Application of bacteriophages in biopolymer-based functional food packaging films

Recently, food spoilage caused by pathogens has been increasing. Therefore, applying control strategies is essential. Bacteriophages can potentially reduce this problem due to their host specificity, ability to inhibit bacterial growth, and extend the shelf life of food. When bacteriophages are applied directly to food, their antibacterial activity is lost. In this regard, bacteriophage-loaded biopolymers offer an excellent option to improve food safety by extending their shelf life. Applying bacteriophages in food preservation requires comprehensive and structured information on their isolation, culturing, storage, and encapsulation in biopolymers for active food packaging applications. This review focuses on using bacteriophages in food packaging and preservation. It discusses the methods for phage application on food, their use for polymer formulation and functionalization, and their effect in enhancing food matrix properties to obtain maximum antibacterial activity in food model systems.

Postharvest handling of ethylene with oxidative and absorptive means

Fruit ripening is an unfolding of a series of genetically-programmed modifications and tend to be highly orchestrated irrevocable phenomenon mediated by ethylene. Phytohormone ethylene also leads to over-ripening, senescence, loss of texture, microbial attack, reduced post-harvest life and other associated problems during storage and transportation of fruits. Its harmful impacts on fresh fruits, vegetables, and ornamentals result in substantial product losses even up to 80%. Curbing of this inevitable menace is therefore need of the hour. Accrual of ethylene in packaging system should fundamentally be ducked to extend the shelf-life and uphold an adequate superiority of perishables in visual and organoleptic terms. The current review discusses about properties, factors affecting and impact of ethylene, intimidation of its impact at gene vis-à-vis activity level using gene-modification/inhibition techniques, chemical/physical in conjunction with other suitable approaches. It also entails the most commercially cultivated approaches worldwide viz. KMnO4-based oxidation together with adsorption-based scrubbing of ethylene in thorough details. Future ethylene removal strategies should focus on systematic evaluation of KMnO4-based scavenging, exploring the mechanism of adsorption, adsorbent(s) behavior in the presence of other gases and their partial pressures, volatiles, temperature, relative humidity, development of hydrophobic adsorbents to turn-up under high RH, regeneration of adsorbent by desorption, improvement in photocatalytic oxidation etc. and further improvements thereof.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-023-05777-1.

High-throughput diagnostic markers for foliar fungal disease resistance and high oleic acid content in groundnut

BACKGROUND

Foliar diseases namely late leaf spot (LLS) and leaf rust (LR) reduce yield and deteriorate fodder quality in groundnut. Also the high oleic acid content has emerged as one of the most important traits for industries and consumers due to its increased shelf life and health benefits.

RESULTS

Genetic mapping combined with pooled sequencing approaches identified candidate resistance genes (LLSR1 and LLSR2 for LLS and LR1 for LR) for both foliar fungal diseases. The LLS-A02 locus housed LLSR1 gene for LLS resistance, while, LLS-A03 housed LLSR2 and LR1 genes for LLS and LR resistance, respectively. A total of 49 KASPs markers were developed from the genomic regions of important disease resistance genes, such as NBS-LRR, purple acid phosphatase, pentatricopeptide repeat-containing protein, and serine/threonine-protein phosphatase. Among the 49 KASP markers, 41 KASPs were validated successfully on a validation panel of contrasting germplasm and breeding lines. Of the 41 validated KASPs, 39 KASPs were designed for rust and LLS resistance, while two KASPs were developed using fatty acid desaturase (FAD) genes to control high oleic acid levels. These validated KASP markers have been extensively used by various groundnut breeding programs across the world which led to development of thousands of advanced breeding lines and few of them also released for commercial cultivation.

CONCLUSION

In this study, high-throughput and cost-effective KASP assays were developed, validated and successfully deployed to improve the resistance against foliar fungal diseases and oleic acid in groundnut. So far deployment of allele-specific and KASP diagnostic markers facilitated development and release of two rust- and LLS-resistant varieties and five high-oleic acid groundnut varieties in India. These validated markers provide opportunities for routine deployment in groundnut breeding programs.

Molecular insights into Pashmina fiber production: comparative skin transcriptomic analysis of Changthangi goats and sheep

Ladakh, one of the highest inhabited regions globally, hosts the unique Changthangi goat, renowned for producing Pashmina, the world's most luxurious natural fiber. In comparison, the fiber derived from Changthangi sheep is considered next only to Pashmina. This research endeavors to compare the skin transcriptome profiles of Changthangi goats and Changthangi sheep, aiming to discern the molecular determinants behind the recognition of Changthangi goats as the source of Pashmina. Drawing upon previously conducted studies, a collective of 225 genes correlated with fiber characteristics were extracted from the differentially expressed genes noticed between the two species (p-value of ≤ 0.05 and a log2 fold change of ≥ 1.5). These genes were analyzed using DAVID software to understand their biological functions and to identify enriched KEGG and Reactome pathways. The protein-protein interaction networks were constructed using Cytoscape, cytoHubba, and STRING to focus on key genes and infer their biological significance. Comparative transcriptome analysis revealed significantly higher expression of genes involved in signaling pathways like Wnt, MAPK, PI3K-Akt, Hedgehog, associated with fiber development and quality in Changthangi goats. These pathways play crucial roles in hair follicle (HF) formation, maintenance of epidermal stem cells, and fiber characteristics. Findings also highlight the enrichment of cell adhesion molecules and ECM-receptor interaction, emphasizing their roles in HF structure, growth, and signaling. This investigation offers an in-depth understanding of the molecular intricacies governing Pashmina production in Changthangi goats, providing valuable insights into their unique genetic makeup and underlying mechanisms influencing the exceptional quality of Pashmina fibers.

Significance of dietary quinoa husk (Chenopodium quinoa) in gene regulation for stress mitigation in fish

The persistent challenges posed by pollution and climate change are significant factors disrupting ecosystems, particularly aquatic environments. Numerous contaminants found in aquatic systems, such as ammonia and metal toxicity, play a crucial role in adversely affecting aquaculture production. Against this backdrop, fish feed was developed using quinoa husk (the byproduct of quinoa) as a substitute for fish meal. Six isonitrogenous diets (30%) and isocaloric diets were formulated by replacing fish meal with quinoa husk at varying percentages: 0% quinoa (control), 15, 20, 25, 30 and 35%. An experiment was conducted to explore the potential of quinoa husk in replacing fish meal and assess its ability to mitigate ammonia and arsenic toxicity as well as high-temperature stress in Pangasianodon hypophthalmus. The formulated feed was also examined for gene regulation related to antioxidative status, immunity, stress proteins, growth regulation, and stress markers. The gene regulation of sod, cat, and gpx in the liver was notably upregulated under concurrent exposure to ammonia, arsenic, and high-temperature (NH3 + As + T) stress. However, quinoa husk at 25% downregulated sod, cat, and gpx expression compared to the control group. Furthermore, genes associated with stress proteins HSP70 and DNA damage-inducible protein (DDIP) were significantly upregulated in response to stressors (NH3 + As + T), but quinoa husk at 25% considerably downregulated HSP70 and DDIP to mitigate the impact of stressors. Growth-responsive genes such as myostatin (MYST) and somatostatin (SMT) were remarkably downregulated, whereas growth hormone receptor (GHR1 and GHRβ), insulin-like growth factors (IGF1X, IGF2X), and growth hormone gene were significantly upregulated with quinoa husk at 25%. The gene expression of apoptosis (Caspase 3a and Caspase 3b) and nitric oxide synthase (iNOS) were also noticeably downregulated with quinoa husk (25%) reared under stressful conditions. Immune-related gene expression, including immunoglobulin (Ig), toll-like receptor (TLR), tumor necrosis factor (TNFα), and interleukin (IL), strengthened fish immunity with quinoa husk feed. The results revealed that replacing 25% of fish meal with quinoa husk could improve the gene regulation of P. hypophthalmus involved in mitigating ammonia, arsenic, and high-temperature stress in fish.

A novel action of insulin sensitizing drug as a potential promotor of preovulatory follicles, ovulation rate and prolificacy in sheep

The effect of the insulin-sensitizing drug metformin on preovulatory follicle (POF) number, ovulation rate, fetal rate and prolificacy was studied in forty-six cyclic Malpura ewes. After estrus synchronization, the ewes were equally divided into two groups (n = 23). The treatment group (MET) received a daily oral dose of metformin at a rate of 500 mg/animal for approximately 12 weeks, spanning five estrous cycles, as against untreated control (CON). All the ewes were bred to proven rams at the end of treatment. Ovarian ultrasound scans were performed at each estrus and day 9 of each cycle to assess the number and diameter of POFs and corpora lutea (CL), respectively. A comprehensive assessment of circulating hormones including, estradiol, progesterone, androstenedione, and insulin as well as metabolic indicators such as glucose, and lipid profile parameters was performed. At the end of treatment on the day of estrus (E5D0), the treatment showed a stimulatory effect on follicular development with a 53.2% (P < 0.001) increase in the number of POFs. It also increased the ovulation rate by 67.4% (P < 0.01), with a higher proportion (χ2df1 = 10.7, P < 0.001) of ewes in the MET group having multiple ovulations compared to the CON group (82.6 vs. 30.4%). With 1.48 ± 0.12 prolificacy rate in MET ewes, the proportion of ewes giving birth to multiple lambs was 2.9-fold higher than in the CON group. Plasma estradiol, insulin, glucose, total cholesterol, and LDL-cholesterol concentrations were lower (P < 0.05) in the MET ewes than in the CON. The results of the present study indicate that metformin can increase the number of POF, ovulation rate, fetal rate and prolificacy in ewes, while reducing the plasma estradiol, insulin, glucose and cholesterol in MET ewes.

