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Greatens N, Jin Y, Olivera Firpo PD. Aecial and Telial Host Specificity of Puccinia coronata var. coronata, a Eurasian Crown Rust Fungus of Two Highly Invasive Wetland Species in North America. PLANT DISEASE 2024; 108:175-181. [PMID: 37606959 DOI: 10.1094/pdis-04-23-0776-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
The Eurasian crown rust fungus Puccinia coronata var. coronata (Pcc) was recently reported in North America and is widespread across the Midwest and Northeast United States. Pcc is a close relative of major pathogens of oats, barley, and turfgrasses. It infects two highly invasive wetland plants, glossy buckthorn (Frangula alnus) and reed canarygrass (Phalaris arundinacea), and could be useful as an augmentative biological control agent. We conducted large greenhouse trials to assess the host specificity of Pcc and determine any threat to cultivated cereals, turfgrasses, or native North American species. A total of 1,830 accessions of cereal crop species and 783 accessions of 110 other gramineous species were evaluated. Young plants were first inoculated with a composite uredinial inoculum derived from aecia. Accessions showing sporulation were further tested with pure urediniospore isolates. Sixteen potential aecial hosts in the families Rhamnaceae and Elaeagnaceae were tested for susceptibility through inoculation with germinating teliospores. Thirteen grass species within five genera in the tribe Poeae (Apera, Calamagrostis, Lamarckia, Phalaris, and Puccinellia) and four species in Rhamnaceae (Frangula alnus, F. californica, F. caroliniana, and Rhamnus lanceolata) were found to be susceptible to Pcc, with some species native to North America. All assessed crop species and turfgrasses were resistant. Limited sporulation, however, was observed on some resistant species within Poeae and four other tribes: Brachypodieae, Bromeae, Meliceae, and Triticeae. Among these species are oats, barley, and Brachypodium distachyon, suggesting the possible use of Pcc in studies of nonhost resistance.
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Affiliation(s)
- Nicholas Greatens
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Yue Jin
- USDA-ARS Cereal Disease Laboratory, St. Paul, MN 55108
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Abdedayem W, Patpour M, Laribi M, Justesen AF, Kouki H, Fakhfakh M, Hovmøller MS, Yahyaoui AH, Hamza S, Ben M’Barek S. Wheat Stem Rust Detection and Race Characterization in Tunisia. PLANTS (BASEL, SWITZERLAND) 2023; 12:552. [PMID: 36771636 PMCID: PMC9919909 DOI: 10.3390/plants12030552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/12/2023] [Accepted: 01/14/2023] [Indexed: 06/18/2023]
Abstract
Climate changes over the past 25 years have led to conducive conditions for invasive and transboundary fungal disease occurrence, including the re-emergence of wheat stem rust disease, caused by Puccinia graminis f.sp. tritici (Pgt) in East Africa, Europe, and the Mediterranean basin. Since 2018, sporadic infections have been observed in Tunisia. In this study, we investigated Pgt occurrence at major Tunisian wheat growing areas. Pgt monitoring, assessment, and sampling from planted trap nurseries at five different locations over two years (2021 and 2022) revealed the predominance of three races, namely TTRTF (Clade III-B), TKKTF (Clade IV-F), and TKTTF (Clade IV-B). Clade III-B was the most prevalent in 2021 as it was detected at all locations, while in 2022 Pgt was only reported at Beja and Jendouba, with the prevalence of Clade IV-B. The low levels of disease incidence during these two years and Pgt population diversity suggest that this fungus most likely originated from exotic incursions and that climate factors could have caused disease establishment in Tunisia. Further evaluation under the artificial disease pressure of Tunisian wheat varieties and weather-based modeling for early disease detection in the Mediterranean area could be helpful in monitoring and predicting wheat stem rust emergence and epidemics.
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Affiliation(s)
- Wided Abdedayem
- National Agronomic Institute of Tunisia (INAT), 43 Avenue Charles Nicolle, Tunis 1002, Tunisia
- CRP Wheat Septoria Precision Phenotyping Platform, Tunis 1082, Tunisia
| | - Mehran Patpour
- Department of Agroecology, Aarhus University, 4200 Slagelse, Denmark
| | - Marwa Laribi
- CRP Wheat Septoria Precision Phenotyping Platform, Tunis 1082, Tunisia
| | | | - Hajer Kouki
- CRP Wheat Septoria Precision Phenotyping Platform, Tunis 1082, Tunisia
| | - Moez Fakhfakh
- Comptoir Multiservices Agricoles, 82, Avenue Louis Brailles, Tunis 1002, Tunisia
| | | | - Amor H. Yahyaoui
- CRP Wheat Septoria Precision Phenotyping Platform, Tunis 1082, Tunisia
- Borlaug Training Foundation, Colorado State University, Fort Collins, CO 80523-1170, USA
| | - Sonia Hamza
- National Agronomic Institute of Tunisia (INAT), 43 Avenue Charles Nicolle, Tunis 1002, Tunisia
| | - Sarrah Ben M’Barek
- CRP Wheat Septoria Precision Phenotyping Platform, Tunis 1082, Tunisia
- Laboratory of ‘Appui à la Durabilité des Systèmes de Production Agricole Dans la Région du Nord-Ouest’, Higher School of Agriculture of Kef (ESAK), Regional Field Crops Research Center of Beja (CRRGC) BP 350, Beja 9000, Tunisia
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3
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Graph Pangenomes Track Genetic Variants for Crop Improvement. Int J Mol Sci 2022; 23:ijms232113420. [DOI: 10.3390/ijms232113420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/28/2022] [Accepted: 10/29/2022] [Indexed: 11/06/2022] Open
Abstract
Global climate change and the urgency to transform crops require an exhaustive genetic evaluation. The large polyploid genomes of food crops, such as cereals, make it difficult to identify candidate genes with confirmed hereditary. Although genome-wide association studies (GWAS) have been proficient in identifying genetic variants that are associated with complex traits, the resolution of acquired heritability faces several significant bottlenecks such as incomplete detection of structural variants (SV), genetic heterogeneity, and/or locus heterogeneity. Consequently, a biased estimate is generated with respect to agronomically complex traits. The graph pangenomes have resolved this missing heritability and provide significant details in terms of specific loci segregating among individuals and evolving to variations. The graph pangenome approach facilitates crop improvements through genome-linked fast breeding.
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Wang N, Fan X, He M, Hu Z, Tang C, Zhang S, Lin D, Gan P, Wang J, Huang X, Gao C, Kang Z, Wang X. Transcriptional repression of TaNOX10 by TaWRKY19 compromises ROS generation and enhances wheat susceptibility to stripe rust. THE PLANT CELL 2022; 34:1784-1803. [PMID: 34999846 PMCID: PMC9048928 DOI: 10.1093/plcell/koac001] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/02/2022] [Indexed: 06/14/2023]
Abstract
Reactive oxygen species (ROS) are vital for plant immunity and regulation of their production is crucial for plant health. While the mechanisms that elicit ROS production have been relatively well studied, those that repress ROS generation are less well understood. Here, via screening Brachypodium distachyon RNA interference mutants, we identified BdWRKY19 as a negative regulator of ROS generation whose knockdown confers elevated resistance to the rust fungus Puccinia brachypodii. The three wheat paralogous genes TaWRKY19 are induced during infection by virulent P. striiformis f. sp. tritici (Pst) and have partially redundant roles in resistance. The stable overexpression of TaWRKY19 in wheat increased susceptibility to an avirulent Pst race, while mutations in all three TaWRKY19 copies conferred strong resistance to Pst by enhancing host plant ROS accumulation. We show that TaWRKY19 is a transcriptional repressor that binds to a W-box element in the promoter of TaNOX10, which encodes an NADPH oxidase and is required for ROS generation and host resistance to Pst. Collectively, our findings reveal that TaWRKY19 compromises wheat resistance to the fungal pathogen and suggest TaWRKY19 as a potential target to improve wheat resistance to the commercially important wheat stripe rust fungus.
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Affiliation(s)
- Ning Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
- Pioneering Innovation Center for Wheat Stress Tolerance Improvement, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xin Fan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
- Pioneering Innovation Center for Wheat Stress Tolerance Improvement, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mengying He
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
- Pioneering Innovation Center for Wheat Stress Tolerance Improvement, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zeyu Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
- Pioneering Innovation Center for Wheat Stress Tolerance Improvement, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chunlei Tang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
- Pioneering Innovation Center for Wheat Stress Tolerance Improvement, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
- Pioneering Innovation Center for Wheat Stress Tolerance Improvement, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dexing Lin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Pengfei Gan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
- Pioneering Innovation Center for Wheat Stress Tolerance Improvement, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jianfeng Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
- Pioneering Innovation Center for Wheat Stress Tolerance Improvement, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xueling Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
- Pioneering Innovation Center for Wheat Stress Tolerance Improvement, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
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Compatible interaction of Brachypodium distachyon and endophytic fungus Microdochium bolleyi. PLoS One 2022; 17:e0265357. [PMID: 35286339 PMCID: PMC8920291 DOI: 10.1371/journal.pone.0265357] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 03/01/2022] [Indexed: 11/19/2022] Open
Abstract
Brachypodium distachyon is a useful model organism for studying interaction of cereals with phytopathogenic fungi. The present study tested the possibility of a compatible interaction of B. distachyon with the endophytic fungus Microdochium bolleyi originated from wheat roots. There was evaluated the effect of this endophytic fungus on the intensity of the attack by pathogen Fusarium culmorum in B. distachyon and wheat, and also changes in expression of genes (in B. distachyon: BdChitinase1, BdPR1-5, BdLOX3, BdPAL, BdEIN3, and BdAOS; and in wheat: TaB2H2(chitinase), TaPR1.1, TaLOX, TaPAL, TaEIN2, and TaAOS) involved in defence against pathogens. Using light microscopy and newly developed specific primers was found to be root colonization of B. distachyon by the endophyte M. bolleyi. B. distachyon plants, as well as wheat inoculated with M. bolleyi showed significantly weaker symptoms on leaves from infection by fungus F. culmorum than did plants without the endophyte. Expression of genes BdPR1-5, BdChitinase1, and BdLOX3 in B. distachyon and of TaPR1.1 and TaB2H2 in wheat was upregulated after infection with F. culmorum. M. bolleyi-mediated resistance in B. distachyon was independent of the expression of the most tested genes. Taken together, the results of the present study show that B. distachyon can be used as a model host system for endophytic fungus M. bolleyi.
