1
|
Qu L, Huang X, Su X, Zhu G, Zheng L, Lin J, Wang J, Xue H. Potato: from functional genomics to genetic improvement. MOLECULAR HORTICULTURE 2024; 4:34. [PMID: 39160633 PMCID: PMC11331666 DOI: 10.1186/s43897-024-00105-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 07/17/2024] [Indexed: 08/21/2024]
Abstract
Potato is the most widely grown non-grain crop and ranks as the third most significant global food crop following rice and wheat. Despite its long history of cultivation over vast areas, slow breeding progress and environmental stress have led to a scarcity of high-yielding potato varieties. Enhancing the quality and yield of potato tubers remains the ultimate objective of potato breeding. However, conventional breeding has faced challenges due to tetrasomic inheritance, high genomic heterozygosity, and inbreeding depression. Recent advancements in molecular biology and functional genomic studies of potato have provided valuable insights into the regulatory network of physiological processes and facilitated trait improvement. In this review, we present a summary of identified factors and genes governing potato growth and development, along with progress in potato genomics and the adoption of new breeding technologies for improvement. Additionally, we explore the opportunities and challenges in potato improvement, offering insights into future avenues for potato research.
Collapse
Affiliation(s)
- Li Qu
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xueqing Huang
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xin Su
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Guoqing Zhu
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lingli Zheng
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jing Lin
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiawen Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hongwei Xue
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
| |
Collapse
|
2
|
Azizi-Dargahlou S, Pouresmaeil M. Agrobacterium tumefaciens-Mediated Plant Transformation: A Review. Mol Biotechnol 2024; 66:1563-1580. [PMID: 37340198 DOI: 10.1007/s12033-023-00788-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/07/2023] [Indexed: 06/22/2023]
Abstract
Agrobacterium tumefaciens-mediated plant transformation is the most dominant technique for the transformation of plants. It is used to transform monocotyledonous and dicotyledonous plants. A. tumefaciens apply for stable and transient transformation, random and targeted integration of foreign genes, as well as genome editing of plants. The Advantages of this method include cheapness, uncomplicated operation, high reproducibility, a low copy number of integrated transgenes, and the possibility of transferring larger DNA fragments. Engineered endonucleases such as CRISPR/Cas9 systems, TALENs, and ZFNs can be delivered with this method. Nowadays, Agrobacterium-mediated transformation is used for the Knock in, Knock down, and Knock out of genes. The transformation effectiveness of this method is not always desirable. Researchers applied various strategies to improve the effectiveness of this method. Here, a general overview of the characteristics and mechanism of gene transfer with Agrobacterium is presented. Advantages, updated data on the factors involved in optimizing this method, and other useful materials that lead to maximum exploitation as well as overcoming obstacles of this method are discussed. Moreover, the application of this method in the generation of genetically edited plants is stated. This review can help researchers to establish a rapid and highly effective Agrobacterium-mediated transformation protocol for any plant species.
Collapse
Affiliation(s)
| | - Mahin Pouresmaeil
- Department of Biotechnology, Azarbaijan Shahid Madani University, Tabriz, Iran
| |
Collapse
|
3
|
Hajibarat Z, Saidi A, Zeinalabedini M, Mousapour Gorji A, Ghaffari MR, Shariati V, Ahmadvand R. Genotyping-by-sequencing and weighted gene co-expression network analysis of genes responsive against Potato virus Y in commercial potato cultivars. PLoS One 2024; 19:e0303783. [PMID: 38787845 PMCID: PMC11125566 DOI: 10.1371/journal.pone.0303783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
Potato is considered a key component of the global food system and plays a vital role in strengthening world food security. A major constraint to potato production worldwide is the Potato Virus Y (PVY), belonging to the genus Potyvirus in the family of Potyviridae. Selective breeding of potato with resistance to PVY pathogens remains the best method to limit the impact of viral infections. Understanding the genetic diversity and population structure of potato germplasm is important for breeders to improve new cultivars for the sustainable use of genetic materials in potato breeding to PVY pathogens. While, genetic diversity improvement in modern potato breeding is facing increasingly narrow genetic basis and the decline of the genetic diversity. In this research, we performed genotyping-by-sequencing (GBS)-based diversity analysis on 10 commercial potato cultivars and weighted gene co-expression network analysis (WGCNA) to identify candidate genes related to PVY-resistance. WGCNA is a system biology technique that uses the WGCNA R software package to describe the correlation patterns between genes in multiple samples. In terms of consumption, these cultivars are a high rate among Iranian people. Using population structure analysis, the 10 cultivars were clustered into three groups based on the 118343 single nucleotide polymorphisms (SNPs) generated by GBS. Read depth ranged between 5 and 18. The average data size and Q30 of the reads were 145.98 Mb and 93.63%, respectively. Based on the WGCNA and gene expression analysis, the StDUF538, StGTF3C5, and StTMEM161A genes were associated with PVY resistance in the potato genome. Further, these three hub genes were significantly involved in defense mechanism where the StTMEM161A was involved in the regulation of alkalization apoplast, the StDUF538 was activated in the chloroplast degradation program, and the StGTF3C5 regulated the proteins increase related to defense in the PVY infected cells. In addition, in the genetic improvement programs, these hub genes can be used as genetic markers for screening commercial cultivars for PVY resistance. Our survey demonstrated that the combination of GBS-based genetic diversity germplasm analysis and WGCNA can assist breeders to select cultivars resistant to PVY as well as help design proper crossing schemes in potato breeding.
Collapse
Affiliation(s)
- Zahra Hajibarat
- Faculty of Life Sciences & Biotechnology, Department of Cell & Molecular Biology, Shahid Beheshti University, Tehran, Iran
| | - Abbas Saidi
- Faculty of Life Sciences & Biotechnology, Department of Cell & Molecular Biology, Shahid Beheshti University, Tehran, Iran
| | - Mehrshad Zeinalabedini
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Ahmad Mousapour Gorji
- Department of Vegetable Research, Seed and Plant Improvement Institute (SPII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Mohammad Reza Ghaffari
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Vahid Shariati
- National Institute of Genetic Engineering and Biotechnology, NIGEB Genome Center, Tehran, Iran
| | - Rahim Ahmadvand
- Department of Vegetable Research, Seed and Plant Improvement Institute (SPII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| |
Collapse
|
4
|
Azariadis A, Andrzejczak OA, Carlsen FM, Westberg I, Brinch-Pedersen H, Petersen BL, Hebelstrup KH. A Walk on the Wild Side: Genome Editing of Tuber-Bearing Solanum bulbocastanum. PLANTS (BASEL, SWITZERLAND) 2024; 13:1044. [PMID: 38611572 PMCID: PMC11013279 DOI: 10.3390/plants13071044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/23/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024]
Abstract
Solanum bulbocastanum is a wild diploid tuber-bearing plant. We here demonstrate transgene-free genome editing of S. bulbocastanum protoplasts and regeneration of gene-edited plants. We use ribonucleoproteins, consisting of Cas9 and sgRNA, assembled in vitro, to target a gene belonging to the nitrate and peptide transporter family. Four different sgRNAs were designed and we observed efficiency in gene-editing in the protoplast pool between 8.5% and 12.4%. Twenty-one plants were re-generated from microcalli developed from individual protoplasts. In three of the plants we found that the target gene had been edited. Two of the edited plants had deletion mutations introduced into both alleles, whereas one only had a mutation in one of the alleles. Our work demonstrates that protocols for the transformation of Solanum tuberosum can be optimized to be applied to a wild Solanum species.
Collapse
Affiliation(s)
- Aristotelis Azariadis
- Section for Crop Genetics & Biotechnology, Department of Agroecology, Aarhus University, Flakkebjerg, 4200 Slagelse, Denmark; (A.A.); (H.B.-P.)
| | - Olga A. Andrzejczak
- Section for Crop Genetics & Biotechnology, Department of Agroecology, Aarhus University, Flakkebjerg, 4200 Slagelse, Denmark; (A.A.); (H.B.-P.)
| | - Frida M. Carlsen
- Section for Plant Glycobiology, Department of Plant and Environmental Sciences, Copenhagen University, 1871 Frederiksberg C, Denmark; (F.M.C.); (I.W.); (B.L.P.)
| | - Ida Westberg
- Section for Plant Glycobiology, Department of Plant and Environmental Sciences, Copenhagen University, 1871 Frederiksberg C, Denmark; (F.M.C.); (I.W.); (B.L.P.)
| | - Henrik Brinch-Pedersen
- Section for Crop Genetics & Biotechnology, Department of Agroecology, Aarhus University, Flakkebjerg, 4200 Slagelse, Denmark; (A.A.); (H.B.-P.)
| | - Bent L. Petersen
- Section for Plant Glycobiology, Department of Plant and Environmental Sciences, Copenhagen University, 1871 Frederiksberg C, Denmark; (F.M.C.); (I.W.); (B.L.P.)
| | - Kim H. Hebelstrup
- Section for Crop Genetics & Biotechnology, Department of Agroecology, Aarhus University, Flakkebjerg, 4200 Slagelse, Denmark; (A.A.); (H.B.-P.)
| |
Collapse
|
5
|
Norouzi M, Nazarain-Firouzabadi F, Ismaili A, Ahmadvand R, Poormazaheri H. CRISPR/Cas StNRL1 gene knockout increases resistance to late blight and susceptibility to early blight in potato. FRONTIERS IN PLANT SCIENCE 2024; 14:1278127. [PMID: 38304452 PMCID: PMC10830690 DOI: 10.3389/fpls.2023.1278127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 12/28/2023] [Indexed: 02/03/2024]
Abstract
With the development of genome editing technologies, editing susceptible genes is a promising method to modify plants for resistance to stress. NPH3/RPT2-LIKE1 protein (NRL1) interacts with effector Pi02860 of Phytophthora infestans and creates a protein complex, promoting the proteasome-mediated degradation of the guanine nucleotide exchange factor SWAP70. SWAP70, as a positive regulator, enhances cell death triggered by the perception of the P. infestans pathogen-associated molecular pattern (PAMP) INF1. Using a clustered regularly interspaced short palindrome repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system, a construct was made to introduce four guide RNAs into the potato cultivar Agria. A total of 60 putative transgenic lines were regenerated, in which 10 transgenic lines with deletions were selected and analyzed. A mutant line with a four-allelic knockdown of StNRL1 gene was obtained, showing an ~90% reduction in StNRL1 expression level, resulting in enhanced resistance to P. infestans. Surprisingly, mutant lines were susceptible to Alternaria alternata, suggesting that StNRL1 may play a role as a resistance gene; hence, silencing StNRL1 enhances resistance to P. infestans.
Collapse
Affiliation(s)
- Moshen Norouzi
- Production Engineering and Plant Genetics Department, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
| | - Farhad Nazarain-Firouzabadi
- Production Engineering and Plant Genetics Department, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
| | - Ahmad Ismaili
- Production Engineering and Plant Genetics Department, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
| | - Rahim Ahmadvand
- Associate Professor, Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran
| | - Helen Poormazaheri
- Department of Biology, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
| |
Collapse
|
6
|
Guo K, Liang W, Wang S, Guo D, Liu F, Persson S, Herburger K, Petersen BL, Liu X, Blennow A, Zhong Y. Strategies for starch customization: Agricultural modification. Carbohydr Polym 2023; 321:121336. [PMID: 37739487 DOI: 10.1016/j.carbpol.2023.121336] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/24/2023]
Abstract
Raw starch is commonly modified to enhance its functionality for industrial applications. There is increasing demand for 'green' modified starches from both end-consumers and producers. It is well known that environmental conditions are key factors that determine plant growth and yield. An increasing number of studies suggest growth conditions can expand affect starch structure and functionality. In this review, we summarized how water, heat, high nitrogen, salinity, shading, CO2 stress affect starch biosynthesis and physicochemical properties. We define these treatments as a fifth type of starch modification method - agricultural modification - in addition to chemical, physical, enzymatic and genetic methods. In general, water stress decreases peak viscosity and gelatinization enthalpy of starch, and high temperature stress increases starch gelatinization enthalpy and temperature. High nitrogen increases total starch content and regulates starch viscosity. Salinity stress mainly regulates starch and amylose content, both of which are genotype-dependent. Shading stress and CO2 stress can both increase starch granule size, but these have different effects on amylose content and amylopectin structure. Compared with other modification methods, agricultural modification has the advantage of operating at a large scale and a low cost and can help meet the ever-rising market of clean-label foods and ingredients.
