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Genome editing in Wheat

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https://www.readbyqxmd.com/read/30477421/targeted-mutagenesis-using-the-agrobacterium-tumefaciens-mediated-crispr-cas9-system-in-common-wheat
#1
Shujuan Zhang, Rongzhi Zhang, Guoqi Song, Jie Gao, Wei Li, Xiaodong Han, Mingli Chen, Yulian Li, Genying Li
BACKGROUND: Recently, the CRISPR/Cas9 system has been widely used to precisely edit plant genomes. Due to the difficulty in Agrobacterium-mediated genetic transformation of wheat, the reported applications in CRISPR/Cas9 system were all based on the biolistic transformation. RESULTS: In the present study, we efficiently applied targeted mutagenesis in common wheat (Triticum aestivum L.) protoplasts and transgenic T0 plants using the CRISPR/Cas9 system delivered via Agrobacterium tumefaciens...
November 26, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/30446870/hi-tom-a-platform-for-high-throughput-tracking-of-mutations-induced-by-crispr-cas-systems
#2
Qing Liu, Chun Wang, Xiaozhen Jiao, Huawei Zhang, Lili Song, Yanxin Li, Caixia Gao, Kejian Wang
The CRISPR/Cas system has been extensively applied to make precise genetic modifications in various organisms. Despite its importance and widespread use, large-scale mutation screening remains time-consuming, labour-intensive and costly. Here, we developed Hi-TOM (available at https://doi.org/www.hi-tom.net/hi-tom/ ), an online tool to track the mutations with precise percentage for multiple samples and multiple target sites. We also described a corresponding next-generation sequencing (NGS) library construction strategy by fixing the bridge sequences and barcoding primers...
November 13, 2018: Science China. Life Sciences
https://www.readbyqxmd.com/read/30407665/applying-the-latest-advances-in-genomics-and-phenomics-for-trait-discovery-in-polyploid-wheat
#3
Philippa Borrill, Sophie A Harrington, Cristobal Uauy
Improving traits in wheat has historically been challenging due to its large and polyploid genome, limited genetic diversity, and in-field phenotyping constraints. However, within recent years many of these barriers have been lowered. The availability of a chromosome-level assembly of the wheat genome now facilitates a step-change in wheat genetics and provides a common platform for resources including variation data, gene expression data, and genetic markers. The development of sequenced mutant populations and gene-editing techniques now enable the rapid assessment of gene function in wheat directly...
November 8, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30352590/genetic-transformation-of-einkorn-triticum-monococcum-l-ssp-monococcum-l-a-diploid-cultivated-wheat-species
#4
Dmitry Miroshnichenko, Danila Ashin, Alexander Pushin, Sergey Dolgov
BACKGROUND: Domesticated einkorn (Triticum monococcum L.) is one of the oldest cultivated cereal crops in the world. Its small genome size (~ 5.7 GB), low ploidy (2n = 2x = 14, Am Am ) and high genetic polymorphism make this species very attractive for use as a diploid model for understanding the genomics and proteomics of Triticeae. Einkorn, however, is still a recalcitrant monocotyledonous species for the application of modern biotechnologies, including transgenesis. This paper reports the factors that may influence transgene delivery, integration, expression and inheritance in einkorn...
October 23, 2018: BMC Biotechnology
https://www.readbyqxmd.com/read/30302531/a-to-i-mrna-editing-in-fungi-occurrence-function-and-evolution
#5
REVIEW
Zhuyun Bian, Yajia Ni, Jin-Rong Xu, Huiquan Liu
A-to-I RNA editing is an important post-transcriptional modification that converts adenosine (A) to inosine (I) in RNA molecules via hydrolytic deamination. Although editing of mRNAs catalyzed by adenosine deaminases acting on RNA (ADARs) is an evolutionarily conserved mechanism in metazoans, organisms outside the animal kingdom lacking ADAR orthologs were thought to lack A-to-I mRNA editing. However, recent discoveries of genome-wide A-to-I mRNA editing during the sexual stage of the wheat scab fungus Fusarium graminearum, model filamentous fungus Neurospora crassa, Sordaria macrospora, and an early diverging filamentous ascomycete Pyronema confluens indicated that A-to-I mRNA editing is likely an evolutionarily conserved feature in filamentous ascomycetes...