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Zanini SF, Bayer PE, Wells R, Snowdon RJ, Batley J, Varshney RK, Nguyen HT, Edwards D, Golicz AA. Pangenomics in crop improvement-from coding structural variations to finding regulatory variants with pangenome graphs. THE PLANT GENOME 2022; 15:e20177. [PMID: 34904403 DOI: 10.1002/tpg2.20177] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/07/2021] [Indexed: 05/15/2023]
Abstract
Since the first reported crop pangenome in 2014, advances in high-throughput and cost-effective DNA sequencing technologies facilitated multiple such studies including the pangenomes of oilseed rape (Brassica napus L.), soybean [Glycine max (L.) Merr.], rice (Oryza sativa L.), wheat (Triticum aestivum L.), and barley (Hordeum vulgare L.). Compared with single-reference genomes, pangenomes provide a more accurate representation of the genetic variation present in a species. By combining the genomic data of multiple accessions, pangenomes allow for the detection and annotation of complex DNA polymorphisms such as structural variations (SVs), one of the major determinants of genetic diversity within a species. In this review we summarize the current literature on crop pangenomics, focusing on their application to find candidate SVs involved in traits of agronomic interest. We then highlight the potential of pangenomes in the discovery and functional characterization of noncoding regulatory sequences and their variations. We conclude with a summary and outlook on innovative data structures representing the complete content of plant pangenomes including annotations of coding and noncoding elements and outcomes of transcriptomic and epigenomic experiments.
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Affiliation(s)
- Silvia F Zanini
- Dep. of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig Univ. Giessen, Giessen, 35392, Germany
| | - Philipp E Bayer
- School of Biological Sciences and Institute of Agriculture, Univ. of Western Australia, Perth, Western Australia, Australia
| | - Rachel Wells
- Dep. of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR47UH, UK
| | - Rod J Snowdon
- Dep. of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig Univ. Giessen, Giessen, 35392, Germany
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, Univ. of Western Australia, Perth, Western Australia, Australia
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- State Agricultural Biotechnology Centre, Centre for Crop Food Innovation, Food Futures Institute, Murdoch Univ., Murdoch, WA, Australia
| | - Henry T Nguyen
- Division of Plant Sciences, Univ. of Missouri, Columbia, MO, USA
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, Univ. of Western Australia, Perth, Western Australia, Australia
| | - Agnieszka A Golicz
- Dep. of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig Univ. Giessen, Giessen, 35392, Germany
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Della Coletta R, Lavell AA, Garvin DF. A Homolog of the Arabidopsis TIME FOR COFFEE Gene Is Involved in Nonhost Resistance to Wheat Stem Rust in Brachypodium distachyon. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1298-1306. [PMID: 34340534 DOI: 10.1094/mpmi-06-21-0137-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Plants resist infection by pathogens using both preexisting barriers and inducible defense responses. Inducible responses are governed in a complex manner by various hormone signaling pathways. The relative contribution of hormone signaling pathways to nonhost resistance to pathogens is not well understood. In this study, we examined the molecular basis of disrupted nonhost resistance to the fungal species Puccinia graminis, which causes stem rust of wheat, in an induced mutant of the model grass Brachypodium distachyon. Through bioinformatic analysis, a 1-bp deletion in the mutant genotype was identified that introduces a premature stop codon in the gene Bradi1g24100, which is a homolog of the Arabidopsis thaliana gene TIME FOR COFFEE (TIC). In Arabidopsis, TIC is central to the regulation of the circadian clock and plays a crucial role in jasmonate signaling by attenuating levels of the transcription factor protein MYC2, and its mutational disruption results in enhanced susceptibility to the hemibiotroph Pseudomonas syringae. Our similar finding for an obligate biotroph suggests that the biochemical role of TIC in mediating disease resistance to biotrophs is conserved in grasses, and that the correct modulation of jasmonate signaling during infection by Puccinia graminis may be essential for nonhost resistance to wheat stem rust in B. distachyon.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Rafael Della Coletta
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
- CAPES Foundation, Ministry of Education of Brazil, Brasilia, DF, Brazil
| | - Anastasiya A Lavell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - David F Garvin
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
- Plant Science Research Unit, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN 55108, U.S.A
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Lichius A. Concentration, cellular exposure and specificity of organelle selective fluorescent dyes in fungal cell biology. FUNGAL BIOL REV 2021. [DOI: 10.1016/j.fbr.2021.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Henningsen EC, Omidvar V, Della Coletta R, Michno JM, Gilbert E, Li F, Miller ME, Myers CL, Gordon SP, Vogel JP, Steffenson BJ, Kianian SF, Hirsch CD, Figueroa M. Identification of Candidate Susceptibility Genes to Puccinia graminis f. sp. tritici in Wheat. FRONTIERS IN PLANT SCIENCE 2021; 12:657796. [PMID: 33968112 PMCID: PMC8097158 DOI: 10.3389/fpls.2021.657796] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/22/2021] [Indexed: 05/30/2023]
Abstract
Wheat stem rust disease caused by Puccinia graminis f. sp. tritici (Pgt) is a global threat to wheat production. Fast evolving populations of Pgt limit the efficacy of plant genetic resistance and constrain disease management strategies. Understanding molecular mechanisms that lead to rust infection and disease susceptibility could deliver novel strategies to deploy crop resistance through genetic loss of disease susceptibility. We used comparative transcriptome-based and orthology-guided approaches to characterize gene expression changes associated with Pgt infection in susceptible and resistant Triticum aestivum genotypes as well as the non-host Brachypodium distachyon. We targeted our analysis to genes with differential expression in T. aestivum and genes suppressed or not affected in B. distachyon and report several processes potentially linked to susceptibility to Pgt, such as cell death suppression and impairment of photosynthesis. We complemented our approach with a gene co-expression network analysis to identify wheat targets to deliver resistance to Pgt through removal or modification of putative susceptibility genes.
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Affiliation(s)
- Eva C. Henningsen
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Vahid Omidvar
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Rafael Della Coletta
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States
| | - Jean-Michel Michno
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN, United States
| | - Erin Gilbert
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Feng Li
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Marisa E. Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Chad L. Myers
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN, United States
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, United States
| | | | - John P. Vogel
- Joint Genome Institute, Walnut Creek, CA, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Brian J. Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Shahryar F. Kianian
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
- USDA-ARS Cereal Disease Laboratory, St. Paul, MN, United States
| | - Cory D. Hirsch
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
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Liu W, Huang L, Komorek R, Handakumbura PP, Zhou Y, Hu D, Engelhard MH, Jiang H, Yu XY, Jansson C, Zhu Z. Correlative surface imaging reveals chemical signatures for bacterial hotspots on plant roots. Analyst 2020; 145:393-401. [DOI: 10.1039/c9an01954e] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A universal sample holder allows correlative imaging analysis of plant roots to reveal chemical signatures for bacterial hotspots.
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11
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Bartaula R, Melo ATO, Kingan S, Jin Y, Hale I. Mapping non-host resistance to the stem rust pathogen in an interspecific barberry hybrid. BMC PLANT BIOLOGY 2019; 19:319. [PMID: 31311507 PMCID: PMC6636152 DOI: 10.1186/s12870-019-1893-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 06/19/2019] [Indexed: 05/17/2023]
Abstract
BACKGROUND Non-host resistance (NHR) presents a compelling long-term plant protection strategy for global food security, yet the genetic basis of NHR remains poorly understood. For many diseases, including stem rust of wheat [causal organism Puccinia graminis (Pg)], NHR is largely unexplored due to the inherent challenge of developing a genetically tractable system within which the resistance segregates. The present study turns to the pathogen's alternate host, barberry (Berberis spp.), to overcome this challenge. RESULTS In this study, an interspecific mapping population derived from a cross between Pg-resistant Berberis thunbergii (Bt) and Pg-susceptible B. vulgaris was developed to investigate the Pg-NHR exhibited by Bt. To facilitate QTL analysis and subsequent trait dissection, the first genetic linkage maps for the two parental species were constructed and a chromosome-scale reference genome for Bt was assembled (PacBio + Hi-C). QTL analysis resulted in the identification of a single 13 cM region (~ 5.1 Mbp spanning 13 physical contigs) on the short arm of Bt chromosome 3. Differential gene expression analysis, combined with sequence variation analysis between the two parental species, led to the prioritization of several candidate genes within the QTL region, some of which belong to gene families previously implicated in disease resistance. CONCLUSIONS Foundational genetic and genomic resources developed for Berberis spp. enabled the identification and annotation of a QTL associated with Pg-NHR. Although subsequent validation and fine mapping studies are needed, this study demonstrates the feasibility of and lays the groundwork for dissecting Pg-NHR in the alternate host of one of agriculture's most devastating pathogens.
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Affiliation(s)
- Radhika Bartaula
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03824 USA
| | - Arthur T. O. Melo
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH 03824 USA
| | | | - Yue Jin
- USDA-ARS Cereal Disease Laboratory, St. Paul, MN 55108 USA
| | - Iago Hale
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH 03824 USA
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Onda Y, Inoue K, Sawada Y, Shimizu M, Takahagi K, Uehara-Yamaguchi Y, Hirai MY, Garvin DF, Mochida K. Genetic Variation for Seed Metabolite Levels in Brachypodium distachyon. Int J Mol Sci 2019; 20:ijms20092348. [PMID: 31083584 PMCID: PMC6540107 DOI: 10.3390/ijms20092348] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/26/2019] [Accepted: 04/27/2019] [Indexed: 12/27/2022] Open
Abstract
Metabolite composition and concentrations in seed grains are important traits of cereals. To identify the variation in the seed metabolotypes of a model grass, namely Brachypodium distachyon, we applied a widely targeted metabolome analysis to forty inbred lines of B. distachyon and examined the accumulation patterns of 183 compounds in the seeds. By comparing the metabolotypes with the population structure of these lines, we found signature metabolites that represent different accumulation patterns for each of the three B. distachyon subpopulations. Moreover, we found that thirty-seven metabolites exhibited significant differences in their accumulation between the lines Bd21 and Bd3-1. Using a recombinant inbred line (RIL) population from a cross between Bd3-1 and Bd21, we identified the quantitative trait loci (QTLs) linked with this variation in the accumulation of thirteen metabolites. Our metabolite QTL analysis illustrated that different genetic factors may presumably regulate the accumulation of 4-pyridoxate and pyridoxamine in vitamin B6 metabolism. Moreover, we found two QTLs on chromosomes 1 and 4 that affect the accumulation of an anthocyanin, chrysanthemin. These QTLs genetically interacted to regulate the accumulation of this compound. This study demonstrates the potential for metabolite QTL mapping in B. distachyon and provides new insights into the genetic dissection of metabolomic traits in temperate grasses.
