51
|
Aamir M, Karmakar P, Singh VK, Kashyap SP, Pandey S, Singh BK, Singh PM, Singh J. A novel insight into transcriptional and epigenetic regulation underlying sex expression and flower development in melon (Cucumis melo L.). PHYSIOLOGIA PLANTARUM 2021; 173:1729-1764. [PMID: 33547804 DOI: 10.1111/ppl.13357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Melon (Cucumis melo L.) is an important cucurbit and has been considered as a model plant for studying sex determination. The four most common sexual morphotypes in melon are monoecious (A-G-M), gynoecious (--ggM-), andromonoecious (A-G-mm), and hermaphrodite (--ggmm). Sex expression in melons is complex, as the genes and associated networks that govern the sex expression are not fully explored. Recently, RNA-seq transcriptomic profiling, ChIP-qPCR analysis integrated with gene ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathways predicted the differentially expressed genes including sex-specific ACS and ACO genes, in regulating the sex-expression, phytohormonal cross-talk, signal transduction, and secondary metabolism in melons. Integration of transcriptional control through genetic interaction in between the ACS7, ACS11, and WIP1 in epistatic or hypostatic manner, along with the recruitment of H3K9ac and H3K27me3, epigenetically, overall determine sex expression. Alignment of protein sequences for establishing phylogenetic evolution, motif comparison, and protein-protein interaction supported the structural conservation while presence of the conserved hydrophilic and charged residues across the diverged evolutionary group predicted the functional conservation of the ACS protein. Presence of the putative cis-binding elements or DNA motifs, and its further comparison with DAP-seq-based cistrome and epicistrome of Arabidopsis, unraveled strong ancestry of melons with Arabidopsis. Motif comparison analysis also characterized putative genes and transcription factors involved in ethylene biosynthesis, signal transduction, and hormonal cross-talk related to sex expression. Overall, we have comprehensively reviewed research findings for a deeper insight into transcriptional and epigenetic regulation of sex expression and flower development in melons.
Collapse
Affiliation(s)
- Mohd Aamir
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Pradip Karmakar
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Vinay Kumar Singh
- Centre for Bioinformatics, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Sarvesh Pratap Kashyap
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Sudhakar Pandey
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Binod Kumar Singh
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Prabhakar Mohan Singh
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Jagdish Singh
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| |
Collapse
|
52
|
Recent advances in CRISPR/Cas9 and applications for wheat functional genomics and breeding. ABIOTECH 2021; 2:375-385. [PMID: 36304421 PMCID: PMC9590522 DOI: 10.1007/s42994-021-00042-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/17/2021] [Indexed: 12/21/2022]
Abstract
Common wheat (Triticum aestivum L.) is one of the three major food crops in the world; thus, wheat breeding programs are important for world food security. Characterizing the genes that control important agronomic traits and finding new ways to alter them are necessary to improve wheat breeding. Functional genomics and breeding in polyploid wheat has been greatly accelerated by the advent of several powerful tools, especially CRISPR/Cas9 genome editing technology, which allows multiplex genome engineering. Here, we describe the development of CRISPR/Cas9, which has revolutionized the field of genome editing. In addition, we emphasize technological breakthroughs (e.g., base editing and prime editing) based on CRISPR/Cas9. We also summarize recent applications and advances in the functional annotation and breeding of wheat, and we introduce the production of CRISPR-edited DNA-free wheat. Combined with other achievements, CRISPR and CRISPR-based genome editing will speed progress in wheat biology and promote sustainable agriculture.
Collapse
|
53
|
Xiao L, Du Q, Fang Y, Quan M, Lu W, Wang D, Si J, El-Kassaby YA, Zhang D. Genetic architecture of the metabolic pathway of salicylic acid biosynthesis in Populus. TREE PHYSIOLOGY 2021; 41:2198-2215. [PMID: 33987676 DOI: 10.1093/treephys/tpab068] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
Salicylic acid (SA) is a vital hormone for adaptive responses to biotic and abiotic stresses, which facilitates growth-immunity trade-offs in plants. However, the genetic regulatory networks underlying the metabolic pathway of SA biosynthesis in perennial species remain unclear. Here, we integrated genome-wide association study (GWAS) with metabolite and expression profiling methodologies to dissect the genetic architecture of SA biosynthesis in Populus. First, we quantified nine intermediate metabolites of SA biosynthesis in 300 unrelated Populus tomentosa Carr. individuals. Then, we used a systematic genetic strategy to identify candidate genes for constructing the genetic regulatory network of SA biosynthesis. We focused on WRKY70, an efficient transcription factor, as the key causal gene in the regulatory network, and combined the novel genes coordinating the accumulation of SA. Finally, we identified eight GWAS signals and eight expression quantitative trait loci situated in a selective sweep, and showed the presence of large allele frequency differences among the three geographic populations, revealing that candidate genes subject to selection were involved in SA biosynthesis. This study provides an integrated strategy for dissecting the genetic architecture of the metabolic pathway of SA biosynthesis in Populus, thereby enhancing our understanding of genetic regulation of SA biosynthesis in trees, and accelerating marker-assisted breeding efforts toward high-resistance elite varieties of Populus.
Collapse
Affiliation(s)
- Liang Xiao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Qingzhang Du
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Yuanyuan Fang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Mingyang Quan
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Wenjie Lu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Dan Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Jingna Si
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| |
Collapse
|
54
|
Verma AK, Mandal S, Tiwari A, Monachesi C, Catassi GN, Srivastava A, Gatti S, Lionetti E, Catassi C. Current Status and Perspectives on the Application of CRISPR/Cas9 Gene-Editing System to Develop a Low-Gluten, Non-Transgenic Wheat Variety. Foods 2021; 10:foods10102351. [PMID: 34681400 PMCID: PMC8534962 DOI: 10.3390/foods10102351] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/10/2021] [Accepted: 09/28/2021] [Indexed: 12/23/2022] Open
Abstract
Wheat gluten contains epitopes that trigger celiac disease (CD). A life-long strict gluten-free diet is the only treatment accepted for CD. However, very low-gluten wheat may provide an alternative treatment to CD. Conventional plant breeding methods have not been sufficient to produce celiac-safe wheat. RNA interference technology, to some extent, has succeeded in the development of safer wheat varieties. However, these varieties have multiple challenges in terms of their implementation. Clustered Regularly Interspaced Short Palindromic Repeats-associated nuclease 9 (CRISPR/Cas9) is a versatile gene-editing tool that has the ability to edit immunogenic gluten genes. So far, only a few studies have applied CRISPR/Cas9 to modify the wheat genome. In this article, we reviewed the published literature that applied CRISPR/Cas9 in wheat genome editing to investigate the current status of the CRISPR/Cas9 system to produce a low-immunogenic wheat variety. We found that in recent years, the CRISPR/Cas9 system has been continuously improved to edit the complex hexaploid wheat genome. Although some reduced immunogenic wheat varieties have been reported, CRISPR/Cas9 has still not been fully explored in terms of editing the wheat genome. We conclude that further studies are required to apply the CRISPR/Cas9 gene-editing system efficiently for the development of a celiac-safe wheat variety and to establish it as a "tool to celiac safe wheat".
Collapse
Affiliation(s)
- Anil K. Verma
- Celiac Disease Research Laboratory, Polytechnic University of Marche, 60123 Ancona, Italy;
- Correspondence: or ; Tel.: +39-0715962834
| | - Sayanti Mandal
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune 411007, Maharashtra, India;
| | - Aadhya Tiwari
- Department of System Biology, MD Anderson Cancer Center, Houston, TX 77030, USA;
- Laboratory of Cell Biology, Department of Orthopaedic Surgery, University Hospital of Tübingen, Waldhörnlestraße 22, D-72072 Tübingen, Germany
| | - Chiara Monachesi
- Celiac Disease Research Laboratory, Polytechnic University of Marche, 60123 Ancona, Italy;
| | - Giulia N. Catassi
- Division of Pediatrics, DISCO Department, Polytechnic University of Marche, 60123 Ancona, Italy; (G.N.C.); (S.G.); (E.L.); (C.C.)
| | - Akash Srivastava
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02906, USA;
| | - Simona Gatti
- Division of Pediatrics, DISCO Department, Polytechnic University of Marche, 60123 Ancona, Italy; (G.N.C.); (S.G.); (E.L.); (C.C.)
| | - Elena Lionetti
- Division of Pediatrics, DISCO Department, Polytechnic University of Marche, 60123 Ancona, Italy; (G.N.C.); (S.G.); (E.L.); (C.C.)
| | - Carlo Catassi
- Division of Pediatrics, DISCO Department, Polytechnic University of Marche, 60123 Ancona, Italy; (G.N.C.); (S.G.); (E.L.); (C.C.)
- Mucosal Immunology and Biology Research Center, Division of Pediatric Gastroenterology and Nutrition, Massachusetts General Hospital, Boston, MA 02114, USA
| |
Collapse
|
55
|
Bhowmik P, Bilichak A. Advances in Gene Editing of Haploid Tissues in Crops. Genes (Basel) 2021; 12:1410. [PMID: 34573392 PMCID: PMC8468125 DOI: 10.3390/genes12091410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/07/2021] [Accepted: 09/09/2021] [Indexed: 01/14/2023] Open
Abstract
Emerging threats of climate change require the rapid development of improved varieties with a higher tolerance to abiotic and biotic factors. Despite the success of traditional agricultural practices, novel techniques for precise manipulation of the crop's genome are needed. Doubled haploid (DH) methods have been used for decades in major crops to fix desired alleles in elite backgrounds in a short time. DH plants are also widely used for mapping of the quantitative trait loci (QTLs), marker-assisted selection (MAS), genomic selection (GS), and hybrid production. Recent discoveries of genes responsible for haploid induction (HI) allowed engineering this trait through gene editing (GE) in non-inducer varieties of different crops. Direct editing of gametes or haploid embryos increases GE efficiency by generating null homozygous plants following chromosome doubling. Increased understanding of the underlying genetic mechanisms responsible for spontaneous chromosome doubling in haploid plants may allow transferring this trait to different elite varieties. Overall, further improvement in the efficiency of the DH technology combined with the optimized GE could accelerate breeding efforts of the major crops.
Collapse
Affiliation(s)
- Pankaj Bhowmik
- Aquatic and Crop Resource Development, National Research Council of Canada, Saskatoon, SK S7N 0W9, Canada;
| | - Andriy Bilichak
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, Morden, MB R6M 1Y5, Canada
| |
Collapse
|
56
|
Zhang J, Zhang H, Li S, Li J, Yan L, Xia L. Increasing yield potential through manipulating of an ARE1 ortholog related to nitrogen use efficiency in wheat by CRISPR/Cas9. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1649-1663. [PMID: 34270164 DOI: 10.1111/jipb.13151] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 07/15/2021] [Indexed: 05/22/2023]
Abstract
Wheat (Triticum aestivum L.) is a staple food crop consumed by more than 30% of world population. Nitrogen (N) fertilizer has been applied broadly in agriculture practice to improve wheat yield to meet the growing demands for food production. However, undue N fertilizer application and the low N use efficiency (NUE) of modern wheat varieties are aggravating environmental pollution and ecological deterioration. Under nitrogen-limiting conditions, the rice (Oryza sativa) abnormal cytokinin response1 repressor1 (are1) mutant exhibits increased NUE, delayed senescence and consequently, increased grain yield. However, the function of ARE1 ortholog in wheat remains unknown. Here, we isolated and characterized three TaARE1 homoeologs from the elite Chinese winter wheat cultivar ZhengMai 7698. We then used CRISPR/Cas9-mediated targeted mutagenesis to generate a series of transgene-free mutant lines either with partial or triple-null taare1 alleles. All transgene-free mutant lines showed enhanced tolerance to N starvation, and showed delayed senescence and increased grain yield in field conditions. In particular, the AABBdd and aabbDD mutant lines exhibited delayed senescence and significantly increased grain yield without growth defects compared to the wild-type control. Together, our results underscore the potential to manipulate ARE1 orthologs through gene editing for breeding of high-yield wheat as well as other cereal crops with improved NUE.
