Genome-wide analysis and prediction of chloroplast and mitochondrial RNA editing sites of AGC gene family in cotton (Gossypium hirsutum L.) for abiotic stress tolerance.

BACKGROUND: Cotton is one of the topmost fiber crops throughout the globe. During the last decade, abrupt changes in the climate resulted in drought, heat, and salinity. These stresses have seriously affected cotton production and significant losses all over the textile industry. The GhAGC kinase, a subfamily of AGC group and member of serine/threonine (Ser/Thr) protein kinases group and is highly conserved among eukaryotic organisms. The AGC kinases are compulsory elements of cell development, metabolic processes, and cell death in mammalian systems. The investigation of RNA editing sites within the organelle genomes of multicellular vascular plants, such as Gossypium hirsutum holds significant importance in understanding the regulation of gene expression at the post-transcriptional level. METHODS: In present work, we characterized twenty-eight GhAGC genes in cotton and constructed phylogenetic tree using nine different species from the most primitive to the most recent. RESULTS: In sequence logos analyses, highly conserved amino acid residues were found in G. hirsutum, G. arboretum, G. raimondii and A. thaliana. The occurrence of cis-acting growth and stress-related elements in the promoter regions of GhAGCs highlight the significance of these factors in plant development and abiotic stress tolerance. Ka/Ks levels demonstrated that purifying selection pressure resulting from segmental events was applied to GhAGC with little functional divergence. We focused on identifying RNA editing sites in G. hirsutum organelles, specifically in the chloroplast and mitochondria, across all 28 AGC genes. CONCLUSION: The positive role of GhAGCs was explored by quantifying the expression in the plant tissues under abiotic stress. These findings help in understanding the role of GhAGC genes under abiotic stresses which may further be used in cotton breeding for the development of climate smart varieties in abruptly changing climate.

Exploring the mechanism of transformation in Acacia nilotica (Linn.) triggered by colchicine seed treatment.

BACKGROUND: Acacia nilotica Linn. is a widely distributed tree known for its applications in post-harvest and medicinal horticulture. However, its seed-based growth is relatively slow. Seed is a vital component for the propagation of A. nilotica due to its cost-effectiveness, genetic diversity, and ease of handling. Colchicine, commonly used for polyploidy induction in plants, may act as a pollutant at elevated levels. Its optimal concentration for Acacia nilotica's improved growth and development has not yet been determined, and the precise mechanism underlying this phenomenon has not been established. Therefore, this study investigated the impact of optimized colchicine (0.07%) seed treatment on A. nilotica's morphological, anatomical, physiological, fluorescent, and biochemical attributes under controlled conditions, comparing it with a control. RESULTS: Colchicine seed treatment significantly improved various plant attributes compared to control. This included increased shoot length (84.6%), root length (53.5%), shoot fresh weight (59.1%), root fresh weight (42.8%), shoot dry weight (51.5%), root dry weight (40%), fresh biomass (23.6%), stomatal size (35.9%), stomatal density (41.7%), stomatal index (51.2%), leaf thickness (11 times), leaf angle (2.4 times), photosynthetic rate (40%), water use efficiency (2.2 times), substomatal CO2 (36.6%), quantum yield of photosystem II (13.1%), proton flux (3.1 times), proton conductivity (2.3 times), linear electron flow (46.7%), enzymatic activities of catalase (25%), superoxide dismutase (33%), peroxidase (13.5%), and ascorbate peroxidase (28%), 2,2-diphenyl-1-picrylhydrazyl-radical scavenging activities(23%), total antioxidant capacity (59%), total phenolic (23%), and flavonoid content (37%) with less number of days to 80% germination (57.1%), transpiration rate (53.9%), stomatal conductance (67.1%), non-photochemical quenching (82.8%), non-regulatory energy dissipation (24.3%), and H2O2 (25%) and O-2 levels (30%). CONCLUSION: These findings elucidate the intricate mechanism behind the morphological, anatomical, physiological, fluorescent, and biochemical transformative effects of colchicine seed treatment on Acacia nilotica Linn. and offer valuable insights for quick production of A. nilotica's plants with modification and enhancement from seeds through an eco-friendly approach.

