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Brant EJ, Eid A, Kannan B, Baloglu MC, Altpeter F. The extent of multiallelic, co-editing of LIGULELESS1 in highly polyploid sugarcane tunes leaf inclination angle and enables selection of the ideotype for biomass yield. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38776398 DOI: 10.1111/pbi.14380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/09/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024]
Abstract
Sugarcane (Saccharum spp. hybrid) is a prime feedstock for commercial production of biofuel and table sugar. Optimizing canopy architecture for improved light capture has great potential for elevating biomass yield. LIGULELESS1 (LG1) is involved in leaf ligule and auricle development in grasses. Here, we report CRISPR/Cas9-mediated co-mutagenesis of up to 40 copies/alleles of the putative LG1 in highly polyploid sugarcane (2n = 100-120, x = 10-12). Next generation sequencing revealed co-editing frequencies of 7.4%-100% of the LG1 reads in 16 of the 78 transgenic lines. LG1 mutations resulted in a tuneable leaf angle phenotype that became more upright as co-editing frequency increased. Three lines with loss of function frequencies of ~12%, ~53% and ~95% of lg1 were selected following a randomized greenhouse trial and grown in replicated, multi-row field plots. The co-edited LG1 mutations were stably maintained in vegetative progenies and the extent of co-editing remained constant in field tested lines L26 and L35. Next generation sequencing confirmed the absence of potential off targets. The leaf inclination angle corresponded to light transmission into the canopy and tiller number. Line L35 displaying loss of function in ~12% of the lg1 NGS reads exhibited an 18% increase in dry biomass yield supported by a 56% decrease in leaf inclination angle, a 31% increase in tiller number, and a 25% increase in internode number. The scalable co-editing of LG1 in highly polyploid sugarcane allows fine-tuning of leaf inclination angle, enabling the selection of the ideotype for biomass yield.
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Affiliation(s)
- Eleanor J Brant
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, IFAS, Gainesville, Florida, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, Florida, USA
| | - Ayman Eid
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, IFAS, Gainesville, Florida, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, Florida, USA
| | - Baskaran Kannan
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, IFAS, Gainesville, Florida, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, Florida, USA
| | - Mehmet Cengiz Baloglu
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, IFAS, Gainesville, Florida, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, Florida, USA
| | - Fredy Altpeter
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, IFAS, Gainesville, Florida, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, Florida, USA
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Biswal AK, Hernandez LRB, Castillo AIR, Debernardi JM, Dhugga KS. An efficient transformation method for genome editing of elite bread wheat cultivars. FRONTIERS IN PLANT SCIENCE 2023; 14:1135047. [PMID: 37275249 PMCID: PMC10234211 DOI: 10.3389/fpls.2023.1135047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 04/17/2023] [Indexed: 06/07/2023]
Abstract
An efficient genetic transformation protocol is necessary to edit genes for trait improvement directly in elite bread wheat cultivars. We used a protein fusion between a wheat growth-regulating factor 4 (GRF4) and its interacting factor (GIF1) to develop a reproducible genetic transformation and regeneration protocol, which we then used to successfully transform elite bread wheat cultivars Baj, Kachu, Morocco, Reedling, RL6077, and Sujata in addition to the experimental cultivar Fielder. Immature embryos were transformed with the vector using particle bombardment method. Transformation frequency increased nearly 60-fold with the GRF4-GIF1-containing vectors as compared to the control vector and ranged from ~5% in the cultivar Kachu to 13% in the cultivar RL6077. We then edited two genes that confer resistance against leaf rust and powdery mildew directly in the aforementioned elite cultivars. A wheat promoter, TaU3 or TaU6, to drive the expression of guide RNA was effective in gene editing whereas the OsU3 promoter failed to generate any edits. Editing efficiency was nearly perfect with the wheat promoters. Our protocol has made it possible to edit genes directly in elite wheat cultivars and would be useful for gene editing in other wheat varieties, which have been recalcitrant to transformation thus far.
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Affiliation(s)
- Akshaya K. Biswal
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | | | - Ana I. R. Castillo
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Juan M. Debernardi
- Plant Transformation Facility, University of California, Davis, Davis, CA, United States
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Szala K, Dmochowska-Boguta M, Bocian J, Orczyk W, Nadolska-Orczyk A. Transgenerational Paternal Inheritance of TaCKX GFMs Expression Patterns Indicate a Way to Select Wheat Lines with Better Parameters for Yield-Related Traits. Int J Mol Sci 2023; 24:ijms24098196. [PMID: 37175902 PMCID: PMC10179260 DOI: 10.3390/ijms24098196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/18/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Members of the TaCKX gene family (GFMs) encode the cytokinin oxygenase/dehydrogenase enzyme (CKX), which irreversibly degrades cytokinins in the organs of wheat plants; therefore, these genes perform a key role in the regulation of yield-related traits. The purpose of the investigation was to determine how expression patterns of these genes, together with the transcription factor-encoding gene TaNAC2-5A, and yield-related traits are inherited to apply this knowledge to speed up breeding processes. The traits were tested in 7 days after pollination (DAP) spikes and seedling roots of maternal and paternal parents and their F2 progeny. The expression levels of most of them and the yield were inherited in F2 from the paternal parent. Some pairs or groups of genes cooperated, and some showed opposite functions. Models of up- or down-regulation of TaCKX GFMs and TaNAC2-5A in low-yielding maternal plants crossed with higher-yielding paternal plants and their high-yielding F2 progeny reproduced gene expression and yield of the paternal parent. The correlation coefficients between TaCKX GFMs, TaNAC2-5A, and yield-related traits in high-yielding F2 progeny indicated which of these genes were specifically correlated with individual yield-related traits. The most common was expressed in 7 DAP spikes TaCKX2.1, which positively correlated with grain number, grain yield, spike number, and spike length, and seedling root mass. The expression levels of TaCKX1 or TaNAC2-5A in the seedling roots were negatively correlated with these traits. In contrast, the thousand grain weight (TGW) was negatively regulated by TaCKX2.2.2, TaCKX2.1, and TaCKX10 in 7 DAP spikes but positively correlated with TaCKX10 and TaNAC2-5A in seedling roots. Transmission of TaCKX GFMs and TaNAC2-5A expression patterns and yield-related traits from parents to the F2 generation indicate their paternal imprinting. These newly shown data of nonmendelian epigenetic inheritance shed new light on crossing strategies to obtain a high-yielding F2 generation.
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Affiliation(s)
- Karolina Szala
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow, 05-870 Blonie, Poland
| | - Marta Dmochowska-Boguta
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow, 05-870 Blonie, Poland
| | - Joanna Bocian
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow, 05-870 Blonie, Poland
| | - Waclaw Orczyk
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow, 05-870 Blonie, Poland
| | - Anna Nadolska-Orczyk
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow, 05-870 Blonie, Poland
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Basu U, Riaz Ahmed S, Bhat BA, Anwar Z, Ali A, Ijaz A, Gulzar A, Bibi A, Tyagi A, Nebapure SM, Goud CA, Ahanger SA, Ali S, Mushtaq M. A CRISPR way for accelerating cereal crop improvement: Progress and challenges. Front Genet 2023; 13:866976. [PMID: 36685816 PMCID: PMC9852743 DOI: 10.3389/fgene.2022.866976] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 11/21/2022] [Indexed: 01/09/2023] Open
Abstract
Humans rely heavily on cereal grains as a key source of nutrients, hence regular improvement of cereal crops is essential for ensuring food security. The current food crisis at the global level is due to the rising population and harsh climatic conditions which prompts scientists to develop smart resilient cereal crops to attain food security. Cereal crop improvement in the past generally depended on imprecise methods like random mutagenesis and conventional genetic recombination which results in high off targeting risks. In this context, we have witnessed the application of targeted mutagenesis using versatile CRISPR-Cas systems for cereal crop improvement in sustainable agriculture. Accelerated crop improvement using molecular breeding methods based on CRISPR-Cas genome editing (GE) is an unprecedented tool for plant biotechnology and agriculture. The last decade has shown the fidelity, accuracy, low levels of off-target effects, and the high efficacy of CRISPR technology to induce targeted mutagenesis for the improvement of cereal crops such as wheat, rice, maize, barley, and millets. Since the genomic databases of these cereal crops are available, several modifications using GE technologies have been performed to attain desirable results. This review provides a brief overview of GE technologies and includes an elaborate account of the mechanisms and applications of CRISPR-Cas editing systems to induce targeted mutagenesis in cereal crops for improving the desired traits. Further, we describe recent developments in CRISPR-Cas-based targeted mutagenesis through base editing and prime editing to develop resilient cereal crop plants, possibly providing new dimensions in the field of cereal crop genome editing.
