Review
Environmental Sciences
Shafeeq Ur Rahman, Muhammad Farrakh Nawaz, Sadaf Gul, Ghulam Yasin, Babar Hussain, Yanliang Li, Hefa Cheng
Summary: Environmental pollution caused by heavy metals from anthropogenic activities has become a topic of increasing concern. Heavy metals, especially non-essential carcinogens, have been identified as major air, water, and soil pollutants that negatively impact the quantity, quality, and safety of plant-based food worldwide. Plants exposed to heavy metals experience reduced growth and yield, but they have developed complex defense mechanisms to avoid or tolerate the toxic effects. OMICS strategies have been widely used to understand the mechanisms of plant response and adaptation to heavy metal stress. Recent advancements in the understanding of the interaction between heavy metals and plants at molecular and cellular levels, as well as plants' defense strategies, are summarized in this review. The use of transcriptomics, genomics, metabolomics, proteomics, and ionomics for studying plant responses to heavy metal toxicity is reviewed, and challenges and future recommendations are discussed.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2022)
Review
Plant Sciences
Rong Zhou, Fangling Jiang, Lifei Niu, Xiaoming Song, Lu Yu, Yuwen Yang, Zhen Wu
Summary: The urgent need for crop varieties with high resilience to feed the growing population in climate change conditions suggests the importance of understanding crops' responses to abiotic stresses at various levels using multi-omics methods. This approach can provide valuable insights into plant biology and open possibilities for improving crop resilience and tolerance. However, challenges remain in interpreting and translating multidimensional data from multi-omics studies into meaningful biological context.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Biochemistry & Molecular Biology
Muhammad Naeem, Zeeshan Ali, Anzal Khan, Sami-Ul-Allah, Hassan Javed Chaudhary, Javeria Ashraf, Faheem Shahzad Baloch
Summary: Rice, as a crucial food crop for half of the world population, has a small genome size and its whole sequenced genome has proven to be valuable for genome research. The sequenced rice genome provides insights into molecular biology, transcriptomics, and genetic variability, which are essential for improving yield, quality, and stress resistance in rice crop.
MOLECULAR BIOLOGY REPORTS
(2022)
Review
Biotechnology & Applied Microbiology
Ali Raza, Javaria Tabassum, Himabindu Kudapa, Rajeev K. Varshney
Summary: Plants face various stresses including heat stress, chilling stress, and freezing stress due to adverse climate fluctuations. Responses to temperature stress involve complex mechanisms at cellular, molecular, and physiological levels, showcasing the importance of omics technologies in understanding stress adaptation and tolerance mechanisms. Efforts in exploring temperature stress responses in plants are crucial for achieving the goal of zero hunger worldwide.
CRITICAL REVIEWS IN BIOTECHNOLOGY
(2021)
Review
Plant Sciences
Umer Mahmood, Xiaodong Li, Yonghai Fan, Wei Chang, Yue Niu, Jiana Li, Cunmin Qu, Kun Lu
Summary: Crop production is facing challenges from increasing food demand and climate change. Advances in omics techniques and machine learning algorithms can accelerate crop breeding to cope with these challenges. Plant breeding and genetic engineering can develop nutrient sufficient and climate-resilient crops.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Plant Sciences
Theivanayagam Maharajan, T. P. Ajeesh Krishna, Kasinathan Rakkammal, Stanislaus Antony Ceasar, Manikandan Ramesh
Summary: Application of CRISPR/Cas tools can enhance cereals' growth and yield under biotic and abiotic stresses. However, studies on the mechanism of biotic and abiotic stress tolerance in cereals using the CRISPR/Cas system are limited. Rice is the most studied cereal in this aspect, while other major cereals have not been extensively explored. Understanding the role of specific genes in response to stresses through the CRISPR/Cas system may help improve cereals' growth and yield under various stress conditions.
Review
Plant Sciences
Vikas Mangal, Milan Kumar Lal, Rahul Kumar Tiwari, Muhammad Ahsan Altaf, Salej Sood, Vijay Gahlaut, Ashish Bhatt, Ajay Kumar Thakur, Ravinder Kumar, Vinay Bhardwaj, Vinod Kumar, Brajesh Singh, Rajender Singh, Devendra Kumar
Summary: Abiotic stresses have a negative impact on vegetable crops, but research on crop genomes can help identify stress-responsive genes. Understanding omics approaches and advanced molecular tools is crucial for studying the biology of abiotic stresses.
