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Gupta P, Dholaniya PS, Princy K, Madhavan AS, Sreelakshmi Y, Sharma R. Augmenting tomato functional genomics with a genome-wide induced genetic variation resource. FRONTIERS IN PLANT SCIENCE 2024; 14:1290937. [PMID: 38328621 PMCID: PMC10848261 DOI: 10.3389/fpls.2023.1290937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/22/2023] [Indexed: 02/09/2024]
Abstract
Induced mutations accelerate crop improvement by providing novel disease resistance and yield alleles. However, the alleles with no perceptible phenotype but have an altered function remain hidden in mutagenized plants. The whole-genome sequencing (WGS) of mutagenized individuals uncovers the complete spectrum of mutations in the genome. Genome-wide induced mutation resources can improve the targeted breeding of tomatoes and facilitate functional genomics. In this study, we sequenced 132 doubly ethyl methanesulfonate (EMS)-mutagenized lines of tomato and detected approximately 41 million novel mutations and 5.5 million short InDels not present in the parental cultivar. Approximately 97% of the genome had mutations, including the genes, promoters, UTRs, and introns. More than one-third of genes in the mutagenized population had one or more deleterious mutations predicted by Sorting Intolerant From Tolerant (SIFT). Nearly one-fourth of deleterious genes mapped on tomato metabolic pathways modulate multiple pathway steps. In addition to the reported GC>AT transition bias for EMS, our population also had a substantial number of AT>GC transitions. Comparing mutation frequency among synonymous codons revealed that the most preferred codon is the least mutagenic toward EMS. The validation of a potato leaf-like mutation, reduction in carotenoids in ζ-carotene isomerase mutant fruits, and chloroplast relocation loss in phototropin1 mutant validated the mutation discovery pipeline. Our database makes a large repertoire of mutations accessible to functional genomics studies and breeding of tomatoes.
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Affiliation(s)
- Prateek Gupta
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
- Department of Biological Sciences, SRM University-AP, Amaravati, Andhra Pradesh, India
| | - Pankaj Singh Dholaniya
- Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, India
| | - Kunnappady Princy
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Athira Sethu Madhavan
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Yellamaraju Sreelakshmi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Rameshwar Sharma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
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Till BJ, Jiménez-Madrigal JP, Gatica-Arias A. Identification of Novel Induced Mutations in Seed and Vegetatively Propagated Plants from Reduced Representation or Whole Genome Sequencing Data. Methods Mol Biol 2024; 2787:123-139. [PMID: 38656486 DOI: 10.1007/978-1-0716-3778-4_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Treatment of plants with chemical mutagens results primarily in the production of novel single nucleotide variants. Mutagenesis is a mostly random process and as such plants derived from mutagenesis of different seeds or in vitro material are expected to accumulate different mutations. An important step in the creation of a mutant population for forward or reverse genetics is the choice of treatment conditions (e.g., dosage) such that sufficient mutations accumulate while not adversely affecting propagation of the plant. DNA sequencing provides a quick method to evaluate the effect of different treatment conditions and their effect on the density and spectrum of accumulated mutations. Whole genome sequencing or reduced representation sequencing is carried out followed by mapping to a reference genome and production of a Variant Call Format (VCF) file. We provide here a method for generating a multi-sample VCF from mutagenized plants and describe a new tool to streamline the process of recovering unique induced mutations and determining their possible effect on gene function.
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Affiliation(s)
- Bradley J Till
- Veterinary Genetics Laboratory, University of California, Davis, CA, USA.
| | - José P Jiménez-Madrigal
- Instituto Tecnológico de Costa Rica, Escuela de Ciencias Naturales y Exactas, Alajuela, Costa Rica
| | - Andrés Gatica-Arias
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
- Capacity Building for Bioinformatics in Latin America (CABANA), San José, Costa Rica
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Huang L, Gao G, Jiang C, Guo G, He Q, Zong Y, Liu C, Yang P. Generating homozygous mutant populations of barley microspores by ethyl methanesulfonate treatment. ABIOTECH 2023; 4:202-212. [PMID: 37970468 PMCID: PMC10638298 DOI: 10.1007/s42994-023-00108-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/31/2023] [Indexed: 11/17/2023]
Abstract
Induced mutations are important for genetic research and breeding. Mutations induced by physical or chemical mutagenesis are usually heterozygous during the early generations. However, mutations must be fixed prior to phenotyping or field trials, which requires additional rounds of self-pollination. Microspore culture is an effective method to produce double-haploid (DH) plants that are fixed homozygotes. In this study, we conducted ethyl methanesulfonate (EMS)-induced mutagenesis of microspore cultures of barley (Hordeum vulgare) cultivar 'Hua30' and landrace 'HTX'. The EMS concentrations were negatively correlated with the efficiency of callus induction and the frequency of mutant plant regeneration. The two genotypes showed different regeneration efficiencies. The phenotypic variation of the regenerated M1 plants and the presence of genome-wide nucleotide mutations, revealed by whole-genome sequencing, highlight the utility of EMS-induced mutagenesis of isolated microspore cultures for developing DH mutants. Genome-wide analysis of the mutation frequency in the regenerated plants revealed that a considerable proportion of mutations resulted from microspore culture (somaclonal variation) rather than EMS-induced mutagenesis. In addition to producing a population of 1972 homozygous mutant lines that are available for future field trials, this study lays the foundation for optimizing the regeneration efficiency of DH plants and the richness of mutations (mainly by fine-tuning the mutagen dosage).
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Affiliation(s)
- Linli Huang
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106 China
| | - Guangqi Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Congcong Jiang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Guimei Guo
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106 China
| | - Qiang He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yingjie Zong
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106 China
| | - Chenghong Liu
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106 China
| | - Ping Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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Shahwar D, Ahn N, Kim D, Ahn W, Park Y. Mutagenesis-based plant breeding approaches and genome engineering: A review focused on tomato. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 792:108473. [PMID: 37716439 DOI: 10.1016/j.mrrev.2023.108473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/18/2023]
Abstract
Breeding is the most important and efficient method for crop improvement involving repeated modification of the genetic makeup of a plant population over many generations. In this review, various accessible breeding approaches, such as conventional breeding and mutation breeding (physical and chemical mutagenesis and insertional mutagenesis), are discussed with respect to the actual impact of research on the economic improvement of tomato agriculture. Tomatoes are among the most economically important fruit crops consumed worldwide because of their high nutritional content and health-related benefits. Additionally, we summarize mutation-based mapping approaches, including Mutmap and MutChromeSeq, for the efficient mapping of several genes identified by random indel mutations that are beneficial for crop improvement. Difficulties and challenges in the adaptation of new genome editing techniques that provide opportunities to demonstrate precise mutations are also addressed. Lastly, this review focuses on various effective and convenient genome editing tools, such as RNA interference (RNAi), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR/Cas9), and their potential for the improvement of numerous desirable traits to allow the development of better varieties of tomato and other horticultural crops.