Collapse
Affiliation(s)
- Ke Guo
- Lab of Food Soft Matter Structure and Advanced Manufacturing, College of Food Science and Engineering, Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing University of Finance and Economics, Nanjing 210023, China; Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Wenxin Liang
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Shujun Wang
- State Key Laboratory of Food Nutrition and Safety and School of Food Engineering and Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Dongwei Guo
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Fulai Liu
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Staffan Persson
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | | | - Bent L Petersen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Xingxun Liu
- Lab of Food Soft Matter Structure and Advanced Manufacturing, College of Food Science and Engineering, Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing University of Finance and Economics, Nanjing 210023, China.
| | - Andreas Blennow
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark.
| | - Yuyue Zhong
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark; Department of Sustainable and Bio-inspired Materials, Max Planck Institute of Colloids and Interfaces, Am Muhlenberg 1, D-14476 Potsdam, Germany.
| |
Collapse
|
7
|
Abeuova L, Kali B, Tussipkan D, Akhmetollayeva A, Ramankulov Y, Manabayeva S. CRISPR/Cas9-mediated multiple guide RNA-targeted mutagenesis in the potato. Transgenic Res 2023; 32:383-397. [PMID: 37330986 DOI: 10.1007/s11248-023-00356-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 06/01/2023] [Indexed: 06/20/2023]
Abstract
CRISPR/Cas9 technology has become the most efficient method for genome editing in many plant species, including important industrial crops such as potatoes. This study used three target regions (T1, T2, and T3) in gbss exon I, whose sequences were first inserted into the BbsI sites in the appropriate guide RNA (gRNA) vector (pEn-Chimera, pMR203, pMR204, and pMR205), and then localized between the AtU6 promoter and the gRNA scaffold sequence. Expression vectors were constructed by introducing gRNA genes into the pMR287 (pYUCas9Plus) plasmids using the MultiSite Gateway system by attR and attL sites. The three target regions of mutant potato lines were analyzed. The use of CRISPR/Cas9-mediated multiple guide RNA-targeted mutagenesis allowed tri- or tetra-allelic mutant potato lines to be generated. Multiple nucleotide substitutions and indels within and around the three target sites caused a frameshift mutation that led to a premature stop codon, resulting in the production of gbss-knockout plants. Mutation frequencies and analysis of mutation patterns suggested that the stably transformed Cas9/multiple guide RNA expression constructs used in this study can induce targeted mutations efficiently in the potato genome. Full knockout of the gbss gene was analyzed by CAPS, Sanger sequencing and iodine staining. The present study demonstrated successful CRISPR/Cas9-mediated multiple guide RNA-targeted mutagenesis in the potato gbss gene by Agrobacterium-mediated transformation, resulting in an amylose-free phenotype.
Collapse
Affiliation(s)
- Laura Abeuova
- National Center for Biotechnology (NCB), Astana, 010000, Kazakhstan
- L.N. Gumilyov Eurasian National University, Astana, 010000, Kazakhstan
| | - Balnur Kali
- National Center for Biotechnology (NCB), Astana, 010000, Kazakhstan
| | - Dilnur Tussipkan
- National Center for Biotechnology (NCB), Astana, 010000, Kazakhstan
| | | | - Yerlan Ramankulov
- National Center for Biotechnology (NCB), Astana, 010000, Kazakhstan
- National Laboratory Astana, Nazarbayev University, Astana, 010000, Kazakhstan
| | - Shuga Manabayeva
- L.N. Gumilyov Eurasian National University, Astana, 010000, Kazakhstan.
| |
Collapse
|
8
|
Maybery-Reupert K, Isenegger D, Hayden M, Cogan N. Development of genomic resources for Rhodes grass ( Chloris gayana), draft genome and annotated variant discovery. FRONTIERS IN PLANT SCIENCE 2023; 14:1239290. [PMID: 37731974 PMCID: PMC10507473 DOI: 10.3389/fpls.2023.1239290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/18/2023] [Indexed: 09/22/2023]
Abstract
Genomic resources for grasses, especially warm-season grasses are limited despite their commercial and environmental importance. Here, we report the first annotated draft whole genome sequence for diploid Rhodes grass (Chloris gayana), a tropical C4 species. Generated using long read nanopore sequencing and assembled using the Flye software package, the assembled genome is 603 Mbp in size and comprises 5,233 fragments that were annotated using the GenSas pipeline. The annotated genome has 46,087 predicted genes corresponding to 92.0% of the expected genomic content present via BUSCO analysis. Gene ontology terms and repetitive elements are identified and discussed. An additional 94 individual plant genotypes originating from three diploid and two tetraploid Rhodes grass cultivars were short-read whole genome resequenced (WGR) to generate a single nucleotide polymorphism (SNP) resource for the species that can be used to elucidate inter- and intra-cultivar relationships across both ploidy levels. A total of 75,777 high quality SNPs were used to generate a phylogenetic tree, highlighting the diversity present within the cultivars which agreed with the known breeding history. Differentiation was observed between diploid and tetraploid cultivars. The WGR data were also used to provide insights into the nature and evolution of the tetraploid status of the species, with results largely agreeing with the published literature that the tetraploids are autotetraploid.
Collapse
Affiliation(s)
- Kellie Maybery-Reupert
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Daniel Isenegger
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Matthew Hayden
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Noel Cogan
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| |
Collapse
|
9
|
Westberg I, Carlsen FM, Johansen IE, Petersen BL. Cytosine base editors optimized for genome editing in potato protoplasts. Front Genome Ed 2023; 5:1247702. [PMID: 37719877 PMCID: PMC10502308 DOI: 10.3389/fgeed.2023.1247702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 08/03/2023] [Indexed: 09/19/2023] Open
Abstract
In this study, we generated and compared three cytidine base editors (CBEs) tailor-made for potato (Solanum tuberosum), which conferred up to 43% C-to-T conversion of all alleles in the protoplast pool. Earlier, gene-edited potato plants were successfully generated by polyethylene glycol-mediated CRISPR/Cas9 transformation of protoplasts followed by explant regeneration. In one study, a 3-4-fold increase in editing efficiency was obtained by replacing the standard Arabidopsis thaliana AtU6-1 promotor with endogenous potato StU6 promotors driving the expression of the gRNA. Here, we used this optimized construct (SpCas9/StU6-1::gRNA1, target gRNA sequence GGTC4C5TTGGAGC12AAAAC17TGG) for the generation of CBEs tailor-made for potato and tested for C-to-T base editing in the granule-bound starch synthase 1 gene in the cultivar Desiree. First, the Streptococcus pyogenes Cas9 was converted into a (D10A) nickase (nCas9). Next, one of three cytosine deaminases from human hAPOBEC3A (A3A), rat (evo_rAPOBEC1) (rA1), or sea lamprey (evo_PmCDA1) (CDA1) was C-terminally fused to nCas9 and a uracil-DNA glycosylase inhibitor, with each module interspaced with flexible linkers. The CBEs were overall highly efficient, with A3A having the best overall base editing activity, with an average 34.5%, 34.5%, and 27% C-to-T conversion at C4, C5, and C12, respectively, whereas CDA1 showed an average base editing activity of 34.5%, 34%, and 14.25% C-to-T conversion at C4, C5, and C12, respectively. rA1 exhibited an average base editing activity of 18.75% and 19% at C4 and C5 and was the only base editor to show no C-to-T conversion at C12.
Collapse
Affiliation(s)
| | | | | | - Bent Larsen Petersen
- Department of Plant and Environmental Sciences, Faculty of Science, The University of Copenhagen, Frederiksberg, Denmark
| |
Collapse
|
10
|
Anuradha, Kumari M, Zinta G, Chauhan R, Kumar A, Singh S, Singh S. Genetic resources and breeding approaches for improvement of amaranth ( Amaranthus spp.) and quinoa ( Chenopodium quinoa). Front Nutr 2023; 10:1129723. [PMID: 37554703 PMCID: PMC10405290 DOI: 10.3389/fnut.2023.1129723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 07/03/2023] [Indexed: 08/10/2023] Open
Abstract
Nowadays, the human population is more concerned about their diet and very specific in choosing their food sources to ensure a healthy lifestyle and avoid diseases. So people are shifting to more smart nutritious food choices other than regular cereals and staple foods they have been eating for a long time. Pseudocereals, especially, amaranth and quinoa, are important alternatives to traditional cereals due to comparatively higher nutrition, essential minerals, amino acids, and zero gluten. Both Amaranchaceae crops are low-input demanding and hardy plants tolerant to stress, drought, and salinity conditions. Thus, these crops may benefit developing countries that follow subsistence agriculture and have limited farming resources. However, these are underutilized orphan crops, and the efforts to improve them by reducing their saponin content remain ignored for a long time. Furthermore, these crops have very rich variability, but the progress of their genetic gain for getting high-yielding genotypes is slow. Realizing problems in traditional cereals and opting for crop diversification to tackle climate change, research should be focused on the genetic improvement for low saponin, nutritionally rich, tolerant to biotic and abiotic stresses, location-specific photoperiod, and high yielding varietal development of amaranth and quinoa to expand their commercial cultivation. The latest technologies that can accelerate the breeding to improve yield and quality in these crops are much behind and slower than the already established major crops of the world. We could learn from past mistakes and utilize the latest trends such as CRISPR/Cas, TILLING, and RNA interference (RNAi) technology to improve these pseudocereals genetically. Hence, the study reviewed important nutrition quality traits, morphological descriptors, their breeding behavior, available genetic resources, and breeding approaches for these crops to shed light on future breeding strategies to develop superior genotypes.
Collapse
Affiliation(s)
- Anuradha
- Division of Agrotechnology, Council of Scientific and Industrial Research–Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Manisha Kumari
- Division of Agrotechnology, Council of Scientific and Industrial Research–Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Gaurav Zinta
- Division of Biotechnology, Council of Scientific and Industrial Research–Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Ramesh Chauhan
- Division of Agrotechnology, Council of Scientific and Industrial Research–Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Ashok Kumar
- Division of Agrotechnology, Council of Scientific and Industrial Research–Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Sanatsujat Singh
- Division of Agrotechnology, Council of Scientific and Industrial Research–Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Satbeer Singh
- Division of Agrotechnology, Council of Scientific and Industrial Research–Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| |
Collapse
|
11
|
Kanai M, Hikino K, Mano S. Cloning and Functional Verification of Endogenous U6 Promoters for the Establishment of Efficient CRISPR/Cas9-Based Genome Editing in Castor ( Ricinus communis). Genes (Basel) 2023; 14:1327. [PMID: 37510232 PMCID: PMC10379810 DOI: 10.3390/genes14071327] [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: 05/19/2023] [Revised: 06/19/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023] Open
Abstract
Castor (Ricinus communis) seeds are rich in a type of hydroxy fatty acid called ricinoleic acid, which is in high demand for the production of plant-based plastics, lubricants, and hydraulic oils. However, the high content of ricin, a toxic protein, in these seeds has restricted further expansion in the area of castor cultivation. Therefore, the development of ricin-free castor is needed. Genome editing technology, although successfully applied in several plant species, is still in the developing stages in castor and awaits the identification of an endogenous U6 promoter with robust function. Here, we searched for U6 small nuclear RNA (snRNA) genes in the castor genome. This led to the identification of six U6 snRNA genes. The promoters of these U6 snRNA genes were cloned, and their function was examined in castor cells using the particle delivery method. The results showed that a U6 promoter length of approximately 300 bp from the transcription start site was sufficient to activate gene expression. This study provides insights into the endogenous castor U6 promoter sequences and outlines a method for verifying the function of U6 promoters in plants using the particle delivery system.
Collapse
Affiliation(s)
- Masatake Kanai
- Laboratory of Organelle Regulation, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Kazumi Hikino
- Laboratory of Organelle Regulation, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Shoji Mano
- Laboratory of Organelle Regulation, National Institute for Basic Biology, Okazaki 444-8585, Japan
- Basic Biology Program, Graduate Institute for Advanced Studies, The Graduate University for Advanced Studies, SOKENDAI, Okazaki 444-8585, Japan
| |
Collapse
|
12
|
Ahmad N, Fatima S, Mehmood MA, Zaman QU, Atif RM, Zhou W, Rahman MU, Gill RA. Targeted genome editing in polyploids: lessons from Brassica. FRONTIERS IN PLANT SCIENCE 2023; 14:1152468. [PMID: 37409308 PMCID: PMC10318174 DOI: 10.3389/fpls.2023.1152468] [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: 01/27/2023] [Accepted: 04/11/2023] [Indexed: 07/07/2023]
Abstract
CRISPR-mediated genome editing has emerged as a powerful tool for creating targeted mutations in the genome for various applications, including studying gene functions, engineering resilience against biotic and abiotic stresses, and increasing yield and quality. However, its utilization is limited to model crops for which well-annotated genome sequences are available. Many crops of dietary and economic importance, such as wheat, cotton, rapeseed-mustard, and potato, are polyploids with complex genomes. Therefore, progress in these crops has been hampered due to genome complexity. Excellent work has been conducted on some species of Brassica for its improvement through genome editing. Although excellent work has been conducted on some species of Brassica for genome improvement through editing, work on polyploid crops, including U's triangle species, holds numerous implications for improving other polyploid crops. In this review, we summarize key examples from genome editing work done on Brassica and discuss important considerations for deploying CRISPR-mediated genome editing more efficiently in other polyploid crops for improvement.
