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Mamrutha HM, Zeenat W, Kapil D, Budhagatapalli N, Tikaniya D, Rakesh K, Krishnappa G, Singh G, Singh GP. Evidence and opportunities for developing non-transgenic genome edited crops using site-directed nuclease 1 approach. Crit Rev Biotechnol 2024; 44:1140-1150. [PMID: 37915126 DOI: 10.1080/07388551.2023.2270581] [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: 02/04/2022] [Revised: 07/21/2023] [Accepted: 09/18/2023] [Indexed: 11/03/2023]
Abstract
The innovations and progress in genome editing/new breeding technologies have revolutionized research in the field of functional genomics and crop improvement. This revolution has expanded the horizons of agricultural research, presenting fresh possibilities for creating novel plant varieties equipped with desired traits that can effectively combat the challenges posed by climate change. However, the regulation and social acceptance of genome-edited crops still remain as major barriers. Only a few countries considered the site-directed nuclease 1 (SDN1) approach-based genome-edited plants under less or no regulation. Hence, the present review aims to comprise information on the research work conducted using SDN1 in crops by various genome editing tools. It also elucidates the promising candidate genes that can be used for editing and has listed the studies on non-transgenic crops developed through SDN1 either by Agrobacterium-mediated transformation or by ribo nucleoprotein (RNP) complex. The review also hoards the existing regulatory landscape of genome editing and provides an overview of globally commercialized genome-edited crops. These compilations will enable confidence in researchers and policymakers, across the globe, to recognize the full potential of this technology and reconsider the regulatory aspects associated with genome-edited crops. Furthermore, this compilation serves as a valuable resource for researchers embarking on the development of customized non-transgenic crops through the utilization of SDN1.
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Affiliation(s)
- H M Mamrutha
- ICAR - Indian Institute of Wheat and Barley Research, Karnal, India
| | - Wadhwa Zeenat
- ICAR - Indian Institute of Wheat and Barley Research, Karnal, India
| | - Deswal Kapil
- ICAR - Indian Institute of Wheat and Barley Research, Karnal, India
- Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - Nagaveni Budhagatapalli
- Institute of Plant Biochemistry, Center for Plant Genome Engineering, Heinrich-Heine-University, Düsseldorf, Germany
| | - Divya Tikaniya
- ICAR - Indian Institute of Wheat and Barley Research, Karnal, India
- Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - Kumar Rakesh
- Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | | | - Gyanendra Singh
- ICAR - Indian Institute of Wheat and Barley Research, Karnal, India
| | - G P Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
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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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Abu Risha M, Rick EM, Plum M, Jappe U. Legume Allergens Pea, Chickpea, Lentil, Lupine and Beyond. Curr Allergy Asthma Rep 2024:10.1007/s11882-024-01165-7. [PMID: 38990406 DOI: 10.1007/s11882-024-01165-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2024] [Indexed: 07/12/2024]
Abstract
PURPOSE OF THE REVIEW In the last decade, an increasing trend towards a supposedly healthier vegan diet could be observed. However, recently, more cases of allergic reactions to plants and plant-based products such as meat-substitution products, which are often prepared with legumes, were reported. Here, we provide the current knowledge on legume allergen sources and the respective single allergens. We answer the question of which legumes beside the well-known food allergen sources peanut and soybean should be considered for diagnostic and therapeutic measures. RECENT FINDINGS These "non-priority" legumes, including beans, pea, lentils, chickpea, lupine, cowpea, pigeon pea, and fenugreek, are potentially new important allergen sources, causing mild-to-severe allergic reactions. Severe reactions have been described particularly for peas and lupine. An interesting aspect is the connection between anaphylactic reactions and exercise (food-dependent exercise-induced anaphylaxis), which has only recently been highlighted for legumes such as soybean, lentils and chickpea. Most allergic reactions derive from IgE cross-reactions to homologous proteins, for example between peanut and lupine, which is of particular importance for peanut-allergic individuals ignorant to these cross-reactions. From our findings we conclude that there is a need for large-scale studies that are geographically distinctive because most studies are case reports, and geographic differences of allergic diseases towards these legumes have already been discovered for well-known "Big 9" allergen sources such as peanut and soybean. Furthermore, the review illustrates the need for a better molecular diagnostic for these emerging non-priority allergen sources to evaluate IgE cross-reactivities to known allergens and identify true allergic reactions.
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Affiliation(s)
- Marua Abu Risha
- Clinical and Molecular Allergology, Priority Research Area Chronic Lung Diseases, Research Center Borstel, Borstel, Germany
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Borstel, Germany
| | - Eva-Maria Rick
- Clinical and Molecular Allergology, Priority Research Area Chronic Lung Diseases, Research Center Borstel, Borstel, Germany
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Borstel, Germany
| | - Melanie Plum
- Clinical and Molecular Allergology, Priority Research Area Chronic Lung Diseases, Research Center Borstel, Borstel, Germany
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Borstel, Germany
| | - Uta Jappe
- Clinical and Molecular Allergology, Priority Research Area Chronic Lung Diseases, Research Center Borstel, Borstel, Germany.
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Borstel, Germany.
- Interdisciplinary Allergy Outpatient Clinic, Department of Pneumology, University of Lübeck, Lübeck, Germany.
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Li H, Che R, Zhu J, Yang X, Li J, Fernie AR, Yan J. Multi-omics-driven advances in the understanding of triacylglycerol biosynthesis in oil seeds. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:999-1017. [PMID: 38009661 DOI: 10.1111/tpj.16545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 11/01/2023] [Indexed: 11/29/2023]
Abstract
Vegetable oils are rich sources of polyunsaturated fatty acids and energy as well as valuable sources of human food, animal feed, and bioenergy. Triacylglycerols, which are comprised of three fatty acids attached to a glycerol backbone, are the main component of vegetable oils. Here, we review the development and application of multiple-level omics in major oilseeds and emphasize the progress in the analysis of the biological roles of key genes underlying seed oil content and quality in major oilseeds. Finally, we discuss future research directions in functional genomics research based on current omics and oil metabolic engineering strategies that aim to enhance seed oil content and quality, and specific fatty acids components according to either human health needs or industrial requirements.
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Affiliation(s)
- Hui Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Ronghui Che
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Jiantang Zhu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Xiaohong Yang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Jiansheng Li
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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Szurman-Zubrzycka M, Kurowska M, Till BJ, Szarejko I. Is it the end of TILLING era in plant science? FRONTIERS IN PLANT SCIENCE 2023; 14:1160695. [PMID: 37674734 PMCID: PMC10477672 DOI: 10.3389/fpls.2023.1160695] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/19/2023] [Indexed: 09/08/2023]
Abstract
Since its introduction in 2000, the TILLING strategy has been widely used in plant research to create novel genetic diversity. TILLING is based on chemical or physical mutagenesis followed by the rapid identification of mutations within genes of interest. TILLING mutants may be used for functional analysis of genes and being nontransgenic, they may be directly used in pre-breeding programs. Nevertheless, classical mutagenesis is a random process, giving rise to mutations all over the genome. Therefore TILLING mutants carry background mutations, some of which may affect the phenotype and should be eliminated, which is often time-consuming. Recently, new strategies of targeted genome editing, including CRISPR/Cas9-based methods, have been developed and optimized for many plant species. These methods precisely target only genes of interest and produce very few off-targets. Thus, the question arises: is it the end of TILLING era in plant studies? In this review, we recap the basics of the TILLING strategy, summarize the current status of plant TILLING research and present recent TILLING achievements. Based on these reports, we conclude that TILLING still plays an important role in plant research as a valuable tool for generating genetic variation for genomics and breeding projects.
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Affiliation(s)
- Miriam Szurman-Zubrzycka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Marzena Kurowska
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Bradley J. Till
- Veterinary Genetics Laboratory, University of California, Davis, Davis, United States
| | - Iwona Szarejko
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
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Khan N, Zhang J, Islam S, Appels R, Dell B. Wheat Water-Soluble Carbohydrate Remobilisation under Water Deficit by 1-FEH w3. Curr Issues Mol Biol 2023; 45:6634-6650. [PMID: 37623238 PMCID: PMC10453044 DOI: 10.3390/cimb45080419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/03/2023] [Accepted: 08/08/2023] [Indexed: 08/26/2023] Open
Abstract
Fructan 1-exohydrolase (1-FEH) is one of the major enzymes in water-soluble carbohydrate (WSC) remobilisation for grains in wheat. We investigated the functional role of 1-FEH w1, w2, and w3 isoforms in WSC remobilisation under post-anthesis water deficit using mutation lines derived from the Australian wheat variety Chara. F1 seeds, developed by backcrossing the 1-FEH w1, w2, and w3 mutation lines with Chara, were genotyped using the Infinium 90K SNP iSelect platform to characterise the mutated region. Putative deletions were identified in FEH mutation lines encompassing the FEH genomic regions. Mapping analysis demonstrated that mutations affected significantly longer regions than the target FEH gene regions. Functional roles of the non-target genes were carried out utilising bioinformatics and confirmed that the non-target genes were unlikely to confound the effects considered to be due to the influence of 1-FEH gene functions. Glasshouse experiments revealed that the 1-FEH w3 mutation line had a slower degradation and remobilisation of fructans than the 1-FEH w2 and w1 mutation lines and Chara, which reduced grain filling and grain yield. Thus, 1-FEH w3 plays a vital role in reducing yield loss under drought. This insight into the distinct role of the 1-FEH isoforms provides new gene targets for water-deficit-tolerant wheat breeding.
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Affiliation(s)
- Nusrat Khan
- Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6163, Australia; (N.K.); (J.Z.); (S.I.)
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Jingjuan Zhang
- Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6163, Australia; (N.K.); (J.Z.); (S.I.)
| | - Shahidul Islam
- Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6163, Australia; (N.K.); (J.Z.); (S.I.)
