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Naithani S, Mohanty B, Elser J, D'Eustachio P, Jaiswal P. Biocuration of a Transcription Factors Network Involved in Submergence Tolerance during Seed Germination and Coleoptile Elongation in Rice ( Oryza sativa). Plants (Basel) 2023; 12:plants12112146. [PMID: 37299125 DOI: 10.3390/plants12112146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023]
Abstract
Modeling biological processes and genetic-regulatory networks using in silico approaches provides a valuable framework for understanding how genes and associated allelic and genotypic differences result in specific traits. Submergence tolerance is a significant agronomic trait in rice; however, the gene-gene interactions linked with this polygenic trait remain largely unknown. In this study, we constructed a network of 57 transcription factors involved in seed germination and coleoptile elongation under submergence. The gene-gene interactions were based on the co-expression profiles of genes and the presence of transcription factor binding sites in the promoter region of target genes. We also incorporated published experimental evidence, wherever available, to support gene-gene, gene-protein, and protein-protein interactions. The co-expression data were obtained by re-analyzing publicly available transcriptome data from rice. Notably, this network includes OSH1, OSH15, OSH71, Sub1B, ERFs, WRKYs, NACs, ZFP36, TCPs, etc., which play key regulatory roles in seed germination, coleoptile elongation and submergence response, and mediate gravitropic signaling by regulating OsLAZY1 and/or IL2. The network of transcription factors was manually biocurated and submitted to the Plant Reactome Knowledgebase to make it publicly accessible. We expect this work will facilitate the re-analysis/re-use of OMICs data and aid genomics research to accelerate crop improvement.
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Affiliation(s)
- Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Bijayalaxmi Mohanty
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Peter D'Eustachio
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
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Gajardo HA, Gómez-Espinoza O, Boscariol Ferreira P, Carrer H, Bravo LA. The Potential of CRISPR/Cas Technology to Enhance Crop Performance on Adverse Soil Conditions. Plants (Basel) 2023; 12:plants12091892. [PMID: 37176948 PMCID: PMC10181257 DOI: 10.3390/plants12091892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
Worldwide food security is under threat in the actual scenery of global climate change because the major staple food crops are not adapted to hostile climatic and soil conditions. Significant efforts have been performed to maintain the actual yield of crops, using traditional breeding and innovative molecular techniques to assist them. However, additional strategies are necessary to achieve the future food demand. Clustered regularly interspaced short palindromic repeat/CRISPR-associated protein (CRISPR/Cas) technology, as well as its variants, have emerged as alternatives to transgenic plant breeding. This novelty has helped to accelerate the necessary modifications in major crops to confront the impact of abiotic stress on agriculture systems. This review summarizes the current advances in CRISPR/Cas applications in crops to deal with the main hostile soil conditions, such as drought, flooding and waterlogging, salinity, heavy metals, and nutrient deficiencies. In addition, the potential of extremophytes as a reservoir of new molecular mechanisms for abiotic stress tolerance, as well as their orthologue identification and edition in crops, is shown. Moreover, the future challenges and prospects related to CRISPR/Cas technology issues, legal regulations, and customer acceptance will be discussed.
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Affiliation(s)
- Humberto A Gajardo
- Laboratorio de Fisiología y Biología Molecular Vegetal, Instituto de Agroindustria, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente & Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 1145, Chile
| | - Olman Gómez-Espinoza
- Laboratorio de Fisiología y Biología Molecular Vegetal, Instituto de Agroindustria, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente & Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 1145, Chile
- Centro de Investigación en Biotecnología, Escuela de Biología, Instituto Tecnológico de Costa Rica, Cartago 30101, Costa Rica
| | - Pedro Boscariol Ferreira
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba 13418-900, Brazil
| | - Helaine Carrer
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba 13418-900, Brazil
| | - León A Bravo
- Laboratorio de Fisiología y Biología Molecular Vegetal, Instituto de Agroindustria, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente & Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 1145, Chile