Collapse
Affiliation(s)
- Jiahui Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huating Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Shaoya Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jingying Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lei Yan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lanqin Xia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| |
Collapse
|
57
|
Stephens C, Ölmez F, Blyth H, McDonald M, Bansal A, Turgay EB, Hahn F, Saintenac C, Nekrasov V, Solomon P, Milgate A, Fraaije B, Rudd J, Kanyuka K. Remarkable recent changes in the genetic diversity of the avirulence gene AvrStb6 in global populations of the wheat pathogen Zymoseptoria tritici. MOLECULAR PLANT PATHOLOGY 2021; 22:1121-1133. [PMID: 34258838 PMCID: PMC8358995 DOI: 10.1111/mpp.13101] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 04/02/2021] [Accepted: 06/03/2021] [Indexed: 06/13/2023]
Abstract
Septoria tritici blotch (STB), caused by the fungus Zymoseptoria tritici, is one of the most economically important diseases of wheat. Recently, both factors of a gene-for-gene interaction between Z. tritici and wheat, the wheat receptor-like kinase Stb6 and the Z. tritici secreted effector protein AvrStb6, have been identified. Previous analyses revealed a high diversity of AvrStb6 haplotypes present in earlier Z. tritici isolate collections, with up to c.18% of analysed isolates possessing the avirulence isoform of AvrStb6 identical to that originally identified in the reference isolate IPO323. With Stb6 present in many commercial wheat cultivars globally, we aimed to assess potential changes in AvrStb6 genetic diversity and the incidence of haplotypes allowing evasion of Stb6-mediated resistance in more recent Z. tritici populations. Here we show, using targeted resequencing of AvrStb6, that this gene is universally present in field isolates sampled from major wheat-growing regions of the world in 2013-2017. However, in contrast to the data from previous AvrStb6 population studies, we report a complete absence of the originally described avirulence isoform of AvrStb6 amongst modern Z. tritici isolates. Moreover, a remarkably small number of haplotypes, each encoding AvrStb6 protein isoforms conditioning virulence on Stb6-containing wheat, were found to predominate among modern Z. tritici isolates. A single virulence isoform of AvrStb6 was found to be particularly abundant throughout the global population. These findings indicate that, despite the ability of Z. tritici to sexually reproduce on resistant hosts, AvrStb6 avirulence haplotypes tend to be eliminated in subsequent populations.
Collapse
Affiliation(s)
| | - Fatih Ölmez
- Department of Plant ProtectionSivas Science and Technology UniversitySivasTurkey
| | - Hannah Blyth
- Department of Biointeractions and Crop ProtectionRothamsted ResearchHarpendenUK
| | - Megan McDonald
- Division of Plant SciencesResearch School of BiologyAustralian National UniversityCanberraAustralia
- Present address:
Megan McDonald, School of BiosciencesUniversity of BirminghamBirminghamUK
| | - Anuradha Bansal
- Department of Biointeractions and Crop ProtectionRothamsted ResearchHarpendenUK
- Present address:
British American TobaccoSouthamptonUK
| | - Emine Burcu Turgay
- Department of Plant PathologyPlant Protection Central Research InstituteField Crops Central Research InstituteAnkaraTurkey
| | - Florian Hahn
- Department of Plant SciencesRothamsted ResearchHarpendenUK
- Present address:
Department of Plant SciencesUniversity of OxfordOxfordUK
| | | | | | - Peter Solomon
- Division of Plant SciencesResearch School of BiologyAustralian National UniversityCanberraAustralia
| | - Andrew Milgate
- NSW Department of Primary IndustriesWagga Wagga Agricultural InstituteWagga WaggaAustralia
| | - Bart Fraaije
- Department of Biointeractions and Crop ProtectionRothamsted ResearchHarpendenUK
- Present address:
NIABCambridgeUK
| | - Jason Rudd
- Department of Biointeractions and Crop ProtectionRothamsted ResearchHarpendenUK
| | - Kostya Kanyuka
- Department of Biointeractions and Crop ProtectionRothamsted ResearchHarpendenUK
| |
Collapse
|
58
|
Zhang S, Zhang R, Gao J, Song G, Li J, Li W, Qi Y, Li Y, Li G. CRISPR/Cas9-mediated genome editing for wheat grain quality improvement. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1684-1686. [PMID: 34143557 PMCID: PMC8428824 DOI: 10.1111/pbi.13647] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 06/01/2021] [Accepted: 06/03/2021] [Indexed: 05/15/2023]
Affiliation(s)
- Shujuan Zhang
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of Agriculture and Rural AffairsKey Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Laboratory for Wheat and MaizeJinanShandongChina
| | - Rongzhi Zhang
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of Agriculture and Rural AffairsKey Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Laboratory for Wheat and MaizeJinanShandongChina
| | - Jie Gao
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of Agriculture and Rural AffairsKey Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Laboratory for Wheat and MaizeJinanShandongChina
| | - Guoqi Song
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of Agriculture and Rural AffairsKey Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Laboratory for Wheat and MaizeJinanShandongChina
| | - Jihu Li
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of Agriculture and Rural AffairsKey Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Laboratory for Wheat and MaizeJinanShandongChina
| | - Wei Li
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of Agriculture and Rural AffairsKey Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Laboratory for Wheat and MaizeJinanShandongChina
| | - Yiping Qi
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMDUSA
- Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMDUSA
| | - Yulian Li
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of Agriculture and Rural AffairsKey Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Laboratory for Wheat and MaizeJinanShandongChina
| | - Genying Li
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of Agriculture and Rural AffairsKey Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Laboratory for Wheat and MaizeJinanShandongChina
| |
Collapse
|
59
|
Sato K, Abe F, Mascher M, Haberer G, Gundlach H, Spannagl M, Shirasawa K, Isobe S. Chromosome-scale genome assembly of the transformation-amenable common wheat cultivar 'Fielder'. DNA Res 2021; 28:6319722. [PMID: 34254113 PMCID: PMC8320877 DOI: 10.1093/dnares/dsab008] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/07/2021] [Indexed: 12/21/2022] Open
Abstract
We have established a high-quality, chromosome-level genome assembly for the hexaploid common wheat cultivar ‘Fielder’, an American, soft, white, pastry-type wheat released in 1974 and known for its amenability to Agrobacterium tumefaciens-mediated transformation and genome editing. Accurate, long-read sequences were obtained using PacBio circular consensus sequencing with the HiFi approach. Sequence reads from 16 SMRT cells assembled using the hifiasm assembler produced assemblies with N50 greater than 20 Mb. We used the Omni-C chromosome conformation capture technique to order contigs into chromosome-level assemblies, resulting in 21 pseudomolecules with a cumulative size of 14.7 and 0.3 Gb of unanchored contigs. Mapping of published short reads from a transgenic wheat plant with an edited seed-dormancy gene, TaQsd1, identified four positions of transgene insertion into wheat chromosomes. Detection of guide RNA sequences in pseudomolecules provided candidates for off-target mutation induction. These results demonstrate the efficiency of chromosome-scale assembly using PacBio HiFi reads and their application in wheat genome-editing studies.
Collapse
Affiliation(s)
- Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Fumitaka Abe
- Institute of Crop Science, NARO, Tsukuba, 305-8666, Japan
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Georg Haberer
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Heidrun Gundlach
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Manuel Spannagl
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | | | - Sachiko Isobe
- Kazusa DNA Research Institute, Kisarazu, 292-0818, Japan
| |
Collapse
|
60
|
Raffan S, Sparks C, Huttly A, Hyde L, Martignago D, Mead A, Hanley SJ, Wilkinson PA, Barker G, Edwards KJ, Curtis TY, Usher S, Kosik O, Halford NG. Wheat with greatly reduced accumulation of free asparagine in the grain, produced by CRISPR/Cas9 editing of asparagine synthetase gene TaASN2. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1602-1613. [PMID: 33638281 PMCID: PMC8384593 DOI: 10.1111/pbi.13573] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 05/05/2023]
Abstract
Free asparagine is the precursor for acrylamide, which forms during the baking, toasting and high-temperature processing of foods made from wheat. In this study, CRISPR/Cas9 was used to knock out the asparagine synthetase gene, TaASN2, of wheat (Triticum aestivum) cv. Cadenza. A 4-gRNA polycistronic gene was introduced into wheat embryos by particle bombardment and plants were regenerated. T1 plants derived from 11 of 14 T0 plants were shown to carry edits. Most edits were deletions (up to 173 base pairs), but there were also some single base pair insertions and substitutions. Editing continued beyond the T1 generation. Free asparagine concentrations in the grain of plants carrying edits in all six TaASN2 alleles (both alleles in each genome) were substantially reduced compared with wildtype, with one plant showing a more than 90 % reduction in the T2 seeds. A plant containing edits only in the A genome alleles showed a smaller reduction in free asparagine concentration in the grain, but the concentration was still lower than in wildtype. Free asparagine concentration in the edited plants was also reduced as a proportion of the free amino acid pool. Free asparagine concentration in the T3 seeds remained substantially lower in the edited lines than wildtype, although it was higher than in the T2 seeds, possibly due to stress. In contrast, the concentrations of free glutamine, glutamate and aspartate were all higher in the edited lines than wildtype. Low asparagine seeds showed poor germination but this could be overcome by exogenous application of asparagine.
Collapse
Affiliation(s)
- Sarah Raffan
- Department of Plant SciencesRothamsted ResearchHarpendenUK
| | | | - Alison Huttly
- Department of Plant SciencesRothamsted ResearchHarpendenUK
| | - Lucy Hyde
- Department of Plant SciencesRothamsted ResearchHarpendenUK
- Present address:
School of Biological SciencesLife Sciences BuildingUniversity of Bristol24 Tyndall AvenueBristolBS8 1TQUK
| | - Damiano Martignago
- Department of Plant SciencesRothamsted ResearchHarpendenUK
- Present address:
Department of BiosciencesUniversity of MilanVia Celoria 26Milano20133Italy
| | - Andrew Mead
- Department of Computational and Analytical SciencesRothamsted ResearchHarpendenUK
| | - Steven J. Hanley
- Department of Computational and Analytical SciencesRothamsted ResearchHarpendenUK
| | - Paul A. Wilkinson
- Functional GenomicsSchool of Biological SciencesUniversity of BristolBristolUK
| | - Gary Barker
- Functional GenomicsSchool of Biological SciencesUniversity of BristolBristolUK
| | - Keith J. Edwards
- Functional GenomicsSchool of Biological SciencesUniversity of BristolBristolUK
| | - Tanya Y. Curtis
- Curtis Analytics LimitedRothamsted Research CampusHarpendenUK
| | - Sarah Usher
- Curtis Analytics LimitedRothamsted Research CampusHarpendenUK
| | - Ondrej Kosik
- Curtis Analytics LimitedRothamsted Research CampusHarpendenUK
| | | |
Collapse
|
61
|
Matres JM, Hilscher J, Datta A, Armario-Nájera V, Baysal C, He W, Huang X, Zhu C, Valizadeh-Kamran R, Trijatmiko KR, Capell T, Christou P, Stoger E, Slamet-Loedin IH. Genome editing in cereal crops: an overview. Transgenic Res 2021; 30:461-498. [PMID: 34263445 PMCID: PMC8316241 DOI: 10.1007/s11248-021-00259-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 05/15/2021] [Indexed: 02/06/2023]
Abstract
Genome-editing technologies offer unprecedented opportunities for crop improvement with superior precision and speed. This review presents an analysis of the current state of genome editing in the major cereal crops- rice, maize, wheat and barley. Genome editing has been used to achieve important agronomic and quality traits in cereals. These include adaptive traits to mitigate the effects of climate change, tolerance to biotic stresses, higher yields, more optimal plant architecture, improved grain quality and nutritional content, and safer products. Not all traits can be achieved through genome editing, and several technical and regulatory challenges need to be overcome for the technology to realize its full potential. Genome editing, however, has already revolutionized cereal crop improvement and is poised to shape future agricultural practices in conjunction with other breeding innovations.