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Rudi Appels
- Faculty of Science, University of Melbourne, Parkville, VIC 3010, Australia;
| | - Bernard Dell
- Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6163, Australia; (N.K.); (J.Z.); (S.I.)
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Salgotra RK, Stewart CN. Genetic Augmentation of Legume Crops Using Genomic Resources and Genotyping Platforms for Nutritional Food Security. PLANTS 2022; 11:plants11141866. [PMID: 35890499 PMCID: PMC9325189 DOI: 10.3390/plants11141866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 11/24/2022]
Abstract
Recent advances in next generation sequencing (NGS) technologies have led the surge of genomic resources for the improvement legume crops. Advances in high throughput genotyping (HTG) and high throughput phenotyping (HTP) enable legume breeders to improve legume crops more precisely and efficiently. Now, the legume breeder can reshuffle the natural gene combinations of their choice to enhance the genetic potential of crops. These genomic resources are efficiently deployed through molecular breeding approaches for genetic augmentation of important legume crops, such as chickpea, cowpea, pigeonpea, groundnut, common bean, lentil, pea, as well as other underutilized legume crops. In the future, advances in NGS, HTG, and HTP technologies will help in the identification and assembly of superior haplotypes to tailor the legume crop varieties through haplotype-based breeding. This review article focuses on the recent development of genomic resource databases and their deployment in legume molecular breeding programmes to secure global food security.
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Affiliation(s)
- Romesh K. Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, Chatha, Jammu 190008, India
- Correspondence: (R.K.S.); (C.N.S.J.)
| | - Charles Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
- Correspondence: (R.K.S.); (C.N.S.J.)
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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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Karaman K, Kizil S, Başak M, Uzun B, Yol E. Development of EMS-induced Mutagenized Groundnut Population and Discovery of Point Mutations in the ahFAD2 and Ara h 1 Genes by TILLING. J Oleo Sci 2021; 70:1631-1640. [PMID: 34732635 DOI: 10.5650/jos.ess21075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Reducing allergenicity and increasing oleic content are important goals in groundnut breeding studies. Ara h 1 is a major allergen gene and Delta(12)-fatty-acid desaturase (FAD2) is responsible for converting oleic into linoleic acid. These genes have homoeologues with one copy in each subgenome, identified as Ara h 1.01, Ara h 1.02, ahFAD2A and ahFAD2B in tetraploid groundnut. To alter functional properties of these genes we have generated an Ethyl Methane Sulfonate (EMS) induced mutant population to be used in Targeting Induced Local Lesions in Genomes (TILLING) approach. Seeds were exposed to two EMS concentrations and the germination rates were calculated as 90.1% (1353 plants) for 0.4% and 60.4% (906 plants) for 1.2% EMS concentrations in the M1 generation. Among the 1541 M2 mutants, 768 were analyzed by TILLING using four homoeologous genes. Two heterozygous mutations were identified in the ahFAD2B and ahFAD2A gene regions from 1.2% and 0.4% EMS-treated populations, respectively. The mutation in ahFAD2B resulted in an amino acid change, which was serine to threonine predicted to be tolerated according to SIFT analysis. The other mutation causing amino acid change, glycine to aspartic acid was predicted to affect protein function in ahFAD2A. No mutations were detected in Ara h 1.01 and Ara h 1.02 for both EMS-treatments after sequencing. We estimated the overall mutation rate to be 1 mutation every 2139 kb. The mutation frequencies were also 1/317 kb for ahFAD2A in 0.4% EMS and 1/466 kb for ahFAD2B in 1.2% EMS treatments. The results demonstrated that TILLING is a powerful tool to interfere with gene function in crops and the mutagenized population developed in this study can be used as an efficient reverse genetics tool for groundnut improvement and functional genomics.
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Affiliation(s)
- Kürşat Karaman
- Department of Field Crops, Faculty of Agriculture, Akdeniz University
| | - Sibel Kizil
- Department of Field Crops, Faculty of Agriculture, Akdeniz University
| | - Merve Başak
- Department of Medicinal and Aromatic Plants, Akev University
| | - Bülent Uzun
- Department of Field Crops, Faculty of Agriculture, Akdeniz University
| | - Engin Yol
- Department of Field Crops, Faculty of Agriculture, Akdeniz University
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Yang Y, Saand MA, Huang L, Abdelaal WB, Zhang J, Wu Y, Li J, Sirohi MH, Wang F. Applications of Multi-Omics Technologies for Crop Improvement. FRONTIERS IN PLANT SCIENCE 2021; 12:563953. [PMID: 34539683 PMCID: PMC8446515 DOI: 10.3389/fpls.2021.563953] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/06/2021] [Indexed: 05/19/2023]
Abstract
Multiple "omics" approaches have emerged as successful technologies for plant systems over the last few decades. Advances in next-generation sequencing (NGS) have paved a way for a new generation of different omics, such as genomics, transcriptomics, and proteomics. However, metabolomics, ionomics, and phenomics have also been well-documented in crop science. Multi-omics approaches with high throughput techniques have played an important role in elucidating growth, senescence, yield, and the responses to biotic and abiotic stress in numerous crops. These omics approaches have been implemented in some important crops including wheat (Triticum aestivum L.), soybean (Glycine max), tomato (Solanum lycopersicum), barley (Hordeum vulgare L.), maize (Zea mays L.), millet (Setaria italica L.), cotton (Gossypium hirsutum L.), Medicago truncatula, and rice (Oryza sativa L.). The integration of functional genomics with other omics highlights the relationships between crop genomes and phenotypes under specific physiological and environmental conditions. The purpose of this review is to dissect the role and integration of multi-omics technologies for crop breeding science. We highlight the applications of various omics approaches, such as genomics, transcriptomics, proteomics, metabolomics, phenomics, and ionomics, and the implementation of robust methods to improve crop genetics and breeding science. Potential challenges that confront the integration of multi-omics with regard to the functional analysis of genes and their networks as well as the development of potential traits for crop improvement are discussed. The panomics platform allows for the integration of complex omics to construct models that can be used to predict complex traits. Systems biology integration with multi-omics datasets can enhance our understanding of molecular regulator networks for crop improvement. In this context, we suggest the integration of entire omics by employing the "phenotype to genotype" and "genotype to phenotype" concept. Hence, top-down (phenotype to genotype) and bottom-up (genotype to phenotype) model through integration of multi-omics with systems biology may be beneficial for crop breeding improvement under conditions of environmental stresses.
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Affiliation(s)
- Yaodong Yang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- *Correspondence: Yaodong Yang
| | - Mumtaz Ali Saand
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- Department of Botany, Shah Abdul Latif University, Khairpur, Pakistan
| | - Liyun Huang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Walid Badawy Abdelaal
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Jun Zhang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Yi Wu
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Jing Li
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | | | - Fuyou Wang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
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Janni M, Gullì M, Maestri E, Marmiroli M, Valliyodan B, Nguyen HT, Marmiroli N. Molecular and genetic bases of heat stress responses in crop plants and breeding for increased resilience and productivity. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3780-3802. [PMID: 31970395 PMCID: PMC7316970 DOI: 10.1093/jxb/eraa034] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 01/20/2020] [Indexed: 05/21/2023]
Abstract
To ensure the food security of future generations and to address the challenge of the 'no hunger zone' proposed by the FAO (Food and Agriculture Organization), crop production must be doubled by 2050, but environmental stresses are counteracting this goal. Heat stress in particular is affecting agricultural crops more frequently and more severely. Since the discovery of the physiological, molecular, and genetic bases of heat stress responses, cultivated plants have become the subject of intense research on how they may avoid or tolerate heat stress by either using natural genetic variation or creating new variation with DNA technologies, mutational breeding, or genome editing. This review reports current understanding of the genetic and molecular bases of heat stress in crops together with recent approaches to creating heat-tolerant varieties. Research is close to a breakthrough of global relevance, breeding plants fitter to face the biggest challenge of our time.
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Affiliation(s)
- Michela Janni
- Institute of Bioscience and Bioresources (IBBR), National Research Council (CNR), Via Amendola, Bari, Italy
- Institute of Materials for Electronics and Magnetism (IMEM), National Research Council (CNR), Parco Area delle Scienze, Parma, Italy
| | - Mariolina Gullì
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, Parma, Italy
| | - Elena Maestri
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, Parma, Italy
| | - Marta Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, Parma, Italy
| | - Babu Valliyodan
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
- Lincoln University, Jefferson City, MO, USA
| | - Henry T Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Nelson Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, Parma, Italy
- CINSA Interuniversity Consortium for Environmental Sciences, Parma/Venice, Italy
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Gao YL, Yao XF, Li WZ, Song ZB, Wang BW, Wu YP, Shi JL, Liu GS, Li YP, Liu CM. An efficient TILLING platform for cultivated tobacco. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:165-180. [PMID: 30697931 DOI: 10.1111/jipb.12784] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 01/23/2019] [Indexed: 06/09/2023]
Abstract
Targeting-induced local lesions in genomes (TILLING) is a powerful reverse-genetics tool that enables high-throughput screening of genomic variations in plants. Although TILLING has been developed for many diploid plants, the technology has been used in very few polyploid species due to their genomic complexity. Here, we established an efficient capillary electrophoresis-based TILLING platform for allotetraploid cultivated tobacco (Nicotiana tabacum L.) using an ethyl methanesulfonate (EMS)-mutagenized population of 1,536 individuals. We optimized the procedures for endonuclease preparation, leaf tissue sampling, DNA extraction, normalization, pooling, PCR amplification, heteroduplex formation, and capillary electrophoresis. In a test screen using seven target genes with eight PCR fragments, we obtained 118 mutants. The mutation density was estimated to be approximately one mutation per 106 kb on average. Phenotypic analyses showed that mutations in two heavy metal transporter genes, HMA2S and HMA4T, led to reduced accumulation of cadmium and zinc, which was confirmed independently using CRISPR/Cas9 to generate knockout mutants. Our results demonstrate that this powerful TILLING platform (available at http://www.croptilling.org) can be used in tobacco to facilitate functional genomics applications.