Review
Plant Sciences
Kasinathan Rakkammal, Arumugam Priya, Subramani Pandian, Theivanayagam Maharajan, Periyasamy Rathinapriya, Lakkakula Satish, Stanislaus Antony Ceasar, Soo-In Sohn, Manikandan Ramesh
Summary: Cereals have developed various tolerance mechanisms to cope with abiotic stress. The omics field, including genomics, transcriptomics, and proteomics, has made significant progress in understanding these mechanisms. Integrated omics and bioinformatics approaches are crucial for studying genome-wide stress-regulation mechanisms.
Article
Biochemical Research Methods
Mohammad Arefian, Thottethodi Subrahmanya Keshava Prasad
Summary: This study characterized the early effects of salt stress on the proteome and metabolome of rice tissues. It identified numerous signaling pathways that were rapidly induced or partially induced by salt stress. Through a combined analysis, it revealed the most sensitive components of signaling pathways causing salt-susceptibility in rice and suggested potential targets for crop improvement.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Mohammad Arefian, Thottethodi Subrahmanya Keshava Prasad
Summary: Rice, a staple food crop worldwide, is estimated to have its global production reduced by 50% due to salinity stress. However, limited knowledge exists regarding the initial molecular signaling and proteins associated with sensing salinity in crop plants. In this study, we characterized the early effects of salt on the proteome and metabolome of rice tissues and identified numerous signaling pathways induced by salinity. By combining omics data and physiological changes, we identified the most susceptible proteins and metabolites in each pathway, providing potential targets for improving rice's sensitivity to salinity.
JOURNAL OF PROTEOME RESEARCH
(2023)
Review
Plant Sciences
Zahra Iqbal, Mohammed Shariq Iqbal, M. Iqbal R. Khan, Mohammad Israil Ansari
Summary: Rice, a crucial staple crop for a large portion of the world's population, faces challenges from environmental stresses, necessitating continuous improvement to meet the needs of a growing population. Omics technologies have been instrumental in studying the regulatory mechanisms and genetic resources of rice, contributing to enhanced yield and quality.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Plant Sciences
Dhanawantari L. Singha, Debajit Das, Yogita N. Sarki, Naimisha Chowdhury, Monica Sharma, Jitendra Maharana, Channakeshavaiah Chikkaputtaiah
Summary: Tissue-specific CRISPR/Cas genome editing is a promising approach for crop improvement, bypassing the issues associated with constitutive genome editing and allowing targeted improvement of crops.
Review
Agronomy
Shubham Joshi, Viswanathan Chinnusamy, Rohit Joshi
Summary: This review discusses the changes in root system architecture under different environmental stimuli using high-throughput omics technologies, and highlights the importance of these technologies in improving crop productivity and developing resistant varieties.
Article
Plant Sciences
Viktoria Voronezhskaya, Polina Volkova, Sofia Bitarishvili, Ekaterina Shesterikova, Mikhail Podlutskii, Gilles Clement, Christian Meyer, Gustavo Turqueto Duarte, Maksim Kudin, Dmitrii Garbaruk, Larisa Turchin, Elizaveta Kazakova
Summary: By analyzing multiple omics of Vicia cracca L. plants grown under chronic radiation exposure, we found that these plants exhibited complex and multidirectional biological effects, including significant changes in metabolism and gene expression patterns. Profound alterations in carbon metabolism, nitrogen reallocation, and photosynthesis were observed, along with signs of DNA damage, redox imbalance, and stress responses. Upregulation of histones, chaperones, peroxidases, and secondary metabolism was also noted.
Review
Genetics & Heredity
Rajib Roychowdhury, Soumya Prakash Das, Amber Gupta, Parul Parihar, Kottakota Chandrasekhar, Umakanta Sarker, Ajay Kumar, Devade Pandurang Ramrao, Chinta Sudhakar
Summary: Global warming and climate change have negative effects on plants by imposing environmental stresses and disease pressure. Multi-omics approaches, including genomics, transcriptomics, proteomics, metabolomics, etc., have become useful tools to understand plant responses to abiotic stress and develop climate-smart crops.
Review
Biotechnology & Applied Microbiology
Wei Su, Ali Raza, Ang Gao, Liu Zeng, Yan Lv, Xiaoyu Ding, Yong Cheng, Xiling Zou
Summary: This article summarizes the research progress of lipid phosphate phosphatases (LPPs) in plants, emphasizing the structural and biochemical characteristics of LPPs and their role in spatio-temporal regulation. Further studies are needed to enhance our understanding of the key role of plant LPPs and lipid metabolism in signal regulation, stress tolerance pathway, and plant growth and development.