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Affiliation(s)
- Durre Shahwar
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Republic of Korea
| | - Namju Ahn
- Daenong Seed Company, Hwasun-gun 58155, Republic of Korea
| | - Donghyun Kim
- Daenong Seed Company, Hwasun-gun 58155, Republic of Korea
| | - Wooseong Ahn
- Daenong Seed Company, Hwasun-gun 58155, Republic of Korea
| | - Younghoon Park
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Republic of Korea.
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Selvakumar R, Jat GS, Manjunathagowda DC. Allele mining through TILLING and EcoTILLING approaches in vegetable crops. PLANTA 2023; 258:15. [PMID: 37311932 DOI: 10.1007/s00425-023-04176-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/01/2023] [Indexed: 06/15/2023]
Abstract
MAIN CONCLUSION The present review illustrates a comprehensive overview of the allele mining for genetic improvement in vegetable crops, and allele exploration methods and their utilization in various applications related to pre-breeding of economically important traits in vegetable crops. Vegetable crops have numerous wild descendants, ancestors and terrestrial races that could be exploited to develop high-yielding and climate-resilient varieties resistant/tolerant to biotic and abiotic stresses. To further boost the genetic potential of economic traits, the available genomic tools must be targeted and re-opened for exploitation of novel alleles from genetic stocks by the discovery of beneficial alleles from wild relatives and their introgression to cultivated types. This capability would be useful for giving plant breeders direct access to critical alleles that confer higher production, improve bioactive compounds, increase water and nutrient productivity as well as biotic and abiotic stress resilience. Allele mining is a new sophisticated technique for dissecting naturally occurring allelic variants in candidate genes that influence important traits which could be used for genetic improvement of vegetable crops. Target-induced local lesions in genomes (TILLINGs) is a sensitive mutation detection avenue in functional genomics, particularly wherein genome sequence information is limited or not available. Population exposure to chemical mutagens and the absence of selectivity lead to TILLING and EcoTILLING. EcoTILLING may lead to natural induction of SNPs and InDels. It is anticipated that as TILLING is used for vegetable crops improvement in the near future, indirect benefits will become apparent. Therefore, in this review we have highlighted the up-to-date information on allele mining for genetic enhancement in vegetable crops and methods of allele exploration and their use in pre-breeding for improvement of economic traits.
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Affiliation(s)
- Raman Selvakumar
- ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110 012, India
| | - Gograj Singh Jat
- ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110 012, India.
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Tyagi K, Sunkum A, Gupta P, Kilambi HV, Sreelakshmi Y, Sharma R. Reduced γ-glutamyl hydrolase activity likely contributes to high folate levels in Periyakulam-1 tomato. HORTICULTURE RESEARCH 2022; 10:uhac235. [PMID: 36643736 PMCID: PMC9832877 DOI: 10.1093/hr/uhac235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/12/2022] [Indexed: 06/17/2023]
Abstract
Tomato cultivars show wide variation in nutraceutical folate in ripe fruits, yet the loci regulating folate levels in fruits remain unexplored. To decipher regulatory points, we compared two contrasting tomato cultivars: Periyakulam-1 (PKM-1) with high folate and Arka Vikas (AV) with low folate. The progression of ripening in PKM-1 was nearly similar to AV but had substantially lower ethylene emission. In parallel, the levels of phytohormones salicylic acid, ABA, and jasmonic acid were substantially lower than AV. The fruits of PKM-1 were metabolically distinct from AV, with upregulation of several amino acids. Consistent with higher °Brix, the red ripe fruits also showed upregulation of sugars and sugar-derived metabolites. In parallel with higher folate, PKM-1 fruits also had higher carotenoid levels, especially lycopene and β-carotene. The proteome analysis showed upregulation of carotenoid sequestration and folate metabolism-related proteins in PKM-1. The deglutamylation pathway mediated by γ-glutamyl hydrolase (GGH) was substantially reduced in PKM-1 at the red-ripe stage. The red-ripe fruits had reduced transcript levels of GGHs and lower GGH activity than AV. Conversely, the percent polyglutamylation of folate was much higher in PKM-1. Our analysis indicates the regulation of GGH activity as a potential target to elevate folate levels in tomato fruits.
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Affiliation(s)
| | - Anusha Sunkum
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad-500046, India
| | - Prateek Gupta
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad-500046, India
| | - Himabindu Vasuki Kilambi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad-500046, India
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Tyagi K, Sunkum A, Rai M, Yadav A, Sircar S, Sreelakshmi Y, Sharma R. Seeing the unseen: a trifoliate (MYB117) mutant allele fortifies folate and carotenoids in tomato fruits. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:38-54. [PMID: 35899408 DOI: 10.1111/tpj.15925] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/13/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
In tomato (Solanum lycopersicum), mutations in the gene encoding the R2R3-MYB117 transcription factor elicit trifoliate leaves and initiate the formation of axillary meristems; however, their effects on fruit ripening remain unexplored. The fruits of a new trifoliate (tf) mutant (tf-5) were firmer and had higher °Brix values and higher folate and carotenoid contents. The transcriptome, proteome, and metabolome profiling of tf-5 reflected a broad-spectrum change in cellular homeostasis. The tf-5 allele enhanced the fruit firmness by suppressing cell wall softening-related proteins. tf-5 fruit displayed a substantial increase in amino acids, particularly γ-aminobutyric acid, with a parallel reduction in aminoacyl-tRNA synthases. The increased lipoxygenase protein and transcript levels seemingly elevated jasmonic acid levels. In addition, increased abscisic acid hydrolase transcript levels coupled with reduced precursor supply lowered abscisic acid levels. The upregulation of carotenoids was mediated by modulation of methylerythreitol and plastoquinone pathways and increased the levels of carotenoid isomerization proteins. The upregulation of folate in tf-5 was connoted by the increase in the precursor p-aminobenzoic acid and transcript levels of several folate biosynthesis genes. The reduction in pterin-6-carboxylate levels and γ-glutamyl hydrolase activity indicated that reduced folate degradation in tf-5 increased folate levels. Our study delineates that in addition to leaf development, MYB117 also influences fruit metabolism. The tf-5 allele can be used to increase γ-aminobutyric acid, carotenoid, and folate levels in tomato.