Transcriptomic analysis reveals candidate genes associated with salinity stress tolerance during the early vegetative stage in fababean genotype, Hassawi-2.

Abiotic stresses are a significant constraint to plant production globally. Identifying stress-related genes can aid in the development of stress-tolerant elite genotypes and facilitate trait and crop manipulation. The primary aim of this study was to conduct whole transcriptome analyses of the salt-tolerant faba bean genotype, Hassawi-2, under different durations of salt stress (6 h, 12 h, 24 h, 48 h, and 72 h) at the early vegetative stage, to better understand the molecular basis of salt tolerance. After de novo assembly, a total of 140,308 unigenes were obtained. The up-regulated differentially expressed genes (DEGs) were 2380, 2863, 3057, 3484, and 4820 at 6 h, 12 h, 24 h, 48 h, and 72 h of salt stress, respectively. Meanwhile, 1974, 3436, 2371, 3502, and 5958 genes were downregulated at 6 h, 12 h, 24 h, 48 h, and 72 h of salt stress, respectively. These DEGs encoded various regulatory and functional proteins, including kinases, plant hormone proteins, transcriptional factors (TFs) basic helix-loop-helix (bHLH), Myeloblastosis (MYB), and (WRKY), heat shock proteins (HSPs), late embryogenesis abundant (LEA) proteins, dehydrin, antioxidant enzymes, and aquaporin proteins. This suggests that the faba bean genome possesses an abundance of salinity resistance genes, which trigger different adaptive mechanisms under salt stress. Some selected DEGs validated the RNA sequencing results, thus confirming similar gene expression levels. This study represents the first transcriptome analysis of faba bean leaves subjected to salinity stress offering valuable insights into the mechanisms governing salt tolerance in faba bean during the vegetative stage. This comprehensive investigation enhances our understanding of precise gene regulatory mechanisms and holds promise for the development of novel salt-tolerant faba bean salt-tolerant cultivars.

Combined application of hot water treatment and eucalyptus leaf extract postpones senescence in harvested green chilies by conserving their antioxidants: a sustainable approach.

BACKGROUND: Green chili is the predominant vegetable in tropical and subtropical regions with high economic value. However, after harvest, it exhibits vigorous metabolic activities due to the high moisture level, leading to a reduction in bioactive compounds and hence reduced shelf life and nutritional quality. Low temperature storage results in the onset of chilling injury symptoms. Therefore, developing techniques to increase the shelf life of green chilies and safeguard their nutritional value has become a serious concern for researchers. In this regard, an experiment was conducted to evaluate the impact of the alone or combined application of hot water treatment (HWT) (45 °C for 15 min) and eucalyptus leaf extract (ELE) (30%) on 'Golden Hot' chilies in comparison to the control. After treatment, chilies were stored at 20 ± 1.5 °C for 20 days. RESULTS: HWT + ELE-treated chilies had a significant reduction in fruit weight loss (14.6%), fungal decay index (35%), red chili percentage (41.2%), soluble solid content (42.9%), ripening index (48.9%), and reactive oxygen species production like H2O2 (55.1%) and O-2 (46.5%) during shelf in comparison to control, followed by the alone application of HWT and ELE. Furthermore, the combined use of HWT and ELE effectively improved the antioxidative properties of stored chilies including DPPH radical scavenging activities (54.6%), ascorbic acid content (28.4%), phenolic content (31.8%), as well as the enzyme activities of POD (103%), CAT (128%), SOD (26.5%), and APX (43.8%) in comparison to the control. Additionally, the green chilies underwent HWT + ELE treatment also exhibited higher chlorophyll levels (100%) and general appearance (79.6%) with reduced anthocyanin content (40.8%) and wrinkling (43%), leading to a higher marketable fruit (41.3%) than the control. CONCLUSION: The pre-storage application of HWT and ELE could be used as an antimicrobial, non-chemical, non-toxic, and eco-friendly treatment for preserving the postharvest quality of green chilies at ambient temperature (20 ± 1.5 °C).

Spatial differences influence nitrogen uptake, grain yield, and land-use advantage of wheat/soybean relay intercropping systems.

