and successful breeding techniques as well as research. During the single-cell revolution, one of the most advanced sequencing tools for examining the transcriptome landscape is single-cell RNA sequencing (scRNA-seq). Comprehensive resources for genetic improvement of soybeans may be found in the SoyBase and other genomics databases. CRISPR-Cas9 genome editing technology provides promising prospects for precise genetic modifications in soybean. This method has enhanced several soybean traits, including as yield, nutritional value, and resistance to both biotic and abiotic stresses. With base editing techniques that allow for precise DNA modifications, the use of CRISPR-Cas9 is further increased. With the availability of the reference genome for soybeans and the following assembly of wild and cultivated soybeans, significant chromosomal rearrangements and gene duplication events have been identified, offering new perspectives on the complex genomic structure of soybeans. Furthermore, major single nucleotide polymorphisms (SNPs) linked to stachyose and sucrose content have been found through genome-wide association studies (GWAS), providing important tools for enhancing soybean carbohydrate profiles. In order to open up new avenues for soybean genetic improvement, future research approaches include investigating transcriptional divergence processes, enhancing genetic resources, and incorporating CRISPR-Cas9 technologies.

Effect of biochar amendment on bacterial community and their role in nutrient acquisition in spinach (Spinacia oleracea L.) grown under elevated CO2

Global climate change is anticipated to shift the soil bacterial community structure and plant nutrient utilization. The use of biochar amendment can positively influence soil bacterial community structure, soil properties, and nutrient use efficiency of crops. However, little is known about the underlying mechanism and response of bacterial community structure to biochar amendment, and its role in nutrient enhancement in soil and plants under elevated CO2. Herein, the effect of biochar amendment (0, 0.5, 1.5%) on soil bacterial community structure, spinach growth, physiology, and soil and plant nutrient status were investigated under two CO2 concentrations (400 and 600 μmol mol-1). Findings showed that biochar application 1.5% (B.2.E) significantly increased the abundance of the bacterial community responsible for growth and nutrient uptake i.e. Firmicutes (42.25%) Bacteroidetes (10.46%), and Gemmatimonadetes (125.75%) as compared to respective control (CK.E) but interestingly abundance of proteobacteria decreased (9.18%) under elevated CO2. Furthermore, the soil available N, P, and K showed a significant increase in higher biochar-amended treatments under elevated CO2. Spinach plants exhibited a notable enhancement in growth and photosynthetic pigments when exposed to elevated CO2 levels and biochar, as compared to ambient CO2 conditions. However, there was variability observed in the leaf gas exchange attributes. Elevated CO2 reduced spinach roots and leaves nutrient concentration. In contrast, the biochar amendment (B2.E) enhanced root and shoot Zinc (494.99%-155.33%), magnesium (261.15%-183.37%), manganese (80.04%-152.86%), potassium (576.24%-355.17%), calcium (261.88%-165.65%), copper (325.42%-282.53%) and iron (717.63%-177.90%) concentration by influencing plant physiology and bacterial community. These findings provide insights into the interaction between plant and bacterial community under future agroecosystems in response to the addition of biochar contributing to a deeper understanding of ecological dynamics.

MdABCI17 acts as a positive regulator to enhance apple resistance to Botryosphaeria dothidea

The ATP-binding cassette (ABC) superfamily is involved in numerous complex biological processes. However, the understanding of ABCs in plant pathogen defense, particularly against Botryosphaeria dothidea, remains limited. In this study, we identified MdABCI17 that plays a positive role in apple resistance to B. dothidea. Overexpression of MdABCI17 significantly enhanced the resistance of apple calli and fruits to B. dothidea. Our findings revealed that the jasmonic acid (JA) content and the expression of genes associated with JA biosynthesis and signal transduction were higher in stable MdABCI17-overexpressing apple calli than that of wild-type after inoculation with B. dothidea. Similar results were obtained for apple fruits with transient overexpression of MdABCI17. Our research indicates that MdABCI17 enhances apple resistance to B. dothidea through the JA signaling pathway. We further determined that MdABCI17 plays a crucial role in the apple's response to JA signaling. Moreover, exogenous methyl jasmonate (MeJA) treatment significantly enhanced the effectiveness of MdABCI17 in boosting apple resistance to B. dothidea. We proposed a positive feedback regulatory loop between MdABCI17-mediated apple resistance to B. dothidea and JA signal. In summary, our study offers new insights into the role of ABC superfamily members in the control of plant disease resistance.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01501-9.

Less is more: CRISPR/Cas9-based mutations in DND1 gene enhance tomato resistance to powdery mildew with low fitness costs

Powdery mildew (PM), triggered by Oidium neolycopersici, represents a significant threat and a major concern for the productivity of tomato plants (Solanum lycopersicum L.). The presence of susceptibility (S) genes in plants facilitates pathogen proliferation and their dysfunction can lead to a recessively inherited broad-spectrum and durable type of resistance. Past studies have demonstrated that disrupting the function of DND1 (Defense No Death 1) increases plant resilience against various pathogens, such as powdery mildew (PM), but this comes at the cost of negatively affecting the overall health and vigor of the plant. To investigate the possibility of minimizing the adverse effects of the dnd1 mutation while boosting disease resistance, a CRISPR-Cas9 construct with four single guide RNAs targeting three exons of SlDND1 (Solyc02g088560.4.1) was designed and introduced into the tomato variety Moneymaker (MM) through Agrobacterium tumefaciens-mediated transformation. Three T1 lines (named E1, E3 and E4) were crossed with MM and then selfed to produce TF2 families. All the TF2 plants in homozygous state dnd1/dnd1, showed reduced PM symptoms compared to the heterozygous (DND1/dnd1) and wild type (DND1/DND1) ones. Two full knock-out (KO) mutant events (E1 and E4) encoding truncated DND1 proteins, exhibited clear dwarfness and auto-necrosis phenotypes, while mutant event E3 harbouring deletions of 3 amino acids, showed normal growth in height with less auto-necrotic spots. Analysis of the 3D structures of both the reference and the mutant proteins revealed significant conformational alterations in the protein derived from E3, potentially impacting its function. A dnd1/dnd1 TF2 line (TV181848-9, E3) underwent whole-genome sequencing using Illumina technology, which confirmed the absence of off-target mutations in selected genomic areas. Additionally, no traces of the Cas9 gene were detected, indicating its elimination through segregation. Our findings confirm the role of DND1 as an S-gene in tomato because impairment of this gene leads to a notable reduction in susceptibility to O. neolycopersici. Moreover, we provide, for the first time, a dnd1 mutant allele (E3) that exhibits fitness advantages in comparison with previously reported dnd1 mutant alleles, indicating a possible way to breed with dnd1 mutants.

