Integrating genomics and genome editing for orphan crop improvement: a bridge between orphan crops and modern agriculture system

Yaqoob, Huwaida; Tariq, Arooj; Bhat, Basharat Ahmad; Bhat, Kaisar Ahmad; Nehvi, Iqra Bashir; Raza, Ali; Djalović, Ivica; Prasad, P. V. Vara; Mir, Rakeeb Ahmad

doi:10.1080/21645698.2022.2146952

Cited by 27 publications

(16 citation statements)

References 148 publications

(172 reference statements)

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“…And this study will be a base for further work on peanut germin-like proteins. Along with genomics, gene editing tools could be applied for orphan crop improvement, including cultivated peanut (Yaqoob et al, 2023). Transcriptome expression of AhGLPs in different tissues.…”

Section: Discussionmentioning

confidence: 99%

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Genome-wide identification of germin-like proteins in peanut (Arachis hypogea L.) and expression analysis under different abiotic stresses

et al. 2023

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Peanut is an important food and feed crop, providing oil and protein nutrients. Germins and germin-like proteins (GLPs) are ubiquitously present in plants playing numerous roles in defense, growth and development, and different signaling pathways. However, the GLP members have not been comprehensively studied in peanut at the genome-wide scale. We carried out a genome-wide identification of the GLP genes in peanut genome. GLP members were identified comprehensively, and gene structure, genomic positions, motifs/domains distribution patterns, and phylogenetic history were studied in detail. Promoter Cis-elements, gene duplication, collinearity, miRNAs, protein-protein interactions, and expression were determined. A total of 84 GLPs (AhGLPs ) were found in the genome of cultivated peanut. These GLP genes were clustered into six groups. Segmental duplication events played a key role in the evolution of AhGLPs, and purifying selection pressure was underlying the duplication process. Most AhGLPs possessed a well-maintained gene structure and motif organization within the same group. The promoter regions of AhGLPs contained several key cis-elements responsive to ‘phytohormones’, ‘growth and development’, defense, and ‘light induction’. Seven microRNAs (miRNAs) from six families were found targeting 25 AhGLPs. Gene Ontology (GO) enrichment analysis showed that AhGLPs are highly enriched in nutrient reservoir activity, aleurone grain, external encapsulating structure, multicellular organismal reproductive process, and response to acid chemicals, indicating their important biological roles. AhGLP14, AhGLP38, AhGLP54, and AhGLP76 were expressed in most tissues, while AhGLP26, AhGLP29, and AhGLP62 showed abundant expression in the pericarp. AhGLP7, AhGLP20, and AhGLP21, etc., showed specifically high expression in embryo, while AhGLP12, AhGLP18, AhGLP40, AhGLP78, and AhGLP82 were highly expressed under different hormones, water, and temperature stress. The qRT-PCR results were in accordance with the transcriptome expression data. In short, these findings provided a foundation for future functional investigations on the AhGLPs for peanut breeding programs.

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Section: Discussionmentioning

confidence: 99%

“…Several biotic and abiotic stress agents affect the peanut plant throughout its lifecycle ( Ali et al., 2020 ). Identification and application of novel genetic, genomics and gene editing resources can help to improve peanut growth and stress resistance ( Yaqoob et al, 2023 ).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification of germin-like proteins in peanut (Arachis hypogea L.) and expression analysis under different abiotic stresses

et al. 2023

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“…Researchers are trying to understand the heat and cold response mechanisms which can help produce improved vegetable cultivars and strengthen the breeding program (Aleem et al 2020;Raza et al 2021b;Kang et al 2022;Chaudhary et al 2022). New genomic tools such as recombinant DNA technology, mutation breeding, and genome editing can help speed up the process of producing temperature-resilient crops (Aleem et al 2020;Raza et al 2021b;Varshney et al 2020Varshney et al , 2021aYaqoob et al 2023). Conventional breeding combined with genome editing can play a part in introducing/altering the functions of genes of interest in the crop and can produce transgene-free plants.…”

Section: Introductionmentioning

confidence: 99%

Developing future heat-resilient vegetable crops

Saeed

Chaudhry

Raza

et al. 2023

Funct Integr Genomics

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Climate 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.

