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Kapp N, Barnes WJ, Richard TL, Anderson CT. Imaging with the fluorogenic dye Basic Fuchsin reveals subcellular patterning and ecotype variation of lignification in Brachypodium distachyon. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:4295-304. [PMID: 25922482 PMCID: PMC4493785 DOI: 10.1093/jxb/erv158] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Lignin is a complex polyphenolic heteropolymer that is abundant in the secondary cell walls of plants and functions in growth and defence. It is also a major barrier to the deconstruction of plant biomass for bioenergy production, but the spatiotemporal details of how lignin is deposited in actively lignifying tissues and the precise relationships between wall lignification in different cell types and developmental events, such as flowering, are incompletely understood. Here, the lignin-detecting fluorogenic dye, Basic Fuchsin, was adapted to enable comparative fluorescence-based imaging of lignin in the basal internodes of three Brachypodium distachyon ecotypes that display divergent flowering times. It was found that the extent and intensity of Basic Fuchsin fluorescence increase over time in the Bd21-3 ecotype, that Basic Fuchsin staining is more widespread and intense in 4-week-old Bd21-3 and Adi-10 basal internodes than in Bd1-1 internodes, and that Basic Fuchsin staining reveals subcellular patterns of lignin in vascular and interfascicular fibre cell walls. Basic Fuchsin fluorescence did not correlate with lignin quantification by acetyl bromide analysis, indicating that whole-plant and subcellular lignin analyses provide distinct information about the extent and patterns of lignification in B. distachyon. Finally, it was found that flowering time correlated with a transient increase in total lignin, but did not correlate strongly with the patterning of stem lignification, suggesting that additional developmental pathways might regulate secondary wall formation in grasses. This study provides a new comparative tool for imaging lignin in plants and helps inform our views of how lignification proceeds in grasses.
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Affiliation(s)
- Nikki Kapp
- Center for Lignocellulose Structure and Formation, The Pennsylvania State University, University Park, PA 16802, USA Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA Department of Agricultural and Biological Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - William J Barnes
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Tom L Richard
- Center for Lignocellulose Structure and Formation, The Pennsylvania State University, University Park, PA 16802, USA Department of Agricultural and Biological Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Charles T Anderson
- Center for Lignocellulose Structure and Formation, The Pennsylvania State University, University Park, PA 16802, USA Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
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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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Kim DY, Hong MJ, Park CS, Seo YW. The effects of chronic radiation of gamma ray on protein expression and oxidative stress inBrachypodium distachyon. Int J Radiat Biol 2015; 91:407-19. [DOI: 10.3109/09553002.2015.1012307] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Brutnell TP, Bennetzen JL, Vogel JP. Brachypodium distachyon and Setaria viridis: Model Genetic Systems for the Grasses. ANNUAL REVIEW OF PLANT BIOLOGY 2015; 66:465-85. [PMID: 25621515 DOI: 10.1146/annurev-arplant-042811-105528] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The family of grasses encompasses the world's most important food, feed, and bioenergy crops, yet we are only now beginning to develop the genetic resources to explore the diversity of form and function that underlies economically important traits. Two emerging model systems, Brachypodium distachyon and Setaria viridis, promise to greatly accelerate the process of gene discovery in the grasses and to serve as bridges in the exploration of panicoid and pooid grasses, arguably two of the most important clades of plants from a food security perspective. We provide both a historical view of the development of plant model systems and highlight several recent reports that are providing these developing communities with the tools for gene discovery and pathway engineering.