Agrobacterium tumefaciens-Mediated Plant Transformation: A Review

Agrobacterium tumefaciens-mediated plant transformation is the most dominant technique for the transformation of plants. It is used to transform monocotyledonous and dicotyledonous plants. A. tumefaciens apply for stable and transient transformation, random and targeted integration of foreign genes, as well as genome editing of plants. The Advantages of this method include cheapness, uncomplicated operation, high reproducibility, a low copy number of integrated transgenes, and the possibility of transferring larger DNA fragments. Engineered endonucleases such as CRISPR/Cas9 systems, TALENs, and ZFNs can be delivered with this method. Nowadays, Agrobacterium-mediated transformation is used for the Knock in, Knock down, and Knock out of genes. The transformation effectiveness of this method is not always desirable. Researchers applied various strategies to improve the effectiveness of this method. Here, a general overview of the characteristics and mechanism of gene transfer with Agrobacterium is presented. Advantages, updated data on the factors involved in optimizing this method, and other useful materials that lead to maximum exploitation as well as overcoming obstacles of this method are discussed. Moreover, the application of this method in the generation of genetically edited plants is stated. This review can help researchers to establish a rapid and highly effective Agrobacterium-mediated transformation protocol for any plant species.

Heat-stress-responsive HvHSFA2e gene regulates the heat and drought tolerance in barley through modulation of phytohormone and secondary metabolic pathways

KEY MESSAGE

The heat stress transcription factor HSFA2e regulates both temperature and drought response via hormonal and secondary metabolism alterations. High temperature and drought are the primary yield-limiting environmental constraints for staple food crops. Heat shock transcription factors (HSF) terminally regulate the plant abiotic stress responses to maintain growth and development under extreme environmental conditions. HSF genes of subclass A2 predominantly express under heat stress (HS) and activate the transcriptional cascade of defense-related genes. In this study, a highly heat-inducible HSF, HvHSFA2e was constitutively expressed in barley (Hordeum vulgare L.) to investigate its role in abiotic stress response and plant development. Transgenic barley plants displayed enhanced heat and drought tolerance in terms of increased chlorophyll content, improved membrane stability, reduced lipid peroxidation, and less accumulation of ROS in comparison to wild-type (WT) plants. Transcriptome analysis revealed that HvHSFA2e positively regulates the expression of abiotic stress-related genes encoding HSFs, HSPs, and enzymatic antioxidants, contributing to improved stress tolerance in transgenic plants. The major genes of ABA biosynthesis pathway, flavonoid, and terpene metabolism were also upregulated in transgenics. Our findings show that HvHSFA2e-mediated upregulation of heat-responsive genes, modulation in ABA and flavonoid biosynthesis pathways enhance drought and heat stress tolerance.

A genome-wide association study reveals novel loci and candidate genes associated with plant height variation in Medicago sativa

BACKGROUND

Plant height (PH) is an important agronomic trait influenced by a complex genetic network. However, the genetic basis for the variation in PH in Medicago sativa remains largely unknown. In this study, a comprehensive genome-wide association analysis was performed to identify genomic regions associated with PH using a diverse panel of 220 accessions of M. sativa worldwide.

RESULTS

Our study identified eight novel single nucleotide polymorphisms (SNPs) significantly associated with PH evaluated in five environments, explaining 8.59-12.27% of the phenotypic variance. Among these SNPs, the favorable genotype of chr6__31716285 had a low frequency of 16.4%. Msa0882400, located proximal to this SNP, was annotated as phosphate transporter 3;1, and its role in regulating alfalfa PH was supported by transcriptome and candidate gene association analysis. In addition, 21 candidate genes were annotated within the associated regions that are involved in various biological processes related to plant growth and development.

CONCLUSIONS

Our findings provide new molecular markers for marker-assisted selection in M. sativa breeding programs. Furthermore, this study enhances our understanding of the underlying genetic and molecular mechanisms governing PH variations in M. sativa.

Adoption of CRISPR-Cas for crop production: present status and future prospects

Background

Global food systems in recent years have been impacted by some harsh environmental challenges and excessive anthropogenic activities. The increasing levels of both biotic and abiotic stressors have led to a decline in food production, safety, and quality. This has also contributed to a low crop production rate and difficulty in meeting the requirements of the ever-growing population. Several biotic stresses have developed above natural resistance in crops coupled with alarming contamination rates. In particular, the multiple antibiotic resistance in bacteria and some other plant pathogens has been a hot topic over recent years since the food system is often exposed to contamination at each of the farm-to-fork stages. Therefore, a system that prioritizes the safety, quality, and availability of foods is needed to meet the health and dietary preferences of everyone at every time.

Methods

This review collected scattered information on food systems and proposes methods for plant disease management. Multiple databases were searched for relevant specialized literature in the field. Particular attention was placed on the genetic methods with special interest in the potentials of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and Cas (CRISPR associated) proteins technology in food systems and security.

Results

The review reveals the approaches that have been developed to salvage the problem of food insecurity in an attempt to achieve sustainable agriculture. On crop plants, some systems tend towards either enhancing the systemic resistance or engineering resistant varieties against known pathogens. The CRISPR-Cas technology has become a popular tool for engineering desired genes in living organisms. This review discusses its impact and why it should be considered in the sustainable management, availability, and quality of food systems. Some important roles of CRISPR-Cas have been established concerning conventional and earlier genome editing methods for simultaneous modification of different agronomic traits in crops.

Conclusion

Despite the controversies over the safety of the CRISPR-Cas system, its importance has been evident in the engineering of disease- and drought-resistant crop varieties, the improvement of crop yield, and enhancement of food quality.