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Affiliation(s)
- Yu-Long Gao
- Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Xue-Feng Yao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- The University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen-Zheng Li
- Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Zhong-Bang Song
- Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Bing-Wu Wang
- Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Yu-Ping Wu
- Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Jun-Li Shi
- Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Guan-Shan Liu
- Tobacco Research Institute, the Chinese Agriculture Academy of Sciences, Qingdao, 266101, China
| | - Yong-Ping Li
- Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Chun-Ming Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- Institute of Crop Sciences, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Desmae H, Janila P, Okori P, Pandey MK, Motagi BN, Monyo E, Mponda O, Okello D, Sako D, Echeckwu C, Oteng‐Frimpong R, Miningou A, Ojiewo C, Varshney RK. Genetics, genomics and breeding of groundnut ( Arachis hypogaea L.). PLANT BREEDING = ZEITSCHRIFT FUR PFLANZENZUCHTUNG 2019; 138:425-444. [PMID: 31598026 PMCID: PMC6774334 DOI: 10.1111/pbr.12645] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 04/10/2018] [Accepted: 07/13/2018] [Indexed: 05/04/2023]
Abstract
Groundnut is an important food and oil crop in the semiarid tropics, contributing to household food consumption and cash income. In Asia and Africa, yields are low attributed to various production constraints. This review paper highlights advances in genetics, genomics and breeding to improve the productivity of groundnut. Genetic studies concerning inheritance, genetic variability and heritability, combining ability and trait correlations have provided a better understanding of the crop's genetics to develop appropriate breeding strategies for target traits. Several improved lines and sources of variability have been identified or developed for various economically important traits through conventional breeding. Significant advances have also been made in groundnut genomics including genome sequencing, marker development and genetic and trait mapping. These advances have led to a better understanding of the groundnut genome, discovery of genes/variants for traits of interest and integration of marker-assisted breeding for selected traits. The integration of genomic tools into the breeding process accompanied with increased precision of yield trialing and phenotyping will increase the efficiency and enhance the genetic gain for release of improved groundnut varieties.
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Affiliation(s)
- Haile Desmae
- International Crop Research Institute for the Semi‐Arid Tropics (ICRISAT)BamakoMali
| | | | | | | | | | | | - Omari Mponda
- Division of Research and Development (DRD)Tanzania Agricultural Research Institute (TARI) ‐ NaliendeleMtwaraTanzania
| | - David Okello
- National Agricultural Research Organization (NARO)EntebbeUganda
| | | | | | | | - Amos Miningou
- Institut National d'Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
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14
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Yuan C, Sun Q, Kong Y. Genome-wide mining seed-specific candidate genes from peanut for promoter cloning. PLoS One 2019; 14:e0214025. [PMID: 30921362 PMCID: PMC6438489 DOI: 10.1371/journal.pone.0214025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 03/05/2019] [Indexed: 01/18/2023] Open
Abstract
Peanut seeds are ideal bioreactors for the production of foreign recombinant proteins and/or nutrient metabolites. Seed-Specific Promoters (SSPs) are important molecular tools for bioreactor research. However, few SSPs have been characterized in peanut seeds. The mining of Seed-Specific Candidate Genes (SSCGs) is a prerequisite for promoter cloning. Here, we described an approach for the genome-wide mining of SSCGs via comparative gene expression between seed and nonseed tissues. Three hundred thirty-seven SSCGs were ultimately identified, and the top 108 SSCGs were characterized. Gene Ontology (GO) analysis revealed that some SSCGs were involved in seed development, allergens, seed storage and fatty acid metabolism. RY REPEAT and GCN4 motifs, which are commonly found in SSPs, were dispersed throughout most of the promoters of SSCGs. Expression pattern analysis revealed that all 108 SSCGs were expressed specifically or preferentially in the seed. These results indicated that the promoters of the 108 SSCGs may perform functions in a seed-specific and/or seed-preferential manner. Moreover, a novel SSP was cloned and characterized from a paralogous gene of SSCG29 from cultivated peanut. Together with the previously characterized SSP of the SSCG5 paralogous gene in cultivated peanut, these results implied that the method for SSCG identification in this study was feasible and accurate. The SSCGs identified in this work could be widely applied to SSP cloning by other researchers. Additionally, this study identified a low-cost, high-throughput approach for exploring tissue-specific genes in other crop species.
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Affiliation(s)
- Cuiling Yuan
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, Shandong, China
- Shandong Peanut Research Institute, Qingdao, Shandong, China
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Quanxi Sun
- Shandong Peanut Research Institute, Qingdao, Shandong, China
- * E-mail: (YK); (QS)
| | - Yingzhen Kong
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, Shandong, China
- * E-mail: (YK); (QS)
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15
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Koval T, Dohnálek J. Characteristics and application of S1–P1 nucleases in biotechnology and medicine. Biotechnol Adv 2018; 36:603-612. [DOI: 10.1016/j.biotechadv.2017.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 12/08/2017] [Accepted: 12/13/2017] [Indexed: 12/18/2022]
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16
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Jeyaramraja P, Meenakshi SN, Woldesenbet F. Relationship between drought and preharvest aflatoxin contamination in groundnut (Arachis hypogaea L.). WORLD MYCOTOXIN J 2018. [DOI: 10.3920/wmj2017.2248] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Groundnut is a commercial oilseed crop that is prone to infection by Aspergillus flavus or Aspergillus parasiticus. Drought impairs the defence mechanism of the plant and favours the production of aflatoxin by the fungus. Aflatoxin is a carcinogen and its presence in food and feed causes significant economic loss. The answer to the question, ‘how drought tolerance and aflatoxin resistance are related?’ is not clear. In this review paper, the relationship of drought and preharvest aflatoxin contamination (AC), the relationship of drought tolerance traits and AC, and the approaches to enhance resistance to AC are discussed using up-to-date literature. Factors leading to AC are drought, high geocarposphere temperature, kernel/pod damage, and reduced phytoalexin synthesis by the plant. If the fungus colonises a kernel with reduced water activity, the plant cannot synthesise phytoalexin and then, the fungus synthesises aflatoxin. Breeding for resistance to AC is complicated because aflatoxin concentration is costly to measure, highly variable, and influenced by the environment. Since drought tolerant cultivars have resistance to AC, traits of drought tolerance have been used as indirect selection tools for reduced AC. The genetics of aflatoxin resistance mechanisms have not been made clear as the environment influences the host-pathogen relationship. Host-pathogen interactions under the influence of environment should be studied at molecular level to identify plant resistant factors using the tools of genomics, proteomics, and metabolomics in order to develop cultivars with durable resistance. Many candidate genes involved in host-pathogen interactions have been identified due to improvements in fungal expressed sequence tags, microarrays, and genome sequencing techniques. Moreover, research projects are underway on identifying genes coding for antifungal compounds, resistance associated proteins and quantitative trait loci associated with aflatoxin resistance. This review is expected to help those who wish to work on reducing AC in groundnuts.
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Affiliation(s)
- P.R. Jeyaramraja
- Department of Biology, College of Natural Sciences, Arba Minch University, P.O. Box 21, Arba Minch, Gamo Gofa Zone, Ethiopia
| | - S. Nithya Meenakshi
- Department of Botany, PSGR Krishnammal College for Women, Peelamedu, Coimbatore 641 004, Tamilnadu, India
| | - F. Woldesenbet
- Department of Biology, College of Natural Sciences, Arba Minch University, P.O. Box 21, Arba Minch, Gamo Gofa Zone, Ethiopia
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17
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Jacob P, Avni A, Bendahmane A. Translational Research: Exploring and Creating Genetic Diversity. TRENDS IN PLANT SCIENCE 2018; 23:42-52. [PMID: 29126790 DOI: 10.1016/j.tplants.2017.10.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/10/2017] [Accepted: 10/18/2017] [Indexed: 05/21/2023]
Abstract
The crop selection process has created a genetic bottleneck ultimately restricting breeding output. Wild relatives of major crops as well as the so-called 'neglected plant' species represent a reservoir of genetic diversity that remains underutilized. These species could be used as a tool to discover new alleles of agronomic interest or could be the target of breeding programs. Targeted induced local lesions in the genome (TILLING) can be used to translate in neglected crops what has been discovered in major crops and reciprocally. However, random mutagenesis, used in TILLING approaches, provides only a limited density of mutational events at a defined target locus. Alternatively, clustered regularly interspaced short palindromic repeats (CRISPR) associated 9 (Cas9) fused to a cytidine deaminase could serve as a localized mutagenic agent to produce high-density mutant populations. Artificial evolution is at hand.
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Affiliation(s)
- Pierre Jacob
- Institute of Plant Science - Paris-Saclay, INRA, 91190 Gif-sur-Yvette, France
| | - Adi Avni
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
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18
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Abstract
Gene space: the final frontier in plant functional genomics. These are the voyages of TILLING, the reverse-genetics strategy that sought to boldly go where no-one had gone before by combining high-density chemical mutagenesis with high-throughput mutation discovery. Its 18-year mission has been to explore new technologies such as next generation sequencing and to seek out new strategies like in silico databases of catalogued EMS-induced mutations from entire mutant plant populations. This chapter is a clip show highlighting key milestones in the development of TILLING. Use of different technologies for the discovery of induced mutations, establishment of TILLING in different plant species, what has been learned about the effect of chemical mutagens on the plant genome, development of exome capture sequencing in wheat, and a look to the future of reverse-genetics with targeted genome editing are discussed. Graphical Abstract.
