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Singh D, Chaudhary P, Taunk J, Singh CK, Chinnusamy V, Sevanthi AM, Singh VJ, Pal M. Targeting Induced Local Lesions in Genomes (TILLING): advances and opportunities for fast tracking crop breeding. Crit Rev Biotechnol 2024; 44:817-836. [PMID: 37455414 DOI: 10.1080/07388551.2023.2231630] [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: 02/14/2021] [Accepted: 06/01/2023] [Indexed: 07/18/2023]
Abstract
The intensification of food production via conventional crop breeding alone is inadequate to cater for global hunger. The development of precise and expeditious high throughput reverse genetics approaches has hugely benefited modern plant breeding programs. Targeting Induced Local Lesions in Genomes (TILLING) is one such reverse genetics approach which employs chemical/physical mutagenesis to create new genetic sources and identifies superior/novel alleles. Owing to technical limitations and sectional applicability of the original TILLING protocol, it has been timely modified. Successions include: EcoTILLING, Double stranded EcoTILLING (DEcoTILLING), Self-EcoTILLING, Individualized TILLING (iTILLING), Deletion-TILLING (De-TILLING), PolyTILLING, and VeggieTILLING. This has widened its application to a variety of crops and needs. They can characterize mutations in coding as well as non-coding regions and can overcome complexities associated with the large genomes. Combining next generation sequencing tools with the existing TILLING protocols has enabled screening of huge germplasm collections and mutant populations for the target genes. In silico TILLING platforms have transformed TILLING into an exciting breeding approach. The present review outlines these multifarious TILLING modifications for precise mutation detection and their application in advance breeding programmes together with relevant case studies. Appropriate use of these protocols will open up new avenues for crop improvement in the twenty first century.
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Affiliation(s)
- Dharmendra Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Priya Chaudhary
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Jyoti Taunk
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Chandan Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Vikram Jeet Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Madan Pal
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Kumar S, Singh A, Bist CMS, Sharma M. Advancements in genetic techniques and functional genomics for enhancing crop traits and agricultural sustainability. Brief Funct Genomics 2024:elae017. [PMID: 38679487 DOI: 10.1093/bfgp/elae017] [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: 02/08/2024] [Revised: 04/03/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
Genetic variability is essential for the development of new crop varieties with economically beneficial traits. The traits can be inherited from wild relatives or induced through mutagenesis. Novel genetic elements can then be identified and new gene functions can be predicted. In this study, forward and reverse genetics approaches were described, in addition to their applications in modern crop improvement programs and functional genomics. By using heritable phenotypes and linked genetic markers, forward genetics searches for genes by using traditional genetic mapping and allele frequency estimation. Despite recent advances in sequencing technology, omics and computation, genetic redundancy remains a major challenge in forward genetics. By analyzing close-related genes, we will be able to dissect their functional redundancy and predict possible traits and gene activity patterns. In addition to these predictions, sophisticated reverse gene editing tools can be used to verify them, including TILLING, targeted insertional mutagenesis, gene silencing, gene targeting and genome editing. By using gene knock-down, knock-up and knock-out strategies, these tools are able to detect genetic changes in cells. In addition, epigenome analysis and editing enable the development of novel traits in existing crop cultivars without affecting their genetic makeup by increasing epiallelic variants. Our understanding of gene functions and molecular dynamics of various biological phenomena has been revised by all of these findings. The study also identifies novel genetic targets in crop species to improve yields and stress tolerances through conventional and non-conventional methods. In this article, genetic techniques and functional genomics are specifically discussed and assessed for their potential in crop improvement.
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Affiliation(s)
- Surender Kumar
- Department of Biotechnology, College of Horticulture, Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan-173230, Himachal Pradesh, India
| | - Anupama Singh
- Department of Biotechnology, College of Horticulture, Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan-173230, Himachal Pradesh, India
| | - Chander Mohan Singh Bist
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla-171001, Himachal Pradesh, India
| | - Munish Sharma
- Department of Plant Sciences, Central University of Himachal Pradesh, Dharamshala-176215, Himachal Pradesh, India
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Singh H, Sekhon BS, Kumar P, Dhall RK, Devi R, Dhillon TS, Sharma S, Khar A, Yadav RK, Tomar BS, Ntanasi T, Sabatino L, Ntatsi G. Genetic Mechanisms for Hybrid Breeding in Vegetable Crops. PLANTS (BASEL, SWITZERLAND) 2023; 12:2294. [PMID: 37375919 DOI: 10.3390/plants12122294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/25/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023]
Abstract
To address the complex challenges faced by our planet such as rapidly changing climate patterns, food and nutritional insecurities, and the escalating world population, the development of hybrid vegetable crops is imperative. Vegetable hybrids could effectively mitigate the above-mentioned fundamental challenges in numerous countries. Utilizing genetic mechanisms to create hybrids not only reduces costs but also holds significant practical implications, particularly in streamlining hybrid seed production. These mechanisms encompass self-incompatibility (SI), male sterility, and gynoecism. The present comprehensive review is primarily focused on the elucidation of fundamental processes associated with floral characteristics, the genetic regulation of floral traits, pollen biology, and development. Specific attention is given to the mechanisms for masculinizing and feminizing cucurbits to facilitate hybrid seed production as well as the hybridization approaches used in the biofortification of vegetable crops. Furthermore, this review provides valuable insights into recent biotechnological advancements and their future utilization for developing the genetic systems of major vegetable crops.
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Affiliation(s)
- Hira Singh
- Department of Vegetable Science, Punjab Agriculture University, Ludhiana 141004, India
| | - Bhallan Singh Sekhon
- Department of Vegetable Science, Punjab Agriculture University, Ludhiana 141004, India
| | - Pradeep Kumar
- ICAR-Central Arid Zone Research Institute, Jodhpur 342003, India
| | - Rajinder Kumar Dhall
- Department of Vegetable Science, Punjab Agriculture University, Ludhiana 141004, India
| | - Ruma Devi
- Department of Vegetable Science, Punjab Agriculture University, Ludhiana 141004, India
| | - Tarsem Singh Dhillon
- Department of Vegetable Science, Punjab Agriculture University, Ludhiana 141004, India
| | - Suman Sharma
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88003, USA
| | - Anil Khar
- ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | | | | | - Theodora Ntanasi
- Laboratory of Vegetable Production, Department of Crop Science, Agricultural University of Athens, IeraOdos 75, 11855 Athens, Greece
| | - Leo Sabatino
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy
| | - Georgia Ntatsi
- Laboratory of Vegetable Production, Department of Crop Science, Agricultural University of Athens, IeraOdos 75, 11855 Athens, Greece
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Adeyinka OS, Tabassum B, Koloko BL, Ogungbe IV. Enhancing the quality of staple food crops through CRISPR/Cas-mediated site-directed mutagenesis. PLANTA 2023; 257:78. [PMID: 36913066 DOI: 10.1007/s00425-023-04110-6] [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: 11/20/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
The enhancement of CRISPR-Cas gene editing with robust nuclease activity promotes genetic modification of desirable agronomic traits, such as resistance to pathogens, drought tolerance, nutritional value, and yield-related traits in crops. The genetic diversity of food crops has reduced tremendously over the past twelve millennia due to plant domestication. This reduction presents significant challenges for the future especially considering the risks posed by global climate change to food production. While crops with improved phenotypes have been generated through crossbreeding, mutation breeding, and transgenic breeding over the years, improving phenotypic traits through precise genetic diversification has been challenging. The challenges are broadly associated with the randomness of genetic recombination and conventional mutagenesis. This review highlights how emerging gene-editing technologies reduce the burden and time necessary for developing desired traits in plants. Our focus is to provide readers with an overview of the advances in CRISPR-Cas-based genome editing for crop improvement. The use of CRISPR-Cas systems in generating genetic diversity to enhance the quality and nutritional value of staple food crops is discussed. We also outlined recent applications of CRISPR-Cas in developing pest-resistant crops and removing unwanted traits, such as allergenicity from crops. Genome editing tools continue to evolve and present unprecedented opportunities to enhance crop germplasm via precise mutations at the desired loci of the plant genome.
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Affiliation(s)
- Olawale Samuel Adeyinka
- Department of Chemistry, Physics and Atmospheric Sciences Jackson State University, Jackson, MS, 39217, USA.
| | - Bushra Tabassum
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | | | - Ifedayo Victor Ogungbe
- Department of Chemistry, Physics and Atmospheric Sciences Jackson State University, Jackson, MS, 39217, USA
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Depuydt T, De Rybel B, Vandepoele K. Charting plant gene functions in the multi-omics and single-cell era. TRENDS IN PLANT SCIENCE 2023; 28:283-296. [PMID: 36307271 DOI: 10.1016/j.tplants.2022.09.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 09/09/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Despite the increased access to high-quality plant genome sequences, the set of genes with a known function remains far from complete. With the advent of novel bulk and single-cell omics profiling methods, we are entering a new era where advanced and highly integrative functional annotation strategies are being developed to elucidate the functions of all plant genes. Here, we review different multi-omics approaches to improve functional and regulatory gene characterization and highlight the power of machine learning and network biology to fully exploit the complementary information embedded in different omics layers. Finally, we discuss the potential of emerging single-cell methods and algorithms to further increase the resolution, allowing generation of functional insights about plant biology.
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Affiliation(s)
- Thomas Depuydt
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; Vlaams Instituut voor Biotechnologie, Center for Plant Systems Biology, Ghent, Belgium
| | - Bert De Rybel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; Vlaams Instituut voor Biotechnologie, Center for Plant Systems Biology, Ghent, Belgium
| | - Klaas Vandepoele
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; Vlaams Instituut voor Biotechnologie, Center for Plant Systems Biology, Ghent, Belgium; Ghent University, Bioinformatics Institute Ghent, Ghent, Belgium.