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Affiliation(s)
- Kamal Tyagi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Anusha Sunkum
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Meenakshi Rai
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Amita Yadav
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Sanchari Sircar
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Yellamaraju Sreelakshmi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Rameshwar Sharma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
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Next-Generation Sequencing of Local Romanian Tomato Varieties and Bioinformatics Analysis of the Ve Locus. Int J Mol Sci 2022; 23:ijms23179750. [PMID: 36077147 PMCID: PMC9456471 DOI: 10.3390/ijms23179750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 01/17/2023] Open
Abstract
Genetic variability is extremely important, not only for the species’ adaptation to environmental challenges, but also for the creation of novel varieties through plant breeding. Tomato is an important vegetable crop, as well as a model species in numerous genomic studies. Its genome was fully sequenced in 2012 for the ‘Heinz 1706’ variety, and since then, resequencing efforts have revealed genetic variability data that can be used for multiple purposes, including triggering mechanisms of biotic and abiotic stress resistance. The present study focused on the analysis of the genome variation for eight Romanian local tomato varieties using next-generation sequencing technique, and as a case study, the sequence analysis of the Ve1 and Ve2 loci, to determine which genotypes might be good candidates for future breeding of tomato varieties resistant to Verticillium species. The analysis of the Ve locus identified several genotypes that could be donors of the Ve1 gene conferring resistance to Verticillium race 1. Sequencing for the first time Romanian genotypes enriched the existing data on various world tomato genetic resources, but also opened the way for the molecular breeding in Romania. Plant breeders can use these data to create novel tomato varieties adapted to the ever-changing environment.
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Jiang C, Lei M, Guo Y, Gao G, Shi L, Jin Y, Cai Y, Himmelbach A, Zhou S, He Q, Yao X, Kan J, Haberer G, Duan F, Li L, Liu J, Zhang J, Spannagl M, Liu C, Stein N, Feng Z, Mascher M, Yang P. A reference-guided TILLING by amplicon-sequencing platform supports forward and reverse genetics in barley. PLANT COMMUNICATIONS 2022; 3:100317. [PMID: 35605197 PMCID: PMC9284286 DOI: 10.1016/j.xplc.2022.100317] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 02/13/2022] [Accepted: 03/11/2022] [Indexed: 05/26/2023]
Abstract
Barley is a diploid species with a genome smaller than those of other members of the Triticeae tribe, making it an attractive model for genetic studies in Triticeae crops. The recent development of barley genomics has created a need for a high-throughput platform to identify genetically uniform mutants for gene function investigations. In this study, we report an ethyl methanesulfonate (EMS)-mutagenized population consisting of 8525 M3 lines in the barley landrace "Hatiexi" (HTX), which we complement with a high-quality de novo assembly of a reference genome for this genotype. The mutation rate within the population ranged from 1.51 to 4.09 mutations per megabase, depending on the treatment dosage of EMS and the mutation discrimination platform used for genotype analysis. We implemented a three-dimensional DNA pooling strategy combined with multiplexed amplicon sequencing to create a highly efficient and cost-effective TILLING (targeting induced locus lesion in genomes) platform in barley. Mutations were successfully identified from 72 mixed amplicons within a DNA pool containing 64 individual mutants and from 56 mixed amplicons within a pool containing 144 individuals. We discovered abundant allelic mutants for dozens of genes, including the barley Green Revolution contributor gene Brassinosteroid insensitive 1 (BRI1). As a proof of concept, we rapidly determined the causal gene responsible for a chlorotic mutant by following the MutMap strategy, demonstrating the value of this resource to support forward and reverse genetic studies in barley.
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Affiliation(s)
- Congcong Jiang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Miaomiao Lei
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China; College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yu Guo
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Guangqi Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lijie Shi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China; College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yanlong Jin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Cai
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China; College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Shenghui Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiang He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuefeng Yao
- Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jinhong Kan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Georg Haberer
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Fengying Duan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Manuel Spannagl
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Chunming Liu
- Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Zongyun Feng
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany.
| | - Ping Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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Gupta P, Rodriguez-Franco M, Bodanapu R, Sreelakshmi Y, Sharma R. Phytoene synthase 2 in tomato fruits remains functional and contributes to abscisic acid formation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 316:111177. [PMID: 35151443 DOI: 10.1016/j.plantsci.2022.111177] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/27/2021] [Accepted: 01/02/2022] [Indexed: 06/14/2023]
Abstract
In ripening tomato fruits, the leaf-specific carotenoids biosynthesis mediated by phytoene synthase 2 (PSY2) is replaced by a fruit-specific pathway by the expression of two chromoplast-specific genes: phytoene synthase 1 (PSY1) and lycopene-β-cyclase (CYCB). Though both PSY1 and PSY2 genes express in tomato fruits, the functional role of PSY2 is not known. To decipher whether PSY2-mediated carotenogenesis operates in ripening fruits, we blocked the in vivo activity of lycopene-β-cyclases in fruits of several carotenoids and ripening mutants by CPTA (2-(4-Chlorophenylthio)triethylamine hydrochloride), an inhibitor of lycopene-β-cyclases. The CPTA-treatment induced accumulation of lycopene in leaves, immature-green and ripening fruits. Even in psy1 mutants V7 and r that are deficient in fruit-specific carotenoid biosynthesis, CPTA triggered lycopene accumulation but lowered the abscisic acid level. Differing from fruit-specific carotenogenesis, CPTA-treated V7 and r mutant fruits accumulated lycopene but not phytoene and phytofluene. The lack of phytoene and phytofluene accumulation was reminiscent of PSY2-mediated leaf-like carotenogenesis, where phytoene and phytofluene accumulation is never seen. The lycopene accumulation was associated with the partial transformation of chloroplasts to chromoplasts bearing thread-like structures. Our study uncovers the operation of a parallel carotenogenesis pathway mediated by PSY2 that provides precursors for abscisic acid biosynthesis in ripening tomato fruits.