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Affiliation(s)
- Umer Basu
- Division of Entomology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Syed Riaz Ahmed
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | | | - Zunaira Anwar
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Ahmad Ali
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Aqsa Ijaz
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Addafar Gulzar
- Division of Plant Pathology, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Wadura Sopore, India
| | - Amir Bibi
- Department of Plant Breeding and Genetics, Faculty of Agriculture Sciences, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Anshika Tyagi
- Department of Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Suresh M. Nebapure
- Division of Entomology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Chengeshpur Anjali Goud
- Institute of Biotechnology, Professor Jayashanker Telangana State Agriculture University, Hyderabad, India
| | - Shafat Ahmad Ahanger
- Division of Plant Pathology, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Wadura Sopore, India,*Correspondence: Shafat Ahmad Ahanger, ; Sajad Ali, ; Muntazir Mushtaq,
| | - Sajad Ali
- Department of Biotechnology, Yeungnam University, Gyeongsan, South Korea,*Correspondence: Shafat Ahmad Ahanger, ; Sajad Ali, ; Muntazir Mushtaq,
| | - Muntazir Mushtaq
- ICAR-National Bureau of Plant Genetic Resources, Division of Germplasm Evaluation, Pusa Campus, New Delhi, India,*Correspondence: Shafat Ahmad Ahanger, ; Sajad Ali, ; Muntazir Mushtaq,
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Movahedi A, Wei H, Kadkhodaei S, Sun W, Zhuge Q, Yang L, Xu C. CRISPR-mediated genome editing in poplar issued by efficient transformation. FRONTIERS IN PLANT SCIENCE 2023; 14:1159615. [PMID: 37139106 PMCID: PMC10149819 DOI: 10.3389/fpls.2023.1159615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/23/2023] [Indexed: 05/05/2023]
Abstract
Background CRISPR has been increasingly used for plant genetic improvements because of its high efficiency and precision. Recently, the authors have reported the possibility of homology-directed repair (HDR) using CRISPR/Cas9 through woody plants such as poplar. HDR often replaces nucleotides with one donor DNA template (DDT), including homologous sequences. Methods CRISPR-Cas9 was recruited, and three variables, Agrobacteria inoculator concentration, pDDT/pgRNA ratio, and homologous arm length, were designed to integrate nptII and 2XCamV 35S into the MKK2 promoter zone. Results Here, we showed that recovered poplars on kanamycin-supplemented media exhibited enhanced expression of MKK2 affected by the precise integration of 2XcamV 35S and nptII, improving biochemical and phenotypic properties. Our findings confirmed that Agrobacterium inoculator OD600 = 2.5, increased DDT numbers during cell division to 4:1 pDDT/pgRNA, and optimized homologous arms 700 bp caused efficient HDR and increased MKK2 expression. Conclusion Efficient transformations resulted from optimized variables, directly affecting the HDR efficiency through woody plants such as poplar.
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Affiliation(s)
- Ali Movahedi
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- College of Arts and Sciences, Arlington International University, Wilmington, DE, United States
| | - Hui Wei
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China
| | - Saeid Kadkhodaei
- Agricultural Biotechnology Research Institute of Iran, Isfahan Branch, Agricultural Research, Education and Extension Organization, Isfahan, Iran
| | - Weibo Sun
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Qiang Zhuge
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Liming Yang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Chen Xu
- Nanjing Key Laboratory of Quality and Safety of Agricultural Product, Nanjing Xiaozhuang University, Nanjing, China
- *Correspondence: Chen Xu,
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Zhang H, Zheng Y, Zhang G, Miao Y, Liu C, Huang L. A Bibliometric Study for Plant RNA Editing Research: Trends and Future Challenges. Mol Biotechnol 2022:10.1007/s12033-022-00641-7. [PMID: 36562872 DOI: 10.1007/s12033-022-00641-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
RNA editing is a post-transcriptional process that introduces changes in RNA sequences encoded by nuclear, mitochondrial, or plastid genomes. To understand the research progress of plant RNA editing, we comprehensively analyze the articles on plant RNA editing from 2001 to 2022 through bibliometric methods. Nucleic Acids Research, Plant Journal and Plant cell are the journals that deserve attention with their high production, total local citation scores (TLCS), and h-indexes. The USA, China, and Germany are the top three countries with highly productive publications. Ulm University, Cornell University, and Chinese Acad Sci are excellent cooperative institutions with a high level of influence in the field, and KNOOP V and TAKENAKA M are good partnership. Plant RNA editing researches concentrate on the subject categories of Biochemistry & Molecular Biology, Plant Sciences, Genetics & Heredity, etc. Plant mitochondria, genome editing and messenger-RNA may be the research hotspots in the future. The main plant RNA editing research tools are JACUSA, SPRINT, and REDO, and the main databases are REDIdb, PED, and dbRES. At present, the research streams are (1) RNA editing sites; (2) Pentapeptide repeat protein (PPR) involved in RNA editing; (3) RNA editing factors. Overall, this article summarizes the research overview of plant RNA editing until 2022 and provides theoretical implications for its possible future directions.
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Affiliation(s)
- Huihui Zhang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
- Jiangxi University of Chinese Medicine, Nanchang, 330000, Jiangxi, China
| | - Yan Zheng
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
- Jiangxi University of Chinese Medicine, Nanchang, 330000, Jiangxi, China
| | - Guoshuai Zhang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Yujing Miao
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Chang Liu
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China.
| | - Linfang Huang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China.
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Ul Haq SI, Zheng D, Feng N, Jiang X, Qiao F, He JS, Qiu QS. Progresses of CRISPR/Cas9 genome editing in forage crops. JOURNAL OF PLANT PHYSIOLOGY 2022; 279:153860. [PMID: 36371870 DOI: 10.1016/j.jplph.2022.153860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) mediated-genome editing has evolved into a powerful tool that is widely used in plant species to induce editing in the genome for analyzing gene function and crop improvement. CRISPR/Cas9 is an RNA-guided genome editing tool consisting of a Cas9 nuclease and a single-guide RNA (sgRNA). The CRISPR/Cas9 system enables more accurate and efficient genome editing in crops. In this review, we summarized the advances of the CRISPR/Cas9 technology in plant genome editing and its applications in forage crops. We described briefly about the development of CRISPR/Cas9 technology in plant genome editing. We assessed the progress of CRISPR/Cas9-mediated targeted-mutagenesis in various forage crops, including alfalfa, Medicago truncatula, Hordeum vulgare, Sorghum bicolor, Setaria italica and Panicum virgatum. The potentials and challenges of CRISPR/Cas9 in forage breeding were discussed.
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Affiliation(s)
- Syed Inzimam Ul Haq
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Dianfeng Zheng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China
| | - Naijie Feng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China
| | - Xingyu Jiang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China
| | - Feng Qiao
- Academy of Plateau Science and Sustainability, School of Life Sciences, Qinghai Normal University, Xining, Qinghai, 810016, China
| | - Jin-Sheng He
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Quan-Sheng Qiu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China; State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, Gansu, 730000, China; Academy of Plateau Science and Sustainability, School of Life Sciences, Qinghai Normal University, Xining, Qinghai, 810016, China; College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China.
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8
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Tanaka J, Minkenberg B, Poddar S, Staskawicz B, Cho MJ. Improvement of Gene Delivery and Mutation Efficiency in the CRISPR-Cas9 Wheat (Triticum aestivum L.) Genomics System via Biolistics. Genes (Basel) 2022; 13:genes13071180. [PMID: 35885963 PMCID: PMC9318839 DOI: 10.3390/genes13071180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/25/2022] [Accepted: 06/27/2022] [Indexed: 11/16/2022] Open
Abstract
Discovery of the CRISPR-Cas9 gene editing system revolutionized the field of plant genomics. Despite advantages in the ease of designing gRNA and the low cost of the CRISPR-Cas9 system, there are still hurdles to overcome in low mutation efficiencies, specifically in hexaploid wheat. In conjunction with gene delivery and transformation frequency, the mutation efficiency bottleneck has the potential to slow down advancements in genomic editing of wheat. In this study, nine bombardment parameter combinations using three gold particle sizes and three rupture disk pressures were tested to establish optimal stable transformation frequencies in wheat. Utilizing the best transformation protocol and a knockout cassette of the phytoene desaturase gene, we subjected transformed embryos to four temperature treatments and compared mutation efficiencies. The use of 0.6 μm gold particles for bombardment increased transformation frequencies across all delivery pressures. A heat treatment of 34 °C for 24 h resulted in the highest mutation efficiency with no or minimal reduction in transformation frequency. The 34 °C treatment produced two M0 mutant events with albino phenotypes, requiring biallelic mutations in all three genomes of hexaploid wheat. Utilizing optimal transformation and heat treatment parameters greatly increases mutation efficiency and can help advance research efforts in wheat genomics.
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Affiliation(s)
- Jaclyn Tanaka
- Innovative Genomics Institute, University of California, Berkeley, CA 94704, USA; (J.T.); (B.M.); (S.P.); (B.S.)
| | - Bastian Minkenberg
- Innovative Genomics Institute, University of California, Berkeley, CA 94704, USA; (J.T.); (B.M.); (S.P.); (B.S.)
| | - Snigdha Poddar
- Innovative Genomics Institute, University of California, Berkeley, CA 94704, USA; (J.T.); (B.M.); (S.P.); (B.S.)
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Brian Staskawicz
- Innovative Genomics Institute, University of California, Berkeley, CA 94704, USA; (J.T.); (B.M.); (S.P.); (B.S.)
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Myeong-Je Cho
- Innovative Genomics Institute, University of California, Berkeley, CA 94704, USA; (J.T.); (B.M.); (S.P.); (B.S.)
- Correspondence:
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Awan MJA, Pervaiz K, Rasheed A, Amin I, Saeed NA, Dhugga KS, Mansoor S. Genome edited wheat- current advances for the second green revolution. Biotechnol Adv 2022; 60:108006. [PMID: 35732256 DOI: 10.1016/j.biotechadv.2022.108006] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 05/21/2022] [Accepted: 06/15/2022] [Indexed: 11/15/2022]
Abstract
Common wheat is a major source of nutrition around the globe, but unlike maize and rice hybrids, no breakthrough has been made to enhance wheat yield since Green Revolution. With the availability of reference genome sequence of wheat and advancement of allied genomics technologies, understanding of genes involved in grain yield components and disease resistance/susceptibility has opened new avenues for crop improvement. Wheat has a huge hexaploidy genome of approximately 17 GB with 85% repetition, and it is a daunting task to induce any mutation across three homeologues that can be helpful for the enhancement of agronomic traits. The CRISPR-Cas9 system provides a promising platform for genome editing in a site-specific manner. In wheat, CRISPR-Cas9 is being used in the improvement of yield, grain quality, biofortification, resistance against diseases, and tolerance against abiotic factors. The promising outcomes of the CRISPR-based multiplexing approach circumvent the constraint of targeting merely one gene at a time. Deployment of clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) 9 endonuclease (CRISPR-Cas9) and Cas9 variant systems such as cytidine base editing, adenosine base editing, and prime editing in wheat has been used to induce point mutations more precisely. Scientists have acquired major events such as induction of male sterility, fertility restoration, and alteration of seed dormancy through Cas9 in wheat that can facilitate breeding programs for elite variety development. Furthermore, a recent discovery in tissue culturing enables scientists to significantly enhance regeneration efficiency in wheat by transforming the GRF4-GIF1 cassette. Rapid generation advancement by speed breeding technology provides the opportunity for the generation advancement of the desired plants to segregate out unwanted transgenes and allows rapid integration of gene-edited wheat into the breeding pipeline. The combination of these novel technologies addresses some of the most important limiting factors for sustainable and climate-smart wheat that should lead to the second "Green Revolution" for global food security.