Effect of exogenous melatonin implant on post-thaw semen quality of buffalo bulls

Melatonin is an intracellular antioxidant of sperm membrane that protects the cells from lipid peroxidation. Yet, its role as an antioxidant on semen quality of buffalo bulls is still obscure. The present study was undertaken to assess the effect of exogenous melatonin implant (18 mg/50 kg bodyweight) on post-thaw sperm characteristics, oxidative stress, endocrinological profiles and fertility of buffalo bulls. Six apparently healthy breeding Murrah buffalo bulls were randomly selected at bull farm, Guru Angad Dev Veterinary and Animal Sciences University for the present study and divided into two groups viz. control (n = 3) and melatonin implanted group (n = 3). A total of 120 ejaculates were collected from bulls of both groups (n = 60 each) throughout the study period. Most beneficial effects of melatonin implants were observed during post-implantation period. The percentages of post-thaw sperm total and progressive motility, viability and mitochondrial membrane potential were higher (p < .05) in melatonin implanted buffalo bulls compared to controls during post-implantation period. Following melatonin implantation, MDA production in post-thaw semen was lower (p < .05) in melatonin implanted group than in control group. Plasma melatonin and testosterone concentrations were higher (p < .05) in buffalo bulls implanted with melatonin as compared to their control counterparts. No differences (p > .05) in plasma LH concentrations were observed in both groups. First service pregnancy rate was 43.3% using semen of melatonin implanted bulls and 30.0% with semen of controls (p > .05). Thus, melatonin was able to protect sperm membrane against oxidative damage and improve post-thaw semen quality, thereby resulting in higher fertilizing potential of spermatozoa.

Profiling the antioxidant biomarkers in marine fish larvae: a comparative assessment of different storage conditions to select the optimal strategy

Research on antioxidant biomarkers can generate profound insights into the defense mechanisms of fish larvae against different stressors and can reveal manipulation strategies for improved growth and survival. However, the number of samples to process and unavailability of required infrastructure in larval-rearing facilities limit the immediate processing, requiring the preservation of specimens. Silver pompano (Trachinotus blochii), a potential marine aquaculture species, shows a low larval survival rate due to poorly developed antioxidant mechanism. In this context, 39 storage conditions, including three storage temperatures and different buffers, were scrutinized to select the most suitable preservation strategy for five important antioxidant biomarkers of fish larvae, viz. catalase activity, superoxide dismutase (SOD) activity, measurement of lipid peroxidation, reduced glutathione (GSH), and ascorbic acid contents. The paper proposes the optimum larval storage conditions for these five evaluated antioxidant biomarkers to generate similar results in preserved and non-preserved larval samples. Larval samples preserved in PBS at lower temperatures (- 20 °C and - 80 °C) are recommended for evaluating catalase activity and ascorbic acid content. Catalase activity can also be evaluated by preserving the larval samples at - 20 °C or - 80 °C without buffers. Larval samples held in PBS or without any buffers at - 20 °C and at - 80 °C were found to be suitable for SOD and GSH evaluation, respectively. Preservation in 50% glacial acetic acid at - 80 °C or - 20 °C was preferred for the lipid peroxidation assays. Apart from methodological perspectives, the paper provides insights into the dynamics of larval antioxidant profiles of T. blochii, for the first time.

Isolation, Characterization, and Expression Analysis of NAC Transcription Factor from Andrographis paniculata (Burm. f.) Nees and Their Role in Andrographolide Production

Andrographis paniculata (Burm. f.) Nees is an important medicinal plant known for its bioactive compound andrographolide. NAC transcription factors (NAM, ATAF1/2, and CUC2) play a crucial role in secondary metabolite production, stress responses, and plant development through hormonal signaling. In this study, a putative partial transcript of three NAC family genes (ApNAC83, ApNAC21 22 and ApNAC02) was used to isolate full length genes using RACE. Bioinformatics analyses such as protein structure prediction, cis-acting regulatory elements, and gene ontology analysis were performed. Based on in silico predictions, the diterpenoid profiling of the plant's leaves (five-week-old) and the real-time PCR-based expression analysis of isolated NAC genes under abscisic acid (ABA) treatment were performed. Additionally, the expression analysis of isolated NAC genes under MeJA treatment and transient expression in Nicotiana tabacum was performed. Full-length sequences of three members of the NAC transcription factor family, ApNAC83 (1102 bp), ApNAC21 22 (996 bp), and ApNAC02 (1011 bp), were isolated and subjected to the promoter and gene ontology analysis, which indicated their role in transcriptional regulation, DNA binding, ABA-activated signaling, and stress management. It was observed that ABA treatment leads to a higher accumulation of andrographolide and 14-deoxyandrographolide content, along with the upregulation of ApNAC02 (9.6-fold) and the downregulation of ApNAC83 and ApNAC21 22 in the leaves. With methyl jasmonate treatment, ApNAC21 22 expression decreased, while ApNAC02 increased (1.9-fold), with no significant change being observed in ApNAC83. The transient expression of the isolated NAC genes in a heterologous system (Nicotiana benthamiana) demonstrated their functional transcriptional activity, leading to the upregulation of the NtHMGR gene, which is related to the terpene pathway in tobacco. The expression analysis and heterologous expression of ApNAC21 22 and ApNAC02 indicated their role in andrographolide biosynthesis.

Structure predictions and functional insights into Amidase_3 domain containing N-acetylmuramyl-L-alanine amidases from Deinococcus indicus DR1

BACKGROUND

N-acetylmuramyl-L-alanine amidases are cell wall modifying enzymes that cleave the amide bond between the sugar residues and stem peptide in peptidoglycan. Amidases play a vital role in septal cell wall cleavage and help separate daughter cells during cell division. Most amidases are zinc metalloenzymes, and E. coli cells lacking amidases grow as chains with daughter cells attached to each other. In this study, we have characterized two amidase enzymes from Deinococcus indicus DR1. D. indicus DR1 is known for its high arsenic tolerance and unique cell envelope. However, details of their cell wall biogenesis remain largely unexplored.

RESULTS

We have characterized two amidases Ami1Di and Ami2Di from D. indicus DR1. Both Ami1Di and Ami2Di suppress cell separation defects in E. coli amidase mutants, suggesting that these enzymes are able to cleave septal cell wall. Ami1Di and Ami2Di proteins possess the Amidase_3 catalytic domain with conserved -GHGG- motif and Zn2+ binding sites. Zn2+- binding in Ami1Di is crucial for amidase activity. AlphaFold2 structures of both Ami1Di and Ami2Di were predicted, and Ami1Di was a closer homolog to AmiA of E. coli.

CONCLUSION

Our results indicate that Ami1Di and Ami2Di enzymes can cleave peptidoglycan, and structural prediction studies revealed insights into the activity and regulation of these enzymes in D. indicus DR1.

Genetic enhancement of reproductive stage drought tolerance in RPHR-1005R and derivative rice hybrids through marker-assisted backcross breeding in rice (Oryza sativa L.)

BACKGROUND

Drought stress is considered as one of the major production constraints in rice. RPHR-1005R is a restorer line (R-Line) with a popular, medium-slender grain type, and is the male parent of the popular Indian rice hybrid, DRR-H3. However, both the hybrid and its restorer are highly vulnerable to the drought stress, which limits the adoption of the hybrid. Therefore, the selection of the restorer line RPHR-1005R has been made with the objective of enhancing drought tolerance.

METHODS AND RESULTS

In this study, we have introgressed a major QTL for grain yield under drought (qDTY 1.1) from Nagina22 through a marker-assisted backcross breeding (MABB) strategy. PCR based SSR markers linked to grain yield under drought (qDTY1.1 - RM431, RM11943), fertility restorer genes (Rf3-DRRM-Rf3-10, Rf4-RM6100) and wide compatibility (S5n allele) were deployed for foreground selection. At BC2F1, a single plant (RPHR6339-4-16-14) with target QTL in heterozygous condition and with the highest recurrent parent genome recovery (85.41%) and phenotypically like RPHR-1005R was identified and selfed to generate BC2F2. Fifty-eight homozygous lines were advanced to BC2F4 and six promising restorer lines and a hybrid combination (APMS6A/RPHR6339-4-16-14-3) were identified.

CONCLUSIONS

In summary, the six improved restorer lines could be employed for developing heterotic hybrids possessing reproductive stage drought tolerance. The hybrid combination (APMS6A/RPHR6339-4-16-14-3) was estimated to ensure stable yields in drought-prone irrigated lowlands as well as in directly seeded aerobic and upland areas of India.

Intestinal Histopathological Aberrations in Oreochromis niloticus Juveniles upon Dietary Florfenicol Administration

The aquaculture use of antibiotics can cause detrimental effects on fish organs and gut microbial dysbiosis. The impact of florfenicol (FFC) on fish intestinal histology, an approved antibiotic, remains unclear. This study aimed to investigate the effects of FFC on Oreochromis niloticus juveniles by administering FFC at 10 mg and 30 mg/kg biomass/day for 30 consecutive days to mimic long-term use. A dose-dependent reduction in feed intake, survival and biomass, with an upsurge in mortalities was observed. Even the therapeutic dose instigated mortalities on day 30 of FFC dosing (FD). Histopathological analysis revealed mild to moderate alterations, including loss of absorptive regions, epithelial degeneration, necrotized areas, intercellular enterocytic space and swollen laminar propria. Post-dosing, the observation of the detachment of lamina propria from the epithelium indicated imminent irritability. Goblet cells reduced drastically on day 30 FD, accompanied by an increase in intraepithelial lymphocytes. However, cessation of dosing for 13 days resulted in the reclamation of goblet cells and absorptive regions, indicating that the intestinal tissues underwent considerable repair after lifting antibiotic pressure. These findings suggested that O. niloticus can tolerate dietary FFC but emphasize the need for responsible use of antibiotics in aquaculture.

Safety, tolerability and biological responses of Oreochromis niloticus juveniles upon oral oxolinic acid administration

In aquaculture, oxolinic acid (OA) is used as a second-line treatment at 12 mg/kg biomass/day for seven consecutive days. The present study evaluated the biosafety of 21 days of dietary administration of OA at 0, 12, 36, 60 and 120 mg by assessing the growth, biochemical, erythrocytic morphological and histopathological alterations and residue levels in Oreochromis niloticus. A significant dose-dependent reduction in feed intake and biomass and an increase in mortalities and erythrocytic cellular and nuclear changes were recorded. Significant elevations in plasma glucose, creatinine, alkaline phosphatase, alanine transaminase and aspartate transaminase and a decline in calcium and chloride levels were documented. The kidney, liver and intestine histoarchitecture showed mild to marked alterations. The edible tissue OA residues peaked on day 21 and decreased upon cessation of administration in all the dosing groups. The residue levels in the muscle of the recommended dose group were well within the maximum residue limit set by the European Medicines Evaluation Agency. Although the current study hinted at the safety and tolerability of OA even during long-term usage in O. niloticus in Indian conditions, care must be exercised for its aquacultural application because of its listing as a critically important medicine for humans.

