The Intervention of Multi-Omics Approaches for Developing Abiotic Stress Resistance in Cotton Crop Under Climate Change

Khan, Muhammad Kashif Riaz; Ditta, Allah; Wang, Baohua; Liu, Fang; Anwar, Zunaira; Ijaz, Aqsa; Ahmed, Syed Riaz; Khan, Sana Muhy-Ud-Din

doi:10.1007/978-3-031-15568-0_3

Cited by 9 publications

(7 citation statements)

References 290 publications

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“…Recently existing base editors, encompassing adenine base editors (ABEs) and cytosine base editors (CBEs), have been engineered by fusing the inactive Cas9 (dCas9) or Cas9 nickase (D10A) (nCas9) with adenine deaminase or cytidine deaminase, respectively ( Komor et al, 2016 ; Gaudelli et al, 2017 ). In this manner, single-point mutations such as the conversion of A*T to G*C or C*G to T*A in crop plants can be generated using ABEs or CBEs ( Bharat et al, 2020 ; Ali et al, 2023 ; Khan et al, 2023 ). So far, base editing has been effectively used to target several important traits in various crops like maize, cotton, Arabidopsis thaliana , rice and others.…”

Section: Revolutionizing Genetics: Genome Editing and Beyondmentioning

confidence: 99%

“…In the recent years, genome map construction has gained an immense significance in MAS. MAS has been acquired as a molecular tool for the selection of desirable phenotypes using DNA markers such as RFLP, RAPD and AFLP on the basis of agriculturally important traits and the genes linked with tolerance against several abiotic and biotic factors ( Jones et al, 1997 ; Khan et al, 2023 ). Use of MAS in plant breeding has opened new doors in crop improvement ( Winter and Kahl, 1995 ).…”

Section: Next-generation Sequencing Applications In Cotton Genomicsmentioning

confidence: 99%

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A comprehensive review on Gossypium hirsutum resistance against cotton leaf curl virus

Nadeem,

Riaz Ahmed,

Luqman

et al. 2024

Front. Genet.

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Cotton (Gossypium hirsutum L.) is a significant fiber crop. Being a major contributor to the textile industry requires continuous care and attention. Cotton is subjected to various biotic and abiotic constraints. Among these, biotic factors including cotton leaf curl virus (CLCuV) are dominant. CLCuV is a notorious disease of cotton and is acquired, carried, and transmitted by the whitefly (Bemisia tabaci). A cotton plant affected with CLCuV may show a wide range of symptoms such as yellowing of leaves, thickening of veins, upward or downward curling, formation of enations, and stunted growth. Though there are many efforts to protect the crop from CLCuV, long-term results are not yet obtained as CLCuV strains are capable of mutating and overcoming plant resistance. However, systemic-induced resistance using a gene-based approach remained effective until new virulent strains of CLCuV (like Cotton Leaf Curl Burewala Virus and others) came into existence. Disease control by biological means and the development of CLCuV-resistant cotton varieties are in progress. In this review, we first discussed in detail the evolution of cotton and CLCuV strains, the transmission mechanism of CLCuV, the genetic architecture of CLCuV vectors, and the use of pathogen and nonpathogen-based approaches to control CLCuD. Next, we delineate the uses of cutting-edge technologies like genome editing (with a special focus on CRISPR-Cas), next-generation technologies, and their application in cotton genomics and speed breeding to develop CLCuD resistant cotton germplasm in a short time. Finally, we delve into the current obstacles related to cotton genome editing and explore forthcoming pathways for enhancing precision in genome editing through the utilization of advanced genome editing technologies. These endeavors aim to enhance cotton’s resilience against CLCuD.

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Section: Revolutionizing Genetics: Genome Editing and Beyondmentioning

confidence: 99%

Section: Next-generation Sequencing Applications In Cotton Genomicsmentioning

confidence: 99%

A comprehensive review on Gossypium hirsutum resistance against cotton leaf curl virus

Nadeem,

Riaz Ahmed,

Luqman

et al. 2024

Front. Genet.