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Zaulda FA, Yang SH, Han J, Mlotshwa S, Dorrance A, Qu F. A cowpea severe mosaic virus-based vector simplifies virus-induced gene silencing and foreign protein expression in soybean. PLANT METHODS 2022; 18:116. [PMID: 36307846 PMCID: PMC9617382 DOI: 10.1186/s13007-022-00950-7] [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: 03/17/2022] [Accepted: 09/04/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Soybean gene functions cannot be easily interrogated through transgenic disruption (knock-out) of genes-of-interest, or transgenic overexpression of proteins-of-interest, because soybean transformation is time-consuming and technically challenging. An attractive alternative is to administer transient gene silencing or overexpression with a plant virus-based vector. However, existing virus-induced gene silencing (VIGS) and/or overexpression vectors suitable for soybean have various drawbacks that hinder their widespread adoption. RESULTS We describe the development of a new vector based on cowpea severe mosaic virus (CPSMV), a plus-strand RNA virus with its genome divided into two RNA segments, RNA1 and RNA2. This vector, designated FZ, incorporates a cloning site in the RNA2 cDNA, permitting insertion of nonviral sequences. When paired with an optimized RNA1 construct, FZ readily infects both Nicotiana benthamiana and soybean. As a result, FZ constructs destined for soybean can be first delivered to N. benthamiana in order to propagate the modified viruses to high titers. FZ-based silencing constructs induced robust silencing of phytoene desaturase genes in N. benthamiana, multiple soybean accessions, and cowpea. Meanwhile, FZ supported systemic expression of fluorescent proteins mNeonGreen and mCherry in N. benthamiana and soybean. Finally, FZ-mediated expression of the Arabidopsis transcription factor MYB75 caused N. benthamiana to bear brown leaves and purple, twisted flowers, indicating that MYB75 retained the function of activating anthocyanin synthesis pathways in a different plant. CONCLUSIONS The new CPSMV-derived FZ vector provides a convenient and versatile soybean functional genomics tool that is expected to accelerate the characterization of soybean genes controlling crucial productivity traits.
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Affiliation(s)
- Fides Angeli Zaulda
- Department of Plant Pathology, The Ohio State University, Wooster, OH, 44691, USA
| | - Seung Hyun Yang
- Department of Plant Pathology, The Ohio State University, Wooster, OH, 44691, USA
| | - Junping Han
- Department of Plant Pathology, The Ohio State University, Wooster, OH, 44691, USA
| | | | - Anne Dorrance
- Department of Plant Pathology, The Ohio State University, Wooster, OH, 44691, USA
| | - Feng Qu
- Department of Plant Pathology, The Ohio State University, Wooster, OH, 44691, USA.
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Jagadeesan SK, Potter T, Al-Gafari M, Hooshyar M, Hewapathirana CM, Takallou S, Hajikarimlou M, Burnside D, Samanfar B, Moteshareie H, Smith M, Golshani A. Discovery and identification of genes involved in DNA damage repair in yeast. Gene 2022; 831:146549. [PMID: 35569766 DOI: 10.1016/j.gene.2022.146549] [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: 09/13/2021] [Revised: 02/16/2022] [Accepted: 05/06/2022] [Indexed: 11/04/2022]
Abstract
DNA repair defects are common in tumour cells and can lead to misrepair of double-strand breaks (DSBs), posing a significant challenge to cellular integrity. The overall mechanisms of DSB have been known for decades. However, the list of the genes that affect the efficiency of DSB repair continues to grow. Additional factors that play a role in DSB repair pathways have yet to be identified. In this study, we present a computational approach to identify novel gene functions that are involved in DNA damage repair in Saccharomyces cerevisiae. Among the primary candidates, GAL7, YMR130W, and YHI9 were selected for further analysis since they had not previously been identified as being active in DNA repair pathways. Originally, GAL7 was linked to galactose metabolism. YHI9 and YMR130W encode proteins of unknown functions. Laboratory testing of deletion strains gal7Δ, ymr130wΔ, and yhi9Δ implicated all 3 genes in Homologous Recombination (HR) and/or Non-Homologous End Joining (NHEJ) repair pathways, and enhanced sensitivity to DNA damage-inducing drugs suggested involvement in the broader DNA damage repair machinery. A subsequent genetic interaction analysis revealed interconnections of these three genes, most strikingly through SIR2, SIR3 and SIR4 that are involved in chromatin regulation and DNA damage repair network.
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Affiliation(s)
- Sasi Kumar Jagadeesan
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Taylor Potter
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Mustafa Al-Gafari
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Mohsen Hooshyar
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | | | - Sarah Takallou
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Maryam Hajikarimlou
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Daniel Burnside
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Bahram Samanfar
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre (ORDC), Ottawa, Ontario, Canada.
| | - Houman Moteshareie
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Myron Smith
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada.
| | - Ashkan Golshani
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
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Kumar J, Kumar A, Sen Gupta D, Kumar S, DePauw RM. Reverse genetic approaches for breeding nutrient-rich and climate-resilient cereal and food legume crops. Heredity (Edinb) 2022; 128:473-496. [PMID: 35249099 PMCID: PMC9178024 DOI: 10.1038/s41437-022-00513-5] [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: 09/14/2021] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 12/21/2022] Open
Abstract
In the last decade, advancements in genomics tools and techniques have led to the discovery of many genes. Most of these genes still need to be characterized for their associated function and therefore, such genes remain underutilized for breeding the next generation of improved crop varieties. The recent developments in different reverse genetic approaches have made it possible to identify the function of genes controlling nutritional, biochemical, and metabolic traits imparting drought, heat, cold, salinity tolerance as well as diseases and insect-pests. This article focuses on reviewing the current status and prospects of using reverse genetic approaches to breed nutrient-rich and climate resilient cereal and food legume crops.
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Affiliation(s)
- Jitendra Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India.
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Debjyoti Sen Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sachin Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India
| | - Ron M DePauw
- Advancing Wheat Technologies, 118 Strathcona Rd SW, Calgary, AB, T3H 1P3, Canada
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Shin NR, Shin YH, Kim HS, Park YD. Function Analysis of the PR55/ B Gene Related to Self-Incompatibility in Chinese Cabbage Using CRISPR/Cas9. Int J Mol Sci 2022; 23:ijms23095062. [PMID: 35563453 PMCID: PMC9102814 DOI: 10.3390/ijms23095062] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 02/06/2023] Open
Abstract
Chinese cabbage, a major crop in Korea, shows self-incompatibility (SI). SI is controlled by the type 2A serine/threonine protein phosphatases (PP2As). The PP2A gene is controlled by regulatory subunits that comprise a 36 kDa catalyst C subunit, a 65 kDa regulatory A subunit, and a variety of regulatory B subunits (50–70 kDa). Among them, the PP2A 55 kDa B regulatory subunit (PR55/B) gene located in the A05 chromosome has 13 exons spanning 2.9 kb, and two homologous genes, Bra018924 and Bra014296, were found to be present on the A06 and A08 chromosome, respectively. In this study, we performed a functional analysis of the PR55/B gene using clustered regularly interspaced short palindromic repeats/CRISPR-associated system 9 (CRISPR/Cas9)-mediated gene mutagenesis. CRISPR/Cas9 technology can be used to easily introduce mutations in the target gene. Tentative gene-edited lines were generated by the Agrobacterium-mediated transfer and were selected by PCR and Southern hybridization analysis. Furthermore, pods were confirmed to be formed in flower pollination (FP) as well as bud pollination (BP) in some gene-edited lines. Seed fertility of gene-edited lines indicated that the PR55/B gene plays a key role in SI. Finally, self-compatible T-DNA-free T2 gene-edited plants and edited sequences of target genes were secured. The self-compatible Chinese cabbage developed in this study is expected to contribute to Chinese cabbage breeding.
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Singh D, Chaudhary P, Taunk J, Singh CK, Singh D, Tomar RSS, Aski M, Konjengbam NS, Raje RS, Singh S, Sengar RS, Yadav RK, Pal M. Fab Advances in Fabaceae for Abiotic Stress Resilience: From 'Omics' to Artificial Intelligence. Int J Mol Sci 2021; 22:10535. [PMID: 34638885 PMCID: PMC8509049 DOI: 10.3390/ijms221910535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/17/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022] Open
Abstract
Legumes are a better source of proteins and are richer in diverse micronutrients over the nutritional profile of widely consumed cereals. However, when exposed to a diverse range of abiotic stresses, their overall productivity and quality are hugely impacted. Our limited understanding of genetic determinants and novel variants associated with the abiotic stress response in food legume crops restricts its amelioration. Therefore, it is imperative to understand different molecular approaches in food legume crops that can be utilized in crop improvement programs to minimize the economic loss. 'Omics'-based molecular breeding provides better opportunities over conventional breeding for diversifying the natural germplasm together with improving yield and quality parameters. Due to molecular advancements, the technique is now equipped with novel 'omics' approaches such as ionomics, epigenomics, fluxomics, RNomics, glycomics, glycoproteomics, phosphoproteomics, lipidomics, regulomics, and secretomics. Pan-omics-which utilizes the molecular bases of the stress response to identify genes (genomics), mRNAs (transcriptomics), proteins (proteomics), and biomolecules (metabolomics) associated with stress regulation-has been widely used for abiotic stress amelioration in food legume crops. Integration of pan-omics with novel omics approaches will fast-track legume breeding programs. Moreover, artificial intelligence (AI)-based algorithms can be utilized for simulating crop yield under changing environments, which can help in predicting the genetic gain beforehand. Application of machine learning (ML) in quantitative trait loci (QTL) mining will further help in determining the genetic determinants of abiotic stress tolerance in pulses.
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Affiliation(s)
- Dharmendra Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Priya Chaudhary
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Jyoti Taunk
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Chandan Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Deepti Singh
- Department of Botany, Meerut College, Meerut 250001, India
| | - Ram Sewak Singh Tomar
- College of Horticulture and Forestry, Rani Lakshmi Bai Central Agricultural University, Jhansi 284003, India
| | - Muraleedhar Aski
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Noren Singh Konjengbam
- College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University, Imphal 793103, India
| | - Ranjeet Sharan Raje
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Sanjay Singh
- ICAR- National Institute of Plant Biotechnology, LBS Centre, Pusa Campus, New Delhi 110012, India
| | - Rakesh Singh Sengar
- College of Biotechnology, Sardar Vallabh Bhai Patel Agricultural University, Meerut 250001, India
| | - Rajendra Kumar Yadav
- Department of Genetics and Plant Breeding, Chandra Shekhar Azad University of Agriculture and Technology, Kanpur 208002, India
| | - Madan Pal
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
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Hu XL, Lu H, Hassan MM, Zhang J, Yuan G, Abraham PE, Shrestha HK, Villalobos Solis MI, Chen JG, Tschaplinski TJ, Doktycz MJ, Tuskan GA, Cheng ZMM, Yang X. Advances and perspectives in discovery and functional analysis of small secreted proteins in plants. HORTICULTURE RESEARCH 2021; 8:130. [PMID: 34059650 PMCID: PMC8167165 DOI: 10.1038/s41438-021-00570-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 04/26/2021] [Indexed: 05/02/2023]
Abstract
Small secreted proteins (SSPs) are less than 250 amino acids in length and are actively transported out of cells through conventional protein secretion pathways or unconventional protein secretion pathways. In plants, SSPs have been found to play important roles in various processes, including plant growth and development, plant response to abiotic and biotic stresses, and beneficial plant-microbe interactions. Over the past 10 years, substantial progress has been made in the identification and functional characterization of SSPs in several plant species relevant to agriculture, bioenergy, and horticulture. Yet, there are potentially a lot of SSPs that have not been discovered in plant genomes, which is largely due to limitations of existing computational algorithms. Recent advances in genomics, transcriptomics, and proteomics research, as well as the development of new computational algorithms based on machine learning, provide unprecedented capabilities for genome-wide discovery of novel SSPs in plants. In this review, we summarize known SSPs and their functions in various plant species. Then we provide an update on the computational and experimental approaches that can be used to discover new SSPs. Finally, we discuss strategies for elucidating the biological functions of SSPs in plants.