In-package cold plasma treatment to extend the shelf life of food

Conventional food preservation methods such as heat treatment, irradiation, chemical treatment, refrigeration, and coating have various disadvantages, like loss of food quality, nutrition, and cost-effectiveness. Accordingly, cold plasma is one of the new technologies for food processing and has played an important role in preventing food spoilage. Specifically, in-package cold plasma has become a modern trend to decontaminate, process, and package food simultaneously. This strategy has proven successful in processing various fresh food ingredients, including spinach, fruits, vegetables, and meat. In particular, cold plasma treatment within the package reduces the risk of post-processing contamination. Cryoplasm decontamination within packaging has been reported to reduce significantly the microbial load of many foods' spoilage-causing pathogens. However, studies are needed to focus more on the effects of in-package treatments on endogenous enzyme activity, pest control, and removal of toxic pesticide residues. In this review, we comprehensively evaluated the efficacy of in-package low-temperature plasma treatment to extend the shelf life of various foods. The mechanisms by which cold plasma interacts with food were investigated, emphasizing its effects on pathogen reduction, spoilage mitigation, and surface modification. The review also critically assessed the effects of the treatments on food quality, regulatory considerations, and their potential as viable technologies to improve food safety and packaging life. In-package cold plasma treatment could revolutionize food storage when combined with other sophisticated technologies such as nanotechnology.

Unveiling the dynamic expression of PR-1 during Musa spp. infection by Fusarium oxysporum fsp. Cubense: a cloning and characterization study

BACKGROUND

Pathogen-related proteins (PR) are pivotal in plant defense, combating diverse biotic and abiotic stresses. While multiple gene families contribute to banana resistance against Fusarium oxysporum f sp. cubense (Foc), Pseudocercospora eumusae, and Pratylenchus coffeae, the significance of PR-1 genes in defense is paramount.

METHODS

Three PR-1 genes, up-regulated under diverse biotic stresses, were cloned from both resistant and susceptible cultivars of Foc, P. eumusae, and P. coffeae. Molecular characterization, phylogenetic analysis, and docking studies with the Foc TR4 CP gene were conducted.

RESULTS

Through transcriptomic and real-time studies, three PR-1 genes (Ma02_g15050, Ma02_g15060, and Ma04_g34800) from Musa spp. were identified. These genes exhibited significant up-regulation in resistant cultivars when exposed to Foc, P. eumusae, and P. coffeae. Cloning of these genes was successfully performed from both resistant and susceptible cultivars of Foc race 1 and TR4, P. eumusae, and P. coffeae. Distinct characteristics were observed among the PR-1 genes, with groups 1 and 2 being acidic with signal peptides, and group 3 being basic without signal peptides. All cloned PR-1 proteins belonged to the CAP superfamily (PF00188). Phylogenetic analysis revealed clustering patterns for acidic PR-1 proteins, and KEGG orthology showed associations with vital pathways, including MAPK signaling, plant hormone signal transduction, and plant-pathogen interaction. Secondary and tertiary structure analyses confirmed sequence conservation across studied species. Docking studies explored interactions between the cerato-platanin (CP) gene from Foc TR4 and Ma02_g15060 from banana, suggesting the potential hindrance of PR-1 antifungal activity through direct interaction.

CONCLUSIONS

The findings underscore the crucial role of cloned PR-1 genes in banana plant defense mechanisms against a broad spectrum of biotic stresses. These genes, especially those in groups 1 and 2, hold promise as candidates for developing stress-tolerant banana cultivars. The study provides valuable insights into the molecular aspects of banana defense strategies, emphasizing the potential applications of PR-1 genes in enhancing banana resilience.

Optimizing speed breeding and seed/pod chip based genotyping techniques in pigeonpea: A way forward for high throughput line development

BACKGROUND

The challenge of pigeonpea breeding lies in its photosensitivity and seasonal specificity. This poses a problem to the breeder, as it restricts to single generation advancement in a year. Currently, the cross to cultivar gap is twelve to thirteen years resulting in a limited number of varietal releases over the past six decades. Shortening the breeding cycle was need of the hour, unlikely achieved by conventional breeding. To overcome these hindrances speed breeding was a necessary leap. An experiment was planned to optimize the speed breeding coupled with single seed descent and seed or pod chip-based genotyping to shorten the breeding cycle in pigeonpea at ICRISAT, Hyderabad. Monitored photoperiod, light wavelength, temperature and crop management regime were the indicators attributing to the success of speed breeding.

RESULT

A photoperiod of 13 h: 8 h: 13 h at vegetative: flowering and pod filling stages is ideal for shortening the breeding cycle. Broad spectrum light (5700 K LED) hastened early vegetative growth and pod formation. Whereas far-red (735 nm) light favoured early flowering. A significant difference between the photoperiods, genotypes as well as photoperiod x genotype interaction for both days to flowering and plant height was noted.

CONCLUSION

The optimized protocol serves as a road map for rapid generation advancement in pigeonpea. Deploying this protocol, it is possible to advance 2-4 generations per year. The breeding cycle can be reduced to 2-4 years which otherwise takes 7 years under conventional breeding. Single Seed Descent and seed or pod chip-based genotyping for early generation marker assisted selection, strengthened the precision of this technique aiding in high throughput line development.

Unraveling determinants of integrated farming systems adoption for sustainable livelihood and dietary diversity

Introduction

Over the years, smallholder farmers have faced more vulnerability to risk and uncertainty in India due to their dependence on cereal crops. One way to reduce this risk is through diversified agriculture, integrating different practices for efficient resource utilization, and adopting a farming systems approach. An integrated farming system (IFS) is one such technique that provides year-round income from different components of enterprises. However, the decision to adopt IFS may be determined by several characteristics of farmers, which needs to be delineated through impact analysis to harness the benefits of a systems approach.

Methods

This study analyzes the economic effects of integrated farming systems and assesses their determinants, as well as the dietary diversity patterns of farmers in two states of southern India, i.e., Kerala and Tamil Nadu. A multistage sampling technique was used to obtain cross-sectional data from 367 farmers randomly chosen from one district in Kerala and two districts in Tamil Nadu. The participants have Crop + Horticulture + Animal husbandry (45.45%) as their major system, whereas non-participants have Crop + Animal husbandry (44.35%) as their predominant system. Coarsened exact matching and logit regression methods were used to evaluate the economic impacts of IFS and its influencing factors.

Results

The findings of the study indicate that age, education, livestock holding, access to credit, and plantation area have a positive and significant effect on participation by farmers in the program. The matching results show that adoption of IFS resulted in a significant economic impact, generating an additional gross income of Rs. 36,165 ha-1 and a net income of Rs. 35,852 ha-1 and improving the dietary diversity of farm households by 8.6% as compared to non-adopters.

Discussion

This study suggests that IFS is a promising approach for improving farmers' livelihoods, economic gains, and nutritional security. Therefore, the integrated farming systems models need to be upscaled through the convergence of government schemes in other regions of India to support smallholder farmers' farming.

Elevated CO2 ameliorates the high temperature stress effects on physio-biochemical, growth, yield traits of maize hybrids

The rising temperatures and levels of carbon dioxide in the atmosphere are anticipated to have a significant impact on the productivity of agricultural crops. Although, the individual effects of elevated CO2 and temperature have been extensively studied in C3 and C4 crops, there remains a scarcity of research investigating their interactive effects specifically on maize hybrids. The impact of elevated temperature and its interaction with elevated CO2 on phenology, physiology, biomass, and grain yield of maize hybrids was assessed in a field experiment using Free Air Temperature Elevation (FATE) facility. The results showed that elevated temperature (eT) increased the anthesis silking interval (ASI), while the presence of elevated CO2 along with elevated temperature (eT + eCO2) mitigated this effect. The differential expression were observed between hybrids depending on their genetic potential. Furthermore, the net photosynthetic rate (Anet), stomatal conductance (gs), and transpiration rate (Tr) of hybrids decreased under elevated temperature but eT + eCO2 condition helped in reverting its impact to some extent. In term of leaf composition, the highest level of total soluble sugars (TSS) and starch was observed under eT + eCO2 conditions, possibly due to improved Anet in the presence of elevated eCO2. The negative impact of eT was also evident through increased proline and MDA content, but eT + eCO2 ameliorated the adverse effect of eT. The biomass and grain yield also responded similarly, among the hybrids 900M GOLD recorded superior performance for grain yield at eT condition exceeding 35 °C. On the other hand, DHM117 experienced a significant reduction in grain yield under eT, but performed better under eT + eCO2 due to its improved physiological response to eCO2. The study indicated that elevated levels of carbon dioxide can actually mitigate the detrimental effects of elevated temperature on maize crop. This positive impact on maize crop can be attributed to an enhanced physiological performance in the presence of eCO2 which enables the plants to maintain satisfactory yield levels despite the challenging environmental conditions.

Genetic diversity, population structure analysis and codon substitutions of Indicine Badri cattle using ddRAD sequencing

The present study was carried out on 96 animals representing three distinct colour variants of Badri cattle to investigate the genetic diversity, population structure and substitution mutations in the genetic codons due to single nucleotide variations. The DNA samples of 96 Badri cows were genotyped using a double digestion restriction associated DNA (ddRAD) sequencing approach. A standardized bioinformatics pipeline was employed to identify single nucleotide polymorphisms (SNPs), initially detecting 7,168,552 SNPs through alignment with the Bos indicus reference genome assembly. Subsequent stringent quality filtration yielded 65,483 high-confidence SNPs for downstream analysis. Genetic diversity analysis of the Badri cattle population resulted in average values of 0.145, 0.088, and 0.091 for Shannon's diversity Index (I), Simpson's Diversity (h), and Simpson's Unbiased Diversity (uh), respectively. Genetic similarities between the black and brown, black and grey, and brown and grey Badri variants were found to be 0.9972, 0.9980 and 0.9970, respectively. Tajima's D diversity value was observed to be significant and positive for 99.29% of high-confidence SNPs (65,483). STRUCTURE analysis showed admixture among the three Badri colour variants, suggesting a lack of genetic differentiation. Annotation of high-confidence SNPs regarding genetic codon changes indicated maximum substitutions in the GGC with GGT (22 occurrences), followed by AAC to AGC (20 occurrences), GAA to TAA (19 occurrences) and CAA to CAG (19 occurrences). The study concludes there are genetic similarities among colour variants, lack of rare alleles, balancing selection, sudden population contraction and genetic codon substitutions within the Badri cattle population. Insights derived from SNP data analysis hold potential significance for conservation initiatives and breed improvement programs for indicine cattle.