Collapse
Affiliation(s)
- Jerlie Mhay Matres
- Genetic Design and Validation Unit, International Rice Research Institute, Los Banos, Philippines
| | - Julia Hilscher
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Akash Datta
- Genetic Design and Validation Unit, International Rice Research Institute, Los Banos, Philippines
| | - Victoria Armario-Nájera
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Can Baysal
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Wenshu He
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Xin Huang
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Changfu Zhu
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Rana Valizadeh-Kamran
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
- Department of Biotechnology, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Kurniawan R Trijatmiko
- Genetic Design and Validation Unit, International Rice Research Institute, Los Banos, Philippines
| | - Teresa Capell
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Paul Christou
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
- ICREA, Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Eva Stoger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria.
| | - Inez H Slamet-Loedin
- Genetic Design and Validation Unit, International Rice Research Institute, Los Banos, Philippines.
| |
Collapse
|
62
|
Choi SH, Lee MH, Jin DM, Ju SJ, Ahn WS, Jie EY, Lee JM, Lee J, Kim CY, Kim SW. TSA Promotes CRISPR/Cas9 Editing Efficiency and Expression of Cell Division-Related Genes from Plant Protoplasts. Int J Mol Sci 2021; 22:7817. [PMID: 34360584 PMCID: PMC8346083 DOI: 10.3390/ijms22157817] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 12/15/2022] Open
Abstract
Trichostatin A (TSA) is a representative histone deacetylase (HDAC) inhibitor that modulates epigenetic gene expression by regulation of chromatin remodeling in cells. To investigate whether the regulation of chromatin de-condensation by TSA can affect the increase in the efficiency of Cas9 protein-gRNA ribonucleoprotein (RNP) indel formation from plant cells, genome editing efficiency using lettuce and tobacco protoplasts was examined after several concentrations of TSA treatments (0, 0.1, 1 and 10 μM). RNP delivery from protoplasts was conducted by conventional polyethylene glycol (PEG) transfection protocols. Interestingly, the indel frequency of the SOC1 gene from TSA treatments was about 3.3 to 3.8 times higher than DMSO treatment in lettuce protoplasts. The TSA-mediated increase of indel frequency of the SOC1 gene in lettuce protoplasts occurred in a concentration-dependent manner, although there was not much difference. Similar to lettuce, TSA also increased the indel frequency by 1.5 to 1.8 times in a concentration-dependent manner during PDS genome editing using tobacco protoplasts. The MNase test clearly showed that chromatin accessibility with TSA treatments was higher than that of DMSO treatment. Additionally, TSA treatment significantly increased the level of histone H3 and H4 acetylation from lettuce protoplasts. The qRT-PCR analysis showed that expression of cell division-related genes (LsCYCD1-1, LsCYCD3-2, LsCYCD6-1, and LsCYCU4-1) was increased by TSA treatment. These findings could contribute to increasing the efficiency of CRISPR/Cas9-mediated genome editing. Furthermore, this could be applied for the development of useful genome-edited crops using the CRISPR/Cas9 system with plant protoplasts.
Collapse
Affiliation(s)
- Seung Hee Choi
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsingil, Jeongeup-si 56212, Korea; (S.H.C.); (D.M.J.); (S.J.J.); (W.S.A.); (E.Y.J.); (J.M.L.); (J.L.); (C.Y.K.)
| | - Myoung Hui Lee
- National Institute of Crop Science, RDA, Wanju 55365, Korea;
| | - Da Mon Jin
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsingil, Jeongeup-si 56212, Korea; (S.H.C.); (D.M.J.); (S.J.J.); (W.S.A.); (E.Y.J.); (J.M.L.); (J.L.); (C.Y.K.)
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju 61186, Korea
| | - Su Ji Ju
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsingil, Jeongeup-si 56212, Korea; (S.H.C.); (D.M.J.); (S.J.J.); (W.S.A.); (E.Y.J.); (J.M.L.); (J.L.); (C.Y.K.)
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Korea
| | - Woo Seok Ahn
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsingil, Jeongeup-si 56212, Korea; (S.H.C.); (D.M.J.); (S.J.J.); (W.S.A.); (E.Y.J.); (J.M.L.); (J.L.); (C.Y.K.)
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju 61186, Korea
| | - Eun Yee Jie
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsingil, Jeongeup-si 56212, Korea; (S.H.C.); (D.M.J.); (S.J.J.); (W.S.A.); (E.Y.J.); (J.M.L.); (J.L.); (C.Y.K.)
| | - Ji Min Lee
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsingil, Jeongeup-si 56212, Korea; (S.H.C.); (D.M.J.); (S.J.J.); (W.S.A.); (E.Y.J.); (J.M.L.); (J.L.); (C.Y.K.)
| | - Jiyoung Lee
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsingil, Jeongeup-si 56212, Korea; (S.H.C.); (D.M.J.); (S.J.J.); (W.S.A.); (E.Y.J.); (J.M.L.); (J.L.); (C.Y.K.)
| | - Cha Young Kim
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsingil, Jeongeup-si 56212, Korea; (S.H.C.); (D.M.J.); (S.J.J.); (W.S.A.); (E.Y.J.); (J.M.L.); (J.L.); (C.Y.K.)
| | - Suk Weon Kim
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsingil, Jeongeup-si 56212, Korea; (S.H.C.); (D.M.J.); (S.J.J.); (W.S.A.); (E.Y.J.); (J.M.L.); (J.L.); (C.Y.K.)
| |
Collapse
|
63
|
Hahn F, Sanjurjo Loures L, Sparks CA, Kanyuka K, Nekrasov V. Efficient CRISPR/Cas-Mediated Targeted Mutagenesis in Spring and Winter Wheat Varieties. PLANTS (BASEL, SWITZERLAND) 2021; 10:1481. [PMID: 34371684 PMCID: PMC8309376 DOI: 10.3390/plants10071481] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 11/16/2022]
Abstract
CRISPR/Cas technology has recently become the molecular tool of choice for gene function studies in plants as well as crop improvement. Wheat is a globally important staple crop with a well annotated genome and there is plenty of scope for improving its agriculturally important traits using genome editing technologies, such as CRISPR/Cas. As part of this study we targeted three different genes in hexaploid wheat Triticum aestivum: TaBAK1-2 in the spring cultivar Cadenza as well as Ta-eIF4E and Ta-eIF(iso)4E in winter cultivars Cezanne, Goncourt and Prevert. Primary transgenic lines carrying CRISPR/Cas-induced indels were successfully generated for all targeted genes. While BAK1 is an important regulator of plant immunity and development, Ta-eIF4E and Ta-eIF(iso)4E act as susceptibility (S) factors required for plant viruses from the Potyviridae family to complete their life cycle. We anticipate the resultant homozygous tabak1-2 mutant lines will facilitate studies on the involvement of BAK1 in immune responses in wheat, while ta-eif4e and ta-eif(iso)4e mutant lines have the potential to become a source of resistance to wheat spindle streak mosaic virus (WSSMV) and wheat yellow mosaic virus (WYMV), both of which are important pathogens of wheat. As winter wheat varieties are generally less amenable to genetic transformation, the successful experimental methodology for transformation and genome editing in winter wheat presented in this study will be of interest to the research community working with this crop.
Collapse
Affiliation(s)
- Florian Hahn
- Plant Sciences Department, Rothamsted Research, Harpenden AL5 2JQ, UK; (F.H.); (L.S.L.); (C.A.S.)
| | - Laura Sanjurjo Loures
- Plant Sciences Department, Rothamsted Research, Harpenden AL5 2JQ, UK; (F.H.); (L.S.L.); (C.A.S.)
| | - Caroline A. Sparks
- Plant Sciences Department, Rothamsted Research, Harpenden AL5 2JQ, UK; (F.H.); (L.S.L.); (C.A.S.)
| | - Kostya Kanyuka
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden AL5 2JQ, UK;
| | - Vladimir Nekrasov
- Plant Sciences Department, Rothamsted Research, Harpenden AL5 2JQ, UK; (F.H.); (L.S.L.); (C.A.S.)
| |
Collapse
|
64
|
Maximiano MR, Távora FTPK, Prado GS, Dias SC, Mehta A, Franco OL. CRISPR Genome Editing Technology: A Powerful Tool Applied to Developing Agribusiness. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:6379-6395. [PMID: 34097395 DOI: 10.1021/acs.jafc.1c01062] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The natural increase of the world's population implies boosting agricultural demand. In the current non-optimistic global scenario, where adverse climate changes come associated with substantial population growth, the main challenge in agribusiness is food security. Recently, the CRISPR/Cas system has emerged as a friendly gene editing biotechnological tool, enabling a precise manipulation of genomes and enhancement of desirable traits in several organisms. This review highlights the CRISPR/Cas system as a paramount tool for the improvement of agribusiness products and brings up-to-date findings showing its potential applications in improving agricultural-related traits in major plant crops and farm animals, all representing economic-relevant commodities responsible for feeding the world. Several applied pieces of research have successfully demonstrated the CRISPR/Cas ability in boosting interesting traits in agribusiness products, including animal productivity and welfare, crop yield growth, and seed quality, reflecting positive impacts in both socioeconomics and human health aspects. Hence, the CRISPR/Cas system has revolutionized bioscience and biotechnology, and its concrete application in agribusiness goods is on the horizon.
Collapse
Affiliation(s)
- Mariana Rocha Maximiano
- S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul 79117-900, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal 70790-160, Brazil
| | - Fabiano T P K Távora
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal 70770-917, Brazil
- Programa de Pós Graduação em Ciências Biológicas (Imunologia e DIP/Genética e Biotecnologia), Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais 36036-900, Brazil
| | - Guilherme Souza Prado
- Laboratório de Biotecnologia, Embrapa Arroz e Feijão, Goiânia, Goiás 75375-000, Brazil
| | - Simoni Campos Dias
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal 70790-160, Brazil
| | - Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal 70770-917, Brazil
| | - Octávio Luiz Franco
- S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul 79117-900, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal 70790-160, Brazil
- Programa de Pós Graduação em Ciências Biológicas (Imunologia e DIP/Genética e Biotecnologia), Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais 36036-900, Brazil
| |
Collapse
|
65
|
Huang X, Hilscher J, Stoger E, Christou P, Zhu C. Modification of cereal plant architecture by genome editing to improve yields. PLANT CELL REPORTS 2021; 40:953-978. [PMID: 33559722 DOI: 10.1007/s00299-021-02668-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 01/22/2021] [Indexed: 06/12/2023]
Abstract
We summarize recent genome editing studies that have focused on the examination (or reexamination) of plant architectural phenotypes in cereals and the modification of these traits for crop improvement. Plant architecture is defined as the three-dimensional organization of the entire plant. Shoot architecture refers to the structure and organization of the aboveground components of a plant, reflecting the developmental patterning of stems, branches, leaves and inflorescences/flowers. Root system architecture is essentially determined by four major shape parameters-growth, branching, surface area and angle. Interest in plant architecture has arisen from the profound impact of many architectural traits on agronomic performance, and the genetic and hormonal regulation of these traits which makes them sensitive to both selective breeding and agronomic practices. This is particularly important in staple crops, and a large body of literature has, therefore, accumulated on the control of architectural phenotypes in cereals, particularly rice due to its twin role as one of the world's most important food crops as well as a model organism in plant biology and biotechnology. These studies have revealed many of the molecular mechanisms involved in the regulation of tiller/axillary branching, stem height, leaf and flower development, root architecture and the grain characteristics that ultimately help to determine yield. The advent of genome editing has made it possible, for the first time, to introduce precise mutations into cereal crops to optimize their architecture and close in on the concept of the ideotype. In this review, we consider recent genome editing studies that have focused on the examination (or reexamination) of plant architectural phenotypes in cereals and the modification of these traits for crop improvement.