CRISPR/Cas9 based genome editing of Phytoene desaturase (PDS) gene in chilli pepper (Capsicum annuum L.)

An effective CRISPR/Cas9 reagent delivery system has been developed in a commercially significant crop, the chilli pepper using a construct harboring two distinct gRNAs targeting exons 14 and 15 of the Phytoene desaturase (CaPDS) gene, whose loss-of-function mutation causes a photo-bleaching phenotype and impairs the biosynthesis of carotenoids. The construct carrying two sgRNAs was observed to create visible albino phenotypes in cotyledons regenerating on a medium containing 80 mg/L kanamycin, and plants regenerated therefrom after biolistic-mediated transfer of CRISPR/Cas9 reagents into chilli pepper cells. Analysis of CRISPR/Cas9 genome-editing events, including kanamycin screening of mutants and assessing homozygosity using the T7 endonuclease assay (T7E1), revealed 62.5 % of transformed plants exhibited successful editing at the target region and displayed both albino and mosaic phenotypes. Interestingly, the sequence analysis showed that insertions and substitutions were present in all the plant lines in the targeted CaPDS region. The detected mutations were mostly 12- to 24-bp deletions that disrupted the exon-intron junction, along with base substitutions and the insertion of 1-bp at the protospacer adjacent motif (PAM) region of the target site. The reduction in essential photosynthetic pigments (chlorophyll a, chlorophyll b and carotenoid) in knockout chilli pepper lines provided further evidence that the CaPDS gene had been functionally disrupted. In this present study, we report that the biolistic delivery of CRISPR/Cas9 reagents into chilli peppers is very effective and produces multiple mutation events in a short span of time.

Pectin as a biofunctional food: comprehensive overview of its therapeutic effects and antidiabetic-associated mechanisms

Pectin is a complex polysaccharide found in a variety of fruits and vegetables. It has been shown to have potential antidiabetic activity along with other biological activities, including cholesterol-lowering properties, antioxidant activity, anti-inflammatory and immune-modulatory effects, augmented healing of diabetic foot ulcers and other health benefits. There are several pectin-associated antidiabetic mechanisms, such as the regulation of glucose metabolism, reduction of oxidative stress, increased insulin sensitivity, appetite suppression and modulation of the gut microbiome. Studies have shown that pectin supplementation has antidiabetic effects in different animal models and in vitro. In human studies, pectin has been found to have a positive effect on blood glucose control, particularly in individuals with type 2 diabetes. Pectin also shows synergistic effects by enhancing the potency and efficacy of antidiabetic drugs when taken together. In conclusion, pectin has the potential to be an effective antidiabetic agent. However, further research is needed to fully understand its detailed molecular mechanisms in various animal models, functional food formulations and safety profiles for the treatment and management of diabetes and associated complications in humans. The current study was carried out to provide the critical approach towards therapeutical potential, anti-diabetic potential and underlying molecular mechanisms on the basis of existing knowledge.

Selenium and other heavy metal levels in different rice brands commonly consumed in Pretoria, South Africa

For centuries, rice has been a dietary staple food partially due to its accessibility, affordability, and nutritional content. However, it has been documented that plants can bioaccumulate trace elements from soil and store them in their tissues therefore necessitating monitoring of its nutritional quality. The current study investigated the Selenium and heavy metal contents of various brands of rice obtained from different retail stores in Pretoria, South Africa. The analysis was carried out using different rice samples and different methods/stages of cooking rice including the analysis of rinsed rice water (RW), raw rice (RR), cooked rice (CR), and cooked rice water (CW), for trace elements content using the Inductive Couple Plasma Mass Spectrometry. The results revealed that the Se content ranged from 0.013 ± 0.01 mg/kg - 0.089 ± 0.06 mg/kg in RR, 0.013 ± 0.01 mg/kg - 0.046 ± 0.01 mg/kg in CR, 0.01 ± 0.01mg/kg- 0.028 ± 0.00 mg/kg in RW and 0.01 ± 0.01 mg/kg - 0.048 ± 0.01 mg/kg in CW. The calculated estimated dietary intake (EDI) of Se was recorded as follows; raw rice (7.06 × 10-5 mg/day), cooked rice (5.01 × 10-5 mg/day), water from cooked rice (4.54 × 10-5 mg/day) and rinsed water of raw rice (3.97 × 10-5 mg/day). The concentrations of all other heavy metals measured were within the WHO-recommended limits. The HQ for all the trace metals in all the samples did not exceed one, implying that there is no health risk from trace metals analysed in this study from the consumption of the rice brands used in this study. The results of this study demonstrated that reliance on rice alone for the supply of Se may be inadequate owing to the values obtained in our study. Constant monitoring of the nutritional contents of food products may be required to improve the overall nutritional well-being of the consumers.

Exploring low-dose gamma radiation effects on monoterpene biosynthesis in Thymus vulgaris: insights into plant defense mechanisms

Thymus vulgaris, commonly known as thyme, is a plant renowned for producing monoterpenes. This study aimed to understand the effects of low-dose gamma radiation, specifically in the range of 1-5 Gy, on various traits of Thymus vulgaris, providing context on its importance in agricultural and medicinal applications. The research explored morpho-physiological, biochemical, and gene-expression responses in thyme plants under no gamma- and gamma-ray exposure conditions. The study revealed complex relationships between gamma-ray doses and plant characteristics. In particular, shoot and root lengths initially increased with low doses (1-3 Gy) but decreased at higher doses (5 Gy), suggesting a dose-dependent threshold effect. Similarly, shoot and root fresh weights displayed an initial increase followed by a decline with increasing doses. Biochemical parameters showed dose-dependent responses, with low to moderate doses (1-3 Gy) stimulating enzyme activities and high doses (5 Gy) inhibiting them. Gene expression analysis was focused on the following specific genes: thymol synthase, γ-terpinene synthase, and carvacrol synthase. Low to moderate doses increased the expression of these genes, resulting in increased production of bioactive compounds. However, higher doses had diminished effects or suppressed gene expression. Metabolite analysis demonstrated dose-dependent responses, with moderate doses enhancing secondary metabolite production, while higher doses provided limited benefits. These findings underscore the implications of using gamma radiation to enhance secondary metabolite production in plants and its potential applications in agriculture, medicine, and environmental science. The study emphasizes the potential of gamma radiation as an external stressor to influence plant responses and highlights the importance of understanding such effects in various fields.