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Affiliation(s)
- Prateek Gupta
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India.
| | - Marta Rodriguez-Franco
- Department of Cell Biology, Faculty of Biology, University of Freiburg, Freiburg, D-79104, Germany.
| | - Reddaiah Bodanapu
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Yellamaraju Sreelakshmi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India.
| | - Rameshwar Sharma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India.
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Sharma V, Mishra A, Sharma H, Kumar P, Roy JK. Unraveling novel and rare mutations for alpha-amylase and key transcription factors in EMS-induced wheat mutants for amylose by TILLING. Mol Biol Rep 2022; 49:5427-5436. [PMID: 35092561 DOI: 10.1007/s11033-022-07155-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 01/17/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND TILLING (Targeting Induced Local Lesions in Genomes) is a reverse-genetic strategy that is used to locate an allelic series of induced point mutations in genes of interest. High-throughput TILLING allows the rapid and cost-effective detection of induced point mutations in populations of chemically mutagenized individuals. Grain amylose content is the major constraints for its nutritional quality and have drawn research interest. Identification of allelic variations in genes involved in starch biosynthesis in wheat endosperm is pre-requisite to amenable for nutritional quality improvement. METHODS AND RESULTS In this study, 44 EMS-induced (M4 generation) mutant lines having variation for amylose content were used for TILLING sequencing. Overall 2098.08 kb of the sequence was analyzed, and the average mutation density was 1/65.56 kb. In analysis, at the high depth score a total of 32 variations were identified including three natural variations, 76% transitions, 10% transversions, and 14% InDels respectively. The substitutions led to intronic variants, UTRs and up-downstream gene variants in Alpha-amylase, TabZIP77.1, TabZIP1 and Myb respectively. In the Myb transcription factor two missense mutations recorded namely Myb_7B c.680G > A and c.1358 T > C led to p.Gly227Asp and p.Met453Thr and c.1390G > A one substitution in Myb_7D led to p.Val464Ile. CONCLUSION The identified missense substitutions were predicted to affect the protein function; hence they may have a probable role in context to the amylose content in mutants. The mutations ascertained in the current study will help in gene discovery in wheat and identified mutants can be used as genetic resources to improve nutritional quality of wheat.
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Affiliation(s)
- Vinita Sharma
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, 140 306, Mohali, Punjab, India.,Indian Institute of Science Education & Research, Sector-81, SAS Nagar, 140 306, Mohali, Punjab, India
| | - Ankita Mishra
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, 140 306, Mohali, Punjab, India
| | - Himanshu Sharma
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, 140 306, Mohali, Punjab, India.
| | - Pankaj Kumar
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, 140 306, Mohali, Punjab, India
| | - Joy K Roy
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, 140 306, Mohali, Punjab, India.
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12
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Singh R, Kumar K, Bharadwaj C, Verma PK. Broadening the horizon of crop research: a decade of advancements in plant molecular genetics to divulge phenotype governing genes. PLANTA 2022; 255:46. [PMID: 35076815 DOI: 10.1007/s00425-022-03827-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
Advancements in sequencing, genotyping, and computational technologies during the last decade (2011-2020) enabled new forward-genetic approaches, which subdue the impediments of precise gene mapping in varied crops. The modern crop improvement programs rely heavily on two major steps-trait-associated QTL/gene/marker's identification and molecular breeding. Thus, it is vital for basic and translational crop research to identify genomic regions that govern the phenotype of interest. Until the advent of next-generation sequencing, the forward-genetic techniques were laborious and time-consuming. Over the last 10 years, advancements in the area of genome assembly, genotyping, large-scale data analysis, and statistical algorithms have led faster identification of genomic variations regulating the complex agronomic traits and pathogen resistance. In this review, we describe the latest developments in genome sequencing and genotyping along with a comprehensive evaluation of the last 10-year headways in forward-genetic techniques that have shifted the focus of plant research from model plants to diverse crops. We have classified the available molecular genetic methods under bulk-segregant analysis-based (QTL-seq, GradedPool-Seq, QTG-Seq, Exome QTL-seq, and RapMap), target sequence enrichment-based (RenSeq, AgRenSeq, and TACCA), and mutation-based groups (MutMap, NIKS algorithm, MutRenSeq, MutChromSeq), alongside improvements in classical mapping and genome-wide association analyses. Newer methods for outcrossing, heterozygous, and polyploid plant genetics have also been discussed. The use of k-mers has enriched the nature of genetic variants which can be utilized to identify the phenotype-causing genes, independent of reference genomes. We envisage that the recent methods discussed herein will expand the repertoire of useful alleles and help in developing high-yielding and climate-resilient crops.
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Affiliation(s)
- Ritu Singh
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Kamal Kumar
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Chellapilla Bharadwaj
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110020, India
| | - Praveen Kumar Verma
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
- Plant Immunity Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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13
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Gupta P, Hirschberg J. The Genetic Components of a Natural Color Palette: A Comprehensive List of Carotenoid Pathway Mutations in Plants. FRONTIERS IN PLANT SCIENCE 2022; 12:806184. [PMID: 35069664 PMCID: PMC8770946 DOI: 10.3389/fpls.2021.806184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/08/2021] [Indexed: 05/16/2023]
Abstract
Carotenoids comprise the most widely distributed natural pigments. In plants, they play indispensable roles in photosynthesis, furnish colors to flowers and fruit and serve as precursor molecules for the synthesis of apocarotenoids, including aroma and scent, phytohormones and other signaling molecules. Dietary carotenoids are vital to human health as a source of provitamin A and antioxidants. Hence, the enormous interest in carotenoids of crop plants. Over the past three decades, the carotenoid biosynthesis pathway has been mainly deciphered due to the characterization of natural and induced mutations that impair this process. Over the year, numerous mutations have been studied in dozens of plant species. Their phenotypes have significantly expanded our understanding of the biochemical and molecular processes underlying carotenoid accumulation in crops. Several of them were employed in the breeding of crops with higher nutritional value. This compendium of all known random and targeted mutants available in the carotenoid metabolic pathway in plants provides a valuable resource for future research on carotenoid biosynthesis in plant species.
