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Dixon RA, Dickinson AJ. A century of studying plant secondary metabolism-From "what?" to "where, how, and why?". PLANT PHYSIOLOGY 2024; 195:48-66. [PMID: 38163637 PMCID: PMC11060662 DOI: 10.1093/plphys/kiad596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/15/2023] [Indexed: 01/03/2024]
Abstract
Over the past century, early advances in understanding the identity of the chemicals that collectively form a living plant have led scientists to deeper investigations exploring where these molecules localize, how they are made, and why they are synthesized in the first place. Many small molecules are specific to the plant kingdom and have been termed plant secondary metabolites, despite the fact that they can play primary and essential roles in plant structure, development, and response to the environment. The past 100 yr have witnessed elucidation of the structure, function, localization, and biosynthesis of selected plant secondary metabolites. Nevertheless, many mysteries remain about the vast diversity of chemicals produced by plants and their roles in plant biology. From early work characterizing unpurified plant extracts, to modern integration of 'omics technology to discover genes in metabolite biosynthesis and perception, research in plant (bio)chemistry has produced knowledge with substantial benefits for society, including human medicine and agricultural biotechnology. Here, we review the history of this work and offer suggestions for future areas of exploration. We also highlight some of the recently developed technologies that are leading to ongoing research advances.
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Affiliation(s)
- Richard A Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA
| | - Alexandra Jazz Dickinson
- Department of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA 92093, USA
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2
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Xu WB, Guo QH, Liu P, Dai S, Wu CA, Yang GD, Huang JG, Zhang SZ, Song JM, Zheng CC, Yan K. A long non-coding RNA functions as a competitive endogenous RNA to modulate TaNAC018 by acting as a decoy for tae-miR6206. PLANT MOLECULAR BIOLOGY 2024; 114:36. [PMID: 38598012 DOI: 10.1007/s11103-024-01448-7] [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: 09/29/2023] [Accepted: 03/27/2024] [Indexed: 04/11/2024]
Abstract
Increasing evidence indicates a strong correlation between the deposition of cuticular waxes and drought tolerance. However, the precise regulatory mechanism remains elusive. Here, we conducted a comprehensive transcriptome analysis of two wheat (Triticum aestivum) near-isogenic lines, the glaucous line G-JM38 rich in cuticular waxes and the non-glaucous line NG-JM31. We identified 85,143 protein-coding mRNAs, 4,485 lncRNAs, and 1,130 miRNAs. Using the lncRNA-miRNA-mRNA network and endogenous target mimic (eTM) prediction, we discovered that lncRNA35557 acted as an eTM for the miRNA tae-miR6206, effectively preventing tae-miR6206 from cleaving the NAC transcription factor gene TaNAC018. This lncRNA-miRNA interaction led to higher transcript abundance for TaNAC018 and enhanced drought-stress tolerance. Additionally, treatment with mannitol and abscisic acid (ABA) each influenced the levels of tae-miR6206, lncRNA35557, and TaNAC018 transcript. The ectopic expression of TaNAC018 in Arabidopsis also improved tolerance toward mannitol and ABA treatment, whereas knocking down TaNAC018 transcript levels via virus-induced gene silencing in wheat rendered seedlings more sensitive to mannitol stress. Our results indicate that lncRNA35557 functions as a competing endogenous RNA to modulate TaNAC018 expression by acting as a decoy target for tae-miR6206 in glaucous wheat, suggesting that non-coding RNA has important roles in the regulatory mechanisms responsible for wheat stress tolerance.
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Affiliation(s)
- Wei-Bo Xu
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Qian-Huan Guo
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Peng Liu
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Shuang Dai
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250100, People's Republic of China
| | - Chang-Ai Wu
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Guo-Dong Yang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Jin-Guang Huang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Shi-Zhong Zhang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Jian-Min Song
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250100, People's Republic of China.
| | - Cheng-Chao Zheng
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China.
| | - Kang Yan
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China.
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3
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Yan Y, Gagalova KK, Gerbrandt EM, Castellarin SD. Cuticular wax biosynthesis in blueberries ( Vaccinium corymbosum L.): Transcript and metabolite changes during ripening and storage affect key fruit quality traits. HORTICULTURE RESEARCH 2024; 11:uhae004. [PMID: 38464479 PMCID: PMC10923646 DOI: 10.1093/hr/uhae004] [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: 08/10/2023] [Accepted: 12/30/2023] [Indexed: 03/12/2024]
Abstract
In fruits, cuticular waxes affect fruit quality traits such as surface color at harvest and water loss during postharvest storage. This study investigated the transcriptional regulation of cuticular wax deposition in northern highbush blueberries (Vaccinium corymbosum L.) in relation to fruit water loss and surface color during ripening and postharvest storage, as well as the effects of abscisic acid (ABA)-mediated changes in cuticular wax deposition on these fruit quality traits. Total cuticular wax content (μg∙cm-2) decreased during fruit ripening and increased during postharvest storage. Transcriptome analysis revealed a transcript network for cuticular wax deposition in blueberries. Particularly, five OSC-Likes were identified as putative genes for triterpene alcohol production, with OSC-Like1 and OSC-Like2 encoding mixed amyrin synthases, OSC-Like3 encoding a lupeol synthase, and OSC-Like4 and OSC-Like5 encoding cycloartenol synthases. The expression of three CYP716A-like genes correlated to the accumulation of two triterpene acids oleanolic acid and ursolic acid, the major wax compounds in blueberries. Exogenous ABA application induced the expression of triterpenoid biosynthetic genes and the accumulation of β-amyrin and oleanolic acid, as well as increased the ratio of oleanolic acid to ursolic acid. These changes were associated with reduced fruit water loss. The content of β-diketones was also increased by ABA application, and this increase was associated with increased fruit lightness (measured as L* using CIELAB Color Space by a colorimeter). This study provided key insights on the molecular basis of cuticular wax deposition and its implications on fruit quality traits in blueberries.
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Affiliation(s)
- Yifan Yan
- Wine Research Centre, Faculty of Land and Food Systems, The University of British Columbia, 2205 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Kristina K Gagalova
- Canada’s Michael Smith Genome Sciences Centre, 570 W 7th Ave, Vancouver, BC V5Z 4S6, Canada
| | - Eric M Gerbrandt
- British Columbia Blueberry Council, 32160 South Fraser Way #275, Abbotsford, BC V2T 1W5, Canada
| | - Simone D Castellarin
- Wine Research Centre, Faculty of Land and Food Systems, The University of British Columbia, 2205 East Mall, Vancouver, BC V6T 1Z4, Canada
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Chen JY, Kuruparan A, Zamani-Babgohari M, Gonzales-Vigil E. Dynamic changes to the plant cuticle include the production of volatile cuticular wax-derived compounds. Proc Natl Acad Sci U S A 2023; 120:e2307012120. [PMID: 38019866 PMCID: PMC10710056 DOI: 10.1073/pnas.2307012120] [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: 04/29/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
The cuticle is a hydrophobic structure that seals plant aerial surfaces from the surrounding environment. To better understand how cuticular wax composition changes over development, we conducted an untargeted screen of leaf surface lipids from black cottonwood (Populus trichocarpa). We observed major shifts to the lipid profile across development, from a phenolic and terpene-dominated profile in young leaves to an aliphatic wax-dominated profile in mature leaves. Contrary to the general pattern, levels of aliphatic cis-9-alkenes decreased in older leaves following their accumulation. A thorough examination revealed that the decrease in cis-9-alkenes was accompanied by a concomitant increase in aldehydes, one of them being the volatile compound nonanal. By applying exogenous alkenes to P. trichocarpa leaves, we show that unsaturated waxes in the cuticle undergo spontaneous oxidative cleavage to generate aldehydes and that this process occurs similarly in other alkene-accumulating systems such as balsam poplar (Populus balsamifera) leaves and corn (Zea mays) silk. Moreover, we show that the production of cuticular wax-derived compounds can be extended to other wax components. In bread wheat (Triticum aestivum), 9-hydroxy-14,16-hentriacontanedione likely decomposes to generate 2-heptadecanone and 7-octyloxepan-2-one (a caprolactone). These findings highlight an unusual route to the production of plant volatiles that are structurally encoded within cuticular wax precursors. These processes could play a role in modulating ecological interactions and open the possibility for engineering bioactive volatile compounds into plant waxes.
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Affiliation(s)
- Jeff Y Chen
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Aswini Kuruparan
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Mahbobeh Zamani-Babgohari
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Eliana Gonzales-Vigil
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
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5
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Jolliffe JB, Pilati S, Moser C, Lashbrooke JG. Beyond skin-deep: targeting the plant surface for crop improvement. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6468-6486. [PMID: 37589495 PMCID: PMC10662250 DOI: 10.1093/jxb/erad321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/09/2023] [Indexed: 08/18/2023]
Abstract
The above-ground plant surface is a well-adapted tissue layer that acts as an interface between the plant and its surrounding environment. As such, its primary role is to protect against desiccation and maintain the gaseous exchange required for photosynthesis. Further, this surface layer provides a barrier against pathogens and herbivory, while attracting pollinators and agents of seed dispersal. In the context of agriculture, the plant surface is strongly linked to post-harvest crop quality and yield. The epidermal layer contains several unique cell types adapted for these functions, while the non-lignified above-ground plant organs are covered by a hydrophobic cuticular membrane. This review aims to provide an overview of the latest understanding of the molecular mechanisms underlying crop cuticle and epidermal cell formation, with focus placed on genetic elements contributing towards quality, yield, drought tolerance, herbivory defence, pathogen resistance, pollinator attraction, and sterility, while highlighting the inter-relatedness of plant surface development and traits. Potential crop improvement strategies utilizing this knowledge are outlined in the context of the recent development of new breeding techniques.
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Affiliation(s)
- Jenna Bryanne Jolliffe
- South African Grape and Wine Research Institute, Stellenbosch University, Stellenbosch, 7600, South Africa
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all’Adige, 38098, Italy
| | - Stefania Pilati
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all’Adige, 38098, Italy
| | - Claudio Moser
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all’Adige, 38098, Italy
| | - Justin Graham Lashbrooke
- South African Grape and Wine Research Institute, Stellenbosch University, Stellenbosch, 7600, South Africa
- Department of Genetics, Stellenbosch University, Stellenbosch, 7600, South Africa
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6
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Sun Y, Ruiz Orduna A, Zhang Z, Feakins SJ, Jetter R. Biosynthesis of barley wax β-diketones: a type-III polyketide synthase condensing two fatty acyl units. Nat Commun 2023; 14:7284. [PMID: 37949901 PMCID: PMC10638390 DOI: 10.1038/s41467-023-42917-9] [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: 10/20/2022] [Accepted: 10/25/2023] [Indexed: 11/12/2023] Open
Abstract
The surface coatings of cereal plants are dominated by waxy β-diketones crucial for drought resistance and, therefore, grain yield. Here, barley (Hordeum vulgare) wax analyses reveal β-diketone and associated 2-alkanol ester profiles suggesting a common C16 3-ketoacid precursor. Isotope analysis further shows that the major (C31) diketone is synthesized from two plastidial C16 acyl units. Previous studies identified a gene cluster encoding enzymes responsible for β-diketone formation in barley, but left their biochemical functions unknown. Various assays now characterize one of these enzymes as a thioesterase producing long-chain (mainly C16) 3-ketoacids, and another one as a polyketide synthase (PKS) condensing the 3-ketoacids with long-chain (mainly C16) acyl-CoAs into β-diketones. The two enzymes are localized to the plastids and Endoplasmic Reticulum (ER), respectively, implying substrate transfer between these two sub-cellular compartments. Overall, our findings define a two-step pathway involving an unprecedented PKS reaction leading directly to the β-diketone products.
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Affiliation(s)
- Yulin Sun
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Alberto Ruiz Orduna
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Zhonghang Zhang
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Sarah J Feakins
- Department of Earth Sciences, University of Southern California, 3651 Trousdale Pkwy, Los Angeles, CA, 90089, USA
| | - Reinhard Jetter
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada.
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7
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Ciuca MD, Racovita RC. Curcumin: Overview of Extraction Methods, Health Benefits, and Encapsulation and Delivery Using Microemulsions and Nanoemulsions. Int J Mol Sci 2023; 24:ijms24108874. [PMID: 37240220 DOI: 10.3390/ijms24108874] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/14/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Curcumin is the principal curcuminoid found in the rhizomes of turmeric. Due to its therapeutic action against cancer, depression, diabetes, some bacteria, and oxidative stress, it has been used widely in medicine since ancient times. Due to its low solubility, the human organism cannot completely absorb it. Advanced extraction technologies, followed by encapsulation in microemulsion and nanoemulsion systems, are currently being used to improve bioavailability. This review discusses the different methods available for curcumin extraction from plant material, methods for the identification of curcumin in the resulting extracts, its beneficial effects on human health, and the encapsulation techniques into small colloidal systems that have been used over the past decade to deliver this compound.