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Affiliation(s)
- Xiao-Li Hu
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Haiwei Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Jin Zhang
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Him K Shrestha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | | | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Gerald A Tuskan
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Zong-Ming Max Cheng
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA.
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China.
| | - Xiaohan Yang
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA.
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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Malik A, Gul A, Munir F, Amir R, Alipour H, Babar MM, Bakhtiar SM, Paracha RZ, Khalid Z, Hayat MQ. Evaluating the cleavage efficacy of CRISPR-Cas9 sgRNAs targeting ineffective regions of Arabidopsis thaliana genome. PeerJ 2021; 9:e11409. [PMID: 34055482 PMCID: PMC8142926 DOI: 10.7717/peerj.11409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 04/14/2021] [Indexed: 12/26/2022] Open
Abstract
The CRISPR-Cas9 system has recently evolved as a powerful mutagenic tool for targeted genome editing. The impeccable functioning of the system depends on the optimal design of single guide RNAs (sgRNAs) that mainly involves sgRNA specificity and on-target cleavage efficacy. Several research groups have designed algorithms and models, trained on mammalian genomes, for predicting sgRNAs cleavage efficacy. These models are also implemented in most plant sgRNA design tools due to the lack of on-target cleavage efficacy studies in plants. However, one of the major drawbacks is that almost all of these models are biased for considering only coding regions of the DNA while excluding ineffective regions, which are of immense importance in functional genomics studies especially for plants, thus making prediction less reliable. In the present study, we evaluate the on-target cleavage efficacy of experimentally validated sgRNAs designed against diverse ineffective regions of Arabidopsis thaliana genome using various statistical tests. We show that nucleotide preference in protospacer adjacent motif (PAM) proximal region, GC content in the PAM proximal seed region, intact RAR and 3rd stem loop structures, and free accessibility of nucleotides in seed and tracrRNA regions of sgRNAs are important determinants associated with their high on-target cleavage efficacy. Thus, our study describes the features important for plant sgRNAs high on-target cleavage efficacy against ineffective genomic regions previously shown to give rise to ineffective sgRNAs. Moreover, it suggests the need of developing an elaborative plant-specific sgRNA design model considering the entire genomic landscape including ineffective regions for enabling highly efficient genome editing without wasting time and experimental resources.
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Affiliation(s)
- Afsheen Malik
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Alvina Gul
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Faiza Munir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Rabia Amir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Hadi Alipour
- Department of Plant Production and Genetics, Faculty of Agriculture and Natural Resources, Urmia University, Urmia, Iran
| | - Mustafeez Mujtaba Babar
- Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Syeda Marriam Bakhtiar
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Rehan Zafar Paracha
- Research Center for Modeling and Simulation, National University of Sciences and Technology, Islamabad, Pakistan
| | - Zoya Khalid
- Computational Biology Research Lab, Department of Computer Science, National University of Computer and Emerging Sciences-FAST, Islamabad, Pakistan
| | - Muhammad Qasim Hayat
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
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Dar MS, Dholakia BB, Kulkarni AP, Oak PS, Shanmugam D, Gupta VS, Giri AP. Influence of domestication on specialized metabolic pathways in fruit crops. PLANTA 2021; 253:61. [PMID: 33538903 DOI: 10.1007/s00425-020-03554-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 12/23/2020] [Indexed: 05/08/2023]
Abstract
During the process of plant domestication, the selection and traditional breeding for desired characters such as flavor, juiciness and nutritional value of fruits, probably have resulted in gain or loss of specialized metabolites contributing to these traits. Their appearance in fruits is likely due to the acquisition of novel and specialized metabolic pathways and their regulation, driven by systematic molecular evolutionary events facilitated by traditional breeding. Plants change their armory of specialized metabolism to adapt and survive in diverse ecosystems. This may occur through molecular evolutionary events, such as single nucleotide polymorphism, gene duplication and transposition, leading to convergent or divergent evolution of biosynthetic pathways producing such specialized metabolites. Breeding and selection for improved specific and desired traits (fruit size, color, taste, flavor, etc.) in fruit crops through conventional breeding approaches may further alter content and profile of specialized metabolites. Biosynthetic routes of these metabolites have been studied in various plants. Here, we explore the influence of plant domestication and breeding processes on the selection of biosynthetic pathways of favorable specialized metabolites in fruit crops. An orderly clustered arrangement of genes associated with their production is observed in many fruit crops. We further analyzed selection-based acquisition of specialized metabolic pathways comparing first the metabolic profiles and genes involved in their biosynthesis, followed by the genomic organization of such genes between wild and domesticated horticultural crops. Domestication of crop plants favored the acquisition and retention of metabolic pathways that enhanced the fruit value while eliminated those which produced toxic or unfavorable metabolites. Interestingly, unintentional reorganization of complex metabolic pathways by selection and traditional breeding processes has endowed us with flavorful, juicy and nutritionally rich fruits.
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Affiliation(s)
- M Saleem Dar
- Plant Molecular Biology Unit, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, 201002, India
| | - Bhushan B Dholakia
- Plant Molecular Biology Unit, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411008, India.
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, MS, 411008, India.
| | - Abhijeet P Kulkarni
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, MS, 411007, India
| | - Pranjali S Oak
- Plant Molecular Biology Unit, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, 201002, India
| | - Dhanasekaran Shanmugam
- Plant Molecular Biology Unit, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, 201002, India
| | - Vidya S Gupta
- Plant Molecular Biology Unit, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, 201002, India
| | - Ashok P Giri
- Plant Molecular Biology Unit, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411008, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, 201002, India.
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14
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Wu L, Han L, Li Q, Wang G, Zhang H, Li L. Using Interactome Big Data to Crack Genetic Mysteries and Enhance Future Crop Breeding. MOLECULAR PLANT 2021; 14:77-94. [PMID: 33340690 DOI: 10.1016/j.molp.2020.12.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 05/27/2023]
Abstract
The functional genes underlying phenotypic variation and their interactions represent "genetic mysteries". Understanding and utilizing these genetic mysteries are key solutions for mitigating the current threats to agriculture posed by population growth and individual food preferences. Due to advances in high-throughput multi-omics technologies, we are stepping into an Interactome Big Data era that is certain to revolutionize genetic research. In this article, we provide a brief overview of current strategies to explore genetic mysteries. We then introduce the methods for constructing and analyzing the Interactome Big Data and summarize currently available interactome resources. Next, we discuss how Interactome Big Data can be used as a versatile tool to dissect genetic mysteries. We propose an integrated strategy that could revolutionize genetic research by combining Interactome Big Data with machine learning, which involves mining information hidden in Big Data to identify the genetic models or networks that control various traits, and also provide a detailed procedure for systematic dissection of genetic mysteries,. Finally, we discuss three promising future breeding strategies utilizing the Interactome Big Data to improve crop yields and quality.
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Affiliation(s)
- Leiming Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Linqian Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoying Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongwei Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
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15
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Miki D, Zinta G, Zhang W, Peng F, Feng Z, Zhu JK. CRISPR/Cas9-Based Genome Editing Toolbox for Arabidopsis thaliana. Methods Mol Biol 2021; 2200:121-146. [PMID: 33175375 DOI: 10.1007/978-1-0716-0880-7_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
CRISPR/Cas9 system has emerged as a powerful genome engineering tool to study gene function and improve plant traits. Genome editing is achieved at a specific genome sequence by Cas9 endonuclease to generate double standard breaks (DSBs) directed by short guide RNAs (sgRNAs). The DSB is repaired by error-prone nonhomologous end joining (NHEJ) or error-free homology-directed repair (HDR) pathways, resulting in gene mutation or sequence replacement, respectively. These cellular DSB repair pathways can be exploited to knock out or replace genes. Also, cytidine or adenine base editors (CBEs or ABEs) fused to catalytically dead Cas9 (dCas9) or nickase Cas9 (nCas9) are used to perform precise base editing without generating DSBs. In this chapter, we describe a detailed procedure to carry out single/multiple gene mutations and precise base editing in the Arabidopsis genome by using CRISPR/Cas9-based system. Specifically, the steps of target gene selection, sgRNA design, vector construction, transformation, and analysis of transgenic lines are described. The protocol is potentially adaptable to perform genome editing in other plant species such as rice.
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Affiliation(s)
- Daisuke Miki
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Gaurav Zinta
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wenxin Zhang
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fangnan Peng
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhengyan Feng
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA
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16
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Saikia B, Singh S, Debbarma J, Velmurugan N, Dekaboruah H, Arunkumar KP, Chikkaputtaiah C. Multigene CRISPR/Cas9 genome editing of hybrid proline rich proteins (HyPRPs) for sustainable multi-stress tolerance in crops: the review of a promising approach. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:857-869. [PMID: 32377037 PMCID: PMC7196567 DOI: 10.1007/s12298-020-00782-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 01/07/2020] [Accepted: 02/21/2020] [Indexed: 05/05/2023]
Abstract
The recent global climate change has directly impacted major biotic and abiotic stress factors affecting crop productivity worldwide. Therefore, the need of the hour is to develop sustainable multiple stress tolerant crops through modern biotechnological approaches to cope with climate change. Hybrid proline rich proteins (HyPRPs) are the cell-wall structural proteins, which contain an N-terminal repetitive proline-rich domain and a C-terminal conserved eight-cysteine motif domain. HyPRPs are known to regulate multiple abiotic and biotic stress responses in plants. Recently, a few HyPRPs have been characterized as negative regulators of abiotic and biotic stress responses in different plants. Disruption of such negative regulators for desirable positive phenotypic traits has been made possible through the advent of advanced genome engineering tools. In the past few years, CRISPR/Cas9 has emerged as a novel breakthrough technology for crop improvement by target specific editing of known negative regulatory host genes. Here, we have described the mechanism of action and the role of known HyPRPs in regulating different biotic and abiotic stress responses in major crop plants. We have also discussed the importance of the CRISPR/Cas9 based genome editing system in targeting known negative regulatory HyPRPs for multi-stress crop tolerance using the tomato crop model. Application of genome editing to manipulate the HyPRPs of major crop plants holds promise in developing newer stress management methods in this rapidly changing climate and would lead in the future to sustain crop productivity.
