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McLeod L, Barchi L, Tumino G, Tripodi P, Salinier J, Gros C, Boyaci HF, Ozalp R, Borovsky Y, Schafleitner R, Barchenger D, Finkers R, Brouwer M, Stein N, Rabanus-Wallace MT, Giuliano G, Voorrips R, Paran I, Lefebvre V. Multi-environment association study highlights candidate genes for robust agronomic quantitative trait loci in a novel worldwide Capsicum core collection. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1508-1528. [PMID: 37602679 DOI: 10.1111/tpj.16425] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/13/2023] [Accepted: 08/04/2023] [Indexed: 08/22/2023]
Abstract
Investigating crop diversity through genome-wide association studies (GWAS) on core collections helps in deciphering the genetic determinants of complex quantitative traits. Using the G2P-SOL project world collection of 10 038 wild and cultivated Capsicum accessions from 10 major genebanks, we assembled a core collection of 423 accessions representing the known genetic diversity. Since complex traits are often highly dependent upon environmental variables and genotype-by-environment (G × E) interactions, multi-environment GWAS with a 10 195-marker genotypic matrix were conducted on a highly diverse subset of 350 Capsicum annuum accessions, extensively phenotyped in up to six independent trials from five climatically differing countries. Environment-specific and multi-environment quantitative trait loci (QTLs) were detected for 23 diverse agronomic traits. We identified 97 candidate genes potentially implicated in 53 of the most robust and high-confidence QTLs for fruit flavor, color, size, and shape traits, and for plant productivity, vigor, and earliness traits. Investigating the genetic architecture of agronomic traits in this way will assist the development of genetic markers and pave the way for marker-assisted selection. The G2P-SOL pepper core collection will be available upon request as a unique and universal resource for further exploitation in future gene discovery and marker-assisted breeding efforts by the pepper community.
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Affiliation(s)
- Louis McLeod
- INRAE, GAFL, Montfavet, France
- INRAE, A2M, Montfavet, France
| | - Lorenzo Barchi
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Giorgio Tumino
- Plant Breeding, Wageningen University and Research (WUR), Wageningen, The Netherlands
| | - Pasquale Tripodi
- Research Centre for Vegetable and Ornamental Crops, Council for Agricultural Research and Economics (CREA), Pontecagnano Faiano, Italy
| | | | | | | | - Ramazan Ozalp
- Bati Akdeniz Agricultural Research Institute (BATEM), Antalya, Türkiye
| | - Yelena Borovsky
- The Volcani Center, Institute of Plant Sciences, Agricultural Research Organization (ARO), Rishon LeZion, Israel
| | - Roland Schafleitner
- Vegetable Diversity and Improvement, World Vegetable Center, Shanhua, Taiwan
| | - Derek Barchenger
- Vegetable Diversity and Improvement, World Vegetable Center, Shanhua, Taiwan
| | - Richard Finkers
- Plant Breeding, Wageningen University and Research (WUR), Wageningen, The Netherlands
| | - Matthijs Brouwer
- Plant Breeding, Wageningen University and Research (WUR), Wageningen, The Netherlands
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Corre, Gatersleben, Germany
- Department of Crop Sciences, Center for Integrated Breeding Research, Georg-August-University, Göttingen, Germany
| | | | - Giovanni Giuliano
- Casaccia Research Centre, Italian National Agency for New Technologies, Energy, and Sustainable Economic Development (ENEA), Rome, Italy
| | - Roeland Voorrips
- Plant Breeding, Wageningen University and Research (WUR), Wageningen, The Netherlands
| | - Ilan Paran
- The Volcani Center, Institute of Plant Sciences, Agricultural Research Organization (ARO), Rishon LeZion, Israel
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Tariq H, Asif S, Andleeb A, Hano C, Abbasi BH. Flavonoid Production: Current Trends in Plant Metabolic Engineering and De Novo Microbial Production. Metabolites 2023; 13:metabo13010124. [PMID: 36677049 PMCID: PMC9864322 DOI: 10.3390/metabo13010124] [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: 10/19/2022] [Revised: 12/23/2022] [Accepted: 01/10/2023] [Indexed: 01/14/2023] Open
Abstract