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Affiliation(s)
- Maria D Ciuca
- Department of Inorganic Chemistry, Physical Chemistry and Electrochemistry, Faculty of Chemical Engineering and Biotechnologies, University Politehnica of Bucharest, 1-7 Gh. Polizu St., District 1, 011061 Bucharest, Romania
| | - Radu C Racovita
- Department of Inorganic Chemistry, Physical Chemistry and Electrochemistry, Faculty of Chemical Engineering and Biotechnologies, University Politehnica of Bucharest, 1-7 Gh. Polizu St., District 1, 011061 Bucharest, Romania
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8
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Gozdzik J, Busta L, Jetter R. Leaf cuticular waxes of wild-type Welsh onion (Allium fistulosum L.) and a wax-deficient mutant: Compounds with terminal and mid-chain functionalities. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 198:107679. [PMID: 37121165 DOI: 10.1016/j.plaphy.2023.107679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/21/2023] [Accepted: 04/02/2023] [Indexed: 05/02/2023]
Abstract
Plant cuticles cover aerial organs to limit non-stomatal water loss and protect against insects and pathogens. Cuticles contain complex mixtures of fatty acid-derived waxes, with various chain lengths and diverse functional groups. To further our understanding of the chemical diversity and biosynthesis of these compounds, this study investigated leaf cuticular waxes of Welsh onion (Allium fistulosum L.) wild type and a wax-deficient mutant. Leaf waxes were extracted with chloroform, separated using thin layer chromatography (TLC), and analyzed using gas chromatography-mass spectrometry (GC-MS). The extracts contained typical wax compound classes found in nearly all plant lineages but also two uncommon compound classes. Analyses of characteristic MS fragmentation patterns followed by comparisons with synthetic standards identified the latter as very-long-chain ketones and primary ketols. The ketols were minor compounds, with chain lengths ranging from C28 to C32 and carbonyls mainly on C-18 and C-20 in wild type wax, and a C28 chain with C-16 carbonyl in the mutant. The ketones made up 70% of total wax in the wild type, consisting mainly of C31 isomers with carbonyl group on C-14 or C-16. In contrast, the mutant wax comprised only 4% ketones, with chain lengths C27 and C29 and carbonyls predominantly on C-12 and C-14, respectively. A two-carbon homolog shift between wild type and mutant was also observed in the primary alcohols (a major wax compound class), whilst alkanes exhibited a four-carbon shift. Overall, the compositional data shed light on possible biosynthetic pathways to wax ketones that can be tested in future studies.
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Affiliation(s)
- Jedrzej Gozdzik
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Lucas Busta
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, 55812, USA
| | - Reinhard Jetter
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada; Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
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Gerasimova SV, Kolosovskaya EV, Vikhorev AV, Korotkova AM, Hertig CW, Genaev MA, Domrachev DV, Morozov SV, Chernyak EI, Shmakov NA, Vasiliev GV, Kochetov AV, Kumlehn J, Khlestkina EK. WAX INDUCER 1 Regulates β-Diketone Biosynthesis by Mediating Expression of the Cer-cqu Gene Cluster in Barley. Int J Mol Sci 2023; 24:ijms24076762. [PMID: 37047735 PMCID: PMC10095013 DOI: 10.3390/ijms24076762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/17/2023] [Accepted: 03/27/2023] [Indexed: 04/14/2023] Open
Abstract
Plant surface properties are crucial determinants of resilience to abiotic and biotic stresses. The outer layer of the plant cuticle consists of chemically diverse epicuticular waxes. The WAX INDUCER1/SHINE subfamily of APETALA2/ETHYLENE RESPONSIVE FACTORS regulates cuticle properties in plants. In this study, four barley genes homologous to the Arabidopsis thaliana AtWIN1 gene were mutated using RNA-guided Cas9 endonuclease. Mutations in one of them, the HvWIN1 gene, caused a recessive glossy sheath phenotype associated with β-diketone deficiency. A complementation test for win1 knockout (KO) and cer-x mutants showed that Cer-X and WIN1 are allelic variants of the same genomic locus. A comparison of the transcriptome from leaf sheaths of win1 KO and wild-type plants revealed a specific and strong downregulation of a large gene cluster residing at the previously known Cer-cqu locus. Our findings allowed us to postulate that the WIN1 transcription factor in barley is a master mediator of the β-diketone biosynthesis pathway acting through developmental stage- and organ-specific transactivation of the Cer-cqu gene cluster.
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Affiliation(s)
- Sophia V Gerasimova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | | | - Alexander V Vikhorev
- Vavilov Institute of Plant Genetic Resources (VIR), 190000 Saint Petersburg, Russia
| | - Anna M Korotkova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Christian W Hertig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
| | - Mikhail A Genaev
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Dmitry V Domrachev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Sergey V Morozov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Elena I Chernyak
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Nikolay A Shmakov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Gennady V Vasiliev
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Alex V Kochetov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
| | - Elena K Khlestkina
- Vavilov Institute of Plant Genetic Resources (VIR), 190000 Saint Petersburg, Russia
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10
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Yang J, Busta L, Jetter R, Sun Y, Wang T, Zhang W, Ni Y, Guo Y. Diversified chemical profiles of cuticular wax on alpine meadow plants of the Qinghai-Tibet Plateau. PLANTA 2023; 257:74. [PMID: 36879182 DOI: 10.1007/s00425-023-04107-1] [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: 12/12/2022] [Accepted: 02/25/2023] [Indexed: 06/18/2023]
Abstract
The alpine meadow plants showed great intra- and inter-genera variations of chemical profiles of cuticular waxes. Developing an understanding of wax structure-function relationships that will help us tackle global climate change requires a detailed understanding of plant wax chemistry. The goal in this study was to provide a catalog of wax structures, abundances, and compositions on alpine meadow plants. Here, leaf waxes from 33 plant species belonging to 11 families were sampled from alpine meadows of the east side of the Qinghai-Tibet Plateau. Across these species, total wax coverage varied from 2.30 μg cm-2 to 40.70 μg cm-2, showing variation both within as well as between genera and suggesting that wax variation is subject to both environmental and genetic effects. Across all wax samples, more than 140 wax compounds belonging to 13 wax compound classes were identified, including both ubiquitous wax compounds and lineage-specific compounds. Among the ubiquitous compounds (primary alcohols, alkyl esters, aldehydes, alkanes, and fatty acids), chain length profiles across a wide range of species point to key differences in the chain length specificity of alcohol and alkane formation machinery. The lineage-specific wax compound classes (diols, secondary alcohols, lactones, iso-alkanes, alkyl resorcinols, phenylethyl esters, cinnamate esters, alkyl benzoates, and triterpenoids) nearly all consisted of isomers with varying chain lengths or functional group positions, making the diversity of specialized wax compounds immense. The comparison of species relationships between chemical data and genetic data highlighted the importance of inferring phylogenetic relationships from data sets that contain a large number of variables that do not respond to environmental stimuli.
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Affiliation(s)
- Jianfeng Yang
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao Agricultural University, Qingdao, 266109, China
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- College of Animal Science and Technology, Southwest University, Chongqing, 400716, China
| | - Lucas Busta
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, 55812, USA
| | - Reinhard Jetter
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| | - Yingpeng Sun
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao Agricultural University, Qingdao, 266109, China
| | - Tianyu Wang
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao Agricultural University, Qingdao, 266109, China
| | - Wenlan Zhang
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yu Ni
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yanjun Guo
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao Agricultural University, Qingdao, 266109, China.
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China.
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11
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Negin B, Hen-Avivi S, Almekias-Siegl E, Shachar L, Jander G, Aharoni A. Tree tobacco (Nicotiana glauca) cuticular wax composition is essential for leaf retention during drought, facilitating a speedy recovery following rewatering. THE NEW PHYTOLOGIST 2023; 237:1574-1589. [PMID: 36369885 DOI: 10.1111/nph.18615] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/05/2022] [Indexed: 05/20/2023]
Abstract
Despite decades of extensive study, the role of cuticular lipids in sustaining plant fitness is far from being understood. We utilized genome-edited tree tobacco (Nicotiana glauca) to investigate the significance of different classes of epicuticular wax in abiotic stress such as cuticular water loss, drought, and light response. We generated mutants displaying a range of wax compositions. Four wax mutants and one cutin mutant were extensively investigated for alterations in their response to abiotic factors. Although the mutations led to elevated cuticular water loss, the wax mutants did not display elevated transpiration or reduced growth under nonstressed conditions. However, under drought, plants lacking alkanes were unable to reduce their transpiration, leading to leaf death, impaired recovery, and stem cracking. By contrast, plants deficient in fatty alcohols exhibited elevated drought tolerance, which was part of a larger trend of plant phenotypes not clustering by a glossy/glaucous appearance in the parameters examined in this study. We conclude that although alkanes have little effect on whole N. glauca transpiration and biomass gain under normal, nonstressed conditions, they are essential during drought responses, since they enable plants to seal their cuticle upon stomatal closure, thereby reducing leaf death and facilitating a speedy recovery.
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Affiliation(s)
- Boaz Negin
- Plant and Environmental Science Department, Weizmann Institute of Science, Rehovot, 7610001, Israel
- Boyce Thompson Institute, 533 Tower Road, Ithaca, NY, 14853, USA
| | - Shelly Hen-Avivi
- Plant and Environmental Science Department, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Efrat Almekias-Siegl
- Plant and Environmental Science Department, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Lior Shachar
- Plant and Environmental Science Department, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Georg Jander
- Boyce Thompson Institute, 533 Tower Road, Ithaca, NY, 14853, USA
| | - Asaph Aharoni
- Plant and Environmental Science Department, Weizmann Institute of Science, Rehovot, 7610001, Israel
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12
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Laskoś K, Myśków B, Dziurka M, Warchoł M, Dziurka K, Juzoń K, Czyczyło-Mysza IM. Variation between glaucous and non-glaucous near-isogenic lines of rye (Secale cereale L.) under drought stress. Sci Rep 2022; 12:22486. [PMID: 36577794 PMCID: PMC9797576 DOI: 10.1038/s41598-022-26869-6] [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: 04/19/2022] [Accepted: 12/21/2022] [Indexed: 12/29/2022] Open
Abstract
Glaucous (811, L35, and RXL10) and non-glaucous (811bw, L35bw, and RXL10bw) near-isogenic lines (NILs) of rye (Secale cereale L.) forming three pairs of inbred lines were the subject of the research. The research aimed to study the relationship between wax cover attributes and the physio-biochemical drought reactions and yield of rye NILs and to uncover the differences in drought resistance levels of these lines. The greatest differences between glaucous and non-glaucous NILs were observed in the RXL10/RXL10bw pair. Of particular note were the stable grain number and the thousand grain weight of the non-glaucous line RXL10bw under drought and the accompanying reactions, such as an approximately 60% increase in MDA and a two-fold increase in wax amount, both of which were significantly higher than in the glaucous line RXL10 and in other NILs. The surprisingly high level of MDA in the RXL10bw line requires further analysis. Moreover, additional wax crystal aggregates were found under drought conditions on the abaxial leaf surface of the glaucous lines 811 and RXL10. The use of rye NILs indicated that line-specific drought resistance could be associated with wax biosynthetic pathways involved in physiological and biochemical responses important for increased drought resistance.
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Affiliation(s)
- Kamila Laskoś
- grid.460372.4The Franciszek Górski Institute of Plant Physiology Polish Academy of Sciences, Niezapominajek 21, 30-239 Kraków, Poland
| | - Beata Myśków
- grid.411391.f0000 0001 0659 0011Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Słowackiego 17, 71-434 Szczecin, Poland
| | - Michał Dziurka
- grid.460372.4The Franciszek Górski Institute of Plant Physiology Polish Academy of Sciences, Niezapominajek 21, 30-239 Kraków, Poland
| | - Marzena Warchoł
- grid.460372.4The Franciszek Górski Institute of Plant Physiology Polish Academy of Sciences, Niezapominajek 21, 30-239 Kraków, Poland
| | - Kinga Dziurka
- grid.460372.4The Franciszek Górski Institute of Plant Physiology Polish Academy of Sciences, Niezapominajek 21, 30-239 Kraków, Poland
| | - Katarzyna Juzoń
- grid.460372.4The Franciszek Górski Institute of Plant Physiology Polish Academy of Sciences, Niezapominajek 21, 30-239 Kraków, Poland
| | - Ilona M. Czyczyło-Mysza
- grid.460372.4The Franciszek Górski Institute of Plant Physiology Polish Academy of Sciences, Niezapominajek 21, 30-239 Kraków, Poland
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13
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Wang X, Chang C. Exploring and exploiting cuticle biosynthesis for abiotic and biotic stress tolerance in wheat and barley. FRONTIERS IN PLANT SCIENCE 2022; 13:1064390. [PMID: 36438119 PMCID: PMC9685406 DOI: 10.3389/fpls.2022.1064390] [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: 10/08/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Wheat and barley are widely distributed cereal crops whose yields are adversely affected by environmental stresses such as drought, salinity, extreme temperatures, and attacks of pathogens and pests. As the interphase between aerial plant organs and their environments, hydrophobic cuticle largely consists of a cutin matrix impregnated and sealed with cuticular waxes. Increasing evidence supports that the cuticle plays a key role in plant adaptation to abiotic and biotic stresses, which could be harnessed for wheat and barley improvement. In this review, we highlighted recent advances in cuticle biosynthesis and its multifaceted roles in abiotic and biotic stress tolerance of wheat and barley. Current strategies, challenges, and future perspectives on manipulating cuticle biosynthesis for abiotic and biotic stress tolerance in wheat and barley are discussed.
