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Bethke G, Huang Y, Hensel G, Heinen S, Liu C, Wyant SR, Li X, Quin MB, McCormick S, Morrell PL, Dong Y, Kumlehn J, Salvi S, Berthiller F, Muehlbauer GJ. UDP-glucosyltransferase HvUGT13248 confers type II resistance to Fusarium graminearum in barley. PLANT PHYSIOLOGY 2023; 193:2691-2710. [PMID: 37610244 DOI: 10.1093/plphys/kiad467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/18/2023] [Accepted: 08/01/2023] [Indexed: 08/24/2023]
Abstract
Fusarium head blight (FHB) of barley (Hordeum vulgare) causes yield losses and accumulation of trichothecene mycotoxins (e.g. deoxynivalenol [DON]) in grains. Glucosylation of DON to the nontoxic DON-3-O-glucoside (D3G) is catalyzed by UDP-glucosyltransferases (UGTs), such as barley UGT13248. We explored the natural diversity of UGT13248 in 496 barley accessions and showed that all carried potential functional alleles of UGT13248, as no genotypes showed strongly increased seedling sensitivity to DON. From a TILLING population, we identified 2 mutant alleles (T368I and H369Y) that, based on protein modeling, likely affect the UDP-glucose binding of UGT13248. In DON feeding experiments, DON-to-D3G conversion was strongly reduced in spikes of these mutants compared to controls, and plants overexpressing UGT13248 showed increased resistance to DON and increased DON-to-D3G conversion. Moreover, field-grown plants carrying the T368I or H369Y mutations inoculated with Fusarium graminearum showed increased FHB disease severity and reduced D3G production. Barley is generally considered to have type II resistance that limits the spread of F. graminearum from the infected spikelet to adjacent spikelets. Point inoculation experiments with F. graminearum showed increased infection spread in T368I and H369Y across the spike compared to wild type, while overexpression plants showed decreased spread of FHB symptoms. Confocal microscopy revealed that F. graminearum spread to distant rachis nodes in T368I and H369Y mutants but was arrested at the rachis node of the inoculated spikelet in wild-type plants. Taken together, our data reveal that UGT13248 confers type II resistance to FHB in barley via conjugation of DON to D3G.
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Affiliation(s)
- Gerit Bethke
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Yadong Huang
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Goetz Hensel
- Department of Physiology and Cell Biology, Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben 06466, Germany
| | - Shane Heinen
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Chaochih Liu
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Skylar R Wyant
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Xin Li
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Maureen B Quin
- Department of Biochemistry, Molecular Biology and Biophysics, Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108, USA
| | - Susan McCormick
- Mycotoxin Prevention and Applied Microbiology Research, USDA-ARS NCAUR, Peoria, IL 61604, USA
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Yanhong Dong
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Jochen Kumlehn
- Department of Physiology and Cell Biology, Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben 06466, Germany
| | - Silvio Salvi
- Department of Agricultural and Food Sciences, University of Bologna, Bologna 40126, Italy
| | - Franz Berthiller
- Department of Agrobiotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln 3430, Austria
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
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Selva C, Yang X, Shirley NJ, Whitford R, Baumann U, Tucker MR. HvSL1 and HvMADS16 promote stamen identity to restrict multiple ovary formation in barley. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5039-5056. [PMID: 37279531 PMCID: PMC10498024 DOI: 10.1093/jxb/erad218] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 06/01/2023] [Indexed: 06/08/2023]
Abstract
Correct floral development is the result of a sophisticated balance of molecular cues. Floral mutants provide insight into the main genetic determinants that integrate these cues, as well as providing opportunities to assess functional variation across species. In this study, we characterize the barley (Hordeum vulgare) multiovary mutants mov2.g and mov1, and propose causative gene sequences: a C2H2 zinc-finger gene HvSL1 and a B-class gene HvMADS16, respectively. In the absence of HvSL1, florets lack stamens but exhibit functional supernumerary carpels, resulting in multiple grains per floret. Deletion of HvMADS16 in mov1 causes homeotic conversion of lodicules and stamens into bract-like organs and carpels that contain non-functional ovules. Based on developmental, genetic, and molecular data, we propose a model by which stamen specification in barley is defined by HvSL1 acting upstream of HvMADS16. The present work identifies strong conservation of stamen formation pathways with other cereals, but also reveals intriguing species-specific differences. The findings lay the foundation for a better understanding of floral architecture in Triticeae, a key target for crop improvement.
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Affiliation(s)
- Caterina Selva
- Waite Research Institute, School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae 5064, South Australia, Australia
| | - Xiujuan Yang
- Waite Research Institute, School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae 5064, South Australia, Australia
| | - Neil J Shirley
- Waite Research Institute, School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae 5064, South Australia, Australia
| | - Ryan Whitford
- Waite Research Institute, School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae 5064, South Australia, Australia
| | - Ute Baumann
- Waite Research Institute, School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae 5064, South Australia, Australia
| | - Matthew R Tucker
- Waite Research Institute, School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae 5064, South Australia, Australia
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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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Agronomic Trait Analysis and Genetic Mapping of a New Wheat Semidwarf Gene Rht-SN33d. Int J Mol Sci 2022; 24:ijms24010583. [PMID: 36614025 PMCID: PMC9820066 DOI: 10.3390/ijms24010583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/01/2022] [Accepted: 12/21/2022] [Indexed: 12/31/2022] Open
Abstract
Plant height is a key agronomic trait that is closely to the plant morphology and lodging resistance in wheat. However, at present, the few dwarf genes widely used in wheat breeding have narrowed wheat genetic diversity. In this study, we selected a semi-dwarf wheat mutant dwarf33 that exhibits decreased plant height with little serious negative impact on other agronomic traits. Genetic analysis and mutant gene mapping indicated that dwarf33 contains a new recessive semi-dwarf gene Rht-SN33d, which was mapped into ~1.3 Mb interval on the 3DL chromosome. The gibberellin metabolism-related gene TraesCS3D02G542800, which encodes gibberellin 2-beta-dioxygenase, is considered a potential candidate gene of Rht-SN33d. Rht-SN33d reduced plant height by approximately 22.4% in mutant dwarf33. Further study revealed that shorter stem cell length may be the main factor causing plant height decrease. In addition, the coleoptile length of dwarf33 was just 9.3% shorter than that of wild-type Shaannong33. These results will help to expand our understanding of new mechanisms of wheat height regulation, and obtain new germplasm for wheat improvement.
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Luo G, Najafi J, Correia PMP, Trinh MDL, Chapman EA, Østerberg JT, Thomsen HC, Pedas PR, Larson S, Gao C, Poland J, Knudsen S, DeHaan L, Palmgren M. Accelerated Domestication of New Crops: Yield is Key. PLANT & CELL PHYSIOLOGY 2022; 63:1624-1640. [PMID: 35583202 PMCID: PMC9680862 DOI: 10.1093/pcp/pcac065] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/17/2022] [Accepted: 05/17/2022] [Indexed: 05/05/2023]
Abstract
Sustainable agriculture in the future will depend on crops that are tolerant to biotic and abiotic stresses, require minimal input of water and nutrients and can be cultivated with a minimal carbon footprint. Wild plants that fulfill these requirements abound in nature but are typically low yielding. Thus, replacing current high-yielding crops with less productive but resilient species will require the intractable trade-off of increasing land area under cultivation to produce the same yield. Cultivating more land reduces natural resources, reduces biodiversity and increases our carbon footprint. Sustainable intensification can be achieved by increasing the yield of underutilized or wild plant species that are already resilient, but achieving this goal by conventional breeding programs may be a long-term prospect. De novo domestication of orphan or crop wild relatives using mutagenesis is an alternative and fast approach to achieve resilient crops with high yields. With new precise molecular techniques, it should be possible to reach economically sustainable yields in a much shorter period of time than ever before in the history of agriculture.
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Affiliation(s)
| | | | | | | | | | | | | | - Pai Rosager Pedas
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V DK-1799, Denmark
| | - Steve Larson
- US Department of Agriculture (USDA), USDA–ARS Forage & Range Research Lab, Utah State University Logan, Logan, UT 84322, USA
| | - Caixia Gao
- Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jesse Poland
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Makkah 23955, Saudi Arabia
| | - Søren Knudsen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V DK-1799, Denmark
| | - Lee DeHaan
- The Land Institute, Salina, KS 67401, USA
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6
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Knudsen S, Wendt T, Dockter C, Thomsen HC, Rasmussen M, Egevang Jørgensen M, Lu Q, Voss C, Murozuka E, Østerberg JT, Harholt J, Braumann I, Cuesta-Seijo JA, Kale SM, Bodevin S, Tang Petersen L, Carciofi M, Pedas PR, Opstrup Husum J, Nielsen MTS, Nielsen K, Jensen MK, Møller LA, Gojkovic Z, Striebeck A, Lengeler K, Fennessy RT, Katz M, Garcia Sanchez R, Solodovnikova N, Förster J, Olsen O, Møller BL, Fincher GB, Skadhauge B. FIND-IT: Accelerated trait development for a green evolution. SCIENCE ADVANCES 2022; 8:eabq2266. [PMID: 36001660 PMCID: PMC9401622 DOI: 10.1126/sciadv.abq2266] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Improved agricultural and industrial production organisms are required to meet the future global food demands and minimize the effects of climate change. A new resource for crop and microbe improvement, designated FIND-IT (Fast Identification of Nucleotide variants by droplet DigITal PCR), provides ultrafast identification and isolation of predetermined, targeted genetic variants in a screening cycle of less than 10 days. Using large-scale sample pooling in combination with droplet digital PCR (ddPCR) greatly increases the size of low-mutation density and screenable variant libraries and the probability of identifying the variant of interest. The method is validated by screening variant libraries totaling 500,000 barley (Hordeum vulgare) individuals and isolating more than 125 targeted barley gene knockout lines and miRNA or promoter variants enabling functional gene analysis. FIND-IT variants are directly applicable to elite breeding pipelines and minimize time-consuming technical steps to accelerate the evolution of germplasm.
