Cultivating resilience in wheat: mitigating arsenic toxicity with seaweed extract and Azospirillum brasilense.

Arsenic (As) toxicity is a serious hazard to agricultural land due to growing industrialization, which has a negative effect on wheat crop yields. To address this issue, using seaweed extract and Azospirillum brasilense has emerged as an effective strategy for improving yield under stress conditions. However, the combined application of A. brasilense and seaweed extract in wheat crops under As toxicity has not been fully explored. The effectiveness of combining A. brasilense and seaweed extract in reducing As toxicity in wheat production was examined in this study through a 2-year pot experiment with nine treatments. These treatments included a control with no additives and two As concentrations (50 and 70 µM). At 50 and 70 µM, As was tested alone, with seaweed extract, with A. brasilense, and both. Significant results were achieved in reducing As toxicity in wheat crops. Arsenic at 70 µM proved more harmful than at 50 µM. The application of A. brasilense and seaweed extract was more effective in improving crop growth rates, chlorophyll levels, and stomatal conductance. The combined application notably decreased As concentration in wheat plants. It was concluded that applying A. brasilense and seaweed extract not only improves wheat growth but can also improve soil parameters under As toxicity conditions by increasing organic matter contents, boosting nutrient availability, and increasing the production of antioxidant enzymes.

Underlying mechanism of Dendrobium huoshanense resistance to lead stress using the quantitative proteomics method.

Lead affects photosynthesis and growth and has serious toxic effects on plants. Here, the differential expressed proteins (DEPs) in D. huoshanense were investigated under different applications of lead acetate solutions. Using label-free quantitative proteomics methods, more than 12,000 peptides and 2,449 proteins were identified. GO and KEGG functional annotations show that these differential proteins mainly participate in carbohydrate metabolism, energy metabolism, amino acid metabolism, translation, protein folding, sorting, and degradation, as well as oxidation and reduction processes. A total of 636 DEPs were identified, and lead could induce the expression of most proteins. KEGG enrichment analysis suggested that proteins involved in processes such as homologous recombination, vitamin B6 metabolism, flavonoid biosynthesis, cellular component organisation or biogenesis, and biological regulation were significantly enriched. Nearly 40 proteins are involved in DNA replication and repair, RNA synthesis, transport, and splicing. The effect of lead stress on D. huoshanense may be achieved through photosynthesis, oxidative phosphorylation, and the production of excess antioxidant substances. The expression of 9 photosynthesis-related proteins and 12 oxidative phosphorylation-related proteins was up-regulated after lead stress. Furthermore, a total of 3 SOD, 12 POD, 3 CAT, and 7 ascorbate-related metabolic enzymes were identified. Under lead stress, almost all key enzymes involved in the synthesis of antioxidant substances are up-regulated, which may facilitate the scavenging of oxygen-free radical scavenging. The expression levels of some key enzymes involved in sugar and glycoside synthesis, the phenylpropanoid synthesis pathway, and the terpene synthesis pathway also increased. More than 30 proteins involved in heavy metal transport were also identified. Expression profiling revealed a significant rise in the expression of the ABC-type multidrug resistance transporter, copper chaperone, and P-type ATPase with exposure to lead stress. Our findings lay the basis for research on the response and resistance of D. huoshanense to heavy metal stress.

Exogenous melatonin alleviates sodium chloride stress and increases vegetative growth in Lonicera japonica seedlings via gene regulation.

