Brassica juncea Genome Sequencing: Structural and Functional Insights

Ramkumar, Thakku R.; Arya, Sagar S.; Kumari, Divyani; Lenka, Sangram K.

doi:10.1007/978-3-030-91507-0_12

Cited by 3 publications

(5 citation statements)

References 61 publications

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“…It is an annual herb with a maximum height of one meter. B. juncea is a key oil seed crop that is largely grown in arid and semi-arid areas [ 21 ]. In India, it is the second most significant crop for the production of edible oil, accounting for almost 27.8% of the Indian oilseed economy [ 22 ], with a global production of around 7% [ 23 ].…”

Section: Introductionmentioning

confidence: 99%

CuO Nanoparticle-Mediated Seed Priming Improves Physio-Biochemical and Enzymatic Activities of Brassica juncea

Faraz

Faizan

Rajput

et al. 2023

Plants

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The use of nanoparticles (NPs) in agricultural fields has risen to a level where people are considering NPs as an alternative to commercial fertilizers. The input of copper oxide NPs (CuO NPs) as seed primers was investigated in this study, and the growth indices of Brassica juncea such as phenotypic parameters, photosynthetic attributes, and biochemical parameters were measured during maximum vegetative growth stage, i.e., at 45 days after sowing. Surface sterilized seeds were soaked in varying concentrations (0, 2, 4, 8 and 16 mg/L) of CuO NPs for 15, 30, and/or 45 min. After those priming periods, the seeds were planted in pots and allowed to grow naturally. Among the different tested concentrations of CuO NPs, 4 mg/L of CuO NPs for 30 min seed priming proved to be best, and considerably increased the, shoot length (30%), root length (27%), net photosynthetic rate (30%), internal CO2 concentration (28%), and proline content (41%). Besides, the performance of the antioxidant enzymes, viz, superoxide dismutase, catalase, peroxidase, and biochemical parameters such as nitrate reductase and carbonic anhydrase were also increased by several folds after the application of CuO NPs in B. juncea. The present study suggests that CuO NPs can be effectively used to increase the performance of B. juncea and may also be suitable for testing on other crop species.

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Section: Introductionmentioning

confidence: 99%

CuO Nanoparticle-Mediated Seed Priming Improves Physio-Biochemical and Enzymatic Activities of Brassica juncea

Faraz

Faizan

Rajput

et al. 2023

Plants

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“…By causing DNA double-strand breaks, which promote error-prone non-homologous end joining (NHEJ) or homology-directed repair (HDR) at specified genomic loci, ZFNs and TALENs have been used to carry out a variety of genetic changes ( Li et al., 2011 ; Miller et al., 2011 ; Jinek et al., 2012 ; Li et al., 2012 ; Gaj et al., 2013 ; Ahmad M., 2022 ). The DNA cleavage domain of the restriction enzyme FokI and zinc-finger-based DNA recognition modules make up the ZFN family of targeted drugs ( Podevin et al., 2013 ; Pinto-Carbó et al., 2016 ; Verhaegen and De Smet, 2017 ; Ramkumar et al., 2022 ). Before joining together to cling to particular DNA sequences, each zinc finger locates and bonds to a nucleotide triplet.…”

Section: Why Crispr-cas Ge Better Than Zfns and Talens Genome Editing?mentioning

confidence: 99%

“…Thus, the nuclear and organellar genome sequencing work in B. juncea improved our comprehension of the intricate allotetraploid architecture and laid the groundwork for future use of the data in translational genomics and precession breeding. Their findings suggest that orf352 is required for CMS and that the amino acids 179 to 210 from orf352 may aid in pollen abortion ( Ramkumar et al., 2022 ). Pal Maliga and colleagues after a decade successfully used a multiplexing CRISPR system comprised of four gRNAs and egg-cell-specific Cas9 expression to create transgenic B. napus seedlings with dysfunctional ACC2 genes, they exhibit a spectinomycin hypersensitive phenotype, it is hoped that these mutant plants will be appropriate for chloroplast transformation in significant foods like rice, wheat, tomato, banana, citrus, grapes, cassava, and cucumber have all shown signs of pathogen resistance when they were grown on CRISPR-engineered plants ( Table 1 ) ( LaManna et al., 2022 ; Li et al., 2022 ; Liu et al., 2022a ; Liu et al., 2022b ).…”