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Affiliation(s)
- Muhammad Jawad Akbar Awan
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Komal Pervaiz
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Awais Rasheed
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS) & CIMMYT-China office, 12 Zhongguanccun South Street, Beijing 100081, China
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Nasir A Saeed
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Kanwarpal S Dhugga
- Corteva Agriscience, Johnston, IA, USA; International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan.
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Mattiello L, Rütgers M, Sua-Rojas MF, Tavares R, Soares JS, Begcy K, Menossi M. Molecular and Computational Strategies to Increase the Efficiency of CRISPR-Based Techniques. FRONTIERS IN PLANT SCIENCE 2022; 13:868027. [PMID: 35712599 PMCID: PMC9194676 DOI: 10.3389/fpls.2022.868027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
The prokaryote-derived Clustered Regularly Interspaced Palindromic Repeats (CRISPR)/Cas mediated gene editing tools have revolutionized our ability to precisely manipulate specific genome sequences in plants and animals. The simplicity, precision, affordability, and robustness of this technology have allowed a myriad of genomes from a diverse group of plant species to be successfully edited. Even though CRISPR/Cas, base editing, and prime editing technologies have been rapidly adopted and implemented in plants, their editing efficiency rate and specificity varies greatly. In this review, we provide a critical overview of the recent advances in CRISPR/Cas9-derived technologies and their implications on enhancing editing efficiency. We highlight the major efforts of engineering Cas9, Cas12a, Cas12b, and Cas12f proteins aiming to improve their efficiencies. We also provide a perspective on the global future of agriculturally based products using DNA-free CRISPR/Cas techniques. The improvement of CRISPR-based technologies efficiency will enable the implementation of genome editing tools in a variety of crop plants, as well as accelerate progress in basic research and molecular breeding.
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Affiliation(s)
- Lucia Mattiello
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Mark Rütgers
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Maria Fernanda Sua-Rojas
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Rafael Tavares
- Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - José Sérgio Soares
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Kevin Begcy
- Environmental Horticulture Department, University of Florida, Gainesville, FL, United States
| | - Marcelo Menossi
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Brazil
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11
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Naik BJ, Shimoga G, Kim SC, Manjulatha M, Subramanyam Reddy C, Palem RR, Kumar M, Kim SY, Lee SH. CRISPR/Cas9 and Nanotechnology Pertinence in Agricultural Crop Refinement. FRONTIERS IN PLANT SCIENCE 2022; 13:843575. [PMID: 35463432 PMCID: PMC9024397 DOI: 10.3389/fpls.2022.843575] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 02/07/2022] [Indexed: 05/08/2023]
Abstract
The CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9) method is a versatile technique that can be applied in crop refinement. Currently, the main reasons for declining agricultural yield are global warming, low rainfall, biotic and abiotic stresses, in addition to soil fertility issues caused by the use of harmful chemicals as fertilizers/additives. The declining yields can lead to inadequate supply of nutritional food as per global demand. Grains and horticultural crops including fruits, vegetables, and ornamental plants are crucial in sustaining human life. Genomic editing using CRISPR/Cas9 and nanotechnology has numerous advantages in crop development. Improving crop production using transgenic-free CRISPR/Cas9 technology and produced fertilizers, pesticides, and boosters for plants by adopting nanotechnology-based protocols can essentially overcome the universal food scarcity. This review briefly gives an overview on the potential applications of CRISPR/Cas9 and nanotechnology-based methods in developing the cultivation of major agricultural crops. In addition, the limitations and major challenges of genome editing in grains, vegetables, and fruits have been discussed in detail by emphasizing its applications in crop refinement strategy.
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Affiliation(s)
- Banavath Jayanna Naik
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Jeju, South Korea
| | - Ganesh Shimoga
- Interaction Laboratory, Future Convergence Engineering, Advanced Technology Research Center, Korea University of Technology and Education, Cheonan-si, South Korea
| | - Seong-Cheol Kim
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Jeju, South Korea
| | | | | | | | - Manu Kumar
- Department of Life Science, College of Life Science and Biotechnology, Dongguk University, Seoul, South Korea
| | - Sang-Youn Kim
- Interaction Laboratory, Future Convergence Engineering, Advanced Technology Research Center, Korea University of Technology and Education, Cheonan-si, South Korea
| | - Soo-Hong Lee
- Department of Medical Biotechnology, Dongguk University, Seoul, South Korea
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12
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Gupta P, Hirschberg J. The Genetic Components of a Natural Color Palette: A Comprehensive List of Carotenoid Pathway Mutations in Plants. FRONTIERS IN PLANT SCIENCE 2022; 12:806184. [PMID: 35069664 PMCID: PMC8770946 DOI: 10.3389/fpls.2021.806184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/08/2021] [Indexed: 05/16/2023]
Abstract
Carotenoids comprise the most widely distributed natural pigments. In plants, they play indispensable roles in photosynthesis, furnish colors to flowers and fruit and serve as precursor molecules for the synthesis of apocarotenoids, including aroma and scent, phytohormones and other signaling molecules. Dietary carotenoids are vital to human health as a source of provitamin A and antioxidants. Hence, the enormous interest in carotenoids of crop plants. Over the past three decades, the carotenoid biosynthesis pathway has been mainly deciphered due to the characterization of natural and induced mutations that impair this process. Over the year, numerous mutations have been studied in dozens of plant species. Their phenotypes have significantly expanded our understanding of the biochemical and molecular processes underlying carotenoid accumulation in crops. Several of them were employed in the breeding of crops with higher nutritional value. This compendium of all known random and targeted mutants available in the carotenoid metabolic pathway in plants provides a valuable resource for future research on carotenoid biosynthesis in plant species.
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Affiliation(s)
| | - Joseph Hirschberg
- Department of Genetics, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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Hu J, Yu M, Chang Y, Tang H, Wang W, Du L, Wang K, Yan Y, Ye X. Functional analysis of TaPDI genes on storage protein accumulation by CRISPR/Cas9 edited wheat mutants. Int J Biol Macromol 2021; 196:131-143. [PMID: 34942204 DOI: 10.1016/j.ijbiomac.2021.12.048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/24/2021] [Accepted: 12/07/2021] [Indexed: 11/05/2022]
Abstract
Wheat protein disulfide isomerase (PDI) is involved in the formation of glutenin macropolymers (GMP) and the correct folding and accumulation of storage proteins in endosperm. In present study, seven types of homozygous TaPDI gene edited mutants were obtained by CRISPR/Cas9 technology, which were confirmed by PCR-RE and sequencing. Compared with other mutants and wild type (WT), the grain length and width in mutant PDI-abd-6 which was edited for the three TaPDI homoeologous genes were reduced, and the grain middle parts were slumped. The GMP size in PDI-abd-6 was not significantly different from that in WT, whereas the accumulation of protein bodies (PBs) increased during grain development. The endosperm cells became denser in PDI-abd-6 without sheet-like structure, and the expression level of TaBiP gene was significantly decreased. Particularly, the GMP content in PDI-abd-6 is also decreased significantly. The basic bread and flour rheological parameters in the mutant were negatively changed compared with those in WT. Our results indicated that TaPDI genes affects wheat flour-processing quality by the order of TaPDI-4B, TaPDI-4D, and TaPDI-4A from high to low; the expression of either one TaPDI could be enough to maintain the GMP accumulation and processing properties of wheat dough.
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Affiliation(s)
- Jinxin Hu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, China; Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Mei Yu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Yanan Chang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, China; Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Huali Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Wanxin Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Lipu Du
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Ke Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, China.
| | - Yueming Yan
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Science, Capital Normal University, 100048 Beijing, China.
| | - Xingguo Ye
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, China.
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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.
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Hassan MM, Zhang Y, Yuan G, De K, Chen JG, Muchero W, Tuskan GA, Qi Y, Yang X. Construct design for CRISPR/Cas-based genome editing in plants. TRENDS IN PLANT SCIENCE 2021; 26:1133-1152. [PMID: 34340931 DOI: 10.1016/j.tplants.2021.06.015] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 05/06/2023]
Abstract
CRISPR construct design is a key step in the practice of genome editing, which includes identification of appropriate Cas proteins, design and selection of guide RNAs (gRNAs), and selection of regulatory elements to express gRNAs and Cas proteins. Here, we review the choices of CRISPR-based genome editors suited for different needs in plant genome editing applications. We consider the technical aspects of gRNA design and the associated computational tools. We also discuss strategies for the design of multiplex CRISPR constructs for high-throughput manipulation of complex biological processes or polygenic traits. We provide recommendations for different elements of CRISPR constructs and discuss the remaining challenges of CRISPR construct optimization in plant genome editing.
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Affiliation(s)
- Md Mahmudul Hassan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali-8602, Bangladesh
| | - Yingxiao Zhang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Kuntal De
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA.