CRITICAL REVIEWS IN BIOTECHNOLOGY
(2023)
Article
Plant Sciences
Shiva Najafi-Kakavand, Naser Karimi, Hamid-Reza Ghasempour, Ali Raza, Mehrdad Chaichi, Masoud Modarresi
Summary: The study shows that the external application of salicylic acid (SA) and jasmonic acid (JA) can improve the root antioxidative response of two populations of Alyssum inflatum Nyar. against nickel (Ni) toxicity. The combination of SA and JA is especially effective in restricting Ni translocation to the shoot, accumulating in roots, and enhancing antioxidant defense systems, thereby improving root biomass and plant tolerance.
JOURNAL OF PLANT GROWTH REGULATION
(2023)
Review
Genetics & Heredity
Faisal Saeed, Usman Khalid Chaudhry, Ali Raza, Sidra Charagh, Allah Bakhsh, Abhishek Bohra, Sumbul Ali, Annapurna Chitikineni, Yasir Saeed, Richard G. F. Visser, Kadambot H. M. Siddique, Rajeev K. Varshney
Summary: Climate change directly impacts the yield of vegetables through rising temperatures. Breeding for climate-resilient crops requires significant time and effort, but advancements in omics technologies have improved the efficiency of identifying pathways for high-temperature stress resilience in vegetable crops. Genomics-assisted breeding, gene editing, and speed breeding offer new approaches to develop temperature-resilient vegetables more efficiently. This review discusses the effects of heat stress on vegetables and highlights the use of omics and genome editing in producing temperature-resilient vegetables.
FUNCTIONAL & INTEGRATIVE GENOMICS
(2023)
Article
Agronomy
Sadia Shahid, Abida Kausar, Noreen Zahra, Muhammad Bilal Hafeez, Ali Raza, Muhammad Yasin Ashraf
Summary: This study investigated the effects of amino acid application on maize under salt stress. The results showed that proper methionine levels can alleviate the negative effects of salinity, improving photosynthetic efficiency and antioxidant activities in plants.
Review
Agronomy
Huwaida Yaqoob, Arooj Tariq, Basharat Ahmad Bhat, Kaisar Ahmad Bhat, Iqra Bashir Nehvi, Ali Raza, Ivica Djalovic, P. V. Vara Prasad, Rakeeb Ahmad Mir
Summary: Genome editing can be used to domesticate orphan crops by editing their genomes. This technique shows promise in increasing agricultural output, especially in crops that possess undesirable traits similar to their wild cousins. By applying knowledge from model crops to orphan crops, breeders can quickly generate desired genetic diversity and innovative breeding materials. This review highlights the practicality of genome editing as a tool to accelerate the domestication of semi-domesticated or wild plants, providing a more diverse foundation for future food and fodder supplies. It also emphasizes the importance of investing in research to advance our understanding of plant genomes, genes, and cellular systems. Planting more of these abandoned orphan crops could help mitigate food shortages in the face of future climate crises.
GM CROPS & FOOD-BIOTECHNOLOGY IN AGRICULTURE AND THE FOOD CHAIN
(2023)
Review
Plant Sciences
A. Raza, S. Charagh, S. Abbas, M. U. Hassan, F. Saeed, S. Haider, R. Sharif, A. Anand, F. J. Corpas, W. Jin, R. K. Varshney
Summary: Climate change and abiotic stress factors have a significant impact on crop losses, particularly extreme temperatures. Plants have developed strategies to cope with temperature stress, such as accumulating the amino acid proline which helps in stress tolerance and maintaining plant metabolism. Manipulating the biosynthesis of proline through genetic engineering can lead to the development of temperature-smart crops.
Review
Plant Sciences
Aaliya Batool, Noreen Zahra, Rubina Naseer, Sobia Shahzad, Shahid Iqbal, Abida Kausar, Ali Raza
Summary: Plant architecture is the three-dimensional organization of aerial parts of plants, including branching pattern, leaf structure and position, and floral organ arrangement. Environmental stresses can alter plant architecture, impacting overall fitness and productivity. Genetic and molecular studies have identified key genes involved in maintaining plant architecture and understanding their function can lead to desired traits and improved crop yield. This review discusses how these genes control leaf features, flowering regulation, and branching patterns, and the impact of functional genomics-based approaches on plant development.