Melatonin (Mt) functions as a growth regulator and multifunctional signaling molecule in plants, thereby playing a crucial role in promoting growth and orchestrating protective responses to various abiotic stresses. However, the mechanism whereby exogenous Mt protects Lonicera japonica Thunb. (L. japonica) against salt stress has not been fully elucidated. Therefore, this study aimed to elucidate how exogenous Mt alleviates sodium chloride (NaCl) stress in L. japonica seedlings. Salt-sensitive L. japonica seedlings were treated with an aqueous solution containing 150 mM of NaCl and aqueous solutions containing various concentrations of Mt. The results revealed that treatment of NaCl-stressed L. japonica seedlings with a 60 µM aqueous solution of Mt significantly enhanced vegetative plant growth by scavenging reactive oxygen species and thus reducing oxidative stress. The latter was evidenced by decreases in electrical conductivity and malondialdehyde (MDA) concentrations. Moreover, Mt treatment led to increases in the NaCl-stressed L. japonica seedlings' total chlorophyll content, soluble sugar content, and flavonoid content, demonstrating that Mt treatment improved the seedlings' tolerance of NaCl stress. This was also indicated by the NaCl-stressed L. japonica seedlings exhibiting marked increases in the activities of antioxidant enzymes (superoxide dismutase, peroxidase, catalase, and ascorbate peroxidase) and in photosynthetic functions. Furthermore, Mt treatment of NaCl-stressed L. japonica seedlings increased their expression of phenylalanine ammonia-lyase 1 (PAL1), phenylalanine ammonia-lyase 2 (PAL2), calcium-dependent protein kinase (CPK), cinnamyl alcohol dehydrogenase (CAD), flavanol synthase (FLS), and chalcone synthase (CHS). In conclusion, our results demonstrate that treatment of L. japonica seedlings with a 60 µM aqueous solution of Mt significantly ameliorated the detrimental effects of NaCl stress in the seedlings. Therefore, such treatment has substantial potential for use in safeguarding medicinal plant crops against severe salinity.

Functional analysis of two caffeoyl-coenzyme 3 a-o-methyltransferase involved in pear lignin metabolism.

Caffeoyl-coenzyme 3 A-O-methyltransferase (CCoAOMT) plays a crucial role in the lignin synthesis in many higher plants. In this study, nine PbCCoAOMT genes in total were identified from pear, and classified into six categories. We treated pear fruits with hormones abscisic acid (ABA) and methyl jasmonate (MeJA) and salicylic acid (SA) and observed differential expression levels of these genes. Through qRT-PCR, we also preliminarily identified candidate PbCCoAOMT gene, potentially involved in lignin synthesis in pear fruits. Additionally, the overexpression of PbCCoAOMT1/2 in Arabidopsis and pear fruits increased in lignin content. Enzymatic assays showed that recombinant PbCCoAOMT1/2 proteins have similar enzymatic activity in vitro. The Y1H (Yeast one-hybrid) and dual luciferase (dual-LUC) experiments demonstrated that PbMYB25 can bind to the AC elements in the promoter region of the PbCCoAOMT1 gene. Our findings suggested that the PbCCoAOMT1 and PbCCoAOMT2 genes may contribute to the synthesis of lignin and provide insights into the mechanism of lignin biosynthesis and stone cell development in pear fruits.

Development of oleogel by structuring the blend of corn oil and sunflower oil with beeswax to replace margarine in cookies.

Oleogel significantly affects the product's sensory properties, texture, and shelf life. The goal of this study was to create oleogel by combining corn oil and sunflower oil and utilizing beeswax as a structural agent. A variety of physicochemical analyses were done to evaluate the quality of oleogel, including peroxide value, iodine value, saponification value, fatty acid, rheological parameters and firmness. Different percentages of oleogel, ranging from 0% to 75%, were used to substitute margarine in cookies. The cookies' quality was evaluated using proximate analysis, color analysis, texture analysis, calorific value, and sensory analysis. The study yielded substantial results by finding the ideal margarine-to-oleogel mix ratio, allowing for the manufacturing of high-quality cookies with a greater degree of unsaturation. Cookies with oleogel showed higher levels of unsaturation and better properties, making them the preferred option among consumers.

The nexus between ecology of foraging and food security: cross-cultural perceptions of wild food plants in Kashmir Himalaya.