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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16
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Molina-Risco M, Ibarra O, Faion-Molina M, Kim B, Septiningsih EM, Thomson MJ. Optimizing Agrobacterium-Mediated Transformation and CRISPR-Cas9 Gene Editing in the tropical japonica Rice Variety Presidio. Int J Mol Sci 2021; 22:ijms222010909. [PMID: 34681568 PMCID: PMC8535416 DOI: 10.3390/ijms222010909] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 09/28/2021] [Accepted: 10/04/2021] [Indexed: 01/07/2023] Open
Abstract
Bottlenecks in plant transformation and regeneration have slowed progress in applying CRISPR/Cas-based genome editing for crop improvement. Rice (Oryza sativa L.) has highly efficient temperate japonica transformation protocols, along with reasonably efficient indica protocols using immature embryos. However, rapid and efficient protocols are not available for transformation and regeneration in tropical japonica varieties, even though they represent the majority of rice production in the U.S. and South America. The current study has optimized a protocol using callus induction from mature seeds with both Agrobacterium-mediated and biolistic transformation of the high-yielding U.S. tropical japonica cultivar Presidio. Gene editing efficiency was tested by evaluating knockout mutations in the phytoene desaturase (PDS) and young seedling albino (YSA) genes, which provide a visible phenotype at the seedling stage for successful knockouts. Using the optimized protocol, transformation of 648 explants with particle bombardment and 532 explants with Agrobacterium led to a 33% regeneration efficiency. The YSA targets had ambiguous phenotypes, but 60% of regenerated plants for PDS showed an albino phenotype. Sanger sequencing of edited progeny showed a number of insertions, deletions, and substitutions at the gRNA target sites. These results pave the way for more efficient gene editing of tropical japonica rice varieties.
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Affiliation(s)
- Marco Molina-Risco
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (M.M.-R.); (O.I.); (M.F.-M.); (B.K.); (E.M.S.)
| | - Oneida Ibarra
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (M.M.-R.); (O.I.); (M.F.-M.); (B.K.); (E.M.S.)
- Avance Biosciences Inc., Houston, TX 77040, USA
| | - Mayra Faion-Molina
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (M.M.-R.); (O.I.); (M.F.-M.); (B.K.); (E.M.S.)
| | - Backki Kim
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (M.M.-R.); (O.I.); (M.F.-M.); (B.K.); (E.M.S.)
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (M.M.-R.); (O.I.); (M.F.-M.); (B.K.); (E.M.S.)
| | - Michael J. Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (M.M.-R.); (O.I.); (M.F.-M.); (B.K.); (E.M.S.)
- Correspondence:
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17
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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".
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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
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18
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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.
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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
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19
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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.
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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.
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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.
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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
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21
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Marsh JI, Hu H, Gill M, Batley J, Edwards D. Crop breeding for a changing climate: integrating phenomics and genomics with bioinformatics. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1677-1690. [PMID: 33852055 DOI: 10.1007/s00122-021-03820-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/18/2021] [Indexed: 05/05/2023]
Abstract
Safeguarding crop yields in a changing climate requires bioinformatics advances in harnessing data from vast phenomics and genomics datasets to translate research findings into climate smart crops in the field. Climate change and an additional 3 billion mouths to feed by 2050 raise serious concerns over global food security. Crop breeding and land management strategies will need to evolve to maximize the utilization of finite resources in coming years. High-throughput phenotyping and genomics technologies are providing researchers with the information required to guide and inform the breeding of climate smart crops adapted to the environment. Bioinformatics has a fundamental role to play in integrating and exploiting this fast accumulating wealth of data, through association studies to detect genomic targets underlying key adaptive climate-resilient traits. These data provide tools for breeders to tailor crops to their environment and can be introduced using advanced selection or genome editing methods. To effectively translate research into the field, genomic and phenomic information will need to be integrated into comprehensive clade-specific databases and platforms alongside accessible tools that can be used by breeders to inform the selection of climate adaptive traits. Here we discuss the role of bioinformatics in extracting, analysing, integrating and managing genomic and phenomic data to improve climate resilience in crops, including current, emerging and potential approaches, applications and bottlenecks in the research and breeding pipeline.
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Affiliation(s)
- Jacob I Marsh
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, 6009, Australia
| | - Haifei Hu
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, 6009, Australia
| | - Mitchell Gill
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, 6009, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, 6009, Australia.
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Eid A, Mohan C, Sanchez S, Wang D, Altpeter F. Multiallelic, Targeted Mutagenesis of Magnesium Chelatase With CRISPR/Cas9 Provides a Rapidly Scorable Phenotype in Highly Polyploid Sugarcane. Front Genome Ed 2021; 3:654996. [PMID: 34713257 PMCID: PMC8525377 DOI: 10.3389/fgeed.2021.654996] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/15/2021] [Indexed: 12/12/2022] Open
Abstract
Genome editing with sequence-specific nucleases, such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9), is revolutionizing crop improvement. Developing efficient genome-editing protocols for highly polyploid crops, including sugarcane (x = 10-13), remains challenging due to the high level of genetic redundancy in these plants. Here, we report the efficient multiallelic editing of magnesium chelatase subunit I (MgCh) in sugarcane. Magnesium chelatase is a key enzyme for chlorophyll biosynthesis. CRISPR/Cas9-mediated targeted co-mutagenesis of 49 copies/alleles of magnesium chelatase was confirmed via Sanger sequencing of cloned PCR amplicons. This resulted in severely reduced chlorophyll contents, which was scorable at the time of plant regeneration in the tissue culture. Heat treatment following the delivery of genome editing reagents elevated the editing frequency 2-fold and drastically promoted co-editing of multiple alleles, which proved necessary to create a phenotype that was visibly distinguishable from the wild type. Despite their yellow leaf color, the edited plants were established well in the soil and did not show noticeable growth retardation. This approach will facilitate the establishment of genome editing protocols for recalcitrant crops and support further optimization, including the evaluation of alternative RNA-guided nucleases to overcome the limitations of the protospacer adjacent motif (PAM) site or to develop novel delivery strategies for genome editing reagents.
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Affiliation(s)
- Ayman Eid
- Agronomy Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, United States
| | - Chakravarthi Mohan
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, United States
| | - Sara Sanchez
- Agronomy Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, United States
| | - Duoduo Wang
- Agronomy Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, United States
| | - Fredy Altpeter
- Agronomy Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, United States
- Genetics Institute, University of Florida, Gainesville, FL, United States
- Plant Molecular and Cellular Biology Program, Institute of Food and Agricultural Sciences, Gainesville, FL, United States
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23
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Calderini DF, Castillo FM, Arenas‐M A, Molero G, Reynolds MP, Craze M, Bowden S, Milner MJ, Wallington EJ, Dowle A, Gomez LD, McQueen‐Mason SJ. Overcoming the trade-off between grain weight and number in wheat by the ectopic expression of expansin in developing seeds leads to increased yield potential. THE NEW PHYTOLOGIST 2021; 230:629-640. [PMID: 33124693 PMCID: PMC8048851 DOI: 10.1111/nph.17048] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/21/2020] [Indexed: 05/19/2023]
Abstract
Wheat is the most widely grown crop globally, providing 20% of all human calories and protein. Achieving step changes in genetic yield potential is crucial to ensure food security, but efforts are thwarted by an apparent trade-off between grain size and number. Expansins are proteins that play important roles in plant growth by enhancing stress relaxation in the cell wall, which constrains cell expansion. Here, we describe how targeted overexpression of an α-expansin in early developing wheat seeds leads to a significant increase in grain size without a negative effect on grain number, resulting in a yield boost under field conditions. The best-performing transgenic line yielded 12.3% higher average grain weight than the control, and this translated to an increase in grain yield of 11.3% in field experiments using an agronomically appropriate plant density. This targeted transgenic approach provides an opportunity to overcome a common bottleneck to yield improvement across many crops.
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Affiliation(s)
- Daniel F. Calderini
- Institute of Plant Production and ProtectionUniversidad Austral de ChileCampus Isla TejaValdivia5090000Chile
| | - Francisca M. Castillo
- Institute of Plant Production and ProtectionUniversidad Austral de ChileCampus Isla TejaValdivia5090000Chile
- Institute of Biochemistry and MicrobiologyFaculty of SciencesUniversidad Austral de ChileValdivia5090000Chile
| | - Anita Arenas‐M
- Institute of Plant Production and ProtectionUniversidad Austral de ChileCampus Isla TejaValdivia5090000Chile
- Institute of Biochemistry and MicrobiologyFaculty of SciencesUniversidad Austral de ChileValdivia5090000Chile
| | - Gemma Molero
- International Maize and Wheat Improvement Center (CIMMYT)El BatánTexcocoCP 56237Mexico
| | - Matthew P. Reynolds
- International Maize and Wheat Improvement Center (CIMMYT)El BatánTexcocoCP 56237Mexico
| | | | | | | | | | - Adam Dowle
- CNAPBiology DepartmentUniversity of YorkWentworth Way, HeslingtonYorkYO10 5YWUK
| | - Leonardo D. Gomez
- CNAPBiology DepartmentUniversity of YorkWentworth Way, HeslingtonYorkYO10 5YWUK
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Numan M, Khan AL, Asaf S, Salehin M, Beyene G, Tadele Z, Ligaba-Osena A. From Traditional Breeding to Genome Editing for Boosting Productivity of the Ancient Grain Tef [ Eragrostis tef (Zucc.) Trotter]. PLANTS (BASEL, SWITZERLAND) 2021; 10:628. [PMID: 33806233 PMCID: PMC8066236 DOI: 10.3390/plants10040628] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 02/07/2023]
Abstract
Tef (Eragrostis tef (Zucc.) Trotter) is a staple food crop for 70% of the Ethiopian population and is currently cultivated in several countries for grain and forage production. It is one of the most nutritious grains, and is also more resilient to marginal soil and climate conditions than major cereals such as maize, wheat and rice. However, tef is an extremely low-yielding crop, mainly due to lodging, which is when stalks fall on the ground irreversibly, and prolonged drought during the growing season. Climate change is triggering several biotic and abiotic stresses which are expected to cause severe food shortages in the foreseeable future. This has necessitated an alternative and robust approach in order to improve resilience to diverse types of stresses and increase crop yields. Traditional breeding has been extensively implemented to develop crop varieties with traits of interest, although the technique has several limitations. Currently, genome editing technologies are receiving increased interest among plant biologists as a means of improving key agronomic traits. In this review, the potential application of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (CRISPR-Cas) technology in improving stress resilience in tef is discussed. Several putative abiotic stress-resilient genes of the related monocot plant species have been discussed and proposed as target genes for editing in tef through the CRISPR-Cas system. This is expected to improve stress resilience and boost productivity, thereby ensuring food and nutrition security in the region where it is needed the most.