October 9, 2018: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/30285624/efficient-generation-of-stable-heritable-gene-edits-in-wheat-using-crispr-cas9
#6
Rhian M Howells, Melanie Craze, Sarah Bowden, Emma J Wallington
BACKGROUND: The use of CRISPR/Cas9 systems could prove to be a valuable tool in crop research, providing the ability to fully knockout gene function in complex genomes or to precisely adjust gene function by knockout of individual alleles. RESULTS: We compare gene editing in hexaploid wheat (Triticum aestivum) with diploid barley (Hordeum vulgare), using a combination of single genome and tri-genome targeting. High efficiency gene editing, 11-17% for single genome targeted guides and 5% for tri-genome targeted guides, was achieved in wheat using stable Agrobacterium-mediated transformation...
October 3, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/30258105/biolistic-delivery-based-transient-crispr-cas9-expression-enables-in-planta-genome-editing-in-wheat
#7
Haruyasu Hamada, Yuelin Liu, Yozo Nagira, Ryuji Miki, Naoaki Taoka, Ryozo Imai
The current application of genome editing to crop plants is limited to cultivars that are amenable to in vitro culture and regeneration. Here, we report an in planta genome-editing which does not require callus culture and regeneration. Shoot apical meristems (SAMs) contain a subepidermal cell layer, L2, from which germ cells later develop during floral organogenesis. The biolistic delivery of gold particles coated with plasmids expressing CRISPR/Cas9 components designed to target TaGASR7 were bombarded into SAM-exposed embryos of imbibed seeds...
September 26, 2018: Scientific Reports
https://www.readbyqxmd.com/read/30249481/perspective-on-wheat-yield-and-quality-with-reduced-nitrogen-supply
#8
REVIEW
Christian Zörb, Uwe Ludewig, Malcolm J Hawkesford
Wheat is an important cereal crop with a high demand for nitrogen (N) fertilizer to enable the grain protein accumulation that is necessary for baking and processing quality. Here, perspectives for the development of improved wheat genotypes with higher yield stability, better grain quality, and improved N use efficiency to lower environmental impacts are discussed. The development of improved wheat genotypes, for example, genotypes that lack storage proteins that do not contribute to baking quality (e.g., by genome editing), in combination with appropriate N fertilizer management to prevent N losses into the environment underpins a novel approach to improving N use efficiency...
November 2018: Trends in Plant Science
https://www.readbyqxmd.com/read/30197654/the-enhancement-of-plant-disease-resistance-using-crispr-cas9-technology
#9
REVIEW
Virginia M G Borrelli, Vittoria Brambilla, Peter Rogowsky, Adriano Marocco, Alessandra Lanubile
Genome editing technologies have progressed rapidly and become one of the most important genetic tools in the implementation of pathogen resistance in plants. Recent years have witnessed the emergence of site directed modification methods using meganucleases, zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindrome repeats (CRISPR)/CRISPR-associated protein 9 (Cas9). Recently, CRISPR/Cas9 has largely overtaken the other genome editing technologies due to the fact that it is easier to design and implement, has a higher success rate, and is more versatile and less expensive...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/30136108/gene-editing-and-mutagenesis-reveal-inter-cultivar-differences-and-additivity-in-the-contribution-of-tagw2-homoeologues-to-grain-size-and-weight-in-wheat
#10
Wei Wang, James Simmonds, Qianli Pan, Dwight Davidson, Fei He, Abdulhamit Battal, Alina Akhunova, Harold N Trick, Cristobal Uauy, Eduard Akhunov
CRISPR-Cas9-based genome editing and EMS mutagenesis revealed inter-cultivar differences and additivity in the contribution of TaGW2 homoeologues to grain size and weight in wheat. The TaGW2 gene homoeologues have been reported to be negative regulators of grain size (GS) and thousand grain weight (TGW) in wheat. However, the contribution of each homoeologue to trait variation among different wheat cultivars is not well documented. We used the CRISPR-Cas9 system and TILLING to mutagenize each homoeologous gene copy in cultivars Bobwhite and Paragon, respectively...
