CRISPR/Cas-mediated editing of cis-regulatory elements for crop improvement

Saeed, Sumbul; Usman, Babar; Shim, Su-Hyeon; Khan, Shahid Ullah; Nizamuddin, Sabzoi; Saeed, Sundus; Shoaib, Yasira; Jeon, Jong‐Seong; Jung, Ki-Hong

doi:10.1016/j.plantsci.2022.111435

Cited by 19 publications

(6 citation statements)

References 90 publications

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“…In this scenario, crop research should focus on achieving the activation of cold‐temperature pathways at higher temperatures. Promoter editing by CRISPR has been successfully applied in agronomically relevant species (Saeed et al, 2022) and could offer the possibility of optimizing the expression of vernalization‐responsive genes at slightly higher temperatures. One interesting milestone in the Brassicas would perhaps be achieving the activation of VIN3 at the higher average winter temperatures predicted for the future.…”

Section: Perspectives and Challenges For Improving Plant Resilience T...mentioning

confidence: 99%

Is winter coming? Impact of the changing climate on plant responses to cold temperature

Larran

Pajoro

Qüesta

2023

Plant Cell & Environment

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Climate change is causing alterations in annual temperature regimes worldwide. Important aspects of this include the reduction of winter chilling temperatures as well as the occurrence of unpredicted frosts, both significantly affecting plant growth and yields. Recent studies advanced the knowledge of the mechanisms underlying cold responses and tolerance in the model plant Arabidopsis thaliana. However, how these cold‐responsive pathways will readjust to ongoing seasonal temperature variation caused by global warming remains an open question. In this review, we highlight the plant developmental programmes that depend on cold temperature. We focus on the molecular mechanisms that plants have evolved to adjust their development and stress responses upon exposure to cold. Covering both genetic and epigenetic aspects, we present the latest insights into how alternative splicing, noncoding RNAs and the formation of biomolecular condensates play key roles in the regulation of cold responses. We conclude by commenting on attractive targets to accelerate the breeding of increased cold tolerance, bringing up biotechnological tools that might assist in overcoming current limitations. Our aim is to guide the reflection on the current agricultural challenges imposed by a changing climate and to provide useful information for improving plant resilience to unpredictable cold regimes.

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Section: Perspectives and Challenges For Improving Plant Resilience T...mentioning

confidence: 99%

Is winter coming? Impact of the changing climate on plant responses to cold temperature

Larran

Pajoro

Qüesta

2023

Plant Cell & Environment

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“…In particular, the tradeoff effects caused by gene pleiotropy have become the bottleneck of multi-traits pyramiding breeding [63][64][65][66]. Recently, CRISPR/Cas-mediated editing of cis-regulatory regions was used in different crops to generate novel beneficial alleles with improved stress resistance, yield, and quality [67,68]. Unlike editing a coding region, editing a cis-regulatory region can fine-tune the expression level or profile of the target gene without disrupting its function, thereby optimizing the tradeoff effects of the pleiotropic gene [67,69].…”

Section: Breaking Breeding Bottlenecks Of Tradeoff Effectsmentioning

confidence: 99%

“…Recently, CRISPR/Cas-mediated editing of cis-regulatory regions was used in different crops to generate novel beneficial alleles with improved stress resistance, yield, and quality [67,68]. Unlike editing a coding region, editing a cis-regulatory region can fine-tune the expression level or profile of the target gene without disrupting its function, thereby optimizing the tradeoff effects of the pleiotropic gene [67,69]. Recently, various tradeoff effects have been subtly solved in rice, maize, and wheat using CRISPR/Cas technology.…”

Section: Breaking Breeding Bottlenecks Of Tradeoff Effectsmentioning

confidence: 99%

CRISPR/Cas Technology Revolutionizes Crop Breeding

Tang,

Wang,

Jin

et al. 2023

Plants

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Crop breeding is an important global strategy to meet sustainable food demand. CRISPR/Cas is a most promising gene-editing technology for rapid and precise generation of novel germplasm and promoting the development of a series of new breeding techniques, which will certainly lead to the transformation of agricultural innovation. In this review, we summarize recent advances of CRISPR/Cas technology in gene function analyses and the generation of new germplasms with increased yield, improved product quality, and enhanced resistance to biotic and abiotic stress. We highlight their applications and breakthroughs in agriculture, including crop de novo domestication, decoupling the gene pleiotropy tradeoff, crop hybrid seed conventional production, hybrid rice asexual reproduction, and double haploid breeding; the continuous development and application of these technologies will undoubtedly usher in a new era for crop breeding. Moreover, the challenges and development of CRISPR/Cas technology in crops are also discussed.

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“…This becomes a mainstream of the targeted breeding in agricultural plants [ 1 ]. Among whole-genome technologies, CRISPR/Cas-mediated editing of cis-regulatory elements is the most widespread for crop improvement [ 2 , 3 , 4 ]. For genome-editing of TATA-binding protein (TBP)-binding sites (TBP-sites) [ 5 ], the most evolutionally conservative [ 6 ] and obligatory [ 7 , 8 ] transcription initiation site in eukaryotic promoters [ 9 , 10 ], a Faecalibaculum rodentium Cas9 protein was recently discovered [ 5 ].…”

Section: Introductionmentioning

confidence: 99%

AtSNP_TATAdb: Candidate Molecular Markers of Plant Advantages Related to Single Nucleotide Polymorphisms within Proximal Promoters of Arabidopsis thaliana L.

Bogomolov,

Zolotareva,

Filonov

et al. 2024

IJMS

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The mainstream of the post-genome target-assisted breeding in crop plant species includes biofortification such as high-throughput phenotyping along with genome-based selection. Therefore, in this work, we used the Web-service Plant_SNP_TATA_Z-tester, which we have previously developed, to run a uniform in silico analysis of the transcriptional alterations of 54,013 protein-coding transcripts from 32,833 Arabidopsis thaliana L. genes caused by 871,707 SNPs located in the proximal promoter region. The analysis identified 54,993 SNPs as significantly decreasing or increasing gene expression through changes in TATA-binding protein affinity to the promoters. The existence of these SNPs in highly conserved proximal promoters may be explained as intraspecific diversity kept by the stabilizing natural selection. To support this, we hand-annotated papers on some of the Arabidopsis genes possessing these SNPs or on their orthologs in other plant species and demonstrated the effects of changes in these gene expressions on plant vital traits. We integrated in silico estimates of the TBP-promoter affinity in the AtSNP_TATAdb knowledge base and showed their significant correlations with independent in vivo experimental data. These correlations appeared to be robust to variations in statistical criteria, genomic environment of TATA box regions, plants species and growing conditions.

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CRISPR/Cas-mediated editing of cis-regulatory elements for crop improvement

Cited by 19 publications

References 90 publications

Is winter coming? Impact of the changing climate on plant responses to cold temperature

Is winter coming? Impact of the changing climate on plant responses to cold temperature

CRISPR/Cas Technology Revolutionizes Crop Breeding

AtSNP_TATAdb: Candidate Molecular Markers of Plant Advantages Related to Single Nucleotide Polymorphisms within Proximal Promoters of Arabidopsis thaliana L.

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