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Affiliation(s)
- Muhammad Numan
- Laboratory of Molecular Biology and Biotechnology, Department of Biology, University of North Carolina at Greensboro, Greensboro, NC 27412, USA; (M.N.); (M.S.)
| | - Abdul Latif Khan
- Natural and Medical Sciences Research Center, Biotechnology and OMICs Laboratory, University of Nizwa, Nizwa 616, Oman; (A.L.K.); (S.A.)
| | - Sajjad Asaf
- Natural and Medical Sciences Research Center, Biotechnology and OMICs Laboratory, University of Nizwa, Nizwa 616, Oman; (A.L.K.); (S.A.)
| | - Mohammad Salehin
- Laboratory of Molecular Biology and Biotechnology, Department of Biology, University of North Carolina at Greensboro, Greensboro, NC 27412, USA; (M.N.); (M.S.)
| | - Getu Beyene
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA;
| | - Zerihun Tadele
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, CH-3013 Bern, Switzerland;
| | - Ayalew Ligaba-Osena
- Laboratory of Molecular Biology and Biotechnology, Department of Biology, University of North Carolina at Greensboro, Greensboro, NC 27412, USA; (M.N.); (M.S.)
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25
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Zhang L, Wang Y, Li T, Qiu H, Xia Z, Dong Y. Target-specific mutations efficiency at multiple loci of CRISPR/Cas9 system using one sgRNA in soybean. Transgenic Res 2021; 30:51-62. [PMID: 33387102 DOI: 10.1007/s11248-020-00228-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 12/04/2020] [Indexed: 12/24/2022]
Abstract
Soybean has a palaeopolyploid genome with nearly 75% of the genes present in multiple copies. Although the CRISPR/Cas9 system has been employed in soybean to generate site-directed mutagenesis, a systematical assessment of mutation efficiency of the CRISPR/Cas9 system for the multiple-copy genes is still urgently needed. Here, we successfully optimize one sgRNA CRISPR/Cas9 system in soybean by testing the efficiency, pattern, specificity of the mutations at multiple loci of GmFAD2 and GmALS. The results showed that simultaneous site-directed mutagenesis of two homoeologous loci by one sgRNA, the mutation frequency in the T0 generation were 64.71% for GmPDS, 60.0% for GmFAD2 and 42.86% for GmALS, respectively. The chimeric and heterozygous mutations were dominant types. Moreover, association of phenotypes with mutation pattern at target loci of GmPDS11 and GmPDS18 could help us further demonstrate that the CRISPR/Cas9 system can efficiently generate target specific mutations at multiple loci using one sgRNA in soybean, albeit with a relatively low transformation efficiency.
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Affiliation(s)
- Ling Zhang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, Jilin, China
| | - Yingzhe Wang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, Jilin, China
| | - Tong Li
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, Jilin, China
| | - Hongmei Qiu
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, Jilin, China
| | - Zhengjun Xia
- Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Yingshan Dong
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, Jilin, China.
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26
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Eid A, Mohan C, Sanchez S, Wang D, Altpeter F. Multiallelic, Targeted Mutagenesis of Magnesium Chelatase With CRISPR/Cas9 Provides a Rapidly Scorable Phenotype in Highly Polyploid Sugarcane. Front Genome Ed 2021. [PMID: 34713257 DOI: 10.3389/fgeed.2021.65499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023] Open
Abstract
Genome editing with sequence-specific nucleases, such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9), is revolutionizing crop improvement. Developing efficient genome-editing protocols for highly polyploid crops, including sugarcane (x = 10-13), remains challenging due to the high level of genetic redundancy in these plants. Here, we report the efficient multiallelic editing of magnesium chelatase subunit I (MgCh) in sugarcane. Magnesium chelatase is a key enzyme for chlorophyll biosynthesis. CRISPR/Cas9-mediated targeted co-mutagenesis of 49 copies/alleles of magnesium chelatase was confirmed via Sanger sequencing of cloned PCR amplicons. This resulted in severely reduced chlorophyll contents, which was scorable at the time of plant regeneration in the tissue culture. Heat treatment following the delivery of genome editing reagents elevated the editing frequency 2-fold and drastically promoted co-editing of multiple alleles, which proved necessary to create a phenotype that was visibly distinguishable from the wild type. Despite their yellow leaf color, the edited plants were established well in the soil and did not show noticeable growth retardation. This approach will facilitate the establishment of genome editing protocols for recalcitrant crops and support further optimization, including the evaluation of alternative RNA-guided nucleases to overcome the limitations of the protospacer adjacent motif (PAM) site or to develop novel delivery strategies for genome editing reagents.
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Affiliation(s)
- Ayman Eid
- Agronomy Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, United States
| | - Chakravarthi Mohan
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, United States
| | - Sara Sanchez
- Agronomy Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, United States
| | - Duoduo Wang
- Agronomy Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, United States
| | - Fredy Altpeter
- Agronomy Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, United States
- Genetics Institute, University of Florida, Gainesville, FL, United States
- Plant Molecular and Cellular Biology Program, Institute of Food and Agricultural Sciences, Gainesville, FL, United States
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Křenek P, Chubar E, Vadovič P, Ohnoutková L, Vlčko T, Bergougnoux V, Cápal P, Ovečka M, Šamaj J. CRISPR/Cas9-Induced Loss-of-Function Mutation in the Barley Mitogen-Activated Protein Kinase 6 Gene Causes Abnormal Embryo Development Leading to Severely Reduced Grain Germination and Seedling Shootless Phenotype. FRONTIERS IN PLANT SCIENCE 2021; 12:670302. [PMID: 34394137 PMCID: PMC8361755 DOI: 10.3389/fpls.2021.670302] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 06/07/2021] [Indexed: 05/12/2023]
Abstract
The diverse roles of mitogen-activated protein kinases (MAPKs, MPKs) in plant development could be efficiently revealed by reverse genetic studies. In Arabidopsis, mpk6 knockout mutants complete the life cycle; however, ~40% of their embryos show defects in the development leading to abnormal phenotypes of seeds and seedlings' roots. Contrary to the Arabidopsis MPK6, the rice MPK6 (OsMPK6) is an essential gene as transfer DNA (T-DNA) insertion and CRISPR/Cas9 induced loss-of-function mutations in the OsMPK6 cause early embryo arrest. In this study, we successfully developed a viable transgenic barley line with the CRISPR/Cas9-induced heterozygous single base pair cytosine-guanine (CG) deletion [wild type (WT)/-1C] in the third exon of the HvMPK6 gene, a barley ortholog of the Arabidopsis and rice MPK6. There were no obvious macroscopic phenotype differences between the WT/-1C plants and WT plants. All the grains collected from the WT/-1C plants were of similar size and appearance. However, seedling emergence percentage (SEP) from these grains was substantially decreased in the soil in the T2 and T3 generation. The mutation analysis of the 248 emerged T2 and T3 generation plants showed that none of them was a biallelic mutant in the HvMPK6 gene, suggesting lethality of the -1C/-1C homozygous knockout mutation. In the soil, the majority of the -1C/-1C grains did not germinate and the minority of them developed into abnormal seedlings with a shootless phenotype and a reduced root system. Some of the -1C/-1C seedlings also developed one or more small chlorotic leaf blade-like structure/structures. The -1C/-1C grains contained the late-stage developed abnormal embryos with the morphologically obvious scutellum and root part of the embryonic axis but with the missing or substantially reduced shoot part of the embryonic axis. The observed embryonic abnormalities correlated well with the shootless phenotype of the seedlings and suggested that the later-stage defect is predetermined already during the embryo development. In conclusion, our results indicate that barley MPK6 is essential for the embryologically predetermined shoot formation, but not for the most aspects of the embryo and early seedling development.
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Affiliation(s)
- Pavel Křenek
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
- *Correspondence: Pavel Křenek
| | - Elizaveta Chubar
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | - Pavol Vadovič
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | - Ludmila Ohnoutková
- Laboratory of Growth Regulators, Faculty of Science, Institute of Experimental Botany of the Czech Academy of Sciences, Palacký University Olomouc, Olomouc, Czechia
| | - Tomáš Vlčko
- Laboratory of Growth Regulators, Faculty of Science, Institute of Experimental Botany of the Czech Academy of Sciences, Palacký University Olomouc, Olomouc, Czechia
| | - Véronique Bergougnoux
- Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czechia
| | - Petr Cápal
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Miroslav Ovečka
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | - Jozef Šamaj
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
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28
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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.
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29
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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.
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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.
