Dark response genes: a group of endogenous pendulum/timing players in maize?

Dong, Ming-You; Ling, Lei; Fan, Xian‐Wei; Li, Youzhi

doi:10.1007/s00425-020-03403-4

Cited by 34 publications

(11 citation statements)

References 83 publications

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“…The CRISPR/Cas9, and related versions, are the most advanced third-generation GETs in plant biology [ 29 ]. The Cas9 system requires a short guide sequence (sgRNA) to direct Cas9 nuclease to cleave the target site [ 30 ].…”

Section: Evolution Of Getsmentioning

confidence: 99%

Evolution and Application of Genome Editing Techniques for Achieving Food and Nutritional Security

Fiaz

Ahmar

Saeed

et al. 2021

IJMS

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A world with zero hunger is possible only through a sustainable increase in food production and distribution and the elimination of poverty. Scientific, logistical, and humanitarian approaches must be employed simultaneously to ensure food security, starting with farmers and breeders and extending to policy makers and governments. The current agricultural production system is facing the challenge of sustainably increasing grain quality and yield and enhancing resistance to biotic and abiotic stress under the intensifying pressure of climate change. Under present circumstances, conventional breeding techniques are not sufficient. Innovation in plant breeding is critical in managing agricultural challenges and achieving sustainable crop production. Novel plant breeding techniques, involving a series of developments from genome editing techniques to speed breeding and the integration of omics technology, offer relevant, versatile, cost-effective, and less time-consuming ways of achieving precision in plant breeding. Opportunities to edit agriculturally significant genes now exist as a result of new genome editing techniques. These range from random (physical and chemical mutagens) to non-random meganucleases (MegaN), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein system 9 (CRISPR/Cas9), the CRISPR system from Prevotella and Francisella1 (Cpf1), base editing (BE), and prime editing (PE). Genome editing techniques that promote crop improvement through hybrid seed production, induced apomixis, and resistance to biotic and abiotic stress are prioritized when selecting for genetic gain in a restricted timeframe. The novel CRISPR-associated protein system 9 variants, namely BE and PE, can generate transgene-free plants with more frequency and are therefore being used for knocking out of genes of interest. We provide a comprehensive review of the evolution of genome editing technologies, especially the application of the third-generation genome editing technologies to achieve various plant breeding objectives within the regulatory regimes adopted by various countries. Future development and the optimization of forward and reverse genetics to achieve food security are evaluated.

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Section: Evolution Of Getsmentioning

confidence: 99%

Evolution and Application of Genome Editing Techniques for Achieving Food and Nutritional Security

Fiaz

Ahmar

Saeed

et al. 2021

IJMS

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“…Accurate plant gene sequences are critical for gene editing. The improved genome editing efficiency in M. truncatula [ 34 ] should increase CRISPR/Cas9 technology use. Due to significant differences in the transformation efficiencies between A17 and R108, R108 is the first choice for genome editing practices.…”

Section: Discussionmentioning

confidence: 99%

Delineating the Tnt1 Insertion Landscape of the Model Legume Medicago truncatula cv. R108 at the Hi-C Resolution Using a Chromosome-Length Genome Assembly

Kaur

Lui

Dudchenko

et al. 2021

IJMS

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Legumes are of great interest for sustainable agricultural production as they fix atmospheric nitrogen to improve the soil. Medicago truncatula is a well-established model legume, and extensive studies in fundamental molecular, physiological, and developmental biology have been undertaken to translate into trait improvements in economically important legume crops worldwide. However, M. truncatula reference genome was generated in the accession Jemalong A17, which is highly recalcitrant to transformation. M. truncatula R108 is more attractive for genetic studies due to its high transformation efficiency and Tnt1-insertion population resource for functional genomics. The need to perform accurate synteny analysis and comprehensive genome-scale comparisons necessitates a chromosome-length genome assembly for M. truncatula cv. R108. Here, we performed in situ Hi-C (48×) to anchor, order, orient scaffolds, and correct misjoins of contigs in a previously published genome assembly (R108 v1.0), resulting in an improved genome assembly containing eight chromosome-length scaffolds that span 97.62% of the sequenced bases in the input assembly. The long-range physical information data generated using Hi-C allowed us to obtain a chromosome-length ordering of the genome assembly, better validate previous draft misjoins, and provide further insights accurately predicting synteny between A17 and R108 regions corresponding to the known chromosome 4/8 translocation. Furthermore, mapping the Tnt1 insertion landscape on this reference assembly presents an important resource for M. truncatula functional genomics by supporting efficient mutant gene identification in Tnt1 insertion lines. Our data provide a much-needed foundational resource that supports functional and molecular research into the Leguminosae for sustainable agriculture and feeding the future.

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“…The full-length elements of the Gypsy superfamily were much more frequent than Copia , similarly to other species, such as poplar [ 9 ]. At the lineage level, for the Copia superfamily, Ale elements were the most frequent, similar to other species, such as Erythrostemon hughesii [ 43 ]. For the Gypsy superfamily, the Chromovirus lineage (in particular, the Tekay sublineage) showed the highest abundance as already reported in other species, like pepper and Hieracium [ 37 , 44 ].…”

Section: Discussionmentioning

confidence: 99%

LTR-retrotransposon dynamics in common fig (Ficus carica L.) genome

et al. 2021

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Background Long Terminal Repeat retrotransposons (LTR-REs) are repetitive DNA sequences that constitute a large part of the genome. The improvement of sequencing technologies and sequence assembling strategies has achieved genome sequences with much greater reliability than those of the past, especially in relation to repetitive DNA sequences. Results In this study, we analysed the genome of Ficus carica L., obtained using third generation sequencing technologies and recently released, to characterise the complete complement of full-length LTR-REs to study their dynamics during fig genome evolution. A total of 1867 full-length elements were identified. Those belonging to the Gypsy superfamily were the most abundant; among these, the Chromovirus/Tekay lineage was the most represented. For the Copia superfamily, Ale was the most abundant lineage. Measuring the estimated insertion time of each element showed that, on average, Ivana and Chromovirus/Tekay were the youngest lineages of Copia and Gypsy superfamilies, respectively. Most elements were inactive in transcription, both constitutively and in leaves of plants exposed to an abiotic stress, except for some elements, mostly belonging to the Copia/Ale lineage. A relationship between the inactivity of an element and inactivity of genes lying in close proximity to it was established. Conclusions The data reported in this study provide one of the first sets of information on the genomic dynamics related to LTR-REs in a plant species with highly reliable genome sequence. Fig LTR-REs are highly heterogeneous in abundance and estimated insertion time, and only a few elements are transcriptionally active. In general, the data suggested a direct relationship between estimated insertion time and abundance of an element and an inverse relationship between insertion time (or abundance) and transcription, at least for Copia LTR-REs.

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Dark response genes: a group of endogenous pendulum/timing players in maize?

Cited by 34 publications

References 83 publications

Evolution and Application of Genome Editing Techniques for Achieving Food and Nutritional Security

Evolution and Application of Genome Editing Techniques for Achieving Food and Nutritional Security

Delineating the Tnt1 Insertion Landscape of the Model Legume Medicago truncatula cv. R108 at the Hi-C Resolution Using a Chromosome-Length Genome Assembly

LTR-retrotransposon dynamics in common fig (Ficus carica L.) genome

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