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Öğe Developing future heat-resilient vegetable crops(Springer Heidelberg, 2023) Saeed, Faisal; Chaudhry, Usman Khalid; Raza, Ali; Charagh, Sidra; Bakhsh, Allah; Bohra, Abhishek; Ali, SumbulClimate change seriously impacts global agriculture, with rising temperatures directly affecting the yield. Vegetables are an essential part of daily human consumption and thus have importance among all agricultural crops. The human population is increasing daily, so there is a need for alternative ways which can be helpful in maximizing the harvestable yield of vegetables. The increase in temperature directly affects the plants' biochemical and molecular processes; having a significant impact on quality and yield. Breeding for climate-resilient crops with good yields takes a long time and lots of breeding efforts. However, with the advent of new omics technologies, such as genomics, transcriptomics, proteomics, and metabolomics, the efficiency and efficacy of unearthing information on pathways associated with high-temperature stress resilience has improved in many of the vegetable crops. Besides omics, the use of genomics-assisted breeding and new breeding approaches such as gene editing and speed breeding allow creation of modern vegetable cultivars that are more resilient to high temperatures. Collectively, these approaches will shorten the time to create and release novel vegetable varieties to meet growing demands for productivity and quality. This review discusses the effects of heat stress on vegetables and highlights recent research with a focus on how omics and genome editing can produce temperature-resilient vegetables more efficiently and faster.Öğe Doubled Haploid Production – Mechanism and Utilization in Plant Breeding(Springer International Publishing, 2023) Yel, Ilknur; Dönmez, Betül Ayça; Yeşil, Binnur; Tekinsoy, Merve; Saeed, Faisal; Bakhsh, AllahThe discovery of haploids in plants led plant breeders to help to produce double haploids. The chromosome numbers of double haploids are different from haploids. This technique shortens the time to produce homozygous plants as compared to the conventional breeding method. After doubling the chromosome, it produces two identical homologous chromosomes. This helps to achieve homozygosity of crop up to one generation early as compared to conventional breeding. Once an interesting gene combination is achieved through conventional breeding; further mixing of genes is considered a real challenge. The production of double haploids is dependent on haploid inducer lines. The current breakthroughs of molecular actors triggering induction of haploid in plants have an important role of processes related to the development of gamete, interactions, and stability of the genome. These findings allowed translation of induction of haploid, and genome editing technologies can be helpful to produce haploid inducer lines. These recent discoveries can be helpful for improved breeding strategies. Besides that, it also provides deeper information regarding sexual reproduction in plants. In this chapter, we discussed how we can produce haploid inducer lines and with the help of new biotechnological tools to produce double haploid plants. © The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Switzerland AG 2023.Öğe Establishment of highly efficient and reproducible Agrobacterium-mediated transformation system for tomato (Solanum lycopersicum L.)(Springer, 2022) Hashmi, Muneeb Hassan; Saeed, Faisal; Demirel, Ufuk; Bakhsh, AllahA simple and improved Agrobacterium-mediated transformation protocol of tomato (Solanum lycopersicum) cultivar Rio Grande was developed to inspect the potential of producing transgenic tomatoes. In this study, regeneration and transformation efficiency as assessed in response to the seedling age, explant type, co-infection, co-cultivation duration, selection pressure (kanamycin), and the optimal concentration of plant growth regulators (PGR) 6-benzylaminopurine (BAP), gibberellic acid (GA3), and indolebutyric acid (IBA) in a Murashige and Skoog (MS) basal medium. To accomplish this goal, 2- to 4-wk-old tomato explant cotyledons, hypocotyl, and cotyledonary nodes were excised and transformed with the EHA105 Agrobacterium tumefaciens strain harboring pBIN19 binary vector containing uidA reporter gene and nptII as a selectable marker. Results revealed that 14-d-old cotyledonary nodes and leaves inoculated for 15 min with A. tumefaciens strain EHA105 following 48-h co-cultivation were optimal for the highest percent transformation efficiency 27.31. Antibiotic kanamycin (Kan) at 25 mg L-1 in the regeneration selection medium was found to be effective. MS medium containing optimal concentrations of 1.5 mg L-1 of BAP, 0.2 mg L-1 GA(3), and IBA 1.5 mg L-1 showed a significant level of percent regeneration, shoot elongation, and rooting efficiency of transformed plantlets. Molecular analysis of T-0 transgenic tomato plants showed integration and a higher relative expression level of the uidA gene. The optimized A. tumefaciens-mediated transformation method for tomato cultivar Rio Grande showed the highest percent transformation efficiency (TE) and regeneration efficiency (RE) and is likely to give consistent results with different tomato cultivars.