Flavonoids are secondary metabolites that represent a heterogeneous family of plant polyphenolic compounds. Recent research has determined that the health benefits of fruits and vegetables, as well as the therapeutic potential of medicinal plants, are based on the presence of various bioactive natural products, including a high proportion of flavonoids. With current trends in plant metabolite research, flavonoids have become the center of attention due to their significant bioactivity associated with anti-cancer, antioxidant, anti-inflammatory, and anti-microbial activities. However, the use of traditional approaches, widely associated with the production of flavonoids, including plant extraction and chemical synthesis, has not been able to establish a scalable route for large-scale production on an industrial level. The renovation of biosynthetic pathways in plants and industrially significant microbes using advanced genetic engineering tools offers substantial promise for the exploration and scalable production of flavonoids. Recently, the co-culture engineering approach has emerged to prevail over the constraints and limitations of the conventional monoculture approach by harnessing the power of two or more strains of engineered microbes to reconstruct the target biosynthetic pathway. In this review, current perspectives on the biosynthesis and metabolic engineering of flavonoids in plants have been summarized. Special emphasis is placed on the most recent developments in the microbial production of major classes of flavonoids. Finally, we describe the recent achievements in genetic engineering for the combinatorial biosynthesis of flavonoids by reconstructing synthesis pathways in microorganisms via a co-culture strategy to obtain high amounts of specific bioactive compounds.
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Affiliation(s)
- Hasnat Tariq
- Department of Biotechnology, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Saaim Asif
- Department of Biosciences, COMSATS University, Islamabad 45550, Pakistan
| | - Anisa Andleeb
- Department of Biotechnology, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Christophe Hano
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRAE USC1328, Eure et Loir Campus, Université d’Orléans, 28000 Chartres, France
- Correspondence: (C.H.); (B.H.A.)
| | - Bilal Haider Abbasi
- Department of Biotechnology, Quaid-i-Azam University, Islamabad 45320, Pakistan
- Correspondence: (C.H.); (B.H.A.)
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Grover S, Shinde S, Puri H, Palmer N, Sarath G, Sattler SE, Louis J. Dynamic regulation of phenylpropanoid pathway metabolites in modulating sorghum defense against fall armyworm. FRONTIERS IN PLANT SCIENCE 2022; 13:1019266. [PMID: 36507437 PMCID: PMC9732255 DOI: 10.3389/fpls.2022.1019266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
Plants undergo dynamic metabolic changes at the cellular level upon insect infestation to better defend themselves. Phenylpropanoids, a hub of secondary plant metabolites, encompass a wide range of compounds that can contribute to insect resistance. Here, the role of sorghum (Sorghum bicolor) phenylpropanoids in providing defense against the chewing herbivore, fall armyworm (FAW), Spodoptera frugiperda, was explored. We screened a panel of nested association mapping (NAM) founder lines against FAW and identified SC1345 and Ajabsido as most resistant and susceptible lines to FAW, respectively, compared to reference parent, RTx430. Gene expression and metabolomic studies suggested that FAW feeding suppressed the expression level of genes involved in monolignol biosynthetic pathway and their associated phenolic intermediates at 10 days post infestation. Further, SC1345 genotype displayed elevated levels of flavonoid compounds after FAW feeding for 10 days, suggesting a diversion of precursors from lignin biosynthesis to the flavonoid pathway. Additionally, bioassays with sorghum lines having altered levels of flavonoids provided genetic evidence that flavonoids are crucial in providing resistance against FAW. Finally, the application of FAW regurgitant elevated the expression of genes associated with the flavonoid pathway in the FAW-resistant SC1345 genotype. Overall, our study indicates that a dynamic regulation of the phenylpropanoid pathway in sorghum plants imparts resistance against FAW.