Lipid peroxidation and stress-induced signalling molecules in systemic resistance mediated by azelaic acid/AZELAIC ACID INDUCED1: signal initiation and propagation

Systemic acquired resistance protects plants against a broad spectrum of secondary infections by pathogens. A crucial compound involved in the systemic spread of the threat information after primary pathogen infection is the C9 oxylipin azelaic acid (AZA), a breakdown product of unsaturated C18 fatty acids. AZA is generated during lipid peroxidation in the plastids and accumulates in response to various abiotic and biotic stresses. AZA stimulates the expression of AZELAIC ACID INDUCED1 (AZI1), and a pool of AZI1 accumulates in the plastid envelope in association with AZA. AZA and AZI1 utilize the symplastic pathway to travel through the plasmodesmata to neighbouring cells to induce systemic stress resistance responses in distal tissues. Here, we describe the synthesis, travel and function of AZA and AZI1 and discuss open questions of signal initiation and propagation.

Non-Destructive Assessment of Microstructural Changes in Kabuli Chickpeas during Storage

The potential of hyperspectral imaging (HSI) and synchrotron phase-contrast micro computed tomography (SR-µCT) was evaluated to determine changes in chickpea quality during storage. Chickpea samples were stored for 16 wk at different combinations of moisture contents (MC of 9%, 11%, 13%, and 15% wet basis) and temperatures (10 °C, 20 °C, and 30 °C). Hyperspectral imaging was utilized to investigate the overall quality deterioration, and SR-µCT was used to study the microstructural changes during storage. Principal component analysis (PCA) and Partial Least Squares Discriminant Analysis (PLS-DA) were used as multivariate data analysis approaches for HSI data. Principal component analysis successfully grouped the samples based on relative humidity (RH) and storage temperatures, and the PLS-DA classification also resulted in reliable accuracy (between 80 and 99%) for RH-based and temperature-based classification. The SR-µCT results revealed that microstructural changes in kernels (9% and 15% MC) were dominant at higher temperatures (above 20 °C) as compared to lower temperatures (10 °C) during storage due to accelerated spoilage at higher temperatures (above 20 °C). Chickpeas which had internal irregularities like cracked endosperm and air spaces before storage were spoiled at lower moisture from 8 wk of storage.

Genome-wide identification and characterization of NBLRR genes in finger millet (Eleusine coracana L.) and their expression in response to Magnaporthe grisea infection

BACKGROUND

The nucleotide binding site leucine rich repeat (NBLRR) genes significantly regulate defences against phytopathogens in plants. The genome-wide identification and analysis of NBLRR genes have been performed in several species. However, the detailed evolution, structure, expression of NBLRRs and functional response to Magnaporthe grisea are unknown in finger millet (Eleusine coracana (L.) Gaertn.).

RESULTS

The genome-wide scanning of the finger millet genome resulted in 116 NBLRR (EcNBLRRs1-116) encompassing 64 CC-NB-LRR, 47 NB-LRR and 5 CCR-NB-LRR types. The evolutionary studies among the NBLRRs of five Gramineae species, viz., purple false brome (Brachypodium distachyon (L.) P.Beauv.), finger millet (E. coracana), rice (Oryza sativa L.), sorghum (Sorghum bicolor L. (Moench)) and foxtail millet (Setaria italica (L.) P.Beauv.) showed the evolution of NBLRRs in the ancestral lineage of the target species and subsequent divergence through gene-loss events. The purifying selection (Ka/Ks < 1) shaped the expansions of NBLRRs paralogs in finger millet and orthologs among the target Gramineae species. The promoter sequence analysis showed various stress- and phytohormone-responsive cis-acting elements besides growth and development, indicating their potential role in disease defence and regulatory mechanisms. The expression analysis of 22 EcNBLRRs in the genotypes showing contrasting responses to Magnaporthe grisea infection revealed four and five EcNBLRRs in early and late infection stages, respectively. The six of these nine candidate EcNBLRRs proteins, viz., EcNBLRR21, EcNBLRR26, EcNBLRR30, EcNBLRR45, EcNBLRR55 and EcNBLRR76 showed CC, NB and LRR domains, whereas the EcNBLRR23, EcNBLRR32 and EcNBLRR83 showed NB and LRR somains.

CONCLUSION

The identification and expression analysis of EcNBLRRs showed the role of EcNBLRR genes in assigning blast resistance in finger millet. These results pave the foundation for in-depth and targeted functional analysis of EcNBLRRs through genome editing and transgenic approaches.

CRISPR/Cas genome editing revealed non-angiogenic role of VEGFA gene in porcine luteal cells: a preliminary report

BACKGROUND

The angiogenic cytokine vascular endothelial growth factor A (VEGFA) also exerts non-angiogenic effects on endocrine functionality of porcine luteal cells critical for progesterone (P4) production.

METHOD AND RESULTS

The expression dynamics of VEGFA-FLT/KDR system were investigated using RT-qPCR during luteal stages and VEGFA gene knock out (KO) porcine luteal cells were generated using CRISPR/Cas9 technology. The downstream effects of VEGFA ablation were studied using RT-qPCR, Annexin V, MTT, ELISA for P4 estimation and scratch wound assay. Bioinformatics analysis of RNA-Seq data of porcine mid-luteal stage was conducted for exploring protein-protein interaction network, KEGG pathways, transcription factors and kinase mapping for VEGFA-FLT/KDR interactomes. The VEGFA-FLT/KDR system expressed throughout the luteal stages with highest expression during mid- luteal stage. Cellular morphology, structure and oil-red-o staining for lipid droplets did not differ significantly between VEGFA KO and wild type cells, however, VEGFA KO significantly decreased (p < 0.05) viability and proliferation efficiency of edited cells on subsequent passages. Expression of apoptotic gene, CASP3 and hypoxia related gene, HIF1A were significantly (p < 0.05) upregulated in KO cells. The relative mRNA expression of VEGFA and steroidogenic genes STAR, CYP11A1 and HSD3B1 decreased significantly (p < 0.05) upon KO, which was further validated by the significant (p < 0.05) decrease in P4 output from KO cells. Bioinformatics analysis mapped VEGFA-FLT/KDR system to signalling pathways associated with steroidogenic cell functionality and survival, which complemented the findings of the study.

CONCLUSION

The ablation of VEGFA gene resulted in decreased steroidogenic capability of luteal cells, which suggests that VEGFA exerts additional non-angiogenic regulatory effects in luteal cell functionality.

Milk exosomal microRNA profiling identified miR-375 and miR-199-5p for regulation of immune response during subclinical mastitis of crossbred cattle

BACKGROUND

The dairy industry has experienced significant economic losses as a result of mastitis, an inflammatory disease of cows, including both subclinical and clinical cases. Milk exosome microRNAs have gained attention due to their stable and selective wrapping nature, offering potential for the prognosis and diagnosis of bovine mastitis, the most common pathological condition of the mammary gland.

METHODS AND RESULTS

 In the present investigation, the microRNA profile of milk exosomes was explored using high-throughput small RNA sequencing data in sub-clinical mastitic and healthy crossbred Vrindavani cattle. In both groups, 349 microRNAs were identified, with 238 (68.19%) microRNAs co-expressed; however, 35 and 76 distinct microRNAs were found in subclinical mastitic and healthy cattle, respectively. Differential expression analysis revealed 11 microRNAs upregulated, and 18 microRNAs were downregulated in sub-clinical mastitic cattle. The functional annotation of the target genes of differentially expressed known and novel microRNAs including bta-miR-375, bta-miR-199-5p and bta-miR-12030 reveals their involvement in the regulation of immune response and inflammatory mechanisms and could be involved in development of mastitis.

CONCLUSIONS

The analysis of milk exosomal miRNAs cargos hold great promise as an approach to study the underlying molecular mechanisms associated with mastitis in high milk producing dairy cattle. Concurrently, the significantly downregulated miR-375 may upregulate key target genes, including CTLA4, IHH, IRF1, and IL7R. These genes are negative regulators of immune response pathways, which could be associated with impaired inflammatory mechanisms in mammary cells. According to the findings, bta-miR-375 could be a promising biomarker for the development of mastitis in dairy cattle.

Monitoring and method validation of organophosphorus/organochlorine pesticide residues in vegetables and fruits by gas chromatography

In this study, an analytical method was developed and validated for the assessment of pesticide residues in commonly consumed vegetables and fruits. Fresh samples of apple, green peas, tomatoes, and cucumbers were processed and subjected to analysis using a modified QuEChERS (quick, easy, cheap, effective, rugged, safe) extraction technique. Subsequently, quantification of pesticide residues was conducted utilizing gas chromatography (GC)-electron capture detector. Extraction and cleanup parameters were meticulously optimized, resulting in a modification of the original QuEChERS method. This modification aimed to reduce solvent consumption, making the study more environmentally friendly. The developed method was validated in terms of selectivity, specificity, linearity, precision, and accuracy by following the SANTE guidelines. Calibration curves showed good linearity (r > 0.99) within the test range. Precision was evaluated by intra- and inter-day experiments with an acceptable relative standard deviation (<20.0%). Recovery was assessed at the limit of quantification level and was observed to fall within the range of 70%-120%, with relative standard deviations below 5.45%. The validated method presented here can be applied to analyze pesticide residues in various other vegetables, fruits, and cereals. It is essential for ongoing monitoring of pesticide residues to ensure public safety.

Molecular characterization of Red banana and its somaclonal variant: a comprehensive study

The prized Red banana, selected for superior qualities, demands strong genetic uniformity for successful clonal propagation and preservation. Ensuring this uniformity early in the growth of in vitro Red banana plants is essential, as gene mutations and chromosome rearrangements during tissue culture can jeopardize both cloning and germplasm conservation. In this situation, molecular markers play a pivotal role in confirming genetic stability. Thus the study aims to discover a marker that identifies tissue-cultured Red bananas from their virescent variants during initial sub-culturing. A marker linked to anthocyanin has been identified which effectively differentiated Red bananas from virescent variants and it was further validated in various banana cultivars, ornamental Musa species and their interspecific hybrids. The PCR-based marker showed remarkable specificity, discerning Red bananas from virescent variants during tissue culture. It also distinguished green and red offspring, cutting time and resource costs, and shortening the banana breeding cycle.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03868-6.