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Affiliation(s)
- Yoshihiko Onda
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.
| | - Komaki Inoue
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Yuji Sawada
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Minami Shimizu
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Kotaro Takahagi
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Yukiko Uehara-Yamaguchi
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Masami Y Hirai
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - David F Garvin
- Plant Science Research Unit, United States Department of Agriculture, Agricultural Research Service, 1991 Upper Buford Circle, St. Paul, MN 55108, USA.
| | - Keiichi Mochida
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Institute of Plant Science and Resource, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan.
- Microalgae Production Control Technology Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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13
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Della Coletta R, Hirsch CN, Rouse MN, Lorenz A, Garvin DF. Genomic Dissection of Nonhost Resistance to Wheat Stem Rust in Brachypodium distachyon. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:392-400. [PMID: 30261155 DOI: 10.1094/mpmi-08-18-0220-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The emergence of new races of Puccinia graminis f. sp. tritici, the causal pathogen of wheat stem rust, has spurred interest in developing durable resistance to this disease in wheat. Nonhost resistance holds promise to help control this and other diseases because it is durable against nonadapted pathogens. However, the genetic and molecular basis of nonhost resistance to wheat stem rust is poorly understood. In this study, the model grass Brachypodium distachyon, a nonhost of P. graminis f. sp. tritici, was used to genetically dissect nonhost resistance to wheat stem rust. A recombinant inbred line (RIL) population segregating for response to wheat stem rust was evaluated for resistance. Evaluation of genome-wide cumulative single nucleotide polymorphism allele frequency differences between contrasting pools of resistant and susceptible RILs followed by molecular marker analysis identified six quantitative trait loci (QTL) that cumulatively explained 72.5% of the variation in stem rust resistance. Two of the QTLs explained 31.7% of the variation, and their interaction explained another 4.6%. Thus, nonhost resistance to wheat stem rust in B. distachyon is genetically complex, with both major and minor QTLs acting additively and, in some cases, interacting. These findings will guide future research to identify genes essential to nonhost resistance to wheat stem rust.
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Affiliation(s)
- Rafael Della Coletta
- 1 Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, U.S.A
- 2 CAPES Foundation, Ministry of Education of Brazil, Brasilia, DF, Brazil
| | - Candice N Hirsch
- 1 Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, U.S.A
| | - Matthew N Rouse
- 3 USDA-ARS Cereal Disease Laboratory, St. Paul, MN, U.S.A
- 4 Department of Plant Pathology, University of Minnesota; and
| | - Aaron Lorenz
- 1 Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, U.S.A
| | - David F Garvin
- 1 Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, U.S.A
- 5 USDA-ARS Plant Science Research Unit, St. Paul, MN, U.S.A
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14
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Gill US, Lee S, Jia Y, Mysore KS. Exploring natural variation for rice sheath blight resistance in Brachypodium distachyon. PLANT SIGNALING & BEHAVIOR 2018; 14:1546527. [PMID: 30540521 PMCID: PMC6351096 DOI: 10.1080/15592324.2018.1546527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/26/2018] [Accepted: 10/30/2018] [Indexed: 06/09/2023]
Abstract
Sheath blight caused by the soil borne fungus Rhizoctonia solani AG1-IA is one of the major diseases of rice in the world. Genetic resistance in rice against this disease has not been very successful. Brachypodium distachyon is considered as a model species for several cereal crops and it has been studied in the past to identify novel sources of disease resistance against cereal crop diseases. Therefore, the current study was designed to explore nonhost disease resistance in Brachypodium accessions against sheath blight pathogen of rice, Rhizoctonia solani. A total of 19 Brachypodium distachyon accessions were screened for resistance against Rhizoctonia solani AG1-IA. Different levels of resistance reactions were observed among accessions. Quantification of jasmonic acid (JA) and salicylic acid (SA) concentration in selected resistant (Bd3-1), moderately susceptible (Bd21), and susceptible (Bd30-1) inbred accessions revealed that Bd3-1 accumulated more JA upon pathogen infection compared to Bd21 or Bd30-1. In contrary, no differences were observed for SA accumulation in tested accessions suggesting that the resistance to R. solani in Brachypodium is due to an SA-independent defense pathway. Our study provides a new foundation to explore this area for more durable resistance against this disease.
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Affiliation(s)
| | - Seonghee Lee
- Department of Horticultural Science, IFAS Gulf Coast Research and Education Center, University of Florida, Balm, USA
| | - Yulin Jia
- United States Department of Agriculture, Dale Bumpers National Rice Research Center, Stuttgart, AR, USA
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15
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Omidvar V, Dugyala S, Li F, Rottschaefer SM, Miller ME, Ayliffe M, Moscou MJ, Kianian SF, Figueroa M. Detection of Race-Specific Resistance Against Puccinia coronata f. sp. avenae in Brachypodium Species. PHYTOPATHOLOGY 2018; 108:1443-1454. [PMID: 29923800 DOI: 10.1094/phyto-03-18-0084-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Oat crown rust caused by Puccinia coronata f. sp. avenae is the most destructive foliar disease of cultivated oat. Characterization of genetic factors controlling resistance responses to Puccinia coronata f. sp. avenae in nonhost species could provide new resources for developing disease protection strategies in oat. We examined symptom development and fungal colonization levels of a collection of Brachypodium distachyon and B. hybridum accessions infected with three North American P. coronata f. sp. avenae isolates. Our results demonstrated that colonization phenotypes are dependent on both host and pathogen genotypes, indicating a role for race-specific responses in these interactions. These responses were independent of the accumulation of reactive oxygen species. Expression analysis of several defense-related genes suggested that salicylic acid and ethylene-mediated signaling but not jasmonic acid are components of resistance reaction to P. coronata f. sp. avenae. Our findings provide the basis to conduct a genetic inheritance study to examine whether effector-triggered immunity contributes to nonhost resistance to P. coronata f. sp. avenae in Brachypodium spp.
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Affiliation(s)
- Vahid Omidvar
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Sheshanka Dugyala
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Feng Li
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Susan M Rottschaefer
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Marisa E Miller
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Mick Ayliffe
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Matthew J Moscou
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Shahryar F Kianian
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Melania Figueroa
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
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16
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Gilbert B, Bettgenhaeuser J, Upadhyaya N, Soliveres M, Singh D, Park RF, Moscou MJ, Ayliffe M. Components of Brachypodium distachyon resistance to nonadapted wheat stripe rust pathogens are simply inherited. PLoS Genet 2018; 14:e1007636. [PMID: 30265668 PMCID: PMC6161853 DOI: 10.1371/journal.pgen.1007636] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 08/15/2018] [Indexed: 11/19/2022] Open
Abstract
Phytopathogens have a limited range of host plant species that they can successfully parasitise ie. that they are adapted for. Infection of plants by nonadapted pathogens often results in an active resistance response that is relatively poorly characterised because phenotypic variation in this response often does not exist within a plant species, or is too subtle for genetic dissection. In addition, complex polygenic inheritance often underlies these resistance phenotypes and mutagenesis often does not impact upon this resistance, presumably due to genetic or mechanistic redundancy. Here it is demonstrated that phenotypic differences in the resistance response of Brachypodium distachyon to the nonadapted wheat stripe rust pathogen Puccinia striiformis f. sp. tritici (Pst) are genetically tractable and simply inherited. Two dominant loci were identified on B. distachyon chromosome 4 that each reduce attempted Pst colonisation compared with sib and parent lines without these loci. One locus (Yrr1) is effective against diverse Australian Pst isolates and present in two B. distachyon mapping families as a conserved region that was reduced to 5 candidate genes by fine mapping. A second locus, Yrr2, shows Pst race-specificity and encodes a disease resistance gene family typically associated with host plant resistance. These data indicate that some components of resistance to nonadapted pathogens are genetically tractable in some instances and may mechanistically overlap with host plant resistance to avirulent adapted pathogens.
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Affiliation(s)
- Brian Gilbert
- CSIRO Agriculture and Food, Clunies Ross Drive, Canberra, ACT, Australia
| | - Jan Bettgenhaeuser
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Narayana Upadhyaya
- CSIRO Agriculture and Food, Clunies Ross Drive, Canberra, ACT, Australia
| | - Melanie Soliveres
- CSIRO Agriculture and Food, Clunies Ross Drive, Canberra, ACT, Australia
| | - Davinder Singh
- University of Sydney, Plant Breeding Institute, Cobbitty, NSW, Australia
| | - Robert F. Park
- University of Sydney, Plant Breeding Institute, Cobbitty, NSW, Australia
| | - Matthew J. Moscou
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
- University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Michael Ayliffe
- CSIRO Agriculture and Food, Clunies Ross Drive, Canberra, ACT, Australia
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17
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Scholthof KBG, Irigoyen S, Catalan P, Mandadi KK. Brachypodium: A Monocot Grass Model Genus for Plant Biology. THE PLANT CELL 2018; 30:1673-1694. [PMID: 29997238 PMCID: PMC6139682 DOI: 10.1105/tpc.18.00083] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/25/2018] [Accepted: 07/11/2018] [Indexed: 05/21/2023]
Abstract
The genus Brachypodium represents a model system that is advancing our knowledge of the biology of grasses, including small grains, in the postgenomics era. The most widely used species, Brachypodium distachyon, is a C3 plant that is distributed worldwide. B. distachyon has a small genome, short life cycle, and small stature and is amenable to genetic transformation. Due to the intensive and thoughtful development of this grass as a model organism, it is well-suited for laboratory and field experimentation. The intent of this review is to introduce this model system genus and describe some key outcomes of nearly a decade of research since the first draft genome sequence of the flagship species, B. distachyon, was completed. We discuss characteristics and features of B. distachyon and its congeners that make the genus a valuable model system for studies in ecology, evolution, genetics, and genomics in the grasses, review current hot topics in Brachypodium research, and highlight the potential for future analysis using this system in the coming years.