BACKGROUND: Wild food plants (WFPs) play an important role in the traditional dietary habits of various indigenous communities worldwide, particularly in mountainous regions. To understand the dynamics of food preferences, cross-cultural studies on food plants should be conducted across diverse ethnic groups in a given area. In this context, the current study investigated the use of WFPs by seven different cultural groups in the Kashmir Himalayan Region. In this area, people gather wild plants and their parts for direct consumption, traditional foods, or sale in local markets. Despite this reliance, documentation of the food system, especially concerning WFPs, is notably lacking. Hence, our research aimed to document WFPs, along with associated traditional ecological knowledge, and identify major threats to their long-term sustainability in Division Muzaffarabad. METHODS: Through a comprehensive approach involving questionnaires, interviews, focus groups, and market surveys, we gathered data from 321 respondents. PCA was performed to analyze threats and plant use using "factoextra" in R software. Origin Pro was used to create a chord diagram, while R software was used to generate a Polar heat map. Additionally, a Venn diagram was created using Bioinformatics software. RESULTS: The study included 321 informants, of whom 75.38% were men and 24.61% were women. In total, 113 plant taxa from 74 genera and 41 botanical families were reported. Polygonaceae and Rosaceae accounted for the majority (17 species each), followed by Lamiaceae (7 species). Leaves were the most used part as food sources (41.04%), followed by fruits (33.33%). Most of the species are consumed as cooked (46.46%) and as raw snacks (37.80%). A total of 47 plant species were collected and cooked as wild vegetables, followed by 40 species used as fruits. This study is the first to describe the market potential and ecological distribution of WFPs in the study area. Cross-comparison showed that utilization of WFPs varies significantly across the region and communities, including their edible parts and mode of consumption. Jaccard index (JI) value ranged from 5.81 to 25. Furthermore, the current study describes 29 WFPs and 10 traditional food dishes that have rarely been documented in Pakistan's ethnobotanical literature. Climate change, invasive species, expansion of agriculture, and plant diseases are some of the most significant threats to WFPs in the study area. CONCLUSIONS: The older age group has more knowledge about WFPs compared to the younger generation, who are not interested in learning about the utilization of WFPs. This lack of interest in information about WFPs among the younger generation can be attributed to their limited access to markets and availability of food plants in the study area. Traditional gathering of food plants has been reduced in younger generations during recent years; therefore, it is crucial to develop effective conservation strategies. These efforts not only safeguard indigenous flora, food knowledge, and cultural heritage, but they also contribute to food security and public health by utilizing local wild foods in the examined area.

Genome wide identification of the NPR1 gene family in plant defense mechanisms against biotic stress in chili (Capsicum annuum L.).

Chili pepper cultivation in the Indian subcontinent is severely affected by viral diseases, prompting the need for environmentally friendly disease control methods. To achieve this, it is essential to understand the molecular mechanisms of viral resistance in chili pepper. The NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) genes are known to provide broad-spectrum resistance to various phytopathogens by activating systemic acquired resistance (SAR). An in-depth understanding of NPR1 gene expression during begomovirus infection and its correlation with different biochemical and physiological parameters is crucial for enhancing resistance against begomoviruses in chili pepper. Nevertheless, limited information on chili CaNPR genes and their role in biotic stress constrains their potential in breeding for biotic stress resistance. By employing bioinformatics for genome mining, we identify 5 CaNPR genes in chili. The promoter regions of 1,500 bp of CaNPR genes contained cis-elements associated with biotic stress responses, signifying their involvement in biotic stress responses. Furthermore, these gene promoters harbored components linked to light, development, and hormone responsiveness, suggesting their roles in plant hormone responses and development. MicroRNAs played a vital role in regulating these five CaNPR genes, highlighting their significance in the regulation of chili genes. Inoculation with the begomovirus "cotton leaf curl Khokhran virus (CLCuKV)" had a detrimental effect on chili plant growth, resulting in stunted development, fibrous roots, and evident virus symptoms. The qRT-PCR analysis of two local chili varieties inoculated with CLCuKV, one resistant (V1) and the other susceptible (V2) to begomoviruses, indicated that CaNPR1 likely provides extended resistance and plays a role in chili plant defense mechanisms, while the remaining genes are activated during the early stages of infection. These findings shed light on the function of chili's CaNPR in biotic stress responses and identify potential genes for biotic stress-resistant breeding. However, further research, including gene cloning and functional analysis, is needed to confirm the role of these genes in various physiological and biological processes. This in-silico analysis enhances our genome-wide understanding of how chili CaNPR genes respond during begomovirus infection.

Genome wide identification of phenylalanine ammonia-lyase (PAL) gene family in Cucumis sativus (cucumber) against abiotic stress.