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Henderson SW, Henderson ST, Goetz M, Koltunow AMG. Efficient CRISPR/Cas9-Mediated Knockout of an Endogenous PHYTOENE DESATURASE Gene in T1 Progeny of Apomictic Hieracium Enables New Strategies for Apomixis Gene Identification. Genes (Basel) 2020; 11:E1064. [PMID: 32927657 PMCID: PMC7563859 DOI: 10.3390/genes11091064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/06/2020] [Accepted: 09/08/2020] [Indexed: 12/11/2022] Open
Abstract
Most Hieracium subgenus Pilosella species are self-incompatible. Some undergo facultative apomixis where most seeds form asexually with a maternal genotype. Most embryo sacs develop by mitosis, without meiosis and seeds form without fertilization. Apomixis is controlled by dominant loci where recombination is suppressed. Loci deletion by γ-irradiation results in reversion to sexual reproduction. Targeted mutagenesis of genes at identified loci would facilitate causal gene identification. In this study, the efficacy of CRISPR/Cas9 editing was examined in apomictic Hieracium by targeting mutations in the endogenous PHYTOENE DESATURASE (PDS) gene using Agrobacterium-mediated leaf disk transformation. In three experiments, the expected albino dwarf-lethal phenotype, characteristic of PDS knockout, was evident in 11% of T0 plants, 31.4% were sectorial albino chimeras, and the remainder were green. The chimeric plants flowered. Germinated T1 seeds derived from apomictic reproduction in two chimeric plants were phenotyped and sequenced to identify PDS gene edits. Up to 86% of seeds produced albino seedlings with complete PDS knockout. This was attributed to continuing Cas9-mediated editing in chimeric plants during apomictic seed formation preventing Cas9 segregation from the PDS target. This successful demonstration of efficient CRISPR/Cas9 gene editing in apomictic Hieracium, enabled development of the discussed strategies for future identification of causal apomixis genes.
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Affiliation(s)
- Sam W. Henderson
- Correspondence: (S.W.H.); (A.M.G.K.); Tel.: +61-407-323-260 (A.M.G.K.)
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31
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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.
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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.
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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
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33
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Camacho MP. What's all the fuss about? The inheritance of acquired traits is compatible with the Central Dogma. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2020; 42:32. [PMID: 32691291 DOI: 10.1007/s40656-020-00329-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 07/09/2020] [Indexed: 06/11/2023]
Abstract
The Central Dogma of molecular biology, which holds that DNA makes protein and not the other way around, is as influential as it is controversial. Some believe the Dogma has outlived its usefulness, either because it fails to fully capture the ins-and-outs of protein synthesis (Griffiths and Stotz in Genetics and philosophy Cambridge introductions to philosophy and biology, Cambridge University Press, Cambridge, 2013; Stotz in Hist Philos Life Sci 28(4):533-548, 2006), because it turns on a confused notion of information (Sarkar in Molecular models of life, MIT Press, Cambridge, 2004), or because it problematically assumes the unidirectional flow of information from DNA to protein (Gottlieb, in: Oyama, Griffiths, Gray (eds), Cycles of contingency: developmental systems and evolution, MIT Press, Cambridge, 2001). This paper evaluates an underexplored defense of the Dogma, which relies on the assumption that the Dogma and the Inheritance of Acquired Traits, a principle which dates as far back as Jean Baptiste-Lamarck, are incompatible principles (Smith in The theory of evolution, Cambridge University Press, Cambridge, 1993; Judson in The eighth day of creation, Jonathan Cape, London, 1979; Dawkins in The extended phenotype, Oxford University Press, Oxford, 1970; Cobb in PLoS Biol 15(9):e2003243, 2017. https://doi.org/10.1371/journal.pbio.2003243 ; Wilkins in BioEssays 24(10):960-973, 2002. https://doi.org/10.1002/bies.10167 ; Graur The fallacious commingling of two unrelated hypotheses: 'the central dogma' and 'dna makes rna makes protein'. Judge Starling., 2018. http://judgestarling.tumblr.com/post/177554581856/the-fallacious-commingling-of-two-unrelated ). By appealing to empirical evidence in molecular science, I argue that this apparent incompatibility is indeed merely apparent. I conclude by briefly demonstrating how these considerations bear on the topic of conceptual pluralism in the philosophy of science (Stencel and Proszewska in Found Sci 23(4):603-620, 2018. https://doi.org/10.1007/s10699-017-9543-x ; Lu and Bourrat in Br J Philos Sci 69(3):775-800, 2018. https://doi.org/10.1093/bjps/axx019 ).
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Affiliation(s)
- M Polo Camacho
- University of Kansas, 1445 Jayhawk Blvd., Wescoe Hall, Room 3108, Lawrence, KS, 66045-7590, USA.
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34
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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.
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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.
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35
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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.
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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.
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36
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Adamski NM, Borrill P, Brinton J, Harrington SA, Marchal C, Bentley AR, Bovill WD, Cattivelli L, Cockram J, Contreras-Moreira B, Ford B, Ghosh S, Harwood W, Hassani-Pak K, Hayta S, Hickey LT, Kanyuka K, King J, Maccaferrri M, Naamati G, Pozniak CJ, Ramirez-Gonzalez RH, Sansaloni C, Trevaskis B, Wingen LU, Wulff BBH, Uauy C. A roadmap for gene functional characterisation in crops with large genomes: Lessons from polyploid wheat. eLife 2020; 9:e55646. [PMID: 32208137 PMCID: PMC7093151 DOI: 10.7554/elife.55646] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 03/12/2020] [Indexed: 02/04/2023] Open
Abstract
Understanding the function of genes within staple crops will accelerate crop improvement by allowing targeted breeding approaches. Despite their importance, a lack of genomic information and resources has hindered the functional characterisation of genes in major crops. The recent release of high-quality reference sequences for these crops underpins a suite of genetic and genomic resources that support basic research and breeding. For wheat, these include gene model annotations, expression atlases and gene networks that provide information about putative function. Sequenced mutant populations, improved transformation protocols and structured natural populations provide rapid methods to study gene function directly. We highlight a case study exemplifying how to integrate these resources. This review provides a helpful guide for plant scientists, especially those expanding into crop research, to capitalise on the discoveries made in Arabidopsis and other plants. This will accelerate the improvement of crops of vital importance for food and nutrition security.
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Affiliation(s)
| | - Philippa Borrill
- School of Biosciences, University of BirminghamBirminghamUnited Kingdom
| | - Jemima Brinton
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | | | | | | | - William D Bovill
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food (CSIRO)CanberraAustralia
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and BioinformaticsFiorenzuola d'ArdaItaly
| | | | - Bruno Contreras-Moreira
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Brett Ford
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food (CSIRO)CanberraAustralia
| | - Sreya Ghosh
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Wendy Harwood
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | | | - Sadiye Hayta
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of QueenslandSt LuciaAustralia
| | | | - Julie King
- Division of Plant and Crop Sciences, The University of Nottingham, Sutton Bonington CampusLoughboroughUnited Kingdom
| | - Marco Maccaferrri
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna (University of Bologna)BolognaItaly
| | - Guy Naamati
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Curtis J Pozniak
- Crop Development Centre, University of SaskatchewanSaskatoonCanada
| | | | | | - Ben Trevaskis
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food (CSIRO)CanberraAustralia
| | - Luzie U Wingen
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Brande BH Wulff
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Cristobal Uauy
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
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37
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Milner MJ, Craze M, Bowden S, Bates R, Wallington EJ, Keeling A. Identification of genes involved in male sterility in wheat ( Triticum aestivum L.) which could be used in a genic hybrid breeding system. PLANT DIRECT 2020; 4:e00201. [PMID: 32181421 PMCID: PMC7063588 DOI: 10.1002/pld3.201] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/20/2019] [Accepted: 01/13/2020] [Indexed: 05/12/2023]
Abstract
Wheat is grown on more land than any other crop in the world. Current estimates suggest that yields will have to increase sixty percent by 2050 to meet the demand of an ever-increasing human population; however, recent wheat yield gains have lagged behind other major crops such as rice and maize. One of the reasons suggested for the lag in yield potential is the lack of a robust hybrid system to harness the potential yield gains associated with heterosis, also known as hybrid vigor. Here, we set out to identify candidate genes for a genic hybrid system in wheat and characterize their function in wheat using RNASeq on stamens and carpels undergoing meiosis. Twelve genes were identified as potentially playing a role in pollen viability. CalS5- and RPG1-like genes were identified as pre- and post-meiotic genes for further characterization and to determine their role in pollen viability. It appears that all three homoeologues of both CalS5 and RPG1 are functional in wheat as all three homoeologues need to be knocked out in order to cause male sterility. However, one functional homoeologue is sufficient to maintain male fertility in wheat.
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Affiliation(s)
| | | | | | - Ruth Bates
- The John Bingham LaboratoryNIABCambridgeUK
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38
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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.
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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
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Yue JJ, Hong CY, Wei P, Tsai YC, Lin CS. How to start your monocot CRISPR/Cas project: plasmid design, efficiency detection, and offspring analysis. RICE (NEW YORK, N.Y.) 2020; 13:9. [PMID: 32016561 PMCID: PMC6997315 DOI: 10.1186/s12284-019-0354-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/02/2019] [Indexed: 05/28/2023]
Abstract
The breakthrough CRISPR (clustered regularly interspaced short palindromic repeat)/Cas9-mediated genome-editing technology has led to great progress in monocot research; however, several factors need to be considered for the efficient implementation of this technology. To generate genome-edited crops, single guide (sg)RNA and Cas9 DNA are delivered into plant cells and expressed, and the predicted position is targeted. Analyses of successful targeted mutations have revealed that the expression levels, expression timing, and variants of both sgRNA and Cas9 need to be sophisticatedly regulated; therefore, the promoters of these genes and the target site positions are the key factors for genome-editing efficiency. Currently, various vectors and online tools are available to aid sgRNA design. Furthermore, to reduce the sequence limitation of the protospacer adjacent motif (PAM) and for other purposes, many Cas protein variants and base editors can be used in plants. Before the stable transformation of a plant, the evaluation of vectors and target sites is therefore very important. Moreover, the delivery of Cas9-sgRNA ribonucleoproteins (RNPs) is one strategy that can be used to prevent transgene issues with the expression of sgRNA and Cas proteins. RNPs can be used to efficiently generate transgene-free genome-edited crops that can reduce transgene issues related to the generation of genetically modified organisms. In this review, we introduce new techniques for genome editing and identifying marker-free genome-edited mutants in monocot crops. Four topics are covered: the design and construction of plasmids for genome editing in monocots; alternatives to SpCas9; protoplasts and CRISPR; and screening for marker-free CRISPR/Cas9-induced mutants. We have aimed to encompass a full spectrum of information for genome editing in monocot crops.
