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Stovicek V, Lengeler KB, Wendt T, Rasmussen M, Katz M, Förster J. Modifying flavor profiles of Saccharomyces spp. for industrial brewing using FIND-IT, a non-GMO approach for metabolic engineering of yeast. N Biotechnol 2024; 82:92-106. [PMID: 38788897 DOI: 10.1016/j.nbt.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 05/13/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
Abstract
Species of Saccharomyces genus have played an irreplaceable role in alcoholic beverage and baking industry for centuries. S. cerevisiae has also become an organism of choice for industrial production of alcohol and other valuable chemicals and a model organism shaping the rise of modern genetics and genomics in the past few decades. Today´s brewing industry faces challenges of decreasing consumption of traditional beer styles and increasing consumer demand for new styles, flavors and aromas. The number of currently used brewer's strains and their genetic diversity is yet limited and implementation of more genetic and phenotypic variation is seen as a solution to cope with the market challenges. This requires modification of current production strains or introduction of novel strains from other settings, e.g. industrial or wild habitats into the brewing industry. Due to legal regulation in many countries and negative customer perception of GMO organisms, the production of food and beverages requires non-GMO production organisms, whose development can be difficult and time-consuming. Here, we apply FIND-IT (Fast Identification of Nucleotide variants by DigITal PCR), an ultrafast genome-mining method, for isolation of novel yeast variants with varying flavor profiles. The FIND-IT method uses combination of random mutagenesis, droplet digital PCR with probes that target a specific desired mutation and a sub-isolation of the mutant clone. Such an approach allows the targeted identification and isolation of specific mutant strains with eliminated production of certain flavor and off-flavors and/or changes in the strain metabolism. We demonstrate that the technology is useful for the identification of loss-of function or gain of function mutations in unrelated industrial and wild strains differing in ploidy. Where no other phenotypic selection exists, this technology serves together with standard breeding techniques as a modern tool facilitating a modification of (brewer's) yeast strains leading to diversification of the product portfolio.
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Affiliation(s)
- Vratislav Stovicek
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark
| | - Klaus B Lengeler
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark
| | - Toni Wendt
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark; Traitomic A/S, J.C. Jacobsens Gade 1, DK-1799 Copenhagen V, Denmark
| | - Magnus Rasmussen
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark
| | - Michael Katz
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark.
| | - Jochen Förster
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark; DTU Biosustain, The Novo Nordisk Foundation Center for Biosustainability, Søltofts Plads, Building 220, 2800 Kongens Lyngby, Denmark
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2
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Swamidatta SH, Lichman BR. Beyond co-expression: pathway discovery for plant pharmaceuticals. Curr Opin Biotechnol 2024; 88:103147. [PMID: 38833915 DOI: 10.1016/j.copbio.2024.103147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 06/06/2024]
Abstract
Plant natural products have been an important source of medicinal molecules since ancient times. To gain access to the whole diversity of these molecules for pharmaceutical applications, it is important to understand their biosynthetic origins. Whilst co-expression is a reliable tool for identifying gene candidates, a variety of complementary methods can aid in screening or refining candidate selection. Here, we review recently employed plant biosynthetic pathway discovery approaches, and highlight future directions in the field.
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Affiliation(s)
- Sandesh H Swamidatta
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| | - Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK.