Phenylalanine ammonia lyase (PAL) is a widely studied enzyme in plant biology due to its role in connecting primary metabolism to secondary phenylpropanoid metabolism, significantly influencing plant growth, development, and stress response. Although PAL genes have been extensively studied in various plant species but their exploration in cucumber has been limited. This study successfully identified 11 CsPAL genes in Cucumis sativus (cucumber). These CsPAL genes were categorized based on their conserved sequences revealing patterns through MEME analysis and multiple sequence alignment. Interestingly, cis-elements related to stress were found in the promoter regions of CsPAL genes, indicating their involvement in responding to abiotic stress. Furthermore, these gene's promoters contained components associated with light, development and hormone responsiveness. This suggests that they may have roles in hormone developmental processes. MicroRNAs were identified as a key regulators for the CsPAL genes, playing a crucial role in modulating their expression. This discovery underscores the complex regulatory network involved in the plant's response to various stress conditions. The influence of these microRNAs further highlights the complicated mechanisms that plants use to manage stress. Gene expression patterns were analyzed using RNA-seq data. The significant upregulation of CsPAL9 during HT3h (heat stress for 3 h) and the heightened upregulation of both CsPAL9 and CsPAL7 under HT6h (heat stress for 6 h) in the transcriptome study suggest a potential role for these genes in cucumber's tolerance to heat stress. This comprehensive investigation aims to enhance our understanding of the PAL gene family's versatility, offering valuable insights for advancements in cucumber genetics.

Genome-wide analysis and identification of Carotenoid Cleavage Oxygenase (CCO) gene family in coffee (coffee arabica) under abiotic stress.

The coffee industry holds importance, providing livelihoods for millions of farmers globally and playing a vital role in the economies of coffee-producing countries. Environmental conditions such as drought and temperature fluctuations can adversely affect the quality and yield of coffee crops.Carotenoid cleavage oxygenases (CCO) enzymes are essential for coffee plants as they help break down carotenoids contributing to growth and stress resistance. However, knowledge about the CCO gene family in Coffee arabica was limited. In this study identified 21 CCO genes in Coffee arabica (C. arabica) revealing two subfamilies carotenoid cleavage dioxygenases (CCDs) and 9-cis-epoxy carotenoid dioxygenases (NCED) through phylogenic analysis. These subfamilies exhibited distribution patterns in terms of gene structure, domains, and motifs. The 21 CaCCO genes, comprising 5 NCED and 16 CCD genes were found across chromosomes. Promoter sequencing analysis revealed cis-elements that likely interact with plant stress-responsive, growth-related, and phytohormones, like auxin and abscisic acid. A comprehensive genome-wide comparison, between C. arabica and A. thaliana was conducted to understand the characteristics of CCO genes. RTqPCR data indicated that CaNCED5, CaNCED6, CaNCED12, and CaNCED20 are target genes involved in the growth of drought coffee plants leading to increased crop yield, in a conditions, with limited water availability. This reveals the role of coffee CCOs in responding to abiotic stress and identifies potential genes useful for breeding stress-resistant coffee varieties.

Soy protein-polyphenols conjugates interaction mechanism, characterization, techno-functional and biological properties: An updated review.

Soy protein is a promising nutritional source with improved functionality and bioactivities due to conjugation with polyphenols (PP)-the conjugates between soy protein and PP held by covalent and noncovalent bonds. Different approaches, including thermodynamics, spectroscopy, and molecular docking simulations, can demonstrate the outcomes and mechanism of these conjugates. The soy protein, PP structure, matrix properties (temperature, pH), and interaction mechanism alter the ζ-potential, secondary structure, thermal stability, and surface hydrophobicity of proteins and also improve the techno-functional properties such as gelling ability, solubility, emulsifying, and foaming properties. Soy protein-PP conjugates also reveal enhanced in vitro digestibility, anti-allergic, antioxidant, anticancer, anti-inflammatory, and antimicrobial activities. Thus, these conjugates may be employed as edible film additives, antioxidant emulsifiers, hydrogels, and nanoparticles in the food industry. Future research is needed to specify the structure-function associations of soy protein-PP conjugates that may affect their functionality and application in the food industry.

Efficacy of various amendments for immobilization of potentially toxic elements in wastewater contaminated soils.