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56
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Isozyme variation and differentiation of morphologically cryptic species in the Brachypodium distachyon complex. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.04.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Dell'Acqua M, Zuccolo A, Tuna M, Gianfranceschi L, Pè ME. Targeting environmental adaptation in the monocot model Brachypodium distachyon: a multi-faceted approach. BMC Genomics 2014; 15:801. [PMID: 25236859 PMCID: PMC4177692 DOI: 10.1186/1471-2164-15-801] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 09/04/2014] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The local environment plays a major role in the spatial distribution of plant populations. Natural plant populations have an extremely poor displacing capacity, so their continued survival in a given environment depends on how well they adapt to local pedoclimatic conditions. Genomic tools can be used to identify adaptive traits at a DNA level and to further our understanding of evolutionary processes. Here we report the use of genotyping-by-sequencing on local groups of the sequenced monocot model species Brachypodium distachyon. Exploiting population genetics, landscape genomics and genome wide association studies, we evaluate B. distachyon role as a natural probe for identifying genomic loci involved in environmental adaptation. RESULTS Brachypodium distachyon individuals were sampled in nine locations with different ecologies and characterized with 16,697 SNPs. Variations in sequencing depth showed consistent patterns at 8,072 genomic bins, which were significantly enriched in transposable elements. We investigated the structuration and diversity of this collection, and exploited climatic data to identify loci with adaptive significance through i) two different approaches for genome wide association analyses considering climatic variation, ii) an outlier loci approach, and iii) a canonical correlation analysis on differentially sequenced bins. A linkage disequilibrium-corrected Bonferroni method was applied to filter associations. The two association methods jointly identified a set of 15 genes significantly related to environmental adaptation. The outlier loci approach revealed that 5.7% of the loci analysed were under selection. The canonical correlation analysis showed that the distribution of some differentially sequenced regions was associated to environmental variation. CONCLUSIONS We show that the multi-faceted approach used here targeted different components of B. distachyon adaptive variation, and may lead to the discovery of genes related to environmental adaptation in natural populations. Its application to a model species with a fully sequenced genome is a modular strategy that enables the stratification of biological material and thus improves our knowledge of the functional loci determining adaptation in near-crop species. When coupled with population genetics and measures of genomic structuration, methods coming from genome wide association studies may lead to the exploitation of model species as natural probes to identify loci related to environmental adaptation.
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Affiliation(s)
| | | | | | | | - Mario Enrico Pè
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.
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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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Poiré R, Chochois V, Sirault XRR, Vogel JP, Watt M, Furbank RT. Digital imaging approaches for phenotyping whole plant nitrogen and phosphorus response in Brachypodium distachyon. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:781-96. [PMID: 24666962 DOI: 10.1111/jipb.12198] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 03/24/2014] [Indexed: 05/24/2023]
Abstract
This work evaluates the phenotypic response of the model grass (Brachypodium distachyon (L.) P. Beauv.) to nitrogen and phosphorus nutrition using a combination of imaging techniques and destructive harvest of shoots and roots. Reference line Bd21-3 was grown in pots using 11 phosphorus and 11 nitrogen concentrations to establish a dose-response curve. Shoot biovolume and biomass, root length and biomass, and tissue phosphorus and nitrogen concentrations increased with nutrient concentration. Shoot biovolume, estimated by imaging, was highly correlated with dry weight (R(2) > 0.92) and both biovolume and growth rate responded strongly to nutrient availability. Higher nutrient supply increased nodal root length more than other root types. Photochemical efficiency was strongly reduced by low phosphorus concentrations as early as 1 week after germination, suggesting that this measurement may be suitable for high throughput screening of phosphorus response. In contrast, nitrogen concentration had little effect on photochemical efficiency. Changes in biovolume over time were used to compare growth rates of four accessions in response to nitrogen and phosphorus supply. We demonstrate that a time series image-based approach coupled with mathematical modeling provides higher resolution of genotypic response to nutrient supply than traditional destructive techniques and shows promise for high throughput screening and determination of genomic regions associated with superior nutrient use efficiency.