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Mmbando GS. Challenges and prospects in using biotechnological interventions in O. glaberrima, an African cultivated rice. GM Crops & Food 2022; 13:372-387. [DOI: 10.1080/21645698.2022.2149212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Gideon Sadikiel Mmbando
- Department of Biology, College of Natural and Mathematical Sciences, University of Dodoma (Udom), Dodoma, Tanzania
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Biswas S, Ibarra O, Shaphek M, Molina-Risco M, Faion-Molina M, Bellinatti-Della Gracia M, Thomson MJ, Septiningsih EM. Increasing the level of resistant starch in 'Presidio' rice through multiplex CRISPR-Cas9 gene editing of starch branching enzyme genes. Plant Genome 2022:e20225. [PMID: 35713092 DOI: 10.1002/tpg2.20225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/15/2022] [Indexed: 06/15/2023]
Abstract
Rice (Oryza sativa L.) is an excellent source of starch, which is composed of amylopectin and amylose. Resistant starch (RS) is a starch product that is not easily digestible and absorbed in the stomach or small intestine and instead is passed on directly to the large intestine. Cereals high in RS may be beneficial to improve human health and reduce the risk of diet-related chronic diseases. It has been reported through chemical mutagenesis and RNA interference studies that starch branching enzymes (SBEs) play a major role in contributing to higher levels of RS in cereal crops. In this study, we used multiplex clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR associated protein 9 (Cas9) genome editing to simultaneously target all four SBE genes in rice using the endogenous transfer RNA (tRNA)-processing system for expressing the single-guide RNAs (sgRNAs) targeting these genes. The CRISPR-Cas9 vector construct with four SBE gene sgRNAs was transformed into the U.S. rice cultivar Presidio using Agrobacterium-mediated transformation. Knockout mutations were identified at all four SBE genes across eight transgene-positive T0 plants. Transgene-free T1 lines with different combinations of disrupted SBE genes were identified, with several SBE-edited lines showing significantly increased RS content up to 15% higher than the wild-type (WT) cultivar Presidio. Although further efforts are needed to fix all of the mutant alleles as homozygous, our study demonstrated the potential of multiplex genome editing to develop high-RS lines.
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Affiliation(s)
- Sudip Biswas
- Dep. of Soil and Crop Sciences, Texas A&M Univ., College Station, TX, 77843, USA
| | - Oneida Ibarra
- Dep. of Soil and Crop Sciences, Texas A&M Univ., College Station, TX, 77843, USA
- Avance Biosciences Inc., Houston, TX, 77040, USA
| | - Mariam Shaphek
- Dep. of Soil and Crop Sciences, Texas A&M Univ., College Station, TX, 77843, USA
- Dep. of Biochemistry and Biophysics, Texas A&M Univ., College Station, TX, 77843, USA
| | - Marco Molina-Risco
- Dep. of Soil and Crop Sciences, Texas A&M Univ., College Station, TX, 77843, USA
| | - Mayra Faion-Molina
- Dep. of Soil and Crop Sciences, Texas A&M Univ., College Station, TX, 77843, USA
| | | | - Michael J Thomson
- Dep. of Soil and Crop Sciences, Texas A&M Univ., College Station, TX, 77843, USA
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Thomson MJ, Biswas S, Tsakirpaloglou N, Septiningsih EM. Functional Allele Validation by Gene Editing to Leverage the Wealth of Genetic Resources for Crop Improvement. Int J Mol Sci 2022; 23:ijms23126565. [PMID: 35743007 PMCID: PMC9223900 DOI: 10.3390/ijms23126565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 02/05/2023] Open
Abstract
Advances in molecular technologies over the past few decades, such as high-throughput DNA marker genotyping, have provided more powerful plant breeding approaches, including marker-assisted selection and genomic selection. At the same time, massive investments in plant genetics and genomics, led by whole genome sequencing, have led to greater knowledge of genes and genetic pathways across plant genomes. However, there remains a gap between approaches focused on forward genetics, which start with a phenotype to map a mutant locus or QTL with the goal of cloning the causal gene, and approaches using reverse genetics, which start with large-scale sequence data and work back to the gene function. The recent establishment of efficient CRISPR-Cas-based gene editing promises to bridge this gap and provide a rapid method to functionally validate genes and alleles identified through studies of natural variation. CRISPR-Cas techniques can be used to knock out single or multiple genes, precisely modify genes through base and prime editing, and replace alleles. Moreover, technologies such as protoplast isolation, in planta transformation, and the use of developmental regulatory genes promise to enable high-throughput gene editing to accelerate crop improvement.