Antioxidant Defence in Labeo rohita to Biotic and Abiotic Stress: Insight from mRNA Expression, Molecular Characterization and Recombinant Protein-Based ELISA of Catalase, Glutathione Peroxidase, CuZn Superoxide Dismutase, and Glutathione S-Transferase

Fish possess numerous enzymatic antioxidant systems as part of their innate immunity. These systems have been poorly studied in Labeo rohita (rohu). The present study characterized and investigated the role of antioxidant genes in the defence mechanisms against two types of stressors, including infection and ammonia stress. Four key genes associated with antioxidant activity-catalase, glutathione peroxidase, glutathione S-transferase, and CuZn superoxide dismutase were successfully cloned and sequenced. These genes were found to be expressed in different tissues and developmental stages of rohu. The expression levels of these antioxidant genes in the liver and anterior kidney tissues of rohu juveniles were modulated in response to bacterial infection (Aeromonas hydrophila), parasite infection (Argulus siamensis), poly I:C stimulation and ammonia stress. Additionally, the recombinant proteins derived from these genes exhibited significant antioxidant and antibacterial activities. These proteins also demonstrated a protective effect against A. hydrophila infection in rohu and had an immunomodulatory role. Furthermore, indirect ELISA assay systems were developed to measure these protein levels in healthy as well as A. hydrophila and ammonia-induced rohu serum. Overall, this study characterized and emphasised the importance of the antioxidant mechanism in rohu's defence against oxidative damage and microbial diseases.

Genetic analyses reveal panmixia in Indian waters and population subdivision across Indian Ocean and Indo-Malay Archipelago for Decapterus russelli

The Indian Scad, Decapterus russelli is an important pelagic carangid widely distributed throughout the Indian Ocean and the Indo-West Pacific. Despite being widely distributed in the Indian Ocean, the information regarding genetic structuring and diversity has been lacking compared to its Indo Malay Archipelago counterparts. The present study was conducted to investigate the genetic stock structure of D. russelli based on mitochondrial (Cyt b) and nuclear (DrAldoB1) markers along Indian waters. The results indicated the presence of a single panmictic stock across the Indian Ocean region. High haplotype diversity associated with low nucleotide diversity suggested a population bottleneck followed by rapid population growth. Phylogenetic analysis revealed the absence of geographical clustering of lineages with the most common haplotype distributed globally. The pelagic life style, migratory capabilities, and larval dispersal may be the contributing factors to the observed spatial homogeneity of D. russelli. However, significant genetic differentiation was observed between the populations from Indian Ocean and Indo-Malay Archipelago. Hierarchical molecular variance analysis (AMOVA), pairwise FST comparisons and SAMOVA showed existence of two distinct genetic stocks of D. russelli in the Indian Ocean and IMA. The observed interpopulation genetic variation was high. A plausible explanation for the genetic differentiation observed between the Indo-Malay Archipelago and the Indian Ocean regions suggest the influence of historic isolation, ocean surface currents and biotic and abiotic features of the ocean. Also, there was a significant relationship between genetic distance and geographical distance between population pairs in a manner consistent with isolation-by-distance. These resulted in the evolution of a phylogeographic break for this species between these regions. The findings of these results suggest that D. russelli from the Indian Ocean shall be managed in its entire area of distribution as a single stock. Further, the Indian Ocean and Indo-Malayan stocks can be managed separately.

Nitrate-responsive transcriptome analysis of rice RGA1 mutant reveals the role of G-protein alpha subunit in negative regulation of nitrogen-sensitivity and use efficiency

KEY MESSAGE

Nitrate-responsive transcriptomic, phenotypic and physiological analyses of rice RGA1 mutant revealed many novel RGA1-regulated genes/processes/traits related to nitrogen use efficiency, and provided robust genetic evidence of RGA1-regulation of NUE. Nitrogen (N) use efficiency (NUE) is important for sustainable agriculture. G-protein signalling was implicated in N-response/NUE in rice, but needed firm genetic characterization of the role of alpha subunit (RGA1). The knock-out mutant of RGA1 in japonica rice exhibited lesser nitrate-dose sensitivity than the wild type (WT), in yield and NUE. We, therefore, investigated its genomewide nitrate-response relative to WT. It revealed 3416 differentially expressed genes (DEGs), including 719 associated with development, grain yield and phenotypic traits for NUE. The upregulated DEGs were related to photosynthesis, chlorophyll, tetrapyrrole and porphyrin biosynthesis, while the downregulated DEGs belonged to cellular protein metabolism and transport, small GTPase signalling, cell redox homeostasis, etc. We validated 26 nitrate-responsive DEGs across functional categories by RT-qPCR. Physiological validation of nitrate-response in the mutant and the WT at 1.5 and 15 mM doses revealed higher chlorophyll and stomatal length but decreased stomatal density, conductance and transpiration. The consequent increase in photosynthesis and water use efficiency may have contributed to better yield and NUE in the mutant, whereas the WT was N-dose sensitive. The mutant was not as N-dose-responsive as the WT in shoot/root growth, productive tillers and heading date, but equally responsive as WT in total N and protein content. The RGA1 mutant was less impacted by higher N-dose or salt stress in terms of yield, protein content, photosynthetic performance, relative water content, water use efficiency and catalase activity. PPI network analyses revealed known NUE-related proteins as RGA1 interactors. Therefore, RGA1 negatively regulates N-dose sensitivity and NUE in rice.

Mineral nutrients in plants under changing environments: A road to future food and nutrition security

Plant nutrition is an important aspect that contributes significantly to sustainable agriculture, whereas minerals enrichment in edible source implies global human health; hence, both strategies need to be bridged to ensure "One Health" strategies. Abiotic stress-induced nutritional imbalance impairs plant growth. In this context, we discuss the molecular mechanisms related to the readjustment of nutrient pools for sustained plant growth under harsh conditions, and channeling the minerals to edible source (seeds) to address future nutritional security. This review particularly highlights interventions on (i) the physiological and molecular responses of mineral nutrients in crop plants under stressful environments; (ii) the deployment of breeding and biotechnological strategies for the optimization of nutrient acquisition, their transport, and distribution in plants under changing environments. Furthermore, the present review also infers the recent advancements in breeding and biotechnology-based biofortification approaches for nutrient enhancement in crop plants to optimize yield and grain mineral concentrations under control and stress-prone environments to address food and nutritional security.

Evidence for the natural infection of cucurbit chlorotic yellows virus (CCYV) in lettuce plants from India

In the years 2021 and 2022, lettuce plants showing blistering, chlorosis, mosaic, rosetting/ excess proliferation, and stunting symptoms were subjected to leaf-dip transmission electron microscopy, RT-PCR followed by sequence analysis and bio-assay to unfold the identity of associated virus(es). The association of long filamentous virions (~ 850 nm in length) as seen through leaf-dip transmission electron microscopy suggested the possible infection by a potyvirus or crinivirus, either singly or in combination. RT-PCR assays using generic primers targeting the RdRp region of criniviruses and the NIb region of potyviruses revealed the association of both a crinivirus as well as a potyvirus. The gel-purified RT-PCR products derived from the RdRp region of criniviruses upon cloning, sequencing, and NCBI BLAST analysis indicated the associated crinivirus as cucurbit chlorotic yellows virus (CCYV). Further, RT-PCR assays using specific primers targeting CP and CP minor genes of CCYV followed by cloning and sequencing confirmed its association with the diseased lettuce plants. Besides, the bioassay based on whitefly-mediated virus transmission followed by RT-PCR confirmed the infectivity of CCYV from diseased to healthy lettuce plants. The results of this study confirmed the natural infection of CCYV in lettuce host for the first time in the world indicating its distribution across the crop families.

Salinity stress tolerance prediction for biomass-related traits in maize (Zea mays L.) using genome-wide markers

Maize (Zea mays L.) is the third most important cereal crop after rice (Oryza sativa) and wheat (Triticum aestivum). Salinity stress significantly affects vegetative biomass and grain yield and, therefore, reduces the food and silage productivity of maize. Selecting salt-tolerant genotypes is a cumbersome and time-consuming process that requires meticulous phenotyping. To predict salt tolerance in maize, we estimated breeding values for four biomass-related traits, including shoot length, shoot weight, root length, and root weight under salt-stressed and controlled conditions. A five-fold cross-validation method was used to select the best model among genomic best linear unbiased prediction (GBLUP), ridge-regression BLUP (rrBLUP), extended GBLUP, Bayesian Lasso, Bayesian ridge regression, BayesA, BayesB, and BayesC. Examination of the effect of different marker densities on prediction accuracy revealed that a set of low-density single nucleotide polymorphisms obtained through filtering based on a combination of analysis of variance and linkage disequilibrium provided the best prediction accuracy for all the traits. The average prediction accuracy in cross-validations ranged from 0.46 to 0.77 across the four derived traits. The GBLUP, rrBLUP, and all Bayesian models except BayesB demonstrated comparable levels of prediction accuracy that were superior to the other modeling approaches. These findings provide a roadmap for the deployment and optimization of genomic selection in breeding for salt tolerance in maize.

Historical shifting in grain mineral density of landmark rice and wheat cultivars released over the past 50 years in India

The 'Green Revolution (GR)' has been successful in meeting food sufficiency in India, but compromising its nutritional security. In a first, we report altered grain nutrients profile of modern-bred rice and wheat cultivars diminishing their mineral dietary significance to the Indian population. To substantiate, we evaluated grain nutrients profile of historical landmark high-yielding cultivars of rice and wheat released in succeeding decades since the GR and its impacts on mineral diet quality and human health, with a prediction for decades ahead. Analysis of grain nutrients profile shows a downward trend in concentrations of essential and beneficial elements, but an upward in toxic elements in past 50 y in both rice and wheat. For example, zinc (Zn) and iron (Fe) concentration in grains of rice decreased by ~ 33.0 (P < 0.001) and 27.0% (P < 0.0001); while for wheat it decreased by ~ 30.0 (P < 0.0001) and 19.0% (P < 0.0001) in past more than 50 y, respectively. A proposed mineral-diet quality index (M-DQI) significantly (P < 0.0001) decreased ~ 57.0 and 36.0% in the reported time span (1960-2010) in rice and wheat, respectively. The impoverished M-DQI could impose hostile effects on non-communicable diseases (NCDs) like iron-deficiency anemia, respiratory, cardiovascular, and musculoskeletal among the Indian population by 2040. Our research calls for an urgency of grain nutrients profiling before releasing a cultivar of staples like rice and wheat in the future.