Farmers are using municipal wastewater either treated or untreated for irrigation because of limited fresh water resources. Wastewater extensively used for irrigation purposes is enriched with many nutrients. The reuse of wastewater is imposing a negative impact on human health and the ecosystem. It is a need of the day to identify and assess issues of the reuse of wastewater. In the current experiment, impact of organic/inorganic amendments was studied to mitigate the toxic effects of pollutants present in wastewater. Soil was brought from the site having consistent use of wastewater and different treatments were applied as per plan. The experiment has 28 treatments with 04 replications. Nine different amendments were used at 3 varying levels. Incubation time of 30 days was given after the addition of all treatments. The results of the study showed the application of FYM @ 5.0% w/w soil reduced soil pH (7.44), EC (2.16 dS m-1), SAR (8.14), lead (8.48 mg kg-1), cadmium (1.14 mg kg-1), nickel (10.55 mg kg-1) and arsenic (2.03 mg kg-1) when compared with control and other treatments. Usage of compost and horse waste followed FYM. On the basis of this study, it is recommended that wastewater can be used for irrigation purpose after treating with FYM preferably and compost in general.

Haplotype-resolved genome assembly for tetraploid Chinese cherry (Prunus pseudocerasus) offers insights into fruit firmness.

Chinese cherry (Prunus pseudocerasus) holds considerable importance as one of the primary stone fruit crops in China. However, artificially improving its traits and genetic analysis are challenging due to lack of high-quality genomic resources, which mainly result from difficulties associated with resolving its tetraploid and highly heterozygous genome. Herein, we assembled a chromosome-level, haplotype-resolved genome of the cultivar 'Zhuji Duanbing', comprising 993.69 Mb assembled into 32 pseudochromosomes using PacBio HiFi, Oxford Nanopore, and Hi-C. Intra-haplotype comparative analyses revealed extensive intra-genomic sequence and expression consistency. Phylogenetic and comparative genomic analyses demonstrated that P. pseudocerasus was a stable autotetraploid species, closely related to wild P. pusilliflora, with the two diverging ~18.34 million years ago. Similar to other Prunus species, P. pseudocerasus underwent a common whole-genome duplication event that occurred ~139.96 million years ago. Because of its low fruit firmness, P. pseudocerasus is unsuitable for long-distance transportation, thereby restricting its rapid development throughout China. At the ripe fruit stage, P. pseudocerasus cv. 'Zhuji Duanbing' was significantly less firm than P. avium cv. 'Heizhenzhu'. The difference in firmness is attributed to the degree of alteration in pectin, cellulose, and hemicellulose contents. In addition, comparative transcriptomic analyses identified GalAK-like and Stv1, two genes involved in pectin biosynthesis, which potentially caused the difference in firmness between 'Zhuji Duanbing' and 'Heizhenzhu'. Transient transformations of PpsGalAK-like and PpsStv1 increase protopectin content and thereby enhance fruit firmness. Our study lays a solid foundation for functional genomic studies and the enhancement of important horticultural traits in Chinese cherries.

Genome-scale identification, expression and evolution analysis of B-box members in Dendrobium huoshanense.

B-box (BBX) proteins have been recognized as vital determinants in plant development, morphogenesis, and adaptive responses to a myriad of environmental stresses. These zinc-finger proteins play a pivotal role in various biological processes. Their influence spans photomorphogenesis, the regulation of flowering, and imparting resilience to a wide array of challenges, encompassing both biotic and abiotic factors. Chromosome localization, gene structure and conserved motifs, phylogenetic analysis, collinearity analysis, expression profiling, fluorescence quantitative analysis, and tobacco transient transformation methods were used for functional localization and expression pattern analysis of the DhBBX gene. A total of 23 DhBBX members were identified from Dendrobium huoshanense. Subsequent phylogenetic evaluations effectively segregated these genes into five discrete evolutionary subsets. The predictions of subcellular localizations revealed that all these proteins were localized in the nucleus. The genetic composition and patterns showed that the majority of these genes consisted of several exons, with a few variations that could be attributed to transposon insertion. A comprehensive analysis using qRT-PCR was conducted to unravel the expression patterns of these genes in D. huoshanense, with a specific concentration on their responses to various hormone treatments and cold stress. Subcellular localization reveals that DhBBX21 and DhBBX9 are located in the nucleus. Our results provide a deep comprehension of the complex regulatory mechanisms of BBXs in response to various environmental and hormonal stimuli. These discoveries encourage further detailed and focused investigations into the operational dynamics of the BBX gene family in a wider range of plant species.

