Sentinel plot surveillance of cotton leaf curl disease in Pakistan- a case study at the cultivated cotton-wild host plant interface

An Integrative Computational Approach for Identifying Cotton Host Plant MicroRNAs with Potential to Abate CLCuKoV-Bur Infection

Cotton leaf curl Kokhran virus-Burewala (CLCuKoV-Bur) has a circular single-stranded ssDNA genome of 2759 nucleotides in length and belongs to the genus Begomovirus (family, Geminiviridae). CLCuKoV-Bur causes cotton leaf curl disease (CLCuD) and is transmitted by the whitefly Bemisis tabaci cryptic species. Monopartite begomoviruses encode five open reading frames (ORFs). CLCuKoV-Bur replicates through a dsDNA intermediate. Five open reading frames (ORFs) are organized in the small circular, single-stranded (ss)-DNA genome of CLCuKoV-Bur (2759 bases). RNA interference (RNAi) is a naturally occurring process that has revolutionized the targeting of gene regulation in eukaryotic organisms to combat virus infection. The aim of this study was to elucidate the potential binding attractions of cotton-genome-encoded microRNAs (Gossypium hirsutum-microRNAs, ghr-miRNAs) on CLCuKoV-Bur ssDNA-encoded mRNAs using online bioinformatics target prediction tools, RNA22, psRNATarget, RNAhybrid, and TAPIR. Using this suite of robust algorithms, the predicted repertoire of the cotton microRNA-binding landscape was determined for a CLCuKoV-Bur consensus genome sequence. Previously experimentally validated cotton (Gossypium hirsutum L.) miRNAs (n = 80) were selected from a public repository miRNA registry miRBase (v22) and hybridized in silico into the CLCuKoV-Bur genome (AM421522) coding and non-coding sequences. Of the 80 ghr-miRNAs interrogated, 18 ghr-miRNAs were identified by two to four algorithms evaluated. Among them, the ghr-miR399d (accession no. MIMAT0014350), located at coordinate 1747 in the CLCuKoV-Bur genome, was predicted by a consensus or "union" of all four algorithms and represents an optimal target for designing an artificial microRNA (amiRNA) silencing construct for in planta expression. Based on all robust predictions, an in silico ghr-miRNA-regulatory network was developed for CLCuKoV-Bur ORFs using Circos software version 0.6. These results represent the first predictions of ghr-miRNAs with the therapeutic potential for developing CLCuD resistance in upland cotton plants.

Evaluation of energy potential of MSW in the Tamale metropolis, Ghana: An assessment of solid waste characteristics and energy content

In the present investigation, a thorough examination of waste composition was undertaken in the Tamale Metropolis, Ghana. The methodology employed was carefully designed, incorporating both commercial and residential sectors as well as various socioeconomic classes. Source-based sampling of waste materials covered a range of locations, including households, markets, hotels, and restaurants, while socioeconomic-based categorization followed the zoning of the metropolis. Waste audit sampling involved collecting a total of 90 batches of solid waste over the three-month period from August to October 2023. The primary objectives were to physically characterize the waste and evaluate its chemical properties through proximate and ultimate analysis of waste fractions, aiming to determine the waste-to-energy potential and compatibility with waste-to-energy technologies. The study revealed that the Tamale Metropolis generates 176.1 tons/day of Municipal Solid Waste (MSW) at a rate of 0.47 kg/capita/day.Organic matter constituted the majority (44.9%), followed by inert, miscellaneous, and plastic waste at 20% each. The remaining 14.3% comprised paper, metal, glass, leather, and textile components. Notably, the hospitality sector exhibited the highest organic matter content at 62.3%, contrasting with average households and markets at 44.9% and 13.1%, respectively. Moisture content ranged from 5.4% to 12.6%, volatile solids from 21.8% to 77.2%, and gross calorific values from 7.9 MJ/kg to 28.9 MJ/kg. Household waste demonstrated the highest energy content at 6693.8 kcal/kg, followed by hotels/restaurants (2003.94 kcal/kg) and markets (1883.62 kcal/kg). This study's findings offer valuable insights that can inform the development of effective policies by regulatory bodies such as the Public Utility Regulatory Commission (PURC) and the Ghana Ministry of Energy, as well as city authorities like the Tamale Metropolitan Assembly and the Environmental Protection Agency. These insights can be used to address waste and energy challenges in the metropolis.Implications: The findings reveal critical insights with substantial implications for stakeholders and regulatory bodies. It emphasizes the waste-to-energy potential of various waste fractions, highlighting the need for sustainable municipal waste management strategies. Particularly, the high organic content in the hospitality sector presents significant energy recovery opportunities. For bodies like the Public Utility Regulatory Commission and the Ghana Ministry of Energy, this data is crucial for developing policies that support waste-to-energy technologies. Additionally, the Tamale Metropolitan Assembly and the Environmental Protection Agency can use these insights to improve local waste management practices, customizing interventions to address specific sectoral waste composition. The study also underlines the importance of ongoing monitoring to ensure the effectiveness of these strategies over time.