November 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/30029701/food-processing-and-breeding-strategies-for-coeliac-safe-and-healthy-wheat-products
#11
Aurélie Jouanin, Luud J W J Gilissen, Lesley A Boyd, James Cockram, Fiona J Leigh, Emma J Wallington, Hetty C van den Broeck, Ingrid M van der Meer, Jan G Schaart, Richard G F Visser, Marinus J M Smulders
A strict gluten-free diet is currently the only treatment for the 1-2% of the world population who suffer from coeliac disease (CD). However, due to the presence of wheat and wheat derivatives in many food products, avoiding gluten consumption is difficult. Gluten-free products, made without wheat, barley or rye, typically require the inclusion of numerous additives, resulting in products that are often less healthy than gluten-based equivalents. Here, we present and discuss two broad approaches to decrease wheat gluten immunogenicity for CD patients...
August 2018: Food Research International
https://www.readbyqxmd.com/read/29959543/advancing-agrobacterium-based-crop-transformation-and-genome-modification-technology-for-agricultural-biotechnology
#12
Ajith Anand, Todd J Jones
The last decade has seen significant strides in Agrobacterium-mediated plant transformation technology. This has not only expanded the number of crop species that can be transformed by Agrobacterium, but has also made it possible to routinely transform several recalcitrant crop species including cereals (e.g., maize, sorghum, and wheat). However, the technology is limited by the random nature of DNA insertions, genotype dependency, low frequency of quality events, and variation in gene expression arising from genomic insertion sites...
June 30, 2018: Current Topics in Microbiology and Immunology
https://www.readbyqxmd.com/read/29734518/zinc-finger-nuclease-mediated-precision-genome-editing-of-an-endogenous-gene-in-hexaploid-bread-wheat-triticum-aestivum-using-a-dna-repair-template
#13
Yidong Ran, Nicola Patron, Pippa Kay, Debbie Wong, Margaret Buchanan, Ying-Ying Cao, Tim Sawbridge, John P Davies, John Mason, Steven R Webb, German Spangenberg, William M Ainley, Terence A Walsh, Matthew J Hayden
Sequence-specific nucleases have been used to engineer targeted genome modifications in various plants. While targeted gene knockouts resulting in loss of function have been reported with relatively high rates of success, targeted gene editing using an exogenously supplied DNA repair template and site-specific transgene integration has been more challenging. Here, we report the first application of zinc finger nuclease (ZFN)-mediated, nonhomologous end-joining (NHEJ)-directed editing of a native gene in allohexaploid bread wheat to introduce, via a supplied DNA repair template, a specific single amino acid change into the coding sequence of acetohydroxyacid synthase (AHAS) to confer resistance to imidazolinone herbicides...
December 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29723918/genotyping-genome-edited-mutations-in-plants-using-crispr-ribonucleoprotein-complexes
#14
Zhen Liang, Kunling Chen, Yan Yan, Yi Zhang, Caixia Gao
Despite the great achievements in genome editing, accurately detecting mutations induced by sequence-specific nucleases is still a challenge in plants, especially in polyploidy plants. An efficient detection method is particularly vital when the mutation frequency is low or when a large population needs to be screened. Here, we applied purified CRISPR ribonucleoprotein complexes to cleave PCR products for genome-edited mutation detection in hexaploid wheat and diploid rice. We show that this mutation detection method is more sensitive than Sanger sequencing and more applicable than PCR/RE method without the requirement for restriction enzyme site...
December 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29722792/alphamate-a-program-for-optimizing-selection-maintenance-of-diversity-and-mate-allocation-in-breeding-programs
#15
Gregor Gorjanc, John M Hickey
Summary: AlphaMate is a flexible program that optimizes selection, maintenance of genetic diversity and mate allocation in breeding programs. It can be used in animal and cross- and self-pollinating plant populations. These populations can be subject to selective breeding or conservation management. The problem is formulated as a multi-objective optimization of a valid mating plan that is solved with an evolutionary algorithm. A valid mating plan is defined by a combination of mating constraints (the number of matings, the maximal number of parents, the minimal/equal/maximal number of contributions per parent, or allowance for selfing) that are gender specific or generic...