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14
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He J, Li C, Hu N, Zhu Y, He Z, Sun Y, Wang Z, Wang Y. ECERIFERUM1-6A is required for the synthesis of cuticular wax alkanes and promotes drought tolerance in wheat. PLANT PHYSIOLOGY 2022; 190:1640-1657. [PMID: 36000923 PMCID: PMC9614490 DOI: 10.1093/plphys/kiac394] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/03/2022] [Indexed: 05/27/2023]
Abstract
Cuticular waxes cover the aerial surfaces of land plants and protect them from various environmental stresses. Alkanes are major wax components and contribute to plant drought tolerance, but the biosynthesis and regulation of alkanes remain largely unknown in wheat (Triticum aestivum L.). Here, we identified and functionally characterized a key alkane biosynthesis gene ECERIFERUM1-6A (TaCER1-6A) from wheat. The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated knockout mutation in TaCER1-6A greatly reduced the contents of C27, C29, C31, and C33 alkanes in wheat leaves, while TaCER1-6A overexpression significantly increased the contents of these alkanes in wheat leaves, suggesting that TaCER1-6A is specifically involved in the biosynthesis of C27, C29, C31, and C33 alkanes on wheat leaf surfaces. TaCER1-6A knockout lines exhibited increased cuticle permeability and reduced drought tolerance, whereas TaCER1-6A overexpression lines displayed reduced cuticle permeability and enhanced drought tolerance. TaCER1-6A was highly expressed in flag leaf blades and seedling leaf blades and could respond to abiotic stresses and abscisic acid. TaCER1-6A was located in the endoplasmic reticulum, which is the subcellular compartment responsible for wax biosynthesis. A total of three haplotypes (HapI/II/III) of TaCER1-6A were identified in 43 wheat accessions, and HapI was the dominant haplotype (95%) in these wheat varieties. Additionally, we identified two R2R3-MYB transcription factors TaMYB96-2D and TaMYB96-5D that bound directly to the conserved motif CAACCA in promoters of the cuticular wax biosynthesis genes TaCER1-6A, TaCER1-1A, and fatty acyl-CoA reductase4. Collectively, these results suggest that TaCER1-6A is required for C27, C29, C31, and C33 alkanes biosynthesis and improves drought tolerance in wheat.
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Affiliation(s)
- Jiajia He
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chongzhao Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ning Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuyao Zhu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhaofeng He
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yulin Sun
- Department of Botany, The University of British Columbia, Vancouver, British Columbia, V6T 1Z4 Canada
| | - Zhonghua Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
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15
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Characterization of Glossy Spike Mutants and Identification of Candidate Genes Regulating Cuticular Wax Synthesis in Barley ( Hordeum vulgare L.). Int J Mol Sci 2022; 23:ijms232113025. [PMID: 36361814 PMCID: PMC9658550 DOI: 10.3390/ijms232113025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 10/20/2022] [Accepted: 10/25/2022] [Indexed: 12/04/2022] Open
Abstract
Cuticular waxes comprise the hydrophobic layer that protects crops against nonstomatal water loss and biotic and abiotic stresses. Expanding on our current knowledge of the genes that are involved in cuticular wax biosynthesis and regulation plays an important role in dissecting the processes of cuticular wax metabolism. In this study, we identified the Cer-GN1 barley (Hordeum vulgare L.) mutant that is generated by ethyl methanesulfonate mutagenesis with a glossy spike phenotype that is controlled by a single recessive nuclear gene. A physiological analysis showed that the total cuticular wax loads of Cer-GN1 were one-third that of the progenitor wild-type (WT), and its water loss rate was significantly accelerated (p < 0.05). In addition, Cer-GN1 was defective in the glume’s cuticle according to the toluidine blue dye test, and it was deficient in the tubule-shaped crystals which were observed on the glume surfaces by scanning electron microscopy. Using metabolomics and transcriptomics, we investigated the impacts of cuticular wax composition and waxy regulatory genes on the loss of the glaucous wax in the spikes of Cer-GN1. Among the differential metabolites, we found that 16-hydroxyhexadecanoic acid, which is one of the predominant C16 and C18 fatty acid-derived cutin monomers, was significantly downregulated in Cer-GN1 when it was compared to that of WT. We identified two novel genes that are located on chromosome 4H and are downregulated in Cer-GN1 (HvMSTRG.29184 and HvMSTRG.29185) that encode long-chain fatty acid omega-monooxygenase CYP704B1, which regulates the conversion of C16 palmitic acid to 16-hydroxyhexadecanoic acid. A quantitative real-time PCR revealed that the expression levels of HvMSTRG.29184 and HvMSTRG.29185 were downregulated at 1, 4, 8, 12, and 16 days after the heading stage in Cer-GN1 when it was compared to those of WT. These results suggested that HvMSTRG.29184 and HvMSTRG.29185 have CYP704B1 activity, which could regulate the conversion of C16 palmitic acid to 16-hydroxyhexadecanoic acid in barley. Their downregulation in Cer-GN1 reduced the synthesis of the cuticular wax components and ultimately caused the loss of the glaucous wax in the spikes. It is necessary to verify whether HvMSTRG.29184 and HvMSTRG.29185 truly encode a CYP704B1 that regulates the conversion of C16 palmitic acid to 16-hydroxyhexadecanoic acid in barley.
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16
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Conserved signalling components coordinate epidermal patterning and cuticle deposition in barley. Nat Commun 2022; 13:6050. [PMID: 36229435 PMCID: PMC9561702 DOI: 10.1038/s41467-022-33300-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 09/12/2022] [Indexed: 12/24/2022] Open
Abstract
Faced with terrestrial threats, land plants seal their aerial surfaces with a lipid-rich cuticle. To breathe, plants interrupt their cuticles with adjustable epidermal pores, called stomata, that regulate gas exchange, and develop other specialised epidermal cells such as defensive hairs. Mechanisms coordinating epidermal features remain poorly understood. Addressing this, we studied two loci whose allelic variation causes both cuticular wax-deficiency and misarranged stomata in barley, identifying the underlying genes, Cer-g/ HvYDA1, encoding a YODA-like (YDA) MAPKKK, and Cer-s/ HvBRX-Solo, encoding a single BREVIS-RADIX (BRX) domain protein. Both genes control cuticular integrity, the spacing and identity of epidermal cells, and barley's distinctive epicuticular wax blooms, as well as stomatal patterning in elevated CO2 conditions. Genetic analyses revealed epistatic and modifying relationships between HvYDA1 and HvBRX-Solo, intimating that their products participate in interacting pathway(s) linking epidermal patterning with cuticular properties in barley. This may represent a mechanism for coordinating multiple adaptive features of the land plant epidermis in a cultivated cereal.
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17
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Singh KS, van der Hooft JJJ, van Wees SCM, Medema MH. Integrative omics approaches for biosynthetic pathway discovery in plants. Nat Prod Rep 2022; 39:1876-1896. [PMID: 35997060 PMCID: PMC9491492 DOI: 10.1039/d2np00032f] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Indexed: 12/13/2022]
Abstract
Covering: up to 2022With the emergence of large amounts of omics data, computational approaches for the identification of plant natural product biosynthetic pathways and their genetic regulation have become increasingly important. While genomes provide clues regarding functional associations between genes based on gene clustering, metabolome mining provides a foundational technology to chart natural product structural diversity in plants, and transcriptomics has been successfully used to identify new members of their biosynthetic pathways based on coexpression. Thus far, most approaches utilizing transcriptomics and metabolomics have been targeted towards specific pathways and use one type of omics data at a time. Recent technological advances now provide new opportunities for integration of multiple omics types and untargeted pathway discovery. Here, we review advances in plant biosynthetic pathway discovery using genomics, transcriptomics, and metabolomics, as well as recent efforts towards omics integration. We highlight how transcriptomics and metabolomics provide complementary information to link genes to metabolites, by associating temporal and spatial gene expression levels with metabolite abundance levels across samples, and by matching mass-spectral features to enzyme families. Furthermore, we suggest that elucidation of gene regulatory networks using time-series data may prove useful for efforts to unwire the complexities of biosynthetic pathway components based on regulatory interactions and events.
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Affiliation(s)
- Kumar Saurabh Singh
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, The Netherlands.
| | - Justin J J van der Hooft
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - Saskia C M van Wees
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, The Netherlands.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
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18
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Assessing the role of glaucousness in imparting tolerance to moisture and heat stress in wheat. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01177-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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19
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Lin M, Qiao P, Matschi S, Vasquez M, Ramstein GP, Bourgault R, Mohammadi M, Scanlon MJ, Molina I, Smith LG, Gore MA. Integrating GWAS and TWAS to elucidate the genetic architecture of maize leaf cuticular conductance. PLANT PHYSIOLOGY 2022; 189:2144-2158. [PMID: 35512195 PMCID: PMC9342973 DOI: 10.1093/plphys/kiac198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/28/2022] [Indexed: 05/11/2023]
Abstract
The cuticle, a hydrophobic layer of cutin and waxes synthesized by plant epidermal cells, is the major barrier to water loss when stomata are closed. Dissecting the genetic architecture of natural variation for maize (Zea mays L.) leaf cuticular conductance (gc) is important for identifying genes relevant to improving crop productivity in drought-prone environments. To this end, we performed an integrated genome- and transcriptome-wide association studies (GWAS and TWAS) to identify candidate genes putatively regulating variation in leaf gc. Of the 22 plausible candidate genes identified, 4 were predicted to be involved in cuticle precursor biosynthesis and export, 2 in cell wall modification, 9 in intracellular membrane trafficking, and 7 in the regulation of cuticle development. A gene encoding an INCREASED SALT TOLERANCE1-LIKE1 (ISTL1) protein putatively involved in intracellular protein and membrane trafficking was identified in GWAS and TWAS as the strongest candidate causal gene. A set of maize nested near-isogenic lines that harbor the ISTL1 genomic region from eight donor parents were evaluated for gc, confirming the association between gc and ISTL1 in a haplotype-based association analysis. The findings of this study provide insights into the role of regulatory variation in the development of the maize leaf cuticle and will ultimately assist breeders to develop drought-tolerant maize for target environments.
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Affiliation(s)
- Meng Lin
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Pengfei Qiao
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | | | - Miguel Vasquez
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093, USA
| | | | - Richard Bourgault
- Department of Biology, Algoma University, Sault Ste Marie, ON P6A 2G4, Canada
| | - Marc Mohammadi
- Department of Biology, Algoma University, Sault Ste Marie, ON P6A 2G4, Canada
| | - Michael J Scanlon
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Isabel Molina
- Department of Biology, Algoma University, Sault Ste Marie, ON P6A 2G4, Canada
| | - Laurie G Smith
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093, USA
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20
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Scott S, Cahoon EB, Busta L. Variation on a theme: the structures and biosynthesis of specialized fatty acid natural products in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:954-965. [PMID: 35749584 PMCID: PMC9546235 DOI: 10.1111/tpj.15878] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Plants are able to construct lineage-specific natural products from a wide array of their core metabolic pathways. Considerable progress has been made toward documenting and understanding, for example, phenylpropanoid natural products derived from phosphoenolpyruvate via the shikimate pathway, terpenoid compounds built using isopentyl pyrophosphate, and alkaloids generated by the extensive modification of amino acids. By comparison, natural products derived from fatty acids have received little attention, except for unusual fatty acids in seed oils and jasmonate-like oxylipins. However, scattered but numerous reports show that plants are able to generate many structurally diverse compounds from fatty acids, including some with highly elaborate and unique structural features that have novel bioproduct functionalities. Furthermore, although recent work has shed light on multiple new fatty acid natural product biosynthesis pathways and products in diverse plant species, these discoveries have not been reviewed. The aims of this work, therefore, are to (i) review and systematize our current knowledge of the structures and biosynthesis of fatty acid-derived natural products that are not seed oils or jasmonate-type oxylipins, specifically, polyacetylenic, very-long-chain, and aromatic fatty acid-derived natural products, and (ii) suggest priorities for future investigative steps that will bring our knowledge of fatty acid-derived natural products closer to the levels of knowledge that we have attained for other phytochemical classes.