Collapse
Affiliation(s)
- Xin Huang
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain
| | - Julia Hilscher
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 33, 1180, Vienna, Austria
| | - Eva Stoger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 33, 1180, Vienna, Austria
| | - Paul Christou
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain
- ICREA, Catalan Institute for Research and Advanced Studies, Passeig Lluís Companys 23, 08010, Barcelona, Spain
| | - Changfu Zhu
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain.
| |
Collapse
|
66
|
Biswas S, Zhang D, Shi J. CRISPR/Cas systems: opportunities and challenges for crop breeding. PLANT CELL REPORTS 2021; 40:979-998. [PMID: 33977326 DOI: 10.1007/s00299-021-02708-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 04/28/2021] [Indexed: 05/27/2023]
Abstract
Increasing crop production to meet the demands of a growing population depends largely on crop improvement through new plant-breeding techniques (NPBT) such as genome editing. CRISPR/Cas systems are NPBTs that enable efficient target-specific gene editing in crops, which is supposed to accelerate crop breeding in a way that is different from genetically modified (GM) technology. Herein, we review the applications of CRISPR/Cas systems in crop breeding focusing on crop domestication, heterosis, haploid induction, and synthetic biology, and summarize the screening methods of CRISPR/Cas-induced mutations in crops. We highlight the importance of molecular characterization of CRISPR/Cas-edited crops, and pay special attentions to emerging highly specific genome-editing tools such as base editors and prime editors. We also discuss future improvements of CRISPR/Cas systems for crop improvement.
Collapse
Affiliation(s)
- Sukumar Biswas
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| |
Collapse
|
67
|
Ahmar S, Mahmood T, Fiaz S, Mora-Poblete F, Shafique MS, Chattha MS, Jung KH. Advantage of Nanotechnology-Based Genome Editing System and Its Application in Crop Improvement. FRONTIERS IN PLANT SCIENCE 2021; 12:663849. [PMID: 34122485 PMCID: PMC8194497 DOI: 10.3389/fpls.2021.663849] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/26/2021] [Indexed: 05/05/2023]
Abstract
Agriculture is an important source of human food. However, current agricultural practices need modernizing and strengthening to fulfill the increasing food requirements of the growing worldwide population. Genome editing (GE) technology has been used to produce plants with improved yields and nutritional value as well as with higher resilience to herbicides, insects, and diseases. Several GE tools have been developed recently, including clustered regularly interspaced short palindromic repeats (CRISPR) with nucleases, a customizable and successful method. The main steps of the GE process involve introducing transgenes or CRISPR into plants via specific gene delivery systems. However, GE tools have certain limitations, including time-consuming and complicated protocols, potential tissue damage, DNA incorporation in the host genome, and low transformation efficiency. To overcome these issues, nanotechnology has emerged as a groundbreaking and modern technique. Nanoparticle-mediated gene delivery is superior to conventional biomolecular approaches because it enhances the transformation efficiency for both temporal (transient) and permanent (stable) genetic modifications in various plant species. However, with the discoveries of various advanced technologies, certain challenges in developing a short-term breeding strategy in plants remain. Thus, in this review, nanobased delivery systems and plant genetic engineering challenges are discussed in detail. Moreover, we have suggested an effective method to hasten crop improvement programs by combining current technologies, such as speed breeding and CRISPR/Cas, with nanotechnology. The overall aim of this review is to provide a detailed overview of nanotechnology-based CRISPR techniques for plant transformation and suggest applications for possible crop enhancement.
Collapse
Affiliation(s)
- Sunny Ahmar
- Institute of Biological Sciences, Universidad de Talca, Talca, Chile
| | - Tahir Mahmood
- Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | | | | | | | - Ki-Hung Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| |
Collapse
|
68
|
Li J, Jiao G, Sun Y, Chen J, Zhong Y, Yan L, Jiang D, Ma Y, Xia L. Modification of starch composition, structure and properties through editing of TaSBEIIa in both winter and spring wheat varieties by CRISPR/Cas9. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:937-951. [PMID: 33236499 PMCID: PMC8131058 DOI: 10.1111/pbi.13519] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/16/2020] [Indexed: 05/19/2023]
Abstract
Foods high in amylose content and resistant starch (RS) offer great potential to improve human health and lower the risk of serious noninfectious diseases. Common wheat (Triticum aestivum L.) is a major staple food crop globally. However, the RS contents in the grains of modern wheat varieties are low. Here, we report the generation of high-amylose wheat through targeted mutagenesis of TaSBEIIa in a modern winter wheat cv Zhengmai 7698 (ZM) and a spring wheat cv Bobwhite by CRISPR/Cas9, respectively. We generated a series of transgene-free mutant lines either with partial or triple-null TasbeIIa alleles in ZM and Bobwhite, respectively. Analyses of starch composition, structure and properties revealed that the effects of partial or triple-null alleles were dosage dependent with triple-null lines demonstrated more profound impacts on starch composition, fine structures of amylopectin and physiochemical and nutritional properties. The flours of triple-null lines possessed significantly increased amylose, RS, protein and soluble pentosan contents which benefit human health. Baking quality analyses indicated that the high-amylose flours may be used as additives or for making cookies. Collectively, we successfully modified the starch composition, structure and properties through targeted mutagenesis of TaSBEIIa by CRISPR/Cas9 in both winter and spring wheat varieties and generated transgene-free high-amylose wheat. Our finding provides deep insights on the role of TaSBEIIa in determining starch composition, structure, properties and end-use quality in different genetic backgrounds and improving RS content with multiple breeding and end-use applications in cereal crop species through genome editing for health benefits.
Collapse
Affiliation(s)
- Jingying Li
- Institute of Crop Sciences (ICS)Chinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Guiai Jiao
- China National Rice Research InstituteHangzhouChina
| | - Yongwei Sun
- Institute of Crop Sciences (ICS)Chinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Jun Chen
- Institute of Crop Sciences (ICS)Chinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Yingxin Zhong
- National Technology Innovation Center for Regional Wheat ProductionMinistry of Chinese Agriculture and Rural AffairsNanjing Agricultural UniversityNanjingChina
| | - Lei Yan
- Institute of Crop Sciences (ICS)Chinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Dong Jiang
- National Technology Innovation Center for Regional Wheat ProductionMinistry of Chinese Agriculture and Rural AffairsNanjing Agricultural UniversityNanjingChina
| | - Youzhi Ma
- Institute of Crop Sciences (ICS)Chinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Lanqin Xia
- Institute of Crop Sciences (ICS)Chinese Academy of Agricultural Sciences (CAAS)BeijingChina
| |
Collapse
|
69
|
Syombua ED, Zhang Z, Tripathi JN, Ntui VO, Kang M, George OO, Edward NK, Wang K, Yang B, Tripathi L. A CRISPR/Cas9-based genome-editing system for yam (Dioscorea spp.). PLANT BIOTECHNOLOGY JOURNAL 2021; 19:645-647. [PMID: 33222361 PMCID: PMC8051594 DOI: 10.1111/pbi.13515] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/27/2020] [Accepted: 11/06/2020] [Indexed: 05/21/2023]
Affiliation(s)
- Easter D. Syombua
- International Institute of Tropical Agriculture (IITA)NairobiKenya
- Centre for Biotechnology and BioinformaticsUniversity of NairobiNairobiKenya
| | - Zhengzhi Zhang
- Division of Plant SciencesBond Life Sciences CenterUniversity of MissouriColumbiaMOUSA
| | | | | | - Minjeong Kang
- Department of AgronomyIowa State UniversityAmesIAUSA
| | - Obiero O. George
- Centre for Biotechnology and BioinformaticsUniversity of NairobiNairobiKenya
| | - Nguu K. Edward
- Department of BiochemistryUniversity of NairobiNairobiKenya
| | - Kan Wang
- Department of AgronomyIowa State UniversityAmesIAUSA
| | - Bing Yang
- Division of Plant SciencesBond Life Sciences CenterUniversity of MissouriColumbiaMOUSA
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | - Leena Tripathi
- International Institute of Tropical Agriculture (IITA)NairobiKenya
| |
Collapse
|
70
|
Li J, Zhang S, Zhang R, Gao J, Qi Y, Song G, Li W, Li Y, Li G. Efficient multiplex genome editing by CRISPR/Cas9 in common wheat. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:427-429. [PMID: 33150679 PMCID: PMC7955872 DOI: 10.1111/pbi.13508] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/09/2020] [Accepted: 10/31/2020] [Indexed: 05/06/2023]
Affiliation(s)
- Jihu Li
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of AgricultureKey Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Laboratory for Wheat and MaizeJinanShandongChina
| | - Shujuan Zhang
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of AgricultureKey Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Laboratory for Wheat and MaizeJinanShandongChina
| | - Rongzhi Zhang
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of AgricultureKey Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Laboratory for Wheat and MaizeJinanShandongChina
| | - Jie Gao
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of AgricultureKey Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Laboratory for Wheat and MaizeJinanShandongChina
| | - Yiping Qi
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMDUSA
- Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMDUSA
| | - Guoqi Song
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of AgricultureKey Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Laboratory for Wheat and MaizeJinanShandongChina
| | - Wei Li
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of AgricultureKey Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Laboratory for Wheat and MaizeJinanShandongChina
| | - Yulian Li
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of AgricultureKey Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Laboratory for Wheat and MaizeJinanShandongChina
| | - Genying Li
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of AgricultureKey Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Laboratory for Wheat and MaizeJinanShandongChina
| |
Collapse
|
71
|
Bhoite R, Si P, Siddique KHM, Yan G. Comparative transcriptome analyses for metribuzin tolerance provide insights into key genes and mechanisms restoring photosynthetic efficiency in bread wheat (Triticum aestivum L.). Genomics 2021; 113:910-918. [PMID: 33600945 DOI: 10.1016/j.ygeno.2021.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/12/2021] [Accepted: 02/09/2021] [Indexed: 10/22/2022]
Abstract
Weeds are the biggest threat to cropping system sustainability in wheat. Metribuzin is a versatile herbicide for broad-spectrum weed management. Understanding key genes, mechanisms and functional markers are essential to develop higher metribuzin tolerant wheats. We identified Chuan Mai 25 (tolerant) and Ritchie (susceptible) as contrasting genotypes to metribuzin stress through dose-response analyses. Transcriptome sequencing using NovaSeq 6000 RNA-Seq platform identified a total of 77,443 genes; 59,915 known genes and 17,528 novel genes. The functional enrichment analysis at 0 h, 24 h and 60 h herbicide exposure revealed that endogenous increase of metabolic enzymes, light-harvesting chlorophyll proteins, PSII stability factor HCF136 and glucose metabolism conferred metribuzin tolerance. The validation of DEGs using RT-qPCR and QTL mapping confirmed their responsiveness to metribuzin. Transcription factors MYB, AP2-EREBP, ABI3VP1, bHLH, NAC are significantly expressed during metribuzin stress. Transcripts with significant enrichments revealed 114 SSRs for genomic selection. The master regulators provide promising avenues for enhancing metribuzin tolerance.