Öğe Harnessing plant-mediated RNAi for effective management of Phthorimaea absoluta by targeting AChE1 and SEC23 genes(Elsevier, 2024) Hashmi, Muneeb Hassan; Tariq, Haneef; Saeed, Faisal; Demirel, Ufuk; Gokce, Ayhan; Merzendorfer, Hans; Aksoy, EmreTomato production on a global scale is under persistent pressure due to the devastating impact of Phthorimaea absoluta Meyrick (Lepidoptera: Gelechiidae), the South American tomato leaf miner. To combat this devastating pest, we explored the potential of plant-mediated RNA interference (RNAi) as a novel strategy for its management. Using transgenic techniques, we developed RNAi constructs (p35SÖğe Identification and characterization of RNA polymerase II (RNAP) C-Terminal domain phosphatase-like 3 (SlCPL3) in tomato under biotic stress(Springer, 2023) Saeed, Faisal; Hashmi, Muneeb Hassan; Aksoy, Emre; Demirel, Ufuk; Bakhsh, AllahBackgroundBacterial diseases are a huge threat to the production of tomatoes. During infection intervals, pathogens affect biochemical, oxidant and molecular properties of tomato. Therefore, it is necessary to study the antioxidant enzymes, oxidation state and genes involved during bacterial infection in tomato.Methods and resultsDifferent bioinformatic analyses were performed to conduct homology, gene promoter analysis and determined protein structure. Antioxidant, MDA and H2O2 response was measured in Falcon, Rio grande and Sazlica tomato cultivars. In this study, RNA Polymerase II (RNAP) C-Terminal Domain Phosphatase-like 3 (SlCPL-3) gene was identified and characterized. It contained 11 exons, and encoded for two protein domains i.e., CPDCs and BRCT. SOPMA and Phyre2, online bioinformatic tools were used to predict secondary structure. For the identification of protein pockets CASTp web-based tool was used. Netphos and Pondr was used for prediction of phosphorylation sites and protein disordered regions. Promoter analysis revealed that the SlCPL-3 is involved in defense-related mechanisms. We further amplified two different regions of SlCPL-3 and sequenced them. It showed homology respective to the reference tomato genome. Our results showed that SlCPL-3 gene was triggered during bacterial stress. SlCPL-3 expression was upregulated in response to bacterial stress during different time intervals. Rio grande showed a high level of SICPL-3 gene expression after 72 hpi. Biochemical and gene expression analysis showed that under biotic stress Rio grande cultivar is more sensitive to Pst DC 3000 bacteria.ConclusionThis study lays a solid foundation for the functional characterization of SlCPL-3 gene in tomato cultivars. All these findings would be beneficial for further analysis of SlCPL-3 gene and may be helpful for the development of resilient tomato cultivars.Öğe Melatonin-mediated temperature stress tolerance in plants(Taylor & Francis As, 2022) Raza, Ali; Charagh, Sidra; Garcia-Caparros, Pedro; Rahman, Md Atikur; Ogwugwa, Vincent H.; Saeed, Faisal; Jin, WanmeiGlobal climate changes cause extreme temperatures and a significant reduction in crop production, leading to food insecurity worldwide. Temperature extremes (including both heat and cold stresses) is one of the most limiting factors in plant growth and development and severely affect plant physiology, biochemical, and molecular processes. Biostimulants like melatonin (MET) have a multifunctional role that acts as a defense molecule to safeguard plants against the noxious effects of temperature stress. MET treatment improves plant growth and temperature tolerance by improving several defense mechanisms. Current research also suggests that MET interacts with other molecules, like phytohormones and gaseous molecules, which greatly supports plant adaptation to temperature stress. Genetic engineering via overexpression or CRISPR/Cas system of MET biosynthetic genes uplifts the MET levels in transgenic plants and enhances temperature stress tolerance. This review highlights the critical role of MET in plant production and tolerance against temperature stress. We have documented how MET interacts with other molecules to alleviate temperature stress. MET-mediated molecular breeding would be great potential in helping the adverse effects of temperature stress by creating transgenic plants.