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Affiliation(s)
- Richard Poiré
- CSIRO Plant Industry, Canberra, ACT 2601, Australia; High Resolution Plant Phenomics Centre, CSIRO Plant Industry, Canberra, ACT 2601, Australia
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Ream TS, Woods DP, Schwartz CJ, Sanabria CP, Mahoy JA, Walters EM, Kaeppler HF, Amasino RM. Interaction of photoperiod and vernalization determines flowering time of Brachypodium distachyon. PLANT PHYSIOLOGY 2014; 164:694-709. [PMID: 24357601 PMCID: PMC3912099 DOI: 10.1104/pp.113.232678] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Accepted: 12/09/2013] [Indexed: 05/20/2023]
Abstract
Timing of flowering is key to the reproductive success of many plants. In temperate climates, flowering is often coordinated with seasonal environmental cues such as temperature and photoperiod. Vernalization is an example of temperature influencing the timing of flowering and is defined as the process by which a prolonged exposure to the cold of winter results in competence to flower during the following spring. In cereals, three genes (VERNALIZATION1 [VRN1], VRN2, and FLOWERING LOCUS T [FT]) have been identified that influence the vernalization requirement and are thought to form a regulatory loop to control the timing of flowering. Here, we characterize natural variation in the vernalization and photoperiod responses in Brachypodium distachyon, a small temperate grass related to wheat (Triticum aestivum) and barley (Hordeum vulgare). Brachypodium spp. accessions display a wide range of flowering responses to different photoperiods and lengths of vernalization. In addition, we characterize the expression patterns of the closest homologs of VRN1, VRN2 (VRN2-like [BdVRN2L]), and FT before, during, and after cold exposure as well as in different photoperiods. FT messenger RNA levels generally correlate with flowering time among accessions grown in different photoperiods, and FT is more highly expressed in vernalized plants after cold. VRN1 is induced by cold in leaves and remains high following vernalization. Plants overexpressing VRN1 or FT flower rapidly in the absence of vernalization, and plants overexpressing VRN1 exhibit lower BdVRN2L levels. Interestingly, BdVRN2L is induced during cold, which is a difference in the behavior of BdVRN2L compared with wheat VRN2 during cold.
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Tyler L, Fangel JU, Fagerström AD, Steinwand MA, Raab TK, Willats WGT, Vogel JP. Selection and phenotypic characterization of a core collection of Brachypodium distachyon inbred lines. BMC PLANT BIOLOGY 2014; 14:25. [PMID: 24423101 PMCID: PMC3925370 DOI: 10.1186/1471-2229-14-25] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 01/02/2014] [Indexed: 05/06/2023]
Abstract
BACKGROUND The model grass Brachypodium distachyon is increasingly used to study various aspects of grass biology. A large and genotypically diverse collection of B. distachyon germplasm has been assembled by the research community. The natural variation in this collection can serve as a powerful experimental tool for many areas of inquiry, including investigating biomass traits. RESULTS We surveyed the phenotypic diversity in a large collection of inbred lines and then selected a core collection of lines for more detailed analysis with an emphasis on traits relevant to the use of grasses as biofuel and grain crops. Phenotypic characters examined included plant height, growth habit, stem density, flowering time, and seed weight. We also surveyed differences in cell wall composition using near infrared spectroscopy (NIR) and comprehensive microarray polymer profiling (CoMPP). In all cases, we observed extensive natural variation including a two-fold variation in stem density, four-fold variation in ferulic acid bound to hemicellulose, and 1.7-fold variation in seed mass. CONCLUSION These characterizations can provide the criteria for selecting diverse lines for future investigations of the genetic basis of the observed phenotypic variation.
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Affiliation(s)
- Ludmila Tyler
- USDA-ARS Western Regional Research Center, Albany, CA, USA
- Current address: University of California, Berkeley, CA, USA
- Current address: University of Massachusetts, Amherst, MA, USA
| | | | - Alexandra Dotson Fagerström
- University of Copenhagen, Copenhagen, Denmark
- Current address: Energy Biosciences Institute, Berkeley, CA, USA
| | - Michael A Steinwand
- USDA-ARS Western Regional Research Center, Albany, CA, USA
- Current address: University of California, Berkeley, CA, USA
| | - Theodore K Raab
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | | | - John P Vogel
- USDA-ARS Western Regional Research Center, Albany, CA, USA
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Exploring the interaction between small RNAs and R genes during Brachypodium response to Fusarium culmorum infection. Gene 2013; 536:254-64. [PMID: 24368332 DOI: 10.1016/j.gene.2013.12.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 11/22/2013] [Accepted: 12/10/2013] [Indexed: 01/15/2023]
Abstract
The present study aims to investigate small RNA interactions with putative disease response genes in the model grass species Brachypodium distachyon. The fungal pathogen Fusarium culmorum (Fusarium herein) and phytohormone salicylic acid treatment were used to induce the disease response in Brachypodium. Initially, 121 different putative disease response genes were identified using bioinformatic and homology based approaches. Computational prediction was used to identify 33 candidate new miRNA coding sequences, of which 9 were verified by analysis of small RNA sequence libraries. Putative Brachypodium miRNA target sites were identified in the disease response genes, and a subset of which were screened for expression and possible miRNA interactions in 5 different Brachypodium lines infected with Fusarium. An NBS-LRR family gene, 1g34430, was polymorphic among the lines, forming two major genotypes, one of which has its miRNA target sites deleted, resulting in altered gene expression during infection. There were siRNAs putatively involved in regulation of this gene, indicating a role of small RNAs in the B. distachyon disease response.