Metabolomics of early blight (Alternaria solani) susceptible tomato (Solanum lycopersicum) unfolds key biomarker metabolites and involved metabolic pathways

Tomato (Solanum lycopersicum) is among the most important commercial horticultural crops worldwide. The crop quality and production is largely hampered due to the fungal pathogen Alternaria solani causing necrotrophic foliage early blight disease. Crop plants usually respond to the biotic challenges with altered metabolic composition and physiological perturbations. We have deciphered altered metabolite composition, modulated metabolic pathways and identified metabolite biomarkers in A. solani-challenged susceptible tomato variety Kashi Aman using Liquid Chromatography-Mass Spectrometry (LC-MS) based metabolomics. Alteration in the metabolite feature composition of pathogen-challenged (m/z 9405) and non-challenged (m/z 9667) plant leaves including 8487 infection-exclusive and 8742 non-infection exclusive features was observed. Functional annotation revealed putatively annotated metabolites and pathway mapping indicated their enrichment in metabolic pathways, biosynthesis of secondary metabolites, ubiquinone and terpenoid-quinones, brassinosteroids, steroids, terpenoids, phenylpropanoids, carotenoids, oxy/sphingolipids and metabolism of biotin and porphyrin. PCA, multivariate PLS-DA and OPLS-DA analysis showed sample discrimination. Significantly up regulated 481 and down regulated 548 metabolite features were identified based on the fold change (threshold ≥ 2.0). OPLS-DA model based on variable importance in projection (VIP scores) and FC threshold (> 2.0) revealed 41 up regulated discriminant metabolite features annotated as sphingosine, fecosterol, melatonin, serotonin, glucose 6-phosphate, zeatin, dihydrozeatin and zeatin-β-D-glucoside. Similarly, 23 down regulated discriminant metabolites included histidinol, 4-aminobutyraldehyde, propanoate, tyramine and linalool. Melatonin and serotonin in the leaves were the two indoleamines being reported for the first time in tomato in response to the early blight pathogen. Receiver operating characteristic (ROC)-based biomarker analysis identified apigenin-7-glucoside, uridine, adenosyl-homocysteine, cGMP, tyrosine, pantothenic acid, riboflavin (as up regulated) and adenosine, homocyctine and azmaline (as down regulated) biomarkers. These results could aid in the development of metabolite-quantitative trait loci (mQTL). Furthermore, stress-induced biosynthetic pathways may be the potential targets for modifications through breeding programs or genetic engineering for improving crop performance in the fields.

miRNA profiling of primary lamb testicle cells infected with lumpy skin disease virus

In this study, miRNA profiling of cells infected with lumpy skin disease virus (LSDV) was conducted for the first time. When compared to mock-infected cells, LSDV-infected primary lamb testicle (LT) cells showed dysregulation of 64, 85, and 85 miRNAs at 12 hours postinfection (hpi), 48 hpi, and 72 hpi, respectively. While some of these miRNAs were found to be dysregulated at a particular time point following LSDV infection, others were dysregulated at all three time points. Analysis of the differentially expressed miRNA-mRNA interaction networks, Gene Ontology analysis of the predicted targets, and KEGG analysis of highly enriched pathways revealed several cellular factors/pathways involved in protein/ion/enzyme binding, cell differentiation, movement of subcellular components, calcium reabsorption, aldosterone synthesis and secretion, and melanogenesis. Some selected upregulated (oar-mir-379-5p, oar-let-7d, Chr10-18769, Chr2_5162 and oar-miR-493-5p) and downregulated (ChrX-33741, Chr3_8257 and Chr26_32680) miRNAs were further confirmed by quantitative real-time PCR. These findings contribute to our understanding of virus replication, virus-host interactions, and disease pathogenesis, and the differentially expressed miRNAs and their cellular targets may serve as biomarkers as well as novel targets for therapeutic intervention against LSDV.

Characterization and ecotoxicological risk assessment of sewage sludge from industrial and non-industrial cities

The present study highlights the occurrence and the temporal variations of physicochemical properties, and heavy metals in the sludge from sewage treatment plants (STPs) located in industrial (two sites) and non-industrial (one site) cities of Haryana, India. The sludge was acidic (5.59) to neutral (7.21) with a mean EC of 7.4 dS m-1. Prominent heavy metals present in the sewage sludge from industrial sites were Cd, Ni, and Cr with maximum values of 2.83, 1449.0, and 3918.5 mg kg-1, respectively. The contamination and enrichment factor better explained the buildup of Ni, Cr, and Cu in the sewage sludge from industrial sites. The pH, total carbon, phosphorus, and other water-soluble anions, viz. SO42-, Cl-, HCO3-, and PO43-, were the most important attributes of sludge controlling the binding and removal of the metals with particulate matters during the phase separation in STPs. These attributes explained about 90% of the variation in Cd, Ni, Cr, Cu, Mn, and Zn content of the sludge from different STPs. Sludge from the non-industrial site had a low potential ecological risk index of 74.0 compared to a very high-risk index of 2186.5 associated with the industrial sites. This study concludes that besides the concentration of the heavy metals, the enrichment factor coupled with geo-accumulation or ecological risk index can effectively categorize the sludge. However, these indices need to be linked with bioaccumulation, bioaccessibility, and biomass quality under different agroecologies for guiding the safer use of sewage sludge in agriculture.

Genome-wide identification and expression analysis of the GRAS gene family under abiotic stresses in wheat (Triticum aestivum L.)

The GRAS transcription factors are multifunctional proteins involved in various biological processes, encompassing plant growth, metabolism, and responses to both abiotic and biotic stresses. Wheat is an important cereal crop cultivated worldwide. However, no systematic study of the GRAS gene family and their functions under heat, drought, and salt stress tolerance and molecular dynamics modeling in wheat has been reported. In the present study, we identified the GRAS gene in Triticum aestivum through systematically performing gene structure analysis, chromosomal location, conserved motif, phylogenetic relationship, and expression patterns. A total of 177 GRAS genes were identified within the wheat genome. Based on phylogenetic analysis, these genes were categorically placed into 14 distinct subfamilies. Detailed analysis of the genetic architecture revealed that the majority of TaGRAS genes had no intronic regions. The expansion of the wheat GRAS gene family was proven to be influenced by both segmental and tandem duplication events. The study of collinearity events between TaGRAS and analogous orthologs from other plant species provided valuable insights into the evolution of the GRAS gene family in wheat. It is noteworthy that the promoter regions of TaGRAS genes consistently displayed an array of cis-acting elements that are associated with stress responses and hormone regulation. Additionally, we discovered 14 miRNAs that target key genes involved in three stress-responsive pathways in our study. Moreover, an assessment of RNA-seq data and qRT-PCR results revealed a significant increase in the expression of TaGRAS genes during abiotic stress. These findings highlight the crucial role of TaGRAS genes in mediating responses to different environmental stresses. Our research delved into the molecular dynamics and structural aspects of GRAS domain-DNA interactions, marking the first instance of such information being generated. Overall, the current findings contribute to our understanding of the organization of the GRAS genes in the wheat genome. Furthermore, we identified TaGRAS27 as a candidate gene for functional research, and to improve abiotic stress tolerance in the wheat by molecular breeding.

Study of Microstructural, Nutritional, and Biochemical Changes in Hulled and Hulless Barley during Storage Using X-ray and Infrared Techniques

Four varieties of barley (Esma, AC Metacalf, Tradition, and AB Cattlelac), representing four Canadian barley classes, were stored at 17% moisture content (mc) for 8 week. Stored barely was characterized using synchrotron X-ray phase contrast microcomputed tomography, synchrotron X-ray fluorescence imaging, and mid-infrared spectroscopy at the Canadian Light Source, Saskatoon. The deterioration was observed in all the selected varieties of barley at the end of 8 week of storage. Changes due to spoilage over time were observed in the grain microstructure and its nutrient distribution and composition. This study underscores the critical importance of the initial condition of barley grain microstructure in determining its storage life, particularly under unfavorable conditions. The hulled barley varieties showed more deterioration in microstructure than the hulless varieties of barley, where a direct correlation between microstructural changes and alterations in nutritional content was found. All selected barley classes showed changes in the distribution of nutrients (Ca, Fe, K, Mn, Cu, and Zn), but the two-row AC Metcalf variety exhibited more substantial variations in their nutrient distribution (Zn and Mn) than the other three varieties during storage. The two-row class barley varieties showed more changes in biochemical components (protein, lipids, and carbohydrates) than the six-row class varieties.

Effect of silencing Thrips palmi Btk29A and COL3A1 on fitness and virus acquisition

Thrips palmi (Thysanoptera: Thripidae) is a major agricultural pest infesting over 200 plant species. Along with direct injury caused by feeding, T. palmi spreads several orthotospoviruses. Groundnut bud necrosis orthotospovirus (GBNV, family Tospoviridae, genus Orthotospovirus) is the predominant orthotospovirus in Asia, vectored by T. palmi. It is responsible for almost 89 million USD losses in Asia annually. Several transcripts of T. palmi related to innate immune response, receptor binding, cell signaling, cellular trafficking, viral replication, and apoptosis are responsive to the infection of orthotospoviruses in thrips. Expression of T. palmi tyrosine kinase Btk29A isoform X1 (Btk29A) and collagen alpha-1(III) chain-like (COL3A1) are significantly regulated post-GBNV and capsicum chlorosis orthotospovirus infection. In the present study, T. palmi Btk29A and COL3A1 were silenced and the effect on virus titer and fitness was assessed. The expression of Btk29A and COL3A1 was significantly reduced by 3.62 and 3.15-fold, respectively, 24 h post-dsRNA exposure. Oral administration of Btk29A and COL3A1 dsRNAs induced 60 and 50.9% mortality in T. palmi. The GBNV concentration in T. palmi significantly dropped post-silencing Btk29A. In contrast, the silencing of COL3A1 led to an increase in GBNV concentration in T. palmi compared to the untreated control. To the best of our knowledge, this is the first report on the effect of silencing Btk29A and COL3A1 on the fitness and GBNV titer in T. palmi.