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Affiliation(s)
- Jin-Jun Yue
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Chwan-Yang Hong
- Department of Agricultural Chemistry, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
| | - Pengcheng Wei
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yu-Chang Tsai
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Choun-Sea Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
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40
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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.
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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
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41
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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
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Nemacheck JA, Schemerhorn BJ, Scofield SR, Subramanyam S. Phenotypic and molecular characterization of Hessian fly resistance in diploid wheat, Aegilops tauschii. BMC PLANT BIOLOGY 2019; 19:439. [PMID: 31640550 PMCID: PMC6805508 DOI: 10.1186/s12870-019-2058-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/27/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND The Hessian fly (Mayetiola destructor), belonging to the gall midge family (Cecidomyiidae), is a devastating pest of wheat (Triticum aestivum) causing significant yield losses. Despite identification and characterization of numerous Hessian fly-responsive genes and associated biological pathways involved in wheat defense against this dipteran pest, their functional validation has been challenging. This is largely attributed to the large genome, polyploidy, repetitive DNA, and limited genetic resources in hexaploid wheat. The diploid progenitor Aegilops tauschii, D-genome donor of modern-day hexaploid wheat, offers an ideal surrogate eliminating the need to target all three homeologous chromosomes (A, B and D) individually, and thereby making the functional validation of candidate Hessian fly-responsive genes plausible. Furthermore, the well-annotated sequence of Ae. tauschii genome and availability of genetic resources amenable to manipulations makes the functional assays less tedious and time-consuming. However, prior to utilization of this diploid genome for downstream studies, it is imperative to characterize its physical and molecular responses to Hessian fly. RESULTS In this study we screened five Ae. tauschii accessions for their response to the Hessian fly biotypes L and vH13. Two lines were identified that exhibited a homozygous resistance response to feeding by both Hessian fly biotypes. Studies using physical measurements and neutral red staining showed that the resistant Ae. tauschii accessions resembled hexaploid wheat in their phenotypic responses to Hessian fly, that included similarities in larval developmental stages, leaf and plant growth, and cell wall permeability. Furthermore, molecular responses, characterized by gene expression profiling using quantitative real-time PCR, in select resistant Ae. tauschii lines also revealed similarities with resistant hexaploid wheat. CONCLUSIONS Phenotypic and molecular characterization of Ae. tauschii to Hessian fly infestation revealed resistant accessions that shared similarities to hexaploid wheat. Resembling the resistant hexaploid wheat, the Ae. tauschii accessions mount an early defense strategy involving defense proteins including lectins, secondary metabolites and reactive oxygen species (ROS) radicals. Our results reveal the suitability of the diploid progenitor for use as an ideal tool for functional genomics research in deciphering the wheat-Hessian fly molecular interactions.
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Affiliation(s)
- Jill A Nemacheck
- USDA-ARS Crop Production and Pest Control Research Unit, West Lafayette, IN, 47907, USA
- Department of Entomology, Purdue University, West Lafayette, IN, 47907, USA
| | - Brandon J Schemerhorn
- USDA-ARS Crop Production and Pest Control Research Unit, West Lafayette, IN, 47907, USA
- Department of Entomology, Purdue University, West Lafayette, IN, 47907, USA
| | - Steven R Scofield
- USDA-ARS Crop Production and Pest Control Research Unit, West Lafayette, IN, 47907, USA
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Subhashree Subramanyam
- USDA-ARS Crop Production and Pest Control Research Unit, West Lafayette, IN, 47907, USA.
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA.
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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.
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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.
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Jouanin A, Schaart JG, Boyd LA, Cockram J, Leigh FJ, Bates R, Wallington EJ, Visser RGF, Smulders MJM. Outlook for coeliac disease patients: towards bread wheat with hypoimmunogenic gluten by gene editing of α- and γ-gliadin gene families. BMC PLANT BIOLOGY 2019; 19:333. [PMID: 31370789 PMCID: PMC6670228 DOI: 10.1186/s12870-019-1889-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 06/17/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Wheat grains contain gluten proteins, which harbour immunogenic epitopes that trigger Coeliac disease in 1-2% of the human population. Wheat varieties or accessions containing only safe gluten have not been identified and conventional breeding alone struggles to achieve such a goal, as the epitopes occur in gluten proteins encoded by five multigene families, these genes are partly located in tandem arrays, and bread wheat is allohexaploid. Gluten immunogenicity can be reduced by modification or deletion of epitopes. Mutagenesis technologies, including CRISPR/Cas9, provide a route to obtain bread wheat containing gluten proteins with fewer immunogenic epitopes. RESULTS In this study, we analysed the genetic diversity of over 600 α- and γ-gliadin gene sequences to design six sgRNA sequences on relatively conserved domains that we identified near coeliac disease epitopes. They were combined in four CRISPR/Cas9 constructs to target the α- or γ-gliadins, or both simultaneously, in the hexaploid bread wheat cultivar Fielder. We compared the results with those obtained with random mutagenesis in cultivar Paragon by γ-irradiation. For this, Acid-PAGE was used to identify T1 grains with altered gliadin protein profiles compared to the wild-type endosperm. We first optimised the interpretation of Acid-PAGE gels using Chinese Spring deletion lines. We then analysed the changes generated in 360 Paragon γ-irradiated lines and in 117 Fielder CRISPR/Cas9 lines. Similar gliadin profile alterations, with missing protein bands, could be observed in grains produced by both methods. CONCLUSIONS The results demonstrate the feasibility and efficacy of using CRISPR/Cas9 to simultaneously edit multiple genes in the large α- and γ-gliadin gene families in polyploid bread wheat. Additional methods, generating genomics and proteomics data, will be necessary to determine the exact nature of the mutations generated with both methods.
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Affiliation(s)
- Aurélie Jouanin
- Wageningen University and Research, Plant Breeding, Wageningen, The Netherlands
- The John Bingham Laboratory, NIAB, Huntingdon Road, Cambridge, UK
| | - Jan G. Schaart
- Wageningen University and Research, Plant Breeding, Wageningen, The Netherlands
| | - Lesley A. Boyd
- The John Bingham Laboratory, NIAB, Huntingdon Road, Cambridge, UK
| | - James Cockram
- The John Bingham Laboratory, NIAB, Huntingdon Road, Cambridge, UK
| | - Fiona J. Leigh
- The John Bingham Laboratory, NIAB, Huntingdon Road, Cambridge, UK
| | - Ruth Bates
- The John Bingham Laboratory, NIAB, Huntingdon Road, Cambridge, UK
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Hajiahmadi Z, Movahedi A, Wei H, Li D, Orooji Y, Ruan H, Zhuge Q. Strategies to Increase On-Target and Reduce Off-Target Effects of the CRISPR/Cas9 System in Plants. Int J Mol Sci 2019; 20:E3719. [PMID: 31366028 PMCID: PMC6696359 DOI: 10.3390/ijms20153719] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/21/2019] [Accepted: 07/27/2019] [Indexed: 12/20/2022] Open
Abstract
The CRISPR/Cas9 system (clustered regularly interspaced short palindromic repeat-associated protein 9) is a powerful genome-editing tool in animals, plants, and humans. This system has some advantages, such as a high on-target mutation rate (targeting efficiency), less cost, simplicity, and high-efficiency multiplex loci editing, over conventional genome editing tools, including meganucleases, transcription activator-like effector nucleases (TALENs), and zinc finger nucleases (ZFNs). One of the crucial shortcomings of this system is unwanted mutations at off-target sites. We summarize and discuss different approaches, such as dCas9 and Cas9 paired nickase, to decrease the off-target effects in plants. According to studies, the most effective method to reduce unintended mutations is the use of ligand-dependent ribozymes called aptazymes. The single guide RNA (sgRNA)/ligand-dependent aptazyme strategy has helped researchers avoid unwanted mutations in human cells and can be used in plants as an alternative method to dramatically decrease the frequency of off-target mutations. We hope our concept provides a new, simple, and fast gene transformation and genome-editing approach, with advantages including reduced time and energy consumption, the avoidance of unwanted mutations, increased frequency of on-target changes, and no need for external forces or expensive equipment.
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Affiliation(s)
- Zahra Hajiahmadi
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
- Department of Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht 4199613776, Iran
| | - Ali Movahedi
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China.
| | - Hui Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Dawei Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Yasin Orooji
- College of Materials Science and Engineering, Nanjing Forestry University, No. 159, Longpan Road, Nanjing 210037, China
| | - Honghua Ruan
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Qiang Zhuge
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
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Koeppel I, Hertig C, Hoffie R, Kumlehn J. Cas Endonuclease Technology-A Quantum Leap in the Advancement of Barley and Wheat Genetic Engineering. Int J Mol Sci 2019; 20:ijms20112647. [PMID: 31146387 PMCID: PMC6600890 DOI: 10.3390/ijms20112647] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 05/24/2019] [Accepted: 05/24/2019] [Indexed: 12/21/2022] Open
Abstract
Domestication and breeding have created productive crops that are adapted to the climatic conditions of their growing regions. Initially, this process solely relied on the frequent occurrence of spontaneous mutations and the recombination of resultant gene variants. Later, treatments with ionizing radiation or mutagenic chemicals facilitated dramatically increased mutation rates, which remarkably extended the genetic diversity of crop plants. However, a major drawback of conventionally induced mutagenesis is that genetic alterations occur simultaneously across the whole genome and at very high numbers per individual plant. By contrast, the newly emerging Cas endonuclease technology allows for the induction of mutations at user-defined positions in the plant genome. In fundamental and breeding-oriented research, this opens up unprecedented opportunities for the elucidation of gene functions and the targeted improvement of plant performance. This review covers historical aspects of the development of customizable endonucleases, information on the mechanisms of targeted genome modification, as well as hitherto reported applications of Cas endonuclease technology in barley and wheat that are the agronomically most important members of the temperate cereals. Finally, current trends in the further development of this technology and some ensuing future opportunities for research and biotechnological application are presented.
