Genome editing and chromosome engineering in plants DOI Creative Commons

Arjun Ojha,

Feng Zhang, Gunvant Patil

и другие.

The Plant Genome, Год журнала: 2023, Номер 16(2)

Опубликована: Июнь 1, 2023

In the last two decades, innovations in genomics (genome reading) have advanced crop breeding and played a central role improvement. Since first genome (rice) was published, several genomes are out public domain with an exponential increase number of samples per genome, improved assembly development PAN (Figure 1). The availability reference, whole re-sequencing (WGRS) PAN-genomes essential to map allelic variants (single base pair large variations) our knowledge toward precise gene discovery, marker development, trait introgression (Bevan et al., 2017; Kadam 2016; Patil Valliyodan 2021). WGRS is one many payoffs discovery programs has been conducted variety organism including humans, animals, species dense variation data integrated other omics platforms (transcriptomics, phenomics, metabolomics) improves understanding phenotype–genotype relationship for marker-assisted mapping. Several crop-specific databases developed accelerate mapping, this information become integral part all aspects biological research, basic applied plant biology (Deshmukh 2021; Matthews 2009). With genomic technologies, researchers can now effectively identify casual genetic from wild/landrace relatives. Application robust high throughput engineering technologies will be understand function achieve targeted modification desirable agronomic traits wide range plants, especially species. Over years, evolved rapidly random mutagenesis approaches, such as chemical, physical, or insertional (transposon T-DNA mediated) mutagenesis, more techniques, editing (Graham 2020). Although often requires creating populations mutant screening without much control on mutation outcomes, enables introduction broad modifications efficient controlled manner. past three continuous search efficiency target-specific lead tools, meganucleases, zinc-finger nuclease, TALENs (transcription activator-like effector nucleases) recently CRISPR-Cas (Vats 2019). required laborious efforts engineer their DNA binding domains new sequence recognition activities. By contrary, technology directed by CRISPR guide RNA (gRNA) system search, bind, create through RNA–DNA pairing. Due its simplicity, activity, versatility, multiplexing capability, reagent choice successfully demonstrated various modifications. Compared systems animal mammalian species, present own opportunities challenges. focus issues, collection reviews research articles were published tackle key challenges, building versatile toolkits, polyploid genomes, integration molecular editing, precision assessment current status quo regulatory landscape products 2). Delivery gene-editing reagents largely relies transformation that time-consuming labor intensive. Uranga Daros (2022) reviewed recent advances virus induced (VIGE) discussed application VIGE toolbox special strategies tissue culture free delivery reagents. addition, regent coordinated expression cell depend upon streamlined processes develop vector parts, Cas enzymes, promoters, terminators, selection/reporter genes. Chamness al. reported universal golden gate-based cloning toolkit simplify complex constructs engineering. These publicly available resources would greatly reduce bottleneck technical challenges testing deployment tools. issue, using optimized CRISPR-Cas9 approach, Biswas Nguyen (2021) characterized multiple novel genes involved resistant starch rice N fixation nodule soybean, respectively. Yoon double haploid switchgrass could significantly speed up processes. targeting four functional CENH3 homolog genes, aneuploid lines time engineering, however, redundancy multiple-member families additional practical characterization, May (2023) progress, obstacles, optimizations needed polyploids. To address Zheng showcased generation single, double, triple knockouts 11 members Cytokinin oxidase/dehydrogenase (CKX) family rice. significant identified among OsCKX same phylogenetic clade, findings revealed diversified regulating capabilities modulate height, panicle size, grain panicle. addition mentioned above, reducing off-target effect Zhang investigated impact highly multiplexed CRISPR-Cas12a off-targeting simultaneous stranded breaks chromosome rearrangements. This particularly important implementation policies. end, Kalaitzandonakes analyzed economics potential long-term improvement agriculture then emerging global policy environment, which shape ultimate path overall socioeconomic benefits society. Arjun Ojha: Writing – original draft;Writing review & editing. Feng Zhang: draft; Gunvant Patil: GPB thankful financial support Governor's University Research Initiative (GURI), Texas Tech University. authors declare no conflicts interest.

Язык: Английский

An efficient CRISPR–Cas12a promoter editing system for crop improvement DOI
Jianping Zhou, Guanqing Liu, Yuxin Zhao

и другие.

Nature Plants, Год журнала: 2023, Номер 9(4), С. 588 - 604

Опубликована: Апрель 6, 2023

Язык: Английский

Процитировано

89
High performance TadA-8e derived cytosine and dual base editors with undetectable off-target effects in plants DOI Creative Commons
Tingting Fan, Yanhao Cheng, Yuechao Wu

и другие.