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Affiliation(s)
- Sajjan Grover
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Sanket Shinde
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Heena Puri
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Nathan Palmer
- Wheat, Sorghum, and Forage Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Lincoln, NE, United States
| | - Gautam Sarath
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE, United States
- Wheat, Sorghum, and Forage Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Lincoln, NE, United States
| | - Scott E Sattler
- Wheat, Sorghum, and Forage Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Lincoln, NE, United States
| | - Joe Louis
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
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Lv Y, Chen J, Zhu M, Liu Y, Wu X, Xiao X, Yuyama N, Liu F, Jing H, Cai H. Wall-associated kinase-like gene RL1 contributes to red leaves in sorghum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:135-150. [PMID: 35942607 DOI: 10.1111/tpj.15936] [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: 01/20/2022] [Revised: 06/20/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Red leaves are common in trees but rare in cereal crops. Red leaves can be used as raw materials for anthocyanin extraction and may have some adaptive significance for plants. In this study, we discovered a red leaf phenotype in the F1 hybrids derived from a cross between two sorghum accessions with green leaf. Histological analysis of red leaves and green leaves showed that red compounds accumulate in mesophyll cells and gradually spreads to the entire leaf blade. In addition, we found chloroplasts degraded more quickly in red leaves than in green leaves based on transmission electron microscopy. Metabolic analysis revealed that flavonoids including six anthocyanins are more abundant in red leaves. Moreover, transcriptome analysis revealed that expression of flavonoid biosynthesis genes was upregulated in red leaves. These observations indicate that flavonoids and anthocyanins in particular, are ideal candidates for the red compounds accumulating in red leaves. Segregation analysis of the red leaf phenotype suggested a genetic architecture consisting of three dominant genes, one (RL1 for RED LEAF1) of which we mapped to a 55-kb region on chromosome 7 containing seven genes. Sequencing, reverse transcription-polymerase chain reaction, and transcriptome analysis suggested Sobic.007G214300, encoding a wall-associated kinase, as the most likely candidate for RL1. Fine mapping the red leaf gene and identifying the metabolites that cause red leaf in sorghum provide us with a better understanding of the red leaf phenotype in the natural population of sorghum.
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Affiliation(s)
- Ya Lv
- Department of Plant Genetics, Breeding and Seed Science, China Agricultural University; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, MOE; Beijing, 100193, China
| | - Jun Chen
- Department of Plant Genetics, Breeding and Seed Science, China Agricultural University; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, MOE; Beijing, 100193, China
- College of Grassland Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Mengjiao Zhu
- Department of Plant Genetics, Breeding and Seed Science, China Agricultural University; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, MOE; Beijing, 100193, China
- College of Grassland Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Yishan Liu
- Department of Plant Genetics, Breeding and Seed Science, China Agricultural University; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, MOE; Beijing, 100193, China
| | - Xiaoyuan Wu
- Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xin Xiao
- Department of Plant Genetics, Breeding and Seed Science, China Agricultural University; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, MOE; Beijing, 100193, China
| | - Nana Yuyama
- Forage Crop Research Institute, Japan Grassland Agricultural and Forage Seed Association, 388-5 Higashiakada, Nasushiobara, Tochigi, 329-2742, Japan
| | - Fengxia Liu
- Department of Plant Genetics, Breeding and Seed Science, China Agricultural University; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, MOE; Beijing, 100193, China
| | - Haichun Jing
- Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hongwei Cai
- Department of Plant Genetics, Breeding and Seed Science, China Agricultural University; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, MOE; Beijing, 100193, China
- College of Grassland Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
- Forage Crop Research Institute, Japan Grassland Agricultural and Forage Seed Association, 388-5 Higashiakada, Nasushiobara, Tochigi, 329-2742, Japan
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Backes A, Charton S, Planchon S, Esmaeel Q, Sergeant K, Hausman JF, Renaut J, Barka EA, Jacquard C, Guerriero G. Gene expression and metabolite analysis in barley inoculated with net blotch fungus and plant growth-promoting rhizobacteria. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 168:488-500. [PMID: 34757299 DOI: 10.1016/j.plaphy.2021.10.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/26/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
Net blotch, caused by the ascomycete Drechslera teres, can compromise barley production. Beneficial bacteria strains are of substantial interest as biological agents for plant protection in agriculture. Belonging to the genus Paraburkholderia, a bacterium, referred to as strain B25, has been identified as protective for barley against net blotch. The strain Paraburkholderia phytofirmans (strain PsJN), which has no effect on the pathogen's growth, has been used as control. In this study, the expression of target genes involved in cell wall-related processes, defense responses, carbohydrate and phenylpropanoid pathways was studied under various conditions (with or without pathogen and/or with or without bacterial strains) at different time-points (0-6-12-48 h). The results show that specific genes were subjected to a circadian regulation and that the expression of most of them increased in barley infected with D. teres and/or bacterized with the strain PsJN. On the contrary, a decreased gene expression was observed in the presence of strain B25. To complement and enrich the gene expression analysis, untargeted metabolomics was carried out on the same samples. The data obtained show an increase in the production of lipid compounds in barley in the presence of the pathogen. In addition, the presence of strain B25 leads to a decrease in the production of defense compounds in this crop. The results contribute to advance the knowledge on the mechanisms occurring at the onset of D. teres infection and in the presence of a biocontrol agent limiting the severity of net blotch in barley.