Öğe Moving Beyond DNA Sequence to Improve Plant Stress Responses(Frontiers Media Sa, 2022) Saeed, Faisal; Chaudhry, Usman Khalid; Bakhsh, Allah; Raza, Ali; Saeed, Yasir; Bohra, Abhishek; Varshney, Rajeev K.Plants offer a habitat for a range of interactions to occur among different stress factors. Epigenetics has become the most promising functional genomics tool, with huge potential for improving plant adaptation to biotic and abiotic stresses. Advances in plant molecular biology have dramatically changed our understanding of the molecular mechanisms that control these interactions, and plant epigenetics has attracted great interest in this context. Accumulating literature substantiates the crucial role of epigenetics in the diversity of plant responses that can be harnessed to accelerate the progress of crop improvement. However, harnessing epigenetics to its full potential will require a thorough understanding of the epigenetic modifications and assessing the functional relevance of these variants. The modern technologies of profiling and engineering plants at genome-wide scale provide new horizons to elucidate how epigenetic modifications occur in plants in response to stress conditions. This review summarizes recent progress on understanding the epigenetic regulation of plant stress responses, methods to detect genome-wide epigenetic modifications, and disentangling their contributions to plant phenotypes from other sources of variations. Key epigenetic mechanisms underlying stress memory are highlighted. Linking plant response with the patterns of epigenetic variations would help devise breeding strategies for improving crop performance under stressed scenarios.Öğe Nano-enabled stress-smart agriculture: Can nanotechnology deliver drought and salinity-smart crops?(Wiley, 2023) Raza, Ali; Charagh, Sidra; Salehi, Hajar; Abbas, Saghir; Saeed, Faisal; Poinern, Gerrard E. J.; Siddique, Kadambot H. M.Salinity and drought stress substantially decrease crop yield and superiority, directly threatening the food supply needed to meet the rising food needs of the growing total population. Nanotechnology is a step towards improving agricultural output and stress tolerance by improving the efficacy of inputs in agriculture via targeted delivery, controlled release, and enhanced solubility and adhesion while also reducing significant damage. The direct application of nanoparticles (NPs)/nanomaterials can boost the performance and effectiveness of physio-biochemical and molecular mechanisms in plants under stress conditions, leading to advanced stress tolerance. Therefore, we presented the effects and plant responses to stress conditions, and also explored the potential of nanomaterials for improving agricultural systems, and discussed the advantages of applying NPs at various developmental stages to alleviate the negative effects of salinity and drought stress. Moreover, we feature the recent innovations in state-of-the-art nanobiotechnology, specifically NP-mediated genome editing via CRISPR/Cas system, to develop stress-smart crops. However, further investigations are needed to unravel the role of nanobiotechnology in addressing climate change challenges in modern agricultural systems. We propose that combining nanobiotechnology, genome editing and speed breeding techniques could enable the designing of climate-smart cultivars (particularly bred or genetically modified plant varieties) to meet the food security needs of the rising world population. Salinity and drought stress substantially decrease crop yield and superiority, threatening the world's food security. Nanotechnology holds great potential for designing stress-smart, sustainable crops to feed the growing population. imageÖğe Recent advances in potato (solanum tuberosum L.) breeding(Springer International Publishing, 2021) Aksoy, Emre; Demirel, Ufuk; Bakhsh, Allah; Zia, Muhammad Abu Bakar; Naeem, Muhammad; Saeed, Faisal; Çalişkan, SevgiPotato (Solanum tuberosum L.) is an annual dicotyledonous tuber crop originating from the Americas and now distributed all over the world. A member of the Solanaceae family, potato is the fourth most produced food crop and the first non-cereal crop in the world. Potato is a staple food with its high potentiality in fighting malnutrition in the world since potato tubers are known sources of vitamins, proteins, carbohydrates and minerals. Moreover, it generates higher