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Июнь 14, 2024

Abstract Cytosine base editors (CBEs) and adenine (ABEs) enable precise C-to-T A-to-G edits. Recently, ABE8e, derived from TadA-8e, enhances edits in mammalian cells plants. Interestingly, TadA-8e can also be evolved to confer editing. This study compares engineered CBEs rice tomato cells, identifying TadCBEa, TadCBEd, TadCBEd_V106W as efficient with high purity a narrow editing window. A dual editor, TadDE, promotes simultaneous Multiplexed TadCBEa TadDE is demonstrated transgenic rice, no off-target effects detected by whole genome transcriptome sequencing, indicating specificity. Finally, two crop engineering applications using are shown: introducing herbicide resistance alleles OsALS creating synonymous mutations OsSPL14 resist OsMIR156 -mediated degradation. Together, this presents editor valuable additions the plant toolbox.

Язык: Английский

Процитировано

13
A simple and efficient CRISPR/Cas9 system permits ultra-multiplex genome editing in plants DOI Creative Commons
Suting Wu, Htin Kyaw, Zhijun Tong

и другие.

The Crop Journal, Год журнала: 2024, Номер 12(2), С. 569 - 582

Опубликована: Фев. 15, 2024

The development and maturation of the CRISPR/Cas genome editing system provides a valuable tool for plant functional genomics genetic improvement. Currently available genome-editing tools have limited number targets, restricting their application in research. In this study, we developed novel CRISPR/Cas9 ultra-multiplex consisting two template vectors, eight donor four destination one primer-design software package. By combining advantages Golden Gate cloning to assemble multiple repetitive fragments Gateway recombination large by changing structure amplicons used sgRNA expression cassettes, can single binary vector targeting more than 40 genomic loci. A rice knockout containing 49 cassettes was assembled high co-editing efficiency observed. This advances synthetic biology engineering.

Язык: Английский

Процитировано

10
Recent advances of CRISPR-based genome editing for enhancing staple crops DOI Creative Commons
Feng Chen, Chen D. Lu, Yan Zhao

и другие.

Frontiers in Plant Science, Год журнала: 2024, Номер 15

Опубликована: Сен. 23, 2024

An increasing population, climate change, and diminishing natural resources present severe threats to global food security, with traditional breeding genetic engineering methods often falling short in addressing these rapidly evolving challenges. CRISPR/Cas systems have emerged as revolutionary tools for precise modifications crops, offering significant advancements resilience, yield, nutritional value, particularly staple crops like rice maize. This review highlights the transformative potential of technology, emphasizing recent innovations such prime base editing, development novel CRISPR-associated proteins, which significantly improved specificity, efficiency, scope genome editing agriculture. These enable targeted that enhance tolerance abiotic stresses well biotic stresses. Additionally, plays a crucial role improving crop yield quality by enhancing photosynthetic nutrient uptake, resistance lodging, while also taste, texture, shelf life, content through biofortification. Despite challenges off-target effects, need more efficient delivery methods, ethical regulatory concerns, underscores importance security sustainability It calls continued research integration CRISPR other emerging technologies nanotechnology, synthetic biology, machine learning fully realize its developing resilient, productive, sustainable agricultural systems.

Язык: Английский

Процитировано

10
Strategies and Methods for Improving the Efficiency of CRISPR/Cas9 Gene Editing in Plant Molecular Breeding DOI Creative Commons
Junming Zhou,

Xinchao Luan,

Yixuan Liu

и другие.

Plants, Год журнала: 2023, Номер 12(7), С. 1478 - 1478

Опубликована: Март 28, 2023

Following recent developments and refinement, CRISPR-Cas9 gene-editing technology has become increasingly mature is being widely used for crop improvement. The application of CRISPR/Cas9 enables the generation transgene-free genome-edited plants in a short period advantages simplicity, high efficiency, specificity, low production costs, which greatly facilitate study gene functions. In plant molecular breeding, efficiency system proven to be key step influencing effectiveness with improvements recently becoming focus reported scientific research. This review details strategies methods improving editing including Cas9 variant enzyme engineering, effect multiple promoter driven Cas9, gRNA efficient optimization expression strategies. It also briefly introduces CRISPR/Cas12a BE PE precision editing. These are beneficial further development systems field breeding.

Язык: Английский

Процитировано

19
IsDge10 is a hypercompact TnpB nuclease that confers efficient genome editing in rice DOI Creative Commons
Rui Zhang, Xu Tang,

Yao He

и другие.

Plant Communications, Год журнала: 2024, Номер 5(11), С. 101068 - 101068

Опубликована: Авг. 23, 2024

Язык: Английский

Процитировано

5
Boosting genome editing in plants with single transcript unit surrogate reporter systems DOI Creative Commons
Xu Tang,

Qiurong Ren,

Xiaodan Yan

и другие.