Cereal/legume intercropping is becoming a popular production strategy for higher crop yields and net profits with reduced inputs and environmental impact. However, the effects of different spatial arrangements on the growth, grain yield, nitrogen uptake, and land-use advantage of wheat/soybean relay intercropping are still unclear, particularly under arid irrigated conditions. Therefore, in a three-year field study from 2018 to 2021, soybean was relay intercropped with wheat in different crop configurations (0.9 m, narrow strips; 1.8 m, medium strips; and 2.7 m, wide strips), and the results of intercropping systems were compared with their sole systems. Results revealed that intercrops with wide strips outperformed the narrow and medium strips, when the objective was to obtain higher total leaf area, dry matter, nitrogen uptake, and grain yield on a given land area due to reduced interspecific competition between intercrops. Specifically, at maturity, wide strips increased the dry matter accumulation (37% and 58%) and its distribution in roots (37% and 55%), straw (40% and 61%), and grains (30% and 46%) of wheat and soybean, respectively, compared to narrow strips. This enhanced dry matter in wide strips improved the soybean's competitive ability (by 17%) but reduced the wheat's competitive ability (by 12%) compared with narrow strips. Noticeably, all intercropping systems accumulated a significantly higher amount of nitrogen than sole systems, revealing that wheat/soybean relay intercropping requires fewer anthropogenic inputs (nitrogen) and exerts less pressure on the ecosystem than sole systems. Overall, in wide strips, intercropped wheat and soybean achieved 62% and 71% of sole wheat and soybean yield, respectively, which increased the greater total system yield (by 19%), total land equivalent ratio (by 24%), and net profit (by 34%) of wide strips compared to narrow strips. Our study, therefore, implies that the growth parameters, grain yields, nutrient accumulation, and land-use advantage of intercrop species could be improved with the proper spatial arrangement in cereal/legume intercropping systems.

Postharvest starch and sugars adjustment in potato tubers of wide-ranging dormancy genotypes subjected to various sprout forcing techniques.

The development of an efficient, safe, and environment-friendly technique to terminate tuber dormancy in potatoes (Solanum tuberosum L.) is of great concern due to the immense scope of multiple cropping all over the globe. The breakage of tuber dormancy has been associated with numerous physiological changes, including a decline in the level of starch and an increase in the levels of sugars during storage of freshly harvested seed potatoes, although their consistency across genotypes and various dormancy-breaking techniques have not yet been fully elucidated. The purpose of the present research is to assess the efficacy of four different dormancy-breaking techniques, such as soaking in 90, 60, or 30 mg L-1 solutions of benzyl amino purine (BAP) and 30, 20, or 10 mg L-1 gibberellic acid (GA3) alone and in the combination of optimized concentrations; cold pre-treatment at 6, 4, or 2 °C; electric shock at 80, 60, 40, or 20 Vs; and irradiation at 3.5, 3, 2.5, 2, 1.5, or 1 kGy on the tuber dormancy period and sprout length of six genotypes. Furthermore, the changes that occurred in tuber weight and endogenous starch, sucrose, fructose, and glucose contents in experimental genotypes following the application of these techniques were also examined. Overall, the most effective technique to terminate tuber dormancy and hasten spout growth was the combined application of BAP and GA3, which reduced the length of dormancy by 9.6 days compared to the untreated control, following 6.7 days of electric current, 4.4 days of cold pre-treatment, and finally irradiation (3.3 days). The 60 mg L-1 solution of BAP greatly reduced the dormancy period in all genotypes but did not affect the sprout length at all. The genotypes showed a weak negative correlation (r = - 0.4) (P < 0.05) of endogenous starch contents with dormancy breakage and weight loss or a moderate (r = - 0.5) correlation with sprout length, but a strong positive correlation (r = 0.8) of tuber glucose, fructose, and sucrose contents with dormancy breakage and weight loss. During 3 weeks of storage, sprouting commencement and significant weight loss occurred as tuber dormancy advanced towards breakage due to a reduction in starch and an increase in the sucrose, fructose, and glucose contents of the tubers. These findings could be advantageous for postponing or accelerating seed potato storage as well as investigating related physiological research in the future.