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Subburaj S, Chen G, Han C, Lv D, Li X, Zeller FJ, Hsam SLK, Yan Y. Molecular characterisation and evolution of HMW glutenin subunit genes in Brachypodium distachyon L. J Appl Genet 2013; 55:27-42. [PMID: 24306693 DOI: 10.1007/s13353-013-0187-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 11/10/2013] [Accepted: 11/19/2013] [Indexed: 01/13/2023]
Abstract
Brachypodium distachyon, a small wild grass within the Pooideae family, is a new model organism for exploring the functional genomics of cereal crops. It was shown to have close relationships to wheat, barley and rice. Here, we describe the molecular characterisation and evolutionary relationships of high molecular weight glutenin subunits (HMW-GS) genes from B. distachyon. Sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), high performance capillary electrophoresis (HPCE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses demonstrated that there was no HMW-GS expression in the Brachypodium grains due to the silencing of their encoding genes. Through allele-specific polymerase chain reaction (AS-PCR) amplification and cloning, a total of 13 HMW-GS encoding genes from diploid, tetraploid and hexaploid Brachypodium species were obtained, and all of them had typical structural features of y-type HMW-GS genes from common wheat and related species, particularly more similar to the 1Dy12 gene. However, the presence of an in-frame premature stop codon (TAG) at position 1521 in the coding region resulted in the conversion of all the genes to pseudogenes. Further, quantitative real-time PCR (qRT-PCR) analysis revealed that HMW-GS genes in B. distachyon displayed a similar trend, but with a low transcriptional expression profile during grain development due to the occurrence of the stop codon. Phylogenetic analysis showed that the highly conserved Glu-1-2 loci were presented in B. distachyon, which displayed close phylogenetic evolutionary relationships with Triticum and related species.
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Steinwand MA, Young HA, Bragg JN, Tobias CM, Vogel JP. Brachypodium sylvaticum, a model for perennial grasses: transformation and inbred line development. PLoS One 2013; 8:e75180. [PMID: 24073248 PMCID: PMC3779173 DOI: 10.1371/journal.pone.0075180] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 08/12/2013] [Indexed: 11/19/2022] Open
Abstract
Perennial species offer significant advantages as crops including reduced soil erosion, lower energy inputs after the first year, deeper root systems that access more soil moisture, and decreased fertilizer inputs due to the remobilization of nutrients at the end of the growing season. These advantages are particularly relevant for emerging biomass crops and it is projected that perennial grasses will be among the most important dedicated biomass crops. The advantages offered by perennial crops could also prove favorable for incorporation into annual grain crops like wheat, rice, sorghum and barley, especially under the dryer and more variable climate conditions projected for many grain-producing regions. Thus, it would be useful to have a perennial model system to test biotechnological approaches to crop improvement and for fundamental research. The perennial grass Brachypodiumsylvaticum is a candidate for such a model because it is diploid, has a small genome, is self-fertile, has a modest stature, and short generation time. Its close relationship to the annual model Brachypodiumdistachyon will facilitate comparative studies and allow researchers to leverage the resources developed for B. distachyon. Here we report on the development of two keystone resources that are essential for a model plant: high-efficiency transformation and inbred lines. Using Agrobacterium tumefaciens-mediated transformation we achieved an average transformation efficiency of 67%. We also surveyed the genetic diversity of 19 accessions from the National Plant Germplasm System using SSR markers and created 15 inbred lines.