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Affiliation(s)
| | - Joseph Hirschberg
- Department of Genetics, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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14
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Jung C, Till B. Mutagenesis and genome editing in crop improvement: perspectives for the global regulatory landscape. TRENDS IN PLANT SCIENCE 2021; 26:1258-1269. [PMID: 34465535 DOI: 10.1016/j.tplants.2021.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/09/2021] [Accepted: 08/02/2021] [Indexed: 05/21/2023]
Abstract
Plant breeding depends on broad genetic variation. New allelic variation can be produced by targeted or random mutagenesis. Seemingly, random mutagenesis is outdated because clustered regularly interspaced short palindromic repeats (CRISPR)-Cas technology is much more precise and potentially faster. Unfortunately, genome editing is not accessible to breeders in many countries due to legal constraints. Therefore, random mutagenesis remains a vital method to create new allelic variation. Mutant offspring, however, suffer from a heavy mutation load, and application in polyploid crops is limited because multiple mutations are typically required. Exploiting random mutations became more efficient due to recent technological advancements, such as sequence-based mutant screening and genomic background selection. In this review, random and targeted mutagenesis will be compared, highlighting the legal situation.
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Affiliation(s)
- Christian Jung
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany.
| | - Bradley Till
- Veterinary Genetics Laboratory, University of California, Davis, Old Davis Road, Davis, CA 95616, USA.
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15
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Petit J, Bres C, Reynoud N, Lahaye M, Marion D, Bakan B, Rothan C. Unraveling Cuticle Formation, Structure, and Properties by Using Tomato Genetic Diversity. FRONTIERS IN PLANT SCIENCE 2021; 12:778131. [PMID: 34912361 PMCID: PMC8667768 DOI: 10.3389/fpls.2021.778131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/02/2021] [Indexed: 05/29/2023]
Abstract
The tomato (Solanum lycopersicum) fruit has a thick, astomatous cuticle that has become a model for the study of cuticle formation, structure, and properties in plants. Tomato is also a major horticultural crop and a long-standing model for research in genetics, fruit development, and disease resistance. As a result, a wealth of genetic resources and genomic tools have been established, including collections of natural and artificially induced genetic diversity, introgression lines of genome fragments from wild relatives, high-quality genome sequences, phenotype and gene expression databases, and efficient methods for genetic transformation and editing of target genes. This mini-review reports the considerable progresses made in recent years in our understanding of cuticle by using and generating genetic diversity for cuticle-associated traits in tomato. These include the synthesis of the main cuticle components (cutin and waxes), their role in the structure and properties of the cuticle, their interaction with other cell wall polymers as well as the regulation of cuticle formation. It also addresses the opportunities offered by the untapped germplasm diversity available in tomato and the current strategies available to exploit them.
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Affiliation(s)
- Johann Petit
- INRAE, Univ. Bordeaux, UMR BFP, Villenave d’Ornon, France
| | - Cécile Bres
- INRAE, Univ. Bordeaux, UMR BFP, Villenave d’Ornon, France
| | - Nicolas Reynoud
- Unité Biopolymères, Interactions, Assemblages, INRAE, Nantes, France
| | - Marc Lahaye
- Unité Biopolymères, Interactions, Assemblages, INRAE, Nantes, France
| | - Didier Marion
- Unité Biopolymères, Interactions, Assemblages, INRAE, Nantes, France
| | - Bénédicte Bakan
- Unité Biopolymères, Interactions, Assemblages, INRAE, Nantes, France
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16
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Udagawa H, Ichida H, Takeuchi T, Abe T, Takakura Y. Highly Efficient and Comprehensive Identification of Ethyl Methanesulfonate-Induced Mutations in Nicotiana tabacum L. by Whole-Genome and Whole-Exome Sequencing. FRONTIERS IN PLANT SCIENCE 2021; 12:671598. [PMID: 34140964 PMCID: PMC8204250 DOI: 10.3389/fpls.2021.671598] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
Tobacco (Nicotiana tabacum L.) is a complex allotetraploid species with a large 4.5-Gb genome that carries duplicated gene copies. In this study, we describe the development of a whole-exome sequencing (WES) procedure in tobacco and its application to characterize a test population of ethyl methanesulfonate (EMS)-induced mutations. A probe set covering 50.3-Mb protein coding regions was designed from a reference tobacco genome. The EMS-induced mutations in 19 individual M2 lines were analyzed using our mutation analysis pipeline optimized to minimize false positives/negatives. In the target regions, the on-target rate of WES was approximately 75%, and 61,146 mutations were detected in the 19 M2 lines. Most of the mutations (98.8%) were single nucleotide variants, and 95.6% of them were C/G to T/A transitions. The number of mutations detected in the target coding sequences by WES was 93.5% of the mutations detected by whole-genome sequencing (WGS). The amount of sequencing data necessary for efficient mutation detection was significantly lower in WES (11.2 Gb), which is only 6.2% of the required amount in WGS (180 Gb). Thus, WES was almost comparable to WGS in performance but is more cost effective. Therefore, the developed target exome sequencing, which could become a fundamental tool in high-throughput mutation identification, renders the genome-wide analysis of tobacco highly efficient.
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Affiliation(s)
- Hisashi Udagawa
- Leaf Tobacco Research Center, Japan Tobacco Inc., Oyama, Japan
| | - Hiroyuki Ichida
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Japan
| | | | - Tomoko Abe
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Japan
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17
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Fanelli V, Ngo KJ, Thompson VL, Silva BR, Tsai H, Sabetta W, Montemurro C, Comai L, Harmer SL. A TILLING by sequencing approach to identify induced mutations in sunflower genes. Sci Rep 2021; 11:9885. [PMID: 33972605 PMCID: PMC8110748 DOI: 10.1038/s41598-021-89237-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/15/2021] [Indexed: 02/03/2023] Open
Abstract
The Targeting Induced Local Lesions in Genomes (TILLING) technology is a reverse genetic strategy broadly applicable to every kind of genome and represents an attractive tool for functional genomic and agronomic applications. It consists of chemical random mutagenesis followed by high-throughput screening of point mutations in targeted genomic regions. Although multiple methods for mutation discovery in amplicons have been described, next-generation sequencing (NGS) is the tool of choice for mutation detection because it quickly allows for the analysis of a large number of amplicons. The aim of the present work was to screen a previously generated sunflower TILLING population and identify alterations in genes involved in several important and complex physiological processes. Twenty-one candidate sunflower genes were chosen as targets for the screening. The TILLING by sequencing strategy allowed us to identify multiple mutations in selected genes and we subsequently validated 16 mutations in 11 different genes through Sanger sequencing. In addition to addressing challenges posed by outcrossing, our detection and validation of mutations in multiple regulatory loci highlights the importance of this sunflower population as a genetic resource.