Collapse
Affiliation(s)
- Roopali Bhoite
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia; The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia.
| | - Ping Si
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia; The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia.
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia.
| | - Guijun Yan
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia; The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia.
| |
Collapse
|
72
|
The evolution and history of gene editing technologies. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 178:1-62. [PMID: 33685594 DOI: 10.1016/bs.pmbts.2021.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Scientific enquiry must be the driving force of research. This sentiment is manifested as the profound impact gene editing technologies are having in our current world. There exist three main gene editing technologies today: Zinc Finger Nucleases, TALENs and the CRISPR-Cas system. When these systems were being uncovered, none of the scientists set out to design tools to engineer genomes. They were simply trying to understand the mechanisms existing in nature. If it was not for this simple sense of wonder, we probably would not have these breakthrough technologies. In this chapter, we will discuss the history, applications and ethical issues surrounding these technologies, focusing on the now predominant CRISPR-Cas technology. Gene editing technologies, as we know them now, are poised to have an overwhelming impact on our world. However, it is impossible to predict the route they will take in the future or to comprehend the full impact of its repercussions.
Collapse
|
73
|
Gupta A, Hua L, Lin G, Molnár I, Doležel J, Liu S, Li W. Multiple origins of Indian dwarf wheat by mutations targeting the TREE domain of a GSK3-like kinase for drought tolerance, phosphate uptake, and grain quality. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:633-645. [PMID: 33164159 DOI: 10.1007/s00122-020-03719-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/27/2020] [Indexed: 05/28/2023]
Abstract
Multiple origins of Indian dwarf wheat were due to two mutations targeting the same TREE domain of a GSK3-like kinase, and these mutations confer to enhanced drought tolerance and increased phosphate and nitrogen accumulation for adaptation to the dry climate of Indian and Pakistan. Indian dwarf wheat, featured by the short stature, erect leaves, dense spikes, and small, spherical grains, was a staple crop in India and Pakistan from the Bronze Age until the early 1900s. These morphological features are controlled by a single locus Sphaerococcum 1 (S1), but the genetic identity of the locus and molecular mechanisms underlying the selection of this wheat type are unknown. In this study, we showed that the origin of Indian dwarf wheat was due to two independent missense mutations targeting the conserved TREE domain of a GSK3-like kinase, which is homologous to the Arabidopsis BIN2 protein, a negative regulator in brassinosteroid signaling. The S1 protein is involved in brassinosteroid signaling by physical interaction with the wheat BES1/BZR1 proteins. The dwarf alleles are insensitive to brassinosteroid, upregulates brassinosteroid biosynthetic genes, significantly enhanced drought tolerance, facilitated phosphate accumulation, and increased high molecular weight glutenins. It is the enhanced drought tolerance and accumulation of nitrogen and phosphate that contributed to the adaptation of such a small-grain form of wheat to the dry climate of India and Pakistan. Thus, our research not only identified the genetic events underlying the origin of the Indian dwarf wheat, but also revealed the function of brassinosteroid in the regulation of drought tolerance, phosphate homeostasis, and grain quality.
Collapse
Affiliation(s)
- Ajay Gupta
- 252 McFadden Biostress Laboratory, Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA
| | - Lei Hua
- 252 McFadden Biostress Laboratory, Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA
| | - Guifang Lin
- Plant Pathology Department, Kansas State University, Manhattan, KS, 66502, USA
| | - Istváan Molnár
- Institute of Experimental Botany of the Czech Academy of Sciences, 77900, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, 77900, Olomouc, Czech Republic
| | - Sanzhen Liu
- Plant Pathology Department, Kansas State University, Manhattan, KS, 66502, USA
| | - Wanlong Li
- 252 McFadden Biostress Laboratory, Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA.
| |
Collapse
|
74
|
Milner MJ, Craze M, Hope MS, Wallington EJ. Turning Up the Temperature on CRISPR: Increased Temperature Can Improve the Editing Efficiency of Wheat Using CRISPR/Cas9. FRONTIERS IN PLANT SCIENCE 2020; 11:583374. [PMID: 33324433 PMCID: PMC7726164 DOI: 10.3389/fpls.2020.583374] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/23/2020] [Indexed: 05/24/2023]
Abstract
The application of CRISPR/Cas9 technologies has transformed our ability to target and edit designated regions of a genome. It's broad adaptability to any organism has led to countless advancements in our understanding of many biological processes. Many current tools are designed for simple plant systems such as diploid species, however, efficient deployment in crop species requires a greater efficiency of editing as these often contain polyploid genomes. Here, we examined the role of temperature to understand if CRISPR/Cas9 editing efficiency can be improved in wheat. The recent finding that plant growth under higher temperatures could increase mutation rates was tested with Cas9 expressed from two different promoters in wheat. Increasing the temperature of the tissue culture or of the seed germination and early growth phase increases the frequency of mutation in wheat when the Cas9 enzyme is driven by the ZmUbi promoter but not OsActin. In contrast, Cas9 expression driven by the OsActin promoter did not increase the mutations detected in either transformed lines or during the transformation process itself. These results demonstrate that CRISPR/Cas9 editing efficiency can be significantly increased in a polyploid cereal species with a simple change in growth conditions to facilitate increased mutations for the creation of homozygous or null knock-outs.
Collapse
|
75
|
Sashidhar N, Harloff HJ, Potgieter L, Jung C. Gene editing of three BnITPK genes in tetraploid oilseed rape leads to significant reduction of phytic acid in seeds. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:2241-2250. [PMID: 32191373 PMCID: PMC7589381 DOI: 10.1111/pbi.13380] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/07/2020] [Accepted: 02/28/2020] [Indexed: 05/20/2023]
Abstract
Commercialization of Brassica napus. L (oilseed rape) meal as protein diet is gaining more attention due to its well-balanced amino acid and protein contents. Phytic acid (PA) is a major source of phosphorus in plants but is considered as anti-nutritive for monogastric animals including humans due to its adverse effects on essential mineral absorption. The undigested PA causes eutrophication, which potentially threatens aquatic life. PA accounts to 2-5% in mature seeds of oilseed rape and is synthesized by complex pathways involving multiple enzymes. Breeding polyploids for recessive traits is challenging as gene functions are encoded by several paralogs. Gene redundancy often requires to knock out several gene copies to study their underlying effects. Therefore, we adopted CRISPR-Cas9 mutagenesis to knock out three functional paralogs of BnITPK. We obtained low PA mutants with an increase of free phosphorus in the canola grade spring cultivar Haydn. These mutants could mark an important milestone in rapeseed breeding with an increase in protein value and no adverse effects on oil contents.
Collapse
Affiliation(s)
- Niharika Sashidhar
- Plant Breeding InstituteChristian‐Albrechts‐University of KielKielGermany
| | - Hans J. Harloff
- Plant Breeding InstituteChristian‐Albrechts‐University of KielKielGermany
| | - Lizel Potgieter
- Environmental GenomicsBotanical InstituteChristian‐Albrechts‐University of KielKielGermany
- Environmental GenomicsMax‐Planck‐Institute for Evolutionary BiologyPlönGermany
| | - Christian Jung
- Plant Breeding InstituteChristian‐Albrechts‐University of KielKielGermany
| |
Collapse
|
76
|
Liu H, Wang K, Tang H, Gong Q, Du L, Pei X, Ye X. CRISPR/Cas9 editing of wheat TaQ genes alters spike morphogenesis and grain threshability. J Genet Genomics 2020; 47:563-575. [PMID: 33187879 DOI: 10.1016/j.jgg.2020.08.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 01/13/2023]
Abstract
The TaQ alleles as one of the AP2-like transcription factors in common wheat (Triticum aestivum) play an important role in the evolution of spike characteristics from wild and domesticated emmer to modern wheat cultivars. Its loss-of-function mutant not only changed threshability and spike architecture but also affected plant height, flowering time, and floret structure. However, the comprehensive functions of TaAQ and TaDq genes in wheat have not been fully elucidated yet. Here, CRISPR/SpCas9 was used to edit wheat TaAQ and TaDq. We obtained homozygous plants in the T1 generation with loss of function of only TaAQ or TaDq and simultaneous loss of function of TaAQ and TaDq to analyze the effect of these genes on wheat spikes and floret shapes. The results demonstrated that the TaAQ-edited plants and the TaAQ and TaDq simultaneously-edited plants were nearly similar in spike architecture, whereas the TaDq-edited plants were different from the wild-type ones only in plant height. Moreover, the TaAQ-edited plants or the TaAQ and TaDq simultaneously-edited plants were more brittle than the wild-type and the TaDq-edited plants. Based on the expression profiling, we postulated that the VRN1, FUL2, SEP2, SEP5, and SEP6 genes might affect the number of spikelets and florets per spike in wheat by regulating the expression of TaQ. Combining the results of this report and previous reports, we conceived a regulatory network of wheat traits, including plant height, spike shape, and floral organs, which were influenced by AP2-like family genes. The results achieved in this study will help us to understand the regulating mechanisms of TaAQ and TaDq alleles on wheat floral organs and inflorescence development.
Collapse
Affiliation(s)
- Huiyun Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ke Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huali Tang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qiang Gong
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lipu Du
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xinwu Pei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Xingguo Ye
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| |
Collapse
|
77
|
Applications of CRISPR-Cas in agriculture and plant biotechnology. Nat Rev Mol Cell Biol 2020; 21:661-677. [PMID: 32973356 DOI: 10.1038/s41580-020-00288-9] [Citation(s) in RCA: 306] [Impact Index Per Article: 76.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2020] [Indexed: 12/26/2022]
Abstract
The prokaryote-derived CRISPR-Cas genome editing technology has altered plant molecular biology beyond all expectations. Characterized by robustness and high target specificity and programmability, CRISPR-Cas allows precise genetic manipulation of crop species, which provides the opportunity to create germplasms with beneficial traits and to develop novel, more sustainable agricultural systems. Furthermore, the numerous emerging biotechnologies based on CRISPR-Cas platforms have expanded the toolbox of fundamental research and plant synthetic biology. In this Review, we first briefly describe gene editing by CRISPR-Cas, focusing on the newest, precise gene editing technologies such as base editing and prime editing. We then discuss the most important applications of CRISPR-Cas in increasing plant yield, quality, disease resistance and herbicide resistance, breeding and accelerated domestication. We also highlight the most recent breakthroughs in CRISPR-Cas-related plant biotechnologies, including CRISPR-Cas reagent delivery, gene regulation, multiplexed gene editing and mutagenesis and directed evolution technologies. Finally, we discuss prospective applications of this game-changing technology.
Collapse
|
78
|
López-Marqués RL, Nørrevang AF, Ache P, Moog M, Visintainer D, Wendt T, Østerberg JT, Dockter C, Jørgensen ME, Salvador AT, Hedrich R, Gao C, Jacobsen SE, Shabala S, Palmgren M. Prospects for the accelerated improvement of the resilient crop quinoa. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5333-5347. [PMID: 32643753 PMCID: PMC7501820 DOI: 10.1093/jxb/eraa285] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 06/11/2020] [Indexed: 05/04/2023]
Abstract
Crops tolerant to drought and salt stress may be developed by two approaches. First, major crops may be improved by introducing genes from tolerant plants. For example, many major crops have wild relatives that are more tolerant to drought and high salinity than the cultivated crops, and, once deciphered, the underlying resilience mechanisms could be genetically manipulated to produce crops with improved tolerance. Secondly, some minor (orphan) crops cultivated in marginal areas are already drought and salt tolerant. Improving the agronomic performance of these crops may be an effective way to increase crop and food diversity, and an alternative to engineering tolerance in major crops. Quinoa (Chenopodium quinoa Willd.), a nutritious minor crop that tolerates drought and salinity better than most other crops, is an ideal candidate for both of these approaches. Although quinoa has yet to reach its potential as a fully domesticated crop, breeding efforts to improve the plant have been limited. Molecular and genetic techniques combined with traditional breeding are likely to change this picture. Here we analyse protein-coding sequences in the quinoa genome that are orthologous to domestication genes in established crops. Mutating only a limited number of such genes by targeted mutagenesis appears to be a promising route for accelerating the improvement of quinoa and generating a nutritious high-yielding crop that can meet the future demand for food production in a changing climate.