Organic amendments and conservation tillage improve cotton productivity and soil health indices under arid climate.

Long-term different tillage system field trials can provide vital knowledge about sustainable changes in soil health indices and crop productivity. This study examined cotton productivity and soil health indices under different tillage systems and organic materials. The present study was carried out at MNS University of Agriculture, Multan to explore the effect of different tillage systems: conventional tillage (T1), conservation tillage (T2), and organic materials: control (recommended dose of synthetic fertilizers; 160:90:60 kg ha-1NPK), poultry manure (10 t ha-1 PM), compost (10 t ha-1 CM), farmyard manure (20 t ha-1 FYM), and biochar (7 t ha-1 BC) on cotton productivity and soil health indices. Two years field trials showed that different tillage systems and organic materials significantly improved the growth, morphological, and yield attributes of cotton and soil health indices. The cotton showed highest seed cotton yield (3692-3736 kg ha-1), and soil organic matter (0.809-0.815%), soil available nitrogen (74.3-74.6 mg kg-1), phosphorus (7.29-7.43 mg kg-1), and potassium (213-216 mg kg-1) under T2 in comparison to T1 system during both years of field experiment, respectively. Similarly, PM (10 t ha-1) showed highest seed cotton yield (3888-3933 kg ha-1), and soil organic matter (0.794-0.797%), nitrogen (74.7-75.0 mg kg-1), phosphorus (7.39-7.55 mg kg-1), and potassium (221-223 mg kg-1) when these are compared to FYM (20 t ha-1), CM (10 t ha-1), and BC (7 t ha-1) during both years of field experiment, respectively. These findings indicate that conservation tillage system with application of 10 t ha-1 PM are the best practices for the sustainable cotton production and to ensure improvement in the soil health indices under arid climatic conditions.

Effect of slow-release nitrogenous fertilizers on dry matter accumulation, grain nutritional quality, water productivity and wheat yield under an arid environment.

Slow release nitrogenous fertilizers can improve crops production and reduce the environmental challenges in agro-ecosystem. There is a need to test the efficiency and performance under arid climatic conditions. The study investigates the effect of slow-release fertilizers (urea, neem coated urea (NCU), sulfur coated urea (SCU) and bioactive sulfur coated urea (BSCU)) on the growth, productivity and grain nutritional qualities of wheat crop. Slow-release fertilizers (SRF) with nitrogen levels (130,117,104 and 94 kg ha-1) were applied with equal splits at sowing, 20 and 60 days after sowing (DAS). Research showed that the BSCU with 130 kg ha-1 increased dry matter accumulation (1989 kg ha-1) after anthesis and grain yield 4463 kg ha-1. The higher plant height (102 cm) was attained by 130 kg N ha-1 SCU while the minimum (77.67 cm) recorded for 94 kg N ha-1 as urea source. Maximum grain NPK concentrations (3.54, 0.66 and 1.07%) were recorded by BSCU 130 kg N ha-1 application. While, the minimum NPK (0.77, 0.19 and 0.35%) were observed by Urea 94 kg N ha-1. The high irrigation water use efficiency (WUE) recorded (20.92 kg ha-1 mm-1) and a crop index of 25.52% by BSCU 130 kg N ha-1 application. Research findings show that generally all SRF but particularly BSCU proved effective and can be recommended for wheat crop under arid environment.

Genetic diversity analysis for wild and cultivated accessions of Cymbopogon citratus (D.C.) Stapf using phytochemical and molecular markers.