Unlocking growth potential: Synergistic potassium fertilization for enhanced yield, nutrient uptake, and energy fractions in Chinese cabbage

The implementation of integrated potassium management presents a viable approach for augmenting plant growth, yield, and nutrient uptake while enhancing soil nutrient availability. A field experiment was executed during the rabi season of 2020, employing a randomized complete block design encompassing eight treatments involving standard (100%) and reduced (75% and 50%) rates of the recommended dose of potassium (RDK) administered through muriate of potash (MOP). Treatments included variations in the incorporation/exclusion of plant growth-promoting rhizobacteria (PGPR), farmyard manure (FYM) at 25% of potassium recommendation, and foliar application of nano potash. The use of 100% RDK +25% K augmentation through FYM + PGPR and nano K fertilizer spray at 25 and 40 DAS (T8) exhibited significant enhancements in green fodder yield (64.0 ± 2.2 t ha-1) over control with no potassium application (47.3 ± 3.7 t ha-1) and found at par with and 75% RDK + 25% K augmentation through FYM + PGPR and nano K fertilizer spray at 25 and 40 DAS (T7). These treatments yielded maximum percent increase for plant height (34.9%), leaf count (38.5%), leaf dimensions (28.8-31.5%), stem girth (25.84%), root volume (27.0%), and root length (37.64%), observed at the harvest stage compared to control (T1-no potassium application). The treatment T8 was on par with T7 and recorded highest uptake of macro (N, P, and K) and micro (Zn, Fe, Cu, and Mn) nutrients. While soil parameters such as available nitrogen and potassium levels were notably increased through the application of treatment T7 across various treatment combinations and found significantly superiority over treatment T8. Multivariate analysis also highlighted treatment T7 is more efficient in maintaining sustainability. Hence, based on the present findings it can be concluded that application of 75% RDK +25% K augmentation through FYM + PGPR and nano K fertilizer spray at 25 and 40 DAS (T7) can be recommended for achieving enhanced productivity and soil fertility improvement within agricultural systems.

From genes to ecosystems: Decoding plant tolerance mechanisms to arsenic stress

Arsenic (As), a metalloid of considerable toxicity, has become increasingly bioavailable through anthropogenic activities, raising As contamination levels in groundwater and agricultural soils worldwide. This bioavailability has profound implications for plant biology and farming systems. As can detrimentally affect crop yield and pose risks of bioaccumulation and subsequent entry into the food chain. Upon exposure to As, plants initiate a multifaceted molecular response involving crucial signaling pathways, such as those mediated by calcium, mitogen-activated protein kinases, and various phytohormones (e.g., auxin, methyl jasmonate, cytokinin). These pathways, in turn, activate enzymes within the antioxidant system, which combat the reactive oxygen/nitrogen species (ROS and RNS) generated by As-induced stress. Plants exhibit a sophisticated genomic response to As, involving the upregulation of genes associated with uptake, chelation, and sequestration. Specific gene families, such as those coding for aquaglyceroporins and ABC transporters, are key in mediating As uptake and translocation within plant tissues. Moreover, we explore the gene regulatory networks that orchestrate the synthesis of phytochelatins and metallothioneins, which are crucial for As chelation and detoxification. Transcription factors, particularly those belonging to the MYB, NAC, and WRKY families, emerge as central regulators in activating As-responsive genes. On a post-translational level, we examine how ubiquitination pathways modulate the stability and function of proteins involved in As metabolism. By integrating omics findings, this review provides a comprehensive overview of the complex genomic landscape that defines plant responses to As. Knowledge gained from these genomic and epigenetic insights is pivotal for developing biotechnological strategies to enhance crop As tolerance.

Multiplexed gene editing in citrus by using a multi-intron containing Cas9 gene

Several expression systems have been developed in clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (CRISPR/Cas9) framework allowing for gene editing of disease-associated genes across diverse citrus varieties. In this study, we present a new approach employing a multi-intron containing Cas9 gene plus multiple gRNAs separated with tRNA sequences to target the phytoene desaturase gene in both 'Carrizo' citrange and 'Duncan' grapefruit. Notably, using this unified vector significantly boosted editing efficiency in both citrus varieties, showcasing mutations in all three designated targets. The implementation of this multiplex gene editing system with a multi-intron-containing Cas9 plus a gRNA-tRNA array demonstrates a promising avenue for efficient citrus genome editing, equipping us with potent tools in the ongoing battle against several diseases such as canker and huanglongbing.

Screening for drought tolerance and genetic diversity of wheat varieties using agronomic and molecular markers

BACKGROUND

The future predictions for frequent and severe droughts will represent a significant threat to wheat yield and food security. In this context, breeding has proven to be the most efficient approach to enhance wheat productivity in dry environments.

METHODS AND RESULTS

In this study, both agronomic and molecular-based approaches were used to evaluate the response of twenty-eight Tunisian wheat varieties to drought stress. The primary objective was to screen these varieties for drought tolerance using molecular and agro-morphological markers. All varieties were significantly affected by drought stress regarding various traits including total dry matter, straw length, flag leaf area, number of senescent leaves, SPAD value, grain yield and grain number. Furthermore, substantial variability in drought-stress tolerance was observed among wheat genotypes. The cluster analysis and principal component analyses confirmed the existence of genotypic variation in growth and yield impairments induced by drought. The stress susceptibility index (SSI) and tolerance index (TOL) proved to be the most effective indices and were strongly correlated with the varying levels of genotypic tolerance. The genotyping evaluation resulted in the amplification of 101 alleles using highly polymorphic 12 SSR markers, showed an average polymorphism of 74%.

CONCLUSIONS

Taken together, the combination of agronomic and molecular approaches revealed that Karim, Td7, D117 and Utique are the most drought-tolerant wheat varieties. These varieties are particularly promising candidates for genetic improvements and can be utilized as potential genitors for future breeding programs in arid and semi-arid regions.