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Affiliation(s)
- Søren Knudsen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Toni Wendt
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Christoph Dockter
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Magnus Rasmussen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Qiongxian Lu
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Cynthia Voss
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Emiko Murozuka
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Jesper Harholt
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Ilka Braumann
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Jose A. Cuesta-Seijo
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Sandip M. Kale
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Sabrina Bodevin
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Lise Tang Petersen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Pai Rosager Pedas
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Jeppe Opstrup Husum
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Kasper Nielsen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Mikkel K. Jensen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Lillian Ambus Møller
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Zoran Gojkovic
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Alexander Striebeck
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Klaus Lengeler
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Ross T. Fennessy
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Michael Katz
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Rosa Garcia Sanchez
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Jochen Förster
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Ole Olsen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Centre for Synthetic Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Geoffrey B. Fincher
- Australian Research Council Centre of Excellence in Plant Cell Walls School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
| | - Birgitte Skadhauge
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
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Root angle is controlled by EGT1 in cereal crops employing an antigravitropic mechanism. Proc Natl Acad Sci U S A 2022; 119:e2201350119. [PMID: 35881796 PMCID: PMC9351459 DOI: 10.1073/pnas.2201350119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The growth angle roots adopt are critical for capturing soil resources, such as nutrients and water. Despite its agronomic importance, few regulatory genes have been identified in crops. Here we identify the root angle regulatory gene ENHANCED GRAVITROPISM 1 (EGT1) in barley. Strikingly, mutants lacking EGT1 exhibit a steeper angle in every root class. EGT1 appears to function as a component of an antigravitropic offset mechanism that regulates tissue stiffness, which impacts final root growth angle. EGT1 is a hot spot for selection as natural allelic variation within a conserved Tubby domain that is linked with steeper root angle. Analogous EGT1-dependent regulation of root angle in wheat demonstrates broad significance of EGT1 for trait improvement in cereal crops. Root angle in crops represents a key trait for efficient capture of soil resources. Root angle is determined by competing gravitropic versus antigravitropic offset (AGO) mechanisms. Here we report a root angle regulatory gene termed ENHANCED GRAVITROPISM1 (EGT1) that encodes a putative AGO component, whose loss-of-function enhances root gravitropism. Mutations in barley and wheat EGT1 genes confer a striking root phenotype, where every root class adopts a steeper growth angle. EGT1 encodes an F-box and Tubby domain-containing protein that is highly conserved across plant species. Haplotype analysis found that natural allelic variation at the barley EGT1 locus impacts root angle. Gravitropic assays indicated that Hvegt1 roots bend more rapidly than wild-type. Transcript profiling revealed Hvegt1 roots deregulate reactive oxygen species (ROS) homeostasis and cell wall-loosening enzymes and cofactors. ROS imaging shows that Hvegt1 root basal meristem and elongation zone tissues have reduced levels. Atomic force microscopy measurements detected elongating Hvegt1 root cortical cell walls are significantly less stiff than wild-type. In situ analysis identified HvEGT1 is expressed in elongating cortical and stele tissues, which are distinct from known root gravitropic perception and response tissues in the columella and epidermis, respectively. We propose that EGT1 controls root angle by regulating cell wall stiffness in elongating root cortical tissue, counteracting the gravitropic machinery’s known ability to bend the root via its outermost tissues. We conclude that root angle is controlled by EGT1 in cereal crops employing an antigravitropic mechanism.
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Wang Y, Salt DE, Koornneef M, Aarts MGM. Construction and analysis of a Noccaea caerulescens TILLING population. BMC PLANT BIOLOGY 2022; 22:360. [PMID: 35869423 PMCID: PMC9308233 DOI: 10.1186/s12870-022-03739-x] [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: 12/07/2021] [Accepted: 06/27/2022] [Indexed: 05/11/2023]
Abstract
BACKGROUND Metals such as Zn or Cd are toxic to plant and humans when they are exposed in high quantities through contaminated soil or food. Noccaea caerulescens, an extraordinary Zn/Cd/Ni hyperaccumulating species, is used as a model plant for metal hyperaccumulation and phytoremediation studies. Current reverse genetic techniques to generate mutants based on transgenesis is cumbersome due to the low transformation efficiency of this species. We aimed to establish a mutant library for functional genomics by a non-transgenic approach, to identify mutants with an altered mineral profiling, and to screen for mutations in bZIP19, a regulator of Zn homeostasis in N. caerulescens. RESULTS To generate the N. caerulescens mutant library, 3000 and 5000 seeds from two sister plants of a single-seed recurrent inbred descendant of the southern French accession Saint-Félix-de-Pallières (SF) were mutagenized respectively by 0.3 or 0.4% ethyl methane sulfonate (EMS). Two subpopulations of 5000 and 7000 M2 plants were obtained after 0.3 or 0.4% EMS treatment. The 0.4% EMS treatment population had a higher mutant frequency and was used for TILLING. A High Resolution Melting curve analysis (HRM) mutation screening platform was optimized and successfully applied to detect mutations for NcbZIP19, encoding a transcription factor controlling Zn homeostasis. Of four identified point mutations in NcbZIP19, two caused non-synonymous substitutions, however, these two mutations did not alter the ionome profile compared to the wild type. Forward screening of the 0.4% EMS treatment population by mineral concentration analysis (ionomics) in leaf material of each M2 plant revealed putative mutants affected in the concentration of one or more of the 20 trace elements tested. Several of the low-Zn mutants identified in the ionomic screen did not give progeny, illustrating the importance of Zn for the species. The mutant frequency of the population was evaluated based on an average of 2.3 knockout mutants per tested monogenic locus. CONCLUSIONS The 0.4% EMS treatment population is effectively mutagenized suitable for forward mutant screens and TILLING. Difficulties in seed production in low Zn mutants, obtained by both forward and reverse genetic approach, hampered further analysis of the nature of the low Zn phenotypes.
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Affiliation(s)
- Yanli Wang
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- College of Horticulture Science & Technology, Hebei Normal University of Science & Technology, No 360, West of HeBei street, Qinhuang Dao, China
| | - David E Salt
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Maarten Koornneef
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Mark G M Aarts
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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9
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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: 11] [Impact Index Per Article: 5.5] [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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10
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Holden S, Bergum M, Green P, Bettgenhaeuser J, Hernández-Pinzón I, Thind A, Clare S, Russell JM, Hubbard A, Taylor J, Smoker M, Gardiner M, Civolani L, Cosenza F, Rosignoli S, Strugala R, Molnár I, Šimková H, Doležel J, Schaffrath U, Barrett M, Salvi S, Moscou MJ. A lineage-specific Exo70 is required for receptor kinase-mediated immunity in barley. SCIENCE ADVANCES 2022; 8:eabn7258. [PMID: 35857460 PMCID: PMC9258809 DOI: 10.1126/sciadv.abn7258] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
In the evolution of land plants, the plant immune system has experienced expansion in immune receptor and signaling pathways. Lineage-specific expansions have been observed in diverse gene families that are potentially involved in immunity but lack causal association. Here, we show that Rps8-mediated resistance in barley to the pathogen Puccinia striiformis f. sp. tritici (wheat stripe rust) is conferred by a genetic module: Pur1 and Exo70FX12, which are together necessary and sufficient. Pur1 encodes a leucine-rich repeat receptor kinase and is the ortholog of rice Xa21, and Exo70FX12 belongs to the Poales-specific Exo70FX clade. The Exo70FX clade emerged after the divergence of the Bromeliaceae and Poaceae and comprises from 2 to 75 members in sequenced grasses. These results demonstrate the requirement of a lineage-specific Exo70FX12 in Pur1-mediated immunity and suggest that the Exo70FX clade may have evolved a specialized role in receptor kinase signaling.
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Affiliation(s)
- Samuel Holden
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Molly Bergum
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Phon Green
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jan Bettgenhaeuser
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - Anupriya Thind
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Shaun Clare
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - James M. Russell
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Amelia Hubbard
- NIAB, 93 Lawrence Weaver Road, Cambridge CB3 0LE, England, UK
| | - Jodi Taylor
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Matthew Smoker
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Matthew Gardiner
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Laura Civolani
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
- Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 44, 40127 Bologna, Italy
| | - Francesco Cosenza
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
- Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 44, 40127 Bologna, Italy
| | - Serena Rosignoli
- Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 44, 40127 Bologna, Italy
| | - Roxana Strugala
- Department of Plant Physiology, RWTH Aachen University, 52056 Aachen, Germany
| | - István Molnár
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Hana Šimková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Ulrich Schaffrath
- Department of Plant Physiology, RWTH Aachen University, 52056 Aachen, Germany
| | - Matthew Barrett
- Australian Tropical Herbarium, James Cook University, Smithfield 4878, Australia
| | - Silvio Salvi
- Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 44, 40127 Bologna, Italy
| | - Matthew J. Moscou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
- Corresponding author.