Collapse
Affiliation(s)
- Niaz Ahmad
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Samia Fatima
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Muhammad Aamer Mehmood
- Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Qamar U. Zaman
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Rana Muhammad Atif
- National Center of Genome Editing, Center of Advanced Studies, Agriculture and Food Security, University of Agriculture, Faisalabad, Pakistan
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Weijun Zhou
- Ministry of Agriculture and Rural Affairs Key Lab of Spectroscopy Sensing, Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Mehboob-ur Rahman
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Rafaqat Ali Gill
- Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| |
Collapse
|
13
|
Pfotenhauer AC, Occhialini A, Harbison SA, Li L, Piatek AA, Luckett CR, Yang Y, Stewart CN, Lenaghan SC. Genome-Editing of FtsZ1 for Alteration of Starch Granule Size in Potato Tubers. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091878. [PMID: 37176936 PMCID: PMC10180631 DOI: 10.3390/plants12091878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/06/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
Genome-editing has enabled rapid improvement for staple food crops, such as potato, a key beneficiary of the technology. In potato, starch contained within tubers represents the primary product for use in food and non-food industries. Starch granules are produced in the plastids of tubers with plastid size correlated with the size of starch grana. The division of plastids is controlled by proteins, including the tubulin-like GTPase FtsZ1. The altered expression of FtsZ1 has been shown to disrupt plastid division, leading to the production of "macro-plastid"-containing plants. These macro-chloroplast plants are characterized by cells containing fewer and enlarged plastids. In this work, we utilize CRISPR/Cas9 to generate FtsZ1 edited potato lines to demonstrate that genome-editing can be used to increase the size of starch granules in tubers. Altered plastid morphology was comparable to the overexpression of FtsZ1 in previous work in potato and other crops. Several lines were generated with up to a 1.98-fold increase in starch granule size that was otherwise phenotypically indistinguishable from wild-type plants. Further, starch paste from one of the most promising lines showed a 2.07-fold increase in final viscosity. The advantages of enlarged starch granules and the potential of CRISPR/Cas9-based technologies for food crop improvement are further discussed.
Collapse
Affiliation(s)
- Alexander C Pfotenhauer
- Center for Agricultural Synthetic Biology (CASB), University of Tennessee, Knoxville, TN 37996, USA
| | - Alessandro Occhialini
- Center for Agricultural Synthetic Biology (CASB), University of Tennessee, Knoxville, TN 37996, USA
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37920, USA
| | - Stacee A Harbison
- Center for Agricultural Synthetic Biology (CASB), University of Tennessee, Knoxville, TN 37996, USA
| | - Li Li
- Center for Agricultural Synthetic Biology (CASB), University of Tennessee, Knoxville, TN 37996, USA
| | - Agnieszka A Piatek
- Department of Food Science, University of Tennessee, Knoxville, TN 37920, USA
| | - Curtis R Luckett
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37920, USA
| | - Yongil Yang
- Center for Agricultural Synthetic Biology (CASB), University of Tennessee, Knoxville, TN 37996, USA
| | - C Neal Stewart
- Center for Agricultural Synthetic Biology (CASB), University of Tennessee, Knoxville, TN 37996, USA
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37920, USA
| | - Scott C Lenaghan
- Center for Agricultural Synthetic Biology (CASB), University of Tennessee, Knoxville, TN 37996, USA
- Department of Food Science, University of Tennessee, Knoxville, TN 37920, USA
| |
Collapse
|
14
|
Ravikiran KT, Thribhuvan R, Sheoran S, Kumar S, Kushwaha AK, Vineeth TV, Saini M. Tailoring crops with superior product quality through genome editing: an update. PLANTA 2023; 257:86. [PMID: 36949234 DOI: 10.1007/s00425-023-04112-4] [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: 09/06/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
In this review, using genome editing, the quality trait alterations in important crops have been discussed, along with the challenges encountered to maintain the crop products' quality. The delivery of economic produce with superior quality is as important as high yield since it dictates consumer's acceptance and end use. Improving product quality of various agricultural and horticultural crops is one of the important targets of plant breeders across the globe. Significant achievements have been made in various crops using conventional plant breeding approaches, albeit, at a slower rate. To keep pace with ever-changing consumer tastes and preferences and industry demands, such efforts must be supplemented with biotechnological tools. Fortunately, many of the quality attributes are resultant of well-understood biochemical pathways with characterized genes encoding enzymes at each step. Targeted mutagenesis and transgene transfer have been instrumental in bringing out desired qualitative changes in crops but have suffered from various pitfalls. Genome editing, a technique for methodical and site-specific modification of genes, has revolutionized trait manipulation. With the evolution of versatile and cost effective CRISPR/Cas9 system, genome editing has gained significant traction and is being applied in several crops. The availability of whole genome sequences with the advent of next generation sequencing (NGS) technologies further enhanced the precision of these techniques. CRISPR/Cas9 system has also been utilized for desirable modifications in quality attributes of various crops such as rice, wheat, maize, barley, potato, tomato, etc. The present review summarizes salient findings and achievements of application of genome editing for improving product quality in various crops coupled with pointers for future research endeavors.
Collapse
Affiliation(s)
- K T Ravikiran
- ICAR-Central Soil Salinity Research Institute, Regional Research Station, Lucknow, Uttar Pradesh, India
| | - R Thribhuvan
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, West Bengal, India
| | - Seema Sheoran
- ICAR-Indian Agricultural Research Institute, Regional Station, Karnal, Haryana, India.
| | - Sandeep Kumar
- ICAR-Indian Institute of Natural Resins and Gums, Ranchi, Jharkhand, India
| | - Amar Kant Kushwaha
- ICAR-Central Institute for Subtropical Horticulture, Lucknow, Uttar Pradesh, India
| | - T V Vineeth
- ICAR-Central Soil Salinity Research Institute, Regional Research Station, Bharuch, Gujarat, India
- Department of Plant Physiology, College of Agriculture, Kerala Agricultural University, Vellanikkara, Thrissur, Kerala, India
| | - Manisha Saini
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| |
Collapse
|
15
|
Hou X, Guo X, Zhang Y, Zhang Q. CRISPR/Cas genome editing system and its application in potato. Front Genet 2023; 14:1017388. [PMID: 36861125 PMCID: PMC9968925 DOI: 10.3389/fgene.2023.1017388] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 01/23/2023] [Indexed: 02/17/2023] Open
Abstract
Potato is the largest non-cereal food crop worldwide and a vital substitute for cereal crops, considering its high yield and great nutritive value. It plays an important role in food security. The CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated) system has the advantages of easy operation, high efficiency, and low cost, which shows a potential in potato breeding. In this paper, the action mechanism and derivative types of the CRISPR/Cas system and the application of the CRISPR/Cas system in improving the quality and resistance of potatoes, as well as overcoming the self-incompatibility of potatoes, are reviewed in detail. At the same time, the application of the CRISPR/Cas system in the future development of the potato industry was analyzed and prospected.
Collapse
Affiliation(s)
- Xin Hou
- College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Xiaomeng Guo
- College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Yan Zhang
- *Correspondence: Yan Zhang, ; Qiang Zhang,
| | | |
Collapse
|
16
|
Sánchez-Gómez C, Posé D, Martín-Pizarro C. Genome Editing by CRISPR/Cas9 in Polyploids. Methods Mol Biol 2023; 2545:459-473. [PMID: 36720828 DOI: 10.1007/978-1-0716-2561-3_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
CRISPR/Cas system has been widely used for genome editing in the past few years. Even though it has been performed in many polyploid species to date, its efficient accomplishment in these organisms is still a challenge. The presence of multiple homoeologous genes as targets for their editing requires more rigorous work and specific needs to assess successful genome editing. Here, we describe a general stepwise protocol to select target sites, design sgRNAs, indicate vector requirements, and screen CRISPR/Cas9-mediated genome editing in polyploid species.
Collapse
Affiliation(s)
- Carlos Sánchez-Gómez
- Departamento de Mejora Genética y Biotecnología, Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM), Universidad de Málaga - Consejo Superior de Investigaciones Científicas, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, UMA, Málaga, Spain
| | - David Posé
- Departamento de Mejora Genética y Biotecnología, Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM), Universidad de Málaga - Consejo Superior de Investigaciones Científicas, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, UMA, Málaga, Spain
| | - Carmen Martín-Pizarro
- Departamento de Mejora Genética y Biotecnología, Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM), Universidad de Málaga - Consejo Superior de Investigaciones Científicas, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, UMA, Málaga, Spain.
| |
Collapse
|
17
|
Ly DNP, Iqbal S, Fosu-Nyarko J, Milroy S, Jones MGK. Multiplex CRISPR-Cas9 Gene-Editing Can Deliver Potato Cultivars with Reduced Browning and Acrylamide. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12020379. [PMID: 36679094 PMCID: PMC9864857 DOI: 10.3390/plants12020379] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/19/2022] [Accepted: 01/10/2023] [Indexed: 05/14/2023]
Abstract
Storing potato tubers at cold temperatures, either for transport or continuity of supply, is associated with the conversion of sucrose to reducing sugars. When cold-stored cut tubers are processed at high temperatures, with endogenous asparagine, acrylamide is formed. Acrylamide is classified as a carcinogen. Potato processors prefer cultivars which accumulate fewer reducing sugars and thus less acrylamide on processing, and suitable processing cultivars may not be available. We used CRISPR-Cas9 to disrupt the genes encoding vacuolar invertase (VInv) and asparagine synthetase 1 (AS1) of cultivars Atlantic and Desiree to reduce the accumulation of reducing sugars and the production of asparagine after cold storage. Three of the four guide RNAs employed induced mutation frequencies of 17-98%, which resulted in deletions, insertions and substitutions at the targeted gene sites. Eight of ten edited events had mutations in at least one allele of both genes; for two, only the VInv was edited. No wild-type allele was detected in both genes of events DSpco7, DSpFN4 and DSpco12, suggesting full allelic mutations. Tubers of two Atlantic and two Desiree events had reduced fructose and glucose concentrations after cold storage. Crisps from these and four other Desiree events were lighter in colour and included those with 85% less acrylamide. These results demonstrate that multiplex CRISPR-Cas9 technology can generate improved potato cultivars for healthier processed potato products.
Collapse
Affiliation(s)
- Diem Nguyen Phuoc Ly
- Crop Biotechnology Research Group, School of Agricultural Sciences, College of Environmental and Life Sciences, Murdoch University, Perth, WA 6150, Australia
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Perth, WA 6150, Australia
| | - Sadia Iqbal
- Crop Biotechnology Research Group, School of Agricultural Sciences, College of Environmental and Life Sciences, Murdoch University, Perth, WA 6150, Australia
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Perth, WA 6150, Australia
- Correspondence: (S.I.); (J.F.-N.); (M.G.K.J.)
| | - John Fosu-Nyarko
- Crop Biotechnology Research Group, School of Agricultural Sciences, College of Environmental and Life Sciences, Murdoch University, Perth, WA 6150, Australia
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Perth, WA 6150, Australia
- Correspondence: (S.I.); (J.F.-N.); (M.G.K.J.)
| | - Stephen Milroy
- Crop Biotechnology Research Group, School of Agricultural Sciences, College of Environmental and Life Sciences, Murdoch University, Perth, WA 6150, Australia
- Potato Research Western Australia, Murdoch University, Perth, WA 6150, Australia
| | - Michael G. K. Jones
- Crop Biotechnology Research Group, School of Agricultural Sciences, College of Environmental and Life Sciences, Murdoch University, Perth, WA 6150, Australia
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Perth, WA 6150, Australia
- Potato Research Western Australia, Murdoch University, Perth, WA 6150, Australia
- Correspondence: (S.I.); (J.F.-N.); (M.G.K.J.)
| |
Collapse
|
18
|
Qiao H, Jiang S, Fu H, Xiong Y, Zhang W, Xu L, Cheng D, Wang J. CRISPR/Cas9 establishment-mediated targeted mutagenesis in Macrobrachium nipponense. Front Physiol 2023; 14:1141359. [PMID: 37035655 PMCID: PMC10079998 DOI: 10.3389/fphys.2023.1141359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/13/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction: CRISPR/Cas9 is a gene-editing technology which could specifically cleave dsDNA and induce target gene mutation. CRISPR/Cas9 has been widely used in gene functional studies in many fields, such as medicine, biology, and agriculture due to its simple design, low cost, and high efficiency. Although it has been well developed in model fish and freshwater fish for gene function analysis, it is still novel in the studies dealing with economic crustacean species. Methods: In this study, we established a CRISPR/Cas9 system based on microinjection for M. nipponense, an important economic crustacean aquaculture species. The vitellogenin (Vg) gene and the eyeless (Ey) gene were selected as the targeted genes for mutation. Two sgRNAs were designed for Mn-Vg and Mn-Ey gene editing, respectively. Results and Discussion: For sg-Vg-1, the gastrula survival ratio was 8.69%, and the final hatching ratio was 4.83%. The blastula mutant ratio was 10%, and the hatching individual mutant ratio was 30%. For sg-Vg-2, the gastrula survival ratio was 5.85%, and the final hatching ratio was 3.89%. The blastula mutant ratio was 16.67%, and no mutant sequences were detected in hatching individuals. For sg-Ey-1, the gastrula survival ratio was 6.25%, and the final hatching ratio was 2.34%. The blastula mutant ratio was 10.00%, and the hatching individual mutant ratio was 66.67%. For sg-Ey-2, the gastrula survival ratio was 6.00%, and the final hatching ratio was 2.67%. No mutant sequence was detected in both blastula stage and hatching individuals. There were no significant morphological changes observed in the Mn-Vg group. Two deformed types were detected in sg-Ey-1-injected embryos. An evident developmental delay of the compound eye was detected in Ey-sg1-H1 in the zoea stage. The compound eyes of the Ey-sg1-H2 embryo could not form well-defined spheres, and the whole compound eye appeared to diffuse at the end of the late zoea stage. The establishment of a gene-editing platform based on CRISPR/Cas9 will not only provide an efficient and convenient method for gene function analysis but also provide a powerful tool for molecular-assisted breeding of Macrobrachium nipponense.