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19
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Selb R, Wal JM, Moreno FJ, Lovik M, Mills C, Hoffmann-Sommergruber K, Fernandez A. Assessment of endogenous allergenicity of genetically modified plants exemplified by soybean - Where do we stand? Food Chem Toxicol 2017; 101:139-148. [PMID: 28111299 DOI: 10.1016/j.fct.2017.01.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/21/2016] [Accepted: 01/18/2017] [Indexed: 10/20/2022]
Abstract
According to EU regulation, genetically modified (GM) plants considered to be allergenic have to be assessed concerning their endogenous allergens before placement on the EU market, in line with the international standards described in Codex Alimentarius. Under such premises, a quantitative relevant increase in allergens might occur in GM plants as an unintended effect compared with conventionally produced crops, which could pose a risk to consumers. Currently, data showing a connection between dose and allergic sensitisation are scarce since the pathophysiological mechanisms of sensitisation are insufficiently understood. In contrast, data on population dose-distribution relationships acquired by oral food challenge are available showing a connection between quantity of allergenic protein consumed and the population of allergic individuals experiencing reactions. Soybean is currently the only recognised allergenic GM food by law for which EFSA has received applications and was therefore taken as an example for defining an assessment strategy. Identification of potential allergens, methodology for quantification as well as risk assessment considerations, are discussed. A strategy is proposed for the identification, assessment and evaluation of potential hazards/risks concerning endogenous allergenicity in food derived from plants developed by biotechnology. This approach could be expanded to other allergenic foods in the future, whenever required.
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Affiliation(s)
- R Selb
- European Food Safety Authority, Parma, Italy
| | - J M Wal
- INRA-CEA, Gif sur Yvette Cedex, France
| | - F J Moreno
- Institute of Food Science Research, CIAL (CSIC-UAM), Madrid, Spain
| | - M Lovik
- Norwegian Institute of Public Health, Oslo, Norway
| | - C Mills
- School of Biological Sciences, Manchester Academic Health Sciences Centre, Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - K Hoffmann-Sommergruber
- Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
| | - A Fernandez
- European Food Safety Authority, Parma, Italy.
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20
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Li W, Guo H, Wang Y, Xie Y, Zhao L, Gu J, Zhao S, Zhao B, Wang G, Liu L. Identification of novel alleles induced by EMS-mutagenesis in key genes of kernel hardness and starch biosynthesis in wheat by TILLING. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0504-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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21
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Aslam U, Cheema HMN, Ahmad S, Khan IA, Malik W, Khan AA. COTIP: Cotton TILLING Platform, a Resource for Plant Improvement and Reverse Genetic Studies. FRONTIERS IN PLANT SCIENCE 2016; 7:1863. [PMID: 28082993 PMCID: PMC5183611 DOI: 10.3389/fpls.2016.01863] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 11/25/2016] [Indexed: 05/26/2023]
Abstract
Cotton is cultivated worldwide for its white fiber, of which around 90% is tetraploid upland cotton (Gossypium hirsutum L.) carrying both A and D genome. Since centuries, yield increasing efforts for the cotton crop by conventional breeding approaches have caused an extensive erosion of natural genetic variability. Mutation based improvement strategies provide an effective way of creating new allelic variations. Targeting Induced Local Lesions IN Genomes (TILLING) provides a mutation based reverse genetic strategy to create and evaluate induced genetic variability at DNA level. Here, we report development and testing of TILLING populations of allotetraploid cotton (G. hirsutum) for functional genomic studies and mutation based enrichment of cotton genetic resources. Seed of two cotton cultivars "PB-899 and PB-900" were mutagenized with 0.3 and 0.2% (v/v) ethyl methanesulfonate, respectively. The phenotyping of M1 and M2 populations presented numerous mutants regarding the branching pattern, leaf morphology, disease resistance, photosynthetic lesions and flower sterility. Molecular screening for point mutations was performed by TILLING PCR aided CEL1 mismatch cleavage. To estimate the mutation frequency in the mutant genomes, five gene classes were TILLed in 8000 M2 plants of each var. "PB-899" and "PB-900." These include actin (GhACT), Pectin Methyl Esterase (GhPME), sucrose synthase (GhSUS), resistance gene analog, and defense response gene (DRGs). The var. PB-899 was harboring 47% higher mutation induction rate than PB-900. The highest rate of mutation frequency was identified for NAC-TF5 (EU706348) of DRGs class, ranging from 1/58 kb in PB-899 to 1/105 kb in PB-900. The mutation screening assay revealed the presence of significant proportion of induced mutations in cotton TILLING populations such as 1/153 kb and 1/326 kb in var. "PB-899" and "PB-900," respectively. The establishment of a cotton TILLING platform (COTIP) and data obtained from the resource TILLING population suggest its effectiveness in widening the genetic bases of cotton for improvement and utilizing it for subsequent reverse genetic studies of various genes.
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Affiliation(s)
- Usman Aslam
- Plant Genetic Resources Lab, Department of Plant Breeding and Genetics, University of AgricultureFaisalabad, Pakistan
| | - Hafiza M. N. Cheema
- Plant Genetic Resources Lab, Department of Plant Breeding and Genetics, University of AgricultureFaisalabad, Pakistan
| | - Sheraz Ahmad
- Plant Genetic Resources Lab, Department of Plant Breeding and Genetics, University of AgricultureFaisalabad, Pakistan
| | - Iqrar A. Khan
- Plant Genetic Resources Lab, Department of Plant Breeding and Genetics, University of AgricultureFaisalabad, Pakistan
| | - Waqas Malik
- Genomics Lab, Department of Plant Breeding and Genetics, Bahauddin Zakariya UniversityMultan, Pakistan
| | - Asif A. Khan
- Plant Genetic Resources Lab, Department of Plant Breeding and Genetics, University of AgricultureFaisalabad, Pakistan
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22
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Jankowicz-Cieslak J, Till BJ. Chemical Mutagenesis of Seed and Vegetatively Propagated Plants Using EMS. CURRENT PROTOCOLS IN PLANT BIOLOGY 2016; 1:617-635. [PMID: 31725963 DOI: 10.1002/cppb.20040] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Chemical mutagenesis provides an inexpensive and straightforward way to generate a high density of novel nucleotide diversity in the genomes of plants and animals. Mutagenesis therefore can be used for functional genomic studies and also for plant breeding. The most commonly used chemical mutagen in plants is ethyl methanesulfonate (EMS). EMS has been shown to induce primarily single base point mutations. Hundreds to thousands of heritable mutations can be induced in a single plant line. A relatively small number of plants, therefore, are needed to produce populations harboring deleterious alleles in most genes. EMS mutagenized plant populations can be screened phenotypically (forward-genetics), or mutations in genes can be identified in advance of phenotypic characterization (reverse-genetics). Reverse-genetics using chemically induced mutations is known as Targeting Induced Local Lesions IN Genomes (TILLING). This unit gives information on EMS treatment of seed and vegetative propagules. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Joanna Jankowicz-Cieslak
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, IAEA Laboratories Seibersdorf, International Atomic Energy Agency, Vienna International Centre, Vienna, Austria
| | - Bradley J Till
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, IAEA Laboratories Seibersdorf, International Atomic Energy Agency, Vienna International Centre, Vienna, Austria
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23
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Tadele Z. Mutagenesis and TILLING to Dissect Gene Function in Plants. Curr Genomics 2016; 17:499-508. [PMID: 28217006 PMCID: PMC5282601 DOI: 10.2174/1389202917666160520104158] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 12/01/2015] [Accepted: 12/05/2015] [Indexed: 11/22/2022] Open
Abstract
Mutagenesis can be random or targeted and occur by nature or artificially by humans. However, the bulk of mutagenesis employed in plants are random and caused by physical agents such as x-ray and gamma-ray or chemicals such as ethyl-methane sulfonate (EMS). Researchers are interested in first identifying these mutations and/or polymorphisms in the genome followed by investigating their effects in the plant function as well as their application in crop improvement. The high-throughput technique called TILLING (Targeting Induced Local Lesion IN Genomes) has been already established and become popular for identifying candidate mutant individuals harboring mutations in the gene of interest. TILLING is a non-transgenic and reverse genetics method of identifying a single nucleotide changes. The procedure of TILLING comprises traditional mutagenesis using optimum type and concentration of mutagen, development of a non-chimeric population, DNA extraction and pooling, mutation detection as well as validation of results. In general, TILLING has proved to be robust in identifying useful mutant lines in diverse economically important crops of the world. The main goal of the current mini-review is to show the significance role played by mutagenesis and TILLING in the discovery of DNA lesions which are to be used in the improvement of crops for the trait of interest.
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Affiliation(s)
- Zerihun Tadele
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
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24
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Allergenicity attributes of different peanut market types. Food Chem Toxicol 2016; 91:82-90. [DOI: 10.1016/j.fct.2016.02.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 01/28/2016] [Accepted: 02/19/2016] [Indexed: 11/20/2022]
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25
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Shamoon M, Sajid MW, Safdar W, Haider J, Omar M, Ammar A, Sharif HR, Khalid S, Randhawa MA. An update on hypoallergenicity of peanut and soybean: where are we now? RSC Adv 2016. [DOI: 10.1039/c6ra12515h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Legumes are one of the major sources of proteins and positively correlate with the development of modern society. At the same time, unfortunately, they significantly contribute to the rising prevalence of food allergy.