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3
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Jørgensen ME, Houston K, Jørgensen HJL, Thomsen HC, Tekaat L, Krogh CT, Mellor SB, Braune KB, Damm ML, Pedas PR, Voss C, Rasmussen MW, Nielsen K, Skadhauge B, Motawia MS, Møller BL, Dockter C, Sørensen M. Disentangling hydroxynitrile glucoside biosynthesis in a barley (Hordeum vulgare) metabolon provides access to elite malting barleys for ethyl carbamate-free whisky production. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38652034 DOI: 10.1111/tpj.16768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/26/2024] [Accepted: 04/02/2024] [Indexed: 04/25/2024]
Abstract
Barley produces several specialized metabolites, including five α-, β-, and γ-hydroxynitrile glucosides (HNGs). In malting barley, presence of the α-HNG epiheterodendrin gives rise to undesired formation of ethyl carbamate in the beverage production, especially after distilling. Metabolite-GWAS identified QTLs and underlying gene candidates possibly involved in the control of the relative and absolute content of HNGs, including an undescribed MATE transporter. By screening 325 genetically diverse barley accessions, we discovered three H. vulgare ssp. spontaneum (wild barley) lines with drastic changes in the relative ratios of the five HNGs. Knock-out (KO)-lines, isolated from the barley FIND-IT resource and each lacking one of the functional HNG biosynthetic genes (CYP79A12, CYP71C103, CYP71C113, CYP71U5, UGT85F22 and UGT85F23) showed unprecedented changes in HNG ratios enabling assignment of specific and mutually dependent catalytic functions to the biosynthetic enzymes involved. The highly similar relative ratios between the five HNGs found across wild and domesticated barley accessions indicate assembly of the HNG biosynthetic enzymes in a metabolon, the functional output of which was reconfigured in the absence of a single protein component. The absence or altered ratios of the five HNGs in the KO-lines did not change susceptibility to the fungal phytopathogen Pyrenophora teres causing net blotch. The study provides a deeper understanding of the organization of HNG biosynthesis in barley and identifies a novel, single gene HNG-0 line in an elite spring barley background for direct use in breeding of malting barley, eliminating HNGs as a source of ethyl carbamate formation in whisky production.
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Affiliation(s)
- Morten E Jørgensen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799, Copenhagen V, Denmark
| | - Kelly Houston
- Cell and Molecular Sciences, James Hutton Institute, Errol Road, Invergowrie, Dundee, Scotland
| | - Hans Jørgen L Jørgensen
- Section for Plant and Soil Sciences, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Hanne C Thomsen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799, Copenhagen V, Denmark
| | - Linda Tekaat
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Camilla Timmermann Krogh
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Silas B Mellor
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | | | - Mette L Damm
- 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
| | - Cynthia Voss
- 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
| | - Birgitte Skadhauge
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799, Copenhagen V, Denmark
| | - Mohammed S Motawia
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Birger Lindberg Møller
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Christoph Dockter
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799, Copenhagen V, Denmark
| | - Mette Sørensen
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
- Novo Nordisk Pharmatech, Københavnsvej 216, 4600, Køge, Denmark
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Trinh MDL, Visintainer D, Günther J, Østerberg JT, da Fonseca RR, Fondevilla S, Moog MW, Luo G, Nørrevang AF, Crocoll C, Nielsen PV, Jacobsen SE, Wendt T, Bak S, López-Marqués RL, Palmgren M. Site-directed genotype screening for elimination of antinutritional saponins in quinoa seeds identifies TSARL1 as a master controller of saponin biosynthesis selectively in seeds. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38572508 DOI: 10.1111/pbi.14340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 04/05/2024]
Abstract
Climate change may result in a drier climate and increased salinization, threatening agricultural productivity worldwide. Quinoa (Chenopodium quinoa) produces highly nutritious seeds and tolerates abiotic stresses such as drought and high salinity, making it a promising future food source. However, the presence of antinutritional saponins in their seeds is an undesirable trait. We mapped genes controlling seed saponin content to a genomic region that includes TSARL1. We isolated desired genetic variation in this gene by producing a large mutant library of a commercial quinoa cultivar and screening the library for specific nucleotide substitutions using droplet digital PCR. We were able to rapidly isolate two independent tsarl1 mutants, which retained saponins in the leaves and roots for defence, but saponins were undetectable in the seed coat. We further could show that TSARL1 specifically controls seed saponin biosynthesis in the committed step after 2,3-oxidosqualene. Our work provides new important knowledge on the function of TSARL1 and represents a breakthrough for quinoa breeding.