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Affiliation(s)
- Michael A. Steinwand
- Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service, Albany, California, United States of America
| | - Hugh A. Young
- Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service, Albany, California, United States of America
- Department of Plant & Microbial Biology, University of California, Berkeley, California, United States of America
| | - Jennifer N. Bragg
- Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service, Albany, California, United States of America
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Christian M. Tobias
- Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service, Albany, California, United States of America
| | - John P. Vogel
- Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service, Albany, California, United States of America
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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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Harsant J, Pavlovic L, Chiu G, Sultmanis S, Sage TL. High temperature stress and its effect on pollen development and morphological components of harvest index in the C3 model grass Brachypodium distachyon. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:2971-83. [PMID: 23771979 PMCID: PMC3697958 DOI: 10.1093/jxb/ert142] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The effect of high temperatures on harvest index (HI) and morphological components that contribute to HI was investigated in two lines (Bd21 and Bd21-3) of Brachypodium distachyon, a C3 grass recognized as a tractable plant, to address critical issues associated with enhancing cereal crop yields in the presence of global climate change. The results demonstrated that temperatures ≥32 °C eliminated HI. Reductions in yield at 32 °C were due primarily to declines in pollen viability, retention of pollen in anthers, and pollen germination, while abortion of microspores by the uninucleate stage that was correlated with abnormal tapetal development resulted in yield failure at 36 °C. Increasing temperatures from 24 to 32 °C resulted in reductions in tiller numbers but had no impact on axillary branch numbers per tiller. Grain developed at 24 and 28 °C primarily in tiller spikes, although spikes on axillary branches also formed grain. Grain quantity decreased in tiller spikes but increased in axillary branch spikes as temperatures rose from 24 to 28 °C. Differential patterns of axillary branching and floret development within spikelets between Bd21 and Bd21-3 resulted in higher grain yield in axillary branches of Bd21-3 at 28 °C. The response of male reproductive development and tiller branching patterns in B. distachyon to increasing temperatures mirrors that in other cereal crops, providing support for the use of this C3 grass in assessing the molecular control of HI in the presence of global warming.
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Affiliation(s)
- Jeffrey Harsant
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, Canada, M5S 3B2
| | - Lazar Pavlovic
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, Canada, M5S 3B2
| | - Greta Chiu
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, Canada, M5S 3B2
| | - Stefanie Sultmanis
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, Canada, M5S 3B2
| | - Tammy L. Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, Canada, M5S 3B2
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López-Alvarez D, López-Herranz ML, Betekhtin A, Catalán P. A DNA barcoding method to discriminate between the model plant Brachypodium distachyon and its close relatives B. stacei and B. hybridum (Poaceae). PLoS One 2012; 7:e51058. [PMID: 23240000 PMCID: PMC3519806 DOI: 10.1371/journal.pone.0051058] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 10/29/2012] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Brachypodium distachyon s. l. has been widely investigated across the world as a model plant for temperate cereals and biofuel grasses. However, this annual plant shows three cytotypes that have been recently recognized as three independent species, the diploids B. distachyon (2n = 10) and B. stacei (2n = 20) and their derived allotetraploid B. hybridum (2n = 30). METHODOLOGY/PRINCIPAL FINDINGS We propose a DNA barcoding approach that consists of a rapid, accurate and automatable species identification method using the standard DNA sequences of complementary plastid (trnLF) and nuclear (ITS, GI) loci. The highly homogenous but largely divergent B. distachyon and B. stacei diploids could be easily distinguished (100% identification success) using direct trnLF (2.4%), ITS (5.5%) or GI (3.8%) sequence divergence. By contrast, B. hybridum could only be unambiguously identified through the use of combined trnLF+ITS sequences (90% of identification success) or by cloned GI sequences (96.7%) that showed 5.4% (ITS) and 4% (GI) rate divergence between the two parental sequences found in the allopolyploid. CONCLUSION/SIGNIFICANCE Our data provide an unbiased and effective barcode to differentiate these three closely-related species from one another. This procedure overcomes the taxonomic uncertainty generated from methods based on morphology or flow cytometry identifications that have resulted in some misclassifications of the model plant and its allies. Our study also demonstrates that the allotetraploid B. hybridum has resulted from bi-directional crosses of B. distachyon and B. stacei plants acting either as maternal or paternal parents.