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Affiliation(s)
- Aurélie Backes
- Université de Reims Champagne-Ardenne, RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100, Reims, France.
| | - Sophie Charton
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, Biotechnologies and Environmental Analytics Platform (BEAP), 41 rue du Brill, L-4422, Belvaux, Luxembourg.
| | - Sébastien Planchon
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, Biotechnologies and Environmental Analytics Platform (BEAP), 41 rue du Brill, L-4422, Belvaux, Luxembourg.
| | - Qassim Esmaeel
- Université de Reims Champagne-Ardenne, RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100, Reims, France.
| | - Kjell Sergeant
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, GreenTech Innovation Centre, 5 rue Bommel, Z.A.E. Robert Steichen, L-4940, Hautcharage, Luxembourg.
| | - Jean-Francois Hausman
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, GreenTech Innovation Centre, 5 rue Bommel, Z.A.E. Robert Steichen, L-4940, Hautcharage, Luxembourg.
| | - Jenny Renaut
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, GreenTech Innovation Centre, 5 rue Bommel, Z.A.E. Robert Steichen, L-4940, Hautcharage, Luxembourg.
| | - Essaid Ait Barka
- Université de Reims Champagne-Ardenne, RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100, Reims, France.
| | - Cédric Jacquard
- Université de Reims Champagne-Ardenne, RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100, Reims, France.
| | - Gea Guerriero
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, GreenTech Innovation Centre, 5 rue Bommel, Z.A.E. Robert Steichen, L-4940, Hautcharage, Luxembourg.
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Ackerman A, Wenndt A, Boyles R. The Sorghum Grain Mold Disease Complex: Pathogens, Host Responses, and the Bioactive Metabolites at Play. FRONTIERS IN PLANT SCIENCE 2021; 12:660171. [PMID: 34122480 PMCID: PMC8192977 DOI: 10.3389/fpls.2021.660171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
Grain mold is a major concern in sorghum [Sorghum bicolor (L.) Moench] production systems, threatening grain quality, safety, and nutritional value as both human food and livestock feed. The crop's nutritional value, environmental resilience, and economic promise poise sorghum for increased acreage, especially in light of the growing pressures of climate change on global food systems. In order to fully take advantage of this potential, sorghum improvement efforts and production systems must be proactive in managing the sorghum grain mold disease complex, which not only jeopardizes agricultural productivity and profitability, but is also the culprit of harmful mycotoxins that warrant substantial public health concern. The robust scholarly literature from the 1980s to the early 2000s yielded valuable insights and key comprehensive reviews of the grain mold disease complex. Nevertheless, there remains a substantial gap in understanding the complex multi-organismal dynamics that underpin the plant-pathogen interactions involved - a gap that must be filled in order to deliver improved germplasm that is not only capable of withstanding the pressures of climate change, but also wields robust resistance to disease and mycotoxin accumulation. The present review seeks to provide an updated perspective of the sorghum grain mold disease complex, bolstered by recent advances in the understanding of the genetic and the biochemical interactions among the fungal pathogens, their corresponding mycotoxins, and the sorghum host. Critical components of the sorghum grain mold disease complex are summarized in narrative format to consolidate a collection of important concepts: (1) the current state of sorghum grain mold in research and production systems; (2) overview of the individual pathogens that contribute to the grain mold complex; (3) the mycotoxin-producing potential of these pathogens on sorghum and other substrates; and (4) a systems biology approach to the understanding of host responses.