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Affiliation(s)
- Mai Duy Luu Trinh
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Davide Visintainer
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jan Günther
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Rute R da Fonseca
- Section for Biodiversity, Globe Institute, University of Copenhagen, København Ø, Denmark
| | | | - Max William Moog
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Guangbin Luo
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Anton F Nørrevang
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Christoph Crocoll
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Philip V Nielsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | | | - Søren Bak
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Rosa Laura López-Marqués
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Michael Palmgren
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
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Hansson M, Youssef HM, Zakhrabekova S, Stuart D, Svensson JT, Dockter C, Stein N, Waugh R, Lundqvist U, Franckowiak J. A guide to barley mutants. Hereditas 2024; 161:11. [PMID: 38454479 PMCID: PMC10921644 DOI: 10.1186/s41065-023-00304-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 11/24/2023] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Mutants have had a fundamental impact upon scientific and applied genetics. They have paved the way for the molecular and genomic era, and most of today's crop plants are derived from breeding programs involving mutagenic treatments. RESULTS Barley (Hordeum vulgare L.) is one of the most widely grown cereals in the world and has a long history as a crop plant. Barley breeding started more than 100 years ago and large breeding programs have collected and generated a wide range of natural and induced mutants, which often were deposited in genebanks around the world. In recent years, an increased interest in genetic diversity has brought many historic mutants into focus because the collections are regarded as valuable resources for understanding the genetic control of barley biology and barley breeding. The increased interest has been fueled also by recent advances in genomic research, which provided new tools and possibilities to analyze and reveal the genetic diversity of mutant collections. CONCLUSION Since detailed knowledge about phenotypic characters of the mutants is the key to success of genetic and genomic studies, we here provide a comprehensive description of mostly morphological barley mutants. The review is closely linked to the International Database for Barley Genes and Barley Genetic Stocks ( bgs.nordgen.org ) where further details and additional images of each mutant described in this review can be found.
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Affiliation(s)
- Mats Hansson
- Department of Biology, Lund University, Sölvegatan 35, 22362, Lund, Sweden.
| | - Helmy M Youssef
- Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, Halle, 06120, Germany
| | | | - David Stuart
- Department of Biology, Lund University, Sölvegatan 35, 22362, Lund, Sweden
| | - Jan T Svensson
- Nordic Genetic Resource Center (NordGen), Växthusvägen 12, 23456, Alnarp, Sweden
| | - Christoph Dockter
- Carlsberg Research Laboratory, J. C. Jacobsens Gade 4, 1799, Copenhagen V, Denmark
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Stadt Seeland, E06466, Germany
- Center for Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- Division of Plant Sciences, University of Dundee, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- School of Agriculture Food and Wine, Waite Campus, The University of Adelaide, Urrbrae, 5064, Australia
| | - Udda Lundqvist
- Nordic Genetic Resource Center (NordGen), Växthusvägen 12, 23456, Alnarp, Sweden
| | - Jerome Franckowiak
- Department of Agronomy and Plant Genetics, University of Minnesota Twin Cities, 411 Borlaug Hall, 1991 Upper Buford Circle, St Paul, MN, 55108, USA
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Madsen CK, Brearley CA, Harholt J, Brinch-Pedersen H. Optimized barley phytase gene expression by focused FIND-IT screening for mutations in cis-acting regulatory elements. FRONTIERS IN PLANT SCIENCE 2024; 15:1372049. [PMID: 38495373 PMCID: PMC10940425 DOI: 10.3389/fpls.2024.1372049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 02/12/2024] [Indexed: 03/19/2024]
Abstract
Introduction Induced modification of plant gene expression is of both fundamental and applied importance. Cis-acting regulatory elements (CREs) are major determinants of the spatiotemporal strength of gene expression. Yet, there are few examples where induced genetic variation in predetermined CREs has been exploited to improve or investigate crop plants. Methods The digital PCR based FIND-IT technology was applied to discover barley mutants with CRE variants in the promoter of the nutritional important barley grain phytase (PAPhy_a) gene. Results and discussion Mutants with higher or lower gene expression and ultimately higher or lower mature grain phytase activity (MGPA), respectively, were discovered. Field trials and inositol phosphate profiling during germination showed that PAPhy_a does not influence agronomic performance under the trial conditions but it does shorten the lag time of phosphate mobilization during germination. Higher endogenous MGPA is an improvement of grain quality for feed use as it improves the phosphate bioavailability for monogastric animals. Moreover, as the targeted CRE motifs of the PAPhy_a promoter are shared with a range of seed expressed genes like key cereal and legume storage genes, the current results demonstrates a concept for modulating individual gene expression levels of a range of seed genes.