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Affiliation(s)
- Muhammad Shamoon
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- The Synergetic Innovation Center of Food Safety and Nutrition
- Jiangnan University
- Wuxi 214122
| | - Muhammad Wasim Sajid
- Department of Biosciences
- COMSATS Institute of Information Technology
- Sahiwal 57000
- Pakistan
| | - Waseem Safdar
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- The Synergetic Innovation Center of Food Safety and Nutrition
- Jiangnan University
- Wuxi 214122
| | - Junaid Haider
- Key Laboratory of Food Colloids and Biotechnology
- Ministry of Education
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
| | - Mukama Omar
- Key Laboratory of Carbohydrate Chemistry and Biotechnology
- School of Biotechnology
- Jiangnan University
- Wuxi 214122
- P. R. China
| | - Alfarga Ammar
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- The Synergetic Innovation Center of Food Safety and Nutrition
- Jiangnan University
- Wuxi 214122
| | - Hafiz Rizwan Sharif
- Key Laboratory of Food Colloids and Biotechnology
- Ministry of Education
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
| | - Saud Khalid
- Center for Polymer from Renewable Resources
- School of Food Science and Engineering
- South China University of Technology
- Guangzhou 510640
- P. R China
| | - Muhammad Atif Randhawa
- Faculty of Food
- Nutrition and Home Sciences
- National Institute of Food Science & Technology
- University of Agriculture
- Faisalabad 38040
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26
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Bhatnagar-Mathur P, Sunkara S, Bhatnagar-Panwar M, Waliyar F, Sharma KK. Biotechnological advances for combating Aspergillus flavus and aflatoxin contamination in crops. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 234:119-132. [PMID: 25804815 DOI: 10.1016/j.plantsci.2015.02.009] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 02/17/2015] [Accepted: 02/18/2015] [Indexed: 06/04/2023]
Abstract
Aflatoxins are toxic, carcinogenic, mutagenic, teratogenic and immunosuppressive byproducts of Aspergillus spp. that contaminate a wide range of crops such as maize, peanut, and cotton. Aflatoxin not only affects crop production but renders the produce unfit for consumption and harmful to human and livestock health, with stringent threshold limits of acceptability. In many crops, breeding for resistance is not a reliable option because of the limited availability of genotypes with durable resistance to Aspergillus. Understanding the fungal/crop/environment interactions involved in aflatoxin contamination is therefore essential in designing measures for its prevention and control. For a sustainable solution to aflatoxin contamination, research must be focused on identifying and improving knowledge of host-plant resistance factors to aflatoxin accumulation. Current advances in genetic transformation, proteomics, RNAi technology, and marker-assisted selection offer great potential in minimizing pre-harvest aflatoxin contamination in cultivated crop species. Moreover, developing effective phenotyping strategies for transgenic as well as precision breeding of resistance genes into commercial varieties is critical. While appropriate storage practices can generally minimize post-harvest aflatoxin contamination in crops, the use of biotechnology to interrupt the probability of pre-harvest infection and contamination has the potential to provide sustainable solution.
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Affiliation(s)
- Pooja Bhatnagar-Mathur
- Genetic Transformation Laboratory, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India.
| | - Sowmini Sunkara
- Genetic Transformation Laboratory, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Madhurima Bhatnagar-Panwar
- Genetic Transformation Laboratory, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Farid Waliyar
- Genetic Transformation Laboratory, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Kiran Kumar Sharma
- Genetic Transformation Laboratory, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
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Guo Y, Abernathy B, Zeng Y, Ozias-Akins P. TILLING by sequencing to identify induced mutations in stress resistance genes of peanut (Arachis hypogaea). BMC Genomics 2015; 16:157. [PMID: 25881128 PMCID: PMC4369367 DOI: 10.1186/s12864-015-1348-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 02/16/2015] [Indexed: 11/28/2022] Open
Abstract
Background Targeting Induced Local Lesions in Genomes (TILLING) is a powerful reverse genetics approach for functional genomics studies. We used high-throughput sequencing, combined with a two-dimensional pooling strategy, with either minimum read percentage with non-reference nucleotide or minimum variance multiplier as mutation prediction parameters, to detect genes related to abiotic and biotic stress resistances. In peanut, lipoxygenase genes were reported to be highly induced in mature seeds infected with Aspergillus spp., indicating their importance in plant-fungus interactions. Recent studies showed that phospholipase D (PLD) expression was elevated more quickly in drought sensitive lines than in drought tolerant lines of peanut. A newly discovered lipoxygenase (LOX) gene in peanut, along with two peanut PLD genes from previous publications were selected for TILLING. Additionally, two major allergen genes Ara h 1 and Ara h 2, and fatty acid desaturase AhFAD2, a gene which controls the ratio of oleic to linoleic acid in the seed, were also used in our study. The objectives of this research were to develop a suitable TILLING by sequencing method for this allotetraploid, and use this method to identify mutations induced in stress related genes. Results We screened a peanut root cDNA library and identified three candidate LOX genes. The gene AhLOX7 was selected for TILLING due to its high expression in seeds and roots. By screening 768 M2 lines from the TILLING population, four missense mutations were identified for AhLOX7, three missense mutations were identified for AhPLD, one missense and two silent mutations were identified for Ara h 1.01, three silent and five missense mutations were identified for Ara h 1.02, one missense mutation was identified for AhFAD2B, and one silent mutation was identified for Ara h 2.02. The overall mutation frequency was 1 SNP/1,066 kb. The SNP detection frequency for single copy genes was 1 SNP/344 kb and 1 SNP/3,028 kb for multiple copy genes. Conclusions Our TILLING by sequencing approach is efficient to identify mutations in single and multi-copy genes. The mutations identified in our study can be used to further study gene function and have potential usefulness in breeding programs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1348-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yufang Guo
- Department of Horticulture, University of Georgia -Tifton Campus, 2360 Rainwater Rd, Tifton, GA, 31793-5766, USA.
| | - Brian Abernathy
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA.
| | - Yajuan Zeng
- Department of Horticulture, University of Georgia -Tifton Campus, 2360 Rainwater Rd, Tifton, GA, 31793-5766, USA.
| | - Peggy Ozias-Akins
- Department of Horticulture, University of Georgia -Tifton Campus, 2360 Rainwater Rd, Tifton, GA, 31793-5766, USA.
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Fitzgerald TL, Powell JJ, Stiller J, Weese TL, Abe T, Zhao G, Jia J, McIntyre CL, Li Z, Manners JM, Kazan K. An assessment of heavy ion irradiation mutagenesis for reverse genetics in wheat (Triticum aestivum L.). PLoS One 2015; 10:e0117369. [PMID: 25719507 PMCID: PMC4342231 DOI: 10.1371/journal.pone.0117369] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 12/22/2014] [Indexed: 11/19/2022] Open
Abstract
Reverse genetic techniques harnessing mutational approaches are powerful tools that can provide substantial insight into gene function in plants. However, as compared to diploid species, reverse genetic analyses in polyploid plants such as bread wheat can present substantial challenges associated with high levels of sequence and functional similarity amongst homoeologous loci. We previously developed a high-throughput method to identify deletions of genes within a physically mutagenized wheat population. Here we describe our efforts to combine multiple homoeologous deletions of three candidate disease susceptibility genes (TaWRKY11, TaPFT1 and TaPLDß1). We were able to produce lines featuring homozygous deletions at two of the three homoeoloci for all genes, but this was dependent on the individual mutants used in crossing. Intriguingly, despite extensive efforts, viable lines possessing homozygous deletions at all three homoeoloci could not be produced for any of the candidate genes. To investigate deletion size as a possible reason for this phenomenon, we developed an amplicon sequencing approach based on synteny to Brachypodium distachyon to assess the size of the deletions removing one candidate gene (TaPFT1) in our mutants. These analyses revealed that genomic deletions removing the locus are relatively large, resulting in the loss of multiple additional genes. The implications of this work for the use of heavy ion mutagenesis for reverse genetic analyses in wheat are discussed.
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Affiliation(s)
- Timothy L. Fitzgerald
- Commonwealth Scientific and Industrial Research Organisation, Agriculture Flagship, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane, QLD, 4067, Australia
- * E-mail: (TLF); (KK)
| | - Jonathan J. Powell
- Commonwealth Scientific and Industrial Research Organisation, Agriculture Flagship, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane, QLD, 4067, Australia
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Jiri Stiller
- Commonwealth Scientific and Industrial Research Organisation, Agriculture Flagship, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane, QLD, 4067, Australia
| | - Terri L. Weese
- Commonwealth Scientific and Industrial Research Organisation, Agriculture Flagship, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane, QLD, 4067, Australia
| | - Tomoko Abe
- RIKEN Nishina Center for Accelerator-Based Science, 2-1 Hirosawa, Wako, Saitama, 351–0198, Japan
| | - Guangyao Zhao
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jizeng Jia
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - C. Lynne McIntyre
- Commonwealth Scientific and Industrial Research Organisation, Agriculture Flagship, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane, QLD, 4067, Australia
| | - Zhongyi Li
- Commonwealth Scientific and Industrial Research Organisation, Agriculture Flagship, Black Mountain Laboratories, Clunies Ross St, Acton, ACT, 2601, Australia
| | - John M. Manners
- Commonwealth Scientific and Industrial Research Organisation, Agriculture Flagship, Black Mountain Laboratories, Clunies Ross St, Acton, ACT, 2601, Australia
| | - Kemal Kazan
- Commonwealth Scientific and Industrial Research Organisation, Agriculture Flagship, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane, QLD, 4067, Australia
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, 4072, Australia
- * E-mail: (TLF); (KK)
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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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A mutant Brassica napus (canola) population for the identification of new genetic diversity via TILLING and next generation sequencing. PLoS One 2013; 8:e84303. [PMID: 24376800 PMCID: PMC3869819 DOI: 10.1371/journal.pone.0084303] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Accepted: 11/13/2013] [Indexed: 12/19/2022] Open
Abstract
We have generated a Brassica napus (canola) population of 3,158 EMS-mutagenised lines and used TILLING to demonstrate that the population has a high enough mutation density that it will be useful for identification of mutations in genes of interest in this important crop species. TILLING is a reverse genetics technique that has been successfully used in many plant and animal species. Classical TILLING involves the generation of a mutagenised population, followed by screening of DNA samples using a mismatch-specific endonuclease that cleaves only those PCR products that carry a mutation. Polyacrylamide gel detection is then used to visualise the mutations in any gene of interest. We have used this TILLING technique to identify 432 unique mutations in 26 different genes in B. napus (canola cv. DH12075). This reflects a mutation density ranging from 1/56 kb to 1/308 kb (depending on the locus) with an average of 1/109 kb. We have also successfully verified the utility of next generation sequencing technology as a powerful approach for the identification of rare mutations in a population of plants, even in polyploid species such as B. napus. Most of the mutants we have identified are publically available.