yield compared to the other crops; hence, it is one of the most notable crops to eliminate hunger and poverty. Therefore, sustainable potato production is important for food security and social welfare in future climate-change scenarios. However, it is very sensitive to environmental conditions and climate change due to its shallow root system. Therefore, future potato breeding programs should focus on enhancement of abiotic and biotic stress tolerance by utilizing the natural germplasm conserved in different gene banks. Moreover, potato breeding should benefit from the effectiveness and ease of molecular techniques such as marker-assisted selection, genome-wide association studies, functional genomics and transgenics. Development of new potato varieties can also be achieved via genetic engineering and genome editing. Disease-free potato seed production requires integration of tissue culture methods in plant breeding. As a staple food for millions, the potato has an extraordinarily rich past, and a bright future. The demand for potato will increase in future, which will be the driving force behind the potato research. © Springer Nature Switzerland AG 2021.Öğe Role of genetic engineering in improving potato production(Elsevier, 2022) Saeed, Faisal; Dangol, Sarbesh Das; Hashmi, Muneeb Hassan; Hossain, Md Jakir; Bakhsh, AllahPotato is believed to be one of the most significant noncereal food crops to address the food security concerns in future for the increasing population worldwide. Potatoes are rich in vitamins, minerals, and antioxidants that make them of paramount significance for impressive health benefits besides. Numerous improvements have been introduced in potatoes for yield and yield contributing traits; however, limitation still exist especially when it comes to abiotic and biotic stresses. Recently, developments in genetic engineering have revolutionized potato breeding remarkably by addressing bottlenecks encountered in conventional potato breeding successfully. The new breeding techniques have allowed the researchers to add, remove, alter, and manipulate gene(s) to encode tolerance/resistance against abiotic and biotic stresses. The improvements in cell biology to regenerate plants from single cells or organized tissues provide a prerequisite for the practical use of genetic engineering in crop improvement. In addition to that, the quality of the potato has also been improved significantly for industrial purposes. This chapter provides a comprehensive understanding of how genetic engineering has contributed to potato improvement in terms of quality, insect pests, and diseases. It also discusses how these modern techniques can shape potato breeding programs for the development of climate-resilient cultivars in future. © 2023 Elsevier Inc. All rights reserved.Öğe Transgenic technologies for efficient insect pest management in crop plants(Elsevier, 2020) Saeed, Faisal; Hashmi, Muneeb Hassan; Hossain, Md. Jakir; Ali, Muhammad Amjad; Bakhsh, AllahInsect and pests impose significant yield losses in crops despite the use of pesticidal and nonchemical controls. These increasing yield losses have provided impetus for the development of new management strategies against various pests. In this regard, transgenic technologies have revolutionized agriculture remarkably with the development of pest-resistant crops that have been outstanding in terms of crop productivity and highly advantageous to the farming community worldwide. With the passage of time, these technologies have enabled the scientists to modify and manipulate crop plants and to provide new solutions to solve conventional barriers for the improvement of economic traits of crops. The advancements in cell biology to regenerate plants from single cells or organized tissues provide prerequisite for the practical use of genetic engineering in crops improvement. The use of insect-resistant endotoxins from Bacillus thuringiensis in commercialized crops has resulted in increased crop yield since their introduction. The plant chloroplastic genome has also been engineered to encode resistance against insects pests. Several transgenic approaches have been employed to enhance resistance in plants against plant parasitic nematode as well. More recently, new and robust genetic engineering techniques like RNAi and Crispr-Cas9 have also proved their usefulness as a potential strategy in crop improvement for the control of pests. This chapter provides comprehensive insights and discussion of use of modern transgenic technologies in today’s agriculture and integration to efficient integrated pest management. © 2020 Elsevier Inc. All rights reserved.