Dominance of Cotton leaf curl Multan virus-Rajasthan strain associated with third epidemic of cotton leaf curl disease in Pakistan

Cotton (Gossypium hirsutum) is an economically potent crop in many countries including Pakistan, India, and China. For the last three decades, cotton production is under the constant stress of cotton leaf curl disease (CLCuD) caused by begomoviruses/satellites complex that is transmitted through the insect pest, whitefly (Bemisia tabaci). In 2018, we identified a highly recombinant strain; Cotton leaf curl Multan virus-Rajasthan (CLCuMuV-Raj), associated with the Cotton leaf curl Multan betasatellite-Vehari (CLCuMuBVeh). This strain is dominant in cotton-growing hub areas of central Punjab, Pakistan, causing the third epidemic of CLCuD. In the present study, we have explored the CLCuD diversity from central to southern districts of Punjab (Faisalabad, Lodhran, Bahawalpur, Rahimyar Khan) and the major cotton-growing region of Sindh (Tandojam), Pakistan for 2 years (2020-2021). Interestingly, we found same virus (CLCuMuV-Raj) and associated betasatellite (CLCuMuBVeh) strain that was previously reported with the third epidemic in the central Punjab region. Furthermore, we found minor mutations in two genes of CLCuMuV-Raj C4 and C1 in 2020 and 2021 respectively as compared to its isolates in 2018, which exhibited virus evolution. Surprisingly, we did not find these mutations in CLCuMuV-Raj isolates identified from Sindh province. The findings of the current study represent the stability of CLCuMuV-Raj and its spread toward the Sindh province where previously Cotton leaf curl Kokhran virus (CLCuKoV) and Cotton leaf curl Shahdadpur virus (CLCuShV) have been reported. The findings of the current study demand future research on CLCuD complex to explore the possible reasons for prevalence in the field and how the virus-host-vector compatible interaction can be broken to develop resistant cultivars.

Cotton microbiome profiling and Cotton Leaf Curl Disease (CLCuD) suppression through microbial consortia associated with Gossypium arboreum

The failure of breeding strategies has caused scientists to shift to other means where the new approach involves exploring the microbiome to modulate plant defense mechanisms against Cotton Leaf Curl Disease (CLCuD). The cotton microbiome of CLCuD-resistant varieties may harbor a multitude of bacterial genera that significantly contribute to disease resistance and provide information on metabolic pathways that differ between the susceptible and resistant varieties. The current study explores the microbiome of CLCuD-susceptible Gossypium hirsutum and CLCuD-resistant Gossypium arboreum using 16 S rRNA gene amplification for the leaf endophyte, leaf epiphyte, rhizosphere, and root endophyte of the two cotton species. This revealed that Pseudomonas inhabited the rhizosphere while Bacillus was predominantly found in the phyllosphere of CLCuV-resistant G. arboreum. Using salicylic acid-producing Serratia spp. and Fictibacillus spp. isolated from CLCuD-resistant G. arboreum, and guided by our analyses, we have successfully suppressed CLCuD in the susceptible G. hirsutum through pot assays. The applied strains exhibited less than 10% CLCuD incidence as compared to control group where it was 40% at 40 days post viral inoculation. Through detailed analytics, we have successfully demonstrated that the applied microbes serve as a biocontrol agent to suppress viral disease in Cotton.