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Affiliation(s)
- Iris Koeppel
- Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany.
| | - Christian Hertig
- Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany.
| | - Robert Hoffie
- Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany.
| | - Jochen Kumlehn
- Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany.
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Bao A, Chen H, Chen L, Chen S, Hao Q, Guo W, Qiu D, Shan Z, Yang Z, Yuan S, Zhang C, Zhang X, Liu B, Kong F, Li X, Zhou X, Tran LSP, Cao D. CRISPR/Cas9-mediated targeted mutagenesis of GmSPL9 genes alters plant architecture in soybean. BMC PLANT BIOLOGY 2019; 19:131. [PMID: 30961525 PMCID: PMC6454688 DOI: 10.1186/s12870-019-1746-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 03/28/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND The plant architecture has significant effects on grain yield of various crops, including soybean (Glycine max), but the knowledge on optimization of plant architecture in order to increase yield potential is still limited. Recently, CRISPR/Cas9 system has revolutionized genome editing, and has been widely utilized to edit the genomes of a diverse range of crop plants. RESULTS In the present study, we employed the CRISPR/Cas9 system to mutate four genes encoding SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors of the SPL9 family in soybean. These four GmSPL9 genes are negatively regulated by GmmiR156b, a target for the improvement of soybean plant architecture and yields. The soybean Williams 82 was transformed with the binary CRISPR/Cas9 plasmid, assembled with four sgRNA expression cassettes driven by the Arabidopsis thaliana U3 or U6 promoter, targeting different sites of these four SPL9 genes via Agrobacterium tumefaciens-mediated transformation. A 1-bp deletion was detected in one target site of the GmSPL9a and one target site of the GmSPL9b, respectively, by DNA sequencing analysis of two T0-generation plants. T2-generation spl9a and spl9b homozygous single mutants exhibited no obvious phenotype changes; but the T2 double homozygous mutant spl9a/spl9b possessed shorter plastochron length. In T4 generation, higher-order mutant plants carrying various combinations of mutations showed increased node number on the main stem and branch number, consequently increased total node number per plants at different levels. In addition, the expression levels of the examined GmSPL9 genes were higher in the spl9b-1 single mutant than wild-type plants, which might suggest a feedback regulation on the expression of the investigated GmSPL9 genes in soybean. CONCLUSIONS Our results showed that CRISPR/Cas9-mediated targeted mutagenesis of four GmSPL9 genes in different combinations altered plant architecture in soybean. The findings demonstrated that GmSPL9a, GmSPL9b, GmSPL9c and GmSPL9 function as redundant transcription factors in regulating plant architecture in soybean.
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Affiliation(s)
- Aili Bao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Haifeng Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Limiao Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Shuilian Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Qingnan Hao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Wei Guo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Dezhen Qiu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Zhihui Shan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Zhonglu Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Songli Yuan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Chanjuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Xiaojuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Baohui Liu
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 China
| | - Fanjiang Kong
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 China
| | - Xia Li
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xinan Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Lam-Son Phan Tran
- Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang, Vietnam
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
| | - Dong Cao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 China
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Genetic Modification for Wheat Improvement: From Transgenesis to Genome Editing. BIOMED RESEARCH INTERNATIONAL 2019; 2019:6216304. [PMID: 30956982 PMCID: PMC6431451 DOI: 10.1155/2019/6216304] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 02/08/2019] [Accepted: 02/21/2019] [Indexed: 12/12/2022]
Abstract
To feed the growing human population, global wheat yields should increase to approximately 5 tonnes per ha from the current 3.3 tonnes by 2050. To reach this goal, existing breeding practices must be complemented with new techniques built upon recent gains from wheat genome sequencing, and the accumulated knowledge of genetic determinants underlying the agricultural traits responsible for crop yield and quality. In this review we primarily focus on the tools and techniques available for accessing gene functions which lead to clear phenotypes in wheat. We provide a view of the development of wheat transformation techniques from a historical perspective, and summarize how techniques have been adapted to obtain gain-of-function phenotypes by gene overexpression, loss-of-function phenotypes by expressing antisense RNAs (RNA interference or RNAi), and most recently the manipulation of gene structure and expression using site-specific nucleases, such as CRISPR/Cas9, for genome editing. The review summarizes recent successes in the application of wheat genetic manipulation to increase yield, improve nutritional and health-promoting qualities in wheat, and enhance the crop's resistance to various biotic and abiotic stresses.
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49
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Ward BP, Brown-Guedira G, Kolb FL, Van Sanford DA, Tyagi P, Sneller CH, Griffey CA. Genome-wide association studies for yield-related traits in soft red winter wheat grown in Virginia. PLoS One 2019; 14:e0208217. [PMID: 30794545 PMCID: PMC6386437 DOI: 10.1371/journal.pone.0208217] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/05/2019] [Indexed: 01/19/2023] Open
Abstract
Grain yield is a trait of paramount importance in the breeding of all cereals. In wheat (Triticum aestivum L.), yield has steadily increased since the Green Revolution, though the current rate of increase is not forecasted to keep pace with demand due to growing world population and increasing affluence. While several genome-wide association studies (GWAS) on yield and related component traits have been performed in wheat, the previous lack of a reference genome has made comparisons between studies difficult. In this study, a GWAS for yield and yield-related traits was carried out on a population of 322 soft red winter wheat lines across a total of four rain-fed environments in the state of Virginia using single-nucleotide polymorphism (SNP) marker data generated by a genotyping-by-sequencing (GBS) protocol. Two separate mixed linear models were used to identify significant marker-trait associations (MTAs). The first was a single-locus model utilizing a leave-one-chromosome-out approach to estimating kinship. The second was a sub-setting kinship estimation multi-locus method (FarmCPU). The single-locus model identified nine significant MTAs for various yield-related traits, while the FarmCPU model identified 74 significant MTAs. The availability of the wheat reference genome allowed for the description of MTAs in terms of both genetic and physical positions, and enabled more extensive post-GWAS characterization of significant MTAs. The results indicate a number of promising candidate genes contributing to grain yield, including an ortholog of the rice aberrant panicle organization (APO1) protein and a gibberellin oxidase protein (GA2ox-A1) affecting the trait grains per square meter, an ortholog of the Arabidopsis thaliana mother of flowering time and terminal flowering 1 (MFT) gene affecting the trait seeds per square meter, and a B2 heat stress response protein affecting the trait seeds per head.
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Affiliation(s)
- Brian P. Ward
- Department Of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Gina Brown-Guedira
- Eastern Regional Small Grains Genotyping Laboratory, USDA-ARS, Raleigh, North Carolina, United States of America
| | - Frederic L. Kolb
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - David A. Van Sanford
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky, United States of America
| | - Priyanka Tyagi
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Clay H. Sneller
- Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, United States of America
| | - Carl A. Griffey
- Department Of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
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50
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Cui X, Balcerzak M, Schernthaner J, Babic V, Datla R, Brauer EK, Labbé N, Subramaniam R, Ouellet T. An optimised CRISPR/Cas9 protocol to create targeted mutations in homoeologous genes and an efficient genotyping protocol to identify edited events in wheat. PLANT METHODS 2019; 15:119. [PMID: 31673276 PMCID: PMC6814032 DOI: 10.1186/s13007-019-0500-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/03/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Targeted genome editing using the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 system has been applied in a large number of plant species. Using a gene-specific single guide RNA (sgRNA) and the CRISPR/Cas9 system, small editing events such as deletions of few bases can be obtained. However larger deletions are required for some applications. In addition, identification and characterization of edited events can be challenging in plants with complex genomes, such as wheat. RESULTS In this study, we used the CRISPR/Cas9 system and developed a protocol that yielded high number of large deletions employing a pair of co-expressed sgRNA to target the same gene. The protocol was validated by targeting three genes, TaABCC6, TaNFXL1 and TansLTP9.4 in a wheat protoplast assay. Deletions of sequences located between the two sgRNA in each gene were the most frequent editing events observed for two of the three genes. A comparative assessment of editing frequencies between a codon-optimized Cas9 for expression in algae, crCas9, and a plant codon-optimized Cas9, pcoCas9, showed more consistent results with the vector expressing pcoCas9. Editing of TaNFXL1 by co-expression of sgRNA pair was investigated in transgenic wheat plants. Given the ploidy of bread wheat, a rapid, robust and inexpensive genotyping protocol was also adapted for hexaploid genomes and shown to be a useful tool to identify homoeolog-specific editing events in wheat. CONCLUSIONS Co-expressed pairs of sgRNA targeting single genes in conjunction with the CRISPR/Cas9 system produced large deletions in wheat. In addition, a genotyping protocol to identify editing events in homoeologs of TaNFXL1 was successfully adapted.
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Affiliation(s)
- Xiucheng Cui
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
- Department of Biology, University of Ottawa, 75 Laurier Ave E, Ottawa, ON K1N 6N5 Canada
| | - Margaret Balcerzak
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Johann Schernthaner
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Vivijan Babic
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Raju Datla
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Elizabeth K. Brauer
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Natalie Labbé
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Rajagopal Subramaniam
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Thérèse Ouellet
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
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