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Affiliation(s)
- Banashree Saikia
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam 785006 India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NEIST Campus, Jorhat, Assam 785006 India
| | - Sanjay Singh
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam 785006 India
| | - Johni Debbarma
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam 785006 India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NEIST Campus, Jorhat, Assam 785006 India
| | - Natarajan Velmurugan
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NEIST Campus, Jorhat, Assam 785006 India
- Biological Sciences Division, Branch Laboratory-Itanagar, CSIR-NEIST, Naharlagun, Arunachal Pradesh 791110 India
| | - Hariprasanna Dekaboruah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam 785006 India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NEIST Campus, Jorhat, Assam 785006 India
| | - Kallare P. Arunkumar
- Central Muga Eri Research and Training Institute (CMER&TI), Lahdoigarh, Jorhat, Assam 785700 India
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam 785006 India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NEIST Campus, Jorhat, Assam 785006 India
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17
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Improvement of Commercially Valuable Traits of Industrial Crops by Application of Carbon-based Nanomaterials. Sci Rep 2019; 9:19358. [PMID: 31852946 PMCID: PMC6920410 DOI: 10.1038/s41598-019-55903-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/03/2019] [Indexed: 01/27/2023] Open
Abstract
Carbon-based nanomaterials (CBNs) have great potential as a powerful tool to improve plant productivity. Here, we investigated the biological effects of graphene and carbon nanotubes (CNTs) on fiber-producing species (cotton, Gossypium hirsutum) and ornamental species (vinca, Catharanthus roseus). The exposure of seeds to CNTs or graphene led to the activation of early seed germination in Catharanthus and overall higher germination in cotton and Catharanthus seeds. The application of CBNs resulted in higher root and shoot growth of young seedlings of both tested species. Cultivation of Catharanthus plants in soil supplemented with CBNs resulted in the stimulation of plant reproductive system by inducing early flower development along with higher flower production. Catharanthus plants cultivated in CNTs or graphene supplemented soil accelerated total flower production by 37 and 58%, respectively. Additionally, CBNs reduced the toxic effects caused by NaCl. Long-term application of CBNs to crops cultivated under salt stress conditions improved the desired phenotypical traits of Catharanthus (higher flower number and leaf number) and cotton (increased fiber biomass) compared to untreated plants of both species cultivated at the same stress condition. The drought stress experiments revealed that introduction of CBNs to matured Catharanthus plant increased the plant survival with no symptoms of leaf wilting as compared to untreated Catharanthus growing in water deficit conditions.
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18
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Chaudhary J, Deshmukh R, Sonah H. Mutagenesis Approaches and Their Role in Crop Improvement. PLANTS (BASEL, SWITZERLAND) 2019; 8:E467. [PMID: 31683624 PMCID: PMC6918138 DOI: 10.3390/plants8110467] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 10/29/2019] [Indexed: 12/20/2022]
Abstract
Induced mutagenesis is one of the most efficient tools that has been utilized extensively to create genetic variation as well as for identification of key regulatory genes for economically important traits toward the crop improvement. Mutations can be induced by several techniques such as physical, chemical, and insertional mutagen treatments; however, these methods are not preferred because of cost and tedious process. Nonetheless, with the advancements in next-generation sequencing (NGS) techniques, millions of mutations can be detected in a very short period of time and, therefore, considered as convenient and cost efficient. Furthermore, induced mutagenesis coupled with whole-genome sequencing has provided a robust platform for forward and reverse genetic applications. Moreover, the availability of whole-genome sequence information for large number of crops has enabled target-specific genome editing techniques as a preferable method to engineer desired mutations. The available genome editing approaches such as ZFNs (Zinc Finger Nucleases), transcription activator like effector nucleases (TALENS), and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated9 (Cas9) endonuclease have been utilized to perform site-specific mutations in several plant species. In particular, the CRISPR/Cas9 has transformed the genome editing because of its simplicity and robustness, therefore, have been utilized to enhance biotic and abiotic stress resistance. The Special Issue of Plants highlights the efforts by the scientific community utilizing mutagenesis techniques for the identification of novel genes toward crop improvement.
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Affiliation(s)
- Juhi Chaudhary
- Department of Biology, Oberlin College, Oberlin, OH 44074, USA.
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Sector 80, SAS Nagar, Mohali, Punjab 140306, India.
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Sector 80, SAS Nagar, Mohali, Punjab 140306, India.
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Kumawat S, Rana N, Bansal R, Vishwakarma G, Mehetre ST, Das BK, Kumar M, Kumar Yadav S, Sonah H, Sharma TR, Deshmukh R. Expanding Avenue of Fast Neutron Mediated Mutagenesis for Crop Improvement. PLANTS (BASEL, SWITZERLAND) 2019; 8:E164. [PMID: 31185678 PMCID: PMC6631465 DOI: 10.3390/plants8060164] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 05/27/2019] [Accepted: 06/05/2019] [Indexed: 12/21/2022]
Abstract
: Fast neutron (FN) radiation mediated mutagenesis is a unique approach among the several induced mutagenesis methods being used in plant science in terms of impacted mutations. The FN mutagenesis usually creates deletions from few bases to several million bases (Mb). A library of random deletion generated using FN mutagenesis lines can provide indispensable resources for the reverse genetic approaches. In this review, information from several efforts made using FN mutagenesis has been compiled to understand the type of induced mutations, frequency, and genetic stability. Concerns regarding the utilization of FN mutagenesis technique for a plant with different level of ploidy and genome complexity are discussed. We have highlighted the utility of next-generation sequencing techniques that can be efficiently utilized for the characterization of mutant lines as well as for the mapping of causal mutations. Pros and cons of mapping by mutation (MutMap), mutant chromosome sequencing (MutChromSeq), exon capture, whole genome sequencing, MutRen-Seq, and different tilling approaches that can be used for the detection of FN-induced mutation has also been discussed. Genomic resources developed using the FN mutagenesis have been catalogued wooing to meaningful utilization of the available resources. The information provided here will be helpful for the efficient exploration for the crop improvement programs and for better understanding of genetic regulations.
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Affiliation(s)
- Surbhi Kumawat
- National Agri-food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
| | - Nitika Rana
- National Agri-food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
| | - Ruchi Bansal
- National Agri-food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
| | - Gautam Vishwakarma
- Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India.
| | - Sayaji T Mehetre
- Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India.
| | - Bikram Kishore Das
- Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India.
| | - Manish Kumar
- Department of Seed Science and Technology, College of Horticulture, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Nauni, Solan, Himachal Pradesh 173230, India.
| | | | - Humira Sonah
- National Agri-food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
| | - Tilak Raj Sharma
- National Agri-food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
| | - Rupesh Deshmukh
- National Agri-food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
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20
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Chaudhary J, Alisha A, Bhatt V, Chandanshive S, Kumar N, Mir Z, Kumar A, Yadav SK, Shivaraj SM, Sonah H, Deshmukh R. Mutation Breeding in Tomato: Advances, Applicability and Challenges. PLANTS (BASEL, SWITZERLAND) 2019; 8:E128. [PMID: 31091747 PMCID: PMC6572636 DOI: 10.3390/plants8050128] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/09/2019] [Accepted: 05/11/2019] [Indexed: 02/04/2023]
Abstract
Induced mutagenesis is one of the most effective strategies for trait improvement without altering the well-optimized genetic background of the cultivars. In this review, several currently accessible methods such as physical, chemical and insertional mutagenesis have been discussed concerning their efficient exploration for the tomato crop improvement. Similarly, challenges for the adaptation of genome-editing, a newly developed technique providing an opportunity to induce precise mutation, have been addressed. Several efforts of genome-editing have been demonstrated in tomato and other crops, exploring its effectiveness and convenience for crop improvement. Descriptive data compiled here from such efforts will be helpful for the efficient exploration of technological advances. However, uncertainty about the regulation of genome-edited crops is still a significant concern, particularly when timely trait improvement in tomato cultivars is needed. In this regard, random approaches of induced mutagenesis are still promising if efficiently explored in breeding applications. Precise identification of casual mutation is a prerequisite for the molecular understanding of the trait development as well as its utilization for the breeding program. Recent advances in sequencing techniques provide an opportunity for the precise detection of mutagenesis-induced sequence variations at a large scale in the genome. Here, we reviewed several novel next-generation sequencing based mutation mapping approaches including Mutmap, MutChromeSeq, and whole-genome sequencing-based mapping which has enormous potential to accelerate the mutation breeding in tomato. The proper utilization of the existing well-characterized tomato mutant resources combined with novel mapping approaches would inevitably lead to rapid enhancement of tomato quality and yield. This article provides an overview of the principles and applications of mutagenesis approaches in tomato and discusses the current progress and challenges involved in tomato mutagenesis research.
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Affiliation(s)
- Juhi Chaudhary
- Department of Biology, Oberlin College, Oberlin, OH 44074, USA.
| | - Alisha Alisha
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
| | - Vacha Bhatt
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
| | - Sonali Chandanshive
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
| | - Nirbhay Kumar
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
| | - Zahoor Mir
- National Research Center on Plant Biotechnology, New Delhi, Delhi 110012, India.
| | - Ashwini Kumar
- Division of Plant Pathology, ICAR-IARI, New Delhi, Delhi 110001, Inida.
| | - Satish K Yadav
- National Bureau of Plant Genetic Resources, New Delhi, Delhi 110012, India.
| | - S M Shivaraj
- Faculté des sciences de l'agriculture et de l'alimentation (FSAA), Université Laval, Quebec, QC G1V 0A6, Canada.