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Affiliation(s)
- Karen-Beth G Scholthof
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843
| | - Sonia Irigoyen
- Texas A&M AgriLife Research and Extension Center, Weslaco, Texas 78596
| | - Pilar Catalan
- Universidad de Zaragoza-Escuela Politécnica Superior de Huesca, 22071 Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza E-50059, Spain
- Institute of Biology, Tomsk State University, Tomsk 634050, Russia
| | - Kranthi K Mandadi
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843
- Texas A&M AgriLife Research and Extension Center, Weslaco, Texas 78596
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18
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Nazareno ES, Li F, Smith M, Park RF, Kianian SF, Figueroa M. Puccinia coronata f. sp. avenae: a threat to global oat production. MOLECULAR PLANT PATHOLOGY 2018; 19:1047-1060. [PMID: 28846186 PMCID: PMC6638059 DOI: 10.1111/mpp.12608] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/24/2017] [Accepted: 08/24/2017] [Indexed: 05/20/2023]
Abstract
UNLABELLED Puccinia coronata f. sp. avenae (Pca) causes crown rust disease in cultivated and wild oat (Avena spp.). The significant yield losses inflicted by this pathogen make crown rust the most devastating disease in the oat industry. Pca is a basidiomycete fungus with an obligate biotrophic lifestyle, and is classified as a typical macrocyclic and heteroecious fungus. The asexual phase in the life cycle of Pca occurs in oat, whereas the sexual phase takes place primarily in Rhamnus species as the alternative host. Epidemics of crown rust happens in areas with warm temperatures (20-25 °C) and high humidity. Infection by the pathogen leads to plant lodging and shrivelled grain of poor quality. Disease symptoms: Infection of susceptible oat varieties gives rise to orange-yellow round to oblong uredinia (pustules) containing newly formed urediniospores. Pustules vary in size and can be larger than 5 mm in length. Infection occurs primarily on the surfaces of leaves, although occasional symptoms develop in the oat leaf sheaths and/or floral structures, such as awns. Symptoms in resistant oat varieties vary from flecks to small pustules, typically accompanied by chlorotic halos and/or necrosis. The pycnial and aecial stages are mostly present in the leaves of Rhamnus species, but occasionally symptoms can also be observed in petioles, young stems and floral structures. Aecial structures display a characteristic hypertrophy and can differ in size, occasionally reaching more than 5 mm in diameter. Taxonomy: Pca belongs to the kingdom Fungi, phylum Basidiomycota, class Pucciniomycetes, order Pucciniales and family Pucciniaceae. Host range: Puccinia coronata sensu lato can infect 290 species of grass hosts. Pca is prevalent in all oat-growing regions and, compared with other cereal rusts, displays a broad telial host range. The most common grass hosts of Pca include cultivated hexaploid oat (Avena sativa) and wild relatives, such as bluejoint grass, perennial ryegrass and fescue. Alternative hosts include several species of Rhamnus, with R. cathartica (common buckthorn) as the most important alternative host in Europe and North America. CONTROL Most crown rust management strategies involve the use of rust-resistant crop varieties and the application of fungicides. The attainment of the durability of resistance against Pca is difficult as it is a highly variable pathogen with a great propensity to overcome the genetic resistance of varieties. Thus, adult plant resistance is often exploited in oat breeding programmes to develop new crown rust-resistant varieties. Useful website: https://www.ars.usda.gov/midwest-area/st-paul-mn/cereal-disease-lab/docs/cereal-rusts/race-surveys/.
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Affiliation(s)
- Eric S. Nazareno
- Department of Plant PathologyUniversity of MinnesotaSt. PaulMN 55108USA
| | - Feng Li
- Department of Plant PathologyUniversity of MinnesotaSt. PaulMN 55108USA
| | - Madeleine Smith
- Department of Plant PathologyUniversity of Minnesota‐Northwest Research and Outreach CenterCrookstonMN 56716USA
| | - Robert F. Park
- Plant Breeding InstituteThe University of SydneyNarellanNSW2567Australia
| | - Shahryar F. Kianian
- Cereal Disease Laboratory, US Department of Agriculture‐Agricultural Research ServiceSt. PaulMN 55108USA
| | - Melania Figueroa
- Department of Plant PathologyUniversity of MinnesotaSt. PaulMN 55108USA
- Stakman‐Borlaug Center for Sustainable Plant HealthUniversity of MinnesotaSt. PaulMN 55108USA
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19
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Bartaula R, Melo ATO, Connolly BA, Jin Y, Hale I. An interspecific barberry hybrid enables genetic dissection of non-host resistance to the stem rust pathogen Puccinia graminis. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:2483-2493. [PMID: 29529250 PMCID: PMC5920301 DOI: 10.1093/jxb/ery066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 02/15/2018] [Indexed: 05/28/2023]
Abstract
Stem rust, caused by Puccinia graminis (Pg), remains a devastating disease of wheat, and the emergence of new Pg races virulent on deployed resistance genes fuels the ongoing search for sources of durable resistance. Despite its intrinsic durability, non-host resistance (NHR) is largely unexplored as a protection strategy against Pg, partly due to the inherent challenge of developing a genetically tractable system within which NHR segregates. Here, we demonstrate that Pg's far less studied ancestral host, barberry (Berberis spp.), provides such a unique pathosystem. Characterization of a natural population of B. ×ottawensis, an interspecific hybrid of Pg-susceptible B. vulgaris and Pg-resistant B. thunbergii (Bt), reveals that this uncommon nothospecies can be used to dissect the genetic mechanism(s) of Pg-NHR exhibited by Bt. Artificial inoculation of a natural population of B. ×ottawensis accessions, verified via genotyping by sequencing to be first-generation hybrids, revealed 51% susceptible, 33% resistant, and 16% intermediate phenotypes. Characterization of a B. ×ottawensis full sib family excluded the possibility of maternal inheritance of the resistance. By demonstrating segregation of Pg-NHR in a hybrid population, this study challenges the assumed irrelevance of Bt to Pg epidemiology and lays a novel foundation for the genetic dissection of NHR to one of agriculture's most studied pathogens.
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Affiliation(s)
- Radhika Bartaula
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH, USA
| | - Arthur T O Melo
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH, USA
| | - Bryan A Connolly
- Department of Biology, Framingham State University, Framingham, MA, USA
| | - Yue Jin
- USDA-ARS Cereal Disease Laboratory, St. Paul, MN, USA
| | - Iago Hale
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH, USA
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20
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Dracatos PM, Haghdoust R, Singh D, Park RF. Exploring and exploiting the boundaries of host specificity using the cereal rust and mildew models. THE NEW PHYTOLOGIST 2018; 218:453-462. [PMID: 29464724 DOI: 10.1111/nph.15044] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 01/09/2018] [Indexed: 05/19/2023]
Abstract
Individual plants encounter a vast number of microbes including bacteria, viruses, fungi and oomycetes through their growth cycle, yet few of these pathogens are able to infect them. Plant species have diverged over millions of years, co-evolving with few specific pathogens. The host boundaries of most pathogen species can be clearly defined. In general, the greater the genetic divergence from the preferred host, the less likely that pathogen would be able to infect that plant species. Co-evolution and divergence also occur within pathogen species, leading to highly specialized subspecies with narrow host ranges. For example, cereal rust and mildew pathogens (Puccinia and Blumeria spp.) display high host specificity as a result of ongoing co-evolution with a narrow range of grass species. In rare cases, however, some plant species are in a transition from host to nonhost or are intermediate hosts (near nonhost). Barley was reported as a useful model for genetic and molecular studies of nonhost resistance due to rare susceptibility to numerous heterologous rust and mildew fungi. This review evaluates host specificity in numerous Puccinia/Blumeria-cereal pathosystems and discusses various approaches for transferring nonhost resistance (NHR) genes between crop species to reduce the impact of important diseases in food production.
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Affiliation(s)
- Peter Michael Dracatos
- Plant Breeding Institute, The University of Sydney, Cobbitty, Private Bag 4011, Narellan, NSW, 2567, Australia
| | - Rouja Haghdoust
- Plant Breeding Institute, The University of Sydney, Cobbitty, Private Bag 4011, Narellan, NSW, 2567, Australia
| | - Davinder Singh
- Plant Breeding Institute, The University of Sydney, Cobbitty, Private Bag 4011, Narellan, NSW, 2567, Australia
| | - Robert Fraser Park
- Plant Breeding Institute, The University of Sydney, Cobbitty, Private Bag 4011, Narellan, NSW, 2567, Australia
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21
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Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure. Nat Commun 2017; 8:2184. [PMID: 29259172 PMCID: PMC5736591 DOI: 10.1038/s41467-017-02292-8] [Citation(s) in RCA: 193] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 11/17/2017] [Indexed: 12/17/2022] Open
Abstract
While prokaryotic pan-genomes have been shown to contain many more genes than any individual organism, the prevalence and functional significance of differentially present genes in eukaryotes remains poorly understood. Whole-genome de novo assembly and annotation of 54 lines of the grass Brachypodium distachyon yield a pan-genome containing nearly twice the number of genes found in any individual genome. Genes present in all lines are enriched for essential biological functions, while genes present in only some lines are enriched for conditionally beneficial functions (e.g., defense and development), display faster evolutionary rates, lie closer to transposable elements and are less likely to be syntenic with orthologous genes in other grasses. Our data suggest that differentially present genes contribute substantially to phenotypic variation within a eukaryote species, these genes have a major influence in population genetics, and transposable elements play a key role in pan-genome evolution. The role of differential gene content in the evolution and function of eukaryotic genomes remains poorly explored. Here the authors assemble and annotate the Brachypodium distachyon pan-genome consisting of 54 diverse lines and reveal the differential present genes as a major driver of phenotypic variation.