Collapse
Affiliation(s)
- Hui Qiao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Sufei Jiang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
- *Correspondence: Hongtuo Fu, ; Sufei Jiang,
| | - Hongtuo Fu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
- *Correspondence: Hongtuo Fu, ; Sufei Jiang,
| | - Yiwei Xiong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Wenyi Zhang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Lei Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Dan Cheng
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Jisheng Wang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| |
Collapse
|
19
|
González MN, Massa GA, Andersson M, Storani L, Olsson N, Décima Oneto CA, Hofvander P, Feingold SE. CRISPR/Cas9 Technology for Potato Functional Genomics and Breeding. Methods Mol Biol 2023; 2653:333-361. [PMID: 36995636 DOI: 10.1007/978-1-0716-3131-7_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Cultivated potato (Solanum tuberosum L.) is one of the most important staple food crops worldwide. Its tetraploid and highly heterozygous nature poses a great challenge to its basic research and trait improvement through traditional mutagenesis and/or crossbreeding. The establishment of the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) as a gene editing tool has allowed the alteration of specific gene sequences and their concomitant gene function, providing powerful technology for potato gene functional analysis and improvement of elite cultivars. This technology relies on a short RNA molecule called single guide RNA (sgRNA) that directs the Cas9 nuclease to induce a site-specific double-stranded break (DSB). Further, repair of the DSB by the error-prone non-homologous end joining (NHEJ) mechanism leads to the introduction of targeted mutations, which can be used to produce the loss of function of specific gene(s). In this chapter, we describe experimental procedures to apply the CRISPR/Cas9 technology for potato genome editing. First, we provide strategies for target selection and sgRNA design and describe a Golden Gate-based cloning system to obtain a sgRNA/Cas9-encoding binary vector. We also describe an optimized protocol for ribonucleoprotein (RNP) complex assembly. The binary vector can be used for both Agrobacterium-mediated transformation and transient expression in potato protoplasts, while the RNP complexes are intended to obtain edited potato lines through protoplast transfection and plant regeneration. Finally, we describe procedures to identify the gene-edited potato lines. The methods described here are suitable for potato gene functional analysis and breeding.
Collapse
Affiliation(s)
- Matías Nicolás González
- Laboratorio de Agrobiotecnología, IPADS (INTA - CONICET), Balcarce, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Gabriela Alejandra Massa
- Laboratorio de Agrobiotecnología, IPADS (INTA - CONICET), Balcarce, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - Mariette Andersson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Leonardo Storani
- Laboratorio de Agrobiotecnología, IPADS (INTA - CONICET), Balcarce, Argentina
- Agencia Nacional de Promoción Científica y Tecnológica, Buenos Aires, Argentina
| | - Niklas Olsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Cecilia Andrea Décima Oneto
- Laboratorio de Agrobiotecnología, IPADS (INTA - CONICET), Balcarce, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - Per Hofvander
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | | |
Collapse
|
20
|
Chincinska IA, Miklaszewska M, Sołtys-Kalina D. Recent advances and challenges in potato improvement using CRISPR/Cas genome editing. PLANTA 2022; 257:25. [PMID: 36562862 PMCID: PMC9789015 DOI: 10.1007/s00425-022-04054-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
MAIN CONCLUSION Genome editing using CRISPR/Cas technology improves the quality of potato as a food crop and enables its use as both a model plant in fundamental research and as a potential biofactory for producing valuable compounds for industrial applications. Potato (Solanum tuberosum L.) plays a significant role in ensuring global food and nutritional security. Tuber yield is negatively affected by biotic and abiotic stresses, and enzymatic browning and cold-induced sweetening significantly contribute to post-harvest quality losses. With the dual challenges of a growing population and a changing climate, potato enhancement is essential for its sustainable production. However, due to several characteristics of potato, including high levels of heterozygosity, tetrasomic inheritance, inbreeding depression, and self-incompatibility of diploid potato, conventional breeding practices are insufficient to achieve substantial trait improvement in tetraploid potato cultivars within a relatively short time. CRISPR/Cas-mediated genome editing has opened new possibilities to develop novel potato varieties with high commercialization potential. In this review, we summarize recent developments in optimizing CRISPR/Cas-based methods for potato genome editing, focusing on approaches addressing the challenging biology of this species. We also discuss the feasibility of obtaining transgene-free genome-edited potato varieties and explore different strategies to improve potato stress resistance, nutritional value, starch composition, and storage and processing characteristics. Altogether, this review provides insight into recent advances, possible bottlenecks, and future research directions in potato genome editing using CRISPR/Cas technology.
Collapse
Affiliation(s)
- Izabela Anna Chincinska
- Department of Plant Physiology and Biotechnology, University of Gdańsk, Wita Stwosza 59, 80-308, Gdańsk, Poland.
| | - Magdalena Miklaszewska
- Department of Functional and Evolutionary Ecology, Division of Molecular Systems Biology (MOSYS), Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Dorota Sołtys-Kalina
- Plant Breeding and Acclimatization Institute-National Research Institute, Platanowa 19, 05-831, Młochów, Poland
| |
Collapse
|
21
|
Tuncel A, Qi Y. CRISPR/Cas mediated genome editing in potato: Past achievements and future directions. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 325:111474. [PMID: 36174801 DOI: 10.1016/j.plantsci.2022.111474] [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: 06/20/2022] [Revised: 08/29/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Genome engineering has been re-shaping plant biotechnology and agriculture. Crop improvement using the recently developed gene editing techniques is now easier, faster, and more precise than ever. Although considered to be a global food security crop, potato has not benefitted enough from diverse collection of these techniques. Unique genetic features of cultivated potatoes such as tetrasomic inheritance, high genomic heterozygosity, and inbreeding depression hamper conventional breeding of this important crop. Therefore, genome editing provides an excellent arsenal of tools for trait improvement in potato. Moreover, using specific transformation protocols, it is possible to engineer transgene free commercial varieties. In this review we first describe the past achievements in potato genome editing and highlight some of the missing aspects of these efforts. Then, we discuss about technical challenges of genome editing in potato and present approaches to overcome these difficulties. Finally, we talk about genome editing applications that have not been explored in potato and point out some of the missing venues in literature.
Collapse
Affiliation(s)
- Aytug Tuncel
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA.
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA.
| |
Collapse
|
22
|
Devi R, Chauhan S, Dhillon TS. Genome editing for vegetable crop improvement: Challenges and future prospects. Front Genet 2022; 13:1037091. [PMID: 36482900 PMCID: PMC9723405 DOI: 10.3389/fgene.2022.1037091] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/28/2022] [Indexed: 09/10/2024] Open
Abstract
Vegetable crops are known as protective foods due to their potential role in a balanced human diet, especially for vegetarians as they are a rich source of vitamins and minerals along with dietary fibers. Many biotic and abiotic stresses threaten the crop growth, yield and quality of these crops. These crops are annual, biennial and perennial in breeding behavior. Traditional breeding strategies pose many challenges in improving economic crop traits. As in most of the cases the large number of backcrosses and stringent selection pressure is required for the introgression of the useful traits into the germplasm, which is time and labour-intensive process. Plant scientists have improved economic traits like yield, quality, biotic stress resistance, abiotic stress tolerance, and improved nutritional quality of crops more precisely and accurately through the use of the revolutionary breeding method known as clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein-9 (Cas9). The high mutation efficiency, less off-target consequences and simplicity of this technique has made it possible to attain novel germplasm resources through gene-directed mutation. It facilitates mutagenic response even in complicated genomes which are difficult to breed using traditional approaches. The revelation of functions of important genes with the advancement of whole-genome sequencing has facilitated the CRISPR-Cas9 editing to mutate the desired target genes. This technology speeds up the creation of new germplasm resources having better agro-economical traits. This review entails a detailed description of CRISPR-Cas9 gene editing technology along with its potential applications in olericulture, challenges faced and future prospects.
Collapse
Affiliation(s)
- Ruma Devi
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, India
| | | | | |
Collapse
|
23
|
Functional inhibition of the StERF3 gene by dual targeting through CRISPR/Cas9 enhances resistance to the late blight disease in Solanum tuberosum L. Mol Biol Rep 2022; 49:11675-11684. [PMID: 36178561 DOI: 10.1007/s11033-022-07958-1] [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: 05/20/2022] [Accepted: 09/17/2022] [Indexed: 10/14/2022]
Abstract
BACKGROUND Disease-resistant cultivars are the best solution to get their maximum yield potential and avoid fungicide application. There is no doubt about the contribution, and use of R genes (resistance genes) in resistance development in plants, while S genes (susceptibility genes) also hold a strong position in pathogenesis by resistance repression, and their loss of function contributes to enhanced resistance. Hence, we attempted to knock out the function of the StERF3 gene in potatoes through CRISPR/Cas9-based genome editing and investigated the CRISPR/Cas9 approach as strategic control against late blight disease in potato plants. METHODS AND RESULTS The StERF3 gene was edited in late blight susceptible cv. Lady Rosetta. Full allelic edited plants were identified through DnpI, and N1aIV mediated restriction digestion and then further analyzed through Indel Detection by Amplicon Analysis. Sequence analysis of targeted plants for indel identification showed full allelic editing. The detached leaf assay of full allelic edited plants demonstrated the role of the StERF3 gene in susceptibility to late blight in potatoes. In planta disease assay also showed reduced, slowed, and delayed disease progression in StERF3-loss-of-function mutants compared to wild-type (control) plants. Less fungal biomass was quantified in knockouts through Real-time qPCR that supported less susceptibility of edited plants to late blight. Besides, relatively high expression of pathogens-related genes, StPR1, and StNPR1, were also observed in StERF3-loss-of-function mutants compared to the corresponding control. CONCLUSION The results showed the functional inhibition of StERF3 genes using the CRISPR/Cas9 approach. The functional knockouts (StERF3 gene-edited potato plants) revealed enhanced resistance against Phytophthora infestans, thereby demonstrating the best strategic control for late blight disease in potato plants.
Collapse
|
24
|
Recent Advances in Molecular Improvement for Potato Tuber Traits. Int J Mol Sci 2022; 23:ijms23179982. [PMID: 36077378 PMCID: PMC9456189 DOI: 10.3390/ijms23179982] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022] Open
Abstract
Potato is an important crop due to its nutritional value and high yield potential. Improving the quality and quantity of tubers remains one of the most important breeding objectives. Genetic mapping helps to identify suitable markers for use in the molecular breeding, and combined with transgenic approaches provides an efficient way for gaining desirable traits. The advanced plant breeding tools and molecular techniques, e.g., TALENS, CRISPR-Cas9, RNAi, and cisgenesis, have been successfully used to improve the yield and nutritional value of potatoes in an increasing world population scenario. The emerging methods like genome editing tools can avoid incorporating transgene to keep the food more secure. Multiple success cases have been documented in genome editing literature. Recent advances in potato breeding and transgenic approaches to improve tuber quality and quantity have been summarized in this review.