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Affiliation(s)
- Samuel Scott
- Department of Chemistry and BiochemistryUniversity of Minnesota DuluthDuluth55812MNUSA
| | - Edgar B. Cahoon
- Department of BiochemistryUniversity of Nebraska LincolnLincoln68588NEUSA
- Center for Plant Science InnovationUniversity of Nebraska LincolnLincoln68588NEUSA
| | - Lucas Busta
- Department of Chemistry and BiochemistryUniversity of Minnesota DuluthDuluth55812MNUSA
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21
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Zhai X, Wu H, Wang Y, Zhang Z, Shan L, Zhao X, Wang R, Liu C, Weng Y, Wang Y, Liu X, Ren H. The fruit glossiness locus, dull fruit ( D), encodes a C 2H 2-type zinc finger transcription factor, CsDULL, in cucumber ( Cucumis sativus L.). HORTICULTURE RESEARCH 2022; 9:uhac146. [PMID: 36072836 PMCID: PMC9437717 DOI: 10.1093/hr/uhac146] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Fruit glossiness is an important external fruit quality trait for fresh-consumed cucumber fruit, affecting its marketability. Dull fruit appearance is mainly controlled by a single gene, D (for dull fruit) that is dominant to glossy fruit (dd), but the molecular mechanism controlling fruit glossiness is unknown. In the present study, we conducted map-based cloning of the D locus in cucumber and identified a candidate gene (Csa5G577350) that encodes a C2H2-type zinc finger transcription factor, CsDULL. A 4895-bp deletion including the complete loss of CsDULL resulted in glossy fruit. CsDULL is highly expressed in the peel of cucumber fruit, and its expression level is positively correlated with the accumulation of cutin and wax in the peel. Through transcriptome analysis, yeast one-hybrid and dual-luciferase assays, we identified two genes potentially targeted by CsDULL for regulation of cutin and wax biosynthesis/transportation that included CsGPAT4 and CsLTPG1. The possibility that CsDULL controls both fruit glossiness and wart development in cucumber is discussed. The present work advances our understanding of regulatory mechanisms of fruit epidermal traits, and provides a useful tool for molecular breeding to improve external fruit quality in cucumber.
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Affiliation(s)
- Xuling Zhai
- Engineering Research Center of the Ministry of Education for Horticultural Crops Breeding and Propagation, College of Horticulture, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Haoying Wu
- Engineering Research Center of the Ministry of Education for Horticultural Crops Breeding and Propagation, College of Horticulture, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yaru Wang
- Engineering Research Center of the Ministry of Education for Horticultural Crops Breeding and Propagation, College of Horticulture, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Zhongren Zhang
- Engineering Research Center of the Ministry of Education for Horticultural Crops Breeding and Propagation, College of Horticulture, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Li Shan
- Engineering Research Center of the Ministry of Education for Horticultural Crops Breeding and Propagation, College of Horticulture, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Xi Zhao
- Engineering Research Center of the Ministry of Education for Horticultural Crops Breeding and Propagation, College of Horticulture, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Ruijia Wang
- Engineering Research Center of the Ministry of Education for Horticultural Crops Breeding and Propagation, College of Horticulture, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Chang Liu
- Engineering Research Center of the Ministry of Education for Horticultural Crops Breeding and Propagation, College of Horticulture, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yiqun Weng
- USDA-ARS, Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, 1575 Linden Dr., Madison, WI 53706, USA
| | - Ying Wang
- Heze Agricultural and Rural Bureau, 1021 Shuanghe Road, Mudan District, Heze, Shandong, 274000, China
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22
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Dong Y, Aharoni A. Image to insight: exploring natural products through mass spectrometry imaging. Nat Prod Rep 2022; 39:1510-1530. [PMID: 35735199 DOI: 10.1039/d2np00011c] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: 2017 to 2022Mass spectrometry imaging (MSI) has become a mature molecular imaging technique that is well-matched for natural product (NP) discovery. Here we present a brief overview of MSI, followed by a thorough discussion of different MSI applications in NP research. This review will mainly focus on the recent progress of MSI in plants and microorganisms as they are the main producers of NPs. Specifically, the opportunity and potential of combining MSI with other imaging modalities and stable isotope labeling are discussed. Throughout, we focus on both the strengths and weaknesses of MSI, with an eye on future improvements that are necessary for the progression of MSI toward routine NP studies. Finally, we discuss new areas of research, future perspectives, and the overall direction that the field may take in the years to come.
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Affiliation(s)
- Yonghui Dong
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Asaph Aharoni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
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23
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Kamal N, Tsardakas Renhuldt N, Bentzer J, Gundlach H, Haberer G, Juhász A, Lux T, Bose U, Tye-Din JA, Lang D, van Gessel N, Reski R, Fu YB, Spégel P, Ceplitis A, Himmelbach A, Waters AJ, Bekele WA, Colgrave ML, Hansson M, Stein N, Mayer KFX, Jellen EN, Maughan PJ, Tinker NA, Mascher M, Olsson O, Spannagl M, Sirijovski N. The mosaic oat genome gives insights into a uniquely healthy cereal crop. Nature 2022; 606:113-119. [PMID: 35585233 PMCID: PMC9159951 DOI: 10.1038/s41586-022-04732-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 04/06/2022] [Indexed: 12/19/2022]
Abstract
Cultivated oat (Avena sativa L.) is an allohexaploid (AACCDD, 2n = 6x = 42) thought to have been domesticated more than 3,000 years ago while growing as a weed in wheat, emmer and barley fields in Anatolia1,2. Oat has a low carbon footprint, substantial health benefits and the potential to replace animal-based food products. However, the lack of a fully annotated reference genome has hampered efforts to deconvolute its complex evolutionary history and functional gene dynamics. Here we present a high-quality reference genome of A. sativa and close relatives of its diploid (Avena longiglumis, AA, 2n = 14) and tetraploid (Avena insularis, CCDD, 2n = 4x = 28) progenitors. We reveal the mosaic structure of the oat genome, trace large-scale genomic reorganizations in the polyploidization history of oat and illustrate a breeding barrier associated with the genome architecture of oat. We showcase detailed analyses of gene families implicated in human health and nutrition, which adds to the evidence supporting oat safety in gluten-free diets, and we perform mapping-by-sequencing of an agronomic trait related to water-use efficiency. This resource for the Avena genus will help to leverage knowledge from other cereal genomes, improve understanding of basic oat biology and accelerate genomics-assisted breeding and reanalysis of quantitative trait studies. Assembly of the hexaploid oat genome and its diploid and tetraploid relatives clarifies the evolutionary history of oat and allows mapping of genes for agronomic traits.
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Affiliation(s)
- Nadia Kamal
- Plant Genome and Systems Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, Neuherberg, Germany
| | - Nikos Tsardakas Renhuldt
- ScanOats Industrial Research Centre, Department of Chemistry, Division of Pure and Applied Biochemistry, Lund University, Lund, Sweden
| | - Johan Bentzer
- ScanOats Industrial Research Centre, Department of Chemistry, Division of Pure and Applied Biochemistry, Lund University, Lund, Sweden
| | - Heidrun Gundlach
- Plant Genome and Systems Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, Neuherberg, Germany
| | - Georg Haberer
- Plant Genome and Systems Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, Neuherberg, Germany
| | - Angéla Juhász
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Thomas Lux
- Plant Genome and Systems Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, Neuherberg, Germany
| | - Utpal Bose
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, Western Australia, Australia.,Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, St Lucia, Queensland, Australia
| | - Jason A Tye-Din
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Gastroenterology, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Daniel Lang
- Plant Genome and Systems Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, Neuherberg, Germany.,Department of Microbial Genomics and Bioforensics, Bundeswehr Institute of Microbiology, Munich, Germany
| | - Nico van Gessel
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Yong-Bi Fu
- Plant Gene Resources of Canada, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Peter Spégel
- Department of Chemistry, Centre for Analysis and Synthesis, Lund University, Lund, Sweden
| | | | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Amanda J Waters
- Research and Development Division, PepsiCo, St Paul, MN, USA
| | - Wubishet A Bekele
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Michelle L Colgrave
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, Western Australia, Australia.,Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, St Lucia, Queensland, Australia
| | - Mats Hansson
- Molecular Cell Biology, Department of Biology, Lund University, Lund, Sweden
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany.,Department of Crop Sciences, Center of Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, Neuherberg, Germany.,School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Eric N Jellen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Peter J Maughan
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Nicholas A Tinker
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
| | - Olof Olsson
- CropTailor AB, Department of Chemistry, Division of Pure and Applied Biochemistry, Lund University, Lund, Sweden
| | - Manuel Spannagl
- Plant Genome and Systems Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, Neuherberg, Germany.
| | - Nick Sirijovski
- ScanOats Industrial Research Centre, Department of Chemistry, Division of Pure and Applied Biochemistry, Lund University, Lund, Sweden. .,CropTailor AB, Department of Chemistry, Division of Pure and Applied Biochemistry, Lund University, Lund, Sweden. .,Food Science Organisation, Oatly AB, Lund, Sweden.
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24
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Lee SB, Suh MC. Regulatory mechanisms underlying cuticular wax biosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2799-2816. [PMID: 35560199 DOI: 10.1093/jxb/erab509] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/18/2021] [Indexed: 05/24/2023]
Abstract
Plants are sessile organisms that have developed hydrophobic cuticles that cover their aerial epidermal cells to protect them from terrestrial stresses. The cuticle layer is mainly composed of cutin, a polyester of hydroxy and epoxy fatty acids, and cuticular wax, a mixture of very-long-chain fatty acids (>20 carbon atoms) and their derivatives, aldehydes, alkanes, ketones, alcohols, and wax esters. During the last 30 years, forward and reverse genetic, transcriptomic, and biochemical approaches have enabled the identification of key enzymes, transporters, and regulators involved in the biosynthesis of cutin and cuticular waxes. In particular, cuticular wax biosynthesis is significantly influenced in an organ-specific manner or by environmental conditions, and is controlled using a variety of regulators. Recent studies on the regulatory mechanisms underlying cuticular wax biosynthesis have enabled us to understand how plants finely control carbon metabolic pathways to balance between optimal growth and development and defense against abiotic and biotic stresses. In this review, we summarize the regulatory mechanisms underlying cuticular wax biosynthesis at the transcriptional, post-transcriptional, post-translational, and epigenetic levels.
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Affiliation(s)
- Saet Buyl Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Korea
| | - Mi Chung Suh
- Department of Life Science, Sogang University, Seoul, 04107, Korea
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25
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Haroon M, Wang X, Afzal R, Zafar MM, Idrees F, Batool M, Khan AS, Imran M. Novel Plant Breeding Techniques Shake Hands with Cereals to Increase Production. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11081052. [PMID: 35448780 PMCID: PMC9025237 DOI: 10.3390/plants11081052] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 04/07/2022] [Accepted: 04/10/2022] [Indexed: 06/01/2023]
Abstract
Cereals are the main source of human food on our planet. The ever-increasing food demand, continuously changing environment, and diseases of cereal crops have made adequate production a challenging task for feeding the ever-increasing population. Plant breeders are striving their hardest to increase production by manipulating conventional breeding methods based on the biology of plants, either self-pollinating or cross-pollinating. However, traditional approaches take a decade, space, and inputs in order to make crosses and release improved varieties. Recent advancements in genome editing tools (GETs) have increased the possibility of precise and rapid genome editing. New GETs such as CRISPR/Cas9, CRISPR/Cpf1, prime editing, base editing, dCas9 epigenetic modification, and several other transgene-free genome editing approaches are available to fill the lacuna of selection cycles and limited genetic diversity. Over the last few years, these technologies have led to revolutionary developments and researchers have quickly attained remarkable achievements. However, GETs are associated with various bottlenecks that prevent the scaling development of new varieties that can be dealt with by integrating the GETs with the improved conventional breeding methods such as speed breeding, which would take plant breeding to the next level. In this review, we have summarized all these traditional, molecular, and integrated approaches to speed up the breeding procedure of cereals.