October 1, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29710373/transforming-plant-biology-and-breeding-with-crispr-cas9-cas12-and-cas13
#16
REVIEW
Patrick Schindele, Felix Wolter, Holger Puchta
Currently, biology is revolutionized by ever growing applications of the CRISPR/Cas system. As discussed in this Review, new avenues have opened up for plant research and breeding by the use of the sequence-specific DNases Cas9 and Cas12 (formerly named Cpf1) and, more recently, the RNase Cas13 (formerly named C2c2). Although double strand break-induced gene editing based on error-prone nonhomologous end joining has been applied to obtain new traits, such as powdery mildew resistance in wheat or improved pathogen resistance and increased yield in tomato, improved technologies based on CRISPR/Cas for programmed change in plant genomes via homologous recombination have recently been developed...
June 2018: FEBS Letters
https://www.readbyqxmd.com/read/29695804/targeted-mutagenesis-in-wheat-microspores-using-crispr-cas9
#17
Pankaj Bhowmik, Evan Ellison, Brittany Polley, Venkatesh Bollina, Manoj Kulkarni, Kaveh Ghanbarnia, Halim Song, Caixia Gao, Daniel F Voytas, Sateesh Kagale
CRISPR/Cas9 genome editing is a transformative technology that will facilitate the development of crops to meet future demands. However, application of gene editing is hindered by the long life cycle of many crop species and because desired genotypes generally require multiple generations to achieve. Single-celled microspores are haploid cells that can develop into double haploid plants and have been widely used as a breeding tool to generate homozygous plants within a generation. In this study, we combined the CRISPR/Cas9 system with microspore technology and developed an optimized haploid mutagenesis system to induce genetic modifications in the wheat genome...
April 25, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29559984/rnai-mediated-downregulation-of-inositol-pentakisphosphate-kinase-ipk1-in-wheat-grains-decreases-phytic-acid-levels-and-increases-fe-and-zn-accumulation
#18
Sipla Aggarwal, Anil Kumar, Kaushal K Bhati, Gazaldeep Kaur, Vishnu Shukla, Siddharth Tiwari, Ajay K Pandey
Enhancement of micronutrient bioavailability is crucial to address the malnutrition in the developing countries. Various approaches employed to address the micronutrient bioavailability are showing promising signs, especially in cereal crops. Phytic acid (PA) is considered as a major antinutrient due to its ability to chelate important micronutrients and thereby restricting their bioavailability. Therefore, manipulating PA biosynthesis pathway has largely been explored to overcome the pleiotropic effect in different crop species...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29516116/tilling-the-next-generation
#19
Bradley J Till, Sneha Datta, Joanna Jankowicz-Cieslak
Gene space: the final frontier in plant functional genomics. These are the voyages of TILLING, the reverse-genetics strategy that sought to boldly go where no-one had gone before by combining high-density chemical mutagenesis with high-throughput mutation discovery. Its 18-year mission has been to explore new technologies such as next generation sequencing and to seek out new strategies like in silico databases of catalogued EMS-induced mutations from entire mutant plant populations. This chapter is a clip show highlighting key milestones in the development of TILLING...
2018: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/29472693/a-new-allele-of-the-brachytic2-gene-in-maize-can-efficiently-modify-plant-architecture
#20
Lai Wei, Xuan Zhang, Zhihai Zhang, Huanhuan Liu, Zhongwei Lin
The applications of semi-dwarf genes such as sd1 and Rht1 in rice and wheat resulted in the first "green revolution" in the 1960s. However, such semi-dwarf genes that can efficiently reduce plant stature and have few negative yield traits have not yet been identified in maize. In this study, a new allele of Brachytic2 gene (qpa1) encoding P-glycoprotein was rapidly fine-mapped using a modified method. The qpa1, containing a 241-bp deletion in the last exon, had no negative effect on yield, but greatly modified the plant architecture including significantly reduced plant height and ear height, increased stalk diameter and erected leaf...
July 2018: Heredity
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