Background: Genetic diversity is being lost because of increasing urbanization and decreasing cultivation land, which leads to the abrupt use of wild resources of medicinally aromatic plants (MAPs). Cymbopogon citratus is a morphologically diverse MAP that is largely exploited in the food, cosmetics, and pharmaceutical industries. However, the intraspecific phytochemical and molecular diversity of C. citratus has yet to be explored. Methodology: The germplasm was obtained from four different countries representing Pakistan, India, Bangladesh, and the United States. Oil extraction was performed by hydro distillation, and metabolic profiles of different accessions were generated by GC-MS. Seventeen functional molecular markers based on three genes encoding cytochrome P450, uridyl diphosphate glycosyltransferase and the 5S rRNA gene family were used to explore genetic diversity. Principal component analysis (PCA) and heatmaps were constructed using R software with the help of the gg-plot R package v1.0.5 for data validation. Results: Among the 208 identified metabolites, citral was maximal, with a phytochemical contribution (1.92-27.73%), α-pinene (0.82-15.57%), verbenol (0.24-22.84%), neral (0.23-21.31%) and geranial acetate (0.43-15.65%). In the majority of accessions, citral was the dominant component. The highest concentration of citral was detected in 384541 (27.74%), 384527 (27.52%) belonging to Pakistan and one USA-based accession 38456 (27.71%). Region-specific grouping revealed a relationship between genetic diversity and geographical location. Pakistani accessions 384518, 38452, and 384544 genetically and 384535, 384518, and 384510 were phytochemically diverse. Conclusion: The genetic diversity was more pronounced in cultivated accessions than in wild accessions. Moreover, it was observed that phytochemical diversity correlated with the altitude and temperature of the region.

Effect of arbuscular mycorrhizal fungi on the physiological functioning of maize under zinc-deficient soils.

Zinc (Zn) deficiency can severely inhibit plant growth, yield, and enzymatic activities. Zn plays a vital role in various enzymatic activities in plants. Arbuscular mycorrhizal fungi (AMF) play a crucial role in improving the plant's Zn nutrition and mitigating Zn stress effects on plants. The current study was conducted to compare the response of inoculated and non-inoculated maize (YH 1898) in the presence of different levels of zinc under greenhouse conditions under a Zn deficient condition. There were two mycorrhizal levels (i.e., M + with mycorrhizae, M- without mycorrhizae) and five Zn levels (i.e., 0, 1.5, 3, 6, and 12 mg kg-1), with three replicates following completely randomized design. At the vegetative stage (before tillering), biochemical, physiological, and agronomic attributes were measured. The results showed that maize plants previously inoculated with AMF had higher gaseous exchange traits, i.e., a higher stomatal conductance rate, favoring an increased photosynthetic rate. Improvement in antioxidant enzyme activity was also observed in inoculated compared to non-inoculated maize plants. Moreover, AMF inoculation also played a beneficial role in nutrients availability and its uptake by plants. Higher Zn12 (12 mg Zn kg-1 soil) treatment accumulated a higher Zn concentration in soil, root, and shoot in AMF-inoculated than in non-inoculated maize plants. These results are consistent with mycorrhizal symbiosis beneficial role for maize physiological functioning in Zn deficient soil conditions. Additionally, AMF inoculation mitigated the stress conditions and assisted nutrient uptake by maize.

Lipoic Acid Combined with Melatonin Mitigates Oxidative Stress and Promotes Root Formation and Growth in Salt-Stressed Canola Seedlings (Brassica napus L.).

Lipoic acid (LA) and melatonin (MT) are pleiotropic molecules participating in plant stress resistance by modulating cellular biochemical changes, ion homeostasis, and antioxidant enzyme activities. However, the combined role of these two molecules in counteracting the detrimental impacts of salinity stress is still unknown. In the present study, we determined the effects of exogenous LA (0.5 µM), MT (1 µM) and their combination (LA + MT) on growth performance and biomass accumulation, photosynthetic pigments, enzymatic and non-enzymatic antioxidant activities, and ions homeostatic in canola (Brassica napus L.) seedlings under salinity stress (0, 100 mM) for 40 days. The results indicate that exogenous application of LA + MT improved the phenotypic growth (by 25 to 45%), root thickness (by 68%), number of later lateral roots (by 52%), root viability (by 44%), and root length (by 50%) under salinity stress. Moreover, total soluble protein, chlorophyll pigments, the concentration of superoxide dismutase (SOD), catalase peroxidase (CAT), and ascorbic peroxidase (ASA) increased with the presence of salt concentration into the growth media and then decreased with the addition of LA + MT to saline solution. Leaf protein contents and the degradation of photosynthetic pigments were lower when LA + MT treatments were added into NaCl media. The proline and phenol contents decreased in the exogenous application of LA + MT treatments more than individual LA or MT treatments under the salinity stress. The incorporation of LA or MT or a combination of LA + MT to saline solution decreased salinity-induced malondialdehyde and electrolyte leakage. In conclusion, the alteration of metabolic pathways, redox modulation, and ions homeostasis in plant tissues by the combined LA and MT application are helpful towards the adaptation of Brassica napus L. seedlings in a saline environment. The results of this study provide, for the first time, conclusive evidence about the protective role of exogenous LA + MT in canola seedlings under salinity stress.