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Affiliation(s)
- Muhammad Haroon
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
| | - Xiukang Wang
- College of Life Sciences, Yan’an University, Yan’an 716000, China
| | - Rabail Afzal
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
| | - Muhammad Mubashar Zafar
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Chinese Academy of Agricultural Science, Anyang 455000, China;
| | - Fahad Idrees
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (F.I.); (M.B.)
| | - Maria Batool
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (F.I.); (M.B.)
| | - Abdul Saboor Khan
- Institute of Plant Sciences, University of Cologne, 50667 Cologne, Germany;
| | - Muhammad Imran
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agriculture University, Guangzhou 510642, China;
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26
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Gong J, Peng Y, Yu J, Pei W, Zhang Z, Fan D, Liu L, Xiao X, Liu R, Lu Q, Li P, Shang H, Shi Y, Li J, Ge Q, Liu A, Deng X, Fan S, Pan J, Chen Q, Yuan Y, Gong W. Linkage and association analyses reveal that hub genes in energy-flow and lipid biosynthesis pathways form a cluster in upland cotton. Comput Struct Biotechnol J 2022; 20:1841-1859. [PMID: 35521543 PMCID: PMC9046884 DOI: 10.1016/j.csbj.2022.04.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 04/11/2022] [Accepted: 04/11/2022] [Indexed: 11/25/2022] Open
Abstract
Upland cotton is an important allotetraploid crop that provides both natural fiber for the textile industry and edible vegetable oil for the food or feed industry. To better understand the genetic mechanism that regulates the biosynthesis of storage oil in cottonseed, we identified the genes harbored in the major quantitative trait loci/nucleotides (QTLs/QTNs) of kernel oil content (KOC) in cottonseed via both multiple linkage analyses and genome-wide association studies (GWAS). In ‘CCRI70′ RILs, six stable QTLs were simultaneously identified by linkage analysis of CHIP and SLAF-seq strategies. In ‘0-153′ RILs, eight stable QTLs were detected by consensus linkage analysis integrating multiple strategies. In the natural panel, thirteen and eight loci were associated across multiple environments with two algorithms of GWAS. Within the confidence interval of a major common QTL on chromosome 3, six genes were identified as participating in the interaction network highly correlated with cottonseed KOC. Further observations of gene differential expression showed that four of the genes, LtnD, PGK, LPLAT1, and PAH2, formed hub genes and two of them, FER and RAV1, formed the key genes in the interaction network. Sequence variations in the coding regions of LtnD, FER, PGK, LPLAT1, and PAH2 genes may support their regulatory effects on oil accumulation in mature cottonseed. Taken together, clustering of the hub genes in the lipid biosynthesis interaction network provides new insights to understanding the mechanism of fatty acid biosynthesis and TAG assembly and to further genetic improvement projects for the KOC in cottonseeds.
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Affiliation(s)
- Juwu Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
- Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, Xinjiang, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Yan Peng
- Third Division of the Xinjiang Production and Construction Corps Agricultural Research Institute, Tumushuke, Xijiang 843900, China
| | - Jiwen Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Wenfeng Pei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Zhen Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Daoran Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Linjie Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
- Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, Xinjiang, China
| | - Xianghui Xiao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
- Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, Xinjiang, China
| | - Ruixian Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
- Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, Xinjiang, China
| | - Quanwei Lu
- College of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Pengtao Li
- College of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Yuzhen Shi
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Junwen Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Aiying Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Xiaoying Deng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Senmiao Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Jingtao Pan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Quanjia Chen
- Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, Xinjiang, China
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
- Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, Xinjiang, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Wankui Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
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27
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Shavit R, Batyrshina ZS, Yaakov B, Florean M, Köllner TG, Tzin V. The wheat dioxygenase BX6 is involved in the formation of benzoxazinoids in planta and contributes to plant defense against insect herbivores. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 316:111171. [PMID: 35151455 DOI: 10.1016/j.plantsci.2021.111171] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 12/22/2021] [Accepted: 12/25/2021] [Indexed: 06/14/2023]
Abstract
Benzoxazinoids are plant specialized metabolites with defense properties, highly abundant in wheat (Triticum), one of the world's most important crops. The goal of our study was to characterize dioxygenase BX6 genes in tetraploid and hexaploid wheat genotypes and to elucidate their effects on defense against herbivores. Phylogenetic analysis revealed four BX6 genes in the hexaploid wheat T. aestivum, but only one ortholog was found in the tetraploid (T. turgidum) wild emmer wheat and the cultivated durum wheat. Transcriptome sequencing of durum wheat plants, damaged by either aphids or caterpillars, revealed that several BX genes, including TtBX6, were upregulated upon caterpillar feeding, relative to the undamaged control plants. A virus-induced gene silencing approach was used to reduce the expression of BX6 in T. aestivum plants, which exhibited both reduced transcript levels and reduced accumulation of different benzoxazinoids. To elucidate the effect of BX6 on plant defense, bioassays with different herbivores feeding on BX6-silenced leaves were conducted. The results showed that plants with silenced BX6 were more susceptible to aphids and the two-spotted spider mite than the control. Overall, our study indicates that wheat BX6 is involved in benzoxazinoid formation in planta and contributes to plant resistance against insect herbivores.
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Affiliation(s)
- Reut Shavit
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Zhaniya S Batyrshina
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Beery Yaakov
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Matilde Florean
- Max Planck Institute for Chemical Ecology, Department of Natural Product Biosynthesis, D-07745, Jena, Germany
| | - Tobias G Köllner
- Max Planck Institute for Chemical Ecology, Department of Natural Product Biosynthesis, D-07745, Jena, Germany
| | - Vered Tzin
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel.
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28
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Xu Y, Zhang H, Zhong Y, Jiang N, Zhong X, Zhang Q, Chai S, Li H, Zhang Z. Comparative genomics analysis of bHLH genes in cucurbits identifies a novel gene regulating cucurbitacin biosynthesis. HORTICULTURE RESEARCH 2022; 9:uhac038. [PMID: 35184192 PMCID: PMC9071377 DOI: 10.1093/hr/uhac038] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/22/2022] [Accepted: 01/30/2022] [Indexed: 05/08/2023]
Abstract
The basic helix-loop-helix (bHLH) family of transcription factors (TFs) participate in a variety of biological regulatory processes in plants, and have undergone significant expansion during land plant evolution by gene duplications. In cucurbit crops, several bHLH genes have been found to be responsible for the agronomic traits such as bitterness. However, the characterization of bHLH genes across the genomes of cucurbit species has not been reported, and how they have evolved and diverged remains largely unanswered. Here we identified 1160 bHLH genes in seven cucurbit crops and performed a comprehensive comparative genomics analysis. We determined orthologous and paralogous bHLH genes across cucurbit crops by syntenic analysis between or within species. Orthology and phylogenetic analysis of the tandem-duplicated bHLH genes in the Bt cluster which regulate the biosynthesis of cucurbitacins suggest that this cluster is derived from three ancestral genes after the cucurbit-common tetraploidization event. Interestingly, we identified a new conserved cluster paralogous to the Bt cluster that includes two tandem bHLH genes, and the evolutionary history and expression profiles of these two genes in the new cluster suggest the involvement of one gene (Brp) in the regulation of cucurbitacin biosynthesis in roots. Further biochemical and transgenic assays in melon hairy roots support the function of Brp. This study provides useful information for further investigating the functions of bHLH TFs and novel insights into the regulation of cucurbitacin biosynthesis in cucurbit crops and other plants.
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Affiliation(s)
- Yuanchao Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huimin Zhang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Yang Zhong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Naiyu Jiang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiaoyun Zhong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qiqi Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Sen Chai
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Hongbo Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhonghua Zhang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
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29
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Kanyuka K. Virus-Mediated Protein Overexpression (VOX) in Monocots to Identify and Functionally Characterize Fungal Effectors. Methods Mol Biol 2022; 2523:93-112. [PMID: 35759193 DOI: 10.1007/978-1-0716-2449-4_7] [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] [Indexed: 06/15/2023]
Abstract
One of the important armories that pathogens utilize to successfully colonize the plants is small secreted effector proteins, which could perform a variety of functions from suppression of plant innate immunity to manipulation of plant physiology in favor of the disease. Plants, on the other hand, evolved disease resistance genes that recognize some of the effectors or avirulence (Avr) proteins. Both, identification of the Avr proteins and understanding of the mechanisms of action of other effectors, are important areas of research in the molecular plant-pathogen interactions field as this knowledge is critical for the development of new effective pathogen control measures. To enable functional analysis of the effectors, it is desirable to be able to overexpress them readily in the host plants. Here we describe detailed experimental protocols for transient effector overexpression in wheat and other monocots using binary Barley stripe mosaic virus (BSMV)- and Foxtail mosaic virus (FoMV)-derived vectors. This functional genomics tool, better known as VOX (Virus-mediated protein OvereXpression), is rapid and relatively simple and inexpensive.
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Affiliation(s)
- Kostya Kanyuka
- Plant Pathology and Entomology, NIAB, Cambridge, UK.
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK.
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30
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Zheng J, Yang C, Zheng X, Yan S, Qu F, Zhao J, Pei Y. Lipidomic, Transcriptomic, and BSA-660K Single Nucleotide Polymorphisms Profiling Reveal Characteristics of the Cuticular Wax in Wheat. FRONTIERS IN PLANT SCIENCE 2021; 12:794878. [PMID: 34899814 PMCID: PMC8652291 DOI: 10.3389/fpls.2021.794878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 10/26/2021] [Indexed: 05/15/2023]
Abstract
Plant epidermal wax helps protect plants from adverse environmental conditions, maintains the function of tissues and organs, and ensures normal plant development. However, the constituents of epidermal wax and the regulatory mechanism of their biosynthesis in wheat have not been fully understood. Wheat varieties with different wax content, Jinmai47 and Jinmai84, were selected to comparatively analyze their waxy components and genetic characteristics, using a combination of lipidomic, transcriptomic, and BSA-Wheat 660K chip analysis. Through lipidomic analysis, 1287 lipid molecules were identified representing 31 lipid subclasses. Among these, Diacylglycerols (DG), (O-acyl)-ω-hydroxy fatty acids (OAHFA), wax ester (WE), Triacylglycerols (TG), and Monoradylglycerols (MG) accounted for 96.4% of the total lipids in Jinmai84 and 94.5% in Jinmai47. DG, OAHFA, and WE were higher in Jinmai84 than in Jinmai47 with the content of OAHFA 2.88-fold greater and DG 1.66-fold greater. Transcriptome sequence and bioinformatics analysis revealed 63 differentially expressed genes related to wax biosynthesis. Differentially expressed genes (DEGs) were found to be involved with the OAHFA, DG, and MG of synthesis pathways, which enriched the wax metabolism pathway. Non-glaucous and glaucous bulks from a mapping population were used to identify single nucleotide polymorphisms (SNP) via 660K chip analysis. Two loci centered on chromosomes 2D and 4B were detected and the locus on 4B is likely novel. These data improve understanding of complex lipid metabolism for cuticular wax biosynthesis in wheat and lay the foundation for future detailed investigation of mechanisms regulating wax metabolism.
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Affiliation(s)
- Jun Zheng
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
- College of Life Science, Shanxi University, Taiyuan, China
| | - Chenkang Yang
- College of Life Science, Shanxi University, Taiyuan, China
| | - Xingwei Zheng
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Suxian Yan
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Fei Qu
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Jiajia Zhao
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Yanxi Pei
- College of Life Science, Shanxi University, Taiyuan, China
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Laskoś K, Czyczyło‐Mysza IM, Dziurka M, Noga A, Góralska M, Bartyzel J, Myśków B. Correlation between leaf epicuticular wax composition and structure, physio-biochemical traits and drought resistance in glaucous and non-glaucous near-isogenic lines of rye. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:93-119. [PMID: 34288188 PMCID: PMC9291005 DOI: 10.1111/tpj.15428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 07/10/2021] [Accepted: 07/14/2021] [Indexed: 05/06/2023]
Abstract
The objective of this research was to investigate the differences between glaucous and non-glaucous near-isogenic lines (NILs) of winter rye (Secale cereale L.) in terms of epicuticular wax layer properties (weight, composition, and crystal morphology), selected physiological and biochemical responses, yield components, above-ground biomass, and plant height under soil drought stress. An important aspect of this analysis was to examine the correlation between the above characteristics. Two different NIL pairs were tested, each consisting of a typical glaucous line and a non-glaucous line with a recessive mutation. The drought experiment was conducted twice (2015-2016). Our study showed that wax accumulation during drought was not correlated with higher leaf hydration and glaucousness. Environmental factors had a large impact on the response of the lines to drought in individual years, both in terms of physiological and biochemical reactions, and the composition of epicuticular leaf wax. The analysed pairs displayed significantly different responses to drought. Demonstration of the correlation between the components of rye leaf wax and the physiological and biochemical parameters of rye NILs is a significant achievement of this work. Interestingly, the study showed a correlation between the wax components and the content of photosynthetic pigments and tocopherols, whose biosynthesis, similarly to the biosynthesis of wax precursors, is mainly located in chloroplasts. This suggests a relationship between wax biosynthesis and plant response to various environmental conditions and drought stress.