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
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21
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Kamolsukyeunyong W, Ruengphayak S, Chumwong P, Kusumawati L, Chaichoompu E, Jamboonsri W, Saensuk C, Phoonsiri K, Toojinda T, Vanavichit A. Identification of spontaneous mutation for broad-spectrum brown planthopper resistance in a large, long-term fast neutron mutagenized rice population. RICE (NEW YORK, N.Y.) 2019; 12:16. [PMID: 30888525 PMCID: PMC6424995 DOI: 10.1186/s12284-019-0274-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/25/2019] [Indexed: 05/09/2023]
Abstract
BACKGROUND The development of rice varieties with broad-spectrum resistance to insect pests is the most promising approach for controlling a fast evolving insect pest such as the brown planthopper (BPH). To cope with rapid evolution, discovering new sources of broad-spectrum resistance genes is the ultimate goal. RESULTS We used a forward genetics approach to identify BPH resistance genes in rice (Oryza sativa L.) using double digest restriction site-associated DNA sequencing (ddRADseq) for quantitative trait loci (QTL)-seq of the backcross inbred lines (BILs) derived from a cross between the BPH-susceptible cultivar KDML105 and BPH-resistant cultivar Rathu Heenati (RH). Two major genomic regions, located between 5.78-7.78 Mb (QBPH4.1) and 15.22-17.22 Mb (QBPH4.2) on rice chromosome 4, showed association with BPH resistance in both pooled BILs and individual highly resistant and susceptible BILs. The two most significant candidate resistance genes located within the QBPH4.1 and QBPH4.2 windows were lectin receptor kinase 3 (OsLecRK3) and sesquiterpene synthase 2 (OsSTPS2), respectively. Functional markers identified in these two genes were used for reverse screening 9323 lines of the fast neutron (FN)-mutagenized population developed from the BPH-susceptible, purple-pigmented, indica cultivar Jao Hom Nin (JHN). Nineteen FN-mutagenized lines (0.24%) carried mutations in the OsLecRK3 and/or OsSTPS2 gene. Among these mutant lines, only one highly resistant line (JHN4) and three moderately resistant lines (JHN09962, JHN12005, and JHN19525) were identified using three active, local BPH populations. The 19 mutant lines together with three randomly selected mutant lines, which did not harbor mutations in the two target genes, were screened further for mutations in six known BPH resistance genes including BPH9, BPH14, BPH18, BPH26, BPH29, and BPH32. Multiple single nucleotide polymorphisms (SNPs) and insertion-deletion (Indel) mutations were identified, which formed gene-specific haplotype patterns (HPs) essential for broad-spectrum resistance to BPH in both BILs and JHN mutant populations. CONCLUSION On the one hand, HPs of OsLekRK2-3, OsSTPS2, and BPH32 determined broad-spectrum resistance to BPH among RH-derived BILs. On the other hand, in the JHN mutant population, BPH9 together with seven significant genes on chromosome 4 played a crucial role in BPH resistance.
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Affiliation(s)
- Wintai Kamolsukyeunyong
- Rice Gene Discovery and Utilization Laboratory, Innovative Plant Biotechnology and Precision Agriculture Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani Thailand
| | - Siriphat Ruengphayak
- Rice Science Center, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, Thailand
| | - Pantharika Chumwong
- Rice Gene Discovery and Utilization Laboratory, Innovative Plant Biotechnology and Precision Agriculture Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani Thailand
| | - Lucia Kusumawati
- Rice Gene Discovery and Utilization Laboratory, Innovative Plant Biotechnology and Precision Agriculture Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani Thailand
| | - Ekawat Chaichoompu
- Rice Science Center, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, Thailand
- Interdisciplinary Graduate Program in Genetic Engineering and Bioinformatics, Kasetsart University, Chatuchak, Bangkok Thailand
| | - Watchareewan Jamboonsri
- Rice Gene Discovery and Utilization Laboratory, Innovative Plant Biotechnology and Precision Agriculture Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani Thailand
| | - Chatree Saensuk
- Rice Science Center, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, Thailand
| | - Kunyakarn Phoonsiri
- Rice Science Center, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, Thailand
| | - Theerayut Toojinda
- Rice Gene Discovery and Utilization Laboratory, Innovative Plant Biotechnology and Precision Agriculture Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani Thailand
- Integrative Crop Biotechnology and Management Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani Thailand
| | - Apichart Vanavichit
- Rice Gene Discovery and Utilization Laboratory, Innovative Plant Biotechnology and Precision Agriculture Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani Thailand
- Rice Science Center, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, Thailand
- Agronomy Department, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom Thailand
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Tyagi S, Mazumdar PA, Mayee P, Shivaraj SM, Anand S, Singh A, Madhurantakam C, Sharma P, Das S, Kumar A, Singh A. Natural variation in Brassica FT homeologs influences multiple agronomic traits including flowering time, silique shape, oil profile, stomatal morphology and plant height in B. juncea. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 277:251-266. [PMID: 30466591 DOI: 10.1016/j.plantsci.2018.09.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/17/2018] [Accepted: 09/21/2018] [Indexed: 06/09/2023]
Abstract
Natural structural variants of regulatory proteins causing quantitative phenotypic consequences have not been reported in plants. Herein, we show that 28 natural structural variants of FT homeologs, isolated from 6 species of Brassica, differ with respect to amino-acid substitutions in regions critical for interactions with FD and represent two evolutionarily distinct categories. Analysis of structural models of selected candidates from Brassica juncea (BjuFT_AAMF1) and Brassica napus (BnaFT_CCLF) predicted stronger binding between BjuFT and Arabidopsis thaliana FD. Over-expression of BjuFT and BnaFT in wild type and ft-10 mutant backgrounds of Arabidopsis validated higher potency of BjuFT in triggering floral transition. Analysis of gain-of-function and artificial miRNA mediated silenced lines of B. juncea implicated Brassica FT in multiple agronomic traits beyond flowering, consistent with a pleiotropic effect. Several dependent and independent traits such as lateral branching, silique shape, seed size, oil-profile, stomatal morphology and plant height were found altered in mutant lines. Enhanced FT levels caused early flowering, which in turn was positively correlated to a higher proportion of desirable fatty acids (PUFA). However, higher FT levels also resulted in altered silique shape and reduced seed size, suggesting trait trade-offs. Modulation of FT levels for achieving optimal balance of trait values and parsing pair-wise interactions among a reportoire of regulatory protein homeologs in polyploid genomes are indeed future areas of crop research.
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Affiliation(s)
- Shikha Tyagi
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India
| | | | - Pratiksha Mayee
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India; Department of Research, Ankur Seeds Pvt. Ltd., 27, Nagpur, Maharashtra, 440018, India
| | - S M Shivaraj
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India; Departement de Phytologie, Université Laval, Quebec City, Quebec, G1V 0A6, Canada
| | - Saurabh Anand
- Department of Botany, University of Delhi, New Delhi, 110007, India
| | - Anupama Singh
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India
| | - Chaithanya Madhurantakam
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India
| | - Prateek Sharma
- Department of Energy and Environment, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India
| | - Sandip Das
- Department of Botany, University of Delhi, New Delhi, 110007, India
| | - Arun Kumar
- National Phytotron Facility, IARI, New Delhi, 110012, India
| | - Anandita Singh
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India.
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23
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Kulmanov M, Schofield PN, Gkoutos GV, Hoehndorf R. Ontology-based validation and identification of regulatory phenotypes. Bioinformatics 2018; 34:i857-i865. [PMID: 30423068 PMCID: PMC6129279 DOI: 10.1093/bioinformatics/bty605] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Motivation Function annotations of gene products, and phenotype annotations of genotypes, provide valuable information about molecular mechanisms that can be utilized by computational methods to identify functional and phenotypic relatedness, improve our understanding of disease and pathobiology, and lead to discovery of drug targets. Identifying functions and phenotypes commonly requires experiments which are time-consuming and expensive to carry out; creating the annotations additionally requires a curator to make an assertion based on reported evidence. Support to validate the mutual consistency of functional and phenotype annotations as well as a computational method to predict phenotypes from function annotations, would greatly improve the utility of function annotations. Results We developed a novel ontology-based method to validate the mutual consistency of function and phenotype annotations. We apply our method to mouse and human annotations, and identify several inconsistencies that can be resolved to improve overall annotation quality. We also apply our method to the rule-based prediction of regulatory phenotypes from functions and demonstrate that we can predict these phenotypes with Fmax of up to 0.647. Availability and implementation https://github.com/bio-ontology-research-group/phenogocon.
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Affiliation(s)
- Maxat Kulmanov
- Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Centre, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Paul N Schofield
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Georgios V Gkoutos
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham, Birmingham, UK
- Institute of Translational Medicine, University Hospitals Birmingham, NHS Foundation Trust, Birmingham, UK
- NIHR Experimental Cancer Medicine Centre, Birmingham, UK
- NIHR Surgical Reconstruction and Microbiology Research Centre, Birmingham, UK
- NIHR Biomedical Research Centre, Birmingham, UK
| | - Robert Hoehndorf
- Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Centre, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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24
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Aglawe SB, Barbadikar KM, Mangrauthia SK, Madhav MS. New breeding technique "genome editing" for crop improvement: applications, potentials and challenges. 3 Biotech 2018; 8:336. [PMID: 30073121 PMCID: PMC6056351 DOI: 10.1007/s13205-018-1355-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 07/14/2018] [Indexed: 12/26/2022] Open
Abstract
Crop improvement is a continuous process in agriculture which ensures ample supply of food, fodder and fiber to burgeoning world population. Despite tremendous success in plant breeding and transgenesis to improve the yield-related traits, there have been several limitations primarily with the specificity in genetic modifications and incompatibility of host species. Because of this, new breeding techniques (NBTs) are gaining worldwide attention for crop improvement programs. Among the NBTs, genome editing (GE) using site-directed nucleases (SDNs) is an important and potential technique that overcomes limitations associated with classical breeding and transgenesis. These SDNs specifically target a compatible region in the gene/genome. The meganucleases (MgN), zinc finger nucleases (ZFN), transcription activator-like effectors nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated endonuclease (Cas) are being successfully employed for GE. These can be used for desired or targeted modifications of the native endogenous gene(s) or targeted insertion of cis/trans elements in the genomes of recipient organisms. Applications of these techniques appear to be endless ever since their discovery and several modifications in original technologies have further brought precision and accuracy in these methods. In this review, we present an overview of GE using SDNs with an emphasis on CRISPR/Cas system, their advantages, limitations and also practical considerations while designing experiments have been discussed. The review also emphasizes on the possible applications of CRISPR for improving economic traits in crop plants.