Impact of Seed Dressing and Soil Application of Potassium Humate on Cotton Plants Productivity and Fiber Quality.

Humus is the stable form of added crop and animal residues. The organic matter after a long-term decomposition process converts into humic substances. The naturally occurring humus is present in less amount in soils of the arid and semi-arid regions. The addition of commercially available humic acid can, therefore, contribute to improving soil health and crop yields. The present study was conducted to evaluate the effect of potassium humate, applied through soil seed dressing, on cotton productivity and fiber quality attributes. Seed dressing with potassium humate was done at the rate of 0, 100, 150 and 200 mL kg-1 seed while in soil potassium humate was applied at the rate of 0, 10, 20 and 30 L ha-1. Results showed that the combined application of potassium humate by seed dressing and through soil application improved the soil properties, productivity and fiber quality traits of cotton. All levels of soil applied potassium humate (10, 20 and 30 L ha-1) performed better over seed dressing in terms of cotton productivity and fiber quality attributes. Among the soil application rates, 20 L ha-1 potassium humate proved better as compared to other rates (0, 10 and 30 L ha-1). Higher soil application of potassium humate (30 L ha-1) showed depressing effects on all the traits studied like the reduction of 12.4% and 6.6% in Ginning out turn and fiber length, respectively, at a seeding dressing of 200 mL kg-1. In conclusion, potassium humate seed dressing and soil application at the rate of 200 mL kg-1 and 20 L ha-1, respectively, is a better approach to improve cotton productivity. Soil potassium humate should not exceed a rate of 20 L ha-1 when the seed dressing of potassium is also practiced.

Radiation efficiency and nitrogen fertilizer impacts on sunflower crop in contrasting environments of Punjab, Pakistan.

Sunflower (Helianthus annuus L.) is the leading non-conventional oilseed crop in Pakistan. Nitrogen fertilizer can affect plant growth and productivity by changing canopy size which has an effect on the radiation use efficiency (RUE) of the crop. The response of sunflower hybrids in terms of phenology, fraction of intercepted radiation (F i), and RUE to nitrogenous rates (0, 60, 120, 180, and 240 kg ha-1) was studied in three field experiments conducted in three various environments: Multan (arid), Faisalabad (semi-arid), and Gujranwala (sub-humid) during spring seasons 2008 and 2009. The treatments were laid out according to a randomized complete block design with split plot arrangements, keeping the sunflower hybrids in main plots and nitrogen rates in sub-plots, and replicated three times. The results showed Hysun-38 took a maximum number of days to anthesis (101) as compared to Pioneer-64A93 (100) and Hysun-33 (99). The mean values of F i were 0.850, 0.903, and 0.978, and the estimated values of RUE for total aboveground dry matter were 2.14, 2.47, and 2.65 g MJ-1 at experimental locations of Multan, Faisalabad, and Gujranwala, respectively. The values of RUE for grain yield (RUEGY) were 0.78, 0.98, and 1.26 g MJ-1 at experimental locations of Multan, Faisalabad, and Gujranwala, respectively. The average RUEGY values over three locations were 2.61, 2.60, 2.43, and 2.36 g MJ-2 in N4 (180 kg ha-1), N5 (240 kg ha-1), N3 (120 kg ha-1), and N2 (60 kg ha-1) treatments, respectively. Increasing rates of N increased RUEGY over the standard treatment N3 (120 kg N ha-1); however, the averaged values over three locations were 1.22, 1.08, 0.99, and 0.92 g MJ-2 in N4, N5, N3, and N2 treatments, respectively. Therefore, optimum water and N doses are important for attaining higher RUE, which may enhance sunflower growth and yield.