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Affiliation(s)
- Kamila Laskoś
- The Franciszek Górski Institute of Plant Physiology Polish Academy of SciencesNiezapominajek 2130‐239Kraków
Poland
| | - Ilona M. Czyczyło‐Mysza
- The Franciszek Górski Institute of Plant Physiology Polish Academy of SciencesNiezapominajek 2130‐239Kraków
Poland
| | - Michał Dziurka
- The Franciszek Górski Institute of Plant Physiology Polish Academy of SciencesNiezapominajek 2130‐239Kraków
Poland
| | - Angelika Noga
- The Franciszek Górski Institute of Plant Physiology Polish Academy of SciencesNiezapominajek 2130‐239Kraków
Poland
| | - Magdalena Góralska
- Department of Plant Genetics, Breeding and BiotechnologyWest‐Pomeranian University of TechnologySłowackiego 1771‐434SzczecinPoland
| | - Jakub Bartyzel
- Department of Applied Nuclear PhysicsFaculty of Physics and Applied Computer ScienceAGH University of Science and TechnologyMickiewicza 330‐059KrakówPoland
| | - Beata Myśków
- Department of Plant Genetics, Breeding and BiotechnologyWest‐Pomeranian University of TechnologySłowackiego 1771‐434SzczecinPoland
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Ahmad HM, Wang X, Mahmood-Ur-Rahman, Fiaz S, Azeem F, Shaheen T. Morphological and Physiological Response of Helianthus annuus L. to Drought Stress and Correlation of Wax Contents for Drought Tolerance Traits. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2021. [DOI: 10.1007/s13369-021-06098-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Upadhyaya NM, Mago R, Panwar V, Hewitt T, Luo M, Chen J, Sperschneider J, Nguyen-Phuc H, Wang A, Ortiz D, Hac L, Bhatt D, Li F, Zhang J, Ayliffe M, Figueroa M, Kanyuka K, Ellis JG, Dodds PN. Genomics accelerated isolation of a new stem rust avirulence gene-wheat resistance gene pair. NATURE PLANTS 2021; 7:1220-1228. [PMID: 34294906 DOI: 10.1038/s41477-021-00971-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 06/18/2021] [Indexed: 06/13/2023]
Abstract
Stem rust caused by the fungus Puccinia graminis f. sp. tritici (Pgt) is a devastating disease of the global staple crop wheat. Although this disease was largely controlled in the latter half of the twentieth century, new virulent strains of Pgt, such as Ug99, have recently evolved1,2. These strains have caused notable losses worldwide and their continued spread threatens global wheat production. Breeding for disease resistance provides the most cost-effective control of wheat rust diseases3. A number of rust resistance genes have been characterized in wheat and most encode immune receptors of the nucleotide-binding leucine-rich repeat (NLR) class4, which recognize pathogen effector proteins known as avirulence (Avr) proteins5. However, only two Avr genes have been identified in Pgt so far, AvrSr35 and AvrSr50 (refs. 6,7), and none in other cereal rusts8,9. The Sr27 resistance gene was first identified in a wheat line carrying an introgression of the 3R chromosome from Imperial rye10. Although not deployed widely in wheat, Sr27 is widespread in the artificial crop species Triticosecale (triticale), which is a wheat-rye hybrid and is a host for Pgt11,12. Sr27 is effective against Ug99 (ref. 13) and other recent Pgt strains14,15. Here, we identify both the Sr27 gene in wheat and the corresponding AvrSr27 gene in Pgt and show that virulence to Sr27 can arise experimentally and in the field through deletion mutations, copy number variation and expression level polymorphisms at the AvrSr27 locus.
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Affiliation(s)
- Narayana M Upadhyaya
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Rohit Mago
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Vinay Panwar
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Tim Hewitt
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Ming Luo
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Jian Chen
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jana Sperschneider
- Biological Data Science Institute, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Hoa Nguyen-Phuc
- Department of Ecology and Evolutionary Biology, Vietnam National University, Ho Chi Minh, Vietnam
| | - Aihua Wang
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Diana Ortiz
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
- Génétique et Amélioration des Fruits et Légumes, INRA, Montfavet Cedex, France
| | - Luch Hac
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Dhara Bhatt
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Feng Li
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Jianping Zhang
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Michael Ayliffe
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Kostya Kanyuka
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Jeffrey G Ellis
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia.
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Trivedi P, Nguyen N, Klavins L, Kviesis J, Heinonen E, Remes J, Jokipii-Lukkari S, Klavins M, Karppinen K, Jaakola L, Häggman H. Analysis of composition, morphology, and biosynthesis of cuticular wax in wild type bilberry (Vaccinium myrtillus L.) and its glossy mutant. Food Chem 2021; 354:129517. [PMID: 33756336 DOI: 10.1101/2020.04.01.019893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 02/12/2021] [Accepted: 02/27/2021] [Indexed: 05/18/2023]
Abstract
In this study, cuticular wax load, its chemical composition, and biosynthesis, was studied during development of wild type (WT) bilberry fruit and its natural glossy type (GT) mutant. GT fruit cuticular wax load was comparable with WT fruits. In both, the proportion of triterpenoids decreased during fruit development concomitant with increasing proportions of total aliphatic compounds. In GT fruit, a higher proportion of triterpenoids in cuticular wax was accompanied by a lower proportion of fatty acids and ketones compared to WT fruit as well as lower density of crystalloid structures on berry surfaces. Our results suggest that the glossy phenotype could be caused by the absence of rod-like structures in GT fruit associated with reduction in proportions of ketones and fatty acids in the cuticular wax. Especially CER26-like, FAR2, CER3-like, LTP, MIXTA, and BAS genes showed fruit skin preferential expression patterns indicating their role in cuticular wax biosynthesis and secretion.
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Affiliation(s)
- Priyanka Trivedi
- Department of Ecology and Genetics, University of Oulu, FI-90014 Oulu, Finland.
| | - Nga Nguyen
- Department of Ecology and Genetics, University of Oulu, FI-90014 Oulu, Finland.
| | - Linards Klavins
- Department of Environmental Science, University of Latvia, LV-1004 Riga, Latvia.
| | - Jorens Kviesis
- Department of Environmental Science, University of Latvia, LV-1004 Riga, Latvia.
| | - Esa Heinonen
- Centre for Material Analysis, University of Oulu, FI-90014 Oulu, Finland.
| | - Janne Remes
- Centre for Material Analysis, University of Oulu, FI-90014 Oulu, Finland.
| | | | - Maris Klavins
- Department of Environmental Science, University of Latvia, LV-1004 Riga, Latvia.
| | - Katja Karppinen
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, NO-9037 Tromsø, Norway.
| | - Laura Jaakola
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, NO-9037 Tromsø, Norway; NIBIO, Norwegian Institute of Bioeconomy Research, NO-1431 Ås, Norway.
| | - Hely Häggman
- Department of Ecology and Genetics, University of Oulu, FI-90014 Oulu, Finland.
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Bharadwaj R, Kumar SR, Sharma A, Sathishkumar R. Plant Metabolic Gene Clusters: Evolution, Organization, and Their Applications in Synthetic Biology. FRONTIERS IN PLANT SCIENCE 2021; 12:697318. [PMID: 34490002 PMCID: PMC8418127 DOI: 10.3389/fpls.2021.697318] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/05/2021] [Indexed: 05/21/2023]
Abstract
Plants are a remarkable source of high-value specialized metabolites having significant physiological and ecological functions. Genes responsible for synthesizing specialized metabolites are often clustered together for a coordinated expression, which is commonly observed in bacteria and filamentous fungi. Similar to prokaryotic gene clustering, plants do have gene clusters encoding enzymes involved in the biosynthesis of specialized metabolites. More than 20 gene clusters involved in the biosynthesis of diverse metabolites have been identified across the plant kingdom. Recent studies demonstrate that gene clusters are evolved through gene duplications and neofunctionalization of primary metabolic pathway genes. Often, these clusters are tightly regulated at nucleosome level. The prevalence of gene clusters related to specialized metabolites offers an attractive possibility of an untapped source of highly useful biomolecules. Accordingly, the identification and functional characterization of novel biosynthetic pathways in plants need to be worked out. In this review, we summarize insights into the evolution of gene clusters and discuss the organization and importance of specific gene clusters in the biosynthesis of specialized metabolites. Regulatory mechanisms which operate in some of the important gene clusters have also been briefly described. Finally, we highlight the importance of gene clusters to develop future metabolic engineering or synthetic biology strategies for the heterologous production of novel metabolites.
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Affiliation(s)
- Revuru Bharadwaj
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Sarma R. Kumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Ashutosh Sharma
- Tecnologico de Monterrey, Centre of Bioengineering, Querétaro, Mexico
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
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Qi P, Pendergast TH, Johnson A, Bahri BA, Choi S, Missaoui A, Devos KM. Quantitative trait locus mapping combined with variant and transcriptome analyses identifies a cluster of gene candidates underlying the variation in leaf wax between upland and lowland switchgrass ecotypes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1957-1975. [PMID: 33760937 PMCID: PMC8263549 DOI: 10.1007/s00122-021-03798-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/19/2021] [Indexed: 06/06/2023]
Abstract
Mapping combined with expression and variant analyses in switchgrass, a crop with complex genetics, identified a cluster of candidate genes for leaf wax in a fast-evolving region of chromosome 7K. Switchgrass (Panicum virgatum L.) is a promising warm-season candidate energy crop. It occurs in two ecotypes, upland and lowland, which vary in a number of phenotypic traits, including leaf glaucousness. To initiate trait mapping, two F2 mapping populations were developed by crossing two different F1 sibs derived from a cross between the tetraploid lowland genotype AP13 and the tetraploid upland genotype VS16, and high-density linkage maps were generated. Quantitative trait locus (QTL) analyses of visually scored leaf glaucousness and of hydrophobicity of the abaxial leaf surface measured using a drop shape analyzer identified highly significant colocalizing QTL on chromosome 7K (Chr07K). Using a multipronged approach, we identified a cluster of genes including Pavir.7KG077009, which encodes a Type III polyketide synthase-like protein, and Pavir.7KG013754 and Pavir.7KG030500, two highly similar genes that encode putative acyl-acyl carrier protein (ACP) thioesterases, as strong candidates underlying the QTL. The lack of homoeologs for any of the three genes on Chr07N, the relatively low level of identity with other switchgrass KCS proteins and thioesterases, as well as the organization of the surrounding region suggest that Pavir.7KG077009 and Pavir.7KG013754/Pavir.7KG030500 were duplicated into a fast-evolving chromosome region, which led to their neofunctionalization. Furthermore, sequence analyses showed all three genes to be absent in the two upland compared to the two lowland accessions analyzed. This study provides an example of and practical guide for trait mapping and candidate gene identification in a complex genetic system by combining QTL mapping, transcriptomics and variant analysis.
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Affiliation(s)
- Peng Qi
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
- Institute of Plant Breeding, Genetics and Genomics, and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Thomas H Pendergast
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
- Institute of Plant Breeding, Genetics and Genomics, and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Alex Johnson
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Bochra A Bahri
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
- Institute of Plant Breeding, Genetics and Genomics, and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Pathology, University of Georgia, Griffin, GA, 30223, USA
| | - Soyeon Choi
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Ali Missaoui
- Institute of Plant Breeding, Genetics and Genomics, and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Katrien M Devos
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
- Institute of Plant Breeding, Genetics and Genomics, and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA.
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Polturak G, Osbourn A. The emerging role of biosynthetic gene clusters in plant defense and plant interactions. PLoS Pathog 2021; 17:e1009698. [PMID: 34214143 PMCID: PMC8253395 DOI: 10.1371/journal.ppat.1009698] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Guy Polturak
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, United Kingdom
| | - Anne Osbourn
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, United Kingdom
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Sequence of the supernumerary B chromosome of maize provides insight into its drive mechanism and evolution. Proc Natl Acad Sci U S A 2021; 118:2104254118. [PMID: 34088847 PMCID: PMC8201846 DOI: 10.1073/pnas.2104254118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
B chromosomes are enigmatic elements in thousands of plant and animal genomes that persist in populations despite being nonessential. They circumvent the laws of Mendelian inheritance but the molecular mechanisms underlying this behavior remain unknown. Here we present the sequence, annotation, and analysis of the maize B chromosome providing insight into its drive mechanism. The sequence assembly reveals detailed locations of the elements involved with the cis and trans functions of its drive mechanism, consisting of nondisjunction at the second pollen mitosis and preferential fertilization of the egg by the B-containing sperm. We identified 758 protein-coding genes in 125.9 Mb of B chromosome sequence, of which at least 88 are expressed. Our results demonstrate that transposable elements in the B chromosome are shared with the standard A chromosome set but multiple lines of evidence fail to detect a syntenic genic region in the A chromosomes, suggesting a distant origin. The current gene content is a result of continuous transfer from the A chromosomal complement over an extended evolutionary time with subsequent degradation but with selection for maintenance of this nonvital chromosome.