Vanadium toxicity was alleviated by supplementation of silicon in tomato seedlings: Upregulating antioxidative enzymes and glyoxalase system.

The primary goal of this research is to investigate the mitigating effect of silicon (Si; 2 mM) on the growth of tomato seedlings under vanadium (V; 40 mg) stress. V stress caused higher V uptake in leaf, and enhanced concentration of leaf anthocyanin, H2O2, O2•-, and MDA, but a decreased in plant biomass, root architecture system, leaf pigments content, mineral elements, and Fv/Fm (PSII maximum efficiency). Si application increased the concentrations of crucial antioxidant molecules such as AsA and GSH, as well as the action of key antioxidant enzymes comprising APX, GR, DHAR, and MDHAR. Importantly, oxidative damage was remarkably alleviated by upregulation of these antioxidant enzymes genes. Moreover, Si application enhanced the accumulation of secondary metabolites as well as the expression their related-genes, and these secondary metabolites may restricted the excessive accumulation of H2O2. In addition, Si rescued tomato plants against the damaging effects of MG by boosting the Gly enzymes activity. The results confirmed that spraying Si to plants might diminish the V accessibility to plants, along with promotion of V stress resistance.

Correction: Synthesis of CuSe/PVP/GO and CuSe/MWCNTs for their applications as nonenzymatic electrochemical glucose biosensors.

[This corrects the article DOI: 10.1039/D3RA06713K.].

Characterization, anti-microbial, anti-oxidant and growth promoting effects of biogenically synthesized silver nanoparticles derived from Dicliptera bupleuroides Nees.

One of the most important areas of nanotechnology is the use of nanoparticles (NPs) for a variety of environmental and biological applications, with silver nanoparticles (Ag-NPs) gaining a lot attention due to their distinct properties. The current study deals with the synthesis of Ag-NPs from Dicliptera bupleuroides Nees leaf extract and to determine their antioxidant, antimicrobial potential and effects on wheat seed germination and growth. UV-Visible spectrum revealed a prominent absorption peak at 442 nm, elucidating the conformation of the Ag-NPs synthesis. Scanning electron microscopy (SEM) showed distinctive triangular, pyramidal, and irregular shape. X-ray diffraction (XRD) demonstrated their crystalline nature, with average crystallite size of the Ag-NPs measured at 20.52 nm. Fourier-transform infrared spectroscopy (FT-IR) further confirmed the presence of functional groups such as Phenols (O-H stretch), transition metal carbonyls N-H, ≡C-H, C ≡ N, C ≡ C, C-Cl, C-Br and O-H bonds on the surface Ag-NPs. The antibacterial activity of the Ag-NPs was most pronounced against Bacillus subtilis, with a zone of inhibition (ZOI) measuring 11 mm ± 0.57 at a concentration of 1000 µg/mL (45% inhibition). Likewise, Ag-NPs exhibited highest antioxidant potential (73.2%) at 100 µg/mL compared with standard (ascorbic acid) which showed (76%) at the same concentration. Furthermore, the effect of D. bupleuroides mediated Ag-NPs on wheat seeds growth and germination was recorded maximum at high concentrations (200-300 ppm). In conclusion, D. bupleuroides mediated Ag-NPs showed safe, cost effective and environmentally friendly synthesis which can be used as an antibacterial and antioxidant agent as well as for enhancing the growth and seed germination of crop seeds globally. RESEARCH HIGHLIGHTS: Nanotechnology is the study of nanoparticles for biological and environmental applications. Ag-NPs among other NPs have received broad attention because of their unique properties. D. bupleuroides Ag-NPs: 45% antibacterial, 73.2% antioxidant, enhance wheat germination. D. bupleuroides-mediated Ag-NPs are both cost-effective and environmentally beneficial.

Chromosome-level genome assembly provides insights into the genetic diversity, evolution, and flower development of Prunus conradinae.