The reduced growth due to elevated CO2 concentration hinders the sexual reproduction of mature Northern pipevine (Aristolochia contorta Bunge)

The phenology has gained considerably more attention in recent times of climate change. The transition from vegetative to reproductive phases is a critical process in the life history of plants, closely tied to phenology. In an era of climate change, understanding how environmental factors affect this transition is of paramount importance. This study consisted of field surveys and a greenhouse experiment on the reproductive biology of Northern pipevine (Aristolochia contorta Bunge). During field surveys, we investigated the environmental factors and growth characteristics of mature A. contorta, with a focus on both its vegetative and reproductive phases. In its successful flowering during the reproductive phase, A. contorta grew under the conditions of 40% relative light intensity and 24% soil moisture content, and had a vertical rhizome. In the greenhouse experiments, we examined the impact of increased CO2 concentration on the growth and development of 10-year-old A. contorta, considering the effect of rhizome direction. Planted with a vertical rhizome direction, A. contorta exhibited sufficient growth for flowering under ambient CO2 concentrations. In contrast, when planted with a horizontal rhizome direction, it was noted to significantly impede successful growth and flowering under elevated CO2 concentrations. This hindered the process of flowering, highlighting the pivotal role of substantial vegetative growth in achieving successful flowering. Furthermore, we observed a higher number of underground buds and shoots under the conditions of elevated CO2 concentration and a horizontal rhizome direction instead of flowering. Elevated CO2 concentrations also exhibited diverse effects on mature A. contorta's flower traits, resulting in smaller flower size, shorter longevity, and reduced stigma receptivity, and pollen viability. The study shed light on elevated CO2 concentrations can hinder growth, potentially obstructing sexual reproduction and diminishing genetic diversity.

CRISPR/Cas9-mediated mutagenesis of phytoene desaturase in pigeonpea and groundnut

The CRISPR/Cas9 technology, renowned for its ability to induce precise genetic alterations in various crop species, has encountered challenges in its application to grain legume crops such as pigeonpea and groundnut. Despite attempts at gene editing in groundnut, the low rates of transformation and editing have impeded its widespread adoption in producing genetically modified plants. This study seeks to establish an effective CRISPR/Cas9 system in pigeonpea and groundnut through Agrobacterium-mediated transformation, with a focus on targeting the phytoene desaturase (PDS) gene. The PDS gene is pivotal in carotenoid biosynthesis, and its disruption leads to albino phenotypes and dwarfism. Two constructs (one each for pigeonpea and groundnut) were developed for the PDS gene, and transformation was carried out using different explants (leaf petiolar tissue for pigeonpea and cotyledonary nodes for groundnut). By adjusting the composition of the growth media and refining Agrobacterium infection techniques, transformation efficiencies of 15.2% in pigeonpea and 20% in groundnut were achieved. Mutation in PDS resulted in albino phenotype, with editing efficiencies ranging from 4 to 6%. Sequence analysis uncovered a nucleotide deletion (A) in pigeonpea and an A insertion in groundnut, leading to a premature stop codon and, thereby, an albino phenotype. This research offers a significant foundation for the swift assessment and enhancement of CRISPR/Cas9-based genome editing technologies in legume crops.

Endophytic fungi from Himalayan silver birch as potential source of plant growth enhancement and secondary metabolite production

Mountain biodiversity is under unparalleled pressure due to climate change, necessitating in-depth research on high-altitude plant's microbial associations which are crucial for plant survival under stress conditions. Realizing that high-altitude tree line species of Himalaya are completely unexplored with respect to the microbial association, the present study aimed to elucidate plant growth promoting and secondary metabolite producing potential of culturable endophytic fungi of Himalayan silver birch (Betula utilis D. Don). ITS region sequencing revealed that the fungal isolates belong to Penicillium species, Pezicula radicicola, and Paraconiothyrium archidendri. These endophytes were psychrotolerant in nature with the potential to produce extracellular lytic activities. The endophytes showed plant growth promoting (PGP) traits like phosphorus solubilization and production of siderophore, indole acetic acid (IAA), and ACC deaminase. The fungal extracts also exhibited antagonistic potential against bacterial pathogens. Furthermore, the fungal extracts were found to be a potential source of bioactive compounds including the host-specific compound-betulin. Inoculation with fungal suspension improved seed germination and biomass of soybean and maize crops under net house conditions. In vitro PGP traits of the endophytes, supported by net house experiments, indicated that fungal association may support the growth and survival of the host in extreme cold conditions.

New insights into QTNs and potential candidate genes governing rice yield via a multi-model genome-wide association study

BACKGROUND

Rice (Oryza sativa L.) is one of the globally important staple food crops, and yield-related traits are prerequisites for improved breeding efficiency in rice. Here, we used six different genome-wide association study (GWAS) models for 198 accessions, with 553,229 single nucleotide markers (SNPs) to identify the quantitative trait nucleotides (QTNs) and candidate genes (CGs) governing rice yield.

RESULTS

Amongst the 73 different QTNs in total, 24 were co-localized with already reported QTLs or loci in previous mapping studies. We obtained fifteen significant QTNs, pathway analysis revealed 10 potential candidates within 100kb of these QTNs that are predicted to govern plant height, days to flowering, and plot yield in rice. Based on their superior allelic information in 20 elite and 6 inferior genotypes, we found a higher percentage of superior alleles in the elite genotypes in comparison to inferior genotypes. Further, we implemented expression analysis and enrichment analysis enabling the identification of 73 candidate genes and 25 homologues of Arabidopsis, 19 of which might regulate rice yield traits. Of these candidate genes, 40 CGs were found to be enriched in 60 GO terms of the studied traits for instance, positive regulator metabolic process (GO:0010929), intracellular part (GO:0031090), and nucleic acid binding (GO:0090079). Haplotype and phenotypic variation analysis confirmed that LOC_OS09G15770, LOC_OS02G36710 and LOC_OS02G17520 are key candidates associated with rice yield.

CONCLUSIONS

Overall, we foresee that the QTNs, putative candidates elucidated in the study could summarize the polygenic regulatory networks controlling rice yield and be useful for breeding high-yielding varieties.