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Yang S, Overlander M, Fiedler J. Genetic analysis of the barley variegation mutant, grandpa1.a. BMC PLANT BIOLOGY 2021; 21:134. [PMID: 33711931 PMCID: PMC7955646 DOI: 10.1186/s12870-021-02915-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 03/04/2021] [Indexed: 05/30/2023]
Abstract
BACKGROUND Providing the photosynthesis factory for plants, chloroplasts are critical for crop biomass and economic yield. However, chloroplast development is a complicated process, coordinated by the cross-communication between the nucleus and plastids, and the underlying biogenesis mechanism has not been fully revealed. Variegation mutants have provided ideal models to identify genes or factors involved in chloroplast development. Well-developed chloroplasts are present in the green tissue areas, while the white areas contain undifferentiated plastids that are deficient in chlorophyll. Unlike albino plants, variegation mutants survive to maturity and enable investigation into the signaling pathways underlying chloroplast biogenesis. The allelic variegated mutants in barley, grandpa 1 (gpa1), have long been identified but have not been genetically characterized. RESULTS We characterized and genetically analyzed the grandpa1.a (gpa1.a) mutant. The chloroplast ultrastructure was evaluated using transmission electron microscopy (TEM), and it was confirmed that chloroplast biogenesis was disrupted in the white sections of gpa1.a. To determine the precise position of Gpa1, a high-resolution genetic map was constructed. Segregating individuals were genotyped with the barley 50 k iSelect SNP Array, and the linked SNPs were converted to PCR-based markers for genetic mapping. The Gpa1 gene was mapped to chromosome 2H within a gene cluster functionally related to photosynthesis or chloroplast differentiation. In the variegated gpa1.a mutant, we identified a large deletion in this gene cluster that eliminates a putative plastid terminal oxidase (PTOX). CONCLUSIONS Here we characterized and genetically mapped the gpa1.a mutation causing a variegation phenotype in barley. The PTOX-encoding gene in the delimited region is a promising candidate for Gpa1. Therefore, the present study provides a foundation for the cloning of Gpa1, which will elevate our understanding of the molecular mechanisms underlying chloroplast biogenesis, particularly in monocot plants.
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Affiliation(s)
- Shengming Yang
- USDA-ARS Cereals Research Unit, Edward T. Schafer Agriculture Research Center, Fargo, ND, 58102, USA.
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58102, USA.
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58102, USA.
| | - Megan Overlander
- USDA-ARS Cereals Research Unit, Edward T. Schafer Agriculture Research Center, Fargo, ND, 58102, USA
| | - Jason Fiedler
- USDA-ARS Cereals Research Unit, Edward T. Schafer Agriculture Research Center, Fargo, ND, 58102, USA
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58102, USA
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40
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Trivedi P, Nguyen N, Klavins L, Kviesis J, Heinonen E, Remes J, Jokipii-Lukkari S, Klavins M, Karppinen K, Jaakola L, Häggman H. Analysis of composition, morphology, and biosynthesis of cuticular wax in wild type bilberry (Vaccinium myrtillus L.) and its glossy mutant. Food Chem 2021; 354:129517. [PMID: 33756336 DOI: 10.1016/j.foodchem.2021.129517] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 02/12/2021] [Accepted: 02/27/2021] [Indexed: 10/22/2022]
Abstract
In this study, cuticular wax load, its chemical composition, and biosynthesis, was studied during development of wild type (WT) bilberry fruit and its natural glossy type (GT) mutant. GT fruit cuticular wax load was comparable with WT fruits. In both, the proportion of triterpenoids decreased during fruit development concomitant with increasing proportions of total aliphatic compounds. In GT fruit, a higher proportion of triterpenoids in cuticular wax was accompanied by a lower proportion of fatty acids and ketones compared to WT fruit as well as lower density of crystalloid structures on berry surfaces. Our results suggest that the glossy phenotype could be caused by the absence of rod-like structures in GT fruit associated with reduction in proportions of ketones and fatty acids in the cuticular wax. Especially CER26-like, FAR2, CER3-like, LTP, MIXTA, and BAS genes showed fruit skin preferential expression patterns indicating their role in cuticular wax biosynthesis and secretion.
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Affiliation(s)
- Priyanka Trivedi
- Department of Ecology and Genetics, University of Oulu, FI-90014 Oulu, Finland.
| | - Nga Nguyen
- Department of Ecology and Genetics, University of Oulu, FI-90014 Oulu, Finland.
| | - Linards Klavins
- Department of Environmental Science, University of Latvia, LV-1004 Riga, Latvia.
| | - Jorens Kviesis
- Department of Environmental Science, University of Latvia, LV-1004 Riga, Latvia.
| | - Esa Heinonen
- Centre for Material Analysis, University of Oulu, FI-90014 Oulu, Finland.
| | - Janne Remes
- Centre for Material Analysis, University of Oulu, FI-90014 Oulu, Finland.
| | | | - Maris Klavins
- Department of Environmental Science, University of Latvia, LV-1004 Riga, Latvia.
| | - Katja Karppinen
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, NO-9037 Tromsø, Norway.
| | - Laura Jaakola
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, NO-9037 Tromsø, Norway; NIBIO, Norwegian Institute of Bioeconomy Research, NO-1431 Ås, Norway.
| | - Hely Häggman
- Department of Ecology and Genetics, University of Oulu, FI-90014 Oulu, Finland.
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Li L, Chai L, Xu H, Zhai H, Wang T, Zhang M, You M, Peng H, Yao Y, Hu Z, Xin M, Guo W, Sun Q, Chen X, Ni Z. Phenotypic characterization of the glossy1 mutant and fine mapping of GLOSSY1 in common wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:835-847. [PMID: 33404673 DOI: 10.1007/s00122-020-03734-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/18/2020] [Indexed: 05/14/2023]
Abstract
A novel wax locus GLOSSY1 was finely mapped to an approximately 308.1-kbp genomic interval on chromosome 2DS of wheat. The epicuticular wax, the outermost layer of aerial organs, gives plants their bluish-white (glaucous) appearance. Epicuticular wax is ubiquitous and provides an essential protective function against environmental stresses. In this study, we identified the glossy1 mutant on the basis of its glossy glume from an EMS population in the elite wheat (Triticum aestivum L.) cultivar Jimai22. The mutant had a dramatically different profile in total wax load and composition of individual wax constituents relative to the wild type, resulting in the increased cuticle permeability of glumes. The glossy glume phenotype was controlled by a single, semidominant locus mapping to the short arm of chromosome 2D, within a 308.1-kbp genomic interval that contained ten annotated protein-coding genes. These results pave the way for an in-depth analysis of the underlying genetic basis of wax formation patterns and enrich our understanding of mechanisms regulating wax metabolism.
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Affiliation(s)
- Linghong Li
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Lingling Chai
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Huanwen Xu
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Huijie Zhai
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Tianya Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Mingyi Zhang
- Dryland Agricultural Research Centre, Shanxi Academy of Agricultural Sciences, Taiyuan, 030031, China
| | - Mingshan You
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Weilong Guo
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Xiyong Chen
- Hebei Crop Genetic Breeding Laboratory, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China.
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China.
- National Plant Gene Research Centre, Beijing, 100193, China.
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Dong Y, Sonawane P, Cohen H, Polturak G, Feldberg L, Avivi SH, Rogachev I, Aharoni A. High mass resolution, spatial metabolite mapping enhances the current plant gene and pathway discovery toolbox. THE NEW PHYTOLOGIST 2020; 228:1986-2002. [PMID: 32654288 DOI: 10.1111/nph.16809] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/06/2020] [Indexed: 05/21/2023]
Abstract
Understanding when and where metabolites accumulate provides important cues to the gene function. Mass spectrometry imaging (MSI) enables in situ temporal and spatial measurement of a large assortment of metabolites, providing mapping information regarding their cellular distribution. To describe the current state and technical advances using MSI in plant sciences, we employed MSI to demonstrate its significant contribution to the study of plant specialised metabolism. We show that coupling MSI with: (1) RNA interference (RNAi), (2) virus induced gene silencing (VIGS), (3) agroinfiltration or (4) samples derived from plant natural variation provides great opportunities to understand the accurate gene-metabolite relationship and discover novel gene-associated metabolites. This was exemplified in three plant species (i.e. tomato, tobacco and wheat) by mapping the distribution of metabolites possessing a range of polarities. In particular, we demonstrated that MSI is able to spatially map an entire metabolic pathway, including intermediates and final products, in the intricate biosynthetic route to tomato fruit steroidal glycoalkaloids. We therefore envisage MSI as a key component of the metabolome analysis arsenal employed in plant gene discovery strategies.
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Affiliation(s)
- Yonghui Dong
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 761001, Israel
| | - Prashant Sonawane
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 761001, Israel
| | - Hagai Cohen
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 761001, Israel
| | - Guy Polturak
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 761001, Israel
| | - Liron Feldberg
- Department of Analytical Chemistry, Israel Institute for Biological Research, Ness Ziona, 7410001, Israel
| | - Shelly Hen Avivi
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 761001, Israel
| | - Ilana Rogachev
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 761001, Israel
| | - Asaph Aharoni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 761001, Israel
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Bragg J, Tomasi P, Zhang L, Williams T, Wood D, Lovell JT, Healey A, Schmutz J, Bonnette JE, Cheng P, Chanbusarakum L, Juenger T, Tobias CM. Environmentally responsive QTL controlling surface wax load in switchgrass. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:3119-3137. [PMID: 32803378 DOI: 10.1007/s00122-020-03659-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
KEY MESSAGE Quantitation of leaf surface wax on a population of switchgrass identified three significant QTL present across six environments that contribute to leaf glaucousness and wax composition and that show complex genetic × environmental (G × E) interactions. The C4 perennial grass Panicum virgatum (switchgrass) is a native species of the North American tallgrass prairie. This adaptable plant can be grown on marginal lands and is useful for soil and water conservation, biomass production, and as a forage. Two major switchgrass ecotypes, lowland and upland, differ in a range of desirable traits, and the responsible underlying loci can be localized efficiently in a pseudotestcross design. An outbred four-way cross (4WCR) mapping population of 750 F2 lines was used to examine the genetic basis of differences in leaf surface wax load between two lowland (AP13 and WBC) and two upland (DAC and VS16) tetraploid cultivars. The objective of our experiments was to identify wax compositional variation among the population founders and to map underlying loci responsible for surface wax variation across environments. GCMS analyses of surface wax extracted from 4WCR F0 founders and F1 hybrids reveal higher levels of wax in lowland genotypes and show quantitative differences of β-diketones, primary alcohols, and other wax constituents. The full mapping population was sampled over two seasons from four field sites with latitudes ranging from 30 to 42 °N, and leaf surface wax was measured. We identified three high-confidence QTL, of which two displayed significant G × E effects. Over 50 candidate genes underlying the QTL regions showed similarity to genes in either Arabidopsis or barley known to function in wax synthesis, modification, regulation, and transport.
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Affiliation(s)
- Jennifer Bragg
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Albany, CA, USA
| | - Pernell Tomasi
- Arid-Land Agricultural Research Center, Plant Physiology and Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Maricopa, AZ, USA
| | - Li Zhang
- Department of Integrative Biology, College of Natural Sciences, University of Texas at Austin, Austin, TX, USA
| | - Tina Williams
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Albany, CA, USA
| | - Delilah Wood
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Albany, CA, USA
| | - John T Lovell
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Adam Healey
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jason E Bonnette
- Department of Integrative Biology, College of Natural Sciences, University of Texas at Austin, Austin, TX, USA
| | - Prisca Cheng
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Albany, CA, USA
| | - Lisa Chanbusarakum
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Albany, CA, USA
| | - Thomas Juenger
- Department of Integrative Biology, College of Natural Sciences, University of Texas at Austin, Austin, TX, USA
| | - Christian M Tobias
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Albany, CA, USA.