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Affiliation(s)
| | - Charles Alistair Brearley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Jesper Harholt
- Carlsberg Research Laboratory, J. C. Jacobsens Gade 4, Copenhagen, Denmark
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Daute M, Jack F, Walker G. The potential for Scotch Malt Whisky flavour diversification by yeast. FEMS Yeast Res 2024; 24:foae017. [PMID: 38684485 PMCID: PMC11095643 DOI: 10.1093/femsyr/foae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/13/2024] [Accepted: 04/28/2024] [Indexed: 05/02/2024] Open
Abstract
Scotch Whisky, a product of high importance to Scotland, has gained global approval for its distinctive qualities derived from the traditional production process, which is defined in law. However, ongoing research continuously enhances Scotch Whisky production and is fostering a diversification of flavour profiles. To be classified as Scotch Whisky, the final spirit needs to retain the aroma and taste of 'Scotch'. While each production step contributes significantly to whisky flavour-from malt preparation and mashing to fermentation, distillation, and maturation-the impact of yeast during fermentation is crucially important. Not only does the yeast convert the sugar to alcohol, it also produces important volatile compounds, e.g. esters and higher alcohols, that contribute to the final flavour profile of whisky. The yeast chosen for whisky fermentations can significantly influence whisky flavour, so the yeast strain employed is of high importance. This review explores the role of yeast in Scotch Whisky production and its influence on flavour diversification. Furthermore, an extensive examination of nonconventional yeasts employed in brewing and winemaking is undertaken to assess their potential suitability for adoption as Scotch Whisky yeast strains, followed by a review of methods for evaluating new yeast strains.
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Affiliation(s)
- Martina Daute
- Division of Engineering and Food Sciences, School of Applied Sciences, Abertay University, Bell St, DD1 1HG, Dundee, Scotland
- The Scotch Whisky Research Institute, Research Ave N, EH14 4AP, Edinburgh, Scotland
| | - Frances Jack
- The Scotch Whisky Research Institute, Research Ave N, EH14 4AP, Edinburgh, Scotland
| | - Graeme Walker
- Division of Engineering and Food Sciences, School of Applied Sciences, Abertay University, Bell St, DD1 1HG, Dundee, Scotland
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8
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Marshall M. How CRISPR could yield the next blockbuster crop. Nature 2024; 625:230-232. [PMID: 38195874 DOI: 10.1038/d41586-024-00015-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
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9
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Oliveira-Filho ER, Voiniciuc C, Hanson AD. Adapting enzymes to improve their functionality in plants: why and how. Biochem Soc Trans 2023; 51:1957-1966. [PMID: 37787016 PMCID: PMC10657173 DOI: 10.1042/bst20230532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/17/2023] [Accepted: 09/21/2023] [Indexed: 10/04/2023]
Abstract
Synthetic biology creates new metabolic processes and improves existing ones using engineered or natural enzymes. These enzymes are often sourced from cells that differ from those in the target plant organ with respect to, e.g. redox potential, effector levels, or proteostasis machinery. Non-native enzymes may thus need to be adapted to work well in their new plant context ('plantized') even if their specificity and kinetics in vitro are adequate. Hence there are two distinct ways in which an enzyme destined for use in plants can require improvement: In catalytic properties such as substrate and product specificity, kcat, and KM; and in general compatibility with the milieu of cells that express the enzyme. Continuous directed evolution systems can deliver both types of improvement and are so far the most broadly effective way to deliver the second type. Accordingly, in this review we provide a short account of continuous evolution methods, emphasizing the yeast OrthoRep system because of its suitability for plant applications. We then cover the down-to-earth and increasingly urgent issues of which enzymes and enzyme properties can - or cannot - be improved in theory, and which in practice are the best to target for crop improvement, i.e. those that are realistically improvable and important enough to warrant deploying continuous directed evolution. We take horticultural crops as examples because of the opportunities they present and to sharpen the focus.
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Affiliation(s)
| | - Cătălin Voiniciuc
- Horticultural Sciences Department, University of Florida, Gainesville, FL, U.S.A
| | - Andrew D. Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, U.S.A
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10
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DeHaan LR, Anderson JA, Bajgain P, Basche A, Cattani DJ, Crain J, Crews TE, David C, Duchene O, Gutknecht J, Hayes RC, Hu F, Jungers JM, Knudsen S, Kong W, Larson S, Lundquist PO, Luo G, Miller AJ, Nabukalu P, Newell MT, Olsson L, Palmgren M, Paterson AH, Picasso VD, Poland JA, Sacks EJ, Wang S, Westerbergh A. Discussion: Prioritize perennial grain development for sustainable food production and environmental benefits. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 895:164975. [PMID: 37336402 DOI: 10.1016/j.scitotenv.2023.164975] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/02/2023] [Accepted: 06/15/2023] [Indexed: 06/21/2023]
Abstract
Perennial grains have potential to contribute to ecological intensification of food production by enabling the direct harvest of human-edible crops without requiring annual cycles of disturbance and replanting. Studies of prototype perennial grains and other herbaceous perennials point to the ability of agroecosystems including these crops to protect water quality, enhance wildlife habitat, build soil quality, and sequester soil carbon. However, genetic improvement of perennial grain candidates has been hindered by limited investment due to uncertainty about whether the approach is viable. As efforts to develop perennial grain crops have expanded in past decades, critiques of the approach have arisen. With a recent report of perennial rice producing yields equivalent to those of annual rice over eight consecutive harvests, many theoretical concerns have been alleviated. Some valid questions remain over the timeline for new crop development, but we argue these may be mitigated by implementation of recent technological advances in crop breeding and genetics such as low-cost genotyping, genomic selection, and genome editing. With aggressive research investment in the development of new perennial grain crops, they can be developed and deployed to provide atmospheric greenhouse gas reductions.