Plant Communications, Год журнала: 2024, Номер 5(6), С. 100921 - 100921

Опубликована: Апрель 15, 2024

CRISPR-Cas-based genome editing holds immense promise for advancing plant genomics and crop enhancement. However, the challenge of low activity complicates identification events. In this study, we introduce multiple single transcript unit surrogate reporter (STU-SR) systems to enhance selection genome-edited plants. These use same guide RNAs designed endogenous genes edit genes, establishing a direct link between gene that genes. Various strategies are used restore functional after editing, including efficient single-strand annealing (SSA) homologous recombination in STU-SR-SSA systems. STU-SR-base editor leverage base reinstate start codon, enriching C-to-T A-to-G Our results showcase effectiveness these STU-SR enhancing events monocot rice, encompassing Cas9 nuclease-based targeted mutagenesis, cytosine adenine editing. The exhibit compatibility with variants, such as PAM-less SpRY, shown boost Brassica oleracea, dicot vegetable crop. summary, have developed highly versatile enrichment

Язык: Английский

Процитировано

4
Regulation of Rice Grain Quality by Exogenous Kinetin During Grain-Filling Period DOI Creative Commons
Yunhua Xiao,

Yating Dong,

Meng Zhou

и другие.

Plants, Год журнала: 2025, Номер 14(3), С. 358 - 358

Опубликована: Янв. 24, 2025

Cytokinins (CKs) play important functions in plant growth and development response to adversity stress. However, little is known about the role CK plays rice grain quality. We hypothesized that exogenous cytokinins could improve quality by regulating physiological traits genes related starch synthesis. Therefore, we exogenously applied different concentrations of kinetin (KT), an CK, during grain-filling period. Our results show all KT treatments resulted a significant increase thousand-grain weight. In particular, chalkiness chalky rate were significantly reduced, gel consistency (GC) content alkali spreading value (ASV) increased 10−8 M treatment. Meanwhile, application positively affected transcription some synthesis-related genes, which was contrast 10−5 conclusion, appropriate period can ultimately affect changes relevant indicators, such as appearance (AQ) eating cooking qualities (ECQ).

Язык: Английский

Процитировано

0
Genetic Analysis of the Awn Length Gene in the Rice Chromosome Segment Substitution Line CSSL29 DOI Open Access
Zhengjie Wang, Jun Yang, Tao Huang

и другие.

International Journal of Molecular Sciences, Год журнала: 2025, Номер 26(4), С. 1436 - 1436

Опубликована: Фев. 8, 2025

Awn length is a significant agronomic trait in rice. To analyze the genetic mechanism of awn chromosome segment substitution line 29 (CSSL29) derived from 9311 (recipient) into Nipponbare (NIP, donor), an F2 segregated population was constructed (indica) and CSSL29. The candidate genes were analyzed using quantitative loci sequencing (QTL-seq), yeast two-hybrid assays, 3 k 10 rice databases. results indicated that segregating followed normal distribution, long-awn phenotype CSSL29 controlled by multiple genes. Through BSA data, major QTL qAWN4 associated with identified on 4, containing cloned gene An-2. Further investigation revealed presence An-1, both exhibiting additive effect regulation phenotype. Yeast experiments confirmed no interaction between An-2 suggesting not mediated through simple protein-to-protein binding. Population analysis allele artificially selected during domestication but did significantly differ indica japonica subspecies. These findings enhance our understanding rice, laying groundwork for future research this area.

Язык: Английский

Процитировано

0
Harnessing promoter elements to enhance gene editing in plants: perspectives and advances DOI Creative Commons
Nikita Gondalia, Luis Felipe Quiroz, Linyi Lai

и другие.

Plant Biotechnology Journal, Год журнала: 2025, Номер unknown

Опубликована: Фев. 27, 2025

Summary Genome‐edited plants, endowed with climate‐smart traits, have been promoted as tools for strengthening resilience against climate change. Successful plant gene editing (GE) requires precise regulation of the GE machinery, a process controlled by promoters, which drives its transcription through interactions factors (TFs) and RNA polymerase. While constitutive promoters are extensively used in constructs, their limitations highlight need alternative approaches. This review emphasizes promise tissue/organ specific well inducible enable targeted spatiotemporal manner no effects on other tissues. Advances synthetic biology paved way creation offering refined control over expression augmenting potential GE. The integration these novel systems presents significant opportunities conditional genome editing. Moreover, advent bioinformatic artificial intelligence is revolutionizing characterization regulatory elements, enhancing our understanding roles plants. Thus, this provides insights into strategic use promoter to enhance precision, efficiency specificity GE, setting stage innovative crop improvement strategies.

Язык: Английский

Процитировано

0