Section: Why Crispr-cas Ge Better Than Zfns and Talens Genome Editing?mentioning

confidence: 99%

“…To become a viable alternative to current genetic transformation techniques, the field of NC- and PC-assisted delivery of biomolecules is still in its infancy and needs coordinated efforts at the intersection of nanotechnology, proteomics, and plant transgenics. The developments in NC, PC, and NC-PC conjugates make them particularly appealing for delivering biomolecules to plants ( Arya et al., 2020 ; Yip, 2020 ; Arya et al., 2021 ; Chen M et al., 2021 , Chen S et al., 2021 ; Ganie et al., 2021 ; Osakabe et al., 2021 ; Qin et al., 2020 ; Tsveta et al., 2021 ; Zheng et al., 2021 ; Gardiner et al., 2022 ; Gehrke et al., 2022 ; Huang et al., 2022 ; Ramkumar et al., 2022 ; Takahashi et al., 2022 ; Tanwar et al., 2022 ).…”

Section: What Benefits Might Crispr/cas-based Gene Editing Offermentioning

confidence: 99%

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Plant breeding advancements with “CRISPR-Cas” genome editing technologies will assist future food security

Ahmad

2023

Front. Plant Sci.

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Genome editing techniques are being used to modify plant breeding, which might increase food production sustainably by 2050. A product made feasible by genome editing is becoming better known, because of looser regulation and widespread acceptance. The world’s population and food supply would never have increased proportionally under current farming practices. The development of plants and food production has been greatly impacted by global warming and climate change. Therefore, minimizing these effects is crucial for agricultural production that is sustainable. Crops are becoming more resilient to abiotic stress because of sophisticated agricultural practices and a better understanding of the abiotic stress response mechanism. Both conventional and molecular breeding techniques have been used to create viable crop types both processes are time-consuming. Recently, plant breeders have shown an interest in genome editing approaches for genetic manipulation that use clustered regularly interspaced short palindromic repeats (CRISPR/Cas9). To ensure the security of the food supply in the future, plant kinds with desired traits must be developed. A completely new era in plant breeding has begun because of the revolution in genome editing techniques based on the CRISPR/CRISPR-associated nuclease (Cas9) systems. All plants may effectively target a particular gene or group of loci using Cas9 and single-guide RNA (sgRNA). CRISPR/Cas9 can thereby save time and labor compared to conventional breeding methods. An easy, quick, and efficient method for directly altering the genetic sequences in cells is with the CRISPR and Cas9 systems. The CRISPR-Cas9 system, which was developed from components of the earliest known bacterial immune system, allows for targeted gene breakage and gene editing in a variety of cells/RNA sequences to guide endonuclease cleavage specificity in the CRISPR-Cas9 system. Editing can be directed to practically any genomic site by altering the guide RNA (gRNA) sequence and delivering it to a target cell along with the Cas9 endonuclease. We summarize recent CRISPR/Cas9 plant research findings, investigate potential applications in plant breeding, and make predictions about likely future breakthroughs and approaches to food security through 2050.

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“…Mapping of 1 Gb chromosome of wheat has been possible with the help of the chromosome-by-chromosome approach only [ 76 ]. Mapping compiles genetic mappings into physical contigs as well as providing a framework for the assembly of sequences into the whole genome, and in the absence of a reference genome sequence, this BAC-end shotgun sequence gives details of genome evolution as well as structure [ 77 , 78 ]. Another interesting method for developing a whole genome sequence has been carried out by detecting the QTL using a methodology named QTL-seq.…”

Section: Genomicsmentioning

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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Brassica juncea Genome Sequencing: Structural and Functional Insights

Cited by 3 publications

References 61 publications

CuO Nanoparticle-Mediated Seed Priming Improves Physio-Biochemical and Enzymatic Activities of Brassica juncea

CuO Nanoparticle-Mediated Seed Priming Improves Physio-Biochemical and Enzymatic Activities of Brassica juncea

Plant breeding advancements with “CRISPR-Cas” genome editing technologies will assist future food security

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

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