Revisiting Changes in Growth, Physiology and Stress Responses of Plants under the Effect of Enhanced CO2 and Temperature

Climate change has universally affected the whole ecosystem in a unified manner and is known to have improbable effects on agricultural productivity and food security. Carbon dioxide (CO2) and temperature are the major environmental factors that have been shown to increase sharply during the last century and are directly responsible for affecting plant growth and development. A number of previous investigations have deliberated the positive effects of elevated CO2 on plant growth and development of various C3 crops, while detrimental effects of enhanced temperature on different crop plants like rice, wheat, maize and legumes are generally observed. A combined effect of elevated CO2 and temperature has yet to be studied in great detail; therefore, this review attempts to delineate the interactive effects of enhanced CO2 and temperature on plant growth, development, physiological and molecular responses. Elevated CO2 maintains leaf photosynthesis rate, respiration, transpiration and stomatal conductance in the presence of elevated temperature and sustains plant growth and productivity in the presence of both these environmental factors. Concomitantly, their interaction also affects the nutritional quality of seeds and leads to alterations in the composition of secondary metabolites. Elevated CO2 and temperature modulate phytohormone concentration in plants, and due to this fact, both environmental factors have substantial effects on abiotic and biotic stresses. Elevated CO2 and temperature have been shown to have mitigating effects on plants in the presence of other abiotic stress agents like drought and salinity, while no such pattern has been observed in the presence of biotic stress agents. This review focuses on the interactive effects of enhanced CO2 and temperature on different plants and is the first of its kind to deliver their combined responses in such detail.

Improvement and regulation of steviol glycoside biosynthesis in Stevia rebaudiana Bertoni

Stevia rebaudiana Bertoni is a natural sweetener plant that is progressively used not only for its sweetening properties but also for its medicinal properties. The plant contains steviol glycoside (SG) which is reported to be up to 300 times sweeter than sucrose. The plant is said to have no side effects on human health and has been approved by FDA. On the basis of previous studies and available databases, this review discusses the extensive understanding of the different approaches for enhancements of SG in S. rebaudiana. To improve the SG biosynthesis, application of different stress, elicitors, induction of polyploidy, cell culture, genetic engineering, and transcriptomic approaches have been addressed. A brief discussion about the cloning and characterization of important genes of the metabolic pathway of SG biosynthesis is also discussed along with various metabolic engineering pathways viz. methylerythritol 4- phosphate (MEP) and mevalonate (MVA) pathways. This review paper also discusses the different aspects as well as the effects of various nanoparticles on S. rebaudiana growth and development, as well as SG biosynthesis.

Elevated CO2 concentration enhances drought resistance of soybean by regulating cell structure, cuticular wax synthesis, photosynthesis, and oxidative stress response

The atmospheric [CO2] and the frequency and intensity of extreme weather events such as drought are increased, leading to uncertainty to soybean production. Elevated [CO2] (eCO2) partially mitigates the adverse effects of drought stress on crop growth and photosynthetic performance, but the mitigative mechanism is not well understood. In this study, soybean seedlings under drought stress simulated by PEG-6000 were grown in climate chambers with different [CO2] (400 μmol mol-1 and 700 μmol mol-1). The changes in anatomical structure, wax content, photosynthesis, and antioxidant enzyme were investigated by the analysis of physiology and transcriptome sequencing (RNA-seq). The results showed that eCO2 increased the thickness of mesophyll cells and decreased the thickness of epidermal cells accompanied by reduced stomatal conductance, thus reducing water loss in soybean grown under drought stress. Meanwhile, eCO2 up-regulated genes related to wax anabolism, thus producing more epidermal wax. Under drought stress, eCO2 increased net photosynthetic rate (PN), ribulose-1,5-bisphosphate carboxylase/oxygenase activity, and alerted the gene expressions in photosynthesis. The increased sucrose synthesis and decreased sucrose decomposition contributed to the progressive increase in the soluble saccharide contents under drought stress with or without eCO2. In addition, eCO2 increased the expressions of genes associated with peroxidase (POD) and proline (Pro), thus enhancing POD activity and Pro content and improving the drought resistance in soybean. Taken together, these findings deepen our understanding of the effects of eCO2 on alleviating drought stress in soybean and provide potential target genes for the genetic improvement of drought tolerance in soybean.

Cloning and expression study of a high-affinity nitrate transporter gene from Zea mays L

A nitrate transporter gene, named B46NRT2.1, from salt-tolerant Zea mays L. B46 has been cloned. B46NRT2.1 contained the same domain belonging to the major facilitator superfamily (PLN00028). The results of the phylogenetic tree indicated that B46NRT2.1 exhibits sequence similarity and the closest relationship with those known nitrate transporters of the NRT2 family. Through RT-qPCR, we found that the expression of B46NRT2.1 mainly happens in the root and leaf. Moreover, the treatment with NaCl, Na₂CO₃, and NaHCO₃ could significantly increase the expression of B46NRT2.1. B46NRT2.1 was located in the plasma membrane. Through the study of yeast and plant salt response brought by B46NRT2.1 overexpression, we have preliminary knowledge that the expression of B46NRT2.1 makes yeast and plants respond to salt shock. There are 10 different kinds of cis-acting regulatory elements (CRES) in the promotor sequences of B46NRT2.1 gene using the PlantCARE web server to analyze. It mainly includes hormone response, abscisic acid, salicylic acid, gibberellin, methyl jasmonate, and auxin. The B46NRT2.1 gene's co-expression network showed that it was co-expressed with a number of other genes in several biological pathways, including regulation of NO₃ long-distance transit, modulation of nitrate sensing and metabolism, nitrate assimilation, and transduction of Jasmonic acid-independent wound signal. The results of this work should serve as a good scientific foundation for further research on the functions of the NRT2 gene family in plants (inbred line B46), and this research adds to our understanding of the molecular mechanisms under salt tolerance.