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Affiliation(s)
- Supriya B. Aglawe
- Biotechnology Section, ICAR-Indian Institute of Rice Research (IIRR), Rajendranagar, Hyderabad, 500030 India
| | - Kalyani M. Barbadikar
- Biotechnology Section, ICAR-Indian Institute of Rice Research (IIRR), Rajendranagar, Hyderabad, 500030 India
| | - Satendra K. Mangrauthia
- Biotechnology Section, ICAR-Indian Institute of Rice Research (IIRR), Rajendranagar, Hyderabad, 500030 India
| | - M. Sheshu Madhav
- Biotechnology Section, ICAR-Indian Institute of Rice Research (IIRR), Rajendranagar, Hyderabad, 500030 India
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25
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Tavakol E. Virus-Induced Gene Silencing (VIGS) in Aegilops tauschii and Its Use in Functional Analysis of AetDREB2. Mol Biotechnol 2017; 60:41-48. [PMID: 29196985 DOI: 10.1007/s12033-017-0042-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Among the available reverse genetic approaches for studying gene function, virus-induced gene silencing (VIGS) has several advantages. It allows rapid characterization of gene function independent of stable transformation, which is basically difficult to achieve in monocots, and offers the potential to silence individual or multiple genes of a gene family. In order to establish a VIGS system in Aegilops tauschii, modified vectors derived from Barley stripe mosaic virus (BSMV) were used for silencing a phytoene desaturase gene that provides a convenient visual reporter for silencing. The results demonstrated a high efficiency of BSMV-VIGS in A. tauschii. Moreover, the BSMV-VIGS system was used to target a 354 bp specific region of the Dehydration-responsive element-binding (AetDreb2) gene, resulting in successful silencing of the gene in A. tauschii plants, as verified by real-time qRT-PCR. Indeed, in comparison with plants that were inoculated with an empty vector (BSMV:00), a faster rate of wilting and a lower relative water content were observed in plants inoculated with BSMV:AetDreb2 when they were exposed to drought stress. Therefore, BSMV-VIGS can be efficiently employed as a novel tool for reverse genetics in A. tauschii. It can also be used to study the effects of polyploidization on the gene function by a comparative analysis between bread wheat and its diploid progenitor.
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Affiliation(s)
- Elahe Tavakol
- Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, 7144165186, Shiraz, Iran.
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26
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Hassani-Pak K, Rawlings C. Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes. J Integr Bioinform 2017; 14:/j/jib.ahead-of-print/jib-2016-0002/jib-2016-0002.xml. [PMID: 28609292 PMCID: PMC6042805 DOI: 10.1515/jib-2016-0002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 02/16/2017] [Indexed: 02/06/2023] Open
Abstract
Genetics and “omics” studies designed to uncover genotype to phenotype relationships often identify large numbers of potential candidate genes, among which the causal genes are hidden. Scientists generally lack the time and technical expertise to review all relevant information available from the literature, from key model species and from a potentially wide range of related biological databases in a variety of data formats with variable quality and coverage. Computational tools are needed for the integration and evaluation of heterogeneous information in order to prioritise candidate genes and components of interaction networks that, if perturbed through potential interventions, have a positive impact on the biological outcome in the whole organism without producing negative side effects. Here we review several bioinformatics tools and databases that play an important role in biological knowledge discovery and candidate gene prioritization. We conclude with several key challenges that need to be addressed in order to facilitate biological knowledge discovery in the future.
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Härtl K, Kalinowski G, Hoffmann T, Preuss A, Schwab W. RNAi-mediated endogene silencing in strawberry fruit: detection of primary and secondary siRNAs by deep sequencing. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:658-668. [PMID: 27862816 PMCID: PMC5398998 DOI: 10.1111/pbi.12664] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 10/12/2016] [Accepted: 11/15/2016] [Indexed: 05/10/2023]
Abstract
RNA interference (RNAi) has been exploited as a reverse genetic tool for functional genomics in the nonmodel species strawberry (Fragaria × ananassa) since 2006. Here, we analysed for the first time different but overlapping nucleotide sections (>200 nt) of two endogenous genes, FaCHS (chalcone synthase) and FaOMT (O-methyltransferase), as inducer sequences and a transitive vector system to compare their gene silencing efficiencies. In total, ten vectors were assembled each containing the nucleotide sequence of one fragment in sense and corresponding antisense orientation separated by an intron (inverted hairpin construct, ihp). All sequence fragments along the full lengths of both target genes resulted in a significant down-regulation of the respective gene expression and related metabolite levels. Quantitative PCR data and successful application of a transitive vector system coinciding with a phenotypic change suggested propagation of the silencing signal. The spreading of the signal in strawberry fruit in the 3' direction was shown for the first time by the detection of secondary small interfering RNAs (siRNAs) outside of the primary targets by deep sequencing. Down-regulation of endogenes by the transitive method was less effective than silencing by ihp constructs probably because the numbers of primary siRNAs exceeded the quantity of secondary siRNAs by three orders of magnitude. Besides, we observed consistent hotspots of primary and secondary siRNA formation along the target sequence which fall within a distance of less than 200 nt. Thus, ihp vectors seem to be superior over the transitive vector system for functional genomics in strawberry fruit.
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Affiliation(s)
- Katja Härtl
- Biotechnology of Natural ProductsTechnische Universität MünchenFreisingGermany
| | - Gregor Kalinowski
- Biotechnology of Natural ProductsTechnische Universität MünchenFreisingGermany
| | - Thomas Hoffmann
- Biotechnology of Natural ProductsTechnische Universität MünchenFreisingGermany
| | - Anja Preuss
- Biotechnology of Natural ProductsTechnische Universität MünchenFreisingGermany
| | - Wilfried Schwab
- Biotechnology of Natural ProductsTechnische Universität MünchenFreisingGermany
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28
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Ben-Amar A, Daldoul S, Reustle GM, Krczal G, Mliki A. Reverse Genetics and High Throughput Sequencing Methodologies for Plant Functional Genomics. Curr Genomics 2016; 17:460-475. [PMID: 28217003 PMCID: PMC5282599 DOI: 10.2174/1389202917666160520102827] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 12/12/2015] [Accepted: 01/05/2016] [Indexed: 11/22/2022] Open
Abstract
In the post-genomic era, increasingly sophisticated genetic tools are being developed with the long-term goal of understanding how the coordinated activity of genes gives rise to a complex organism. With the advent of the next generation sequencing associated with effective computational approaches, wide variety of plant species have been fully sequenced giving a wealth of data sequence information on structure and organization of plant genomes. Since thousands of gene sequences are already known, recently developed functional genomics approaches provide powerful tools to analyze plant gene functions through various gene manipulation technologies. Integration of different omics platforms along with gene annotation and computational analysis may elucidate a complete view in a system biology level. Extensive investigations on reverse genetics methodologies were deployed for assigning biological function to a specific gene or gene product. We provide here an updated overview of these high throughout strategies highlighting recent advances in the knowledge of functional genomics in plants.
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Affiliation(s)
- Anis Ben-Amar
- Department of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, Tunisia
- AgroScience.GmbH, AlPlanta-Institute for Plant Research, Neustadt an der Weinstraße, Germany
| | - Samia Daldoul
- Department of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, Tunisia
| | - Götz M. Reustle
- AgroScience.GmbH, AlPlanta-Institute for Plant Research, Neustadt an der Weinstraße, Germany
| | - Gabriele Krczal
- AgroScience.GmbH, AlPlanta-Institute for Plant Research, Neustadt an der Weinstraße, Germany
| | - Ahmed Mliki
- Department of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, Tunisia
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29
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Czarnecki O, Bryan AC, Jawdy SS, Yang X, Cheng ZM, Chen JG, Tuskan GA. Simultaneous knockdown of six non-family genes using a single synthetic RNAi fragment in Arabidopsis thaliana. PLANT METHODS 2016; 12:16. [PMID: 26889205 PMCID: PMC4756541 DOI: 10.1186/s13007-016-0116-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/08/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND Genetic engineering of plants that results in successful establishment of new biochemical or regulatory pathways requires stable introduction of one or more genes into the plant genome. It might also be necessary to down-regulate or turn off expression of endogenous genes in order to reduce activity of competing pathways. An established way to knockdown gene expression in plants is expressing a hairpin-RNAi construct, eventually leading to degradation of a specifically targeted mRNA. Knockdown of multiple genes that do not share homologous sequences is still challenging and involves either sophisticated cloning strategies to create vectors with different serial expression constructs or multiple transformation events that is often restricted by a lack of available transformation markers. RESULTS Synthetic RNAi fragments were assembled in yeast carrying homologous sequences to six or seven non-family genes and introduced into pAGRIKOLA. Transformation of Arabidopsis thaliana and subsequent expression analysis of targeted genes proved efficient knockdown of all target genes. CONCLUSIONS We present a simple and cost-effective method to create constructs to simultaneously knockdown multiple non-family genes or genes that do not share sequence homology. The presented method can be applied in plant and animal synthetic biology as well as traditional plant and animal genetic engineering.