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Chantreau M, Grec S, Gutierrez L, Dalmais M, Pineau C, Demailly H, Paysant-Leroux C, Tavernier R, Trouvé JP, Chatterjee M, Guillot X, Brunaud V, Chabbert B, van Wuytswinkel O, Bendahmane A, Thomasset B, Hawkins S. PT-Flax (phenotyping and TILLinG of flax): development of a flax (Linum usitatissimum L.) mutant population and TILLinG platform for forward and reverse genetics. BMC PLANT BIOLOGY 2013; 13:159. [PMID: 24128060 PMCID: PMC3853753 DOI: 10.1186/1471-2229-13-159] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 10/09/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND Flax (Linum usitatissimum L.) is an economically important fiber and oil crop that has been grown for thousands of years. The genome has been recently sequenced and transcriptomics are providing information on candidate genes potentially related to agronomically-important traits. In order to accelerate functional characterization of these genes we have generated a flax EMS mutant population that can be used as a TILLinG (Targeting Induced Local Lesions in Genomes) platform for forward and reverse genetics. RESULTS A population of 4,894 M2 mutant seed families was generated using 3 different EMS concentrations (0.3%, 0.6% and 0.75%) and used to produce M2 plants for subsequent phenotyping and DNA extraction. 10,839 viable M2 plants (4,033 families) were obtained and 1,552 families (38.5%) showed a visual developmental phenotype (stem size and diameter, plant architecture, flower-related). The majority of these families showed more than one phenotype. Mutant phenotype data are organised in a database and can be accessed and searched at UTILLdb (http://urgv.evry.inra.fr/UTILLdb). Preliminary screens were also performed for atypical fiber and seed phenotypes. Genomic DNA was extracted from 3,515 M2 families and eight-fold pooled for subsequent mutant detection by ENDO1 nuclease mis-match cleavage. In order to validate the collection for reverse genetics, DNA pools were screened for two genes coding enzymes of the lignin biosynthesis pathway: Coumarate-3-Hydroxylase (C3H) and Cinnamyl Alcohol Dehydrogenase (CAD). We identified 79 and 76 mutations in the C3H and CAD genes, respectively. The average mutation rate was calculated as 1/41 Kb giving rise to approximately 9,000 mutations per genome. Thirty-five out of the 52 flax cad mutant families containing missense or codon stop mutations showed the typical orange-brown xylem phenotype observed in CAD down-regulated/mutant plants in other species. CONCLUSIONS We have developed a flax mutant population that can be used as an efficient forward and reverse genetics tool. The collection has an extremely high mutation rate that enables the detection of large numbers of independant mutant families by screening a comparatively low number of M2 families. The population will prove to be a valuable resource for both fundamental research and the identification of agronomically-important genes for crop improvement in flax.
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Affiliation(s)
- Maxime Chantreau
- Université Lille Nord de France, Lille 1 UMR 1281, Villeneuve d'Ascq cedex F-59650, France
- INRA UMR, 281 Stress Abiotiques et Différenciation des Végétaux Cultivés, Villeneuve d’Ascq F-59650, France
| | - Sébastien Grec
- Université Lille Nord de France, Lille 1 UMR 1281, Villeneuve d'Ascq cedex F-59650, France
- INRA UMR, 281 Stress Abiotiques et Différenciation des Végétaux Cultivés, Villeneuve d’Ascq F-59650, France
| | - Laurent Gutierrez
- CRRBM, UFR des Sciences, UPJV, 33 rue Saint Leu, Amiens cedex 80039, France
| | - Marion Dalmais
- URGV, Unité de Recherche en Génomique Végétale, Université d'Evry Val d'Essonne, INRA, 2 rue Gaston Crémieux CP 5708, Evry cedex 91057, France
| | | | - Hervé Demailly
- CRRBM, UFR des Sciences, UPJV, 33 rue Saint Leu, Amiens cedex 80039, France
| | | | | | - Jean-Paul Trouvé
- Terre de Lin, société cooperative agricole, Saint-Pierre-Le-Viger, 76 740, France
| | - Manash Chatterjee
- Bench Bio Pvt Ltd., c/o Jai Research Foundation, Vapi, Gujarat 396195, India
- National University of Ireland Galway (NUIG), University Road, Galway, Ireland
| | | | - Véronique Brunaud
- URGV, Unité de Recherche en Génomique Végétale, Université d'Evry Val d'Essonne, INRA, 2 rue Gaston Crémieux CP 5708, Evry cedex 91057, France
| | - Brigitte Chabbert
- INRA, UMR614 Fractionnement des AgroRessources et Environnement, Reims F-51100, France
- Université de Reims Champagne-Ardenne, UMR614 Fractionnement des AgroRessources et Environnement, Reims F-51100, France
| | | | - Abdelhafid Bendahmane
- URGV, Unité de Recherche en Génomique Végétale, Université d'Evry Val d'Essonne, INRA, 2 rue Gaston Crémieux CP 5708, Evry cedex 91057, France
| | - Brigitte Thomasset
- CNRS-FRE 3580, GEC, Université de Technologie de Compiègne, CS 60319, Compiègnecedex 60203, France
| | - Simon Hawkins
- Université Lille Nord de France, Lille 1 UMR 1281, Villeneuve d'Ascq cedex F-59650, France
- INRA UMR, 281 Stress Abiotiques et Différenciation des Végétaux Cultivés, Villeneuve d’Ascq F-59650, France
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Tsai H, Missirian V, Ngo KJ, Tran RK, Chan SR, Sundaresan V, Comai L. Production of a high-efficiency TILLING population through polyploidization. PLANT PHYSIOLOGY 2013; 161:1604-14. [PMID: 23417087 PMCID: PMC3613442 DOI: 10.1104/pp.112.213256] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Targeting Induced Local Lesions in Genomes (TILLING) provides a nontransgenic method for reverse genetics that is widely applicable, even in species where other functional resources are missing or expensive to build. The efficiency of TILLING, however, is greatly facilitated by high mutation density. Species vary in the number of mutations induced by comparable mutagenic treatments, suggesting that genetic background may affect the response. Allopolyploid species have often yielded higher mutation density than diploids. To examine the effect of ploidy, we autotetraploidized the Arabidopsis (Arabidopsis thaliana) ecotype Columbia, whose diploid has been used for TILLING extensively, and mutagenized it with 50 mm ethylmethane sulfonate. While the same treatment sterilized diploid Columbia, the tetraploid M1 plants produced good seed. To determine the mutation density, we searched 528 individuals for induced mutations in 15 genes for which few or no knockout alleles were previously available. We constructed tridimensional pools from the genomic DNA of M2 plants, amplified target DNA, and subjected them to Illumina sequencing. The results were analyzed with an improved version of the mutation detection software CAMBa that accepts any pooling scheme. This small population provided a rich resource with approximately 25 mutations per queried 1.5-kb fragment, including on average four severe missense and 1.3 truncation mutations. The overall mutation density of 19.4 mutations Mb(-1) is 4 times that achieved in the corresponding diploid accession, indicating that genomic redundancy engenders tolerance to high mutation density. Polyploidization of diploids will allow the production of small populations, such as less than 2,000, that provide allelic series from knockout to mild loss of function for virtually all genes.
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He Y, Dai S, Dufresne CP, Zhu N, Pang Q, Chen S. Integrated proteomics and metabolomics of Arabidopsis acclimation to gene-dosage dependent perturbation of isopropylmalate dehydrogenases. PLoS One 2013; 8:e57118. [PMID: 23533573 PMCID: PMC3606340 DOI: 10.1371/journal.pone.0057118] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 01/10/2013] [Indexed: 12/02/2022] Open
Abstract
Maintaining metabolic homeostasis is critical for plant growth and development. Here we report proteome and metabolome changes when the metabolic homeostasis is perturbed due to gene-dosage dependent mutation of Arabidopsis isopropylmalate dehydrogenases (IPMDHs). By integrating complementary quantitative proteomics and metabolomics approaches, we discovered that gradual ablation of the oxidative decarboxylation step in leucine biosynthesis caused imbalance of amino acid homeostasis, redox changes and oxidative stress, increased protein synthesis, as well as a decline in photosynthesis, which led to rearrangement of central metabolism and growth retardation. Disruption of IPMDHs involved in aliphatic glucosinolate biosynthesis led to synchronized increase of both upstream and downstream biosynthetic enzymes, and concomitant repression of the degradation pathway, indicating metabolic regulatory mechanisms in controlling glucosinolate biosynthesis.