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11
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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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12
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Simons JM, Herbert TC, Kauffman C, Batete MY, Simpson AT, Katsuki Y, Le D, Amundson D, Buescher EM, Weil C, Tuinstra M, Addo‐Quaye C. Systematic prediction of EMS-induced mutations in a sorghum mutant population. PLANT DIRECT 2022; 6:e404. [PMID: 35647479 PMCID: PMC9132608 DOI: 10.1002/pld3.404] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 04/22/2022] [Accepted: 04/24/2022] [Indexed: 05/14/2023]
Abstract
The precise detection of causal DNA mutations (deoxyribonucleic acid) is very crucial for forward genetic studies. Several sources of errors contribute to false-positive detections by current variant-calling algorithms, which impact associating phenotypes with genotypes. To improve the accuracy of mutation detection, we implemented a binning method for the accurate detection of likely ethyl methanesulfonate (EMS)-induced mutations in a sequenced mutant population. We also implemented a clustering algorithm for detecting likely false negatives with high accuracy. Sorghum bicolor is a very valuable crop species with tremendous potential for uncovering novel gene functions associated with highly desirable agronomical traits. We demonstrate the precision of the described approach in the detection of likely EMS-induced mutations from the publicly available low-cost sequencing of the M3 generation from 600 sorghum BTx623 mutants. The approach detected 3,274,606 single nucleotide polymorphisms (SNPs), of which 96% (3,141,908) were G/C to A/T DNA substitutions, as expected by EMS-mutagenesis mode of action. We demonstrated the general applicability of the described method and showed a high concordance, 94% (3,074,759) SNPs overlap between SAMtools-based and GATK-based variant-calling algorithms. Our clustering algorithm uncovered evidence for an additional 223,048 likely false-negative shared EMS-induced mutations. The final 3,497,654 SNPs represent an 87% increase in SNPs detected from the previous analysis of the mutant population, with an average of one SNP per 125 kb in the sorghum genome. Annotation of the final SNPs revealed 10,263 high-impact and 136,639 moderate-impact SNPs, including 7217 stop-gained mutations, which averages 12 stop-gained mutations per mutant, and four high- or medium-impact SNPs per sorghum gene. We have implemented a public search database for this new genetic resource of 30,285 distinct sorghum genes containing medium- or high-impact EMS-induced mutations. Seedstock for a select 486 of the 600 described mutants are publicly available in the Germplasm Resources Information Network (GRIN) database.
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Affiliation(s)
- Jared M. Simons
- Division of Natural Sciences and MathematicsLewis‐Clark State CollegeLewistonIdahoUSA
| | - Tim C. Herbert
- Division of Natural Sciences and MathematicsLewis‐Clark State CollegeLewistonIdahoUSA
| | - Coleby Kauffman
- Division of Natural Sciences and MathematicsLewis‐Clark State CollegeLewistonIdahoUSA
| | - Marc Y. Batete
- Division of Natural Sciences and MathematicsLewis‐Clark State CollegeLewistonIdahoUSA
| | - Andrew T. Simpson
- Division of Natural Sciences and MathematicsLewis‐Clark State CollegeLewistonIdahoUSA
- Present address:
Department of Biological SciencesUniversity of IdahoMoscowIdahoUSA
| | - Yuka Katsuki
- Division of Natural Sciences and MathematicsLewis‐Clark State CollegeLewistonIdahoUSA
| | - Dong Le
- Division of Natural Sciences and MathematicsLewis‐Clark State CollegeLewistonIdahoUSA
| | - Danielle Amundson
- Division of Natural Sciences and MathematicsLewis‐Clark State CollegeLewistonIdahoUSA
| | | | - Clifford Weil
- Department of AgronomyPurdue UniversityWest LafayetteIndianaUSA
| | - Mitch Tuinstra
- Department of AgronomyPurdue UniversityWest LafayetteIndianaUSA
| | - Charles Addo‐Quaye
- Division of Natural Sciences and MathematicsLewis‐Clark State CollegeLewistonIdahoUSA
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13
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Wyant SR, Rodriguez MF, Carter CK, Parrott WA, Jackson SA, Stupar RM, Morrell PL. Fast neutron mutagenesis in soybean enriches for small indels and creates frameshift mutations. G3 (BETHESDA, MD.) 2022; 12:jkab431. [PMID: 35100358 PMCID: PMC9335934 DOI: 10.1093/g3journal/jkab431] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 11/14/2021] [Indexed: 11/13/2022]
Abstract
The mutagenic effects of ionizing radiation have been used for decades to create novel variants in experimental populations. Fast neutron (FN) bombardment as a mutagen has been especially widespread in plants, with extensive reports describing the induction of large structural variants, i.e., deletions, insertions, inversions, and translocations. However, the full spectrum of FN-induced mutations is poorly understood. We contrast small insertions and deletions (indels) observed in 27 soybean lines subject to FN irradiation with the standing indels identified in 107 diverse soybean lines. We use the same populations to contrast the nature and context (bases flanking a nucleotide change) of single-nucleotide variants. The accumulation of new single-nucleotide changes in FN lines is marginally higher than expected based on spontaneous mutation. In FN-treated lines and in standing variation, C→T transitions and the corresponding reverse complement G→A transitions are the most abundant and occur most frequently in a CpG local context. These data indicate that most SNPs identified in FN lines are likely derived from spontaneous de novo processes in generations following mutagenesis rather than from the FN irradiation mutagen. However, small indels in FN lines differ from standing variants. Short insertions, from 1 to 6 bp, are less abundant than in standing variation. Short deletions are more abundant and prone to induce frameshift mutations that should disrupt the structure and function of encoded proteins. These findings indicate that FN irradiation generates numerous small indels, increasing the abundance of loss-of-function mutations that impact single genes.
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Affiliation(s)
- Skylar R Wyant
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
| | - M Fernanda Rodriguez
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Corey K Carter
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Wayne A Parrott
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA 30602, USA
| | - Scott A Jackson
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA 30602, USA
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
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14
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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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15
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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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16
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ENHANCED GRAVITROPISM 2 encodes a STERILE ALPHA MOTIF-containing protein that controls root growth angle in barley and wheat. Proc Natl Acad Sci U S A 2021; 118:2101526118. [PMID: 34446550 PMCID: PMC8536364 DOI: 10.1073/pnas.2101526118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
To date, the potential of utilizing root traits in plant breeding remains largely untapped. In this study, we cloned and characterized the ENHANCED GRAVITROPISM2 (EGT2) gene of barley that encodes a STERILE ALPHA MOTIF domain–containing protein. We demonstrated that EGT2 is a key gene of root growth angle regulation in response to gravity, which is conserved in barley and wheat and could be a promising target for crop improvement in cereals. The root growth angle defines how roots grow toward the gravity vector and is among the most important determinants of root system architecture. It controls water uptake capacity, nutrient use efficiency, stress resilience, and, as a consequence, yield of crop plants. We demonstrated that the egt2 (enhanced gravitropism 2) mutant of barley exhibits steeper root growth of seminal and lateral roots and an auxin-independent higher responsiveness to gravity compared to wild-type plants. We cloned the EGT2 gene by a combination of bulked-segregant analysis and whole genome sequencing. Subsequent validation experiments by an independent CRISPR/Cas9 mutant allele demonstrated that egt2 encodes a STERILE ALPHA MOTIF domain–containing protein. In situ hybridization experiments illustrated that EGT2 is expressed from the root cap to the elongation zone. We demonstrated the evolutionary conserved role of EGT2 in root growth angle control between barley and wheat by knocking out the EGT2 orthologs in the A and B genomes of tetraploid durum wheat. By combining laser capture microdissection with RNA sequencing, we observed that seven expansin genes were transcriptionally down-regulated in the elongation zone. This is consistent with a role of EGT2 in this region of the root where the effect of gravity sensing is executed by differential cell elongation. Our findings suggest that EGT2 is an evolutionary conserved regulator of root growth angle in barley and wheat that could be a valuable target for root-based crop improvement strategies in cereals.
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17
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Kawamoto Y, Toda H, Inoue H, Kobayashi K, Yamaoka N, Araki T, Yaeno T. Fast and Inexpensive Phenotyping and Genotyping Methods for Evaluation of Barley Mutant Population. PLANTS 2020; 9:plants9091153. [PMID: 32899989 PMCID: PMC7569886 DOI: 10.3390/plants9091153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/19/2020] [Accepted: 09/04/2020] [Indexed: 01/13/2023]
Abstract
To further develop barley breeding and genetics, more information on gene functions based on the analysis of the mutants of each gene is needed. However, the mutant resources are not as well developed as the model plants, such as Arabidopsis and rice. Although genome editing techniques have been able to generate mutants, it is not yet an effective method as it can only be used to transform a limited number of cultivars. Here, we developed a mutant population using ‘Mannenboshi’, which produces good quality grains with high yields but is susceptible to disease, to establish a Targeting Induced Local Lesions IN Genomes (TILLING) system that can isolate mutants in a high-throughput manner. To evaluate the availability of the prepared 8043 M3 lines, we investigated the frequency of mutant occurrence using a rapid, visually detectable waxy phenotype as an indicator. Four mutants were isolated and single nucleotide polymorphisms (SNPs) were identified in the Waxy gene as novel alleles. It was confirmed that the mutations could be easily detected using the mismatch endonuclease CELI, revealing that a sufficient number of mutants could be rapidly isolated from our TILLING population.