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Affiliation(s)
- Arlyn Ackerman
- Cereal Grains Breeding and Genetics, Pee Dee Research and Education Center, Department of Plant & Environmental Sciences, Clemson University, Florence, SC, United States
| | - Anthony Wenndt
- Plant Pathology and Plant-Microbe Biology, The School of Integrated Plant Sciences, Cornell University, Ithaca, NY, United States
| | - Richard Boyles
- Cereal Grains Breeding and Genetics, Pee Dee Research and Education Center, Department of Plant & Environmental Sciences, Clemson University, Florence, SC, United States
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Abrouk M, Athiyannan N, Müller T, Pailles Y, Stritt C, Roulin AC, Chu C, Liu S, Morita T, Handa H, Poland J, Keller B, Krattinger SG. Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color. Commun Biol 2021; 4:375. [PMID: 33742098 PMCID: PMC7979816 DOI: 10.1038/s42003-021-01908-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 02/25/2021] [Indexed: 01/25/2023] Open
Abstract
The cloning of agriculturally important genes is often complicated by haplotype variation across crop cultivars. Access to pan-genome information greatly facilitates the assessment of structural variations and rapid candidate gene identification. Here, we identified the red glume 1 (Rg-B1) gene using association genetics and haplotype analyses in ten reference grade wheat genomes. Glume color is an important trait to characterize wheat cultivars. Red glumes are frequent among Central European spelt, a dominant wheat subspecies in Europe before the 20th century. We used genotyping-by-sequencing to characterize a global diversity panel of 267 spelt accessions, which provided evidence for two independent introductions of spelt into Europe. A single region at the Rg-B1 locus on chromosome 1BS was associated with glume color in the diversity panel. Haplotype comparisons across ten high-quality wheat genomes revealed a MYB transcription factor as candidate gene. We found extensive haplotype variation across the ten cultivars, with a particular group of MYB alleles that was conserved in red glume wheat cultivars. Genetic mapping and transient infiltration experiments allowed us to validate this particular MYB transcription factor variants. Our study demonstrates the value of multiple high-quality genomes to rapidly resolve copy number and haplotype variations in regions controlling agriculturally important traits.
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Affiliation(s)
- Michael Abrouk
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Naveenkumar Athiyannan
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Thomas Müller
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, Switzerland
| | - Yveline Pailles
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Christoph Stritt
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, Switzerland
| | - Anne C Roulin
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, Switzerland
| | | | - Shuyu Liu
- Texas A&M AgriLife Research, Amarillo, TX, USA
| | - Takumi Morita
- Department of Agricultural and Life Sciences, Kyoto Prefectural University, Kyoto, Japan
| | - Hirokazu Handa
- Laboratory of Plant Breeding, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, Switzerland
| | - Simon G Krattinger
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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Balasubramanian VK, Dampanaboina L, Cobos CJ, Yuan N, Xin Z, Mendu V. Induced secretion system mutation alters rhizosphere bacterial composition in Sorghum bicolor (L.) Moench. PLANTA 2021; 253:33. [PMID: 33459875 PMCID: PMC7813745 DOI: 10.1007/s00425-021-03569-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
A novel inducible secretion system mutation in Sorghum named Red root has been identified. The mutant plant root exudes pigmented compounds that enriches Actinobacteria in its rhizosphere compared to BTx623. Favorable plant-microbe interactions in the rhizosphere positively influence plant growth and stress tolerance. Sorghum bicolor, a staple biomass and food crop, has been shown to selectively recruit Gram-positive bacteria (Actinobacteria) in its rhizosphere under drought conditions to enhance stress tolerance. However, the genetic/biochemical mechanism underlying the selective enrichment of specific microbial phyla in the sorghum rhizosphere is poorly known due to the lack of available mutants with altered root secretion systems. Using a subset of sorghum ethyl methanesulfonate (EMS) mutant lines, we have isolated a novel Red root (RR) mutant with an increased accumulation and secretion of phenolic compounds in roots. Genetic analysis showed that RR is a single dominant mutation. We further investigated the effect of root-specific phenolic compounds on rhizosphere microbiome composition under well-watered and water-deficit conditions. The microbiome diversity analysis of the RR rhizosphere showed that Actinobacteria were enriched significantly under the well-watered condition but showed no significant change under the water-deficit condition. BTx623 rhizosphere showed a significant increase in Actinobacteria under the water-deficit condition. Overall, the rhizosphere of RR genotype retained a higher bacterial diversity and richness relative to the rhizosphere of BTx623, especially under water-deficit condition. Therefore, the RR mutant provides an excellent genetic resource for rhizosphere-microbiome interaction studies as well as to develop drought-tolerant lines. Identification of the RR gene and the molecular mechanism through which the mutant selectively enriches microbial populations in the rhizosphere will be useful in designing strategies for improving sorghum productivity and stress tolerance.