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Affiliation(s)
- Olaf Czarnecki
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA ; KWS SAAT SE, Grimsehlstraße 31, 37555 Einbeck, Germany
| | - Anthony C Bryan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Sara S Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Zong-Ming Cheng
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
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30
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Han Y, Zhang B, Qin X, Li M, Guo Y. Investigation of a miRNA-Induced Gene Silencing Technique in Petunia Reveals Alterations in miR173 Precursor Processing and the Accumulation of Secondary siRNAs from Endogenous Genes. PLoS One 2015; 10:e0144909. [PMID: 26658695 PMCID: PMC4701714 DOI: 10.1371/journal.pone.0144909] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/26/2015] [Indexed: 11/19/2022] Open
Abstract
MIGS (miRNA-induced gene silencing) is a straightforward and efficient gene silencing technique in Arabidopsis. It works by exploiting miR173 to trigger the production of phasiRNAs (phased small interfering RNAs). MIGS can be used in plant species other than Arabidopsis by co-expression of miR173 and target gene fragments fused to an upstream miR173 target site. However, the efficiency and technical mechanisms have not been thoroughly investigated in other plants. In this work, two vectors, pMIGS-chs and pMIGS-pds, were constructed and transformed into petunia plants. The transgenic plants showed CHS (chalcone synthase) and PDS (phytoene desaturase) gene-silencing phenotypes respectively, indicating that MIGS functions in petunia. MIGS-chs plants were used to investigate the mechanisms of this technique in petunia. Results of 5′- RACE showed that the miR173 target site was cleaved at the expected position and that endogenous CHS genes were cut at multiple positions. Small RNA deep sequencing analysis showed that the processing of Arabidopsis miR173 precursors in MIGS-chs transgenic petunia plants did not occur in exactly the same way as in Arabidopsis, suggesting differences in the machinery of miRNA processing between plant species. Small RNAs in-phase with the miR173 cleavage register were produced immediately downstream from the cleavage site and out-of-phase small RNAs were accumulated at relatively high levels from processing cycle 5 onwards. Secondary siRNAs were generated from multiple sites of endogenous CHS-A and CHS-J genes, indicating that miR173 cleavage induced siRNAs have the same ability to initiate siRNA transitivity as the siRNAs functioning in co-suppression and hpRNA silencing. On account of the simplicity of vector construction and the transitive amplification of signals from endogenous transcripts, MIGS is a good alternative gene silencing method for plants, especially for silencing a cluster of homologous genes with redundant functions.
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Affiliation(s)
- Yao Han
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Bin Zhang
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Xiaoting Qin
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Mingyang Li
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Yulong Guo
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- * E-mail:
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Guidarelli M, Baraldi E. Transient transformation meets gene function discovery: the strawberry fruit case. FRONTIERS IN PLANT SCIENCE 2015; 6:444. [PMID: 26124771 PMCID: PMC4464107 DOI: 10.3389/fpls.2015.00444] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/29/2015] [Indexed: 05/20/2023]
Abstract
Beside the well known nutritional and health benefits, strawberry (FragariaXananassa) crop draws increasing attention as plant model system for the Rosaceae family, due to the short generation time, the rapid in vitro regeneration, and to the availability of the genome sequence of F.Xananassa and F. vesca species. In the last years, the use of high-throughput sequence technologies provided large amounts of molecular information on the genes possibly related to several biological processes of this crop. Nevertheless, the function of most genes or gene products is still poorly understood and needs investigation. Transient transformation technology provides a powerful tool to study gene function in vivo, avoiding difficult drawbacks that typically affect the stable transformation protocols, such as transformation efficiency, transformants selection, and regeneration. In this review we provide an overview of the use of transient expression in the investigation of the function of genes important for strawberry fruit development, defense and nutritional properties. The technical aspects related to an efficient use of this technique are described, and the possible impact and application in strawberry crop improvement are discussed.
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Affiliation(s)
| | - Elena Baraldi
- Laboratory of Plant Pathology and Biotechnology, Department of Agricultural Sciences, University of BolognaBologna, Italy
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First TILLING platform in Cucurbita pepo: a new mutant resource for gene function and crop improvement. PLoS One 2014; 9:e112743. [PMID: 25386735 PMCID: PMC4227871 DOI: 10.1371/journal.pone.0112743] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 10/14/2014] [Indexed: 11/19/2022] Open
Abstract
Although the availability of genetic and genomic resources for Cucurbita pepo has increased significantly, functional genomic resources are still limited for this crop. In this direction, we have developed a high throughput reverse genetic tool: the first TILLING (Targeting Induced Local Lesions IN Genomes) resource for this species. Additionally, we have used this resource to demonstrate that the previous EMS mutant population we developed has the highest mutation density compared with other cucurbits mutant populations. The overall mutation density in this first C. pepo TILLING platform was estimated to be 1/133 Kb by screening five additional genes. In total, 58 mutations confirmed by sequencing were identified in the five targeted genes, thirteen of which were predicted to have an impact on the function of the protein. The genotype/phenotype correlation was studied in a peroxidase gene, revealing that the phenotype of seedling homozygous for one of the isolated mutant alleles was albino. These results indicate that the TILLING approach in this species was successful at providing new mutations and can address the major challenge of linking sequence information to biological function and also the identification of novel variation for crop breeding.
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Chen L, Hao L, Parry MAJ, Phillips AL, Hu YG. Progress in TILLING as a tool for functional genomics and improvement of crops. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:425-43. [PMID: 24618006 DOI: 10.1111/jipb.12192] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 03/11/2014] [Indexed: 05/18/2023]
Abstract
Food security is a global concern and substantial yield increases in crops are required to feed the growing world population. Mutagenesis is an important tool in crop improvement and is free of the regulatory restrictions imposed on genetically modified organisms. Targeting Induced Local Lesions in Genomes (TILLING), which combines traditional chemical mutagenesis with high-throughput genome-wide screening for point mutations in desired genes, offers a powerful way to create novel mutant alleles for both functional genomics and improvement of crops. TILLING is generally applicable to genomes whether small or large, diploid or even allohexaploid, and shows great potential to address the major challenge of linking sequence information to the function of genes and to modulate key traits for plant breeding. TILLING has been successfully applied in many crop species and recent progress in TILLING is summarized below, especially on the developments in mutation detection technology, application of TILLING in gene functional studies and crop breeding. The potential of TILLING/EcoTILLING for functional genetics and crop improvement is also discussed. Furthermore, a small-scale forward strategy including backcross and selfing was conducted to release the potential mutant phenotypes masked in M2 (or M3) plants.
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Affiliation(s)
- Liang Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
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Rhee SY, Mutwil M. Towards revealing the functions of all genes in plants. TRENDS IN PLANT SCIENCE 2014; 19:212-21. [PMID: 24231067 DOI: 10.1016/j.tplants.2013.10.006] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 10/10/2013] [Accepted: 10/16/2013] [Indexed: 05/19/2023]
Abstract
The great recent progress made in identifying the molecular parts lists of organisms revealed the paucity of our understanding of what most of the parts do. In this review, we introduce computational and statistical approaches and omics data used for inferring gene function in plants, with an emphasis on network-based inference. We also discuss caveats associated with network-based function predictions such as performance assessment, annotation propagation, the guilt-by-association concept, and the meaning of hubs. Finally, we note the current limitations and possible future directions such as the need for gold standard data from several species, unified access to data and tools, quantitative comparison of data and tool quality, and high-throughput experimental validation platforms for systematic gene function elucidation in plants.
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Affiliation(s)
- Seung Yon Rhee
- Carnegie Institution for Science, Department of Plant Biology, 260 Panama St, Stanford, CA 94305, USA.
| | - Marek Mutwil
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany.
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Belfield EJ, Brown C, Gan X, Jiang C, Baban D, Mithani A, Mott R, Ragoussis J, Harberd NP. Microarray-based ultra-high resolution discovery of genomic deletion mutations. BMC Genomics 2014; 15:224. [PMID: 24655320 PMCID: PMC3998191 DOI: 10.1186/1471-2164-15-224] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 02/28/2014] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Oligonucleotide microarray-based comparative genomic hybridization (CGH) offers an attractive possible route for the rapid and cost-effective genome-wide discovery of deletion mutations. CGH typically involves comparison of the hybridization intensities of genomic DNA samples with microarray chip representations of entire genomes, and has widespread potential application in experimental research and medical diagnostics. However, the power to detect small deletions is low. RESULTS Here we use a graduated series of Arabidopsis thaliana genomic deletion mutations (of sizes ranging from 4 bp to ~5 kb) to optimize CGH-based genomic deletion detection. We show that the power to detect smaller deletions (4, 28 and 104 bp) depends upon oligonucleotide density (essentially the number of genome-representative oligonucleotides on the microarray chip), and determine the oligonucleotide spacings necessary to guarantee detection of deletions of specified size. CONCLUSIONS Our findings will enhance a wide range of research and clinical applications, and in particular will aid in the discovery of genomic deletions in the absence of a priori knowledge of their existence.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Nicholas P Harberd
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
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Zhang Z, Zhang Q, Wu J, Zheng X, Zheng S, Sun X, Qiu Q, Lu T. Gene knockout study reveals that cytosolic ascorbate peroxidase 2(OsAPX2) plays a critical role in growth and reproduction in rice under drought, salt and cold stresses. PLoS One 2013; 8:e57472. [PMID: 23468992 PMCID: PMC3585366 DOI: 10.1371/journal.pone.0057472] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 01/22/2013] [Indexed: 11/18/2022] Open
Abstract
Plant ascorbate peroxidases (APXs), enzymes catalyzing the dismutation of H2O2 into H2O and O2, play an important role in reactive oxygen species homeostasis in plants. The rice genome has eight OsAPXs, but their physiological functions remain to be determined. In this report, we studied the function of OsAPX2 gene using a T-DNA knockout mutant under the treatment of drought, salt and cold stresses. The Osapx2 knockout mutant was isolated by a genetic screening of a rice T-DNA insertion library under 20% PEG-2000 treatment. Loss of function in OsAPX2 affected the growth and development of rice seedlings, resulting in semi-dwarf seedlings, yellow-green leaves, leaf lesion mimic and seed sterility. OsAPX2 expression was developmental- and spatial-regulated, and was induced by drought, salt, and cold stresses. Osapx2 mutants had lower APX activity and were sensitive to abiotic stresses; overexpression of OsAPX2 increased APX activity and enhanced stress tolerance. H2O2 and MDA levels were high in Osapx2 mutants but low in OsAPX2-OX transgenic lines relative to wild-type plants after stress treatments. Taken together, the cytosolic ascorbate peroxidase OsAPX2 plays an important role in rice growth and development by protecting the seedlings from abiotic stresses through scavenging reactive oxygen species.
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Affiliation(s)
- Zhiguo Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences/National Key facility for Gene Resources And Genetic Improvement, Beijing, China
| | - Quian Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences/National Key facility for Gene Resources And Genetic Improvement, Beijing, China
| | - Jinxia Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences/National Key facility for Gene Resources And Genetic Improvement, Beijing, China
| | - Xia Zheng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences/National Key facility for Gene Resources And Genetic Improvement, Beijing, China
| | - Sheng Zheng
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xuehui Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences/National Key facility for Gene Resources And Genetic Improvement, Beijing, China
| | - Quansheng Qiu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- * E-mail: (QQ); (TL)
| | - Tiegang Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences/National Key facility for Gene Resources And Genetic Improvement, Beijing, China
- * E-mail: (QQ); (TL)
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Abstract
Targeting induced local lesions in genomes (TILLING), initially a functional genomics tool in model plants, has been extended to many plant species and become of paramount importance to reverse genetics in crops species. Because it is readily applicable to most plants, it remains a dominant non-transgenic method for obtaining mutations in known genes. The process has seen many technological changes over the last 10 years; a major recent change has been the application of next-generation sequencing (NGS) to the process, which permits multiplexing of gene targets and genomes. NGS will ultimately lead to TILLING becoming an in silico procedure. We review here the history and technology in brief, but focus more importantly on recent developments in polyploids, vegetatively propagated crops and the future of TILLING for plant breeding.
