scholarly journals Generation and molecular characterization of CRISPR/Cas9-induced mutations in 63 immunity-associated genes in tomato reveals specificity and a range of gene modifications

2019 ◽  
Author(s):  
Ning Zhang ◽  
Holly M. Roberts ◽  
Joyce Van Eck ◽  
Gregory B. Martin
Keyword(s):  
Molecular Characterization ◽  
Gene Editing ◽  
Induced Mutations ◽  
Tomato Plants ◽  
Transgenic Tomato Plants ◽  
Target Sites ◽  
Targeted Gene Editing ◽  
Gene Alterations ◽  
New Mutations

AbstractThe CRISPR/Cas9 system is a powerful tool for targeted gene editing in many organisms including plants. However, most of the reported uses of CRISPR/Cas9 in plants have focused on modifying one or a few genes, and thus the overall specificity, types of mutations, and heritability of gene alterations remain unclear. Here we describe the molecular characterization of 361 T0 transgenic tomato plants that were generated using CRISPR/Cas9 to induce mutations in 63 immunity-associated genes. Among the T0 transformed plants, 245 carried mutations (68%), with 20% of those plants being homozygous for the mutation, 30% being heterozygous, 32% having two different mutations (biallelic) and 18% having multiple mutations (chimeric). The mutations were predominantly short insertions or deletions, with 87% of the affected sequences being smaller than 10 bp. The majority of 1 bp insertions were A (50%) or T (29%). The mutations from the T0 generation were stably transmitted to later generations, although new mutations were detected in some T1 plants. No mutations were detected in 18 potential off-target sites among 144 plants. Our study provides a broad and detailed view into the effectiveness of CRISPR/Cas9 for genome editing in an economically important plant species.

scholarly journals Characterization of theAc/Ds behaviour in transgenic tomato plants using plasmid rescue

1992 ◽  
Vol 20 (1) ◽  
pp. 61-70 ◽  
Author(s):  
Caius M. T. Rommens ◽  
George N. Rudenko ◽  
Paul P. Dijkwel ◽  
Mark J. J. van Haaren ◽  
Pieter B. F. Ouwerkerk ◽  
...  
Keyword(s):  
Transgenic Tomato ◽  
Plasmid Rescue ◽  
Tomato Plants ◽  
Transgenic Tomato Plants

scholarly journals Highly Efficient Targeted Gene Editing in Upland Cotton Using the CRISPR/Cas9 System

2018 ◽  
Vol 19 (10) ◽  
pp. 3000 ◽  
Author(s):  
Shouhong Zhu ◽  
Xiuli Yu ◽  
Yanjun Li ◽  
Yuqiang Sun ◽  
Qianhao Zhu ◽  
...  
Keyword(s):  
Gene Editing ◽  
Crop Improvement ◽  
Targeted Mutagenesis ◽  
Cotton Fibers ◽  
Efficient Tool ◽  
Gene Encoding ◽  
Editing Event ◽  
Highly Efficient ◽  
Target Sites ◽  
Targeted Gene Editing

The clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) gene editing system has been shown to be able to induce highly efficient mutagenesis in the targeted DNA of many plants, including cotton, and has become an important tool for investigation of gene function and crop improvement. Here, we developed a simple and easy to operate CRISPR/Cas9 system and demonstrated its high editing efficiency in cotton by targeting-ALARP, a gene encoding alanine-rich protein that is preferentially expressed in cotton fibers. Based on sequence analysis of the target site in the 10 transgenic cottons containing CRISPR/Cas9, we found that the mutation frequencies of GhALARP-A and GhALARP-D target sites were 71.4–100% and 92.9–100%, respectively. The most common editing event was deletion, but deletion together with large insertion was also observed. Mosaic mutation editing events were detected in most transgenic plants. No off-target mutation event was detected in any the 15 predicted sites analyzed. This study provided mutants for further study of the function of GhALARP in cotton fiber development. Our results further demonstrated the feasibility of use of CRISPR/Cas9 as a targeted mutagenesis tool in cotton, and provided an efficient tool for targeted mutagenesis and functional genomics in cotton.

scholarly journals PB1968 TWO NEW MUTATIONS AND MOLECULAR CHARACTERIZATION OF G6PD GENE AMONG THAI CHILDREN WITH G6PD DEFICIENCY

HemaSphere ◽  
2019 ◽  
Vol 3 (S1) ◽  
pp. 894 ◽  
Author(s):  
C. Traivaree ◽  
B. Boonyawat ◽  
A. Photi-a ◽  
C. Monsereenusorn ◽  
T. Phetthong
Keyword(s):  
Molecular Characterization ◽  
G6pd Deficiency ◽  
G6pd Gene ◽  
New Mutations

Molecular characterization of luminal breast tumors in African American women.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. 550-550
Author(s):  
Yael Simons ◽  
Mohamed Hassan ◽  
George Chlipala ◽  
Oana Cristina Danciu ◽  
Vijayakrishna K. Gadi ◽  
...  
Keyword(s):  
African American ◽  
Racial Disparities ◽  
Molecular Characterization ◽  
Endocrine Resistance ◽  
Breast Tumors ◽  
Driver Gene ◽  
Gene Fusions ◽  
Primary Tumors ◽  
Gene Alterations