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Affiliation(s)
- Vimal Kumar Balasubramanian
- Fiber and Biopolymer Research Institute (FBRI), Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409 USA
| | | | - Christopher Joseph Cobos
- Fiber and Biopolymer Research Institute (FBRI), Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409 USA
| | - Ning Yuan
- Fiber and Biopolymer Research Institute (FBRI), Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409 USA
| | | | - Venugopal Mendu
- Fiber and Biopolymer Research Institute (FBRI), Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409 USA
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Shimada T, Nagayoshi H, Murayama N, Takenaka S, Katahira J, Kim V, Kim D, Komori M, Yamazaki H, Guengerich FP. Liquid chromatography-tandem mass spectrometry analysis of oxidation of 2'-, 3'-, 4'- and 6-hydroxyflavanones by human cytochrome P450 enzymes. Xenobiotica 2020; 51:139-154. [PMID: 33047997 DOI: 10.1080/00498254.2020.1836433] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
2'-Hydroxyflavanone (2'OHFva), 3'OHFva, 4'OHFva, and 6OHFva, the major oxidative products of flavanone by human cytochrome P450 (P450, CYP) enzymes, were studied in regard to further oxidation by human CYP1A1, 1A2, 1B1.1, 1B1.3, and 2A6. The products formed were analyzed with LC-MS/MS and characterized by their positive ion fragmentations on mass spectrometry. Several di-hydroxylated flavanone (diOHFva) and di-hydroxylated flavone (diOHFvo) products, detected by analyzing parent ions at m/z 257 and 255, respectively, were found following incubation of these four hydroxylated flavanones with P450s. The m/z 257 products were produced at higher levels than the latter with four substrates examined. The structures of the m/z 257 products were characterized by LC-MS/MS product ion spectra, and the results suggest that 3'OHFva and 4'OHFva are further oxidized mainly at B-ring by P450s while 6OHFva oxidation was at A-ring. Different diOHFvo products (m/z 255) were also characterized by LC-MS/MS, and the results suggested that most of these diOHFvo products were formed through oxidation or desaturation of the diOHFva products (m/z 257) by P450s. Only when 4'OHFva (m/z 241) was used as a substrate, formation of 4'OHFvo (m/z 239) was detected, indicating that diOHFvo might also be formed through oxidation of 4'OHFvo by P450s. Finally, our results indicated that CYP1 family enzymes were more active than CYP2A6 in catalyzing the oxidation of these four hydroxylated flavanones, and these findings were supported by molecular docking studies of these chemicals with active sites of P450 enzymes.