Collapse
|
25
|
Deng F, Zeng F, Shen Q, Abbas A, Cheng J, Jiang W, Chen G, Shah AN, Holford P, Tanveer M, Zhang D, Chen ZH. Molecular evolution and functional modification of plant miRNAs with CRISPR. TRENDS IN PLANT SCIENCE 2022; 27:890-907. [PMID: 35165036 DOI: 10.1016/j.tplants.2022.01.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 01/06/2022] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Gene editing using clustered regularly interspaced short palindromic repeat/CRISPR-associated proteins (CRISPR/Cas) has revolutionized biotechnology and provides genetic tools for medicine and life sciences. However, the application of this technology to miRNAs, with the function as negative gene regulators, has not been extensively reviewed in plants. Here, we summarize the evolution, biogenesis, and structure of miRNAs, as well as their interactions with mRNAs and computational models for predicting target genes. In addition, we review current advances in CRISPR/Cas for functional analysis and for modulating miRNA genes in plants. Extending our knowledge of miRNAs and their manipulation with CRISPR will provide fundamental understanding of the functions of plant miRNAs and facilitate more sustainable and publicly acceptable genetic engineering of crops.
Collapse
Affiliation(s)
- Fenglin Deng
- Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Fanrong Zeng
- Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Qiufang Shen
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Asad Abbas
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Jianhui Cheng
- Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Wei Jiang
- Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Guang Chen
- Central Laboratory, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khawaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, 64200, Pakistan
| | - Paul Holford
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Mohsin Tanveer
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7004, Australia.
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; School of Agriculture, Food, and Wine, University of Adelaide, Glen Osmond, SA, Australia.
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia; Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia.
| |
Collapse
|
26
|
Ali S, Khan N, Tang Y. Epigenetic marks for mitigating abiotic stresses in plants. JOURNAL OF PLANT PHYSIOLOGY 2022; 275:153740. [PMID: 35716656 DOI: 10.1016/j.jplph.2022.153740] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 03/02/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
Abiotic stressors are one of the major factors affecting agricultural output. Plants have evolved adaptive systems to respond appropriately to various environmental cues. These responses can be accomplished by modulating or fine-tuning genetic and epigenetic regulatory mechanisms. Understanding the response of plants' molecular features to abiotic stress is a priority in the current period of continued environmental changes. Epigenetic modifications are necessary that control gene expression by changing chromatin status and recruiting various transcription regulators. The present study summarized the current knowledge on epigenetic modifications concerning plant responses to various environmental stressors. The functional relevance of epigenetic marks in regulating stress tolerance has been revealed, and epigenetic changes impact the effector genes. This study looks at the epigenetic mechanisms that govern plant abiotic stress responses, especially DNA methylation, histone methylation/acetylation, chromatin remodeling, and various metabolites. Plant breeders will benefit from a thorough understanding of these processes to create alternative crop improvement approaches. Genome editing with clustered regularly interspaced short palindromic repeat/CRISPR-associated proteins (CRISPR/Cas) provides genetic tools to make agricultural genetic engineering more sustainable and publicly acceptable.
Collapse
Affiliation(s)
- Shahid Ali
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong Province, China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China.
| | - Naeem Khan
- Department of Agronomy, Institute of Food and Agricultural Sciences, University of Florida, FL, 32611, USA
| | - Yulin Tang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong Province, China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China.
| |
Collapse
|
27
|
Zhong Y, Qu JZ, Liu X, Ding L, Liu Y, Bertoft E, Petersen BL, Hamaker BR, Hebelstrup KH, Blennow A. Different genetic strategies to generate high amylose starch mutants by engineering the starch biosynthetic pathways. Carbohydr Polym 2022; 287:119327. [DOI: 10.1016/j.carbpol.2022.119327] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/04/2022] [Accepted: 03/06/2022] [Indexed: 01/14/2023]
|
28
|
Andreasson E, Kieu NP, Zahid MA, Carlsen FM, Marit L, Sandgrind S, Petersen BL, Zhu LH. Invited Mini-Review Research Topic: Utilization of Protoplasts to Facilitate Gene Editing in Plants: Schemes for In Vitro Shoot Regeneration From Tissues and Protoplasts of Potato and Rapeseed: Implications of Bioengineering Such as Gene Editing of Broad-Leaved Plants. Front Genome Ed 2022; 4:780004. [PMID: 35845346 PMCID: PMC9276966 DOI: 10.3389/fgeed.2022.780004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Schemes for efficient regenerationand recovery of shoots from in vitro tissues or single cells, such as protoplasts, are only available for limited numbers of plant species and genotypes and are crucial for establishing gene editing tools on a broader scale in agriculture and plant biology. Growth conditions, including hormone and nutrient composition as well as light regimes in key steps of known regeneration protocols, display significant variations, even between the genotypes within the same species, e.g., potato (Solanum tuberosum). As fresh plant material is a prerequisite for successful shoot regeneration, the plant material often needs to be refreshed for optimizing the growth and physiological state prior to genetic transformation. Utilization of protoplasts has become a more important approach for obtaining transgene-free edited plants by genome editing, CRISPR/Cas9. In this approach, callus formation from protoplasts is induced by one set of hormones, followed by organogenesis, i.e., shoot formation, which is induced by a second set of hormones. The requirements on culture conditions at these key steps vary considerably between the species and genotypes, which often require quantitative adjustments of medium compositions. In this mini-review, we outline the protocols and notes for clonal regeneration and cultivation from single cells, particularly protoplasts in potato and rapeseed. We focus mainly on different hormone treatment schemes and highlight the importance of medium compositions, e.g., sugar, nutrient, and light regimes as well as culture durations at the key regeneration steps. We believe that this review would provide important information and hints for establishing efficient regeneration strategies from other closely related and broad-leaved plant species in general.
Collapse
Affiliation(s)
- Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Lomma, Sweden
- *Correspondence: Erik Andreasson,
| | - Nam Phuong Kieu
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Muhammad Awais Zahid
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Frida Meijer Carlsen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Lenman Marit
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Sjur Sandgrind
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Bent Larsen Petersen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Li-Hua Zhu
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| |
Collapse
|
29
|
Tiwari JK, A J, Tuteja N, Khurana SMP. Genome editing (CRISPR-Cas)-mediated virus resistance in potato (Solanum tuberosum L.). Mol Biol Rep 2022; 49:12109-12119. [PMID: 35764748 DOI: 10.1007/s11033-022-07704-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 06/14/2022] [Indexed: 11/26/2022]
Abstract
Plant viruses are the major pathogens that cause heavy yield loss in potato. The important viruses are potato virus X, potato virus Y and potato leaf roll virus around the world. Besides these three viruses, a novel tomato leaf curl New Delhi virus is serious in India. Conventional cum molecular breeding and transgenics approaches have been applied to develop virus resistant potato genotypes. But progress is slow in developing resistant varieties due to lack of host genes and long breeding process, and biosafety concern with transgenics. Hence, CRISPR-Cas mediated genome editing has emerged as a powerful technology to address these issues. CRISPR-Cas technology has been deployed in potato for several important traits. We highlight here CRISPR-Cas approaches of virus resistance through targeting viral genome (DNA or RNA), host factor gene and multiplexing of target genes simultaneously. Further, advancement in CRISPR-Cas research is presented in the area of DNA-free genome editing, virus-induced genome editing, and base editing. CRISPR-Cas delivery, transformation methods, and challenges in tetraploid potato and possible methods are also discussed.
Collapse
Affiliation(s)
- Jagesh Kumar Tiwari
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India.
| | - Jeevalatha A
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala, 673012, India
| | - Narendra Tuteja
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Road, New Delhi, 110067, India
| | | |
Collapse
|
30
|
Li X, Xu S, Fuhrmann-Aoyagi MB, Yuan S, Iwama T, Kobayashi M, Miura K. CRISPR/Cas9 Technique for Temperature, Drought, and Salinity Stress Responses. Curr Issues Mol Biol 2022; 44:2664-2682. [PMID: 35735623 PMCID: PMC9221872 DOI: 10.3390/cimb44060182] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/02/2022] [Accepted: 06/06/2022] [Indexed: 02/07/2023] Open
Abstract
Global warming and climate change have severely affected plant growth and food production. Therefore, minimizing these effects is required for sustainable crop yields. Understanding the molecular mechanisms in response to abiotic stresses and improving agricultural traits to make crops tolerant to abiotic stresses have been going on unceasingly. To generate desirable varieties of crops, traditional and molecular breeding techniques have been tried, but both approaches are time-consuming. Clustered regularly interspaced short palindromic repeat/Cas9 (CRISPR/Cas9) and transcription activator-like effector nucleases (TALENs) are genome-editing technologies that have recently attracted the attention of plant breeders for genetic modification. These technologies are powerful tools in the basic and applied sciences for understanding gene function, as well as in the field of crop breeding. In this review, we focus on the application of genome-editing systems in plants to understand gene function in response to abiotic stresses and to improve tolerance to abiotic stresses, such as temperature, drought, and salinity stresses.
Collapse
Affiliation(s)
- Xiaohan Li
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; (X.L.); (S.X.); (M.B.F.-A.); (S.Y.); (T.I.); (M.K.)
| | - Siyan Xu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; (X.L.); (S.X.); (M.B.F.-A.); (S.Y.); (T.I.); (M.K.)
| | - Martina Bianca Fuhrmann-Aoyagi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; (X.L.); (S.X.); (M.B.F.-A.); (S.Y.); (T.I.); (M.K.)
| | - Shaoze Yuan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; (X.L.); (S.X.); (M.B.F.-A.); (S.Y.); (T.I.); (M.K.)
| | - Takeru Iwama
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; (X.L.); (S.X.); (M.B.F.-A.); (S.Y.); (T.I.); (M.K.)
| | - Misaki Kobayashi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; (X.L.); (S.X.); (M.B.F.-A.); (S.Y.); (T.I.); (M.K.)
| | - Kenji Miura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; (X.L.); (S.X.); (M.B.F.-A.); (S.Y.); (T.I.); (M.K.)
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, Tsukuba 305-8572, Japan
| |
Collapse
|
31
|
Mahto RK, Ambika, Singh C, Chandana BS, Singh RK, Verma S, Gahlaut V, Manohar M, Yadav N, Kumar R. Chickpea Biofortification for Cytokinin Dehydrogenase via Genome Editing to Enhance Abiotic-Biotic Stress Tolerance and Food Security. Front Genet 2022; 13:900324. [PMID: 35669196 PMCID: PMC9164125 DOI: 10.3389/fgene.2022.900324] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
Globally more than two billion people suffer from micronutrient malnutrition (also known as "hidden hunger"). Further, the pregnant women and children in developing nations are mainly affected by micronutrient deficiencies. One of the most important factors is food insecurity which can be mitigated by improving the nutritional values through biofortification using selective breeding and genetic enhancement techniques. Chickpea is the second most important legume with numerous economic and nutraceutical properties. Therefore, chickpea production needs to be increased from the current level. However, various kind of biotic and abiotic stresses hamper global chickpea production. The emerging popular targets for biofortification in agronomic crops include targeting cytokinin dehydrogenase (CKX). The CKXs play essential roles in both physiological and developmental processes and directly impact several agronomic parameters i.e., growth, development, and yield. Manipulation of CKX genes using genome editing tools in several crop plants reveal that CKXs are involved in regulation yield, shoot and root growth, and minerals nutrition. Therefore, CKXs have become popular targets for yield improvement, their overexpression and mutants can be directly correlated with the increased yield and tolerance to various stresses. Here, we provide detailed information on the different roles of CKX genes in chickpea. In the end, we discuss the utilization of genome editing tool clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9 (CRISPR/Cas9) to engineer CKX genes that can facilitate trait improvement. Overall, recent advancements in CKX and their role in plant growth, stresses and nutrient accumulation are highlighted, which could be used for chickpea improvement.