550 Background: Racial disparities in breast cancer (BC) mortality are attributed to later stage diagnoses and a higher incidence of triple-negative BC among African American (AA) women. In previous work, we showed that AA women with ER+ BC are more likely to develop biologically aggressive disease and are more likely to die from early stage, ER+ BC than non-Hispanic White women (Hoskins et al, JAMA Oncol, 2021). The underlying molecular drivers of this disparity are unknown. Here we report the molecular characterization of a series of luminal BC from AA women. Methods: Consecutive breast tumor specimens received in the Pathology Department underwent next generation sequencing (NGS). Unstained FFPE tissue sections were macro-dissected to isolate tumor cells, and nucleic acids were extracted using commercially available kits. DNA and RNA sequencing libraries were prepared with the Oncomine Comprehensive Assay v3 (OCAv3) (Thermo Fisher), which includes 161 driver genes and detects SNVs, CNVs, INDELs and gene fusions. Sequencing was performed on the Ion S5XL sequencer. Sequencing reads were mapped to the UCSC human genome build GRCh37/hg19 using Torrent Suite™ software (version 5.10; Thermo Fisher). Data analysis and variant calling was performed using the Ion Reporter analysis tool. Results: We identified 60 somatic driver gene alterations in luminal tumors from 35 AA patients (primary tumors, n = 26; metastatic tumors, n = 9). Recurrently altered genes identified in > 5% of tumors are listed in the Table. The most frequently altered gene was PIK3CA (42% of tumors). ESR1 gene fusions were seen in 25% of tumors. Interestingly, an equal frequency of ESR1 fusions were detected in primary (27%) and metastatic (22%) tumors, in contrast to activating mutations which are found in recurrent tumors following treatment with aromatase inhibitors. ARID1A alterations were identified in 17% of primary tumors. ARID1A encodes a subunit of the SWI/SNF chromatin remodeling complex. Alterations in ARID1A confer endocrine resistance, and are enriched in recurrent tumors in the literature. We also found a high number of CNVs in members of the FGF gene family (36% of tumors), which are also associated with resistance to endocrine therapy. An in silico analysis comparing our findings with publicly available datasets will be presented. Conclusions: This study of somatic driver gene alterations in a consecutive series of luminal breast tumors from AA patients found a higher than expected frequency of alterations in genes associated with endocrine resistance in untreated primary tumors, suggesting a partial explanation for racial disparities in survival.[Table: see text]

scholarly journals CRISPR/Cas9-mediated efficient and heritable targeted mutagenesis in tomato plants in the first and later generations

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Changtian Pan ◽  
Lei Ye ◽  
Li Qin ◽  
Xue Liu ◽  
Yanjun He ◽  
...  
Keyword(s):  
Average Frequency ◽  
Transformation Method ◽  
Targeted Mutagenesis ◽  
Efficient Tool ◽  
Tomato Plants ◽  
High Frequencies ◽  
High Mutation Frequency ◽  
Transgenic Tomato Plants ◽  
Targeted Gene Editing ◽  
The Stability

Abstract The CRISPR/Cas9 system has successfully been used in various organisms for precise targeted gene editing. Although it has been demonstrated that CRISPR/Cas9 system can induce mutation in tomato plants, the stability of heredity in later generations and mutant specificity induced by the CRISPR/Cas9 system in tomato plants have not yet been elucidated in detail. In this study, two genes, SlPDS and SlPIF4, were used for testing targeted mutagenesis in tomato plants through an Agrobacterium tumefaciens-mediated transformation method. A high mutation frequency was observed in all tested targets in the T0 transgenic tomato plants, with an average frequency of 83.56%. Clear albino phenotypes were observed for the psd mutants. High frequencies of homozygous and biallelic mutants were detected even in T0 plants. The majority of the detected mutations were 1- to 3-nucleotide deletions, followed by 1-bp insertions. The target mutations in the T0 lines were stably transmitted to the T1 and T2 generations, without new modifications or revision. Off-target activities associated with SlPDS and SlPIF4 were also evaluated by sequencing the putative off-target sites and no clear off-target events were detected. Our results demonstrate that the CRISPR/Cas9 system is an efficient tool for generating stable and heritable modifications in tomato plants.

Molecular characterization of radiation- and chemically induced mutations associated with neuromuscular tremors, runting, juvenile lethality, and sperm defects in jdf2 mice

1999 ◽  
Vol 10 (9) ◽  
pp. 870-878 ◽  
Author(s):  
Mitchell Walkowicz ◽  
Yonggang Ji ◽  
Xiaojia Ren ◽  
Bernhard Horsthemke ◽  
Liane B. Russell ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Induced Mutations ◽  
Chemically Induced

Physiological and molecular characterization of Fe acquisition by tomato plants from natural Fe complexes

2012 ◽  
Vol 49 (2) ◽  
pp. 187-200 ◽  
Author(s):  
Nicola Tomasi ◽  
Maria De Nobili ◽  
Stefano Gottardi ◽  
Laura Zanin ◽  
Tanja Mimmo ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Tomato Plants ◽  
Fe Complexes ◽  
Fe Acquisition
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