Collapse
Affiliation(s)
- Rosa L López-Marqués
- NovoCrops Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- Correspondence: or
| | - Anton F Nørrevang
- NovoCrops Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Peter Ache
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Max Moog
- NovoCrops Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Davide Visintainer
- NovoCrops Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Toni Wendt
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V, Denmark
| | - Jeppe T Østerberg
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V, Denmark
| | - Christoph Dockter
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V, Denmark
| | - Morten E Jørgensen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V, Denmark
| | - Andrés Torres Salvador
- The Quinoa Company, Wageningen, The Netherlands
- Plant Biotechnology Laboratory (COCIBA), Universidad San Francisco de Quito USFQ, Cumbayá, Ecuador
| | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | | | - Sergey Shabala
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China
- Tasmanian Institute for Agriculture, College of Science and Engineering, University of Tasmania, Hobart, Tasmania, Australia
| | - Michael Palmgren
- NovoCrops Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China
- Correspondence: or
| |
Collapse
|
79
|
Abe F, Haque E, Hisano H, Tanaka T, Kamiya Y, Mikami M, Kawaura K, Endo M, Onishi K, Hayashi T, Sato K. Genome-Edited Triple-Recessive Mutation Alters Seed Dormancy in Wheat. Cell Rep 2020; 28:1362-1369.e4. [PMID: 31365876 DOI: 10.1016/j.celrep.2019.06.090] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 04/23/2019] [Accepted: 06/25/2019] [Indexed: 01/03/2023] Open
Abstract
Common wheat has three sets of sub-genomes, making mutations difficult to observe, especially for traits controlled by recessive genes. Here, we produced hexaploid wheat lines with loss of function of homeoalleles of Qsd1, which controls seed dormancy in barley, by Agrobacterium-mediated CRISPR/Cas9. Of the eight transformed wheat events produced, three independent events carrying multiple mutations in wheat Qsd1 homeoalleles were obtained. Notably, one line had mutations in every homeoallele. We crossed this plant with wild-type cultivar Fielder to generate a transgene-free triple-recessive mutant, as revealed by Mendelian segregation. The mutant showed a significantly longer seed dormancy period than wild-type, which may result in reduced pre-harvest sprouting of grains on spikes. PCR, southern blotting, and whole-genome shotgun sequencing revealed that this segregant lacked transgenes in its genomic sequence. This technique serves as a model for trait improvement in wheat, particularly for genetically recessive traits, based on locus information from diploid barley.
Collapse
Affiliation(s)
- Fumitaka Abe
- Division of Wheat and Barley Research, Institute of Crop Science, NARO, Tsukuba 305-8518, Japan
| | - Emdadul Haque
- Division of Wheat and Barley Research, Institute of Crop Science, NARO, Tsukuba 305-8518, Japan
| | - Hiroshi Hisano
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| | - Tsuyoshi Tanaka
- Division of Basic Research, Institute of Crop Science, NARO, Tsukuba 305-8518, Japan; Bioinformatics Team, Advanced Analysis Center, NARO, Tsukuba 305-8602, Japan
| | - Yoko Kamiya
- Kihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan
| | - Masafumi Mikami
- Graduate School of Nanobioscience, Yokohama City University, Yokohama 236-0027, Japan; Division of Applied Genetics, Institute of Agrobiological Sciences, NARO, Tsukuba 305-8634, Japan
| | - Kanako Kawaura
- Kihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan
| | - Masaki Endo
- Division of Applied Genetics, Institute of Agrobiological Sciences, NARO, Tsukuba 305-8634, Japan
| | - Kazumitsu Onishi
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, Japan
| | - Takeshi Hayashi
- Division of Basic Research, Institute of Crop Science, NARO, Tsukuba 305-8518, Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan.
| |
Collapse
|
80
|
Camerlengo F, Frittelli A, Sparks C, Doherty A, Martignago D, Larré C, Lupi R, Sestili F, Masci S. CRISPR-Cas9 Multiplex Editing of the α-Amylase/Trypsin Inhibitor Genes to Reduce Allergen Proteins in Durum Wheat. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.00104] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
|
81
|
Kamiya Y, Abe F, Mikami M, Endo M, Kawaura K. A rapid method for detection of mutations induced by CRISPR/Cas9-based genome editing in common wheat. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2020; 37:247-251. [PMID: 32821233 PMCID: PMC7434669 DOI: 10.5511/plantbiotechnology.20.0404b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Genome editing using CRISPR/Cas9 is useful for common wheat because common wheat has allohexaploid nature and it can induce mutations simultaneously in three homoeologous genes. Although Agrobacterium-mediated transformation has advantages in genome editing, it still has low efficiency and requires relatively long time in wheat. Therefore, the use of guide RNAs (gRNAs) with efficient mutagenesis in vivo is one of the critical factors for producing genome-edited mutant lines in a short time. In this study, we targeted three genes in common wheat and established a rapid method for detection of mutations induced by the biolistic transient expression system. Biolistic transient expression of the gRNAs and Cas9 was achieved in immature wheat embryos. Mutations were detected a week later using PCR-RFLP and verified by the sequencing of genomic clones. We confirmed several types of mutations that occurred at different rates depending on the target sequences. Furthermore, frequencies of mutations tended to be higher at the targets that were edited at higher rates in the plants transformed by Agrobacterium. These results show that this method of rapid detection of edited mutations could be used for variety of applications, such as screening of target sequences or modified vectors for efficient CRISPR/Cas9 genome editing in wheat.
Collapse
Affiliation(s)
- Yoko Kamiya
- Kihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan
| | - Fumitaka Abe
- Division of Basic Research, Institute of Crop Science, National Agriculture and Food Research Organization, Ibaraki 305-8518, Japan
| | - Masafumi Mikami
- Division of Applied Genetics, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Ibaraki 305-8604, Japan
| | - Masaki Endo
- Division of Applied Genetics, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Ibaraki 305-8604, Japan
| | - Kanako Kawaura
- Kihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan
- E-mail: Tel: +81-45-820-2401 Fax: +81-45-820-2466
| |
Collapse
|
82
|
Brandt KM, Gunn H, Moretti N, Zemetra RS. A Streamlined Protocol for Wheat ( Triticum aestivum) Protoplast Isolation and Transformation With CRISPR-Cas Ribonucleoprotein Complexes. FRONTIERS IN PLANT SCIENCE 2020; 11:769. [PMID: 32587597 PMCID: PMC7298111 DOI: 10.3389/fpls.2020.00769] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/14/2020] [Indexed: 05/03/2023]
Abstract
The genetic engineering method CRISPR has been touted as an efficient, inexpensive, easily used, and targeted genetic modification technology that is widely suggested as having the potential to solve many of the problems facing agriculture now and in the future. Like all new technologies, however, it is not without challenges. One of the most difficult challenges to anticipate and detect is gene targets that are inaccessible due to the chromatin state at their specific location. There is currently no way to predict this during the process of designing a sgRNA target, and the only way to detect this issue before spending time and resources on full transformations is to test the cleavage ability of the sgRNA in vivo. In wheat, this is possible using protoplast isolation and PEG transformation with Cas9 ribonucleoprotein complexes. Therefore, we have developed a streamlined protocol for testing the accessibility of sgRNA targets in wheat. The first steps involve digesting wheat leaf tissue in an enzymatic solution and then isolating viable protoplasts using filters and a sucrose gradient. The protoplasts are then transformed using Cas9 ribonucleoprotein complexes via PEG-mediated transformation. DNA is isolated from the CRISPR-Cas-edited protoplasts and PCR is performed to amplify the gene target region. The PCR product is then used to assess the editing efficiency of the chosen sgRNA using Sanger sequencing. This simplified protocol for the isolation and transformation of wheat protoplast cells using Cas9 ribonucleoprotein complexes streamlines CRISPR transformation projects by allowing for a fast and easy test of sgRNA accessibility in vivo.
Collapse
Affiliation(s)
- Kali M. Brandt
- Wheat Breeding and Genetics, Crop and Soil Science, Oregon State University, Corvallis, OR, United States
| | | | | | | |
Collapse
|
83
|
Char SN, Lee H, Yang B. Use of CRISPR/Cas9 for Targeted Mutagenesis in Sorghum. ACTA ACUST UNITED AC 2020; 5:e20112. [PMID: 32501639 DOI: 10.1002/cppb.20112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Sorghum (Sorghum bicolor) fulfills the demand for bioenergy resources and also provides substantial diet calories to the world's population. Therefore, many biological studies use sorghum as a research model for improvement of the domesticated food and bioenergy crops. Furthermore, leveraging genome editing systems in a plethora of grass plant species has been extensively studied with no exception in sorghum. However, a protocol that details the genome editing strategies using CRISPR/Cas9 and that combines an efficient tissue culture and transformation platform in sorghum based on Agrobacterium-mediated DNA transfer has yet to be reported. This protocol outlines the steps and workflow from design of sorghum CRISPR target sites using BTx623 as a reference genome, construction of sorghum CRISPR/Cas9 plasmids, tissue culture, to Agrobacterium-mediated transformation followed by genotyping of CRISPR/Cas9 induced mutants. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Construction of CRISPR/Cas9 expression vector to analysis of CRISPR-edited plants Basic Protocol 2: Stable transformation of sorghum Support Protocol: Management of sorghum plants in a greenhouse.
Collapse
Affiliation(s)
- Si Nian Char
- Division of Plant Sciences, University of Missouri, Columbia, Missouri.,Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri
| | - Hyeyoung Lee
- Division of Plant Sciences, University of Missouri, Columbia, Missouri.,Plant Transformation Core Facility, University of Missouri, Columbia, Missouri
| | - Bing Yang
- Division of Plant Sciences, University of Missouri, Columbia, Missouri.,Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri.,Donald Danforth Plant Science Center, St. Louis, Missouri
| |
Collapse
|
84
|
Li J, Wang Z, He G, Ma L, Deng XW. CRISPR/Cas9-mediated disruption of TaNP1 genes results in complete male sterility in bread wheat. J Genet Genomics 2020; 47:263-272. [PMID: 32694014 DOI: 10.1016/j.jgg.2020.05.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/03/2020] [Accepted: 05/06/2020] [Indexed: 02/04/2023]
Abstract
Male sterile genes and mutants are valuable resources in hybrid seed production for monoclinous crops. High genetic redundancy due to allohexaploidy makes it difficult to obtain the nuclear recessive male sterile mutants through spontaneous mutation or chemical or physical mutagenesis methods in wheat. The emerging effective genome editing tool, CRISPR/Cas9 system, makes it possible to achieve simultaneous mutagenesis in multiple homoeoalleles. To improve the genome modification efficiency of the CRISPR/Cas9 system in wheat, we compared four different RNA polymerase (Pol) III promoters (TaU3p, TaU6p, OsU3p, and OsU6p) and three types of sgRNA scaffold in the protoplast system. We show that the TaU3 promoter-driven optimized sgRNA scaffold was most effective. The optimized CRISPR/Cas9 system was used to edit three TaNP1 homoeoalleles, whose orthologs, OsNP1 in rice and ZmIPE1 in maize, encode a putative glucose-methanol-choline oxidoreductase and are required for male sterility. Triple homozygous mutations in TaNP1 genes result in complete male sterility. We further demonstrated that any one wild-type copy of the three TaNP1 genes is sufficient for maintenance of male fertility. Taken together, this study provides an optimized CRISPR/Cas9 vector for wheat genome editing and a complete male sterile mutant for development of a commercially viable hybrid wheat seed production system.