PLANT GROWTH REGULATION
(2023)
Article
Plant Sciences
Ali Raza, Sidra Charagh, Benjamin Karikari, Rahat Sharif, Vivek Yadav, Muhammad Salman Mubarik, Madiha Habib, Yuhui Zhuang, Chong Zhang, Hua Chen, Rajeev K. Varshney, Weijian Zhuang
Summary: Climate change has a significant impact on crop production by causing various abiotic and biotic stresses. To meet the demands of the increasing world population, efforts are needed to improve crop plants through modern biotechnological tools such as microRNAs (miRNAs). miRNAs play crucial roles in gene regulation and have been shown to enhance plant growth and development as well as stress tolerance. This review provides a comprehensive summary of the progress made in breeding stress-tolerant crop plants using miRNAs, including the identification of miRNAs associated with stress tolerance and the use of sequence-based technologies for crop improvement.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Review
Plant Sciences
Ali Raza, Sidra Charagh, Shiva Najafi-Kakavand, Saghir Abbas, Yasira Shoaib, Sultana Anwar, Sara Sharifi, Guangyuan Lu, Kadambot H. M. Siddique
Summary: Global climate variations cause extreme temperatures and reduce crop production, resulting in food insecurity worldwide. Temperature extremes, such as chilling (0-15 degrees C) and freezing (<0 C), severely affect plant growth and physiology. Plants respond to these stresses by activating various endogenous mechanisms, including phytohormone biosynthesis, to tolerate and adapt to stressful environments. This review highlights the importance of phytohormones in regulating plant responses to cold stress and discusses the potential of genetic engineering and omics approaches to develop cold-smart crop plants.
Article
Horticulture
Qamar U. Zaman, Muhammad Azhar Hussain, Latif Ullah Khan, Liu Hui, Darya Khan, Aamir Ali Khokhar, Jianpeng Cui, Ali Raza, Hua-Feng Wang
Summary: Pitaya, an important tropical plant, is rich in antioxidants and dietary fibers. Research has shown that pitaya regulates the expression of antioxidant enzyme genes to counteract the damage caused by reactive oxygen species. Hormone-related elements are abundant in the promoter regions of the pitaya antioxidant enzyme genes. Exogenous melatonin application efficiently induces the expression of antioxidant enzyme genes and enhances the growth and development of pitaya plants.
SCIENTIA HORTICULTURAE
(2023)
Article
Agriculture, Multidisciplinary
Mereen Nizar, Kanval Shaukat, Abdul Samad, Noreen Zahra, Ifra Saleem, Ali Raza
Summary: This study investigated the potential impact of exogenous supplementation with salicylic acid and hydrogen peroxide on milk thistle under cadmium toxicity in two ecological zones of Balochistan province, Pakistan. The results showed that these treatments effectively alleviated the negative impacts of cadmium toxicity, improved plant nutrients, and enhanced the yield and medicinal value of milk thistle seeds.
JOURNAL OF AGRICULTURE AND FOOD RESEARCH
(2023)
Article
Biology
Abdul Samad, Kanval Shaukat, Mahmood-Ur-Rehman Ansari, Mereen Nizar, Noreen Zahra, Ambreen Naz, Hafiz Muhammad Waleed Iqbal, Ali Raza, Vladan Pesic, Ivica Djalovic
Summary: Salinity is a major abiotic factor that limits plant growth and productivity. Foliar application of plant growth regulators (PGRs) has the potential to mitigate the negative impacts of salinity. A field experiment was conducted to investigate the role of PGRs in alleviating salinity stress on Plantago ovata, an important medicinal plant. The results showed that PGRs enhanced photosynthetic pigments and activated defense mechanisms, leading to improved yield under salt stress. The most effective treatments were PRO and MLE, which predominantly ameliorated the harsh impacts of salinity.
Article
Biochemistry & Molecular Biology
Tunisha Verma, Savita Bhardwaj, Ali Raza, Ivica Djalovic, P. V. Vara Prasad, Dhriti Kapoor
Summary: This study aimed to alleviate the negative effects of salt stress on Indian mustard. The application of triacontanol (TRIA) and hydrogen sulfide (H2S) was found to improve growth attributes and the antioxidant defense system in B. juncea under salt stress. Additionally, salt stress resulted in decreased levels of proteins, metabolites, and antioxidant enzymes, but these levels were significantly increased with the application of TRIA and H2S.
PLANT SIGNALING & BEHAVIOR
(2023)
Article
Biochemistry & Molecular Biology
Abida Kausar, Noreen Zahra, Hina Zahra, Muhammad Bilal Hafeez, Sara Zafer, Abida Shahzadi, Ali Raza, Ivica Djalovic, P. V. Vara Prasad
Summary: This study examines the protective effect of foliar application of thiamine on two varieties of pea plants under drought stress. Results show that thiamine can help plants withstand drought stress and improve their growth and antioxidant capacity. One of the pea varieties performs better than the other.
PLANT SIGNALING & BEHAVIOR
(2023)