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18
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Selva C, Riboni M, Baumann U, Würschum T, Whitford R, Tucker MR. Hybrid breeding in wheat: how shaping floral biology can offer new perspectives. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 47:675-694. [PMID: 32534601 DOI: 10.1071/fp19372] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/21/2020] [Indexed: 06/11/2023]
Abstract
Hybrid breeding in wheat (Triticum aestivum L.) has the potential to deliver major yield increases. This is a requisite to guarantee food security for increasing population demands and to counterbalance the effects of extreme environmental conditions. Successful hybrid breeding in wheat relies on forced outcrossing while preventing self-pollination. To achieve this, research has been directed towards identifying and improving fertility control systems. To maximise cross-pollination and seed set, however, fertility control systems need to be complemented by breeding phenotypically distinct male and female lines. This review summarises existing and novel male sterility systems for wheat hybridisation. We also consider the genetic resources that can be used to alter wheat's floral development and spike morphology, with a focus on the genetic variation already available. Exploiting these resources can lead to enhanced outcrossing, a key requirement in the progress towards hybrid wheat breeding.
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Affiliation(s)
- Caterina Selva
- School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Matteo Riboni
- School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Ute Baumann
- School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Tobias Würschum
- State Plant Breeding Institute, University of Hohenheim, 70593 Stuttgart, Germany
| | - Ryan Whitford
- School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia; and Corresponding authors. ;
| | - Matthew R Tucker
- School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia; and Corresponding authors. ;
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19
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Rotasperti L, Sansoni F, Mizzotti C, Tadini L, Pesaresi P. Barley's Second Spring as A Model Organism for Chloroplast Research. PLANTS 2020; 9:plants9070803. [PMID: 32604986 PMCID: PMC7411767 DOI: 10.3390/plants9070803] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 12/19/2022]
Abstract
Barley (Hordeum vulgare) has been widely used as a model crop for studying molecular and physiological processes such as chloroplast development and photosynthesis. During the second half of the 20th century, mutants such as albostrians led to the discovery of the nuclear-encoded, plastid-localized RNA polymerase and the retrograde (chloroplast-to-nucleus) signalling communication pathway, while chlorina-f2 and xantha mutants helped to shed light on the chlorophyll biosynthetic pathway, on the light-harvesting proteins and on the organization of the photosynthetic apparatus. However, during the last 30 years, a large fraction of chloroplast research has switched to the more “user-friendly” model species Arabidopsis thaliana, the first plant species whose genome was sequenced and published at the end of 2000. Despite its many advantages, Arabidopsis has some important limitations compared to barley, including the lack of a real canopy and the absence of the proplastid-to-chloroplast developmental gradient across the leaf blade. These features, together with the availability of large collections of natural genetic diversity and mutant populations for barley, a complete genome assembly and protocols for genetic transformation and gene editing, have relaunched barley as an ideal model species for chloroplast research. In this review, we provide an update on the genomics tools now available for barley, and review the biotechnological strategies reported to increase photosynthesis efficiency in model species, which deserve to be validated in barley.
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20
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Jiang C, Kan J, Ordon F, Perovic D, Yang P. Bymovirus-induced yellow mosaic diseases in barley and wheat: viruses, genetic resistances and functional aspects. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1623-1640. [PMID: 32008056 DOI: 10.1007/s00122-020-03555-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 01/24/2020] [Indexed: 05/20/2023]
Abstract
Bymovirus-induced yellow mosaic diseases seriously threaten global production of autumn-sown barley and wheat, which are two of the presently most important crops around the world. Under natural field conditions, the diseases are caused by infection of soil-borne plasmodiophorid Polymyxa graminis-transmitted bymoviruses of the genus Bymovirus of the family Potyviridae. Focusing on barley and wheat, this article summarizes the achievements on taxonomy, geography and host specificity of these disease-conferring viruses, as well as the genetics of resistance in barley, wheat and wild relatives. Moreover, based on recent progress of barley and wheat genomics, germplasm resources and large-scale sequencing, the exploration and isolation of corresponding resistant genes from wheat and barley as well as relatives, no matter what a large and complicated genome is present, are becoming feasible and are discussed. Furthermore, the foreseen advances on cloning of the resistance or susceptibility-encoding genes, which will provide the possibility to explore the functional interaction between host plants and soil-borne viral pathogens, are discussed as well as the benefits for marker-assisted resistance breeding in barley and wheat.
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Affiliation(s)
- Congcong Jiang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, People's Republic of China
| | - Jinhong Kan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, People's Republic of China
| | - Frank Ordon
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute (JKI), 06484, Quedlinburg, Germany
| | - Dragan Perovic
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute (JKI), 06484, Quedlinburg, Germany
| | - Ping Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, People's Republic of China.
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21
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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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22
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Christov NK. The role of epistasis and its interaction with environment in fine-tuning heading time in barley. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:743-746. [PMID: 31971242 PMCID: PMC6977021 DOI: 10.1093/jxb/erz503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 11/07/2019] [Indexed: 06/10/2023]
Abstract
This article comments on: Afsharyan NP, Sannemann W, Léon J, Ballvora A. 2020. Effect of epistasis and environment on flowering time of barley reveals novel flowering-delaying QTL allele. Journal of Experimental Botany 71, 893–906.
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Affiliation(s)
- Nikolai K Christov
- Functional Genetics Department, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
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23
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Kumar A, Kumar R, Sengupta D, Das SN, Pandey MK, Bohra A, Sharma NK, Sinha P, Sk H, Ghazi IA, Laha GS, Sundaram RM. Deployment of Genetic and Genomic Tools Toward Gaining a Better Understanding of Rice- Xanthomonas oryzae pv. oryzae Interactions for Development of Durable Bacterial Blight Resistant Rice. FRONTIERS IN PLANT SCIENCE 2020; 11:1152. [PMID: 32849710 PMCID: PMC7417518 DOI: 10.3389/fpls.2020.01152] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/15/2020] [Indexed: 05/05/2023]
Abstract
Rice is the most important food crop worldwide and sustainable rice production is important for ensuring global food security. Biotic stresses limit rice production significantly and among them, bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae (Xoo) is very important. BB reduces rice yields severely in the highly productive irrigated and rainfed lowland ecosystems and in recent years; the disease is spreading fast to other rice growing ecosystems as well. Being a vascular pathogen, Xoo interferes with a range of physiological and biochemical exchange processes in rice. The response of rice to Xoo involves specific interactions between resistance (R) genes of rice and avirulence (Avr) genes of Xoo, covering most of the resistance genes except the recessive ones. The genetic basis of resistance to BB in rice has been studied intensively, and at least 44 genes conferring resistance to BB have been identified, and many resistant rice cultivars and hybrids have been developed and released worldwide. However, the existence and emergence of new virulent isolates of Xoo in the realm of a rapidly changing climate necessitates identification of novel broad-spectrum resistance genes and intensification of gene-deployment strategies. This review discusses about the origin and occurrence of BB in rice, interactions between Xoo and rice, the important roles of resistance genes in plant's defense response, the contribution of rice resistance genes toward development of disease resistance varieties, identification and characterization of novel, and broad-spectrum BB resistance genes from wild species of Oryza and also presents a perspective on potential strategies to achieve the goal of sustainable disease management.
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Affiliation(s)
- Anirudh Kumar
- Department of Botany, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
- *Correspondence: Raman Meenakshi Sundaram, ; Anirudh Kumar,
| | - Rakesh Kumar
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Debashree Sengupta
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad (UoH), Hyderabad, India
| | - Subha Narayan Das
- Department of Botany, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Manish K. Pandey
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Abhishek Bohra
- ICAR-Crop Improvement Division, Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Naveen K. Sharma
- Department of Botany, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Pragya Sinha
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Hajira Sk
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Irfan Ahmad Ghazi
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad (UoH), Hyderabad, India
| | - Gouri Sankar Laha
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Raman Meenakshi Sundaram
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
- *Correspondence: Raman Meenakshi Sundaram, ; Anirudh Kumar,
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Liu S, Ge F, Huang W, Lightfoot DA, Peng D. Effective identification of soybean candidate genes involved in resistance to soybean cyst nematode via direct whole genome re-sequencing of two segregating mutants. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2677-2687. [PMID: 31250041 DOI: 10.1007/s00122-019-03381-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/14/2019] [Indexed: 06/09/2023]
Abstract
KEY MESSAGE Three soybean candidate genes involved in resistance to soybean cyst nematode race 4 were identified via direct whole genome re-sequencing of two segregating mutants. The genes conferring resistance to soybean cyst nematode (SCN) race 4 (Hg type 1.2.3.5.7) in soybean (Glycine max L. Merr.) remains unknown. Next generation sequencing-based methods identify a wide range of targets, it is difficult to identify genes underlying traits. Use of the MutMap and QTL-seq methods to identify trait candidate genes needs backcrossing and is very time-consuming. Here we report a simple method to effectively identify candidate genes involved in resistance to SCN race 4. Two ethane methylsulfonate mutagenized mutants of soybean 'PI 437654', whose SCN race 4-infection phenotype altered, were selected. Six relevant whole genomes were re-sequenced, and then calling of genomic variants (SNPs and InDels) was conducted and compared to 'Williams 82'. The comparison eliminated many genomic variants from the mutant lines that overlapped two non-phenotypic but mutant progeny plants, wild-type PI 437654 and 'Zhonghuang 13'. Finally, only 27 mutations were found among 10 genes. Of these 10 genes, 3 genes, Glyma.09g054000, Glyma.16g065700 and Glyma.18g192200 were overlapped between two phenotypic mutant progeny plants. Therefore, the three genes may be the candidate genes involved in resistance of PI 437654 to soybean cyst nematode race 4. This method simplifies the effective identification of candidate genes.