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Affiliation(s)
- Diana López-Alvarez
- Department of Agriculture and Environmental Sciences, University of Zaragoza, Huesca, Spain
| | | | - Alexander Betekhtin
- Department of Agriculture and Environmental Sciences, University of Zaragoza, Huesca, Spain
- Department of Plant Anatomy and Cytology, University of Silesia, Katowice, Poland
| | - Pilar Catalán
- Department of Agriculture and Environmental Sciences, University of Zaragoza, Huesca, Spain
- * E-mail:
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Luo N, Yu X, Liu J, Jiang Y. Nucleotide diversity and linkage disequilibrium in antioxidant genes of Brachypodium distachyon. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 197:122-129. [PMID: 23116679 DOI: 10.1016/j.plantsci.2012.09.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 09/26/2012] [Accepted: 09/28/2012] [Indexed: 06/01/2023]
Abstract
Brachypodium distachyon (Brachypodium) is a powerful model system for studying cereal, bioenergy, forage, and turf grasses. Nucleotide diversity (π) and linkage disequilibrium (LD) in candidate genes involved in the antioxidative pathways in this species are not known. The average π for CAT encoding catalase, GPX encoding glutathione peroxidase, DHAR encoding dehydroascorbate reductase, MDHAR encoding monodehydroascorbate reductase, and APX ecoding ascorbate peroxidase was 0.0027 among 19 accessions contrasting for drought tolerance. The highest value of π was found in APX (0.0046) and the lowest π was in MDHAR (0.0006). The average single nucleotide polymorphism (SNP) frequency across these five genes was one SNP per 131 bp between two randomly sampled sequences for the five genes in the sequence length ranging from 1,447 bp to 1,701 bp. The LD decay was slow and extended to a distance of more than 1.2kb for all genes. The neighbor-joining tree analyses of DHAR, MDHAR, and CAT generally separated accessions differing in drought tolerance. The results indicate a putative role of these candidate genes in increasing general fitness of Brachypodium.
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Affiliation(s)
- Na Luo
- Institute of Botany, Jiangsu Province & Chinese Academy of Science, Nanjing 210014, China
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Bragg JN, Wu J, Gordon SP, Guttman ME, Thilmony R, Lazo GR, Gu YQ, Vogel JP. Generation and characterization of the Western Regional Research Center Brachypodium T-DNA insertional mutant collection. PLoS One 2012; 7:e41916. [PMID: 23028431 PMCID: PMC3444500 DOI: 10.1371/journal.pone.0041916] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 06/29/2012] [Indexed: 11/18/2022] Open
Abstract
The model grass Brachypodium distachyon (Brachypodium) is an excellent system for studying the basic biology underlying traits relevant to the use of grasses as food, forage and energy crops. To add to the growing collection of Brachypodium resources available to plant scientists, we further optimized our Agrobacterium tumefaciens-mediated high-efficiency transformation method and generated 8,491 Brachypodium T-DNA lines. We used inverse PCR to sequence the DNA flanking the insertion sites in the mutants. Using these flanking sequence tags (FSTs) we were able to assign 7,389 FSTs from 4,402 T-DNA mutants to 5,285 specific insertion sites (ISs) in the Brachypodium genome. More than 29% of the assigned ISs are supported by multiple FSTs. T-DNA insertions span the entire genome with an average of 19.3 insertions/Mb. The distribution of T-DNA insertions is non-uniform with a larger number of insertions at the distal ends compared to the centromeric regions of the chromosomes. Insertions are correlated with genic regions, but are biased toward UTRs and non-coding regions within 1 kb of genes over exons and intron regions. More than 1,300 unique genes have been tagged in this population. Information about the Western Regional Research Center Brachypodium insertional mutant population is available on a searchable website (http://brachypodium.pw.usda.gov) designed to provide researchers with a means to order T-DNA lines with mutations in genes of interest.