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Affiliation(s)
- Valentina Fanelli
- grid.7644.10000 0001 0120 3326Department of Soil, Plant and Food Sciences (DiSSPA), University of Bari Aldo Moro, 70124 Bari, Italy ,grid.27860.3b0000 0004 1936 9684Department of Plant Biology, University of California, Davis, CA 95616 USA
| | - Kathie J. Ngo
- grid.27860.3b0000 0004 1936 9684Department of Plant Biology, University of California, Davis, CA 95616 USA
| | - Veronica L. Thompson
- grid.27860.3b0000 0004 1936 9684Department of Plant Biology, University of California, Davis, CA 95616 USA
| | - Brennan R. Silva
- grid.27860.3b0000 0004 1936 9684Department of Plant Biology, University of California, Davis, CA 95616 USA
| | - Helen Tsai
- grid.27860.3b0000 0004 1936 9684Department of Plant Biology, University of California, Davis, CA 95616 USA
| | - Wilma Sabetta
- grid.5326.20000 0001 1940 4177National Research Council, Institute of Bioscience and BioResources-IBBR, 70124 Bari, Italy
| | - Cinzia Montemurro
- grid.7644.10000 0001 0120 3326Department of Soil, Plant and Food Sciences (DiSSPA), University of Bari Aldo Moro, 70124 Bari, Italy
| | - Luca Comai
- grid.27860.3b0000 0004 1936 9684Department of Plant Biology, University of California, Davis, CA 95616 USA
| | - Stacey L. Harmer
- grid.27860.3b0000 0004 1936 9684Department of Plant Biology, University of California, Davis, CA 95616 USA
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18
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Lakhssassi N, Zhou Z, Cullen MA, Badad O, El Baze A, Chetto O, Embaby MG, Knizia D, Liu S, Neves LG, Meksem K. TILLING-by-Sequencing + to Decipher Oil Biosynthesis Pathway in Soybeans: A New and Effective Platform for High-Throughput Gene Functional Analysis. Int J Mol Sci 2021; 22:4219. [PMID: 33921707 PMCID: PMC8073088 DOI: 10.3390/ijms22084219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/08/2021] [Accepted: 04/13/2021] [Indexed: 12/25/2022] Open
Abstract
Reverse genetic approaches have been widely applied to study gene function in crop species; however, these techniques, including gel-based TILLING, present low efficiency to characterize genes in soybeans due to genome complexity, gene duplication, and the presence of multiple gene family members that share high homology in their DNA sequence. Chemical mutagenesis emerges as a genetically modified-free strategy to produce large-scale soybean mutants for economically important traits improvement. The current study uses an optimized high-throughput TILLING by target capture sequencing technology, or TILLING-by-Sequencing+ (TbyS+), coupled with universal bioinformatic tools to identify population-wide mutations in soybeans. Four ethyl methanesulfonate mutagenized populations (4032 mutant families) have been screened for the presence of induced mutations in targeted genes. The mutation types and effects have been characterized for a total of 138 soybean genes involved in soybean seed composition, disease resistance, and many other quality traits. To test the efficiency of TbyS+ in complex genomes, we used soybeans as a model with a focus on three desaturase gene families, GmSACPD, GmFAD2, and GmFAD3, that are involved in the soybean fatty acid biosynthesis pathway. We successfully isolated mutants from all the six gene family members. Unsurprisingly, most of the characterized mutants showed significant changes either in their stearic, oleic, or linolenic acids. By using TbyS+, we discovered novel sources of soybean oil traits, including high saturated and monosaturated fatty acids in addition to low polyunsaturated fatty acid contents. This technology provides an unprecedented platform for highly effective screening of polyploid mutant populations and functional gene analysis. The obtained soybean mutants from this study can be used in subsequent soybean breeding programs for improved oil composition traits.
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Affiliation(s)
- Naoufal Lakhssassi
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | - Zhou Zhou
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | - Mallory A. Cullen
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | - Oussama Badad
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | - Abdelhalim El Baze
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | - Oumaima Chetto
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | - Mohamed G. Embaby
- Department of Animal Science, Food, and Nutrition, Southern Illinois University, Carbondale, IL 62901, USA;
| | - Dounya Knizia
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | - Shiming Liu
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | | | - Khalid Meksem
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
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Salava H, Thula S, Mohan V, Kumar R, Maghuly F. Application of Genome Editing in Tomato Breeding: Mechanisms, Advances, and Prospects. Int J Mol Sci 2021; 22:E682. [PMID: 33445555 PMCID: PMC7827871 DOI: 10.3390/ijms22020682] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 12/31/2020] [Accepted: 01/05/2021] [Indexed: 12/19/2022] Open
Abstract
Plants regularly face the changing climatic conditions that cause biotic and abiotic stress responses. The abiotic stresses are the primary constraints affecting crop yield and nutritional quality in many crop plants. The advances in genome sequencing and high-throughput approaches have enabled the researchers to use genome editing tools for the functional characterization of many genes useful for crop improvement. The present review focuses on the genome editing tools for improving many traits such as disease resistance, abiotic stress tolerance, yield, quality, and nutritional aspects of tomato. Many candidate genes conferring tolerance to abiotic stresses such as heat, cold, drought, and salinity stress have been successfully manipulated by gene modification and editing techniques such as RNA interference, insertional mutagenesis, and clustered regularly interspaced short palindromic repeat (CRISPR/Cas9). In this regard, the genome editing tools such as CRISPR/Cas9, which is a fast and efficient technology that can be exploited to explore the genetic resources for the improvement of tomato and other crop plants in terms of stress tolerance and nutritional quality. The review presents examples of gene editing responsible for conferring both biotic and abiotic stresses in tomato simultaneously. The literature on using this powerful technology to improve fruit quality, yield, and nutritional aspects in tomato is highlighted. Finally, the prospects and challenges of genome editing, public and political acceptance in tomato are discussed.
