Sequence-specific nucleases have been applied to engineer targeted modifications in polyploid genomes, but simultaneous modification of multiple homoeoalleles has not been reported. Here we use transcription activator-like effector nuclease (TALEN) and clustered, regularly interspaced, short palindromic repeats (CRISPR)-Cas9 (refs. 4,5) technologies in hexaploid bread wheat to introduce targeted mutations in the three homoeoalleles that encode MILDEW-RESISTANCE LOCUS (MLO) proteins. Genetic redundancy has prevented evaluation of whether mutation of all three MLO alleles in bread wheat might confer resistance to powdery mildew, a trait not found in natural populations. We show that TALEN-induced mutation of all three TaMLO homoeologs in the same plant confers heritable broad-spectrum resistance to powdery mildew. We further use CRISPR-Cas9 technology to generate transgenic wheat plants that carry mutations in the TaMLO-A1 allele. We also demonstrate the feasibility of engineering targeted DNA insertion in bread wheat through nonhomologous end joining of the double-strand breaks caused by TALENs. Our findings provide a methodological framework to improve polyploid crops.

Editing plant genomes is technically challenging in hard-to-transform plants and usually involves transgenic intermediates, which causes regulatory concerns. Here we report two simple and efficient genome-editing methods in which plants are regenerated from callus cells transiently expressing CRISPR/Cas9 introduced as DNA or RNA. This transient expression-based genome-editing system is highly efficient and specific for producing transgene-free and homozygous wheat mutants in the T0 generation. We demonstrate our protocol to edit genes in hexaploid bread wheat and tetraploid durum wheat, and show that we are able to generate mutants with no detectable transgenes. Our methods may be applicable to other plant species, thus offering the potential to accelerate basic and applied plant genome-engineering research.

Abiotic stress, such as salinity, drought, and cold, causes detrimental yield losses for all major plant crop species. Understanding mechanisms that improve plants' ability to produce biomass, which largely is constituted by the plant cell wall, is therefore of upmost importance for agricultural activities. Cellulose is a principal component of the cell wall and is synthesized by microtubule-guided cellulose synthase enzymes at the plasma membrane. Here, we identified two components of the cellulose synthase complex, which we call companion of cellulose synthase (CC) proteins. The cytoplasmic tails of these membrane proteins bind to microtubules and promote microtubule dynamics. This activity supports microtubule organization, cellulose synthase localization at the plasma membrane, and renders seedlings less sensitive to stress. Our findings offer a mechanistic model for how two molecular components, the CC proteins, sustain microtubule organization and cellulose synthase localization and thus aid plant biomass production during salt stress. VIDEO ABSTRACT.

Genome-editing tools provide advanced biotechnological techniques that enable the precise and efficient targeted modification of an organism’s genome. Genome-editing systems have been utilized in a wide variety of plant species to characterize gene functions and improve agricultural traits. We describe the current applications of genome editing in plants, focusing on its potential for crop improvement in terms of adaptation, resilience, and end-use. In addition, we review novel breakthroughs that are extending the potential of genome-edited crops and the possibilities of their commercialization. Future prospects for integrating this revolutionary technology with conventional and new-age crop breeding strategies are also discussed.

In plants, vacuolar H + -ATPase (V-ATPase) activity acidifies both the trans-Golgi network/early endosome (TGN/EE) and the vacuole. This dual V-ATPase function has impeded our understanding in how the pH homeostasis within the plant TGN/EE controls exo-and endocytosis.⋆ Staffan. Persson@unimelb.au.edu, karin.schumacher@cos.uni-heidelberg.de, and eugenia.russinova@psb.vib-ugent. Additional informationSupplementary information is available on line. Competing interestsThe authors declare no competing financial interests Europe PMC Funders GroupAuthor Manuscript Nat Plants. Author manuscript; available in PMC 2016 June 13. Here, we show that the weak V-ATPase mutant deetiolated3 (det3) displayed a pH increase in the TGN/EE, but not in the vacuole, strongly impairing secretion and recycling of the brassinosteroid receptor and the cellulose synthase complexes to the plasma membrane, in contrast to mutants lacking tonoplast-localized V-ATPase activity only. The brassinosteroid insensitivity and the cellulose deficiency defects in det3 were tightly correlated with reduced Golgi and TGN/EE motility. Thus, our results provide strong evidence that acidification of the TGN/EE, but not of the vacuole, is indispensable for functional secretion and recycling in plants.Plant exo-and endocytic pathways converge at the trans-Golgi network/early endosome (TGN/EE) compartment where different cargos are sorted to further destinations1,2. In animal and yeast cells, acidification of intracellular organelles is crucial for the function of the secretory and endocytic pathways and requires proton pumping activity of the vacuolar H + -ATPases (V-ATPase)3-5. The V-ATPase is conserved across species and consists of multiple subunits that are organized in a cytosolic V1 domain, which is important for the ATP hydrolysis (including A, B, C, D, E, F, G, and H subunits), and an integral membrane V0 domain, which forms the proton pore (including a, d, c, c" and e subunits)3. In Arabidopsis thaliana, the V-ATPase activity is associated with both the TGN/EEs and the tonoplast that are marked by the differential localization of the membraneVHA-a1, VHA-a2 and VHA-a3 isoforms1,6,7. The vha-a3 mutant and the vha-a2 vha-a3 double mutant that lack the tonoplast V-ATPase activity do not display severe defects in cell expansion, whereas the inducible inhibition of the TGN/EE-localized VHA-a1 isoform constrains it7,8. Treatment with the V-ATPase inhibitor concanamycinA (ConcA) resulted in loss of the TGN/EE identity and interfered with the trafficking of endocytic and secretory cargos1,2. Given the differential localization of the V-ATPases, the reduced cell expansion has been concluded to be caused by defects in TGN/EE compartments rather than in the vacuole8, but the nature of these defects has not been clarified. In contrast, the cytosolic V-ATPase subunit C (VHA-C), encoded by the single-copy VHA-C/DEETIOLATED3 (DET3) gene, is required for V-ATPase activity at the TGN/EEs and at the vacuole9. A knockdown allele of DET3 displayed pleiotropic phe...