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Affiliation(s)
- Jennifer N. Bragg
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
- University of California Davis, Davis, California, United States of America
| | - Jiajie Wu
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
- University of California Davis, Davis, California, United States of America
| | - Sean P. Gordon
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
| | - Mara E. Guttman
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
| | - Roger Thilmony
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
| | - Gerard R. Lazo
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
| | - Yong Q. Gu
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
| | - John P. Vogel
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
- * E-mail:
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Giraldo P, Rodríguez-Quijano M, Vázquez JF, Carrillo JM, Benavente E. Validation of microsatellite markers for cytotype discrimination in the model grass Brachypodium distachyon. Genome 2012; 55:523-7. [PMID: 22788413 DOI: 10.1139/g2012-039] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Brachypodium distachyon (L.) P. Beauv. (2n = 2x = 10) is a small annual grass species where the existence of three different cytotypes (10, 20, and 30 chromosomes) has long been regarded as a case of autopolyploid series with x = 5. However, it has been demonstrated that the cytotypes assumed to be polyploids represent two separate Brachypodium species recently named as Brachypodium stacei (2n = 2x = 20) and Brachypodium hybridum (2n = 4x = 30). The aim of this study was to find a PCR-based alternative approach that could replace standard cytotyping methods (i.e., chromosome counting and flow cytometry) to characterize each of the three Brachypodium species. We have analyzed with four microsatellite (SSR) markers 83 B. distachyon-type lines from varied locations in Spain, including the Balearic and Canary Islands. Within this set of lines, 64, 4, and 15 had 10, 20, and 30 chromosomes, respectively. The surveyed markers produced cytotype-specific SSR profiles. So, a single amplification product was generated in the diploid samples, with nonoverlapping allelic ranges between the 2n = 10 and 2n = 20 cytotypes, whereas two bands, one in the size range of each of the diploid cytotypes, were amplified in the 2n = 30 lines. Furthermore, the remarkable size difference obtained with the SSR ALB165 allowed the identification of the Brachypodium species by simple agarose gel electrophoresis.
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Affiliation(s)
- Patricia Giraldo
- Departamento de Biotecnología (Genética), Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, 28040-Madrid, Spain.
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Pacheco-Villalobos D, Hardtke CS. Natural genetic variation of root system architecture from Arabidopsis to Brachypodium: towards adaptive value. Philos Trans R Soc Lond B Biol Sci 2012; 367:1552-8. [PMID: 22527398 PMCID: PMC3321687 DOI: 10.1098/rstb.2011.0237] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Root system architecture is a trait that displays considerable plasticity because of its sensitivity to environmental stimuli. Nevertheless, to a significant degree it is genetically constrained as suggested by surveys of its natural genetic variation. A few regulators of root system architecture have been isolated as quantitative trait loci through the natural variation approach in the dicotyledon model, Arabidopsis. This provides proof of principle that allelic variation for root system architecture traits exists, is genetically tractable, and might be exploited for crop breeding. Beyond Arabidopsis, Brachypodium could serve as both a credible and experimentally accessible model for root system architecture variation in monocotyledons, as suggested by first glimpses of the different root morphologies of Brachypodium accessions. Whether a direct knowledge transfer gained from molecular model system studies will work in practice remains unclear however, because of a lack of comprehensive understanding of root system physiology in the native context. For instance, apart from a few notable exceptions, the adaptive value of genetic variation in root system modulators is unknown. Future studies should thus aim at comprehensive characterization of the role of genetic players in root system architecture variation by taking into account the native environmental conditions, in particular soil characteristics.