Collapse
Affiliation(s)
| | - Ambika
- Department of Genetics and Plant Breeding, UAS, Bangalore, India
| | - Charul Singh
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - B S. Chandana
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | | | - Shruti Verma
- NCoE-SAM, Department of Pediatrics, KSCH, Lady Hardinge Medical College, New Delhi, India
| | - Vijay Gahlaut
- Institute of Himalayan Bioresource Technology (CSIR), Palampur, India
| | - Murli Manohar
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Neelam Yadav
- Centre of Food Technology, University of Allahabad, Prayagraj, India
| | - Rajendra Kumar
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| |
Collapse
|
32
|
CRISPR/Cas9-Mediated Mutagenesis of the Granule-Bound Starch Synthase Gene in the Potato Variety Yukon Gold to Obtain Amylose-Free Starch in Tubers. Int J Mol Sci 2022; 23:ijms23094640. [PMID: 35563030 PMCID: PMC9101600 DOI: 10.3390/ijms23094640] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 02/04/2023] Open
Abstract
Potato (Solanum tuberosum L.) is the third most important food crop after rice and wheat. Its tubers are a rich source of dietary carbohydrates in the form of starch, which has many industrial applications. Starch is composed of two polysaccharides, amylose and amylopectin, and their ratios determine different properties and functionalities. Potato varieties with higher amylopectin have many food processing and industrial applications. Using Agrobacterium-mediated transformation, we delivered Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR/Cas9) reagents to potato (variety Yukon Gold) cells to disrupt the granule-bound starch synthase (gbssI) gene with the aim of eliminating the amylose component of starch. Lugol-Iodine staining of the tubers showed a reduction or complete elimination of amylose in some of the edited events. These results were further confirmed by the perchloric acid and enzymatic methods. One event (T2-7) showed mutations in all four gbss alleles and total elimination of amylose from the tubers. Viscosity profiles of the tuber starch from six different knockout events were determined using a Rapid Visco Analyzer (RVA), and the values reflected the amylopectin/amylose ratio. Follow-up studies will focus on eliminating the CRISPR components from the events and on evaluating the potential of clones with various amylose/amylopectin ratios for food processing and other industrial applications.
Collapse
|
33
|
Luo S, Ma Q, Zhong Y, Jing J, Wei Z, Zhou W, Lu X, Tian Y, Zhang P. Editing of the starch branching enzyme gene SBE2 generates high-amylose storage roots in cassava. PLANT MOLECULAR BIOLOGY 2022; 106:67-84. [PMID: 34792751 DOI: 10.1007/s11103-021-01130-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/09/2021] [Indexed: 05/25/2023]
Abstract
The production of high-amylose cassava through CRISPR/Cas9-mediated mutagenesis of the starch branching enzyme gene SBE2 was firstly achieved. High-amylose cassava (Manihot esculenta Crantz) is desirable for starch industrial applications and production of healthier processed food for human consumption. In this study, we report the production of high-amylose cassava through CRISPR/Cas9-mediated mutagenesis of the starch branching enzyme 2 (SBE2). Mutations in two targeted exons of SBE2 were identified in all regenerated plants; these mutations, which included nucleotide insertions, and short or long deletions in the SBE2 gene, were classified into eight mutant lines. Three mutants, M6, M7 and M8, with long fragment deletions in the second exon of SBE2 showed no accumulation of SBE2 protein. After harvest from the field, significantly higher amylose (up to 56% in apparent amylose content) and resistant starch (up to 35%) was observed in these mutants compared with the wild type, leading to darker blue coloration of starch granules after quick iodine staining and altered starch viscosity with a higher pasting temperature and peak time. Further 1H-NMR analysis revealed a significant reduction in the degree of starch branching, together with fewer short chains (degree of polymerization [DP] 15-25) and more long chains (DP>25 and especially DP>40) of amylopectin, which indicates that cassava SBE2 catalyzes short chain formation during amylopectin biosynthesis. Transition from A- to B-type crystallinity was also detected in the starches. Our study showed that CRISPR/Cas9-mediated mutagenesis of starch biosynthetic genes in cassava is an effective approach for generating novel varieties with valuable starch properties for food and industrial applications.
Collapse
Affiliation(s)
- Shu Luo
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qiuxiang Ma
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Yingying Zhong
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- Shanghai Sanshu Biotechnology Co., LTD, Shanghai, 201210, China
| | - Jianling Jing
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zusheng Wei
- Guangxi Subtropical Crops Research Institute, Nanning, 530001, China
| | - Wenzhi Zhou
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- Shanghai Sanshu Biotechnology Co., LTD, Shanghai, 201210, China
| | - Xinlu Lu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yinong Tian
- Guangxi Subtropical Crops Research Institute, Nanning, 530001, China
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
- University of Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
34
|
Luo S, Ma Q, Zhong Y, Jing J, Wei Z, Zhou W, Lu X, Tian Y, Zhang P. Editing of the starch branching enzyme gene SBE2 generates high-amylose storage roots in cassava. PLANT MOLECULAR BIOLOGY 2022; 108:429-442. [PMID: 34792751 DOI: 10.1007/s11103-021-01215-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Abstract
The production of high-amylose cassava through CRISPR/Cas9-mediated mutagenesis of the starch branching enzyme gene SBE2 was firstly achieved. High-amylose cassava (Manihot esculenta Crantz) is desirable for starch industrial applications and production of healthier processed food for human consumption. In this study, we report the production of high-amylose cassava through CRISPR/Cas9-mediated mutagenesis of the starch branching enzyme 2 (SBE2). Mutations in two targeted exons of SBE2 were identified in all regenerated plants; these mutations, which included nucleotide insertions, and short or long deletions in the SBE2 gene, were classified into eight mutant lines. Three mutants, M6, M7 and M8, with long fragment deletions in the second exon of SBE2 showed no accumulation of SBE2 protein. After harvest from the field, significantly higher amylose (up to 56% in apparent amylose content) and resistant starch (up to 35%) was observed in these mutants compared with the wild type, leading to darker blue coloration of starch granules after quick iodine staining and altered starch viscosity with a higher pasting temperature and peak time. Further 1H-NMR analysis revealed a significant reduction in the degree of starch branching, together with fewer short chains (degree of polymerization [DP] 15-25) and more long chains (DP>25 and especially DP>40) of amylopectin, which indicates that cassava SBE2 catalyzes short chain formation during amylopectin biosynthesis. Transition from A- to B-type crystallinity was also detected in the starches. Our study showed that CRISPR/Cas9-mediated mutagenesis of starch biosynthetic genes in cassava is an effective approach for generating novel varieties with valuable starch properties for food and industrial applications.
Collapse
Affiliation(s)
- Shu Luo
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qiuxiang Ma
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Yingying Zhong
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- Shanghai Sanshu Biotechnology Co., LTD, Shanghai, 201210, China
| | - Jianling Jing
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zusheng Wei
- Guangxi Subtropical Crops Research Institute, Nanning, 530001, China
| | - Wenzhi Zhou
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- Shanghai Sanshu Biotechnology Co., LTD, Shanghai, 201210, China
| | - Xinlu Lu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yinong Tian
- Guangxi Subtropical Crops Research Institute, Nanning, 530001, China
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
- University of Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
35
|
Tiwari JK, Buckseth T, Challam C, Zinta R, Bhatia N, Dalamu D, Naik S, Poonia AK, Singh RK, Luthra SK, Kumar V, Kumar M. CRISPR/Cas Genome Editing in Potato: Current Status and Future Perspectives. Front Genet 2022; 13:827808. [PMID: 35186041 PMCID: PMC8849127 DOI: 10.3389/fgene.2022.827808] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/11/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
| | | | | | - Rasna Zinta
- ICAR-Central Potato Research Institute, Shimla, India.,School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, India
| | - Nisha Bhatia
- ICAR-Central Potato Research Institute, Shimla, India.,School of Biotechnology, Shoolini University, Solan, India
| | - Dalamu Dalamu
- ICAR-Central Potato Research Institute, Shimla, India
| | - Sharmistha Naik
- ICAR-Central Potato Research Institute, Shimla, India.,ICAR-National Research Centre for Grapes, Pune, India
| | - Anuj K Poonia
- School of Biotechnology, Shoolini University, Solan, India
| | | | | | - Vinod Kumar
- ICAR-Central Potato Research Institute, Shimla, India
| | - Manoj Kumar
- ICAR-Central Potato Research Institute, Meerut, India
| |
Collapse
|
36
|
Carlsen FM, Johansen IE, Yang Z, Liu Y, Westberg IN, Kieu NP, Jørgensen B, Lenman M, Andreasson E, Nielsen KL, Blennow A, Petersen BL. Strategies for Efficient Gene Editing in Protoplasts of Solanum tuberosum Theme: Determining gRNA Efficiency Design by Utilizing Protoplast (Research). Front Genome Ed 2022; 3:795644. [PMID: 35128523 PMCID: PMC8811252 DOI: 10.3389/fgeed.2021.795644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
Potato, Solanum tuberosum is a highly diverse tetraploid crop. Elite cultivars are extremely heterozygous with a high prevalence of small length polymorphisms (indels) and single nucleotide polymorphisms (SNPs) within and between cultivars, which must be considered in CRISPR/Cas gene editing strategies and designs to obtain successful gene editing. In the present study, in-depth sequencing of the gene encoding glucan water dikinase (GWD) 1 and the downy mildew resistant 6 (DMR6-1) genes in the potato cultivars Saturna and Wotan, respectively, revealed both indels and a 1.3–2.8 higher SNP prevalence when compared to the heterozygous diploid RH genome sequence as expected for a tetraploid compared to a diploid. This complicates guide RNA (gRNA) and diagnostic PCR designs. At the same time, high editing efficiencies at the cell pool (protoplast) level are pivotal for achieving full allelic knock-out in tetraploids. Furthermore, high editing efficiencies reduce the downstream cumbersome and delicate ex-plant regeneration. Here, CRISPR/Cas ribonucleoprotein particles (RNPs) were delivered transiently to protoplasts by polyethylene glycol (PEG) mediated transformation. For each of GWD1 and the DMR6-1, 6–10 gRNAs were designed to target regions comprising the 5′ and the 3′ end of the two genes. Similar to other studies including several organisms, editing efficiency of the individual RNPs varied significantly, and some generated specific indel patterns. RNP’s targeting the 5′ end of GWD1 yielded significantly higher editing efficiency as compared to targeting the 3′ end. For DMR6-1, such an effect was not seen. Simultaneously targeting each of the two target regions with two RNPs (multiplexing) yielded a clear positive synergistic effect on the total editing when targeting the 3′ end of the GWD1 gene only. Multiplexing of the two genes, residing on different chromosomes, yielded no or a slightly negative effect on editing from the single or combined gRNA/RNPs. These initial findings may instigate much larger studies needed for facilitating and optimizing precision breeding in plants.
Collapse
Affiliation(s)
- Frida Meijer Carlsen
- Department of Plant and Environmental Sciences, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Ida Elisabeth Johansen
- Department of Plant and Environmental Sciences, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
- Kartoffel Mel Centralen Amba, Brande, Denmark
| | - Zhang Yang
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ying Liu
- Department of Plant and Environmental Sciences, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Ida Nøhr Westberg
- Department of Plant and Environmental Sciences, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Nam Phuong Kieu
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Bodil Jørgensen
- Department of Plant and Environmental Sciences, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Marit Lenman
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Andreas Blennow
- Department of Plant and Environmental Sciences, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Bent Larsen Petersen
- Department of Plant and Environmental Sciences, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
- *Correspondence: Bent Larsen Petersen,
| |
Collapse
|
37
|
Nahirñak V, Almasia NI, González MN, Massa GA, Décima Oneto CA, Feingold SE, Hopp HE, Vazquez Rovere C. State of the Art of Genetic Engineering in Potato: From the First Report to Its Future Potential. FRONTIERS IN PLANT SCIENCE 2022; 12:768233. [PMID: 35082806 PMCID: PMC8784693 DOI: 10.3389/fpls.2021.768233] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
Potato (Solanum tuberosum L.) is a crop of world importance that produces tubers of high nutritional quality. It is considered one of the promising crops to overcome the challenges of poverty and hunger worldwide. However, it is exposed to different biotic and abiotic stresses that can cause significant losses in production. Thus, potato is a candidate of special relevance for improvements through conventional breeding and biotechnology. Since conventional breeding is time-consuming and challenging, genetic engineering provides the opportunity to introduce/switch-off genes of interest without altering the allelic combination that characterize successful commercial cultivars or to induce targeted sequence modifications by New Breeding Techniques. There is a variety of methods for potato improvement via genetic transformation. Most of them incorporate genes of interest into the nuclear genome; nevertheless, the development of plastid transformation protocols broadened the available approaches for potato breeding. Although all methods have their advantages and disadvantages, Agrobacterium-mediated transformation is the most used approach. Alternative methods such as particle bombardment, protoplast transfection with polyethylene glycol and microinjection are also effective. Independently of the DNA delivery approach, critical steps for a successful transformation are a rapid and efficient regeneration protocol and a selection system. Several critical factors affect the transformation efficiency: vector type, insert size, Agrobacterium strain, explant type, composition of the subculture media, selective agent, among others. Moreover, transient or stable transformation, constitutive or inducible promoters, antibiotic/herbicide resistance or marker-free strategies can be considered. Although great efforts have been made to optimize all the parameters, potato transformation protocols are highly genotype-dependent. Genome editing technologies provide promising tools in genetic engineering allowing precise modification of targeted sequences. Interestingly, transient expression of genome editing components in potato protoplasts was reported to generate edited plants without the integration of any foreign DNA, which is a valuable aspect from both a scientific and a regulatory perspective. In this review, current challenges and opportunities concerning potato genetic engineering strategies developed to date are discussed. We describe their critical parameters and constrains, and the potential application of the available tools for functional analyses or biotechnological purposes. Public concerns and safety issues are also addressed.