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Affiliation(s)
- Shiming Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, People's Republic of China.
| | - Fengyong Ge
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Wenkun Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - David A Lightfoot
- College of Agricultural Sciences, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Deliang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
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25
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CRISPR-Cas9 system: A new-fangled dawn in gene editing. Life Sci 2019; 232:116636. [DOI: 10.1016/j.lfs.2019.116636] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 06/30/2019] [Accepted: 07/05/2019] [Indexed: 12/24/2022]
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26
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Schreiber M, Barakate A, Uzrek N, Macaulay M, Sourdille A, Morris J, Hedley PE, Ramsay L, Waugh R. A highly mutagenised barley ( cv. Golden Promise) TILLING population coupled with strategies for screening-by-sequencing. PLANT METHODS 2019; 15:99. [PMID: 31462905 PMCID: PMC6708184 DOI: 10.1186/s13007-019-0486-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 08/16/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND We developed and characterised a highly mutagenised TILLING population of the barley (Hordeum vulgare) cultivar Golden Promise. Golden Promise is the 'reference' genotype for barley transformation and a primary objective of using this cultivar was to be able to genetically complement observed mutations directly in order to prove gene function. Importantly, a reference genome assembly of Golden Promise has also recently been developed. As our primary interest was to identify mutations in genes involved in meiosis and recombination, to characterise the population we focused on a set of 46 genes from the literature that are possible meiosis gene candidates. RESULTS Sequencing 20 plants from the population using whole exome capture revealed that the mutation density in this population is high (one mutation every 154 kb), and consequently even in this small number of plants we identified several interesting mutations. We also recorded some issues with seed availability and germination. We subsequently designed and applied a simple two-dimensional pooling strategy to identify mutations in varying numbers of specific target genes by Illumina short read pooled-amplicon sequencing and subsequent deconvolution. In parallel we assembled a collection of semi-sterile mutants from the population and used a custom exome capture array targeting the 46 candidate meiotic genes to identify potentially causal mutations. CONCLUSIONS We developed a highly mutagenised barley TILLING population in the transformation competent cultivar Golden Promise. We used novel and cost-efficient screening approaches to successfully identify a broad range of potentially deleterious variants that were subsequently validated by Sanger sequencing. These resources combined with a high-quality genome reference sequence opens new possibilities for efficient functional gene validation.
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Affiliation(s)
- Miriam Schreiber
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA Scotland UK
| | - Abdellah Barakate
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA Scotland UK
| | - Nicola Uzrek
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA Scotland UK
| | - Malcolm Macaulay
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA Scotland UK
| | - Adeline Sourdille
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA Scotland UK
| | - Jenny Morris
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA Scotland UK
| | - Pete E. Hedley
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA Scotland UK
| | - Luke Ramsay
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA Scotland UK
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA Scotland UK
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA Scotland UK
- School of Agriculture and Wine, University of Adelaide, Plant Genome Building, Waite Campus, Urrbrae, Adelaide, SA Australia
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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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28
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Szurman-Zubrzycka M, Baran B, Stolarek-Januszkiewicz M, Kwaśniewska J, Szarejko I, Gruszka D. The dmc1 Mutant Allows an Insight Into the DNA Double-Strand Break Repair During Meiosis in Barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2019; 10:761. [PMID: 31244877 PMCID: PMC6579892 DOI: 10.3389/fpls.2019.00761] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 05/24/2019] [Indexed: 05/28/2023]
Abstract
Meiosis is a process of essential importance for sexual reproduction, as it leads to production of gametes. The recombination event (crossing-over) generates genetic variation by introducing new combination of alleles. The first step of crossing-over is introduction of a targeted double-strand break (DSB) in DNA. DMC1 (Disrupted Meiotic cDNA1) is a recombinase that is specific only for cells undergoing meiosis and takes part in repair of such DSBs by searching and invading homologous sequences that are subsequently used as a template for the repair process. Although role of the DMC1 gene has been validated in Arabidopsis thaliana, a functional analysis of its homolog in barley, a crop species of significant importance in agriculture, has never been performed. Here, we describe the identification of barley mutants carrying substitutions in the HvDMC1 gene. We performed mutational screening using TILLING (Targeting Induced Local Lesions IN Genomes) strategy and the barley TILLING population, HorTILLUS, developed after double-treatment of spring barley cultivar 'Sebastian' with sodium azide and N-methyl-N-nitrosourea. One of the identified alleles, dmc1.c, was found independently in two different M2 plants. The G2571A mutation identified in this allele leads to a substitution of the highly conserved amino acid (arginine-183 to lysine) in the DMC1 protein sequence. Two mutant lines carrying the same dmc1.c allele show similar disturbances during meiosis. The chromosomal aberrations included anaphase bridges and chromosome fragments in anaphase/telophase I and anaphase/telophase II, as well as micronuclei in tetrads. Moreover, atypical tetrads containing three or five cells were observed. A highly increased frequency of all chromosome aberrations during meiosis have been observed in the dmc1.c mutants compared to parental variety. The results indicated that DMC1 is required for the DSB repair, crossing-over and proper chromosome disjunction during meiosis in barley.
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Affiliation(s)
- Miriam Szurman-Zubrzycka
- Department of Genetics, Faculty of Biology and Environment Protection, The University of Silesia in Katowice, Katowice, Poland
| | - Brygida Baran
- Department of Genetics, Faculty of Biology and Environment Protection, The University of Silesia in Katowice, Katowice, Poland
| | | | - Jolanta Kwaśniewska
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environment Protection, The University of Silesia in Katowice, Katowice, Poland
| | - Iwona Szarejko
- Department of Genetics, Faculty of Biology and Environment Protection, The University of Silesia in Katowice, Katowice, Poland
| | - Damian Gruszka
- Department of Genetics, Faculty of Biology and Environment Protection, The University of Silesia in Katowice, Katowice, Poland
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29
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Abstract
TILLING (Targeting Induced Local Lesions IN Genomes), a popular reverse genetics approach in barley research, combines plant mutagenesis with efficient mutation detection for studying biological function of a specific gene. The high mutation frequency within a TILLING population principally enables the identification of induced variations in (almost) all genes of a given species (more precisely a given genotype of a species) of interest, which can be tested for their functional impact on morphological and/or physiological characteristics of the plant. Several TILLING populations induced by chemical mutagenesis were established for barley (Talame et al., Plant Biotechnol J 6:477-485, 2008; Gottwald et al., BMC Res Notes 2:258, 2009; Caldwell et al. Plant J 40:143-150, 2004) and showed the possibility for adapting protocols to develop further populations. This chapter describes a chemical mutagenesis protocol for barley seeds and two independent procedures for efficient single nucleotide polymorphism (SNP) detection in a large number of mutagenized plants either by slab-gel- or capillary gel-based electrophoreses on the LI-COR 4300 DNA Analyzer and the AdvanCE FS96 instruments, respectively.
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Affiliation(s)
- Matthias Jost
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Miriam Szurman-Zubrzycka
- Faculty of Biology and Environmental Protection, Department of Genetics, University of Silesia, Katowice, Poland
| | - Katarzyna Gajek
- Faculty of Biology and Environmental Protection, Department of Genetics, University of Silesia, Katowice, Poland
| | - Iwona Szarejko
- Faculty of Biology and Environmental Protection, Department of Genetics, University of Silesia, Katowice, Poland
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany.
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30
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Bettgenhaeuser J, Krattinger SG. Rapid gene cloning in cereals. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:699-711. [PMID: 30341495 DOI: 10.1007/s00122-018-3210-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/12/2018] [Indexed: 05/03/2023]
Abstract
The large and complex genomes of many cereals hindered cloning efforts in the past. Advances in genomics now allow the rapid cloning of genes from humanity's most valuable crops. The past two decades were characterized by a genomics revolution that entailed profound changes to crop research, plant breeding, and agriculture. Today, high-quality reference sequences are available for all major cereal crop species. Large resequencing and pan-genome projects start to reveal a more comprehensive picture of the genetic makeup and the diversity among domesticated cereals and their wild relatives. These technological advancements will have a dramatic effect on dissecting genotype-phenotype associations and on gene cloning. In this review, we will highlight the status of the genomic resources available for various cereal crops and we will discuss their implications for gene cloning. A particular focus will be given to the cereal species barley and wheat, which are characterized by very large and complex genomes that have been inaccessible to rapid gene cloning until recently. With the advancements in genomics and the development of several rapid gene-cloning methods, it has now become feasible to tackle the cloning of most agriculturally important genes, even in wheat and barley.