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22
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Periyannan S, Milne RJ, Figueroa M, Lagudah ES, Dodds PN. An overview of genetic rust resistance: From broad to specific mechanisms. PLoS Pathog 2017; 13:e1006380. [PMID: 28704545 PMCID: PMC5509339 DOI: 10.1371/journal.ppat.1006380] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Sambasivam Periyannan
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Canberra, Australian Capital Territory, Australia
- Research School of Biology, The Australian National University, Canberra Australian Capital Territory, Australia
| | - Ricky J. Milne
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Melania Figueroa
- Department of Plant Pathology and The Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Evans S. Lagudah
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Peter N. Dodds
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Canberra, Australian Capital Territory, Australia
- * E-mail:
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Rioux RA, Van Ryzin BJ, Kerns JP. Brachypodium: A Potential Model Host for Fungal Pathogens of Turfgrasses. PHYTOPATHOLOGY 2017; 107:749-757. [PMID: 28134592 DOI: 10.1094/phyto-08-16-0318-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Brachypodium distachyon is a C3 grass that is an attractive model host system for studying pathogenicity of major turfgrass pathogens due to its genetic similarity to many cool-season turfgrasses. Infection assays with two or more isolates of the casual agents of dollar spot, brown patch, and Microdochium patch resulted in compatible interactions with B. distachyon inbred line Bd21-3. The symptoms produced by these pathogens on Bd21-3 closely resembled those observed on the natural turfgrass host (creeping bentgrass), demonstrating that B. distachyon is susceptible to the fungal pathogens that cause dollar spot, brown patch, and Microdochium patch on turfgrasses. The interaction between Sclerotinia homoeocarpa isolates and Brachypodium ecotypes was also investigated. Interestingly, differential responses of these ecotypes to S. homoeocarpa isolates was found, particularly when comparing B. distachyon to B. hybridum ecotypes. Taken together, these findings demonstrate that B. distachyon can be used as a model host system for these turfgrass diseases and leveraged for studies of molecular mechanisms contributing to host resistance.
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Affiliation(s)
- Renee A Rioux
- First author: Department of Plant Pathology, University of Wisconsin-Madison, Madison 53706; and second and third authors: Department of Entomology and Plant Pathology, North Carolina State University, Raleigh 27695
| | - Benjamin J Van Ryzin
- First author: Department of Plant Pathology, University of Wisconsin-Madison, Madison 53706; and second and third authors: Department of Entomology and Plant Pathology, North Carolina State University, Raleigh 27695
| | - James P Kerns
- First author: Department of Plant Pathology, University of Wisconsin-Madison, Madison 53706; and second and third authors: Department of Entomology and Plant Pathology, North Carolina State University, Raleigh 27695
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24
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Rabe F, Bosch J, Stirnberg A, Guse T, Bauer L, Seitner D, Rabanal FA, Czedik-Eysenberg A, Uhse S, Bindics J, Genenncher B, Navarrete F, Kellner R, Ekker H, Kumlehn J, Vogel JP, Gordon SP, Marcel TC, Münsterkötter M, Walter MC, Sieber CMK, Mannhaupt G, Güldener U, Kahmann R, Djamei A. A complete toolset for the study of Ustilago bromivora and Brachypodium sp. as a fungal-temperate grass pathosystem. eLife 2016; 5:e20522. [PMID: 27835569 PMCID: PMC5106213 DOI: 10.7554/elife.20522] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/12/2016] [Indexed: 11/18/2022] Open
Abstract
Due to their economic relevance, the study of plant pathogen interactions is of importance. However, elucidating these interactions and their underlying molecular mechanisms remains challenging since both host and pathogen need to be fully genetically accessible organisms. Here we present milestones in the establishment of a new biotrophic model pathosystem: Ustilago bromivora and Brachypodium sp. We provide a complete toolset, including an annotated fungal genome and methods for genetic manipulation of the fungus and its host plant. This toolset will enable researchers to easily study biotrophic interactions at the molecular level on both the pathogen and the host side. Moreover, our research on the fungal life cycle revealed a mating type bias phenomenon. U. bromivora harbors a haplo-lethal allele that is linked to one mating type region. As a result, the identified mating type bias strongly promotes inbreeding, which we consider to be a potential speciation driver.
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Affiliation(s)
- Franziska Rabe
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jason Bosch
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Alexandra Stirnberg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Tilo Guse
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Lisa Bauer
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Denise Seitner
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Fernando A Rabanal
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | | | - Simon Uhse
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Janos Bindics
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Bianca Genenncher
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Fernando Navarrete
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Ronny Kellner
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Heinz Ekker
- Vienna Biocenter Core Facilities GmbH, Vienna, Austria
| | - Jochen Kumlehn
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, Gatersleben, Germany
| | - John P Vogel
- DOE Joint Genome Institute, California, United States
| | - Sean P Gordon
- DOE Joint Genome Institute, California, United States
| | - Thierry C Marcel
- INRA UMR BIOGER, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Martin Münsterkötter
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Mathias C Walter
- Department of Genome-oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
| | - Christian MK Sieber
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Gertrud Mannhaupt
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Ulrich Güldener
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Genome-oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
| | - Regine Kahmann
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Armin Djamei
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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25
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An T, Cai Y, Zhao S, Zhou J, Song B, Bux H, Qi X. Brachypodium distachyon T-DNA insertion lines: a model pathosystem to study nonhost resistance to wheat stripe rust. Sci Rep 2016; 6:25510. [PMID: 27138687 PMCID: PMC4853781 DOI: 10.1038/srep25510] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 04/18/2016] [Indexed: 11/24/2022] Open
Abstract
Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (PST), is one of the most destructive diseases and can cause severe yield losses in many regions of the world. Because of the large size and complexity of wheat genome, it is difficult to study the molecular mechanism of interaction between wheat and PST. Brachypodium distachyon has become a model system for temperate grasses' functional genomics research. The phenotypic evaluation showed that the response of Brachypodium distachyon to PST was nonhost resistance (NHR), which allowed us to present this plant-pathogen system as a model to explore the immune response and the molecular mechanism underlying wheat and PST. Here we reported the generation of about 7,000 T-DNA insertion lines based on a highly efficient Agrobacterium-mediated transformation system. Hundreds of mutants either more susceptible or more resistant to PST than that of the wild type Bd21 were obtained. The three putative target genes, Bradi5g17540, BdMYB102 and Bradi5g11590, of three T-DNA insertion mutants could be involved in NHR of Brachypodium distachyon to wheat stripe rust. The systemic pathologic study of this T-DNA mutants would broaden our knowledge of NHR, and assist in breeding wheat cultivars with durable resistance.
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Affiliation(s)
- Tianyue An
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100093, China
| | - Yanli Cai
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100093, China
| | - Suzhen Zhao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jianghong Zhou
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Bo Song
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hadi Bux
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Institute of Plant Sciences, University of Sindh, Jamshoro, 76080, Pakistan
| | - Xiaoquan Qi
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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26
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Figueroa M, Upadhyaya NM, Sperschneider J, Park RF, Szabo LJ, Steffenson B, Ellis JG, Dodds PN. Changing the Game: Using Integrative Genomics to Probe Virulence Mechanisms of the Stem Rust Pathogen Puccinia graminis f. sp. tritici. FRONTIERS IN PLANT SCIENCE 2016; 7:205. [PMID: 26941766 PMCID: PMC4764693 DOI: 10.3389/fpls.2016.00205] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/06/2016] [Indexed: 05/03/2023]
Abstract
The recent resurgence of wheat stem rust caused by new virulent races of Puccinia graminis f. sp. tritici (Pgt) poses a threat to food security. These concerns have catalyzed an extensive global effort toward controlling this disease. Substantial research and breeding programs target the identification and introduction of new stem rust resistance (Sr) genes in cultivars for genetic protection against the disease. Such resistance genes typically encode immune receptor proteins that recognize specific components of the pathogen, known as avirulence (Avr) proteins. A significant drawback to deploying cultivars with single Sr genes is that they are often overcome by evolution of the pathogen to escape recognition through alterations in Avr genes. Thus, a key element in achieving durable rust control is the deployment of multiple effective Sr genes in combination, either through conventional breeding or transgenic approaches, to minimize the risk of resistance breakdown. In this situation, evolution of pathogen virulence would require changes in multiple Avr genes in order to bypass recognition. However, choosing the optimal Sr gene combinations to deploy is a challenge that requires detailed knowledge of the pathogen Avr genes with which they interact and the virulence phenotypes of Pgt existing in nature. Identifying specific Avr genes from Pgt will provide screening tools to enhance pathogen virulence monitoring, assess heterozygosity and propensity for mutation in pathogen populations, and confirm individual Sr gene functions in crop varieties carrying multiple effective resistance genes. Toward this goal, much progress has been made in assembling a high quality reference genome sequence for Pgt, as well as a Pan-genome encompassing variation between multiple field isolates with diverse virulence spectra. In turn this has allowed prediction of Pgt effector gene candidates based on known features of Avr genes in other plant pathogens, including the related flax rust fungus. Upregulation of gene expression in haustoria and evidence for diversifying selection are two useful parameters to identify candidate Avr genes. Recently, we have also applied machine learning approaches to agnostically predict candidate effectors. Here, we review progress in stem rust pathogenomics and approaches currently underway to identify Avr genes recognized by wheat Sr genes.
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Affiliation(s)
- Melania Figueroa
- Department of Plant Pathology and the Stakman-Borlaug Center for Sustainable Plant Health, University of MinnesotaSt. Paul, MN, USA
| | - Narayana M. Upadhyaya
- Agriculture, Commonwealth Scientific and Industrial Research OrganisationCanberra, ACT, Australia
| | - Jana Sperschneider
- Agriculture, Centre for Environment and Life Sciences, Commonwealth Scientific and Industrial Research OrganisationPerth, WA, Australia
| | - Robert F. Park
- Faculty of Agriculture and Environment, Plant Breeding Institute, The University of SydneyNarellan, NSW, Australia
| | - Les J. Szabo
- Department of Plant Pathology and the Stakman-Borlaug Center for Sustainable Plant Health, University of MinnesotaSt. Paul, MN, USA
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research ServiceSt. Paul, MN, USA
| | - Brian Steffenson
- Department of Plant Pathology and the Stakman-Borlaug Center for Sustainable Plant Health, University of MinnesotaSt. Paul, MN, USA
| | - Jeff G. Ellis
- Agriculture, Commonwealth Scientific and Industrial Research OrganisationCanberra, ACT, Australia
| | - Peter N. Dodds
- Agriculture, Commonwealth Scientific and Industrial Research OrganisationCanberra, ACT, Australia
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27
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Dugyala S, Borowicz P, Acevedo M. Rapid protocol for visualization of rust fungi structures using fluorochrome Uvitex 2B. PLANT METHODS 2015; 11:54. [PMID: 26692889 PMCID: PMC4676834 DOI: 10.1186/s13007-015-0096-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/02/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Histological examination using fluorochromes is one of the standard methods for observation of microorganisms in tissues and other compartments. In the study of fungi, especially those that cannot be cultured in axenic media such as biotrophic fungi, histological examination of processes associated with the fungal growth, differentiation, infection and other cellular functions can lead to the better understanding of host-parasite interactions. Fluorescence microscopy coupled with Fluorochrome Uvitex 2B have been extensively utilized to study rust fungi structures and host-pathogen interactions. In this study, we report development of a rapid staining protocol of the rust fungus Puccinia triticina using fluorochrome Uvitex 2B. The newly developed rapid procedure was compared with a standard staining technique to observe in planta fungal infection structures development during the wheat-Puccinia triticina interaction. RESULTS While significantly reducing the time for staining, the rapid protocol described here was equally efficient or better compared to standard procedure in detecting fungal infection structures using Uvitex 2B. In the rapid staining procedure, pre-heating of the stain increased efficiency to detect all the infection structures including haustoria with highly reduced background noise from plant tissue. CONCLUSION This staining process described here is simple and quick. It can be completed in 4 h, which is of 6 times faster than the standard Uvitex 2B staining procedure.