Prunus conradinae, a valuable flowering cherry belonging to the Rosaceae family subgenus Cerasus and endemic to China, has high economic and ornamental value. However, a high-quality P. conradinae genome is unavailable, which hinders our understanding of its genetic relationships and phylogenesis, and ultimately, the possibility of mining of key genes for important traits. Herein, we have successfully assembled a chromosome-scale P. conradinae genome, identifying 31,134 protein-coding genes, with 98.22% of them functionally annotated. Furthermore, we determined that repetitive sequences constitute 46.23% of the genome. Structural variation detection revealed some syntenic regions, inversions, translocations, and duplications, highlighting the genetic diversity and complexity of Cerasus. Phylogenetic analysis demonstrated that P. conradinae is most closely related to P. campanulata, from which it diverged ~ 19.1 million years ago (Mya). P. avium diverged earlier than P. cerasus and P. conradinae. Similar to the other Prunus species, P. conradinae underwent a common whole-genome duplication event at ~ 138.60 Mya. Furthermore, 79 MADS-box members were identified in P. conradinae, accompanied by the expansion of the SHORT VEGETATIVE PHASE subfamily. Our findings shed light on the complex genetic relationships, and genome evolution of P. conradinae and will facilitate research on the molecular breeding and functions of key genes related to important horticultural and economic characteristics of subgenus Cerasus.

Genome-wide identification and expression analysis of TIFY genes under MeJA, cold and PEG-induced drought stress treatment in Dendrobium huoshanense.

The TIFY family consists of plant-specific genes that regulates multiple plant functions, including developmental and defense responses. Here, we performed a comprehensive genomic analysis of TIFY genes in Dendrobium huoshanense. Our analysis encompassed their phylogenetic relationships, gene structures, chromosomal distributions, promoter regions, and patterns of collinearity. A total of 16 DhTIFY genes were identified, and classified into distinct clusters named JAZ, PPD, ZIM, and TIFY based on their phylogenetic relationship. These DhTIFYs exhibited an uneven distribution across 7 chromosomes. The expansion of the DhTIFY gene family appears to have been significantly influenced by whole-genome and segmental duplication events. The ratio of non-synonymous to synonymous substitutions (Ka/Ks) implies that the purifying selection has been predominant, maintaining a constrained functional diversification after duplication events. Gene structure analysis indicated that DhTIFYs exhibited significant structural variation, particularly in terms of gene organization and intron numbers. Moreover, numerous cis-acting elements related to hormone signaling, developmental processes, and stress responses were identified within the promoter regions. Subsequently, qRT-PCR experiments demonstrated that the expression of DhTIFYs is modulated in response to MeJA (Methyl jasmonate), cold, and drought treatment. Collectively, these results enhance our understanding of the functional dynamics of TIFY genes in D. huoshanense and may pinpoint potential candidates for detailed examination of the biological roles of TIFY genes. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-024-01442-9.

Comparative analysis of POD genes and their expression under multiple hormones in Pyrus bretschenedri.

BACKGROUND: Class III peroxidase (POD) enzymes play vital roles in plant development, hormone signaling, and stress responses. Despite extensive research on POD families in various plant species, the knowledge regarding the POD family in Chinese pear (Pyrus bretschenedri) is notably limited. RESULTS: We systematically characterized 113 POD family genes, designated as PbPOD1 to PbPOD113 based on their chromosomal locations. Phylogenetic analysis categorized these genes into seven distinct subfamilies (I to VII). The segmental duplication events were identified as a prevalent mechanism driving the expansion of the POD gene family. Microsynteny analysis, involving comparisons with Pyrus bretschenedri, Fragaria vesca, Prunus avium, Prunus mume and Prunus persica, highlighted the conservation of duplicated POD regions and their persistence through purifying selection during the evolutionary process. The expression patterns of PbPOD genes were performed across various plant organs and diverse fruit development stages using transcriptomic data. Furthermore, we identified stress-related cis-acting elements within the promoters of PbPOD genes, underscoring their involvement in hormonal and environmental stress responses. Notably, qRT-PCR analyses revealed distinctive expression patterns of PbPOD genes in response to melatonin (MEL), salicylic acid (SA), abscisic acid (ABA), and methyl jasmonate (MeJA), reflecting their responsiveness to abiotic stress and their role in fruit growth and development. CONCLUSIONS: In this study, we investigated the potential functions and evolutionary dynamics of PbPOD genes in Pyrus bretschenedri, positioning them as promising candidates for further research and valuable indicators for enhancing fruit quality through molecular breeding strategies.