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Affiliation(s)
- Jan Bettgenhaeuser
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Simon G Krattinger
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
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31
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Rawat N, Schoen A, Singh L, Mahlandt A, Wilson DL, Liu S, Lin G, Gill BS, Tiwari VK. TILL-D: An Aegilops tauschii TILLING Resource for Wheat Improvement. FRONTIERS IN PLANT SCIENCE 2018; 9:1665. [PMID: 30487809 PMCID: PMC6246738 DOI: 10.3389/fpls.2018.01665] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 10/26/2018] [Indexed: 05/28/2023]
Abstract
Aegilops tauschii (2n = 2x = 14, genome DD), also known as Tausch's goatgrass, is the D genome donor of bread or hexaploid wheat Triticum aestivum (2n = 2x = 42, AABBDD genome). It is a rich reservoir of useful genes for biotic and abiotic stress tolerance for wheat improvement. We developed a TILLING (Targeting Induced Local Lesions In Genomes) resource for Ae. tauschii for discovery and validation of useful genes in the D genome of wheat. The population, referred to as TILL-D, was developed with ethyl methanesulfonate (EMS) mutagen. The survival rate in M1 generation was 73%, out of which 22% plants were sterile. In the M2 generation 25% of the planted seeds showed phenotypic mutations such as albinos, chlorinas, no germination, variegated, sterile and partially fertile events, and 2,656 produced fertile M2 plants. The waxy gene was used to calculate the mutation frequency (1/70 kb) of the developed population, which was found to be higher than known mutation frequencies for diploid plants (1/89-1/1000 kb), but lower than that for a polyploid species (1/24-1/51 kb). The TILL-D resource, together with the newly published Ae. tauschii reference genome sequence, will facilitate gene discoveries and validations of agronomically important traits and their eventual fine transfer in bread wheat.
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Affiliation(s)
- Nidhi Rawat
- Plant Science and Landscape Architecture Department, University of Maryland, College Park, College Park, MD, United States
| | - Adam Schoen
- Plant Science and Landscape Architecture Department, University of Maryland, College Park, College Park, MD, United States
| | - Lovepreet Singh
- Plant Science and Landscape Architecture Department, University of Maryland, College Park, College Park, MD, United States
| | - Alexander Mahlandt
- Plant Science and Landscape Architecture Department, University of Maryland, College Park, College Park, MD, United States
| | - Duane L. Wilson
- Plant Pathology Department, Kansas State University, Manhattan, KS, United States
| | - Sanzhen Liu
- Plant Pathology Department, Kansas State University, Manhattan, KS, United States
| | - Guifang Lin
- Plant Pathology Department, Kansas State University, Manhattan, KS, United States
| | - Bikram S. Gill
- Plant Pathology Department, Kansas State University, Manhattan, KS, United States
| | - Vijay K. Tiwari
- Plant Pathology Department, Kansas State University, Manhattan, KS, United States
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Hussain M, Iqbal MA, Till BJ, Rahman MU. Identification of induced mutations in hexaploid wheat genome using exome capture assay. PLoS One 2018; 13:e0201918. [PMID: 30102729 PMCID: PMC6089429 DOI: 10.1371/journal.pone.0201918] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 07/24/2018] [Indexed: 12/02/2022] Open
Abstract
Wheat is a staple food crop of many countries. Improving resilience to biotic and abiotic stresses remain key breeding targets. Among these, rust diseases are the most detrimental in terms of depressing wheat production. In the present study, chemical mutagenesis was used to induce mutations in the wheat variety NN-Gandum-1. This cultivar is moderately resistant to leaf and yellow rust. The aim of mutagenesis was to improve resistance to the disease as well as to study function of genes conferring resistance to the disease. In the present investigation, a 0.8% EMS dose was found optimum for supporting 45-55% germination of NN-Gandum-1. A total of 3,634 M2 fertile plants were produced from each of the M1 plant. Out of these, 33 (0.91%) and 20 plants (0.55%) showed absolute resistance to leaf and yellow rust, respectively. While 126 (3.46%) and 127 plants (3.49%) exhibited high susceptibility to the leaf and yellow rust, respectively. In the M4 generation, a total of 11 M4 lines (nine absolute resistant and two highly susceptible) and one wild type were selected for NGS-based exome capture assay. A total of 104,779 SNPs were identified that were randomly distributed throughout the wheat sub genomes (A, B and D). Induced mutations in intronic sequences predominated. The highest total number of SNPs detected in this assay were mapped to chr.2B (14,273 SNPs), which contains the highest number of targeted base pairs in the assay. The average mutation density across all regions interrogated was estimated to be one mutation per 20.91 Mb. The highest mutation frequency was found in chr.2D (1/11.7 kb) and the lowest in chr.7D (1/353.4 kb). Out of the detected mutations, 101 SNPs were filtered using analysis criteria aimed to enrich for mutations that may affect gene function. Out of these, one putative SNP detected in Lr21 were selected for further analysis. The SNP identified in chimeric allele (Lr21) of a resistant mutant (N1-252) was located in a NBS domain of chr.1BS at 3.4 Mb position. Through computational analysis, it was demonstrated that this identified SNP causes a substitution of glutamic acid with alanine, resulting in a predicted altered protein structure. This mutation, therefore, is a candidate for contributing to the resistance phenotype in the mutant line. Based on this work, we conclude that the wheat mutant resource developed is useful as a source of novel genetic variation for forward-genetic screens and also as a useful tool for gaining insights into the important biological circuits of different traits of complex genomes like wheat.
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Affiliation(s)
- Momina Hussain
- Plant Genomics & Mol. Breeding Lab, National Institute for Biotechnology & Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Muhammad Atif Iqbal
- Plant Genomics & Mol. Breeding Lab, National Institute for Biotechnology & Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Bradley J. Till
- University of Vienna, Department fürChromosomenbiologie, Vienna, Austria
| | - Mehboob-ur- Rahman
- Plant Genomics & Mol. Breeding Lab, National Institute for Biotechnology & Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
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Szurman-Zubrzycka ME, Zbieszczyk J, Marzec M, Jelonek J, Chmielewska B, Kurowska MM, Krok M, Daszkowska-Golec A, Guzy-Wrobelska J, Gruszka D, Gajecka M, Gajewska P, Stolarek M, Tylec P, Sega P, Lip S, Kudełko M, Lorek M, Gorniak-Walas M, Malolepszy A, Podsiadlo N, Szyrajew KP, Keisa A, Mbambo Z, Todorowska E, Gaj M, Nita Z, Orlowska-Job W, Maluszynski M, Szarejko I. HorTILLUS-A Rich and Renewable Source of Induced Mutations for Forward/Reverse Genetics and Pre-breeding Programs in Barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2018; 9:216. [PMID: 29515615 PMCID: PMC5826354 DOI: 10.3389/fpls.2018.00216] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 02/05/2018] [Indexed: 05/23/2023]
Abstract
TILLING (Targeting Induced Local Lesions IN Genomes) is a strategy used for functional analysis of genes that combines the classical mutagenesis and a rapid, high-throughput identification of mutations within a gene of interest. TILLING has been initially developed as a discovery platform for functional genomics, but soon it has become a valuable tool in development of desired alleles for crop breeding, alternative to transgenic approach. Here we present the HorTILLUS ( Hordeum-TILLING-University of Silesia) population created for spring barley cultivar "Sebastian" after double-treatment of seeds with two chemical mutagens: sodium azide (NaN3) and N-methyl-N-nitrosourea (MNU). The population comprises more than 9,600 M2 plants from which DNA was isolated, seeds harvested, vacuum-packed, and deposited in seed bank. M3 progeny of 3,481 M2 individuals was grown in the field and phenotyped. The screening for mutations was performed for 32 genes related to different aspects of plant growth and development. For each gene fragment, 3,072-6,912 M2 plants were used for mutation identification using LI-COR sequencer. In total, 382 mutations were found in 182.2 Mb screened. The average mutation density in the HorTILLUS, estimated as 1 mutation per 477 kb, is among the highest mutation densities reported for barley. The majority of mutations were G/C to A/T transitions, however about 8% transversions were also detected. Sixty-one percent of mutations found in coding regions were missense, 37.5% silent and 1.1% nonsense. In each gene, the missense mutations with a potential effect on protein function were identified. The HorTILLUS platform is the largest of the TILLING populations reported for barley and best characterized. The population proved to be a useful tool, both in functional genomic studies and in forward selection of barley mutants with required phenotypic changes. We are constantly renewing the HorTILLUS population, which makes it a permanent source of new mutations. We offer the usage of this valuable resource to the interested barley researchers on cooperative basis.