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Affiliation(s)
- Sheshanka Dugyala
- />Department of Plant Pathology, North Dakota State University, Dept. 7660, PO Box 6050, Fargo, ND 58108-6050 USA
| | - Pawel Borowicz
- />Department of Animal Sciences, North Dakota State University, Dept. #7630, PO Box 6050, Fargo, ND 58108-6050 USA
| | - Maricelis Acevedo
- />Department of Plant Pathology, North Dakota State University, Dept. 7660, PO Box 6050, Fargo, ND 58108-6050 USA
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28
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Dawson AM, Bettgenhaeuser J, Gardiner M, Green P, Hernández-Pinzón I, Hubbard A, Moscou MJ. The development of quick, robust, quantitative phenotypic assays for describing the host-nonhost landscape to stripe rust. FRONTIERS IN PLANT SCIENCE 2015; 6:876. [PMID: 26579142 PMCID: PMC4621417 DOI: 10.3389/fpls.2015.00876] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 10/02/2015] [Indexed: 05/24/2023]
Abstract
Nonhost resistance is often conceptualized as a qualitative separation from host resistance. Classification into these two states is generally facile, as they fail to fully describe the range of states that exist in the transition from host to nonhost. This poses a problem when studying pathosystems that cannot be classified as either host or nonhost due to their intermediate status relative to these two extremes. In this study, we investigate the efficacy of the Poaceae-stripe rust (Puccinia striiformis Westend.) interaction for describing the host-nonhost landscape. First, using barley (Hordeum vulgare L.) and Brachypodium distachyon (L.) P. Beauv. We observed that macroscopic symptoms of chlorosis and leaf browning were associated with hyphal colonization by P. striiformis f. sp. tritici, respectively. This prompted us to adapt a protocol for visualizing fungal structures into a phenotypic assay that estimates the percent of leaf colonized. Use of this assay in intermediate host and intermediate nonhost systems found the frequency of infection decreases with evolutionary divergence from the host species. Similarly, we observed that the pathogen's ability to complete its life cycle decreased faster than its ability to colonize leaf tissue, with no incidence of pustules observed in the intermediate nonhost system and significantly reduced pustule formation in the intermediate host system as compared to the host system, barley-P. striiformis f. sp. hordei. By leveraging the stripe rust pathosystem in conjunction with macroscopic and microscopic phenotypic assays, we now hope to dissect the genetic architecture of intermediate host and intermediate nonhost resistance using structured populations in barley and B. distachyon.
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Affiliation(s)
| | | | | | - Phon Green
- The Sainsbury Laboratory, Norwich Research ParkNorwich, UK
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Figueroa M, Castell-Miller CV, Li F, Hulbert SH, Bradeen JM. Pushing the boundaries of resistance: insights from Brachypodium-rust interactions. FRONTIERS IN PLANT SCIENCE 2015; 6:558. [PMID: 26284085 PMCID: PMC4519692 DOI: 10.3389/fpls.2015.00558] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/07/2015] [Indexed: 05/20/2023]
Abstract
The implications of global population growth urge transformation of current food and bioenergy production systems to sustainability. Members of the family Poaceae are of particular importance both in food security and for their applications as biofuel substrates. For centuries, rust fungi have threatened the production of valuable crops such as wheat, barley, oat, and other small grains; similarly, biofuel crops can also be susceptible to these pathogens. Emerging rust pathogenic races with increased virulence and recurrent rust epidemics around the world point out the vulnerability of monocultures. Basic research in plant immunity, especially in model plants, can make contributions to understanding plant resistance mechanisms and improve disease management strategies. The development of the grass Brachypodium distachyon as a genetically tractable model for monocots, especially temperate cereals and grasses, offers the possibility to overcome the experimental challenges presented by the genetic and genomic complexities of economically valuable crop plants. The numerous resources and tools available in Brachypodium have opened new doors to investigate the underlying molecular and genetic bases of plant-microbe interactions in grasses and evidence demonstrating the applicability and advantages of working with B. distachyon is increasing. Importantly, several interactions between B. distachyon and devastating plant pathogens, such rust fungi, have been examined in the context of non-host resistance. Here, we discuss the use of B. distachyon in these various pathosystems. Exploiting B. distachyon to understand the mechanisms underpinning disease resistance to non-adapted rust fungi may provide effective and durable approaches to fend off these pathogens. The close phylogenetic relationship among Brachypodium spp. and grasses with industrial and agronomic value support harnessing this model plant to improve cropping systems and encourage its use in translational research.
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Affiliation(s)
- Melania Figueroa
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
| | - Claudia V. Castell-Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
| | - Feng Li
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
| | - Scot H. Hulbert
- Department of Plant Pathology, Washington State University, Pullman, WA, USA
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - James M. Bradeen
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
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30
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Wang X, McCallum BD, Fetch T, Bakkeren G, Saville BJ. Sr36- and Sr5-Mediated Resistance Response to Puccinia graminis f. sp. tritici Is Associated with Callose Deposition in Wheat Guard Cells. PHYTOPATHOLOGY 2015; 105:728-737. [PMID: 26056723 DOI: 10.1094/phyto-08-14-0213-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Race-specific resistance of wheat to Puccinia graminis f. sp. tritici is primarily posthaustorial and often involves the induction of a hypersensitive response (HR). The aim of this study was to investigate host defense responses induced in interactions between P. graminis f. sp. tritici races and wheat lines carrying different race-specific stem rust resistance (Sr) genes. In incompatible interactions between wheat lines carrying Sr36 in three genetic backgrounds (LMPG, Prelude, or W2691) and avirulent P. graminis f. sp. tritici races MCCFC or RCCDM, callose accumulated within 24 h in wheat guard cells contacted by a P. graminis f. sp. tritici appressorium, and P. graminis f. sp. tritici ingress was inhibited following appressorium formation. Accordingly, the expression of transcripts encoding a callose synthase increased in the incompatible interaction between LMPG-Sr36 and avirulent P. graminis f. sp. tritici race MCCFC. Furthermore, the inhibition of callose synthesis through the infiltration of 2-deoxy-D-glucose (DDG) increased the ability of P. graminis f. sp. tritici race MCCFC to infect LMPG-Sr36. A similar induction of callose deposition in wheat guard cells was also observed within 24 h after inoculation (hai) with avirulent P. graminis f. sp. tritici race HKCJC on LMPG-Sr5 plants. In contrast, this defense response was not induced in incompatible interactions involving Sr6, Sr24, or Sr30. Instead, the induction of an HR and cellular lignification were noted. The manifestation of the HR and cellular lignification was induced earlier (24 hai) and was more extensive in the resistance response mediated by Sr6 compared with those mediated by Sr24 or Sr30. These results indicate that the resistance mediated by Sr36 is similar to that mediated by Sr5 but different from those triggered by Sr6, Sr24, or Sr30. Resistance responses mediated by Sr5 and Sr36 are prehaustorial, and are a result of very rapid recognition of molecules derived from avirulent isolates of P. graminis f. sp. tritici, in contrast to the responses triggered in lines with Sr6, Sr24, and Sr30.
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Affiliation(s)
- X Wang
- First, second, and third authors: Cereal Research Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada; fourth author: Pacific Agri-Food Research Centre, Agriculture and Agri Food Canada, Summerland, BC, VOH 1ZO, Canada; and fifth author: Forensic Science Program, and Environmental and Life Sciences Graduate Program Trent University, Peterborough, ON, K9J 7B8, Canada
| | - B D McCallum
- First, second, and third authors: Cereal Research Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada; fourth author: Pacific Agri-Food Research Centre, Agriculture and Agri Food Canada, Summerland, BC, VOH 1ZO, Canada; and fifth author: Forensic Science Program, and Environmental and Life Sciences Graduate Program Trent University, Peterborough, ON, K9J 7B8, Canada
| | - T Fetch
- First, second, and third authors: Cereal Research Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada; fourth author: Pacific Agri-Food Research Centre, Agriculture and Agri Food Canada, Summerland, BC, VOH 1ZO, Canada; and fifth author: Forensic Science Program, and Environmental and Life Sciences Graduate Program Trent University, Peterborough, ON, K9J 7B8, Canada
| | - G Bakkeren
- First, second, and third authors: Cereal Research Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada; fourth author: Pacific Agri-Food Research Centre, Agriculture and Agri Food Canada, Summerland, BC, VOH 1ZO, Canada; and fifth author: Forensic Science Program, and Environmental and Life Sciences Graduate Program Trent University, Peterborough, ON, K9J 7B8, Canada
| | - B J Saville
- First, second, and third authors: Cereal Research Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada; fourth author: Pacific Agri-Food Research Centre, Agriculture and Agri Food Canada, Summerland, BC, VOH 1ZO, Canada; and fifth author: Forensic Science Program, and Environmental and Life Sciences Graduate Program Trent University, Peterborough, ON, K9J 7B8, Canada
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Gill US, Uppalapati SR, Nakashima J, Mysore KS. Characterization of Brachypodium distachyon as a nonhost model against switchgrass rust pathogen Puccinia emaculata. BMC PLANT BIOLOGY 2015; 15:113. [PMID: 25953307 PMCID: PMC4424542 DOI: 10.1186/s12870-015-0502-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 04/22/2015] [Indexed: 05/29/2023]
Abstract
BACKGROUND Switchgrass rust, caused by Puccinia emaculata, is an important disease of switchgrass, a potential biofuel crop in the United States. In severe cases, switchgrass rust has the potential to significantly affect biomass yield. In an effort to identify novel sources of resistance against switchgrass rust, we explored nonhost resistance against P. emaculata by characterizing its interactions with six monocot nonhost plant species. We also studied the genetic variations for resistance among Brachypodium inbred accessions and the involvement of various defense pathways in nonhost resistance of Brachypodium. RESULTS We characterized P. emaculata interactions with six monocot nonhost species and identified Brachypodium distachyon (Bd21) as a suitable nonhost model to study switchgrass rust. Interestingly, screening of Brachypodium accessions identified natural variations in resistance to switchgrass rust. Brachypodium inbred accessions Bd3-1 and Bd30-1 were identified as most and least resistant to switchgrass rust, respectively, when compared to tested accessions. Transcript profiling of defense-related genes indicated that the genes which were induced in Bd21after P. emaculata inoculation also had higher basal transcript abundance in Bd3-1 when compared to Bd30-1 and Bd21 indicating their potential involvement in nonhost resistance against switchgrass rust. CONCLUSION In the present study, we identified Brachypodium as a suitable nonhost model to study switchgrass rust which exhibit type I nonhost resistance. Variations in resistance response were also observed among tested Brachypodium accessions. Brachypodium nonhost resistance against P. emaculata may involve various defense pathways as indicated by transcript profiling of defense related genes. Overall, this study provides a new avenue to utilize novel sources of nonhost resistance in Brachypodium against switchgrass rust.