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Dunbar T, Tsakirpaloglou N, Septiningsih EM, Thomson MJ. Carbon Nanotube-Mediated Plasmid DNA Delivery in Rice Leaves and Seeds. Int J Mol Sci 2022; 23:ijms23084081. [PMID: 35456898 PMCID: PMC9028948 DOI: 10.3390/ijms23084081] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/02/2022] [Accepted: 04/05/2022] [Indexed: 02/07/2023] Open
Abstract
CRISPR-Cas gene editing technologies offer the potential to modify crops precisely; however, in vitro plant transformation and regeneration techniques present a bottleneck due to the lengthy and genotype-specific tissue culture process. Ideally, in planta transformation can bypass tissue culture and directly lead to transformed plants, but efficient in planta delivery and transformation remains a challenge. This study investigates transformation methods that have the potential to directly alter germline cells, eliminating the challenge of in vitro plant regeneration. Recent studies have demonstrated that carbon nanotubes (CNTs) loaded with plasmid DNA can diffuse through plant cell walls, facilitating transient expression of foreign genetic elements in plant tissues. To test if this approach is a viable technique for in planta transformation, CNT-mediated plasmid DNA delivery into rice tissues was performed using leaf and excised-embryo infiltration with reporter genes. Quantitative and qualitative data indicate that CNTs facilitate plasmid DNA delivery in rice leaf and embryo tissues, resulting in transient GFP, YFP, and GUS expression. Experiments were also initiated with CRISPR-Cas vectors targeting the phytoene desaturase (PDS) gene for CNT delivery into mature embryos to create heritable genetic edits. Overall, the results suggest that CNT-based delivery of plasmid DNA appears promising for in planta transformation, and further optimization can enable high-throughput gene editing to accelerate functional genomics and crop improvement activities.
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Biswas S, Wahl NJ, Thomson MJ, Cason JM, McCutchen BF, Septiningsih EM. Optimization of Protoplast Isolation and Transformation for a Pilot Study of Genome Editing in Peanut by Targeting the Allergen Gene Ara h 2. Int J Mol Sci 2022; 23:837. [PMID: 35055026 PMCID: PMC8775966 DOI: 10.3390/ijms23020837] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/09/2022] [Accepted: 01/10/2022] [Indexed: 12/22/2022] Open
Abstract
The cultivated peanut (Arachis hypogaea L.) is a legume consumed worldwide in the form of oil, nuts, peanut butter, and candy. Improving peanut production and nutrition will require new technologies to enable novel trait development. Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR-Cas9) is a powerful and versatile genome-editing tool for introducing genetic changes for studying gene expression and improving crops, including peanuts. An efficient in vivo transient CRISPR-Cas9- editing system using protoplasts as a testbed could be a versatile platform to optimize this technology. In this study, multiplex CRISPR-Cas9 genome editing was performed in peanut protoplasts to disrupt a major allergen gene with the help of an endogenous tRNA-processing system. In this process, we successfully optimized protoplast isolation and transformation with green fluorescent protein (GFP) plasmid, designed two sgRNAs for an allergen gene, Ara h 2, and tested their efficiency by in vitro digestion with Cas9. Finally, through deep-sequencing analysis, several edits were identified in our target gene after PEG-mediated transformation in protoplasts with a Cas9 and sgRNA-containing vector. These findings demonstrated that a polyethylene glycol (PEG)-mediated protoplast transformation system can serve as a rapid and effective tool for transient expression assays and sgRNA validation in peanut.
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Affiliation(s)
- Sudip Biswas
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (S.B.); (N.J.W.); (M.J.T.)
| | - Nancy J. Wahl
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (S.B.); (N.J.W.); (M.J.T.)
| | - Michael J. Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (S.B.); (N.J.W.); (M.J.T.)
| | - John M. Cason
- Texas A&M AgriLife Research and Extension Center at Stephenville, Stephenville, TX 76401, USA; (J.M.C.); (B.F.M.)
| | - Bill F. McCutchen
- Texas A&M AgriLife Research and Extension Center at Stephenville, Stephenville, TX 76401, USA; (J.M.C.); (B.F.M.)
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (S.B.); (N.J.W.); (M.J.T.)