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Affiliation(s)
- Miriam E. Szurman-Zubrzycka
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Justyna Zbieszczyk
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Marek Marzec
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Janusz Jelonek
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Beata Chmielewska
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Marzena M. Kurowska
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Milena Krok
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Agata Daszkowska-Golec
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Justyna Guzy-Wrobelska
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Damian Gruszka
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Monika Gajecka
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Patrycja Gajewska
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Magdalena Stolarek
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Piotr Tylec
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Paweł Sega
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Sabina Lip
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Monika Kudełko
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Magdalena Lorek
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Małgorzata Gorniak-Walas
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Anna Malolepszy
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Nina Podsiadlo
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Katarzyna P. Szyrajew
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Anete Keisa
- Department of Microbiology and Biotechnology, Faculty of Biology, University of Latvia, Riga, Latvia
| | - Zodwa Mbambo
- Biosciences, Council for Scientific and Industrial Research, Pretoria, South Africa
| | | | - Marek Gaj
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Zygmunt Nita
- Seed Company Plant Breeding Strzelce Ltd., Plant Breeding and Acclimatization Institute, Błonie, Poland
| | - Wanda Orlowska-Job
- Seed Company Plant Breeding Strzelce Ltd., Plant Breeding and Acclimatization Institute, Błonie, Poland
| | - Miroslaw Maluszynski
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Iwona Szarejko
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
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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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Gupta P, Reddaiah B, Salava H, Upadhyaya P, Tyagi K, Sarma S, Datta S, Malhotra B, Thomas S, Sunkum A, Devulapalli S, Till BJ, Sreelakshmi Y, Sharma R. Next-generation sequencing (NGS)-based identification of induced mutations in a doubly mutagenized tomato (Solanum lycopersicum) population. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:495-508. [PMID: 28779536 DOI: 10.1111/tpj.13654] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/25/2017] [Accepted: 07/26/2017] [Indexed: 05/21/2023]
Abstract
The identification of mutations in targeted genes has been significantly simplified by the advent of TILLING (Targeting Induced Local Lesions In Genomes), speeding up the functional genomic analysis of animals and plants. Next-generation sequencing (NGS) is gradually replacing classical TILLING for mutation detection, as it allows the analysis of a large number of amplicons in short durations. The NGS approach was used to identify mutations in a population of Solanum lycopersicum (tomato) that was doubly mutagenized by ethylmethane sulphonate (EMS). Twenty-five genes belonging to carotenoids and folate metabolism were PCR-amplified and screened to identify potentially beneficial alleles. To augment efficiency, the 600-bp amplicons were directly sequenced in a non-overlapping manner in Illumina MiSeq, obviating the need for a fragmentation step before library preparation. A comparison of the different pooling depths revealed that heterozygous mutations could be identified up to 128-fold pooling. An evaluation of six different software programs (camba, crisp, gatk unified genotyper, lofreq, snver and vipr) revealed that no software program was robust enough to predict mutations with high fidelity. Among these, crisp and camba predicted mutations with lower false discovery rates. The false positives were largely eliminated by considering only mutations commonly predicted by two different software programs. The screening of 23.47 Mb of tomato genome yielded 75 predicted mutations, 64 of which were confirmed by Sanger sequencing with an average mutation density of 1/367 Kb. Our results indicate that NGS combined with multiple variant detection tools can reduce false positives and significantly speed up the mutation discovery rate.
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Affiliation(s)
- Prateek Gupta
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Bodanapu Reddaiah
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Hymavathi Salava
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Pallawi Upadhyaya
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Kamal Tyagi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Supriya Sarma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Sneha Datta
- Plant Breeding and Genetics Laboratory, IAEA Seibersdorf Laboratories, Reaktorstrasse 1, Seibersdorf, Austria
| | - Bharti Malhotra
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Sherinmol Thomas
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Anusha Sunkum
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Sameera Devulapalli
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Bradley John Till
- Plant Breeding and Genetics Laboratory, IAEA Seibersdorf Laboratories, Reaktorstrasse 1, Seibersdorf, Austria
| | - 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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Dwivedi SL, Scheben A, Edwards D, Spillane C, Ortiz R. Assessing and Exploiting Functional Diversity in Germplasm Pools to Enhance Abiotic Stress Adaptation and Yield in Cereals and Food Legumes. FRONTIERS IN PLANT SCIENCE 2017; 8:1461. [PMID: 28900432 PMCID: PMC5581882 DOI: 10.3389/fpls.2017.01461] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/07/2017] [Indexed: 05/03/2023]
Abstract
There is a need to accelerate crop improvement by introducing alleles conferring host plant resistance, abiotic stress adaptation, and high yield potential. Elite cultivars, landraces and wild relatives harbor useful genetic variation that needs to be more easily utilized in plant breeding. We review genome-wide approaches for assessing and identifying alleles associated with desirable agronomic traits in diverse germplasm pools of cereals and legumes. Major quantitative trait loci and single nucleotide polymorphisms (SNPs) associated with desirable agronomic traits have been deployed to enhance crop productivity and resilience. These include alleles associated with variation conferring enhanced photoperiod and flowering traits. Genetic variants in the florigen pathway can provide both environmental flexibility and improved yields. SNPs associated with length of growing season and tolerance to abiotic stresses (precipitation, high temperature) are valuable resources for accelerating breeding for drought-prone environments. Both genomic selection and genome editing can also harness allelic diversity and increase productivity by improving multiple traits, including phenology, plant architecture, yield potential and adaptation to abiotic stresses. Discovering rare alleles and useful haplotypes also provides opportunities to enhance abiotic stress adaptation, while epigenetic variation has potential to enhance abiotic stress adaptation and productivity in crops. By reviewing current knowledge on specific traits and their genetic basis, we highlight recent developments in the understanding of crop functional diversity and identify potential candidate genes for future use. The storage and integration of genetic, genomic and phenotypic information will play an important role in ensuring broad and rapid application of novel genetic discoveries by the plant breeding community. Exploiting alleles for yield-related traits would allow improvement of selection efficiency and overall genetic gain of multigenic traits. An integrated approach involving multiple stakeholders specializing in management and utilization of genetic resources, crop breeding, molecular biology and genomics, agronomy, stress tolerance, and reproductive/seed biology will help to address the global challenge of ensuring food security in the face of growing resource demands and climate change induced stresses.
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Affiliation(s)
| | - Armin Scheben
- School of Biological Sciences, Institute of Agriculture, University of Western Australia, PerthWA, Australia
| | - David Edwards
- School of Biological Sciences, Institute of Agriculture, University of Western Australia, PerthWA, Australia
| | - Charles Spillane
- Plant and AgriBiosciences Research Centre, Ryan Institute, National University of Ireland GalwayGalway, Ireland
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural SciencesAlnarp, Sweden
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Zhang K, Raboanatahiry N, Zhu B, Li M. Progress in Genome Editing Technology and Its Application in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:177. [PMID: 28261237 PMCID: PMC5306361 DOI: 10.3389/fpls.2017.00177] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/27/2017] [Indexed: 05/19/2023]
Abstract
Genome editing technology (GET) is a versatile approach that has progressed rapidly as a mechanism to alter the genotype and phenotype of organisms. However, conventional genome modification using GET cannot satisfy current demand for high-efficiency and site-directed mutagenesis, retrofitting of artificial nucleases has developed into a new avenue within this field. Based on mechanisms to recognize target genes, newly-developed GETs can generally be subdivided into three cleavage systems, protein-dependent DNA cleavage systems (i.e., zinc-finger nucleases, ZFN, and transcription activator-like effector nucleases, TALEN), RNA-dependent DNA cleavage systems (i.e., clustered regularly interspaced short palindromic repeats-CRISPR associated proteins, CRISPR-Cas9, CRISPR-Cpf1, and CRISPR-C2c1), and RNA-dependent RNA cleavage systems (i.e., RNA interference, RNAi, and CRISPR-C2c2). All these techniques can lead to double-stranded (DSB) or single-stranded breaks (SSB), and result in either random mutations via non-homologous end-joining (NHEJ) or targeted mutation via homologous recombination (HR). Thus, site-directed mutagenesis can be induced via targeted gene knock-out, knock-in, or replacement to modify specific characteristics including morphology-modification, resistance-enhancement, and physiological mechanism-improvement along with plant growth and development. In this paper, an non-comprehensive review on the development of different GETs as applied to plants is presented.
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Affiliation(s)
- Kai Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
| | - Nadia Raboanatahiry
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Bin Zhu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
- *Correspondence: Maoteng Li
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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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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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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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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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Singh AK, Singh R, Subramani R, Kumar R, Wankhede DP. Molecular Approaches to Understand Nutritional Potential of Coarse Cereals. Curr Genomics 2016; 17:177-92. [PMID: 27252585 PMCID: PMC4869005 DOI: 10.2174/1389202917666160202215308] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 06/26/2015] [Accepted: 06/29/2015] [Indexed: 01/01/2023] Open
Abstract
Coarse grains are important group of crops that constitutes staple food for large population residing primarily in the arid and semi-arid regions of the world. Coarse grains are designated as nutri-cereals as they are rich in essential amino acids, minerals and vitamins. In spite of having several nutritional virtues in coarse grain as mentioned above, there is still scope for improvement in quality parameters such as cooking qualities, modulation of nutritional constituents and reduction or elimination of anti-nutritional factors. Besides its use in traditional cooking, coarse grains have been used mainly in the weaning food preparation and other malted food production. Improvement in quality parameters will certainly increase consumer's preference for coarse grains and increase their demand. The overall genetic gain in quality traits of economic importance in the cultivated varieties will enhance their industrial value and simultaneously increase income of farmers growing these varieties. The urgent step for improvement of quality traits in coarse grains requires a detailed understanding of molecular mechanisms responsible for varied level of different nutritional contents in different genotypes of these crops. In this review we have discussed the progresses made in understanding of coarse grain biology with various omics tool coupled with modern breeding approaches and the current status with regard to our effort towards dissecting traits related to improvement of quality and nutritional constituents of grains.