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Affiliation(s)
- Upinder S Gill
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, 73401, USA.
| | - Srinivasa R Uppalapati
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, 73401, USA.
- Current address: Biologicals and Fungicide Discovery, DuPont Crop Protection, Newark, DE 19711, USA.
| | - Jin Nakashima
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, 73401, USA.
| | - Kirankumar S Mysore
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, 73401, USA.
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O'Driscoll A, Doohan F, Mullins E. Exploring the utility of Brachypodium distachyon as a model pathosystem for the wheat pathogen Zymoseptoria tritici. BMC Res Notes 2015; 8:132. [PMID: 25888730 PMCID: PMC4397700 DOI: 10.1186/s13104-015-1097-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 03/26/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Zymoseptoria tritici, the causative organism of Septoria tritici blotch disease is a prevalent biotic stressor of wheat production, exerting substantial economic constraints on farmers, requiring intensive chemical control to protect yields. A hemibiotrophic pathogen with a long asymptomless phase of up to 11 days post inoculation (dpi) before a rapid switch to necrotrophy; a deficit exists in our understanding of the events occurring within the host during the two phases of infection. Brachypodium distachyon has demonstrated its potential as a model species for the investigation of fungal disease resistance in cereal and grass species. The aim of this study was to assess the physical interaction between Z. tritici (strain IPO323) and B. distachyon and examine its potential as a model pathosystem for Z. tritici. RESULTS Septoria tritici blotch symptoms developed on the wheat cultivar Riband from 12 dpi with pycnidial formation abundant by 20 dpi. Symptoms on B. distachyon ecotype Bd21-1 were visible from 1 dpi: characteristic pale, water soaked lesions which developed into blotch-like lesions by 4 dpi. These lesions then became necrotic with chlorotic regions expanding up to 7 dpi. Sporulation on B. distachyon tissues was not observed and no evidence of fungal penetration could be obtained, indicating that Z. tritici was unable to complete its life cycle within B. distachyon ecotypes. However, observation of host responses to the Z. tritici strain IPO323 in five B. distachyon ecotypes revealed a variation in resistance responses, ranging from immunity to a chlorotic/necrotic phenotype. CONCLUSIONS The observed interactions suggest that B. distachyon is an incompatible host for Z. tritici infection, with STB symptom development on B. distachyon comparable to that observed during the early infection stages on the natural host, wheat. However first visible symptoms occurred more rapidly on B. distachyon; from 1 dpi in comparison to 12 dpi in wheat. Consequently, we propose that the interaction between B. distachyon and Z. tritici as observed in this study could serve as a suitable model pathosystem with which to investigate mechanisms underpinning an incompatible host response to Z. tritici.
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Affiliation(s)
- Aoife O'Driscoll
- Department of Crop Science, Teagasc Research Centre, Oak Park, Carlow, Ireland.
- UCD Earth Institute and UCD School of Biology and Environmental Sciences, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Fiona Doohan
- UCD Earth Institute and UCD School of Biology and Environmental Sciences, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Ewen Mullins
- Department of Crop Science, Teagasc Research Centre, Oak Park, Carlow, Ireland.
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Zhong S, Ali S, Leng Y, Wang R, Garvin DF. Brachypodium distachyon-Cochliobolus sativus Pathosystem is a New Model for Studying Plant-Fungal Interactions in Cereal Crops. PHYTOPATHOLOGY 2015; 105:482-9. [PMID: 25423068 DOI: 10.1094/phyto-08-14-0214-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cochliobolus sativus (anamorph: Bipolaris sorokiniana) causes spot blotch, common root rot, and kernel blight or black point in barley and wheat. However, little is known about the molecular mechanisms underlying the pathogenicity of C. sativus or the molecular basis of resistance and susceptibility in the hosts. This study aims to establish the model grass Brachypodium distachyon as a new model for studying plant-fungus interactions in cereal crops. Six B. distachyon lines were inoculated with five C. sativus isolates. The results indicated that all six B. distachyon lines were infected by the C. sativus isolates, with their levels of resistance varying depending on the fungal isolates used. Responses ranging from hypersensitive response-mediated resistance to complete susceptibility were observed in a large collection of B. distachyon (2n=2x=10) and B. hybridum (2n=4x=30) accessions inoculated with four of the C. sativus isolates. Evaluation of an F2 population derived from the cross between two of the B. distachyon lines, Bd1-1 and Bd3-1, with isolate Cs07-47-1 showed quantitative and transgressive segregation for resistance to C. sativus, suggesting that the resistance may be governed by quantitative trait loci from both parents. The availability of whole-genome sequences of both the host (B. distachyon) and the pathogen (C. sativus) makes this pathosystem an attractive model for studying this important disease of cereal crops.
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Affiliation(s)
- Shaobin Zhong
- First, second, third, and fourth authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and fifth author: United States Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, University of Minnesota, St. Paul 55108
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Fitzgerald TL, Powell JJ, Schneebeli K, Hsia MM, Gardiner DM, Bragg JN, McIntyre CL, Manners JM, Ayliffe M, Watt M, Vogel JP, Henry RJ, Kazan K. Brachypodium as an emerging model for cereal-pathogen interactions. ANNALS OF BOTANY 2015; 115:717-31. [PMID: 25808446 PMCID: PMC4373291 DOI: 10.1093/aob/mcv010] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 11/03/2014] [Accepted: 12/22/2014] [Indexed: 05/22/2023]
Abstract
BACKGROUND Cereal diseases cause tens of billions of dollars of losses annually and have devastating humanitarian consequences in the developing world. Increased understanding of the molecular basis of cereal host-pathogen interactions should facilitate development of novel resistance strategies. However, achieving this in most cereals can be challenging due to large and complex genomes, long generation times and large plant size, as well as quarantine and intellectual property issues that may constrain the development and use of community resources. Brachypodium distachyon (brachypodium) with its small, diploid and sequenced genome, short generation time, high transformability and rapidly expanding community resources is emerging as a tractable cereal model. SCOPE Recent research reviewed here has demonstrated that brachypodium is either susceptible or partially susceptible to many of the major cereal pathogens. Thus, the study of brachypodium-pathogen interactions appears to hold great potential to improve understanding of cereal disease resistance, and to guide approaches to enhance this resistance. This paper reviews brachypodium experimental pathosystems for the study of fungal, bacterial and viral cereal pathogens; the current status of the use of brachypodium for functional analysis of cereal disease resistance; and comparative genomic approaches undertaken using brachypodium to assist characterization of cereal resistance genes. Additionally, it explores future prospects for brachypodium as a model to study cereal-pathogen interactions. CONCLUSIONS The study of brachypodium-pathogen interactions appears to be a productive strategy for understanding mechanisms of disease resistance in cereal species. Knowledge obtained from this model interaction has strong potential to be exploited for crop improvement.
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Affiliation(s)
- Timothy L Fitzgerald
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Jonathan J Powell
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Katharina Schneebeli
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - M Mandy Hsia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Donald M Gardiner
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Jennifer N Bragg
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - C Lynne McIntyre
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - John M Manners
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Mick Ayliffe
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Michelle Watt
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - John P Vogel
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Robert J Henry
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Kemal Kazan
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
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Bettgenhaeuser J, Gilbert B, Ayliffe M, Moscou MJ. Nonhost resistance to rust pathogens - a continuation of continua. FRONTIERS IN PLANT SCIENCE 2014; 5:664. [PMID: 25566270 PMCID: PMC4263244 DOI: 10.3389/fpls.2014.00664] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 11/07/2014] [Indexed: 05/25/2023]
Abstract
The rust fungi (order: Pucciniales) are a group of widely distributed fungal plant pathogens, which can infect representatives of all vascular plant groups. Rust diseases significantly impact several crop species and considerable research focuses on understanding the basis of host specificity and nonhost resistance. Like many pathogens, rust fungi vary considerably in the number of hosts they can infect, such as wheat leaf rust (Puccinia triticina), which can only infect species in the genera Triticum and Aegilops, whereas Asian soybean rust (Phakopsora pachyrhizi) is known to infect over 95 species from over 42 genera. A greater understanding of the genetic basis determining host range has the potential to identify sources of durable resistance for agronomically important crops. Delimiting the boundary between host and nonhost has been complicated by the quantitative nature of phenotypes in the transition between these two states. Plant-pathogen interactions in this intermediate state are characterized either by (1) the majority of accessions of a species being resistant to the rust or (2) the rust only being able to partially complete key components of its life cycle. This leads to a continuum of disease phenotypes in the interaction with different plant species, observed as a range from compatibility (host) to complete immunity within a species (nonhost). In this review we will highlight how the quantitative nature of disease resistance in these intermediate interactions is caused by a continuum of defense barriers, which a pathogen needs to overcome for successfully establishing itself in the host. To illustrate continua as this underlying principle, we will discuss the advances that have been made in studying nonhost resistance towards rust pathogens, particularly cereal rust pathogens.