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“…For this, it is necessary to understand the genetic basis of a plant's interaction when encountering ecological stress. Several studies considering transcriptomics, genomics, proteomics, metabolomics, and genome editing via CRISPR/Cas technology provide a roadmap toward the acclimatization mechanism in plants and crops (Wang et al, 2019;Raza et al, 2022a;Raza et al, 2022b;Raza et al, 2022c;Raza et al, 2022d;Yaqoob et al, 2023). In-depth molecular studies aid us in developing varieties and cultivars through biotechnology, genetic engineering, and other advanced breeding methods to develop plants that could adapt to different abiotic stresses in a short time (Popescu et al, 2009;Raza et al, 2022a;Raza et al, 2022b;Yaqoob et al, 2023).…”

Section: Introductionmentioning

confidence: 99%

“…Several studies considering transcriptomics, genomics, proteomics, metabolomics, and genome editing via CRISPR/Cas technology provide a roadmap toward the acclimatization mechanism in plants and crops (Wang et al, 2019;Raza et al, 2022a;Raza et al, 2022b;Raza et al, 2022c;Raza et al, 2022d;Yaqoob et al, 2023). In-depth molecular studies aid us in developing varieties and cultivars through biotechnology, genetic engineering, and other advanced breeding methods to develop plants that could adapt to different abiotic stresses in a short time (Popescu et al, 2009;Raza et al, 2022a;Raza et al, 2022b;Yaqoob et al, 2023). Posttranslational modification and signal transduction are mediated by a process called phosphorylation, which changes the expression of genes through transmission of protein signals.…”

Section: Introductionmentioning

confidence: 99%

Harnessing the role of mitogen-activated protein kinases against abiotic stresses in plants

Majeed

Zhu²,

Zhang³

et al. 2023

Front. Plant Sci.

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Crop plants are vulnerable to various biotic and abiotic stresses, whereas plants tend to retain their physiological mechanisms by evolving cellular regulation. To mitigate the adverse effects of abiotic stresses, many defense mechanisms are induced in plants. One of these mechanisms is the mitogen-activated protein kinase (MAPK) cascade, a signaling pathway used in the transduction of extracellular stimuli into intercellular responses. This stress signaling pathway is activated by a series of responses involving MAPKKKs→MAPKKs→MAPKs, consisting of interacting proteins, and their functions depend on the collaboration and activation of one another by phosphorylation. These proteins are key regulators of MAPK in various crop plants under abiotic stress conditions and also related to hormonal responses. It is revealed that in response to stress signaling, MAPKs are characterized as multigenic families and elaborate the specific stimuli transformation as well as the antioxidant regulation system. This pathway is directed by the framework of proteins and stopping domains confer the related associates with unique structure and functions. Early studies of plant MAPKs focused on their functions in model plants. Based on the results of whole-genome sequencing, many MAPKs have been identified in plants, such as Arbodiposis, tomato, potato, alfalfa, poplar, rice, wheat, maize, and apple. In this review, we summarized the recent work on MAPK response to abiotic stress and the classification of MAPK cascade in crop plants. Moreover, we highlighted the modern research methodologies such as transcriptomics, proteomics, CRISPR/Cas technology, and epigenetic studies, which proposed, identified, and characterized the novel genes associated with MAPKs and their role in plants under abiotic stress conditions. In-silico-based identification of novel MAPK genes also facilitates future research on MAPK cascade identification and function in crop plants under various stress conditions.

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Integrating genomics and genome editing for orphan crop improvement: a bridge between orphan crops and modern agriculture system

Cited by 27 publications

References 148 publications

Genome-wide identification of germin-like proteins in peanut (Arachis hypogea L.) and expression analysis under different abiotic stresses

Genome-wide identification of germin-like proteins in peanut (Arachis hypogea L.) and expression analysis under different abiotic stresses

Developing future heat-resilient vegetable crops

Harnessing the role of mitogen-activated protein kinases against abiotic stresses in plants

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