Collapse
Affiliation(s)
- Vanesa Nahirñak
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
| | - Natalia I. Almasia
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
| | - Matías N. González
- Laboratorio de Agrobiotecnología, IPADS (INTA – CONICET), Balcarce, Argentina
| | - Gabriela A. Massa
- Laboratorio de Agrobiotecnología, IPADS (INTA – CONICET), Balcarce, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - Cecilia A. Décima Oneto
- Laboratorio de Agrobiotecnología, IPADS (INTA – CONICET), Balcarce, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - Sergio E. Feingold
- Laboratorio de Agrobiotecnología, IPADS (INTA – CONICET), Balcarce, Argentina
| | - Horacio E. Hopp
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Cecilia Vazquez Rovere
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
| |
Collapse
|
38
|
Zhang S, Wu S, Hu C, Yang Q, Dong T, Sheng O, Deng G, He W, Dou T, Li C, Sun C, Yi G, Bi F. Increased mutation efficiency of CRISPR/Cas9 genome editing in banana by optimized construct. PeerJ 2022; 10:e12664. [PMID: 35036088 PMCID: PMC8742547 DOI: 10.7717/peerj.12664] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/30/2021] [Indexed: 01/07/2023] Open
Abstract
The CRISPR/Cas9-mediated genome editing system has been used extensively to engineer targeted mutations in a wide variety of species. Its application in banana, however, has been hindered because of the species' triploid nature and low genome editing efficiency. This has delayed the development of a DNA-free genome editing approach. In this study, we reported that the endogenous U6 promoter and banana codon-optimized Cas9 apparently increased mutation frequency in banana, and we generated a method to validate the mutation efficiency of the CRISPR/Cas9-mediated genome editing system based on transient expression in protoplasts. The activity of the MaU6c promoter was approximately four times higher than that of the OsU6a promoter in banana protoplasts. The application of this promoter and banana codon-optimized Cas9 in CRISPR/Cas9 cassette resulted in a fourfold increase in mutation efficiency compared with the previous CRISPR/Cas9 cassette for banana. Our results indicated that the optimized CRISPR/Cas9 system was effective for mutating targeted genes in banana and thus will improve the applications for basic functional genomics. These findings are relevant to future germplasm improvement and provide a foundation for developing DNA-free genome editing technology in banana.
Collapse
Affiliation(s)
- Sen Zhang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China,College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Shaoping Wu
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China,College of Life Sciences, Zhaoqing University, Zhaoqing, Guangdong, China
| | - Chunhua Hu
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Qiaosong Yang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Tao Dong
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Ou Sheng
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Guiming Deng
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Weidi He
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Tongxin Dou
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Chunyu Li
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Chenkang Sun
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China,College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong
| | - Ganjun Yi
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Fangcheng Bi
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| |
Collapse
|
39
|
Kumar M, Ayzenshtat D, Marko A, Bocobza S. Optimization of T-DNA configuration with UBIQUITIN10 promoters and tRNA-sgRNA complexes promotes highly efficient genome editing in allotetraploid tobacco. PLANT CELL REPORTS 2022; 41:175-194. [PMID: 34623476 DOI: 10.1007/s00299-021-02796-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
KEY MESSAGE Combination of UBIQUITIN10 promoter-directed CAS9 and tRNA-gRNA complexes in gene-editing assay induces 80% mutant phenotype with a knockout of the four allelic copies in the T0 generation of allotetraploid tobaccos. While gene-editing methodologies, such as CRISPR-Cas9, have been developed and successfully used in many plant species, their use remains challenging, because they most often rely on stable or transient transgene expression. Regrettably, in all plant species, transformation causes epigenetic effects such as gene silencing and variable transgene expression. Here, UBIQUITIN10 promoters from several plant species were characterized and showed their capacity to direct high levels of transgene expression in transient and stable transformation assays, which in turn was used to improve the selection process of regenerated transformants. Furthermore, we compared various sgRNAs delivery systems and showed that the combination of UBIQUITIN10 promoters and tRNA-sgRNA complexes produced 80% mutant phenotype with a complete knockout of the four allelic copies, while the remaining 20% exhibited weaker phenotype, which suggested partial allelic knockout, in the T0 generation of the allotetraploid Nicotiana tabacum. These data provide valuable information to optimize future designs of gene editing constructs for plant research and crop improvement and open the way for valuable gene editing projects in non-model Solanaceae species.
Collapse
MESH Headings
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- DNA, Plant/genetics
- DNA, Plant/metabolism
- Gene Editing/methods
- Genome, Plant
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Promoter Regions, Genetic/genetics
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Tetraploidy
- Nicotiana/genetics
- Ubiquitins/genetics
- Ubiquitins/metabolism
Collapse
Affiliation(s)
- Manoj Kumar
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Rishon LeZion, Israel
| | - Dana Ayzenshtat
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Rishon LeZion, Israel
| | - Adar Marko
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Rishon LeZion, Israel
| | - Samuel Bocobza
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Rishon LeZion, Israel.
| |
Collapse
|
40
|
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.
Collapse
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.
| |
Collapse
|
41
|
Tussipkan D, Manabayeva SA. Employing CRISPR/Cas Technology for the Improvement of Potato and Other Tuber Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:747476. [PMID: 34764969 PMCID: PMC8576567 DOI: 10.3389/fpls.2021.747476] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/04/2021] [Indexed: 05/07/2023]
Abstract
New breeding technologies have not only revolutionized biological science, but have also been employed to generate transgene-free products. Genome editing is a powerful technology that has been used to modify genomes of several important crops. This review describes the basic mechanisms, advantages and disadvantages of genome editing systems, such as ZFNs, TALENs, and CRISPR/Cas. Secondly, we summarize in detail all studies of the CRISPR/Cas system applied to potato and other tuber crops, such as sweet potato, cassava, yam, and carrot. Genes associated with self-incompatibility, abiotic-biotic resistance, nutrient-antinutrient content, and post-harvest factors targeted utilizing the CRISPR/Cas system are analyzed in this review. We hope that this review provides fundamental information that will be useful for future breeding of tuber crops to develop novel cultivars.
Collapse
Affiliation(s)
| | - Shuga A. Manabayeva
- Plant Genetic Engineering Laboratory, National Center for Biotechnology, Nur-Sultan, Kazakhstan
| |
Collapse
|
42
|
|
43
|
Kieu NP, Lenman M, Wang ES, Petersen BL, Andreasson E. Mutations introduced in susceptibility genes through CRISPR/Cas9 genome editing confer increased late blight resistance in potatoes. Sci Rep 2021; 11:4487. [PMID: 33627728 PMCID: PMC7904907 DOI: 10.1038/s41598-021-83972-w] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 02/10/2021] [Indexed: 01/31/2023] Open
Abstract
The use of pathogen-resistant cultivars is expected to increase yield and decrease fungicide use in agriculture. However, in potato breeding, increased resistance obtained via resistance genes (R-genes) is hampered because R-gene(s) are often specific for a pathogen race and can be quickly overcome by the evolution of the pathogen. In parallel, susceptibility genes (S-genes) are important for pathogenesis, and loss of S-gene function confers increased resistance in several plants, such as rice, wheat, citrus and tomatoes. In this article, we present the mutation and screening of seven putative S-genes in potatoes, including two DMR6 potato homologues. Using a CRISPR/Cas9 system, which conferred co-expression of two guide RNAs, tetra-allelic deletion mutants were generated and resistance against late blight was assayed in the plants. Functional knockouts of StDND1, StCHL1, and DMG400000582 (StDMR6-1) generated potatoes with increased resistance against late blight. Plants mutated in StDND1 showed pleiotropic effects, whereas StDMR6-1 and StCHL1 mutated plants did not exhibit any growth phenotype, making them good candidates for further agricultural studies. Additionally, we showed that DMG401026923 (here denoted StDMR6-2) knockout mutants did not demonstrate any increased late blight resistance, but exhibited a growth phenotype, indicating that StDMR6-1 and StDMR6-2 have different functions. To the best of our knowledge, this is the first report on the mutation and screening of putative S-genes in potatoes, including two DMR6 potato homologues.
Collapse
Affiliation(s)
- Nam Phuong Kieu
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Marit Lenman
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Eu Sheng Wang
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Bent Larsen Petersen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsen's vej 40, 1871, Frederiksberg C, Denmark
| | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden.
| |
Collapse
|
44
|
Chauvin L, Sevestre F, Lukan T, Nogué F, Gallois JL, Chauvin JE, Veillet F. Gene Editing in Potato Using CRISPR-Cas9 Technology. Methods Mol Biol 2021; 2354:331-351. [PMID: 34448168 DOI: 10.1007/978-1-0716-1609-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Genome editing in the cultivated potato (Solanum tuberosum), a vegetatively propagated and highly heterozygous species, constitutes a promising trail to directly improve traits into elite cultivars. With the recent and successful development of the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 system in eukaryotic cells, the plant science community has gained access to a powerful, inexpensive, and easy-to-use toolbox to target and inactivate/modify specific genes. The specificity and versatility of the CRISPR-Cas9 system rely on a variable 20 bp spacer sequence at the 5' end of a single-guide RNA (sgRNA), which directs the SpCas9 (Streptococcus pyogenes) nuclease to cut the target DNA at a precise locus with no or low off-target events. Using this system, we and other teams were able to knock out specific genes in potato through the error-prone non-homologous end-joining (NHEJ) DNA repair mechanism. In this chapter, we describe strategies to design and clone spacer sequences into CRISPR-SpCas9 plasmids. We show how these constructs can be used for Agrobacterium-mediated stable transformation or transient transfection of protoplasts, and we describe the optimization of these two delivery methods, as well as of the plant regeneration processes. Finally, the molecular screening and characterization of edited potato plants are also described, mainly relying on PCR-based methods such as high-resolution melt (HRM) analysis.
Collapse
Affiliation(s)
- Laura Chauvin
- IGEPP, INRAE, Institut Agro, Univ Rennes, Ploudaniel, France
| | - François Sevestre
- Unité de Glycobiologie Structurale et Fonctionnelle, Univ. Lille, CNRS, UMR8576, UGSF, Lille, France
- Univ. Lille, CNRS, USR 3290, MSAP, Miniaturisation pour la Synthèse, l'Analyse et la Protéomique, Lille, France
| | - Tjaša Lukan
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | | | | | - Florian Veillet
- IGEPP, INRAE, Institut Agro, Univ Rennes, Ploudaniel, France.
| |
Collapse
|
45
|
Badhan S, Ball AS, Mantri N. First Report of CRISPR/Cas9 Mediated DNA-Free Editing of 4CL and RVE7 Genes in Chickpea Protoplasts. Int J Mol Sci 2021; 22:E396. [PMID: 33401455 PMCID: PMC7795094 DOI: 10.3390/ijms22010396] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 12/13/2022] Open
Abstract
The current genome editing system Clustered Regularly Interspaced Short Palindromic Repeats Cas9 (CRISPR/Cas9) has already confirmed its proficiency, adaptability, and simplicity in several plant-based applications. Together with the availability of a vast amount of genome data and transcriptome data, CRISPR/Cas9 presents a massive opportunity for plant breeders and researchers. The successful delivery of ribonucleoproteins (RNPs), which are composed of Cas9 enzyme and a synthetically designed single guide RNA (sgRNA) and are used in combination with various transformation methods or lately available novel nanoparticle-based delivery approaches, allows targeted mutagenesis in plants species. Even though this editing technique is limitless, it has still not been employed in many plant species to date. Chickpea is the second most crucial winter grain crop cultivated worldwide; there are currently no reports on CRISPR/Cas9 gene editing in chickpea. Here, we selected the 4-coumarate ligase (4CL) and Reveille 7 (RVE7) genes, both associated with drought tolerance for CRISPR/Cas9 editing in chickpea protoplast. The 4CL represents a key enzyme involved in phenylpropanoid metabolism in the lignin biosynthesis pathway. It regulates the accumulation of lignin under stress conditions in several plants. The RVE7 is a MYB transcription factor which is part of regulating circadian rhythm in plants. The knockout of these selected genes in the chickpea protoplast using DNA-free CRISPR/Cas9 editing represents a novel approach for achieving targeted mutagenesis in chickpea. Results showed high-efficiency editing was achieved for RVE7 gene in vivo compared to the 4CL gene. This study will help unravel the role of these genes under drought stress and understand the complex drought stress mechanism pathways. This is the first study in chickpea protoplast utilizing CRISPR/Cas9 DNA free gene editing of drought tolerance associated genes.