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Affiliation(s)
- Lee R DeHaan
- The Land Institute, 2440 E. Water Well Rd, Salina, KS 67401, USA.
| | - James A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, Saint Paul, MN 55108, USA
| | - Prabin Bajgain
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, Saint Paul, MN 55108, USA
| | - Andrea Basche
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, 1875 N. 38th St, 279 PLSH, Lincoln, NE 68583-0915, USA
| | - Douglas J Cattani
- Department of Plant Science, University of Manitoba, 66 Dafoe Rd, Winnipeg, MB R3T 2N2, Canada
| | - Jared Crain
- Department of Plant Pathology, Kansas State University, 1712 Claflin Rd, 4024 Throckmorton PSC, Manhattan, KS 66506, USA
| | - Timothy E Crews
- The Land Institute, 2440 E. Water Well Rd, Salina, KS 67401, USA
| | - Christophe David
- ISARA, Agroecology and Environment Research Unit, 23 rue Jean Baldassini, 69364 Lyon, France
| | - Olivier Duchene
- ISARA, Agroecology and Environment Research Unit, 23 rue Jean Baldassini, 69364 Lyon, France
| | - Jessica Gutknecht
- Department of Soil, Water, and Climate, University of Minnesota, 1991 Upper Buford Circle, Saint Paul, MN 55108, USA
| | - Richard C Hayes
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Pine Gully Rd, NSW 2650, Australia
| | - Fengyi Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center of Perennial Rice Engineering and Technology in Yunnan, School of Agriculture, Yunnan University, 2 Cuihu N Rd, Wuhua District, Kunming 650106, China
| | - Jacob M Jungers
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, Saint Paul, MN 55108, USA
| | - Søren Knudsen
- Carlsberg Research Laboratory, J. C. Jacobsens Gade 4, 1799, Copenhagen, Denmark
| | | | - Steve Larson
- USDA-ARS, Forage and Range Research, 696 North 1100 East, Logan, UT 84321, USA
| | - Per-Olof Lundquist
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology in Uppsala, Swedish University of Agricultural Sciences, Box 7080, 750 07 Uppsala, Sweden
| | - Guangbin Luo
- Department of Plant and Environmental Sciences, University of Copenhagen, Denmark
| | - Allison J Miller
- Saint Louis University, Donald Danforth Plant Science Center, 975 N Warson Rd, Olivette, MO 63132, USA
| | - Pheonah Nabukalu
- NESPAL, University of Georgia, 2356 Rainwater Rd, Tifton, GA 31793, USA
| | - Matthew T Newell
- NSW Department of Primary Industries, Cowra Agricultural Research Station, 296 Binni Creek Rd, Cowra, NSW 2794, Australia
| | - Lennart Olsson
- Lund University Centre for Sustainability Studies, P.O. Box 170, SE-221 Lund, Sweden
| | - Michael Palmgren
- Department of Plant and Environmental Sciences, University of Copenhagen, Denmark
| | | | | | - Jesse A Poland
- King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | | | - Shuwen Wang
- The Land Institute, 2440 E. Water Well Rd, Salina, KS 67401, USA
| | - Anna Westerbergh
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology in Uppsala, Swedish University of Agricultural Sciences, Box 7080, 750 07 Uppsala, Sweden
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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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Huang L, Gao G, Jiang C, Guo G, He Q, Zong Y, Liu C, Yang P. Generating homozygous mutant populations of barley microspores by ethyl methanesulfonate treatment. ABIOTECH 2023; 4:202-212. [PMID: 37970468 PMCID: PMC10638298 DOI: 10.1007/s42994-023-00108-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/31/2023] [Indexed: 11/17/2023]
Abstract
Induced mutations are important for genetic research and breeding. Mutations induced by physical or chemical mutagenesis are usually heterozygous during the early generations. However, mutations must be fixed prior to phenotyping or field trials, which requires additional rounds of self-pollination. Microspore culture is an effective method to produce double-haploid (DH) plants that are fixed homozygotes. In this study, we conducted ethyl methanesulfonate (EMS)-induced mutagenesis of microspore cultures of barley (Hordeum vulgare) cultivar 'Hua30' and landrace 'HTX'. The EMS concentrations were negatively correlated with the efficiency of callus induction and the frequency of mutant plant regeneration. The two genotypes showed different regeneration efficiencies. The phenotypic variation of the