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Affiliation(s)
- Hymavathi Salava
- Department of Plant Sciences, University of Hyderabad, Hyderabad 500064, India;
| | - Sravankumar Thula
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic;
| | - Vijee Mohan
- Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA;
| | - Rahul Kumar
- Plant Translational Research Laboratory, Department of Plant Sciences, University of Hyderabad, Hyderabad 500064, India;
| | - Fatemeh Maghuly
- Plant Functional Genomics, Institute of Molecular Biotechnology, Department of Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
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20
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Hawliczek A, Bolibok L, Tofil K, Borzęcka E, Jankowicz-Cieślak J, Gawroński P, Kral A, Till BJ, Bolibok-Brągoszewska H. Deep sampling and pooled amplicon sequencing reveals hidden genic variation in heterogeneous rye accessions. BMC Genomics 2020; 21:845. [PMID: 33256606 PMCID: PMC7706248 DOI: 10.1186/s12864-020-07240-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/18/2020] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Loss of genetic variation negatively impacts breeding efforts and food security. Genebanks house over 7 million accessions representing vast allelic diversity that is a resource for sustainable breeding. Discovery of DNA variations is an important step in the efficient use of these resources. While technologies have improved and costs dropped, it remains impractical to consider resequencing millions of accessions. Candidate genes are known for most agronomic traits, providing a list of high priority targets. Heterogeneity in seed stocks means that multiple samples from an accession need to be evaluated to recover available alleles. To address this we developed a pooled amplicon sequencing approach and applied it to the out-crossing cereal rye (Secale cereale L.). RESULTS Using the amplicon sequencing approach 95 rye accessions of different improvement status and worldwide origin, each represented by a pooled sample comprising DNA of 96 individual plants, were evaluated for sequence variation in six candidate genes with significant functions on biotic and abiotic stress resistance, and seed quality. Seventy-four predicted deleterious variants were identified using multiple algorithms. Rare variants were recovered including those found only in a low percentage of seed. CONCLUSIONS We conclude that this approach provides a rapid and flexible method for evaluating stock heterogeneity, probing allele diversity, and recovering previously hidden variation. A large extent of within-population heterogeneity revealed in the study provides an important point for consideration during rye germplasm conservation and utilization efforts.
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Affiliation(s)
- Anna Hawliczek
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
| | - Leszek Bolibok
- Department of Silviculture, Institute of Forest Sciences, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
| | - Katarzyna Tofil
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
| | - Ewa Borzęcka
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
| | - Joanna Jankowicz-Cieślak
- 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
| | - Piotr Gawroński
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
| | - Adam Kral
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
| | - 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.
- Veterinary Genetics Laboratory, University of California, Davis, Davis, California, USA.
| | - Hanna Bolibok-Brągoszewska
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland.
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21
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Development and Characterization of an Ethyl Methane Sulfonate (EMS) Induced Mutant Population in Capsicum annuum L. PLANTS 2020; 9:plants9030396. [PMID: 32210121 PMCID: PMC7154856 DOI: 10.3390/plants9030396] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 11/29/2022]
Abstract
Plant breeding explores genetic diversity in useful traits to develop new, high-yielding, and improved cultivars. Ethyl methane sulfonate (EMS) is a chemical widely used to induce mutations at loci that regulate economically essential traits. Additionally, it can knock out genes, facilitating efforts to elucidate gene functions through the analysis of mutant phenotypes. Here, we developed a mutant population using the small and pungent ornamental Capsicum annuum pepper “Micro-Pep”. This accession is particularly suitable for mutation studies and molecular research due to its compact growth habit and small size. We treated 9500 seeds with 1.3% EMS and harvested 3996 M2 lines. We then selected 1300 (32.5%) independent M2 families and evaluated their phenotypes over four years. The mutants displayed phenotypic variations in plant growth, habit, leaf color and shape, and flower and fruit morphology. An experiment to optimize Targeting Induced Local Lesions IN Genomes (TILLING) in pepper detected nine EMS-induced mutations in the eIF4E gene. The M2 families developed here exhibited broad phenotypic variation and should be valuable genetic resources for functional gene analysis in pepper molecular breeding programs using reverse genetics tools, including TILLING.
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22
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Sashidhar N, Harloff HJ, Jung C. Identification of phytic acid mutants in oilseed rape (Brassica napus) by large-scale screening of mutant populations through amplicon sequencing. THE NEW PHYTOLOGIST 2020; 225:2022-2034. [PMID: 31651044 DOI: 10.1111/nph.16281] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 10/11/2019] [Indexed: 05/18/2023]
Abstract
Brassica napus (oilseed rape) is an important oil crop in temperate regions, which originated from hybridization of Brassica oleracea and Brassica rapa. Owing to its polyploidy, the functional study of single genes is cumbersome. Phytic acid is considered as an antinutritive compound, and we aimed to knock out the underlying synthesis and transporter genes to identify low phytic acid mutants. We implemented a high-throughput next-generation sequencing screening protocol for an ethylmethane sulfonate population of 7680 plants in six gene families (BnMIPS, BnMIK, Bn2-PGK, BnIPK1, BnIPK2, and BnMRP5) with two paralogues for each gene. A total of 1487 mutations were revealed, and the vast majority (96%) were confirmed by Sanger sequencing. Furthermore, the characterization of double mutants of Bn.2-PGK2 showed a significant reduction of phytic acid contents. We propose to use three-dimensional pooling combined with amplicon stacking and next-generation sequencing to identify mutations in polyploid oilseed rape in a fast and cost-effective manner for complex metabolic pathways. Furthermore, the mutants identified in Bn2-PGK2 might be a very valuable resource for industrial production of oilseed rape protein for human consumption.