Collapse
Affiliation(s)
- Jian Li
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China
| | - Zheng Wang
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China
| | - Guangming He
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, 100871, China
| | - Ligeng Ma
- College of Life Sciences, Capital Normal University, Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing, 100048, China.
| | - Xing Wang Deng
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China; State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, 100871, China.
| |
Collapse
|
85
|
Hensel G. Genetic transformation of Triticeae cereals – Summary of almost three-decade's development. Biotechnol Adv 2020; 40:107484. [DOI: 10.1016/j.biotechadv.2019.107484] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/23/2019] [Accepted: 11/16/2019] [Indexed: 10/25/2022]
|
86
|
Wang K, Gong Q, Ye X. Recent developments and applications of genetic transformation and genome editing technologies in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1603-1622. [PMID: 31654081 DOI: 10.1007/s00122-019-03464-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/19/2019] [Indexed: 05/24/2023]
Abstract
Wheat (Triticum aestivum) is a staple crop across the world and plays a remarkable role in food supplying security. Over the past few decades, basic and applied research on wheat has lagged behind other cereal crops due to the complex and polyploid genome and difficulties in genetic transformation. A breakthrough called as PureWheat was made in the genetic transformation of wheat in 2014 in Asia, leading to a noticeable progress of wheat genome editing. Due to this great achievement, it is predicated that wheat biotechnology revolution is arriving. Genome editing technologies using zinc finger nucleases, transcription activator-like effector nuclease, and clustered regularly interspaced short palindromic repeats-associated endonucleases (CRISR/Cas) are becoming powerful tools for crop modification which can help biologists and biotechnologists better understand the processes of mutagenesis and genomic alteration. Among the three genome editing systems, CRISR/Cas has high specificity and activity, and therefore it is widely used in genetic engineering. Generally, the genome editing technologies depend on an efficient genetic transformation system. In this paper, we summarize recent progresses and applications on genetic transformation and genome editing in wheat. We also examine the future aspects of genetic transformation and genome editing. We believe that the technologies for wheat efficient genetic engineering and functional studies will become routine with the emergence of high-quality genomic sequences.
Collapse
Affiliation(s)
- Ke Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qiang Gong
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xingguo Ye
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| |
Collapse
|
87
|
Liu H, Wang K, Jia Z, Gong Q, Lin Z, Du L, Pei X, Ye X. Efficient induction of haploid plants in wheat by editing of TaMTL using an optimized Agrobacterium-mediated CRISPR system. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1337-1349. [PMID: 31760434 PMCID: PMC7031065 DOI: 10.1093/jxb/erz529] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/22/2019] [Indexed: 05/20/2023]
Abstract
The use of CRISPR/LbCpf1 and CRISPR/xCas9 systems in wheat have not yet been reported. In this study, we compared the efficiencies of three CRISPR editing systems (SpCas9, LbCpf1, and xCas9), and three different promoters (OsU6a, TaU3, and TaU6) that drive single-guide (sg)RNA, which were introduced into wheat via Agrobacterium-mediated transformation. The results indicated that TaU3 was a better choice than OsU6a or TaU6. The editing efficiency was higher using two sgRNAs than one sgRNA, and mutants with a large fragment deletion between the two sgRNAs were produced. The LbCpf1 and xCas9 systems could both be used successfully. Two endogenous genes, TaWaxy and TaMTL, were edited with high efficiency by the optimized SpCas9 system, with the highest efficiency (80.5%) being achieved when using TaU3 and two sgRNAs to target TaWaxy. Rates of seed set in the TaMTL-edited T0 transgenic plants were much lower than that of the wild-type. A haploid induction rate of 18.9% was found in the TaMTL-edited T1 plants using the CRISPR/SpCas9 system. Mutants with reverse insertion of the deleted sequences of TaMTL and TaWaxy between the two sgRNAs were identified in the edited T0 plants. In addition, wheat grains lacking embryos or endosperms were observed in the TaMTL-edited T1 generation.
Collapse
Affiliation(s)
- Huiyun Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ke Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zimiao Jia
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiang Gong
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhishan Lin
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lipu Du
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinwu Pei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xingguo Ye
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
88
|
Ferrie AMR, Bhowmik P, Rajagopalan N, Kagale S. CRISPR/Cas9-Mediated Targeted Mutagenesis in Wheat Doubled Haploids. Methods Mol Biol 2020; 2072:183-198. [PMID: 31541447 DOI: 10.1007/978-1-4939-9865-4_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CRISPR/Cas9-based genome editing technology has the potential to revolutionize agriculture, but many plant species and/or genotypes are recalcitrant to conventional transformation methods. Additionally, the long generation time of crop plants poses a significant obstacle to effective application of gene editing technology, as it takes a long time to produce modified homozygous genotypes. The haploid single-celled microspores are an attractive target for gene editing experiments, as they enable generation of homozygous doubled haploid mutants in one generation. Here, we describe optimized methods for genome editing of haploid wheat microspores and production of doubled haploid plants by microspore culture.
Collapse
Affiliation(s)
| | | | | | - Sateesh Kagale
- National Research Council Canada, Saskatoon, SK, Canada.
| |
Collapse
|
89
|
Char SN, Yang B. Genome editing in grass plants. ABIOTECH 2020; 1:41-57. [PMID: 36305004 PMCID: PMC9590508 DOI: 10.1007/s42994-019-00005-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/17/2019] [Indexed: 12/16/2022]
Abstract
Cereal crops including maize, rice, wheat, sorghum, barley, millet, oats and rye are the major calorie sources in our daily life and also important bioenergy sources of the world. The rapidly advancing and state-of-the-art genome-editing tools such as zinc finger nucleases, TAL effector nucleases, and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated systems (CRISPR-Cas9-, CRISPR-Cas12a- and CRISPR/Cas-derived base editors) have accelerated the functional genomics and have promising potential for precision breeding of grass crops. With the availability of annotated genomes of the major cereal crops, application of these established genome-editing toolkits to grass plants holds promise to increase the nutritional value and productivity. Furthermore, these easy-to-use and robust genome-editing toolkits have advanced the reverse genetics for discovery of novel gene functions in crop plants. In this review, we document some of important progress in development and utilization of genome-editing tool sets in grass plants. We also highlight present and future uses of genome-editing toolkits that can sustain and improve the quality of cereal grain for food consumption.
Collapse
Affiliation(s)
- Si Nian Char
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
| | - Bing Yang
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
- Donald Danforth Plant Science Center, St. Louis, MO 63132 USA
| |
Collapse
|
90
|
Shan S, Soltis PS, Soltis DE, Yang B. Considerations in adapting CRISPR/Cas9 in nongenetic model plant systems. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11314. [PMID: 31993256 PMCID: PMC6976890 DOI: 10.1002/aps3.11314] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 10/26/2019] [Indexed: 05/03/2023]
Abstract
The past six years have seen the rapid growth of studies of CRISPR/Cas9 in plant genome editing, a method that enormously facilitates both basic research and practical applications. Most studies have focused on genetic model species, but plant species that are not genetic models may also be economically important or biologically significant, or both. However, developing the CRISPR/Cas9 system in a nongenetic model is challenging. Here, we summarize CRISPR/Cas9 applications in 45 plant genera across 24 families and provide a reference for practical application of CRISPR in nongenetic model plant systems. Suggestions for selecting plant species and target genes are given for proof-of-principle CRISPR studies, and the processes of vector construction are reviewed. We recommend using transient assays to identify a desired CRISPR/Cas9 system in a nongenetic model. We then review methods of plant transformation and describe approaches, using regenerated transgenic plants, for evaluating CRISPR editing results. Lastly, potential future applications of CRISPR in nongenetic model plant species are discussed. This review provides a road map for developing CRISPR in nongenetic models, an application that holds enormous potential in plant biology.
Collapse
Affiliation(s)
- Shengchen Shan
- Plant Molecular and Cellular Biology ProgramUniversity of FloridaGainesvilleFlorida32611‐0180USA
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611‐7800USA
| | - Pamela S. Soltis
- Plant Molecular and Cellular Biology ProgramUniversity of FloridaGainesvilleFlorida32611‐0180USA
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611‐7800USA
- Biodiversity InstituteUniversity of FloridaGainesvilleFlorida32611‐5585USA
- Genetics InstituteUniversity of FloridaGainesvilleFlorida32610USA
| | - Douglas E. Soltis
- Plant Molecular and Cellular Biology ProgramUniversity of FloridaGainesvilleFlorida32611‐0180USA
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611‐7800USA
- Biodiversity InstituteUniversity of FloridaGainesvilleFlorida32611‐5585USA
- Genetics InstituteUniversity of FloridaGainesvilleFlorida32610USA
- Department of BiologyUniversity of FloridaGainesvilleFlorida32611‐8525USA
| | - Bing Yang
- Division of Plant SciencesUniversity of MissouriColumbiaMissouri65211USA
- Donald Danforth Plant Science CenterSt. LouisMissouri63132USA
| |
Collapse
|
91
|
Di YH, Sun XJ, Hu Z, Jiang QY, Song GH, Zhang B, Zhao SS, Zhang H. Enhancing the CRISPR/Cas9 system based on multiple GmU6 promoters in soybean. Biochem Biophys Res Commun 2019; 519:819-823. [PMID: 31558318 DOI: 10.1016/j.bbrc.2019.09.074] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 10/25/2022]
Abstract
Small guide RNA (sgRNA) is an important component of the CRISPR/Cas9 system. The gene editing efficiency of the CRISPR/Cas9 system could be enhanced by using highly active U6 promoters to drive the expression of sgRNA. Therefore, we constructed various expression vectors based on the 11 GmU6 promoters predicted and cloned in the whole soybean genome. The expression of truncated GUS driven by 11 GmU6 promoters was tested in hairy roots and by Arabidopsis thaliana transformation. The results indicated that higher transcriptional levels were driven by 5 GmU6 promoters (GmU6-4, GmU6-7, GmU6-8, GmU6-10 and GmU6-11) in both soybean hairy roots and Arabidopsis thaliana. In addition, three genes, Glyma03g36470, Glyma14g04180 and Glyma06g136900, were selected as targets to detect the transcriptional levels of multiple GmU6 promoters. Mutations in these three genes were detected in soybean hairy roots after Agrobacterium rhizogenes infection, indicating efficient target gene editing, including nucleotide insertion, deletion, and substitution. Mutation efficiencies differed among the 11 GmU6 promoters, ranging from 2.8% to 20.6%, and markedly higher efficiencies were obtained with all three genes using the GmU6-8 (20.3%) and GmU6-10 (20.6%) promoters. These two GmU6 promoters also showed higher ability to drive truncated GUS transcription in both soybean hairy roots and transformed Arabidopsis thaliana. These results will help to construct an efficient CRISPR-Cas9 gene editing system and promote the application of the CRISPR-Cas9 genome editing system in soybean molecular breeding.