Transcriptional Regulation of Small Heat Shock Protein 17 (sHSP-17) by Triticum aestivum HSFA2h Transcription Factor Confers Tolerance in Arabidopsis under Heat Stress

Heat shock transcription factors (HSFs) contribute significantly to thermotolerance acclimation. Here, we identified and cloned a putative HSF gene (HSFA2h) of 1218 nucleotide (acc. no. KP257297.1) from wheat cv. HD2985 using a de novo transcriptomic approach and predicted sHSP as its potential target. The expression of HSFA2h and its target gene (HSP17) was observed at the maximum level in leaf tissue under heat stress (HS), as compared to the control. The HSFA2h-pRI101 binary construct was mobilized in Arabidopsis, and further screening of T3 transgenic lines showed improved tolerance at an HS of 38 °C compared with wild type (WT). The expression of HSFA2h was observed to be 2.9- to 3.7-fold higher in different Arabidopsis transgenic lines under HS. HSFA2h and its target gene transcripts (HSP18.2 in the case of Arabidopsis) were observed to be abundant in transgenic Arabidopsis plants under HS. We observed a positive correlation between the expression of HSFA2h and HSP18.2 under HS. Evaluation of transgenic lines using different physio-biochemical traits linked with thermotolerance showed better performance of HS-treated transgenic Arabidopsis plants compared with WT. There is a need to further characterize the gene regulatory network (GRN) of HSFA2h and sHSP in order to modulate the HS tolerance of wheat and other agriculturally important crops.

Assessment of Indian wheat germplasm for Septoria nodorum blotch and tan spot reveals new QTLs conferring resistance along with recessive alleles of Tsn1 and Snn3

The leaf blight diseases, Septoria nodorum blotch (SNB), and tan spot (TS) are emerging due to changing climatic conditions in the northern parts of India. We screened 296 bread wheat cultivars released in India over the past 20 years for seedling resistance against SNB (three experiments) and TS (two experiments). According to a genome-wide association study, six QTLs on chromosome arms 1BL, 2AS, 5BL, and 6BL were particularly significant for SNB across all three years, of which Q.CIM.snb.1BL, Q.CIM.snb.2AS1, Q.CIM.snb.2AS.2, and Q.CIM.snb.6BL appeared novel. In contrast, those on 5BS and 5BL may correspond to Snn3 and Tsn1, respectively. The allelic combination of tsn1/snn3 conferred resistance to SNB, whereas that of Tsn1/Snn3 conferred high susceptibility. As for TS, Tsn1 was the only stably significant locus identified in this panel. Several varieties like PBW 771, DBW 277, and HD 3319, were identified as highly resistant to both diseases that can be used in future wheat improvement programs as resistant donors.

Seroprevalence and associated risk factors of leptospirosis in bovine dairy farms in Telangana state, India

The current cross-sectional study aimed to determine the seroprevalence of Leptospira infection in bovine dairy farms in the Telangana state of India, as well as the associated risk factors, in order to implement effective preventive measures for disease control. A total of 469 blood samples were collected from 67 herds/farms in different areas, covering 20 administrative districts in the state. These samples consisted of 253 from cattle and 216 from buffaloes. Questionnaires were used to collect data on host and epidemiological factors. The collected sera were tested using the gold standard serological test, the Microscopic Agglutination Test (MAT), which employed a panel of 18 reference serovars for Leptospira exposure. The statistical analysis of epidemiological data was carried out to identify the risk factors associated with Leptospira exposure. The overall observed seroprevalence at the animal and farm levels was 41.4% and 77.6%, respectively. The most prevalent anti-leptospiral antibodies were observed against the serogroups Icterohaemorrhagiae (32.4%), Pomona (22.2%), Javanica (19.1%), Australis (17.0%), Bataviae (15.5%), Autumnalis (12.9%), Hebdomadis (12.9%), and others, in the total reacting samples. At the animal level, the significant risk factors associated with exposure to Leptospira species were breed (p = 0.03) and health status (p = 0.03). Furthermore, the multivariate statistical analysis of farm factors revealed that farm size (p = 0.05), presence of dogs (p = 0.04) and rodents (p = 0.01) on the farm, use of fodder from wet soils (p = 0.04), and proximity to water bodies (p = 0.04) were significantly associated with exposure to Leptospira in the studied region. This study provides the first report from India highlighting the important risk factors at the herd/farm and animal level associated with Leptospira infections in cattle and buffaloes. The findings contribute to strengthening the one-health strategy by facilitating the design and planning of appropriate control measures to alleviate the burden of leptospirosis in bovines.

Dissipation kinetics, residue determination and consumer risk assessment of acephate on green pea by gas chromatography-electron capture detector

The present study on "acephate persistence on green pea" was conducted in SKUAST-Kashmir. The study aimed to determine the persistence, dissipation kinetics and waiting period of acephate on green pea. Acephate was sprayed at 75% soluble powder (SP) at 560 g a.i.ha-1 at the fruiting stage followed by another application at a 10 day interval. A rapid and accurate method (quick, easy, cheap, effective, rugged and safe, QuEChERS) was used for extraction and the residue was determined by gas chromatography-electron capture detection on a CPSIL-8CB capillary column (0.25um film thickness, 0.25 mm i.d, 30 m length). At the fortification levels of 0.05, 0.1 and 0.5 mg kg-1 , the percentage recovery of acephate on green pea was found in the range of 71-107%. The initial deposit of green pea was estimated to be 0.37 mg kg-1 . At the indicated dose, the residue of acephate on green pea dissipated below the limit of quantification of 0.05 mg kg-1 after 10 days. Acephate degradation was quick in green pea, with a half-life of 4.07 days. For safe eating of green peas, a 10 day waiting period is recommended. The gas chromatography-electron capture detection technique was validated by following the SANTE standards.

Functional response of an egg parasitoid, Trichogramma chilonis Ishii to sublethal imidacloprid exposure

BACKGROUND

The effectiveness of a biological control agent depends on how well it can control pests and how compatible it is with pesticides. Therefore, we reported the multigenerational effect of a commonly used insecticide, imidacloprid, on the functional response of a widely acclaimed egg parasitoid, Trichogramma chilonis Ishii, to different densities of the host Corcyra cephalonica Stainton eggs. The study investigated the outcomes of the median lethal concentration (LC50 ) and sublethal concentrations (LC5 , LC30 ), along with control treatments for five continuous generations (F1 to F5 ).

RESULTS

The results showed that the F5 generation of LC30 , both of the F1 and F5 generations of LC50 , and the control all had a Type II functional response. A Type I functional response was exhibited for the F1 generation of LC30 and both generations of LC5 . The attack rate on host eggs treated with LC5 and LC30 did not change (decrease) with the shift in the type of functional response as compared to the control. A significant increase in the searching efficiency (a) was observed in the later generation (F5 ) under the exposure of LC5 and LC30 imidacloprid concentrations. A lower handling time (Th ) in both generations of the LC5 followed by LC30 treated individuals was observed when compared with the control and LC50 treatments. The per capita parasitization efficiency (1/Th ) and the rate of parasitization per handling time (a/Th ) were also considerably higher in both the generations of LC5 and LC30 than in the control and LC50 , thereby implying positive effects of imidacloprid on the parasitization potential of T. chilonis.

CONCLUSION

Altogether, these multigenerational outcomes on the functional response of T. chilonis could be leveraged to control the intractable lepidopteran pests under the mild exposure of imidacloprid in integrated pest management (IPM) programs as well as in the mass rearing of the parasitoid, T. chilonis. © 2023 Society of Chemical Industry.

Nano-copper Enhances Gene Regulation of Non-specific Immunity and Antioxidative Status of Fish Reared Under Multiple Stresses

Arsenic pollution, water temperature, and pH are the major concern for aquaculture. Moreover, the aim of the present investigation was to delineate the role of nano-copper (Cu-NPs) in the mitigation of arsenic toxicity, high temperature (34 °C) and low pH (6.5) stress on Pangasianodon hypophthalmus. Four isonitrogenous and isocaloric experimental diets of Cu-NPs at 0, 1.0, 1.5 and 2.0 mg kg-1 were formulated and prepared. Arsenic pollution, low pH and high temperature stress significantly reduced the anti-oxidative status (super oxide dismutase, catalase, glutathione peroxidase and glutathione-s-transferase), lipid peroxidation, total anti-oxidative capacity and lipid profiling (cholesterol, total lipid, phospholipid, very low-density lipoprotein and triglyceride). Further, the supplementation of Cu-NPs at 1.5 and 1.0 mg kg-1 diets noticeably improve the anti-oxidant status and capacity. The stressors groups (As + pH + T, As + T and As) significantly reduced fish immunity viz. albumin, globulin, total protein, albumin globulin ratio (A:G ratio), myeloperoxidase, respiratory burst activities, tumor necrosis factor, total immunoglobulin, and interleukin. Whereas supplementation of Cu-NPs at 1.5 and 1.0 mg kg-1 diets improved the immunity of the fish reared under multiple stresses (As + pH + T). Tail DNA %, DNA damage-inducible protein (DDIP) and inducible nitric oxide (iNOS) synthase gene expression were significantly enhanced with exposure to arsenic, low pH and high temperature but supplementation of Cu-NPs protects the tissues against DNA damage and improved the gene expression of iNOS and DDIP. Cu-NPs at 1.5 and 1.0 mg kg-1 diets significantly enhanced the body weight gain %, protein efficiency ratio, specific growth rate, daily growth index, relative feed intake and reduced the feed conversion ratio. Whereas, the growth-related gene expression such as myostatin (MYST), somatostatin (SMT) was downregulated by Cu supplementation and upregulated the gene expression of growth hormone regulator 1 and β (GHR1 and GHR β) and growth hormone (GH) gene in fish. Dietary Cu-NPs supplementation protects the fish against bacterial infection and enhances arsenic detoxification in different tissues. The present investigation revealed that supplementation of Cu-NPs at 1.5 and 1.0 mg kg-1 diet has the potential to mitigate multiple stress (As + pH + T) in fish.