Collapse
Affiliation(s)
| | | | - Nitin Mantri
- The Pangenomics Lab, School of Science, RMIT University, Melbourne 3000, Australia; (S.B.); (A.S.B.)
| |
Collapse
|
46
|
Bennett EP, Petersen BL, Johansen IE, Niu Y, Yang Z, Chamberlain CA, Met Ö, Wandall HH, Frödin M. INDEL detection, the 'Achilles heel' of precise genome editing: a survey of methods for accurate profiling of gene editing induced indels. Nucleic Acids Res 2020; 48:11958-11981. [PMID: 33170255 PMCID: PMC7708060 DOI: 10.1093/nar/gkaa975] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 10/05/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022] Open
Abstract
Advances in genome editing technologies have enabled manipulation of genomes at the single base level. These technologies are based on programmable nucleases (PNs) that include meganucleases, zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated 9 (Cas9) nucleases and have given researchers the ability to delete, insert or replace genomic DNA in cells, tissues and whole organisms. The great flexibility in re-designing the genomic target specificity of PNs has vastly expanded the scope of gene editing applications in life science, and shows great promise for development of the next generation gene therapies. PN technologies share the principle of inducing a DNA double-strand break (DSB) at a user-specified site in the genome, followed by cellular repair of the induced DSB. PN-elicited DSBs are mainly repaired by the non-homologous end joining (NHEJ) and the microhomology-mediated end joining (MMEJ) pathways, which can elicit a variety of small insertion or deletion (indel) mutations. If indels are elicited in a protein coding sequence and shift the reading frame, targeted gene knock out (KO) can readily be achieved using either of the available PNs. Despite the ease by which gene inactivation in principle can be achieved, in practice, successful KO is not only determined by the efficiency of NHEJ and MMEJ repair; it also depends on the design and properties of the PN utilized, delivery format chosen, the preferred indel repair outcomes at the targeted site, the chromatin state of the target site and the relative activities of the repair pathways in the edited cells. These variables preclude accurate prediction of the nature and frequency of PN induced indels. A key step of any gene KO experiment therefore becomes the detection, characterization and quantification of the indel(s) induced at the targeted genomic site in cells, tissues or whole organisms. In this survey, we briefly review naturally occurring indels and their detection. Next, we review the methods that have been developed for detection of PN-induced indels. We briefly outline the experimental steps and describe the pros and cons of the various methods to help users decide a suitable method for their editing application. We highlight recent advances that enable accurate and sensitive quantification of indel events in cells regardless of their genome complexity, turning a complex pool of different indel events into informative indel profiles. Finally, we review what has been learned about PN-elicited indel formation through the use of the new methods and how this insight is helping to further advance the genome editing field.
Collapse
Affiliation(s)
- Eric Paul Bennett
- Copenhagen Center for Glycomics, Department of Odontology and Molecular and Cellular Medicine, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Bent Larsen Petersen
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Ida Elisabeth Johansen
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Yiyuan Niu
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, China
| | - Zhang Yang
- Copenhagen Center for Glycomics, Department of Odontology and Molecular and Cellular Medicine, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | | | - Özcan Met
- Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hans H Wandall
- Copenhagen Center for Glycomics, Department of Odontology and Molecular and Cellular Medicine, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Morten Frödin
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
47
|
Blennow A, Skryhan K, Tanackovic V, Krunic SL, Shaik SS, Andersen MS, Kirk H, Nielsen KL. Non-GMO potato lines, synthesizing increased amylose and resistant starch, are mainly deficient in isoamylase debranching enzyme. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:2096-2108. [PMID: 32096588 PMCID: PMC7540516 DOI: 10.1111/pbi.13367] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/31/2020] [Accepted: 02/17/2020] [Indexed: 05/04/2023]
Abstract
Solanum tuberosum potato lines with high amylose content were generated by crossing with the wild potato species Solanum sandemanii followed by repeated backcrossing to Solanum tuberosum lines. The trait, termed increased amylose (IAm), was recessive and present after three generations of backcrossing into S. tuberosum lines (6.25% S. sandemanii genes). The tubers of these lines were small, elongated and irregular with small and misshaped starch granules and high sugar content. Additional backcrossing resulted in less irregular tuber morphology, increased starch content (4.3%-9.5%) and increased amylose content (29%-37.9%) but indifferent sugar content. The amylose in the IAm starch granules was mainly located in peripheral spots, and large cavities were found in the granules. Starch pasting was suppressed, and the digestion-resistant starch (RS) content was increased. Comprehensive microarray polymer profiling (CoMPP) analysis revealed specific alterations of major pectic and glycoprotein cell wall components. This complex phenotype led us to search for candidate IAm genes exploiting its recessive trait. Hence, we sequenced genomic DNA of a pool of IAm lines, identified SNPs genome wide against the draft genome sequence of potato and searched for regions of decreased heterozygosity. Three regions, located on chromosomes 3, 7 and 10, respectively, displayed markedly less heterozygosity than average. The only credible starch metabolism-related gene found in these regions encoded the isoamylase-type debranching enzyme Stisa1. Decreased expression of mRNA (>500 fold) and reduced enzyme activity (virtually absent from IAm lines) supported Stisa1 as a candidate gene for IAm.
Collapse
Affiliation(s)
- Andreas Blennow
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Katsiaryna Skryhan
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Vanja Tanackovic
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Susanne L. Krunic
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Shahnoor S. Shaik
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | | | | | - Kåre L. Nielsen
- Department of Chemistry and BiologyAalborg UniversityAalborgDenmark
| |
Collapse
|
48
|
Schenke D, Cai D. Applications of CRISPR/Cas to Improve Crop Disease Resistance: Beyond Inactivation of Susceptibility Factors. iScience 2020; 23:101478. [PMID: 32891884 PMCID: PMC7479627 DOI: 10.1016/j.isci.2020.101478] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/25/2020] [Accepted: 08/17/2020] [Indexed: 12/14/2022] Open
Abstract
Current crop production systems are prone to increasing pathogen pressure. Fundamental understanding of molecular plant-pathogen interactions, the availability of crop and pathogen genomic information, as well as emerging genome editing permits a novel approach for breeding of crop disease resistance. We describe here strategies to identify new targets for resistance breeding with focus on interruption of the compatible plant-pathogen interaction by CRISPR/Cas-mediated genome editing. Basically, crop genome editing can be applied in several ways to achieve this goal. The most common approach focuses on the "simple" knockout by non-homologous end joining repair of plant susceptibility factors required for efficient host colonization. However, genome re-writing via homology-directed repair or base editing can also prevent host manipulation by changing the targets of pathogen-derived effectors or molecules beyond recognition, which also decreases plant susceptibility. We conclude that genome editing by CRISPR/Cas will become increasingly indispensable to generate in relatively short time beneficial resistance traits in crops to meet upcoming challenges.
Collapse
Affiliation(s)
- Dirk Schenke
- Institute of Phytopathology, Department of Molecular Phytopathology and Biotechnology, Christian-Albrechts-University of Kiel, Hermann Rodewald Str. 9, 24118 Kiel, Germany
| | - Daguang Cai
- Institute of Phytopathology, Department of Molecular Phytopathology and Biotechnology, Christian-Albrechts-University of Kiel, Hermann Rodewald Str. 9, 24118 Kiel, Germany
| |
Collapse
|
49
|
López-Marqués RL, Nørrevang AF, Ache P, Moog M, Visintainer D, Wendt T, Østerberg JT, Dockter C, Jørgensen ME, Salvador AT, Hedrich R, Gao C, Jacobsen SE, Shabala S, Palmgren M. Prospects for the accelerated improvement of the resilient crop quinoa. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5333-5347. [PMID: 32643753 PMCID: PMC7501820 DOI: 10.1093/jxb/eraa285] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 06/11/2020] [Indexed: 05/04/2023]
Abstract
Crops tolerant to drought and salt stress may be developed by two approaches. First, major crops may be improved by introducing genes from tolerant plants. For example, many major crops have wild relatives that are more tolerant to drought and high salinity than the cultivated crops, and, once deciphered, the underlying resilience mechanisms could be genetically manipulated to produce crops with improved tolerance. Secondly, some minor (orphan) crops cultivated in marginal areas are already drought and salt tolerant. Improving the agronomic performance of these crops may be an effective way to increase crop and food diversity, and an alternative to engineering tolerance in major crops. Quinoa (Chenopodium quinoa Willd.), a nutritious minor crop that tolerates drought and salinity better than most other crops, is an ideal candidate for both of these approaches. Although quinoa has yet to reach its potential as a fully domesticated crop, breeding efforts to improve the plant have been limited. Molecular and genetic techniques combined with traditional breeding are likely to change this picture. Here we analyse protein-coding sequences in the quinoa genome that are orthologous to domestication genes in established crops. Mutating only a limited number of such genes by targeted mutagenesis appears to be a promising route for accelerating the improvement of quinoa and generating a nutritious high-yielding crop that can meet the future demand for food production in a changing climate.
Collapse
Affiliation(s)
- Rosa L López-Marqués
- NovoCrops Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- Correspondence: or
| | - Anton F Nørrevang
- NovoCrops Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Peter Ache
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Max Moog
- NovoCrops Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Davide Visintainer
- NovoCrops Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Toni Wendt
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V, Denmark
| | - Jeppe T Østerberg
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V, Denmark
| | - Christoph Dockter
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V, Denmark
| | - Morten E Jørgensen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V, Denmark
| | - Andrés Torres Salvador
- The Quinoa Company, Wageningen, The Netherlands
- Plant Biotechnology Laboratory (COCIBA), Universidad San Francisco de Quito USFQ, Cumbayá, Ecuador
| | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | | | - Sergey Shabala
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China
- Tasmanian Institute for Agriculture, College of Science and Engineering, University of Tasmania, Hobart, Tasmania, Australia
| | - Michael Palmgren
- NovoCrops Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China
- Correspondence: or
| |
Collapse
|
50
|
Wolabu TW, Cong L, Park JJ, Bao Q, Chen M, Sun J, Xu B, Ge Y, Chai M, Liu Z, Wang ZY. Development of a Highly Efficient Multiplex Genome Editing System in Outcrossing Tetraploid Alfalfa ( Medicago sativa). FRONTIERS IN PLANT SCIENCE 2020; 11:1063. [PMID: 32765553 PMCID: PMC7380066 DOI: 10.3389/fpls.2020.01063] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 06/26/2020] [Indexed: 05/03/2023]
Abstract
Alfalfa (Medicago sativa) is an outcrossing tetraploid legume species widely cultivated in the world. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (CRISPR/Cas9) system has been successfully used for genome editing in many plant species. However, the use of CRISPR/Cas9 for gene knockout in alfalfa is still very challenging. Our initial single gRNA-CRISPR/Cas9 system had very low mutagenesis efficiency in alfalfa with no mutant phenotype. In order to develop an optimized genome editing system in alfalfa, we constructed multiplex gRNA-CRISPR/Cas9 vectors by a polycistronic tRNA-gRNA approach targeting the Medicago sativa stay-green (MsSGR) gene. The replacement of CaMV35S promoter by the Arabidopsis ubiquitin promoter (AtUBQ10) to drive Cas9 expression in the multiplex gRNA system led to a significant improvement in genome editing efficiency, whereas modification of the gRNA scaffold resulted in lower editing efficiency. The most effective multiplex system exhibited 75% genotypic mutagenesis efficiency, which is 30-fold more efficient than the single gRNA vector. Importantly, phenotypic change was easily observed in the mutants, and the phenotypic mutation efficiency reached 68%. This highly efficient multiplex gRNA-CRISPR/Cas9 genome editing system allowed the generation of homozygous mutants with a complete knockout of the four allelic copies in the T0 generation. This optimized system offers an effective way of testing gene functions and overcomes a major barrier in the utilization of genome editing for alfalfa improvement.
Collapse
Affiliation(s)
| | - Lili Cong
- Noble Research Institute, Ardmore, OK, United States
- College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Jong-Jin Park
- Noble Research Institute, Ardmore, OK, United States
| | - Qinyan Bao
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Miao Chen
- Noble Research Institute, Ardmore, OK, United States
| | - Juan Sun
- Noble Research Institute, Ardmore, OK, United States
- College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Bin Xu
- Noble Research Institute, Ardmore, OK, United States
| | - Yaxin Ge
- Noble Research Institute, Ardmore, OK, United States
| | - Maofeng Chai
- Noble Research Institute, Ardmore, OK, United States
- College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Zhipeng Liu
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Zeng-Yu Wang
- Noble Research Institute, Ardmore, OK, United States
- College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| |
Collapse
|