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Huang L, Xiao Q, Zhao X, Wang D, Wei L, Li X, Liu Y, He Z, Kang L, Guo Y. Responses of cuticular waxes of faba bean to light wavelengths and selection of candidate genes for cuticular wax biosynthesis. THE PLANT GENOME 2020; 13:e20058. [PMID: 33124766 DOI: 10.1002/tpg2.20058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 08/29/2020] [Indexed: 06/11/2023]
Abstract
Cuticular waxes play important eco-physiological roles in protecting plants against abiotic and biotic stresses and show high sensitivity to environmental changes. In order to clarify the responses of cuticular waxes on faba bean (Vicia faba L.) leaves to different light wavelengths, the phenotypic plasticity of cuticular waxes was analyzed when plants were subjected to white, red, yellow, blue, and purple light. Leaf samples from yellow, purple, and white lights were further analyzed, and candidate genes of wax biosynthesis were selected by RNA-seq technology and transcriptome processing. Yellow light increased the total wax coverage and changed the crystal structure compared with leaves under white light. Light wavelengths changed the relative abundance of dominant primary alcohol from C24 under white, yellow, and red lights to C26 under blue and purple lights. In total, 100,194 unigenes were obtained, and 10 genes were annotated in wax biosynthesis pathway, including VLCFAs elongation (KCS1, KCS4, LACS2 and LACS9), acyl reduction pathway (FAR3 and WSD1), and decarboxylation pathway (CER1, CER3 and MAH1). qRT-PCR analysis revealed that yellow and purple lights significantly influenced the expression levels of these genes. Yellow light also increased the water loss rate and decreased the photosynthesis rate. Light at different wavelengths particularly yellow light induced the changes of phenotypic plasticity of cuticular waxes, which thus altered the leaf eco-physiological functions. The expression levels of genes related to wax biosynthesis were also altered by different light wavelengths, suggesting that light at different wavelengths may also be applied in selecting candidate genes involved in wax biosynthesis in other crops.
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Affiliation(s)
- Lei Huang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Qianlin Xiao
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Xiao Zhao
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Dengke Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Liangliang Wei
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Xiaoting Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Yating Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Zhibin He
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Lin Kang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Yanjun Guo
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
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Ahumada-Flores S, Gómez Pando LR, Parra Cota FI, de la Cruz Torres E, Sarsu F, de Los Santos Villalobos S. Technical note: Gamma irradiation induces changes of phenotypic and agronomic traits in wheat (Triticum turgidum ssp. durum). Appl Radiat Isot 2020; 167:109490. [PMID: 33121892 DOI: 10.1016/j.apradiso.2020.109490] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 10/15/2020] [Accepted: 10/21/2020] [Indexed: 10/23/2022]
Abstract
WHEAT VAR CIRNO C2008 was irradiated with gamma rays at 100, 200, and 300 Gy. The irradiated plants obtained at 300 Gy (M1) showed a significant reduction (compared to M0 plants) in germination (i.e. 3.8% at day 5), survival percentage (48%), and plant height (63.3%). Thus, the Probit analysis showed an LD50 of 287.80 Gy. Besides, these irradiated plants, in the field, showed a significant increase (compared to M0 plants) in days to spike initiation (16 days), and maturation (14 days). On the other hand, in the field, fourteen chlorophyll mutants were found (at a different frequency) in the M2 generation, such as Albina, Anthocyanin, Chlorina, Maculata, Tigrina, Striata, Viridis, Viridoalbina, Alboviridis, Xantha, Xanthviridis, Xanthalba, Viridoxantha, and Orange stem. In addition, mutants with changes in agronomic and morphological traits were observed. This nuclear technique is an alternative to obtain promising mutant lines that can be used directly as a variety and/or as parental to transfer these traits to other varieties.
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Affiliation(s)
- Sergio Ahumada-Flores
- -Instituto Tecnológico de Sonora, 5 de Febrero 818 sur, 85000, Cd. Obregón, Sonora, Mexico
| | | | - Fannie Isela Parra Cota
- -Campo Experimental Norman E. Borlaug, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Norman E. Borlaug Km 12, 85000, Cd. Obregón, Sonora, Mexico
| | - Eulogio de la Cruz Torres
- -Instituto Nacional de Investigaciones Nucleares, Carretera México-Toluca S/N, La Marquesa, Ocoyoacac, Edo. México, C.P, 52750, Mexico
| | - Fatma Sarsu
- - Plant Breeding and Genetic Section, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna, Austria
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Formation and diversification of a paradigm biosynthetic gene cluster in plants. Nat Commun 2020; 11:5354. [PMID: 33097700 PMCID: PMC7584637 DOI: 10.1038/s41467-020-19153-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/29/2020] [Indexed: 12/31/2022] Open
Abstract
Numerous examples of biosynthetic gene clusters (BGCs), including for compounds of agricultural and medicinal importance, have now been discovered in plant genomes. However, little is known about how these complex traits are assembled and diversified. Here, we examine a large number of variants within and between species for a paradigm BGC (the thalianol cluster), which has evolved recently in a common ancestor of the Arabidopsis genus. Comparisons at the species level reveal differences in BGC organization and involvement of auxiliary genes, resulting in production of species-specific triterpenes. Within species, the thalianol cluster is primarily fixed, showing a low frequency of deleterious haplotypes. We further identify chromosomal inversion as a molecular mechanism that may shuffle more distant genes into the cluster, so enabling cluster compaction. Antagonistic natural selection pressures are likely involved in shaping the occurrence and maintenance of this BGC. Our work sheds light on the birth, life and death of complex genetic and metabolic traits in plants.
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Góralska M, Bińkowski J, Lenarczyk N, Bienias A, Grądzielewska A, Czyczyło-Mysza I, Kapłoniak K, Stojałowski S, Myśków B. How Machine Learning Methods Helped Find Putative Rye Wax Genes Among GBS Data. Int J Mol Sci 2020; 21:E7501. [PMID: 33053706 PMCID: PMC7593958 DOI: 10.3390/ijms21207501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/23/2020] [Accepted: 10/07/2020] [Indexed: 11/17/2022] Open
Abstract
The standard approach to genetic mapping was supplemented by machine learning (ML) to establish the location of the rye gene associated with epicuticular wax formation (glaucous phenotype). Over 180 plants of the biparental F2 population were genotyped with the DArTseq (sequencing-based diversity array technology). A maximum likelihood (MLH) algorithm (JoinMap 5.0) and three ML algorithms: logistic regression (LR), random forest and extreme gradient boosted trees (XGBoost), were used to select markers closely linked to the gene encoding wax layer. The allele conditioning the nonglaucous appearance of plants, derived from the cultivar Karlikovaja Zelenostebelnaja, was mapped at the chromosome 2R, which is the first report on this localization. The DNA sequence of DArT-Silico 3585843, closely linked to wax segregation detected by using ML methods, was indicated as one of the candidates controlling the studied trait. The putative gene encodes the ABCG11 transporter.
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Affiliation(s)
- Magdalena Góralska
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Szczecin, ul. Słowackiego 17, 71–434 Szczecin, Poland; (M.G.); (J.B.); (N.L.); (A.B.); (S.S.)
| | - Jan Bińkowski
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Szczecin, ul. Słowackiego 17, 71–434 Szczecin, Poland; (M.G.); (J.B.); (N.L.); (A.B.); (S.S.)
| | - Natalia Lenarczyk
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Szczecin, ul. Słowackiego 17, 71–434 Szczecin, Poland; (M.G.); (J.B.); (N.L.); (A.B.); (S.S.)
| | - Anna Bienias
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Szczecin, ul. Słowackiego 17, 71–434 Szczecin, Poland; (M.G.); (J.B.); (N.L.); (A.B.); (S.S.)
| | - Agnieszka Grądzielewska
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, ul. Akademicka, 20–950 Lublin, Poland;
| | - Ilona Czyczyło-Mysza
- Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, Niezapominajek 21, 30–239 Kraków, Poland; (I.C.-M.); (K.K.)
| | - Kamila Kapłoniak
- Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, Niezapominajek 21, 30–239 Kraków, Poland; (I.C.-M.); (K.K.)
| | - Stefan Stojałowski
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Szczecin, ul. Słowackiego 17, 71–434 Szczecin, Poland; (M.G.); (J.B.); (N.L.); (A.B.); (S.S.)
| | - Beata Myśków
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Szczecin, ul. Słowackiego 17, 71–434 Szczecin, Poland; (M.G.); (J.B.); (N.L.); (A.B.); (S.S.)
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von Wettstein-Knowles P. Ecophysiology with barley eceriferum (cer) mutants: the effects of humidity and wax crystal structure on yield and vegetative parameters. ANNALS OF BOTANY 2020; 126:301-313. [PMID: 32361758 PMCID: PMC7380459 DOI: 10.1093/aob/mcaa086] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/26/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND AND AIMS In addition to preventing water loss, plant cuticles must also regulate nutrient loss via leaching. The eceriferum mutants in Hordeum vulgare (barley) potentially influence these functions by altering epicuticular wax structure and composition. METHODS Cultivar 'Bonus' and five of its cer mutants were grown under optimal conditions for vegetative growth and maturation, and nine traits were measured. Nutrient and water amounts going through the soil and the amount of simulated rain as deionized water, affecting phyllosphere humidity, delivered during either the vegetative or maturation phase, were varied. Cer leaf genes and three wilty (wlt) mutations were characterized for reaction to toluidine blue and the rate of non-stomatal water loss. KEY RESULTS Vegetative phase rain on 'Bonus' significantly decreased kernel weight and numbers by 15-30 %, while in cer.j59 and .c36 decreases of up to 42 % occurred. Maturation phase findings corroborated those from the vegetative phase. Significant pleiotropic effects were identified: cer.j59 decreased culm and spike length and 1000-kernel weight, .c36 decreased kernel number and weight, .i16 decreased spike length and .e8 increased culm height. Excepting Cer.zv and .ym mutations, none of the other 27 Cer leaf genes or wlt mutations played significant roles, if any, in preventing water loss. Cer.zv and .ym mutants lost non-stomatal water 13.5 times faster than those of Cer.j, .yi, .ys and .zp and 18.3 times faster than those of four cultivars and the mutants tested here. CONCLUSIONS Using yield to measure the net effect of phyllosphere humidity and wax crystal structure revealed that the former is far more important than the latter. The amenable experimental setup described here can be used to delve deeper. Significant pleiotropic effects were identified for mutations in four Cer genes, of which one is known to participate in wax biosynthesis. Twenty-seven Cer leaf genes and three wlt mutations have little if any effect on water loss.
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Lacchini E, Goossens A. Combinatorial Control of Plant Specialized Metabolism: Mechanisms, Functions, and Consequences. Annu Rev Cell Dev Biol 2020; 36:291-313. [PMID: 32559387 DOI: 10.1146/annurev-cellbio-011620-031429] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Plants constantly perceive internal and external cues, many of which they need to address to safeguard their proper development and survival. They respond to these cues by selective activation of specific metabolic pathways involving a plethora of molecular players that act and interact in complex networks. In this review, we illustrate and discuss the complexity in the combinatorial control of plant specialized metabolism. We hereby go beyond the intuitive concept of combinatorial control as exerted by modular-acting complexes of transcription factors that govern expression of specialized metabolism genes. To extend this discussion, we also consider all known hierarchical levels of regulation of plant specialized metabolism and their interfaces by referring to reported regulatory concepts from the plant field. Finally, we speculate on possible yet-to-be-discovered regulatory principles of plant specialized metabolism that are inspired by knowledge from other kingdoms of life and areas of biological research.
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Affiliation(s)
- Elia Lacchini
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; , .,Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; , .,Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
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Genome-Wide Association Study for Maize Leaf Cuticular Conductance Identifies Candidate Genes Involved in the Regulation of Cuticle Development. G3-GENES GENOMES GENETICS 2020; 10:1671-1683. [PMID: 32184371 PMCID: PMC7202004 DOI: 10.1534/g3.119.400884] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The cuticle, a hydrophobic layer of cutin and waxes synthesized by plant epidermal cells, is the major barrier to water loss when stomata are closed at night and under water-limited conditions. Elucidating the genetic architecture of natural variation for leaf cuticular conductance (gc) is important for identifying genes relevant to improving crop productivity in drought-prone environments. To this end, we conducted a genome-wide association study of gc of adult leaves in a maize inbred association panel that was evaluated in four environments (Maricopa, AZ, and San Diego, CA, in 2016 and 2017). Five genomic regions significantly associated with gc were resolved to seven plausible candidate genes (ISTL1, two SEC14 homologs, cyclase-associated protein, a CER7 homolog, GDSL lipase, and β-D-XYLOSIDASE 4). These candidates are potentially involved in cuticle biosynthesis, trafficking and deposition of cuticle lipids, cutin polymerization, and cell wall modification. Laser microdissection RNA sequencing revealed that all these candidate genes, with the exception of the CER7 homolog, were expressed in the zone of the expanding adult maize leaf where cuticle maturation occurs. With direct application to genetic improvement, moderately high average predictive abilities were observed for whole-genome prediction of gc in locations (0.46 and 0.45) and across all environments (0.52). The findings of this study provide novel insights into the genetic control of gc and have the potential to help breeders more effectively develop drought-tolerant maize for target environments.
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