Collapse
Affiliation(s)
- Yi-Huan Di
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, China; National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xian-Jun Sun
- National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Zheng Hu
- National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qi-Yan Jiang
- National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guo-Hua Song
- National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bo Zhang
- Food Engineering and Biotechnology Institute, Tianjin University of Science and Technology, Tianjin, China
| | - Shan-Shan Zhao
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, China.
| | - Hui Zhang
- National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| |
Collapse
|
92
|
Luo M, Li H, Chakraborty S, Morbitzer R, Rinaldo A, Upadhyaya N, Bhatt D, Louis S, Richardson T, Lahaye T, Ayliffe M. Efficient TALEN-mediated gene editing in wheat. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:2026-2028. [PMID: 31125501 PMCID: PMC6790361 DOI: 10.1111/pbi.13169] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/10/2019] [Accepted: 05/15/2019] [Indexed: 05/02/2023]
Affiliation(s)
- Ming Luo
- CSIRO Agriculture and FoodCanberraACTAustralia
| | - Hongyu Li
- CSIRO Agriculture and FoodCanberraACTAustralia
| | | | - Robert Morbitzer
- Eberhard Karls Universität TübingenZMBP, Allgemeine GenetikTübingenGermany
| | - Amy Rinaldo
- CSIRO Agriculture and FoodCanberraACTAustralia
- The Australian Wine Research InstituteGlen OsmondSouth AustraliaAustralia
| | | | - Dhara Bhatt
- CSIRO Agriculture and FoodCanberraACTAustralia
| | | | | | - Thomas Lahaye
- Eberhard Karls Universität TübingenZMBP, Allgemeine GenetikTübingenGermany
| | | |
Collapse
|
93
|
Wang W, Pan Q, Tian B, He F, Chen Y, Bai G, Akhunova A, Trick HN, Akhunov E. Gene editing of the wheat homologs of TONNEAU1-recruiting motif encoding gene affects grain shape and weight in wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:251-264. [PMID: 31219637 PMCID: PMC6851855 DOI: 10.1111/tpj.14440] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/02/2019] [Accepted: 06/10/2019] [Indexed: 05/08/2023]
Abstract
Grain size and weight are important components of a suite of yield-related traits in crops. Here, we showed that the CRISPR-Cas9 gene editing of TaGW7, a homolog of rice OsGW7 encoding a TONNEAU1-recruiting motif (TRM) protein, affects grain shape and weight in allohexaploid wheat. By editing the TaGW7 homoeologs in the B and D genomes, we showed that mutations in either of the two or both genomes increased the grain width and weight but reduced the grain length. The effect sizes of mutations in the TaGW7 gene homoeologs coincided with the relative levels of their expression in the B and D genomes. The effects of gene editing on grain morphology and weight traits were dosage dependent with the double-copy mutant showing larger effect than the respective single copy mutants. The TaGW7-centered gene co-expression network indicated that this gene is involved in the pathways regulating cell division and organ growth, also confirmed by the cellular co-localization of TaGW7 with α- and β-tubulin proteins, the building blocks of microtubule arrays. The analyses of exome capture data in tetraploid domesticated and wild emmer, and hexaploid wheat revealed the loss of diversity around TaGW7-associated with domestication selection, suggesting that TaGW7 is likely to play an important role in the evolution of yield component traits in wheat. Our study showed how integrating CRISPR-Cas9 system with cross-species comparison can help to uncover the function of a gene fixed in wheat for allelic variants targeted by domestication selection and select targets for engineering new gene variants for crop improvement.
Collapse
Affiliation(s)
- Wei Wang
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Qianli Pan
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Bin Tian
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Fei He
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Yueying Chen
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Guihua Bai
- USDA‐ARS Hard Winter Wheat Genetics Research UnitManhattanKSUSA
| | - Alina Akhunova
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
- Integrated Genomics FacilityKansas State UniversityManhattanKSUSA
| | - Harold N. Trick
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Eduard Akhunov
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| |
Collapse
|
94
|
Zhang S, Zhang R, Gao J, Gu T, Song G, Li W, Li D, Li Y, Li G. Highly Efficient and Heritable Targeted Mutagenesis in Wheat via the Agrobacterium
tumefaciens-Mediated CRISPR/Cas9 System. Int J Mol Sci 2019; 20:E4257. [PMID: 31480315 PMCID: PMC6747105 DOI: 10.3390/ijms20174257] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/24/2019] [Accepted: 08/28/2019] [Indexed: 01/09/2023] Open
Abstract
The CRISPR/Cas9 system has been successfully used in hexaploid wheat. Although it has been reported that the induced mutations can be passed to the next generation, gene editing and transmission patterns in later generations still need to be studied. In this study, we demonstrated that the CRISPR/Cas9 system could achieve efficient mutagenesis in five wheat genes via Agrobacterium-mediated transformation of an sgRNA targeting the D genome, an sgRNA targeting both the A and B homologues and three tri-genome guides targeting the editing of all three homologues. High mutation rates and putative homozygous or biallelic mutations were observed in the T0 plants. The targeted mutations could be stably inherited by the next generation, and the editing efficiency of each mutant line increased significantly across generations. The editing types and inheritance of targeted mutagenesis were similar, which were not related to the targeted subgenome number. The presence of Cas9/sgRNA could cause new mutations in subsequent generations, while mutated lines without Cas9/sgRNA could retain the mutation type. Additionally, off-target mutations were not found in sequences that were highly homologous to the selected sgRNA sequences. Overall, the results suggested that CRISPR/Cas9-induced gene editing via Agrobacterium-mediated transformation plays important roles in wheat genome engineering.
Collapse
Affiliation(s)
- Shujuan Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
- Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River Valley, Ministry of Agriculture, Jinan 250100, Shandong, China
- National Engineering Laboratory for Wheat and Maize, Jinan 250100, Shandong, China
| | - Rongzhi Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
- Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River Valley, Ministry of Agriculture, Jinan 250100, Shandong, China
- National Engineering Laboratory for Wheat and Maize, Jinan 250100, Shandong, China
| | - Jie Gao
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
- Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River Valley, Ministry of Agriculture, Jinan 250100, Shandong, China
- National Engineering Laboratory for Wheat and Maize, Jinan 250100, Shandong, China
| | - Tiantian Gu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
- Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River Valley, Ministry of Agriculture, Jinan 250100, Shandong, China
- National Engineering Laboratory for Wheat and Maize, Jinan 250100, Shandong, China
| | - Guoqi Song
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
- Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River Valley, Ministry of Agriculture, Jinan 250100, Shandong, China
- National Engineering Laboratory for Wheat and Maize, Jinan 250100, Shandong, China
| | - Wei Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
- Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River Valley, Ministry of Agriculture, Jinan 250100, Shandong, China
- National Engineering Laboratory for Wheat and Maize, Jinan 250100, Shandong, China
| | - Dandan Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
- Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River Valley, Ministry of Agriculture, Jinan 250100, Shandong, China
- National Engineering Laboratory for Wheat and Maize, Jinan 250100, Shandong, China
| | - Yulian Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China.
- Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River Valley, Ministry of Agriculture, Jinan 250100, Shandong, China.
- National Engineering Laboratory for Wheat and Maize, Jinan 250100, Shandong, China.
| | - Genying Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China.
- Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River Valley, Ministry of Agriculture, Jinan 250100, Shandong, China.
- National Engineering Laboratory for Wheat and Maize, Jinan 250100, Shandong, China.
| |
Collapse
|
95
|
Razzaq A, Saleem F, Kanwal M, Mustafa G, Yousaf S, Imran Arshad HM, Hameed MK, Khan MS, Joyia FA. Modern Trends in Plant Genome Editing: An Inclusive Review of the CRISPR/Cas9 Toolbox. Int J Mol Sci 2019; 20:E4045. [PMID: 31430902 PMCID: PMC6720679 DOI: 10.3390/ijms20164045] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/14/2019] [Accepted: 08/15/2019] [Indexed: 12/17/2022] Open
Abstract
Increasing agricultural productivity via modern breeding strategies is of prime interest to attain global food security. An array of biotic and abiotic stressors affect productivity as well as the quality of crop plants, and it is a primary need to develop crops with improved adaptability, high productivity, and resilience against these biotic/abiotic stressors. Conventional approaches to genetic engineering involve tedious procedures. State-of-the-art OMICS approaches reinforced with next-generation sequencing and the latest developments in genome editing tools have paved the way for targeted mutagenesis, opening new horizons for precise genome engineering. Various genome editing tools such as transcription activator-like effector nucleases (TALENs), zinc-finger nucleases (ZFNs), and meganucleases (MNs) have enabled plant scientists to manipulate desired genes in crop plants. However, these approaches are expensive and laborious involving complex procedures for successful editing. Conversely, CRISPR/Cas9 is an entrancing, easy-to-design, cost-effective, and versatile tool for precise and efficient plant genome editing. In recent years, the CRISPR/Cas9 system has emerged as a powerful tool for targeted mutagenesis, including single base substitution, multiplex gene editing, gene knockouts, and regulation of gene transcription in plants. Thus, CRISPR/Cas9-based genome editing has demonstrated great potential for crop improvement but regulation of genome-edited crops is still in its infancy. Here, we extensively reviewed the availability of CRISPR/Cas9 genome editing tools for plant biotechnologists to target desired genes and its vast applications in crop breeding research.
Collapse
Affiliation(s)
- Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan
| | - Fozia Saleem
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan
| | - Mehak Kanwal
- Nuclear Institute for Agriculture and Biology (NIAB), P.O. Box 128, Faisalabad 38000, Pakistan
| | - Ghulam Mustafa
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan
| | - Sumaira Yousaf
- Nuclear Institute for Agriculture and Biology (NIAB), P.O. Box 128, Faisalabad 38000, Pakistan
| | | | - Muhammad Khalid Hameed
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Muhammad Sarwar Khan
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan
| | - Faiz Ahmad Joyia
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan.
| |
Collapse
|
96
|
Zhang Y, Malzahn AA, Sretenovic S, Qi Y. The emerging and uncultivated potential of CRISPR technology in plant science. NATURE PLANTS 2019; 5:778-794. [PMID: 31308503 DOI: 10.1038/s41477-019-0461-5] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 05/24/2019] [Indexed: 05/18/2023]
Abstract
The application of clustered regularly interspaced short palindromic repeats (CRISPR) for genetic manipulation has revolutionized life science over the past few years. CRISPR was first discovered as an adaptive immune system in bacteria and archaea, and then engineered to generate targeted DNA breaks in living cells and organisms. During the cellular DNA repair process, various DNA changes can be introduced. The diverse and expanding CRISPR toolbox allows programmable genome editing, epigenome editing and transcriptome regulation in plants. However, challenges in plant genome editing need to be fully appreciated and solutions explored. This Review intends to provide an informative summary of the latest developments and breakthroughs of CRISPR technology, with a focus on achievements and potential utility in plant biology. Ultimately, CRISPR will not only facilitate basic research, but also accelerate plant breeding and germplasm development. The application of CRISPR to improve germplasm is particularly important in the context of global climate change as well as in the face of current agricultural, environmental and ecological challenges.
Collapse
Affiliation(s)
- Yingxiao Zhang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Aimee A Malzahn
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Simon Sretenovic
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA.
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA.
| |
Collapse
|
97
|
Cereal Root Interactions with Soilborne Pathogens—From Trait to Gene and Back. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy9040188] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Realizing the yield potential of crop plants in the presence of shifting pathogen populations, soil quality, rainfall, and other agro-environmental variables remains a challenge for growers and breeders worldwide. In this review, we discuss current approaches for combatting the soilborne phytopathogenic nematodes, Pratylenchus and Heterodera of wheat and barley, and Meloidogyne graminicola Golden and Birchfield, 1965 of rice. The necrotrophic fungal pathogens, Rhizoctonia solani Kühn 1858 AG-8 and Fusarium spp. of wheat and barley, also are discussed. These pathogens constitute major causes of yield loss in small-grain cereals of the Pacific Northwest, USA and throughout the world. Current topics include new sources of genetic resistance, molecular leads from whole genome sequencing and genome-wide patterns of hosts, nematode or fungal gene expression during root-pathogen interactions, host-induced gene silencing, and building a molecular toolbox of genes and regulatory sequences for deployment of resistance genes. In conclusion, improvement of wheat, barley, and rice will require multiple approaches.
Collapse
|