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Affiliation(s)
- Yan He
- Department of Biology, Genetics Institute, and Plant Molecular & Cellular Biology Program, University of Florida, Gainesville, Florida, United States of America
| | - Shaojun Dai
- Department of Biology, Genetics Institute, and Plant Molecular & Cellular Biology Program, University of Florida, Gainesville, Florida, United States of America
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, Heilongjiang, China
| | - Craig P. Dufresne
- Unity Lab Services, Thermo Fisher Scientific Inc., West Palm Beach, Florida, United States of America
| | - Ning Zhu
- Department of Biology, Genetics Institute, and Plant Molecular & Cellular Biology Program, University of Florida, Gainesville, Florida, United States of America
| | - Qiuying Pang
- Department of Biology, Genetics Institute, and Plant Molecular & Cellular Biology Program, University of Florida, Gainesville, Florida, United States of America
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, Heilongjiang, China
| | - Sixue Chen
- Department of Biology, Genetics Institute, and Plant Molecular & Cellular Biology Program, University of Florida, Gainesville, Florida, United States of America
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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Kumar APK, Boualem A, Bhattacharya A, Parikh S, Desai N, Zambelli A, Leon A, Chatterjee M, Bendahmane A. SMART--Sunflower Mutant population And Reverse genetic Tool for crop improvement. BMC PLANT BIOLOGY 2013; 13:38. [PMID: 23496999 PMCID: PMC3606330 DOI: 10.1186/1471-2229-13-38] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 02/13/2013] [Indexed: 05/20/2023]
Abstract
BACKGROUND Sunflower (Helianthus annuus L.) is an important oilseed crop grown widely in various areas of the world. Classical genetic studies have been extensively undertaken for the improvement of this particular oilseed crop. Pertaining to this endeavor, we developed a "chemically induced mutated genetic resource for detecting SNP by TILLING" in sunflower to create new traits. RESULTS To optimize the EMS mutagenesis, we first conducted a "kill curve" analysis with a range of EMS dose from 0.5% to 3%. Based on the observed germination rate, a 50% survival rate i.e. LD50, treatment with 0.6% EMS for 8 hours was chosen to generate 5,000 M2 populations, out of which, 4,763 M3 plants with fertile seed set. Phenotypic characterization of the 5,000 M2 mutagenised lines were undertaken to assess the mutagenesis quality and to identify traits of interest. In the M2 population, about 1.1% of the plants showed phenotypic variations. The sunflower TILLING platform was setup using Endo-1-nuclease as mismatch detection system coupled with an eight fold DNA pooling strategy. As proof-of-concept, we screened the M2 population for induced mutations in two genes related to fatty acid biosynthesis, FatA an acyl-ACP thioesterase and SAD the stearoyl-ACP desaturase and identified a total of 26 mutations. CONCLUSION Based on the TILLING of FatA and SAD genes, we calculated the overall mutation rate to one mutation every 480 kb, similar to other report for this crop so far. As sunflower is a plant model for seed oil biosynthesis, we anticipate that the developed genetic resource will be a useful tool to identify novel traits for sunflower crop improvement.
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Affiliation(s)
- Anish PK Kumar
- Bench Bio Pvt Ltd., c/o Jai Research Foundation, Vapi, Gujarat, 396195, India
| | - Adnane Boualem
- INRA, UMR1165 Unité de Recherche en Génomique Végétale URGV, Evry, F-91057, France
- UEVE, UMR Unité de Recherche en Génomique Végétale URGV, Evry, F-91057, France
- CNRS, ERL8196 UMR Unité de Recherche en Génomique Végétale URGV, Evry, F-91057, France
| | | | - Seema Parikh
- Bench Bio Pvt Ltd., c/o Jai Research Foundation, Vapi, Gujarat, 396195, India
| | - Nirali Desai
- Bench Bio Pvt Ltd., c/o Jai Research Foundation, Vapi, Gujarat, 396195, India
| | - Andres Zambelli
- Biotechnology Research Centre, Nutrisun Business Unit- Advanta Semillas SAIC, Belcarce, Argentina
| | - Alberto Leon
- Biotechnology Research Centre, Nutrisun Business Unit- Advanta Semillas SAIC, Belcarce, Argentina
| | - Manash Chatterjee
- Bench Bio Pvt Ltd., c/o Jai Research Foundation, Vapi, Gujarat, 396195, India
- National University of Ireland Galway (NUIG), Galway, Ireland
| | - Abdelhafid Bendahmane
- INRA, UMR1165 Unité de Recherche en Génomique Végétale URGV, Evry, F-91057, France
- UEVE, UMR Unité de Recherche en Génomique Végétale URGV, Evry, F-91057, France
- CNRS, ERL8196 UMR Unité de Recherche en Génomique Végétale URGV, Evry, F-91057, France
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Varshney RK, Mohan SM, Gaur PM, Gangarao NVPR, Pandey MK, Bohra A, Sawargaonkar SL, Chitikineni A, Kimurto PK, Janila P, Saxena KB, Fikre A, Sharma M, Rathore A, Pratap A, Tripathi S, Datta S, Chaturvedi SK, Mallikarjuna N, Anuradha G, Babbar A, Choudhary AK, Mhase MB, Bharadwaj C, Mannur DM, Harer PN, Guo B, Liang X, Nadarajan N, Gowda CLL. Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics. Biotechnol Adv 2013; 31:1120-34. [PMID: 23313999 DOI: 10.1016/j.biotechadv.2013.01.001] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 12/16/2012] [Accepted: 01/03/2013] [Indexed: 10/27/2022]
Abstract
Advances in next-generation sequencing and genotyping technologies have enabled generation of large-scale genomic resources such as molecular markers, transcript reads and BAC-end sequences (BESs) in chickpea, pigeonpea and groundnut, three major legume crops of the semi-arid tropics. Comprehensive transcriptome assemblies and genome sequences have either been developed or underway in these crops. Based on these resources, dense genetic maps, QTL maps as well as physical maps for these legume species have also been developed. As a result, these crops have graduated from 'orphan' or 'less-studied' crops to 'genomic resources rich' crops. This article summarizes the above-mentioned advances in genomics and genomics-assisted breeding applications in the form of marker-assisted selection (MAS) for hybrid purity assessment in pigeonpea; marker-assisted backcrossing (MABC) for introgressing QTL region for drought-tolerance related traits, Fusarium wilt (FW) resistance and Ascochyta blight (AB) resistance in chickpea; late leaf spot (LLS), leaf rust and nematode resistance in groundnut. We critically present the case of use of other modern breeding approaches like marker-assisted recurrent selection (MARS) and genomic selection (GS) to utilize the full potential of genomics-assisted breeding for developing superior cultivars with enhanced tolerance to various environmental stresses. In addition, this article recommends the use of advanced-backcross (AB-backcross) breeding and development of specialized populations such as multi-parents advanced generation intercross (MAGIC) for creating new variations that will help in developing superior lines with broadened genetic base. In summary, we propose the use of integrated genomics and breeding approach in these legume crops to enhance crop productivity in marginal environments ensuring food security in developing countries.
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Affiliation(s)
- Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; CGIAR Generation Challenge Programme (GCP), c/o CIMMYT, DF 06600, Mexico; The University of Western Australia, Crawley 6009, Australia; Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou 510640, China.
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Scientific opinion addressing the safety assessment of plants developed using Zinc Finger Nuclease 3 and other Site‐Directed Nucleases with similar function. EFSA J 2012. [DOI: 10.2903/j.efsa.2012.2943] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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Chen YZ, Pang QY, He Y, Zhu N, Branstrom I, Yan XF, Chen S. Proteomics and metabolomics of Arabidopsis responses to perturbation of glucosinolate biosynthesis. MOLECULAR PLANT 2012; 5:1138-50. [PMID: 22498773 DOI: 10.1093/mp/sss034] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
To understand plant molecular networks of glucosinolate metabolism, perturbation of aliphatic glucosinolate biosynthesis was established using inducible RNA interference (RNAi) in Arabidopsis. Two RNAi lines were chosen for examining global protein and metabolite changes using complementary proteomics and metabolomics approaches. Proteins involved in metabolism including photosynthesis and hormone metabolism, protein binding, energy, stress, and defense showed marked responses to glucosinolate perturbation. In parallel, metabolomics revealed major changes in the levels of amino acids, carbohydrates, peptides, and hormones. The metabolomics data were correlated with the proteomics results and revealed intimate molecular connections between cellular pathways/processes and glucosinolate metabolism. This study has provided an unprecedented view of the molecular networks of glucosinolate metabolism and laid a foundation towards rationale glucosinolate engineering for enhanced defense and quality.
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Affiliation(s)
- Ya-zhou Chen
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA
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High-throughput discovery of mutations in tef semi-dwarfing genes by next-generation sequencing analysis. Genetics 2012; 192:819-29. [PMID: 22904035 DOI: 10.1534/genetics.112.144436] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Tef (Eragrostis tef) is a major cereal crop in Ethiopia. Lodging is the primary constraint to increasing productivity in this allotetraploid species, accounting for losses of ∼15-45% in yield each year. As a first step toward identifying semi-dwarf varieties that might have improved lodging resistance, an ∼6× fosmid library was constructed and used to identify both homeologues of the dw3 semi-dwarfing gene of Sorghum bicolor. An EMS mutagenized population, consisting of ∼21,210 tef plants, was planted and leaf materials were collected into 23 superpools. Two dwarfing candidate genes, homeologues of dw3 of sorghum and rht1 of wheat, were sequenced directly from each superpool with 454 technology, and 120 candidate mutations were identified. Out of 10 candidates tested, six independent mutations were validated by Sanger sequencing, including two predicted detrimental mutations in both dw3 homeologues with a potential to improve lodging resistance in tef through further breeding. This study demonstrates that high-throughput sequencing can identify potentially valuable mutations in under-studied plant species like tef and has provided mutant lines that can now be combined and tested in breeding programs for improved lodging resistance.
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Development and characterization of a new TILLING population of common bread wheat (Triticum aestivum L.). PLoS One 2012; 7:e41570. [PMID: 22844501 PMCID: PMC3402408 DOI: 10.1371/journal.pone.0041570] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 06/28/2012] [Indexed: 12/04/2022] Open
Abstract
Mutagenesis is an important tool in crop improvement. However, the hexaploid genome of wheat (Triticum aestivum L.) presents problems in identifying desirable genetic changes based on phenotypic screening due to gene redundancy. TILLING (Targeting Induced Local Lesions IN Genomes), a powerful reverse genetic strategy that allows the detection of induced point mutations in individuals of the mutagenized populations, can address the major challenge of linking sequence information to the biological function of genes and can also identify novel variation for crop breeding. Wheat is especially well-suited for TILLING due to the high mutation densities tolerated by polyploids. However, only a few wheat TILLING populations are currently available in the world, which is far from satisfying the requirement of researchers and breeders in different growing environments. In addition, current TILLING screening protocols require costly fluorescence detection systems, limiting their use, especially in developing countries. We developed a new TILLING resource comprising 2610 M2 mutants in a common wheat cultivar ‘Jinmai 47’. Numerous phenotypes with altered morphological and agronomic traits were observed from the M2 and M3 lines in the field. To simplify the procedure and decrease costs, we use unlabeled primers and either non-denaturing polyacrylamide gels or agarose gels for mutation detection. The value of this new resource was tested using PCR with RAPD and Intron-spliced junction (ISJ) primers, and also TILLING in three selected candidate genes, in 300 and 512 mutant lines, revealing high mutation densities of 1/34 kb by RAPD/ISJ analysis and 1/47 kb by TILLING. In total, 31 novel alleles were identified in the 3 targeted genes and confirmed by sequencing. The results indicate that this mutant population represents a useful resource for the wheat research community. We hope that the use of this reverse genetics resource will provide novel allelic diversity for wheat improvement and functional genomics.