Catalase associated with antagonistic changes of abscisic acid and gibberellin response, biosynthesis and catabolism is involved in eugenol-inhibited seed germination in rice

KEY MESSAGE

The inhibitory effect of eugenol on rice germination is mediated by a two-step modulatory process: Eugenol first regulates the antagonism of GA and ABA, followed by activation of catalase activity. The natural monoterpene eugenol has been reported to inhibit preharvest sprouting in rice. However, the inhibitory mechanism remains obscure. In this study, simultaneous monitoring of GA and ABA responses by the in vivo GA and ABA-responsive dual-luciferase reporter system showed that eugenol strongly inhibited the GA response after 6 h of imbibition, whereas eugenol significantly enhanced the ABA response after 12 h of imbibition. Gene expression analysis revealed that eugenol significantly induced the ABA biosynthetic genes OsNCED2, OsNCED3, and OsNCED5, but notably suppressed the ABA catabolic genes OsABA8ox1 and OsABA8ox2. Conversely, eugenol inhibited the GA biosynthetic genes OsGA3ox2 and OsGA20ox4 but significantly induced the GA catabolic genes OsGA2ox1 and OsGA2ox3 during imbibition. OsABI4, the key signaling regulator of ABA and GA antagonism, was notably induced before 12 h and suppressed after 24 h by eugenol. Moreover, eugenol markedly reduced the accumulation of H2O2 in seeds after 36 h of imbibition. Further analysis showed that eugenol strongly induced catalase activity, protein accumulation, and the expression of three catalase genes. Most importantly, mitigation of eugenol-inhibited seed germination was found in the catc mutant. These findings indicate that catalase associated with antagonistic changes of ABA and GA is involved in the sequential regulation of eugenol-inhibited seed germination in rice.

Cucumber grafting on indigenous cucurbit landraces confers salt tolerance and improves fruit yield by enhancing morpho-physio-biochemical and ionic attributes

Pakistan is the 8th most climate-affected country in the globe along with a semi-arid to arid climate, thereby the crops require higher irrigation from underground water. Moreover,  ~ 70% of pumped groundwater in irrigated agriculture is brackish and a major cause of secondary salinization. Cucumber (Cucumis sativus L.) is an important vegetable crop with an annual growth rate of about 3.3% in Pakistan. However, it is a relatively salt-sensitive crop. Therefore, a dire need for an alternate environment-friendly technology like grafting for managing salinity stress in cucumber by utilizing the indigenous cucurbit landraces. In this regard, a non-perforated pot-based study was carried out in a lath house to explore indigenous cucurbit landraces; bottle gourd (Lagenaria siceraria) (cv. Faisalabad Round), pumpkin (Cucurbit pepo. L) (cv. Local Desi Special), sponge gourd (Luffa aegyptiaca) (cv. Local) and ridge gourd (Luffa acutangula) (cv. Desi Special) as rootstocks for inducing salinity tolerance in cucumber (cv. Yahla F1). Four different salts (NaCl) treatments; T0 Control (2.4 dSm-1), T1 (4 dSm-1), T2 (6 dSm-1) and T3 (8 dSm-1) were applied. The grafted cucumber plants were transplanted into the already-induced salinity pots (12-inch). Different morpho-physio-biochemical, antioxidants, ionic, and yield attributes were recorded. The results illustrate that increasing salinity negatively affected the growing cucumber plants. However, grafted cucumber plants showed higher salt tolerance relative to non-grafted ones. Indigenous bottle gourd landrace (cv. Faisalabad Round) exhibited higher salt tolerance compared to non-grafted cucumber plants due to higher up-regulation of morpho-physio-biochemical, ionic, and yield attributes that was also confirmed by principal component analysis (PCA). Shoot and root biomass, chlorophylls contents (a and b), activities of superoxide dismutase (SOD), catalase (CAT) and peroxidase (POX) enzymes, antioxidants scavenging activity (ASA), ionic (↑ K and Ca, ↓ Na), and yield-related attributes were found maximum in cucumber plants grafted onto indigenous bottle gourd landrace. Hence, the indigenous bottle gourd landrace 'cv. Faisalabad round' may be utilized as a rootstock for cucumber under a mild pot-based saline environment. However, indigenous bottle gourd landrace 'cv. Faisalabad round' may further be evaluated as rootstocks in moderate saline field conditions for possible developing hybrid rootstock and, subsequently, sustainable cucumber production.

Trehalose metabolism coordinates transcriptional regulatory control and metabolic requirements to trigger the onset of cassava storage root initiation

Cassava storage roots (SR) are an important source of food energy and raw material for a wide range of applications. Understanding SR initiation and the associated regulation is critical to boosting tuber yield in cassava. Decades of transcriptome studies have identified key regulators relevant to SR formation, transcriptional regulation and sugar metabolism. However, there remain uncertainties over the roles of the regulators in modulating the onset of SR development owing to the limitation of the widely applied differential gene expression analysis. Here, we aimed to investigate the regulation underlying the transition from fibrous (FR) to SR based on Dynamic Network Biomarker (DNB) analysis. Gene expression analysis during cassava root initiation showed the transition period to SR happened in FR during 8 weeks after planting (FR8). Ninety-nine DNB genes associated with SR initiation and development were identified. Interestingly, the role of trehalose metabolism, especially trehalase1 (TRE1), in modulating metabolites abundance and coordinating regulatory signaling and carbon substrate availability via the connection of transcriptional regulation and sugar metabolism was highlighted. The results agree with the associated DNB characters of TRE1 reported in other transcriptome studies of cassava SR initiation and Attre1 loss of function in literature. The findings help fill the knowledge gap regarding the regulation underlying cassava SR initiation.