regenerated M1 plants and the presence of genome-wide nucleotide mutations, revealed by whole-genome sequencing, highlight the utility of EMS-induced mutagenesis of isolated microspore cultures for developing DH mutants. Genome-wide analysis of the mutation frequency in the regenerated plants revealed that a considerable proportion of mutations resulted from microspore culture (somaclonal variation) rather than EMS-induced mutagenesis. In addition to producing a population of 1972 homozygous mutant lines that are available for future field trials, this study lays the foundation for optimizing the regeneration efficiency of DH plants and the richness of mutations (mainly by fine-tuning the mutagen dosage).
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Affiliation(s)
- Linli Huang
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106 China
| | - Guangqi Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Congcong Jiang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Guimei Guo
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106 China
| | - Qiang He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yingjie Zong
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106 China
| | - Chenghong Liu
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106 China
| | - Ping Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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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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Mancinotti D, Czepiel K, Taylor JL, Golshadi Galehshahi H, Møller LA, Jensen MK, Motawia MS, Hufnagel B, Soriano A, Yeheyis L, Kjaerulff L, Péret B, Staerk D, Wendt T, Nelson MN, Kroc M, Geu-Flores F. The causal mutation leading to sweetness in modern white lupin cultivars. SCIENCE ADVANCES 2023; 9:eadg8866. [PMID: 37540741 PMCID: PMC10403207 DOI: 10.1126/sciadv.adg8866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 07/05/2023] [Indexed: 08/06/2023]
Abstract
Lupins are high-protein crops that are rapidly gaining interest as hardy alternatives to soybean; however, they accumulate antinutritional alkaloids of the quinolizidine type (QAs). Lupin domestication was enabled by the discovery of genetic loci conferring low QA levels (sweetness), but the precise identity of the underlying genes remains uncertain. We show that pauper, the most common sweet locus in white lupin, encodes an acetyltransferase (AT) unexpectedly involved in the early QA pathway. In pauper plants, a single-nucleotide polymorphism (SNP) strongly impairs AT activity, causing pathway blockage. We corroborate our hypothesis by replicating the pauper chemotype in narrow-leafed lupin via mutagenesis. Our work adds a new dimension to QA biosynthesis and establishes the identity of a lupin sweet gene for the first time, thus facilitating lupin breeding and enabling domestication of other QA-containing legumes.
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Affiliation(s)
- Davide Mancinotti
- Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Katarzyna Czepiel
- Legume Genomics Team, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, Poznań, Poland
| | - Jemma L. Taylor
- Royal Botanic Gardens Kew, Wakehurst Place, Ardingly, West Sussex RH17 6TN, UK
| | - Hajar Golshadi Galehshahi
- Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | | | | | - Mohammed Saddik Motawia
- Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Bárbara Hufnagel
- IPSiM, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Alexandre Soriano
- IPSiM, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | | | - Louise Kjaerulff
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Benjamin Péret
- IPSiM, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Dan Staerk
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Toni Wendt
- Traitomic A/S, J.C. Jacobsens Gade 14, 1799 Copenhagen, Denmark
| | - Matthew N. Nelson
- Royal Botanic Gardens Kew, Wakehurst Place, Ardingly, West Sussex RH17 6TN, UK
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Floreat, WA 6014, Australia
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Magdalena Kroc
- Legume Genomics Team, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, Poznań, Poland
| | - Fernando Geu-Flores
- Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
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