Rice (Oryza sativa L.) is one of the world's most important staple crops and a powerful model system for studying monocot species because of its relatively small genome, rich genomic resources, and a highly efficient transformation system. With the completion of rice genome sequencing, the challenge of the post-genomic era is to systematically analyze the functions of all rice genes. Gene knockout is a frequently used and effective strategy for achieving this goal. Thus, generation of large-scale mutants at the whole-genome level is of great value for both functional genomics and genetic improvement of rice. Traditionally, large numbers of mutants are produced by physical, chemical, or biological mutagenesis. Mutants created by these methods have made enormous contributions to basic plant research and crop improvement. T-DNA insertion (Jeon et al., 2000), TILLING (targeting-induced local lesions in genomes) (Till et al., 2007) and RNAi (RNA interference) (Wang et al., 2013) are the three most common methods of performing genetic studies. T-DNA insertion and TILLING are time-consuming and labor-intensive in generating genome-wide mutant libraries, because large mutagenized populations must be generated to ensure sufficient genome-wide coverage. In addition, the T-DNA insertions occur randomly and often in intergenic and noncoding regions, for TILLING mutants it is difficult to identify the targeted mutations for the observed phenotypes, and the RNAi method only reduces the expression of targeted genes rather than generating the knockout mutants. Recently, a simple and highly efficient genomic engineering tool, the CRISPR (Clustered Regularly Interspaced Palindromic Repeats)/Cas9 system, has been developed; this technology can create small insertions and deletions (indels) in specific target genes and has been applied to many organisms. Because it is an easy and convenient technique, some CRISPR/Cas9 mutant libraries have been developed for genomewide mutation screens in cultured eukaryotic cells (Shalem et al., 2015). However, no large-scale CRISPR/Cas9 mutant libraries have yet been generated in higher plants. Here, we report the construction of a high-throughput CRISPR/Cas9 mutant library in rice and demonstrate its application for identifying gene functions and its potential use for genetic improvement.

This protocol is an extension to: Nat. Protoc. 9, 2395-2410 (2014); doi:10.1038/nprot.2014.157; published online 18 September 2014In recent years, CRISPR/Cas9 has emerged as a powerful tool for improving crop traits. Conventional plant genome editing mainly relies on plasmid-carrying cassettes delivered by Agrobacterium or particle bombardment. Here, we describe DNA-free editing of bread wheat by delivering in vitro transcripts (IVTs) or ribonucleoprotein complexes (RNPs) of CRISPR/Cas9 by particle bombardment. This protocol serves as an extension of our previously published protocol on genome editing in bread wheat using CRISPR/Cas9 plasmids delivered by particle bombardment. The methods we describe not only eliminate random integration of CRISPR/Cas9 into genomic DNA, but also reduce off-target effects. In this protocol extension article, we present detailed protocols for preparation of IVTs and RNPs; validation by PCR/restriction enzyme (RE) and next-generation sequencing; delivery by biolistics; and recovery of mutants and identification of mutants by pooling methods and Sanger sequencing. To use these protocols, researchers should have basic skills and experience in molecular biology and biolistic transformation. By using these protocols, plants edited without the use of any foreign DNA can be generated and identified within 9-11 weeks.

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