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Affiliation(s)
| | - Brian Gilbert
- Commonwealth Scientific and Industrial Research Organisation, Agriculture FlagshipCanberra, ACT, Australia
| | - Michael Ayliffe
- Commonwealth Scientific and Industrial Research Organisation, Agriculture FlagshipCanberra, ACT, Australia
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Dracatos PM, Ayliffe M, Khatkar MS, Fetch T, Singh D, Park RF. Inheritance of prehaustorial resistance to Puccinia graminis f. sp. avenae in barley (Hordeum vulgare L.). MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:1253-1262. [PMID: 25025780 DOI: 10.1094/mpmi-05-14-0140-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Rust pathogens within the genus Puccinia cause some of the most economically significant diseases of crops. Different formae speciales of P. graminis have co-evolved to mainly infect specific grass hosts; however, some genotypes of other closely related cereals can also be infected. This study investigated the inheritance of resistance to three diverse pathotypes of the oat stem rust pathogen (P. graminis f. sp. avenae) in the 'Yerong' ✕ 'Franklin' (Y/F) barley doubled haploid (DH) population, a host with which it is not normally associated. Both parents, 'Yerong' and 'Franklin', were immune to all P. graminis f. sp. avenae pathotypes; however. there was transgressive segregation within the Y/F population, in which infection types (IT) ranged from complete immunity to mesothetic susceptibility, suggesting the presence of heritable resistance. Both QTL and marker-trait association (MTA) analysis was performed on the Y/F population to map resistance loci in response to P. graminis f. sp. avenae. QTL on chromosome 1H ('Yerong' Rpga1 and Rpga2) were identified using all forms of analysis, while QTL detected on 5H ('Franklin' Rpga3 and Rpga4) and 7H (Rpga5) were only detected using MTA or composite interval mapping-single marker regression analysis respectively. Rpga1 to Rpga5 were effective in response to all P. graminis f. sp. avenae pathotypes used in this study, suggesting resistance is not pathotype specific. Rpga1 co-located to previously mapped QTL in the Y/F population for adult plant resistance to the barley leaf scald pathogen (Rhynchosporium secalis) on chromosome 1H. Histological evidence suggests that the resistance observed within parental and immune DH lines in the population was prehaustorial and caused by callose deposition within the walls of the mesophyll cells, preventing hyphal penetration.
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Girin T, David LC, Chardin C, Sibout R, Krapp A, Ferrario-Méry S, Daniel-Vedele F. Brachypodium: a promising hub between model species and cereals. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5683-96. [PMID: 25262566 DOI: 10.1093/jxb/eru376] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Brachypodium distachyon was proposed as a model species for genetics and molecular genomics in cereals less than 10 years ago. It is now established as a standard for research on C3 cereals on a variety of topics, due to its close phylogenetic relationship with Triticeae crops such as wheat and barley, and to its simple genome, its minimal growth requirement, and its short life cycle. In this review, we first highlight the tools and resources for Brachypodium that are currently being developed and made available by the international community. We subsequently describe how this species has been used for comparative genomic studies together with cereal crops, before illustrating major research fields in which Brachypodium has been successfully used as a model: cell wall synthesis, plant-pathogen interactions, root architecture, and seed development. Finally, we discuss the usefulness of research on Brachypodium in order to improve nitrogen use efficiency in cereals, with the aim of reducing the amount of applied fertilizer while increasing the grain yield. Several paths are considered, namely an improvement of either nitrogen remobilization from the vegetative organs, nitrate uptake from the soil, or nitrate assimilation by the plant. Altogether, these examples position the research on Brachypodium as at an intermediate stage between basic research, carried out mainly in Arabidopsis, and applied research carried out on wheat and barley, enabling a complementarity of the studies and reciprocal benefits.
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Affiliation(s)
- Thomas Girin
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Laure C David
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Camille Chardin
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Richard Sibout
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Anne Krapp
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Sylvie Ferrario-Méry
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Françoise Daniel-Vedele
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
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Gordon SP, Priest H, Des Marais DL, Schackwitz W, Figueroa M, Martin J, Bragg JN, Tyler L, Lee CR, Bryant D, Wang W, Messing J, Manzaneda AJ, Barry K, Garvin DF, Budak H, Tuna M, Mitchell-Olds T, Pfender WF, Juenger TE, Mockler TC, Vogel JP. Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:361-74. [PMID: 24888695 DOI: 10.1111/tpj.12569] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 05/20/2014] [Accepted: 05/23/2014] [Indexed: 05/08/2023]
Abstract
Brachypodium distachyon is small annual grass that has been adopted as a model for the grasses. Its small genome, high-quality reference genome, large germplasm collection, and selfing nature make it an excellent subject for studies of natural variation. We sequenced six divergent lines to identify a comprehensive set of polymorphisms and analyze their distribution and concordance with gene expression. Multiple methods and controls were utilized to identify polymorphisms and validate their quality. mRNA-Seq experiments under control and simulated drought-stress conditions, identified 300 genes with a genotype-dependent treatment response. We showed that large-scale sequence variants had extremely high concordance with altered expression of hundreds of genes, including many with genotype-dependent treatment responses. We generated a deep mRNA-Seq dataset for the most divergent line and created a de novo transcriptome assembly. This led to the discovery of >2400 previously unannotated transcripts and hundreds of genes not present in the reference genome. We built a public database for visualization and investigation of sequence variants among these widely used inbred lines.
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Affiliation(s)
- Sean P Gordon
- USDA-ARS Western Regional Research Center, 800 Buchanan St., Albany, CA, 94710, USA
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Differential gene expression and metabolomic analyses of Brachypodium distachyon infected by deoxynivalenol producing and non-producing strains of Fusarium graminearum. BMC Genomics 2014; 15:629. [PMID: 25063396 PMCID: PMC4124148 DOI: 10.1186/1471-2164-15-629] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 06/18/2014] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Fusarium Head Blight (FHB) caused primarily by Fusarium graminearum (Fg) is one of the major diseases of small-grain cereals including bread wheat. This disease both reduces yields and causes quality losses due to the production of deoxynivalenol (DON), the major type B trichothecene mycotoxin. DON has been described as a virulence factor enabling efficient colonization of spikes by the fungus in wheat, but its precise role during the infection process is still elusive. Brachypodium distachyon (Bd) is a model cereal species which has been shown to be susceptible to FHB. Here, a functional genomics approach was performed in order to characterize the responses of Bd to Fg infection using a global transcriptional and metabolomic profiling of B. distachyon plants infected by two strains of F. graminearum: a wild-type strain producing DON (Fgdon+) and a mutant strain impaired in the production of the mycotoxin (Fgdon-). RESULTS Histological analysis of the interaction of the Bd21 ecotype with both Fg strains showed extensive fungal tissue colonization with the Fgdon+ strain while the florets infected with the Fgdon- strain exhibited a reduced hyphal extension and cell death on palea and lemma tissues. Fungal biomass was reduced in spikes inoculated with the Fgdon- strain as compared with the wild-type strain. The transcriptional analysis showed that jasmonate and ethylene-signalling pathways are induced upon infection, together with genes encoding putative detoxification and transport proteins, antioxidant functions as well as secondary metabolite pathways. In particular, our metabolite profiling analysis showed that tryptophan-derived metabolites, tryptamine, serotonin, coumaroyl-serotonin and feruloyl-serotonin, are more induced upon infection by the Fgdon+ strain than by the Fgdon- strain. Serotonin was shown to exhibit a slight direct antimicrobial effect against Fg. CONCLUSION Our results show that Bd exhibits defense hallmarks similar to those already identified in cereal crops. While the fungus uses DON as a virulence factor, the host plant preferentially induces detoxification and the phenylpropanoid and phenolamide pathways as resistance mechanisms. Together with its amenability in laboratory conditions, this makes Bd a very good model to study cereal resistance mechanisms towards the major disease FHB.
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Mochida K, Shinozaki K. Unlocking Triticeae genomics to sustainably feed the future. PLANT & CELL PHYSIOLOGY 2013; 54:1931-50. [PMID: 24204022 PMCID: PMC3856857 DOI: 10.1093/pcp/pct163] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 11/04/2013] [Indexed: 05/23/2023]
Abstract
The tribe Triticeae includes the major crops wheat and barley. Within the last few years, the whole genomes of four Triticeae species-barley, wheat, Tausch's goatgrass (Aegilops tauschii) and wild einkorn wheat (Triticum urartu)-have been sequenced. The availability of these genomic resources for Triticeae plants and innovative analytical applications using next-generation sequencing technologies are helping to revitalize our approaches in genetic work and to accelerate improvement of the Triticeae crops. Comparative genomics and integration of genomic resources from Triticeae plants and the model grass Brachypodium distachyon are aiding the discovery of new genes and functional analyses of genes in Triticeae crops. Innovative approaches and tools such as analysis of next-generation populations, evolutionary genomics and systems approaches with mathematical modeling are new strategies that will help us discover alleles for adaptive traits to future agronomic environments. In this review, we provide an update on genomic tools for use with Triticeae plants and Brachypodium and describe emerging approaches toward crop improvements in Triticeae.
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Affiliation(s)
- Keiichi Mochida
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 230-0045 Japan
| | - Kazuo Shinozaki
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
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Ayliffe M, Singh D, Park R, Moscou M, Pryor T. Infection of Brachypodium distachyon with selected grass rust pathogens. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2013; 26:946-57. [PMID: 23594350 DOI: 10.1094/mpmi-01-13-0017-r] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The model temperate grass Brachypodium distachyon is considered a nonhost for wheat rust diseases caused by Puccinia graminis f. sp. tritici, P. triticina, and P. striiformis. Up to 140 Brachypodium accessions were infected with these three rust species, in addition to P. graminis ff. spp. avena and phalaridis. Related B. distachyon lines showed similar cytological nonhost resistance (NHR) phenotypes, and an inverse relationship between P. graminis f. sp. tritici and P. striiformis growth was observed in many lines, with accessions that allowed the most growth of P. graminis f. sp. tritici showing the least P. striiformis development and vice versa. Callose deposition patterns during infection by all three rust species showed similarity to the wheat basal defense response while cell death that resulted in autofluorescence did not appear to be a major component of the defense response. Infection of B. distachyon with P. graminis f. sp. avena and P. graminis f. sp. phalaridis produced much greater colonization, indicating that P. graminis rusts with Poeae hosts show greater ability to infect B. distachyon than those with Triticeae hosts. P. striiformis infection of progeny from two B. distachyon families demonstrated that these NHR phenotypes are highly heritable and appear to be under relatively simple genetic control, making this species a powerful tool for elucidating the molecular basis of NHR to cereal rust pathogens.
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