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Affiliation(s)
- Tsutomu Shimada
- Laboratory of Cellular and Molecular Biology, Veterinary Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Haruna Nagayoshi
- Division of Food Sanitation, Osaka Institute of Public Health, Osaka, Japan
| | - Norie Murayama
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, Japan
| | - Shigeo Takenaka
- Graduate School of Comprehensive Rehabilitation, Osaka Prefecture University, Habikino, Osaka, Japan
| | - Jun Katahira
- Laboratory of Cellular and Molecular Biology, Veterinary Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Vitchan Kim
- Department of Biological Sciences, Konkuk University, Seoul, Korea
| | - Donghak Kim
- Department of Biological Sciences, Konkuk University, Seoul, Korea
| | - Masayuki Komori
- Laboratory of Cellular and Molecular Biology, Veterinary Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Hiroshi Yamazaki
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, Japan
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
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Gao J, Xue J, Xue Y, Liu R, Ren X, Wang S, Zhang X. Transcriptome sequencing and identification of key callus browning-related genes from petiole callus of tree peony (Paeonia suffruticosa cv. Kao) cultured on media with three browning inhibitors. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 149:36-49. [PMID: 32035251 DOI: 10.1016/j.plaphy.2020.01.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/18/2020] [Accepted: 01/18/2020] [Indexed: 06/10/2023]
Abstract
Tree peony (Paeonia suffruticosa Andrews) has ornamental, oil, and medicinal values, and demand in the markets for uniform tree peony seedlings is increasing. Micropropagation could quickly propagate uniform seedlings. However, the heavy browning phenomenon hinders large-scale development of uniform tree peony seedlings. In this paper, we measured the total phenolic compounds content, and sequenced the transcriptomes of tree peony 'Kao' petiole calluses cultured on media with three browning antagonist treatments and fresh petioles to identify the key genes involved in callus browning. Polyvinylpyrrolidone (PVP) treatment can reduce production of phenolic compounds and promote callus regeneration. A total of 218,957 unigenes were obtained from fresh petiole and three kinds of browning petiole calluses by transcriptome sequencing. The average sequence length of unigenes was 446 bp with an N50 of 493 bp. Functional annotation analysis revealed that 43,428, 45,357, 31,194, 30,019, and 21,357 unigenes were annotated using the NCBI-NR database, Swiss-Prot, KOG, GO, and KEGG, respectively. In total, 33 differentially expressed genes (DEGs) were identified as potentially associated with callus browning. Among these DEGs, 12 genes were predicted to participate in phenolic compounds biosynthesis, three genes were predicted to be involved in phenolic compounds oxidation, and six genes were predicted to participate in callus regeneration. Moreover, six transcription factors were observed to be differentially expressed in the fresh petiole and three treated petioles in tree peony. This study comprehensively identifies browning-related gene resources and will possibly help in deciphering the molecular mechanisms of callus browning of tree peony in the future.
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Affiliation(s)
- Jie Gao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, PR China, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Institute of Peony, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Jingqi Xue
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, PR China, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Institute of Peony, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Yuqian Xue
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, PR China, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Institute of Peony, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Rong Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, PR China, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Institute of Peony, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Xiuxia Ren
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, PR China, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Institute of Peony, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Shunli Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, PR China, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Institute of Peony, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Xiuxin Zhang
- National Agricultural Science & Technology Center, Chengdu, China.
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Jia Y, Li B, Zhang Y, Zhang X, Xu Y, Li C. Evolutionary dynamic analyses on monocot flavonoid 3'-hydroxylase gene family reveal evidence of plant-environment interaction. BMC PLANT BIOLOGY 2019; 19:347. [PMID: 31395025 PMCID: PMC6686259 DOI: 10.1186/s12870-019-1947-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/26/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Flavonoid 3'-hydroxlase (F3'H) is an important enzyme in determining the B-ring hydroxylation pattern of flavonoids. In monocots, previous studies indicated the presence of two groups of F3'Hs with different enzyme activities. One F3'H in rice was found to display novel chrysoeriol-specific 5'-hydroxylase activity. However, the evolutionary history of monocot F3'Hs and the molecular basis for the observed catalytic difference remained elusive. RESULTS We performed genome-wide survey of 12 common monocot plants, and identified a total of 44 putative F3'H genes. The results showed that F3'H gene family had underwent volatile lineage-specific gene duplication and gene loss events in monocots. The expansion of F3'H gene family was mainly attributed to dispersed gene duplication. Phylogenetic analyses showed that monocot F3'Hs have evolved into two independent lineages (Class I and Class II) after gene duplication in the common ancestor of monocot plants. Evolutionary dynamics analyses had detected positive natural selection in Class II F3'Hs, acting on 7 specific amino acid sites. Protein modelling showed these selected sites were mainly located in the catalytic cavity of F3'H. Sequence alignment revealed that Class I and Class II F3'Hs displayed amino acid substitutions at two critical sites previously found to be responsible for F3'H and flavonoid 3'5'-hydroxylase (F3'5'H) activities. In addition, transcriptional divergence was also observed for Class I and Class II F3'Hs in four monocot species. CONCLUSIONS We concluded that monocot F3'Hs have evolved into two independent lineages (Mono_F3'H Class I and Class II), after gene duplication during the common ancestor of monocot plants. The functional divergence of monocot F3'H Class II has been affected by positive natural selection, which acted on specific amino acid sites only. Critical amino acid sites have been identified to have high possibility to affect the substrate specificity of Class II F3'Hs. Our study provided an evolutionary and protein structural explanation to the previously observed chrysoeriol-specific 5'-hydroxylation activity for CYP75B4 in rice, which may also be true for other Class II F3'Hs in monocots. Our study presented clear evidence of plant-environmental interaction at the gene evolutionary level, and would guide future functional characterization of F3'Hs in cereal plants.