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“…These methods aim to identify relationships and interactions between molecules across different omics layers. ‘Functional analysis’ can interpret the integrated multi-omics data to gain insights into the molecular mechanisms underlying abiotic stress tolerance responses and may involve GO analysis, pathway enrichment analysis and functional annotation of key genes, proteins and metabolites [ 23 ]. ‘Network analysis’ is to construct biological networks that capture the interactions between different molecules identified in the integrated data.…”

Section: Integration Of Multi-omics Data and Interpretation For Abiot...mentioning

confidence: 99%

“…To decipher crops’ abiotic stress tolerance response, both available marker-assisted breeding (MAB) and advanced multiomics-based analysis are complementary to each other, but omics-based tools provide a broader and more comprehensive understanding of plant biology of stress responses than MAB [ 23 ]. Omics technologies provide a comprehensive view of the entire plant system to study the complex interactions between genes, proteins and metabolites underlying molecular mechanisms of abiotic stress tolerance.…”

Section: Introductionmentioning

confidence: 99%

Multi-Omics Pipeline and Omics-Integration Approach to Decipher Plant’s Abiotic Stress Tolerance Responses

Roychowdhury

Das²,

Gupta

et al. 2023

Genes

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The present day’s ongoing global warming and climate change adversely affect plants through imposing environmental (abiotic) stresses and disease pressure. The major abiotic factors such as drought, heat, cold, salinity, etc., hamper a plant’s innate growth and development, resulting in reduced yield and quality, with the possibility of undesired traits. In the 21st century, the advent of high-throughput sequencing tools, state-of-the-art biotechnological techniques and bioinformatic analyzing pipelines led to the easy characterization of plant traits for abiotic stress response and tolerance mechanisms by applying the ‘omics’ toolbox. Panomics pipeline including genomics, transcriptomics, proteomics, metabolomics, epigenomics, proteogenomics, interactomics, ionomics, phenomics, etc., have become very handy nowadays. This is important to produce climate-smart future crops with a proper understanding of the molecular mechanisms of abiotic stress responses by the plant’s genes, transcripts, proteins, epigenome, cellular metabolic circuits and resultant phenotype. Instead of mono-omics, two or more (hence ‘multi-omics’) integrated-omics approaches can decipher the plant’s abiotic stress tolerance response very well. Multi-omics-characterized plants can be used as potent genetic resources to incorporate into the future breeding program. For the practical utility of crop improvement, multi-omics approaches for particular abiotic stress tolerance can be combined with genome-assisted breeding (GAB) by being pyramided with improved crop yield, food quality and associated agronomic traits and can open a new era of omics-assisted breeding. Thus, multi-omics pipelines together are able to decipher molecular processes, biomarkers, targets for genetic engineering, regulatory networks and precision agriculture solutions for a crop’s variable abiotic stress tolerance to ensure food security under changing environmental circumstances.

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“…By using non-destructive methods, it can capture dynamic changes in plant traits over time, offering a more nuanced understanding of plant responses to salinity stress. Hence, HTP serves as a critical tool for breeders to speed up the development of salt-tolerant cotton varieties (Khan et al 2023).…”

Section: Significance Of High Throughput Phenotypingmentioning

confidence: 99%

High Throughput Phenotyping: A Revolutionary Approach to Combat Salinity Stress in Cotton

2023

Trends Biotechnol Plant Sci

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This review paper comprehensively explores the potential of high throughput phenotyping (HTP) in assessing and combating salinity stress in cotton production. Salinity stress presents a significant challenge for global cotton crop, impacting the plant's physiological and molecular functions. HTP emerges as a potentially transformative tool for understanding and addressing this issue, employing advanced imaging techniques, spectral reflectance, and molecular technologies to rapidly and accurately measure plant traits. While HTP holds considerable promise, its implementation is not without challenges. The review dissects these barriers, ranging from technical hurdles associated with data acquisition, storage, and analysis to economic considerations involving equipment and maintenance costs. Notably, advancements in machine learning and artificial intelligence (AI) offer promising solutions to many of these challenges, with proven applications in image analysis, trait prediction and data integration. The review showcases the successful application of HTP across various global case studies, demonstrating its potential to revolutionize plant research and breeding. Further, the integration of AI and machine learning is poised to significantly enhance the capabilities of HTP, ushering in a new era of data-driven, efficient plant phenotyping. The paper concludes with a set of research and policy recommendations to optimize the use of HTP for salinity stress in cotton. These include promoting the integration of genomics and phenomics, improving image analysis algorithms, developing predictive models, and standardizing phenotypic data. At the policy level, the authors call for investments in HTP infrastructure, increased collaboration and data sharing, capacity building, and the incorporation of HTP into breeding programs. This review illustrates the immense potential of HTP to revolutionize our approach to salinity stress in cotton, ultimately contributing to more sustainable and resilient cotton production.

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The Intervention of Multi-Omics Approaches for Developing Abiotic Stress Resistance in Cotton Crop Under Climate Change

Cited by 9 publications

References 290 publications

A comprehensive review on Gossypium hirsutum resistance against cotton leaf curl virus

A comprehensive review on Gossypium hirsutum resistance against cotton leaf curl virus

Multi-Omics Pipeline and Omics-Integration Approach to Decipher Plant’s Abiotic Stress Tolerance Responses

High Throughput Phenotyping: A Revolutionary Approach to Combat Salinity Stress in Cotton

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