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Paulus KE, Schmid B, Zajic D, Schäfer A, Mahler V, Sonnewald U. Hypoallergenic profilin - a new way to identify allergenic determinants. FEBS J 2012; 279:2727-36. [DOI: 10.1111/j.1742-4658.2012.08656.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Shirasawa K, Hirakawa H, Tabata S, Hasegawa M, Kiyoshima H, Suzuki S, Sasamoto S, Watanabe A, Fujishiro T, Isobe S. Characterization of active miniature inverted-repeat transposable elements in the peanut genome. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:1429-38. [PMID: 22294450 PMCID: PMC3336055 DOI: 10.1007/s00122-012-1798-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 01/05/2012] [Indexed: 05/19/2023]
Abstract
Miniature inverted-repeat transposable elements (MITEs), some of which are known as active nonautonomous DNA transposons, are found in the genomes of plants and animals. In peanut (Arachis hypogaea), Ah-MITE1 has been identified in a gene for fatty-acid desaturase, and possessed excision activity. However, the AhMITE1 distribution and frequency of excision have not been determined for the peanut genome. In order to characterize AhMITE1s, their genomic diversity and transposition ability was investigated. Southern blot analysis indicated high AhMITE1 copy number in the genomes of A. hypogaea, A. magna and A. monticola, but not in A. duranensis. A total of 504 AhMITE1s were identified from the MITE-enriched genomic libraries of A. hypogaea. The representative AhMITE1s exhibited a mean length of 205.5 bp and a GC content of 30.1%, with AT-rich, 9 bp target site duplications and 25 bp terminal inverted repeats. PCR analyses were performed using primer pairs designed against both flanking sequences of each AhMITE1. These analyses detected polymorphisms at 169 out of 411 insertional loci in the four peanut lines. In subsequent analyses of 60 gamma-irradiated mutant lines, four Ah-MITE1 excisions showed footprint mutations at the 109 loci tested. This study characterizes AhMITE1s in peanut and discusses their use as DNA markers and mutagens for the genetics, genomics and breeding of peanut and its relatives.
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Affiliation(s)
- Kenta Shirasawa
- Department of Plant Genome Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan.
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Sikora P, Chawade A, Larsson M, Olsson J, Olsson O. Mutagenesis as a tool in plant genetics, functional genomics, and breeding. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2012; 2011:314829. [PMID: 22315587 PMCID: PMC3270407 DOI: 10.1155/2011/314829] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 12/02/2011] [Accepted: 12/15/2011] [Indexed: 05/19/2023]
Abstract
Plant mutagenesis is rapidly coming of age in the aftermath of recent developments in high-resolution molecular and biochemical techniques. By combining the high variation of mutagenised populations with novel screening methods, traits that are almost impossible to identify by conventional breeding are now being developed and characterised at the molecular level. This paper provides a comprehensive overview of the various techniques and workflows available to researchers today in the field of molecular breeding, and how these tools complement the ones already used in traditional breeding. Both genetic (Targeting Induced Local Lesions in Genomes; TILLING) and phenotypic screens are evaluated. Finally, different ways of bridging the gap between genotype and phenotype are discussed.
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Affiliation(s)
- Per Sikora
- Department of Plant and Environmental Sciences, Göteborg University, 40530 Göteborg, Sweden
| | - Aakash Chawade
- CropTailorAB, Erik Dahlbergsgatan 11A, 41126 Göteborg, Sweden
| | - Mikael Larsson
- Department of Chemical and Biological Engineering, Chalmers University of Technology, 41296 Göteborg, Sweden
| | - Johanna Olsson
- CropTailorAB, Erik Dahlbergsgatan 11A, 41126 Göteborg, Sweden
| | - Olof Olsson
- Department of Plant and Environmental Sciences, Göteborg University, 40530 Göteborg, Sweden
- CropTailorAB, Erik Dahlbergsgatan 11A, 41126 Göteborg, Sweden
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Anai T. Potential of a mutant-based reverse genetic approach for functional genomics and molecular breeding in soybean. BREEDING SCIENCE 2012; 61:462-7. [PMID: 23136486 PMCID: PMC3406801 DOI: 10.1270/jsbbs.61.462] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 11/14/2011] [Indexed: 05/04/2023]
Abstract
Mutant-based reverse genetics offers a powerful way to create novel mutant alleles at a selected locus. This approach makes it possible to directly identify plants that carry a specific modified gene from the nucleotide sequence data. Soybean [Glycine max (L.) Merr.] has a highly redundant paleopolyploid genome (approx. 1.1 Gb), which was completely sequenced in 2010. Using reverse genetics to support functional genomics studies designed to predict gene function would accelerate post-genomics research in soybean. Furthermore, the novel mutant alleles created by this approach would be useful genetic resources for improving various traits in soybean. A reverse genetic screening platform in soybean has been developed that combines more than 40,000 mutant lines with a high-throughput method, Targeting Local Lesions IN Genome (TILLING). In this review, the mutant-based reverse genetic approach based on this platform is described, and the likely evolution of this approach in the near future.
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Affiliation(s)
- Toyoaki Anai
- Laboratory of Plant Genetics and Breeding, Faculty of Agriculture, Saga University, Honjyo-machi 1, Saga 840-8502, Japan
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Lochlainn SÓ, Amoah S, Graham NS, Alamer K, Rios JJ, Kurup S, Stoute A, Hammond JP, Østergaard L, King GJ, White PJ, Broadley MR. High Resolution Melt (HRM) analysis is an efficient tool to genotype EMS mutants in complex crop genomes. PLANT METHODS 2011; 7:43. [PMID: 22152063 PMCID: PMC3251530 DOI: 10.1186/1746-4811-7-43] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 12/08/2011] [Indexed: 05/20/2023]
Abstract
BACKGROUND Targeted Induced Loci Lesions IN Genomes (TILLING) is increasingly being used to generate and identify mutations in target genes of crop genomes. TILLING populations of several thousand lines have been generated in a number of crop species including Brassica rapa. Genetic analysis of mutants identified by TILLING requires an efficient, high-throughput and cost effective genotyping method to track the mutations through numerous generations. High resolution melt (HRM) analysis has been used in a number of systems to identify single nucleotide polymorphisms (SNPs) and insertion/deletions (IN/DELs) enabling the genotyping of different types of samples. HRM is ideally suited to high-throughput genotyping of multiple TILLING mutants in complex crop genomes. To date it has been used to identify mutants and genotype single mutations. The aim of this study was to determine if HRM can facilitate downstream analysis of multiple mutant lines identified by TILLING in order to characterise allelic series of EMS induced mutations in target genes across a number of generations in complex crop genomes. RESULTS We demonstrate that HRM can be used to genotype allelic series of mutations in two genes, BraA.CAX1a and BraA.MET1.a in Brassica rapa. We analysed 12 mutations in BraA.CAX1.a and five in BraA.MET1.a over two generations including a back-cross to the wild-type. Using a commercially available HRM kit and the Lightscanner™ system we were able to detect mutations in heterozygous and homozygous states for both genes. CONCLUSIONS Using HRM genotyping on TILLING derived mutants, it is possible to generate an allelic series of mutations within multiple target genes rapidly. Lines suitable for phenotypic analysis can be isolated approximately 8-9 months (3 generations) from receiving M3 seed of Brassica rapa from the RevGenUK TILLING service.
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Affiliation(s)
- Seosamh Ó Lochlainn
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | | | - Neil S Graham
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Khalid Alamer
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Juan J Rios
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | | | | | - John P Hammond
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Lars Østergaard
- Department of Crop Genetics, John Innes Centre, Norwich, NR4 7UH, UK
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, PO Box 157Lismore NSW 2480, Australia
| | - Phillip J White
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Martin R Broadley
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
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Pandey MK, Monyo E, Ozias-Akins P, Liang X, Guimarães P, Nigam SN, Upadhyaya HD, Janila P, Zhang X, Guo B, Cook DR, Bertioli DJ, Michelmore R, Varshney RK. Advances in Arachis genomics for peanut improvement. Biotechnol Adv 2011; 30:639-51. [PMID: 22094114 DOI: 10.1016/j.biotechadv.2011.11.001] [Citation(s) in RCA: 191] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 10/24/2011] [Accepted: 11/01/2011] [Indexed: 01/01/2023]
Abstract
Peanut genomics is very challenging due to its inherent problem of genetic architecture. Blockage of gene flow from diploid wild relatives to the tetraploid; cultivated peanut, recent polyploidization combined with self pollination, and the narrow genetic base of the primary genepool have resulted in low genetic diversity that has remained a major bottleneck for genetic improvement of peanut. Harnessing the rich source of wild relatives has been negligible due to differences in ploidy level as well as genetic drag and undesirable alleles for low yield. Lack of appropriate genomic resources has severely hampered molecular breeding activities, and this crop remains among the less-studied crops. The last five years, however, have witnessed accelerated development of genomic resources such as development of molecular markers, genetic and physical maps, generation of expressed sequenced tags (ESTs), development of mutant resources, and functional genomics platforms that facilitate the identification of QTLs and discovery of genes associated with tolerance/resistance to abiotic and biotic stresses and agronomic traits. Molecular breeding has been initiated for several traits for development of superior genotypes. The genome or at least gene space sequence is expected to be available in near future and this will further accelerate use of biotechnological approaches for peanut improvement.
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Affiliation(s)
- Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
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