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Affiliation(s)
- Niharika Sashidhar
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24118, Kiel, Germany
| | - Hans-Joachim Harloff
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24118, Kiel, Germany
| | - Christian Jung
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24118, Kiel, Germany
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Yano R, Hoshikawa K, Okabe Y, Wang N, Dung PT, Imriani PS, Shiba H, Ariizumi T, Ezura H. Multiplex exome sequencing reveals genome-wide frequency and distribution of mutations in the 'Micro-Tom' Targeting Induced Local Lesions in Genomes (TILLING) mutant library. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2019; 36:223-231. [PMID: 31983876 PMCID: PMC6978505 DOI: 10.5511/plantbiotechnology.19.0830a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 08/30/2019] [Indexed: 06/10/2023]
Abstract
While the 'Micro-Tom' TILLING mutant library is used for a wide range of purposes, including both basic research of gene function and breeding of commercial cultivars, genome-wide distribution and frequency of mutations have not yet been thoroughly elucidated on a population scale. In this study, we developed a 96-plex exome sequencing method to identify and analyze mutations within the TILLING mutants that were developed in the University of Tsukuba. First, an Illumina paired-end sequencing coupled with 96-plex exome capture resulted in the acquisition of an exome sequence dataset with an average read count of 5.6 million for the 95 mutants. Over 98% of the capture target region could be covered by the short reads with an averaged read depth of 12.8, which enabled us to identify single nucleotide polymorphisms and Indels in a genome-wide manner. By subtracting intra-cultivar DNA variations that are present between wild-type 'Micro-Tom' lines, we identified 241,391 mutation candidates in 95 mutant individuals. Of these, 64,319 and 6,480 mutations were expected to cause protein amino acid substitutions or premature stop codon, respectively. Based on the exome mutation dataset, a mutant line designated 'TOMJPW601' was found to carry a premature stop codon mutation (W261*) in a putative auxin influx carrier gene SlLAX1 (Solyc09G014380), consistent with our previous report of its curly leaf phenotype. Our results suggested that a population-scale mutation database developed by multiplexed exome sequencing could be used for in silico mutant screening, which in turn could contribute to both gene function research and breeding programs.
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Affiliation(s)
- Ryoichi Yano
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- Advanced Analysis Center, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
- JST PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Ken Hoshikawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba Plant Innovation Research Center (T-PIRC), University of Tsukuba, 1-1-1Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Yoshihiro Okabe
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba Plant Innovation Research Center (T-PIRC), University of Tsukuba, 1-1-1Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Ning Wang
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba Plant Innovation Research Center (T-PIRC), University of Tsukuba, 1-1-1Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Pham Thi Dung
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Pulungan Sri Imriani
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hiroshi Shiba
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba Plant Innovation Research Center (T-PIRC), University of Tsukuba, 1-1-1Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Tohru Ariizumi
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba Plant Innovation Research Center (T-PIRC), University of Tsukuba, 1-1-1Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba Plant Innovation Research Center (T-PIRC), University of Tsukuba, 1-1-1Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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Tramontano A, Jarc L, Jankowicz-Cieslak J, Hofinger BJ, Gajek K, Szurman-Zubrzycka M, Szarejko I, Ingelbrecht I, Till BJ. Fragmentation of Pooled PCR Products for Highly Multiplexed TILLING. G3 (BETHESDA, MD.) 2019; 9:2657-2666. [PMID: 31213514 PMCID: PMC6686939 DOI: 10.1534/g3.119.400301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/12/2019] [Indexed: 01/16/2023]
Abstract
Improvements to massively parallel sequencing have allowed the routine recovery of natural and induced sequence variants. A broad range of biological disciplines have benefited from this, ranging from plant breeding to cancer research. The need for high sequence coverage to accurately recover single nucleotide variants and small insertions and deletions limits the applicability of whole genome approaches. This is especially true in organisms with a large genome size or for applications requiring the screening of thousands of individuals, such as the reverse-genetic technique known as TILLING. Using PCR to target and sequence chosen genomic regions provides an attractive alternative as the vast reduction in interrogated bases means that sample size can be dramatically increased through amplicon multiplexing and multi-dimensional sample pooling while maintaining suitable coverage for recovery of small mutations. Direct sequencing of PCR products is limited, however, due to limitations in read lengths of many next generation sequencers. In the present study we show the optimization and use of ultrasonication for the simultaneous fragmentation of multiplexed PCR amplicons for TILLING highly pooled samples. Sequencing performance was evaluated in a total of 32 pooled PCR products produced from 4096 chemically mutagenized Hordeum vulgare DNAs pooled in three dimensions. Evaluation of read coverage and base quality across amplicons suggests this approach is suitable for high-throughput TILLING and other applications employing highly pooled complex sampling schemes. Induced mutations previously identified in a traditional TILLING screen were recovered in this dataset further supporting the efficacy of the approach.
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Affiliation(s)
- Andrea Tramontano
- 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, PO Box 100, A-1400 Vienna, Austria and
| | - Luka Jarc
- 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, PO Box 100, A-1400 Vienna, Austria and
| | - 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, PO Box 100, A-1400 Vienna, Austria and
| | - Bernhard J Hofinger
- 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, PO Box 100, A-1400 Vienna, Austria and
| | - Katarzyna Gajek
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032, Katowice, Poland
| | - Miriam Szurman-Zubrzycka
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032, Katowice, Poland
| | - Iwona Szarejko
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032, Katowice, Poland
| | - Ivan Ingelbrecht
- 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, PO Box 100, A-1400 Vienna, Austria and
| | - 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, PO Box 100, A-1400 Vienna, Austria and
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Kawall K. New Possibilities on the Horizon: Genome Editing Makes the Whole Genome Accessible for Changes. FRONTIERS IN PLANT SCIENCE 2019; 10:525. [PMID: 31068963 PMCID: PMC6491833 DOI: 10.3389/fpls.2019.00525] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/04/2019] [Indexed: 05/04/2023]
Abstract
The emergence of new genome editing techniques, such as the site-directed nucleases, clustered regulatory interspaced short palindromic repeats (CRISPRs)/Cas9, transcription activator-like effector nucleases (TALENs), or zinc finger nucleases (ZFNs), has greatly increased the feasibility of introducing any desired changes into the genome of a target organism. The ability to target a Cas nuclease to DNA sequences with a single-guide RNA (sgRNA) has provided a dynamic tool for genome editing and is naturally derived from an adaptive immune system in bacteria and archaea. CRISPR/Cas systems are being rapidly improved and refined, thereby opening up even more possibilities. Classical plant breeding is based on genetic variations that occur naturally and is used to select plants with improved traits. Induced mutagenesis is used to enhance mutational frequency and accelerate this process. Plants have evolved cellular processes, including certain repair mechanisms that ensure DNA integrity and the maintenance of distinct DNA loci. The focus of this review is on the characterization of new potentials in plant breeding through the use of CRISPR/Cas systems that eliminate natural limitations in order to induce thus far unachievable genomic changes.
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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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