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Affiliation(s)
- Trevor L Wang
- John Innes Centre, Norwich Research Park, Norwich, UK.
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Awasthi A, Paul P, Kumar S, Verma SK, Prasad R, Dhaliwal HS. Abnormal endosperm development causes female sterility in rice insertional mutant OsAPC6. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 183:167-174. [PMID: 22195590 DOI: 10.1016/j.plantsci.2011.08.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 08/18/2011] [Accepted: 08/19/2011] [Indexed: 05/28/2023]
Abstract
A T-DNA insertional mutant OsAPC6 of rice, with gibberellic acid insensitivity and reduced height, had up to 45% reduced seed set. The insertion occurred on chromosome 3 of rice in the gene encoding one of the subunits of anaphase promoting complex/Cyclosome APC6. The primary mother cells of the mutant plants had normal meiosis, male gametophyte development and pollen viability. Confocal laser scanning microscopic (CLSM) studies of megagametophyte development showed abnormal mitotic divisions with reduced number or total absence of polar nuclei in about 30-35% megagametophytes of OsAPC6 mutant leading to failure of endosperm and hence embryo and seed development. Abnormal female gametophyte development, high sterility and segregation of tall and gibberellic acid sensitive plants without selectable marker Hpt in the selfed progeny of OsAPC6 mutant plants indicate that the mutant could be maintained in heterozygous condition. The abnormal mitotic divisions during megagametogenesis could be attributed to the inactivation of the APC6/CDC16 of anaphase promoting complex of rice responsible for cell cycle progression during megagametogenesis. Functional validation of the candidate gene through transcriptome profiling and RNAi is in progress.
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Affiliation(s)
- Anjali Awasthi
- Department of Biotechnology, Indian Institute of Technology, Roorkee-247667 India
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Lidder P, Sonnino A. Biotechnologies for the management of genetic resources for food and agriculture. ADVANCES IN GENETICS 2012; 78:1-167. [PMID: 22980921 DOI: 10.1016/b978-0-12-394394-1.00001-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In recent years, the land area under agriculture has declined as also has the rate of growth in agricultural productivity while the demand for food continues to escalate. The world population now stands at 7 billion and is expected to reach 9 billion in 2045. A broad range of agricultural genetic diversity needs to be available and utilized in order to feed this growing population. Climate change is an added threat to biodiversity that will significantly impact genetic resources for food and agriculture (GRFA) and food production. There is no simple, all-encompassing solution to the challenges of increasing productivity while conserving genetic diversity. Sustainable management of GRFA requires a multipronged approach, and as outlined in the paper, biotechnologies can provide powerful tools for the management of GRFA. These tools vary in complexity from those that are relatively simple to those that are more sophisticated. Further, advances in biotechnologies are occurring at a rapid pace and provide novel opportunities for more effective and efficient management of GRFA. Biotechnology applications must be integrated with ongoing conventional breeding and development programs in order to succeed. Additionally, the generation, adaptation, and adoption of biotechnologies require a consistent level of financial and human resources and appropriate policies need to be in place. These issues were also recognized by Member States at the FAO international technical conference on Agricultural Biotechnologies for Developing Countries (ABDC-10), which took place in March 2010 in Mexico. At the end of the conference, the Member States reached a number of key conclusions, agreeing, inter alia, that developing countries should significantly increase sustained investments in capacity building and the development and use of biotechnologies to maintain the natural resource base; that effective and enabling national biotechnology policies and science-based regulatory frameworks can facilitate the development and appropriate use of biotechnologies in developing countries; and that FAO and other relevant international organizations and donors should significantly increase their efforts to support the strengthening of national capacities in the development and appropriate use of pro-poor agricultural biotechnologies.
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Affiliation(s)
- Preetmoninder Lidder
- Office of Knowledge Exchange, Research and Extension, Research and Extension Branch, Food and Agriculture Organization of the UN (FAO), Viale delle Terme di Caracalla, Rome, Italy
| | - Andrea Sonnino
- Office of Knowledge Exchange, Research and Extension, Research and Extension Branch, Food and Agriculture Organization of the UN (FAO), Viale delle Terme di Caracalla, Rome, Italy
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41
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Mohr SE, Perrimon N. RNAi screening: new approaches, understandings, and organisms. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:145-58. [PMID: 21953743 DOI: 10.1002/wrna.110] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
RNA interference (RNAi) leads to sequence-specific knockdown of gene function. The approach can be used in large-scale screens to interrogate function in various model organisms and an increasing number of other species. Genome-scale RNAi screens are routinely performed in cultured or primary cells or in vivo in organisms such as C. elegans. High-throughput RNAi screening is benefitting from the development of sophisticated new instrumentation and software tools for collecting and analyzing data, including high-content image data. The results of large-scale RNAi screens have already proved useful, leading to new understandings of gene function relevant to topics such as infection, cancer, obesity, and aging. Nevertheless, important caveats apply and should be taken into consideration when developing or interpreting RNAi screens. Some level of false discovery is inherent to high-throughput approaches and specific to RNAi screens, false discovery due to off-target effects (OTEs) of RNAi reagents remains a problem. The need to improve our ability to use RNAi to elucidate gene function at large scale and in additional systems continues to be addressed through improved RNAi library design, development of innovative computational and analysis tools and other approaches.
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Affiliation(s)
- Stephanie E Mohr
- Drosophila RNAi Screening Center, Department of Genetics, Harvard Medical School, Boston, MA, USA
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Gonzalez-Ballester D, Pootakham W, Mus F, Yang W, Catalanotti C, Magneschi L, de Montaigu A, Higuera JJ, Prior M, Galván A, Fernandez E, Grossman AR. Reverse genetics in Chlamydomonas: a platform for isolating insertional mutants. PLANT METHODS 2011; 7:24. [PMID: 21794168 PMCID: PMC3161022 DOI: 10.1186/1746-4811-7-24] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 07/27/2011] [Indexed: 05/03/2023]
Abstract
A method was developed to identify insertional mutants of Chlamydomonas reinhardtii disrupted for selected target genes. The approach relies on the generation of thousands of transformants followed by PCR-based screenings that allow for identification of strains harboring the introduced marker gene within specific genes of interest. Our results highlight the strengths and limitations of two independent screens that differed in the nature of the marker DNA used (PCR-amplified fragment containing the plasmid-free marker versus entire linearized plasmid with the marker) and in the strategies used to maintain and store transformants.
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Affiliation(s)
- David Gonzalez-Ballester
- Department of Plant Biology, The Carnegie Institution for Science, Stanford, CA 94305, USA
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba 14071, Spain
| | - Wirulda Pootakham
- Department of Plant Biology, The Carnegie Institution for Science, Stanford, CA 94305, USA
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, 12120, Thailand
| | - Florence Mus
- Department of Plant Biology, The Carnegie Institution for Science, Stanford, CA 94305, USA
- Montana State University, Department of Chemical and Biological Engineering, and Department of Microbiology, Bozeman, MT 59171, USA
| | - Wenqiang Yang
- Department of Plant Biology, The Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Claudia Catalanotti
- Department of Plant Biology, The Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Leonardo Magneschi
- Department of Plant Biology, The Carnegie Institution for Science, Stanford, CA 94305, USA
- PlantLab, Scuola Superiore Sant'Anna, 56127 Pisa, Italy
| | - Amaury de Montaigu
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba 14071, Spain
- Max Planck Insitute for Plant Breeding Research, Department of Plant Developmental Biology, D-50829, Köln, Germany
| | - Jose J Higuera
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba 14071, Spain
| | - Matthew Prior
- Department of Plant Biology, The Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Aurora Galván
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba 14071, Spain
| | - Emilio Fernandez
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba 14071, Spain
| | - Arthur R Grossman
- Department of Plant Biology, The Carnegie Institution for Science, Stanford, CA 94305, USA
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Chen Y, Wilde HD. Mutation scanning of peach floral genes. BMC PLANT BIOLOGY 2011; 11:96. [PMID: 21605436 PMCID: PMC3120741 DOI: 10.1186/1471-2229-11-96] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 05/23/2011] [Indexed: 05/30/2023]
Abstract
BACKGROUND Mutation scanning technology has been used to develop crop species with improved traits. Modifications that improve screening throughput and sensitivity would facilitate the targeted mutation breeding of crops. Technical innovations for high-resolution melting (HRM) analysis are enabling the clinic-based screening for human disease gene polymorphism. We examined the application of two HRM modifications, COLD-PCR and QMC-PCR, to the mutation scanning of genes in peach, Prunus persica. The targeted genes were the putative floral regulators PpAGAMOUS and PpTERMINAL FLOWER I. RESULTS HRM analysis of PpAG and PpTFL1 coding regions in 36 peach cultivars found one polymorphic site in each gene. PpTFL1 and PpAG SNPs were used to examine approaches to increase HRM throughput. Cultivars with SNPs could be reliably detected in pools of twelve genotypes. COLD-PCR was found to increase the sensitivity of HRM analysis of pooled samples, but worked best with small amplicons. Examination of QMC-PCR demonstrated that primary PCR products for further analysis could be produced from variable levels of genomic DNA. CONCLUSIONS Natural SNPs in exons of target peach genes were discovered by HRM analysis of cultivars from a southeastern US breeding program. For detecting natural or induced SNPs in larger populations, HRM efficiency can be improved by increasing sample pooling and template production through approaches such as COLD-PCR and QMC-PCR. Technical advances developed to improve clinical diagnostics can play a role in the targeted mutation breeding of crops.
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Affiliation(s)
- Yihua Chen
- Horticulture Department, University of Georgia, Athens, GA 30602, USA
| | - H Dayton Wilde
- Horticulture Department, University of Georgia, Athens, GA 30602, USA
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