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Affiliation(s)
- Amit Kumar Singh
- Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Rakesh Singh
- Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Rajkumar Subramani
- Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Rajesh Kumar
- Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
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Borrill P, Adamski N, Uauy C. Genomics as the key to unlocking the polyploid potential of wheat. THE NEW PHYTOLOGIST 2015; 208:1008-22. [PMID: 26108556 DOI: 10.1111/nph.13533] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 05/31/2015] [Indexed: 05/19/2023]
Abstract
Polyploidy has played a central role in plant genome evolution and in the formation of new species such as tetraploid pasta wheat and hexaploid bread wheat. Until recently, the high sequence conservation between homoeologous genes, together with the large genome size of polyploid wheat, had hindered genomic analyses in this important crop species. In the past 5 yr, however, the advent of next-generation sequencing has radically changed the wheat genomics landscape. Here, we review a series of advances in genomic resources and tools for functional genomics that are shifting the paradigm of what is possible in wheat molecular genetics and breeding. We discuss how understanding the relationship between homoeologues can inform approaches to modulate the response of quantitative traits in polyploid wheat; we also argue that functional redundancy has 'locked up' a wide range of phenotypic variation in wheat. We explore how genomics provides key tools to inform targeted manipulation of multiple homoeologues, thereby allowing researchers and plant breeders to unlock the full polyploid potential of wheat.
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Affiliation(s)
| | - Nikolai Adamski
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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Pan L, Shah AN, Phelps IG, Doherty D, Johnson EA, Moens CB. Rapid identification and recovery of ENU-induced mutations with next-generation sequencing and Paired-End Low-Error analysis. BMC Genomics 2015; 16:83. [PMID: 25886285 PMCID: PMC4457992 DOI: 10.1186/s12864-015-1263-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 01/22/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Targeting Induced Local Lesions IN Genomes (TILLING) is a reverse genetics approach to directly identify point mutations in specific genes of interest in genomic DNA from a large chemically mutagenized population. Classical TILLING processes, based on enzymatic detection of mutations in heteroduplex PCR amplicons, are slow and labor intensive. RESULTS Here we describe a new TILLING strategy in zebrafish using direct next generation sequencing (NGS) of 250 bp amplicons followed by Paired-End Low-Error (PELE) sequence analysis. By pooling a genomic DNA library made from over 9,000 N-ethyl-N-nitrosourea (ENU) mutagenized F1 fish into 32 equal pools of 288 fish, each with a unique Illumina barcode, we reduce the complexity of the template to a level at which we can detect mutations that occur in a single heterozygous fish in the entire library. MiSeq sequencing generates 250 base-pair overlapping paired-end reads, and PELE analysis aligns the overlapping sequences to each other and filters out any imperfect matches, thereby eliminating variants introduced during the sequencing process. We find that this filtering step reduces the number of false positive calls 50-fold without loss of true variant calls. After PELE we were able to validate 61.5% of the mutant calls that occurred at a frequency between 1 mutant call:100 wildtype calls and 1 mutant call:1000 wildtype calls in a pool of 288 fish. We then use high-resolution melt analysis to identify the single heterozygous mutation carrier in the 288-fish pool in which the mutation was identified. CONCLUSIONS Using this NGS-TILLING protocol we validated 28 nonsense or splice site mutations in 20 genes, at a two-fold higher efficiency than using traditional Cel1 screening. We conclude that this approach significantly increases screening efficiency and accuracy at reduced cost and can be applied in a wide range of organisms.
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Affiliation(s)
- Luyuan Pan
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, USA. .,Current Address: China Zebrafish Resource Center, Institute of Hydrobiology CAS, 430072, Wuhan, China.
| | - Arish N Shah
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, USA.
| | - Ian G Phelps
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, USA.
| | - Dan Doherty
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, USA.
| | - Eric A Johnson
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA.
| | - Cecilia B Moens
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, USA. .,Biology Department, University of Washington, Seattle, WA, USA.
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Schnell J, Steele M, Bean J, Neuspiel M, Girard C, Dormann N, Pearson C, Savoie A, Bourbonnière L, Macdonald P. A comparative analysis of insertional effects in genetically engineered plants: considerations for pre-market assessments. Transgenic Res 2014; 24:1-17. [PMID: 25344849 PMCID: PMC4274372 DOI: 10.1007/s11248-014-9843-7] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 10/16/2014] [Indexed: 01/20/2023]
Abstract
During genetic engineering, DNA is inserted into a plant’s genome, and such insertions are often accompanied by the insertion of additional DNA, deletions and/or rearrangements. These genetic changes are collectively known as insertional effects, and they have the potential to give rise to unintended traits in plants. In addition, there are many other genetic changes that occur in plants both spontaneously and as a result of conventional breeding practices. Genetic changes similar to insertional effects occur in plants, namely as a result of the movement of transposable elements, the repair of double-strand breaks by non-homologous end-joining, and the intracellular transfer of organelle DNA. Based on this similarity, insertional effects should present a similar level of risk as these other genetic changes in plants, and it is within the context of these genetic changes that insertional effects must be considered. Increased familiarity with genetic engineering techniques and advances in molecular analysis techniques have provided us with a greater understanding of the nature and impact of genetic changes in plants, and this can be used to refine pre-market assessments of genetically engineered plants and food and feeds derived from genetically engineered plants.
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Affiliation(s)
- Jaimie Schnell
- Plant and Biotechnology Risk Assessment Unit, Canadian Food Inspection Agency, 1400 Merivale Road, Ottawa, ON, K1A 0Y9, Canada,
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Sparla F, Falini G, Botticella E, Pirone C, Talamè V, Bovina R, Salvi S, Tuberosa R, Sestili F, Trost P. New starch phenotypes produced by TILLING in barley. PLoS One 2014; 9:e107779. [PMID: 25271438 PMCID: PMC4182681 DOI: 10.1371/journal.pone.0107779] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 08/15/2014] [Indexed: 01/08/2023] Open
Abstract
Barley grain starch is formed by amylose and amylopectin in a 1∶3 ratio, and is packed into granules of different dimensions. The distribution of granule dimension is bimodal, with a majority of small spherical B-granules and a smaller amount of large discoidal A-granules containing the majority of the starch. Starch granules are semi-crystalline structures with characteristic X-ray diffraction patterns. Distinct features of starch granules are controlled by different enzymes and are relevant for nutritional value or industrial applications. Here, the Targeting-Induced Local Lesions IN Genomes (TILLING) approach was applied on the barley TILLMore TILLING population to identify 29 new alleles in five genes related to starch metabolism known to be expressed in the endosperm during grain filling: BMY1 (Beta-amylase 1), GBSSI (Granule Bound Starch Synthase I), LDA1 (Limit Dextrinase 1), SSI (Starch Synthase I), SSIIa (Starch Synthase IIa). Reserve starch of nine M3 mutant lines carrying missense or nonsense mutations was analysed for granule size, crystallinity and amylose/amylopectin content. Seven mutant lines presented starches with different features in respect to the wild-type: (i) a mutant line with a missense mutation in GBSSI showed a 4-fold reduced amylose/amylopectin ratio; (ii) a missense mutations in SSI resulted in 2-fold increase in A:B granule ratio; (iii) a nonsense mutation in SSIIa was associated with shrunken seeds with a 2-fold increased amylose/amylopectin ratio and different type of crystal packing in the granule; (iv) the remaining four missense mutations suggested a role of LDA1 in granule initiation, and of SSIIa in determining the size of A-granules. We demonstrate the feasibility of the TILLING approach to identify new alleles in genes related to starch metabolism in barley. Based on their novel physicochemical properties, some of the identified new mutations may have nutritional and/or industrial applications.
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Affiliation(s)
- Francesca Sparla
- Department of Pharmacy and Biotechnology FABIT, University of Bologna, Bologna, Italy
| | - Giuseppe Falini
- Department of Chemistry “G. Ciamician”, University of Bologna, Bologna, Italy
| | - Ermelinda Botticella
- Department of Agriculture, Forestry, Nature & Energy, University of Tuscia, Viterbo, Italy
| | - Claudia Pirone
- Department of Pharmacy and Biotechnology FABIT, University of Bologna, Bologna, Italy
| | - Valentina Talamè
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Riccardo Bovina
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Silvio Salvi
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Roberto Tuberosa
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Francesco Sestili
- Department of Agriculture, Forestry, Nature & Energy, University of Tuscia, Viterbo, Italy
| | - Paolo Trost
- Department of Pharmacy and Biotechnology FABIT, University of Bologna, Bologna, Italy
- * E-mail:
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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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Abstract
To confer resistance against pathogens and pests in plants, typically dominant resistance genes are deployed. However, because resistance is based on recognition of a single pathogen-derived molecular pattern, these narrow-spectrum genes are usually readily overcome. Disease arises from a compatible interaction between plant and pathogen. Hence, altering a plant gene that critically facilitates compatibility could provide a more broad-spectrum and durable type of resistance. Here, such susceptibility (S) genes are reviewed with a focus on the mechanisms underlying loss of compatibility. We distinguish three groups of S genes acting during different stages of infection: early pathogen establishment, modulation of host defenses, and pathogen sustenance. The many examples reviewed here show that S genes have the potential to be used in resistance breeding. However, because S genes have a function other than being a compatibility factor for the pathogen, the side effects caused by their mutation demands a one-by-one assessment of their usefulness for application.
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Induced Genetic Variation, TILLING and NGS-Based Cloning. BIOTECHNOLOGICAL APPROACHES TO BARLEY IMPROVEMENT 2014. [DOI: 10.1007/978-3-662-44406-1_15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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