Role of gibberellins, neem leaf extract, and serine in improving wheat growth and grain yield under drought-triggered oxidative stress

The foliar application of gibberellins (GA3), neem leaf extract (NLE) and serine can be proven as effective growth regulating agents to counter drought stress-related deleterious effects. The literature about the collaborative role of these substances in foliar spray application under drought stress is not available to this date. No single report is available in literature on combine foliar application of GA3, NLE, and serine in improving wheat growth and yield under drought-triggered oxidative stress. The objective of this study was to induct tolerance against drought stress in order to sustain maximum growth and yield of wheat varieties (Anaj-2017 and Galaxy-2013) with foliar applications of GA3, NLE, and serine. The current field trial was designed to disclose the protective role of these substances in wheat varieties (Anaj-2017 and Galaxy-2013) under water-deficit stress. Two irrigation levels, i.e., control (normal irrigation) and water stress (water deficit irrigation), and 5 levels of GA3, NLE and serine i.e., control (water spray), GA3 (10.0 ppm), NLE (10.0%), serine (9.5 mM), and mixture (GA3 + NLE + serine) in a 1:1:1 ratio was applied. Application of these substances improved the pigments (Chlorophyll a, b), carotenoids, growth, biomass, and grain yield traits of both wheat varieties under water-deficit stress. Activities of antioxidant enzymes (POD, CAT and SOD), and non-enzymatic antioxidants (proline, total phenolic contents, anthocyanin and free amino acids) were up-regulated under drought stress and with foliar spray treatments. The foliar applications of these substances reduced the drought triggered overproduction of lipid peroxidation (MDA) and H2O2. The study found that Galaxy-2013 variety is more tolerant to drought stress than Anaj-2017, while co-applied treatments (GA3 + NLE + serine) were shown to be the most effective among all applications.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01402-9.

Identification of quantitative trait loci for drought tolerance in Bukoba/Kijivu Andean mapping population of common bean

KEY MESSAGE

Quantitative Trait Loci "hotspots" for drought tolerance were identified on chromosomes Pv06, Pv07 and Pv10 of common bean. Drought is a major production constraint of common bean (Phaseolus vulgaris L.) worldwide. The objective of this study was to identify the Quantitative Trait Loci (QTL) for drought tolerance in an Andean population of Recombinant Inbred Lines (RILs). A total of 155 F5:7 RILs derived from a cross between Kijivu (drought tolerant) and Bukoba (drought susceptible) were evaluated for drought tolerance in field and pot experiments. Four field experiments were conducted at three locations in Zambia in 2020 and 2021. All field trials were conducted in the dry season under irrigation. The 155 RILs were genotyped with 11,292 SNPs, and composite interval mapping was conducted to identify QTL for drought tolerance. Seed yield for Kijivu under drought stress was consistently higher than for Bukoba across all four field trials. A total of 60 QTL were identified for morphological, agronomic, and physiological traits under drought stress and non-stress conditions. However, the majority of these QTL were specific to drought stress. QTL "hotspots" for drought tolerance were identified on chromosomes Pv06, Pv07, and Pv10. Extensive co-localizations for agronomic and morpho-physiological traits under drought stress were observed at the three drought-tolerance QTL hotspots. Additionally, these three QTL hotspots overlapped with previously identified QTL for drought tolerance, while several others identified QTL are novel. The three identified QTL hotspots could be used in future marker-assisted selection for drought tolerance in common bean.

De novo transcriptome profiling and development of novel secondary metabolites based genic SSRs in medicinal plant Phyllanthus emblica L. (Aonla)

Phyllanthus emblica (Aonla, Indian Gooseberry) is known to have various medicinal properties, but studies to understand its genetic structure are limited. Among the various secondary metabolites, ascorbic acid, flavonoids, terpenoids, phenols and tannins possess great potential for its pharmacological applications. Keeping this consideration, we assembled the transcriptome using the Illumina RNASeq500 platform, generating 39,933,248 high-quality paired-end reads assembled into 1,26,606 transcripts. A total of 87,771 unigenes were recovered after isoforms and unambiguous sequences deletion. Functional annotation of 43,377 coding sequences against the NCBI non-redundant (Nr) database search using BlastX yielded 38,692 sequences containing blast hits and found 4685 coding sequences to be unique. The transcript showed maximum similarity to Hevea brasilensis (16%), followed by to Jatropha curcas (12%). Considering key genes involved in the biosynthesis of flavonoids and various classes of terpenoid compounds, thirty EST-SSR primer sequences were designed based on transcriptomic data. Of which, 12 were found to be highly polymorphic with an average of 86.38%. The average value for marker index (MI), effective multiplicity ratio (EMR), resolution power (Rp) and polymorphic information content (PIC) was 7.20, 8.34, 8.64 and 0.80, respectively. Thus, from this study, we developed newly EST-SSRs linked to important genes involved in the secondary metabolites biosynthesis that will be serving as an invaluable genetic resource for crop improvement including the selection of elite genotypes in P. emblica and its closely related Phyllanthaceae species.

Multiomics reveals the mechanism of B. longum in promoting the formation of mixed-species biofilms

It has been found previously that Bifidobacterium longum, Bacteroides ovatus, Enterococcus faecalis, and Lactobacillus gasseri can form a biofilm better when co-cultured in vitro and B. longum is the core biofilm-formation-promoting strain in this community. B. longum is part of the core microbiota in the gut and is widely recognized as a probiotic. Therefore, it is necessary to explore its role in mixed-species biofilms through transcriptomics and metabolomics. Metabolomics showed that the increase in amino acid and purine content could promote biofilm formation. In transcriptomic analysis, many genes related to carbohydrate metabolism, amino acid metabolism, and environmental tolerance of B. longum were up-regulated. Combined with the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and Gene Ontology (GO) analysis, the differentially expressed genes (DEGs) of B. longum in mixed-species biofilms were mainly correlated to "quorum sensing (QS)", "ABC transporters", "biosynthesis of amino acids", "microbial metabolism in different environments", "carbohydrate metabolism" and "two-component system". In addition, the rpl and rps gene families, which function in the metabolism of organic substances and the biosynthesis of amino acids, were the core DEGs according to the analysis of the protein-protein interaction (PPI) network. Finally, by combining metabolomics and quorum sensing mechanisms, it was found that the metabolism of autoinducer peptides (proliylglycine and glycylleucine), N-acyl homoserine lactone (N-(3-oxo hydroxy) homoserine lactone), and AI-2 can promote the formation of biofilms, both mono- and mixed-species biofilms composed of B. longum. Our research enabled us to understand the critical role of B. longum in mixed-species biofilms and the interactions between biofilm metabolism and gut health. In addition, the generated knowledge will be of great significance for us to develop biofilm products with beneficial functions in future.