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Affiliation(s)
- Yong Jia
- State Agricultural Biotechnology Centre (SABC), School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150 Australia
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA 6150 Australia
| | - Bo Li
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, 434025 Hubei China
| | - Yujuan Zhang
- State Agricultural Biotechnology Centre (SABC), School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150 Australia
| | - Xiaoqi Zhang
- State Agricultural Biotechnology Centre (SABC), School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150 Australia
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA 6150 Australia
| | - Yanhao Xu
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, 434025 Hubei China
| | - Chengdao Li
- State Agricultural Biotechnology Centre (SABC), School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150 Australia
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA 6150 Australia
- Department of Primary Industry and Regional Development, Government of Western Australia, South Perth, WA 6155 Australia
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12
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Mareya CR, Tugizimana F, Piater LA, Madala NE, Steenkamp PA, Dubery IA. Untargeted Metabolomics Reveal Defensome-Related Metabolic Reprogramming in Sorghum bicolor against Infection by Burkholderia andropogonis. Metabolites 2019; 9:metabo9010008. [PMID: 30609758 PMCID: PMC6359421 DOI: 10.3390/metabo9010008] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 12/21/2018] [Accepted: 12/24/2018] [Indexed: 12/27/2022] Open
Abstract
Burkholderia andropogonis is the causal agent of bacterial leaf stripe, one of the three major bacterial diseases affecting Sorghum bicolor. However, the biochemical aspects of the pathophysiological host responses are not well understood. An untargeted metabolomics approach was designed to understand molecular mechanisms underlying S. bicolor⁻B. andropogonis interactions. At the 4-leaf stage, two sorghum cultivars (NS 5511 and NS 5655) differing in disease tolerance, were infected with B. andropogonis and the metabolic changes monitored over time. The NS 5511 cultivar displayed delayed signs of wilting and lesion progression compared to the NS 5655 cultivar, indicative of enhanced resistance. The metabolomics results identified statistically significant metabolites as biomarkers associated with the sorghum defence. These include the phytohormones salicylic acid, jasmonic acid, and zeatin. Moreover, metabolic reprogramming in an array of chemically diverse metabolites that span a wide range of metabolic pathways was associated with the defence response. Signatory biomarkers included aromatic amino acids, shikimic acid, metabolites from the phenylpropanoid and flavonoid pathways, as well as fatty acids. Enhanced synthesis and accumulation of apigenin and derivatives thereof was a prominent feature of the altered metabolomes. The analyses revealed an intricate and dynamic network of the sorghum defence arsenal towards B. andropogonis in establishing an enhanced defensive capacity in support of resistance and disease suppression. The results pave the way for future analysis of the biosynthesis of signatory biomarkers and regulation of relevant metabolic pathways in sorghum.
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Affiliation(s)
- Charity R Mareya
- Centre for Plant Metabolomics Research, Department of Biochemistry, University of Johannesburg, Auckland Park 2006, Johannesburg, South Africa.
| | - Fidele Tugizimana
- Centre for Plant Metabolomics Research, Department of Biochemistry, University of Johannesburg, Auckland Park 2006, Johannesburg, South Africa.
| | - Lizelle A Piater
- Centre for Plant Metabolomics Research, Department of Biochemistry, University of Johannesburg, Auckland Park 2006, Johannesburg, South Africa.
| | - Ntakadzeni E Madala
- Centre for Plant Metabolomics Research, Department of Biochemistry, University of Johannesburg, Auckland Park 2006, Johannesburg, South Africa.
| | - Paul A Steenkamp
- Centre for Plant Metabolomics Research, Department of Biochemistry, University of Johannesburg, Auckland Park 2006, Johannesburg, South Africa.
| | - Ian A Dubery
- Centre for Plant Metabolomics Research, Department of Biochemistry, University of Johannesburg, Auckland Park 2006, Johannesburg, South Africa.
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