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Liang Y, Wang S, Harper CL, Subramanian NK, Tabien RE, Johnson CD, Bailey-Serres J, Septiningsih EM. Reference-Guided De Novo Genome Assembly to Dissect a QTL Region for Submergence Tolerance Derived from Ciherang-Sub1. Plants 2021; 10:plants10122740. [PMID: 34961210 PMCID: PMC8703405 DOI: 10.3390/plants10122740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/02/2021] [Accepted: 12/09/2021] [Indexed: 11/06/2022]
Abstract
Global climate change has increased the number of severe flooding events that affect agriculture, including rice production in the U.S. and internationally. Heavy rainfall can cause rice plants to be completely submerged, which can significantly affect grain yield or completely destroy the plants. Recently, a major effect submergence tolerance QTL during the vegetative stage, qSub8.1, which originated from Ciherang-Sub1, was identified in a mapping population derived from a cross between Ciherang-Sub1 and IR10F365. Ciherang-Sub1 was, in turn, derived from a cross between Ciherang and IR64-Sub1. Here, we characterize the qSub8.1 region by analyzing the sequence information of Ciherang-Sub1 and its two parents (Ciherang and IR64-Sub1) and compare the whole genome profile of these varieties with the Nipponbare and Minghui 63 (MH63) reference genomes. The three rice varieties were sequenced with 150 bp pair-end whole-genome shotgun sequencing (Illumina HiSeq4000), followed by performing the Trimmomatic-SOAPdenovo2-MUMmer3 pipeline for genome assembly, resulting in approximate genome sizes of 354.4, 343.7, and 344.7 Mb, with N50 values of 25.1, 25.4, and 26.1 kb, respectively. The results showed that the Ciherang-Sub1 genome is composed of 59–63% Ciherang, 22–24% of IR64-Sub1, and 15–17% of unknown sources. The genome profile revealed a more detailed genomic composition than previous marker-assisted breeding and showed that the qSub8.1 region is mostly from Ciherang, with some introgressed segments from IR64-Sub1 and currently unknown source(s).
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Affiliation(s)
- Yuya Liang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (Y.L.); (N.K.S.)
| | - Shichen Wang
- Genomics and Bioinformatics Service, Texas A&M AgriLife Research, College Station, TX 77843, USA; (S.W.); (C.D.J.)
| | - Chersty L. Harper
- Texas A&M AgriLife Research Center, Beaumont, TX 77713, USA; (C.L.H.); (R.E.T.)
| | - Nithya K. Subramanian
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (Y.L.); (N.K.S.)
| | - Rodante E. Tabien
- Texas A&M AgriLife Research Center, Beaumont, TX 77713, USA; (C.L.H.); (R.E.T.)
| | - Charles D. Johnson
- Genomics and Bioinformatics Service, Texas A&M AgriLife Research, College Station, TX 77843, USA; (S.W.); (C.D.J.)
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA;
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (Y.L.); (N.K.S.)
- Correspondence:
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Molina-Risco M, Ibarra O, Faion-Molina M, Kim B, Septiningsih EM, Thomson MJ. Optimizing Agrobacterium-Mediated Transformation and CRISPR-Cas9 Gene Editing in the tropical japonica Rice Variety Presidio. Int J Mol Sci 2021; 22:ijms222010909. [PMID: 34681568 PMCID: PMC8535416 DOI: 10.3390/ijms222010909] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 09/28/2021] [Accepted: 10/04/2021] [Indexed: 01/07/2023] Open
Abstract
Bottlenecks in plant transformation and regeneration have slowed progress in applying CRISPR/Cas-based genome editing for crop improvement. Rice (Oryza sativa L.) has highly efficient temperate japonica transformation protocols, along with reasonably efficient indica protocols using immature embryos. However, rapid and efficient protocols are not available for transformation and regeneration in tropical japonica varieties, even though they represent the majority of rice production in the U.S. and South America. The current study has optimized a protocol using callus induction from mature seeds with both Agrobacterium-mediated and biolistic transformation of the high-yielding U.S. tropical japonica cultivar Presidio. Gene editing efficiency was tested by evaluating knockout mutations in the phytoene desaturase (PDS) and young seedling albino (YSA) genes, which provide a visible phenotype at the seedling stage for successful knockouts. Using the optimized protocol, transformation of 648 explants with particle bombardment and 532 explants with Agrobacterium led to a 33% regeneration efficiency. The YSA targets had ambiguous phenotypes, but 60% of regenerated plants for PDS showed an albino phenotype. Sanger sequencing of edited progeny showed a number of insertions, deletions, and substitutions at the gRNA target sites. These results pave the way for more efficient gene editing of tropical japonica rice varieties.
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Affiliation(s)
- Marco Molina-Risco
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (M.M.-R.); (O.I.); (M.F.-M.); (B.K.); (E.M.S.)
| | - Oneida Ibarra
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (M.M.-R.); (O.I.); (M.F.-M.); (B.K.); (E.M.S.)
- Avance Biosciences Inc., Houston, TX 77040, USA
| | - Mayra Faion-Molina
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (M.M.-R.); (O.I.); (M.F.-M.); (B.K.); (E.M.S.)
| | - Backki Kim
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (M.M.-R.); (O.I.); (M.F.-M.); (B.K.); (E.M.S.)
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (M.M.-R.); (O.I.); (M.F.-M.); (B.K.); (E.M.S.)
| | - Michael J. Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (M.M.-R.); (O.I.); (M.F.-M.); (B.K.); (E.M.S.)
- Correspondence:
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