Manganese nanoparticles control the gene regulations against multiple stresses in Pangasianodon hypophthalmus

Ammonia and arsenic pollution, along with the impact of climate change, represent critical factors influencing both the quantity and quality of aquaculture production. Recent developments have underscored the significance of these issues, as they not only disrupt aquatic ecosystems but also have far reaching consequences for human health. To addressed above challenges, an experiment was conducted to delineate the potential of manganese nanoparticles (Mn-NPs) to mitigate arsenic and ammonia pollution as well as high temperature stress in Pangasianodon hypophthalmus. The fish were exposed to different combination of arsenic and ammonia pollution as well as high temperature stress, while simultaneously incorporating diets enriched with Mn-NPs. The inclusion of Mn-NPs at 3 mg kg-1 in the diet led to a noteworthy downregulation of cortisol and HSP 70 gene expression, indicating their potential in mitigating stress responses. Furthermore, immune related gene expressions were markedly altered in response to the stressors but demonstrated improvement with the Mn-NPs diet. Interestingly, the expression of inducible nitric oxide synthase (iNOS), caspase (CAS), metallothionine (MT) and cytochrome P450 (CYP450) genes expression were prominently upregulated, signifying a stress response. Whereas, Mn-NPs at 3 mg kg-1 diet was significantly downregulated theses gene expression and reduces the stress. In addition to stress-related genes, we evaluated the growth-related gene expressions such as growth hormone (GH), growth hormone regulator 1 (GHR1 and GHRβ), Insulin like growth factor (IGF1 and IGF2) were significantly upregulated whereas, myostatin and somatostatin were downregulated upon the supplementation of dietary Mn-NPs with or without stressors in fish. The gene expression of DNA damage inducible protein and DNA damage in response to head DNA % and tail DNA % was protected by Mn-NPs diets. Furthermore, Mn-NPs demonstrated a capacity to enhance the detoxification of arsenic in different fish tissues, resulting in reduced bioaccumulation of arsenic in muscle and other tissues. This finding highlights Mn-NPs as a potential solution for addressing bioaccumulation associated risks. Our study aimed to comprehensively examined the role of dietary Mn-NPs in mitigating the multiple stressors using gene regulation mechanisms, with enhancing the productive performance of P. hypophthalmus.

Geographical distribution of tomato-infecting begomoviruses in major cucurbits in India: a diagnostic analysis using begomovirus species specific PCR

Cucurbits are an essential summer-season vegetable crops, but they are highly vulnerable from a range of abiotic and biotic factors. One of the significant biotic factors posing a growing menace to the production of major cucurbits in India is the emergence of tomato-infecting begomoviruses. In this study, we utilized PCR-based species-specific primers, developed earlier in our laboratory for the detection of begomoviruses infecting tomato and chilli plants, to identify begomoviruses in cucurbits across various regions of India. Leaf samples from major cucurbits were collected from different regions of Haryana, Delhi, Uttar Pradesh, Chhattisgarh, Maharashtra, Telangana and Karnataka, during the year 2020-2021. Total nucleic acid (TNA) was extracted from the samples and subjected to PCR using a generic primer specific to begomoviruses. The samples that exhibited positive amplification were further tested using six different species-specific primers targeting specific begomovirus species, namely Tomato leaf curl New Delhi virus (ToLCNDV), Tomato leaf curl Palampur virus (ToLCPalV), Tomato leaf curl Bangalore virus (ToLCBV), Tomato leaf curl Joydebpur virus (ToLCJoV), Tomato leaf curl Gujarat virus (ToLCGuV), and Chilli leaf curl virus (ChiLCV). The PCR analysis revealed that among the 551 plant samples tested, a total of 124 samples exhibited positive amplification using the universal begomovirus PCR. Specifically, 47 samples tested positive for ToLCNDV, 73 samples were positive for ToLCPalV and only one sample showed positive amplification for ChiLCV. However, none of the samples tested positive for ToLCJoV, ToLCGuV and ToLCBV. These findings from our study indicate the prevalence of ToLCNDV and ToLCPalV in major cucurbits across India. Furthermore, the study highlights the varied distribution of begomoviruses in major cucurbits between northern and southern regions of India.

Genome-wide characterization of 2OGD superfamily for mining of susceptibility factors responding to various biotic stresses in Musa spp

Bananas are an important staple food and cash crop, but they are vulnerable to a variety of pests and diseases that substantially reduce yield and quality. Banana diseases are challenging to control and necessitate an integrated strategy, and development of resistant cultivars is one of the effective ways of managing diseases. Lasting disease resistance is the main goal in crop improvement and resistance mediated by a single resistant (R) gene mostly lack durability. However, long-term resistance can be obtained by inactivating susceptibility factors (S), which facilitate pathogen infection and proliferation. Identification and inactivation of susceptibility factors against the major pathogens like Fusarium oxysporum f. sp. cubense (Foc), Pseudocercospora eumusae and Pratylenchus coffeae in banana will be an effective way in developing banana varieties with more durable resistance. Downy mildew resistance 6 (DMR6) and DMR-like oxygenases (DLO1) are one such susceptibility factors and they belong to 2-oxoglutarate Fe(II) dependent oxygenases (2OGD) superfamily. 2OGDs are known to catalyze a plethora of reactions and also confer resistance to different pathogens in various crops, but not much is known about the 2OGD in Musa species. Through a comprehensive genome-wide analysis, 133 and 122 potential 2OGDs were systematically identified and categorized from the A and B genomes of banana, respectively. Real time expression of dmr6 and dlo1 genes showed positive correlation with transcriptome data upon Foc race1 and TR4 infection and examination of expression pattern of Macma4_04_g22670 (Ma04_g20880) and Macma4_02_g13590 (Ma02_g12040) genes revealed their involvement in Foc race1 and TR4 infections, respectively. Further the expression profile of 2OGDs, specifically Macma4_04_g25310 (Ma04_g23390), Macma4_08_g11980 (Ma08_g12090) and Macma4_04_g38910 (Ma04_g36640) shows that they may play a significant role as a susceptibility factor, particularly against P. eumusae and P. coffeae, implying that they can be exploited as a candidate gene for editing in developing resistant cultivars against these diseases. In summary, our findings contribute to a deeper comprehension of the evolutionary and functional aspects of 2OGDs in Musa spp. Furthermore, they highlight the substantial functions of these family constituents in the progression of diseases. These insights hold significance in the context of enhancing the genetic makeup of bananas to attain extended and more durable resistance against pathogens.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01380-y.

Therapeutics and prophylactic efficacy of novel lytic Escherichia phage vB_EcoS_PJ16 against multidrug-resistant avian pathogenic E. coli using in vivo study

Avian pathogenic Escherichia coli (APEC) is the causative agent of avian colibacillosis, which causes significant economic losses to the poultry industry. The growing resistance of bacteria to antibiotics is a major global public health concern. However, there is limited data on the efficacy of phage therapy in effectively controlling and treating APEC infections. In this study, a novel lytic Escherichia phage, vB_EcoS_PJ16, was isolated from poultry farm wastewater and characterized in both in vitro and in vivo conditions. Transmission electron microscopy analysis revealed the presence of an icosahedral head and a long non-contractile tail, classifying the phage under the Caudoviricetes class. Host range determination showed that Escherichia phage vB_EcoS_PJ16 exhibited lytic activity against multiple strains of pathogenic E. coli, while no significant signs of lysis for Klebsiella pneumoniae, Salmonella Typhimurium, Listeria monocytogenes, and Staphylococcus aureus. Biophysical characterization revealed that the isolated phage was sturdy, as it remained viable for up to 300 days at temperatures of 30 °C, 37 °C, and 42 °C and for up to 24 h at pH 5 to 11, with only minor changes in titer. Kinetic analysis at multiplicity of infection (MOI) 0.1 showed a latency period of about 20 min and a burst size of 26.5 phage particles per infected cell for phage vB_EcoS_PJ16. Whole genome sequencing unveiled that the phage vB_EcoS_PJ16 genome consists of a double-stranded linear DNA molecule with 57,756 bp and a GC content of 43.58%. The Escherichia phage vB_EcoS_PJ16 genome consisted of 98 predicted putative ORFs, with no transfer RNA identified in the genome. Among these 98 genes, 34 genes were predicted to have known functions. A significant reduction in APEC viability was observed at MOI 100 during in vitro bacterial challenge tests conducted at different MOIs (0.01, 1, and 100). In vivo oral evaluation of the isolated phage to limit E. coli infections in day-old chicks indicated a decrease in mortality within both the therapeutic (20%) and prophylactic (30%) groups, when compared to the control group. The findings of this study contribute to our current knowledge of Escherichia phages and suggest a potentially effective role of phages in the therapeutic and prophylactic control of antibiotic-resistant APEC strains.

Pathological analysis and antimicrobial susceptibility of Chryseobacterium balustinum RTFCP 298 isolated from diseased rainbow trout, Oncorhynchus mykiss

In this study, six isolates of Chryseobacterium balustinum were characterized from diseased rainbow trout fingerlings. The virulence characteristics, pathogenicity, and antimicrobial susceptibility pattern of these isolates were investigated. The bacterium showed positive results for catalase, cytochrome oxidase, and aesculin hydrolysis, while negative results were obtained for DNase, gelatinase, methyl red, Voges-Proskauer's reaction, Simon citrate, Hydrogen sulphide, and starch hydrolysis. Amino acid metabolism analysis revealed the inability to metabolize arginine, lysine, and ornithine decarboxylase. Molecular characterization (16S rRNA) and phylogenetic analysis revealed the test isolates as C. balustinum, closely related to strain WLT (99.85% similarity) and C. balustinum P-27 (99.77%). Virulence assay indicated haemolytic activity and biofilm formation by the test bacterium. The challenge test confirmed moderate pathogenicity in rainbow trout and established Koch's postulates. The clinical manifestations of infection included fin erosion, eye and body surface haemorrhage, exophthalmia, and organ liquefaction. The minimum inhibitory concentrations of various antimicrobials ranged from 1 to > 256 µg mL-1. The novel synthetic antimicrobial peptides exhibited MICs of 8 to > 256 µg mL-1, suggesting a potential control method. These findings suggest that C. balustinum is an opportunistic pathogen with moderate pathogenicity in rainbow trout. Further research on the host-pathogen relationship is necessary to understand virulence characteristics and pathogenicity in aquaculture.