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Affiliation(s)
| | - Christian S. Hardtke
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
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Cui Y, Lee MY, Huo N, Bragg J, Yan L, Yuan C, Li C, Holditch SJ, Xie J, Luo MC, Li D, Yu J, Martin J, Schackwitz W, Gu YQ, Vogel JP, Jackson AO, Liu Z, Garvin DF. Fine mapping of the Bsr1 barley stripe mosaic virus resistance gene in the model grass Brachypodium distachyon. PLoS One 2012; 7:e38333. [PMID: 22675544 PMCID: PMC3366947 DOI: 10.1371/journal.pone.0038333] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 05/03/2012] [Indexed: 11/18/2022] Open
Abstract
The ND18 strain of Barley stripe mosaic virus (BSMV) infects several lines of Brachypodium distachyon, a recently developed model system for genomics research in cereals. Among the inbred lines tested, Bd3-1 is highly resistant at 20 to 25°C, whereas Bd21 is susceptible and infection results in an intense mosaic phenotype accompanied by high levels of replicating virus. We generated an F6∶7 recombinant inbred line (RIL) population from a cross between Bd3-1 and Bd21 and used the RILs, and an F2 population of a second Bd21 × Bd3-1 cross to evaluate the inheritance of resistance. The results indicate that resistance segregates as expected for a single dominant gene, which we have designated Barley stripe mosaic virus resistance 1 (Bsr1). We constructed a genetic linkage map of the RIL population using SNP markers to map this gene to within 705 Kb of the distal end of the top of chromosome 3. Additional CAPS and Indel markers were used to fine map Bsr1 to a 23 Kb interval containing five putative genes. Our study demonstrates the power of using RILs to rapidly map the genetic determinants of BSMV resistance in Brachypodium. Moreover, the RILs and their associated genetic map, when combined with the complete genomic sequence of Brachypodium, provide new resources for genetic analyses of many other traits.
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Affiliation(s)
- Yu Cui
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
- Department of Plant and Microbiology, University of California, Berkeley, California, United States of America
| | - Mi Yeon Lee
- Department of Plant and Microbiology, University of California, Berkeley, California, United States of America
| | - Naxin Huo
- USDA-ARS Western Regional Research Center, Albany, California, United States of America
| | - Jennifer Bragg
- USDA-ARS Western Regional Research Center, Albany, California, United States of America
| | - Lijie Yan
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Cheng Yuan
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Cui Li
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Sara J. Holditch
- Department of Plant and Microbiology, University of California, Berkeley, California, United States of America
| | - Jingzhong Xie
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Dawei Li
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Jialin Yu
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Joel Martin
- US DOE Joint Genome Institute, Walnut Creek, California, United States of America
| | - Wendy Schackwitz
- US DOE Joint Genome Institute, Walnut Creek, California, United States of America
| | - Yong Qiang Gu
- USDA-ARS Western Regional Research Center, Albany, California, United States of America
| | - John P. Vogel
- USDA-ARS Western Regional Research Center, Albany, California, United States of America
| | - Andrew O. Jackson
- Department of Plant and Microbiology, University of California, Berkeley, California, United States of America
- * E-mail: (AOJ); (ZL)
| | - Zhiyong Liu
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
- * E-mail: (AOJ); (ZL)
| | - David F. Garvin
- USDA-ARS Plant Science Research Unit and Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America
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Chochois V, Vogel JP, Watt M. Application of Brachypodium to the genetic improvement of wheat roots. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:3467-3474. [PMID: 22467408 DOI: 10.1093/jxb/ers044] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
To meet the demands of a larger and more affluent global population, wheat yields must increase faster this century than last, with less irrigation, fertilizer, and land. Modelling and experiments consistently demonstrate a large potential for increasing wheat productivity by improving root systems; however, application of research to new varieties is slow because of the inherent difficulties associated with working underground. This review makes the case for the use of the model grass Brachypodium distachyon to simplify root research and accelerate the identification of genes underlying wheat root improvement. Brachypodium is a small temperate grass with many genomic, genetic, and experimental resources that make it a tractable model plant. Brachypodium and wheat have very similar root anatomies which are distinct from rice root anatomy that is specialized to help it overcome anaerobic conditions associated with submerged roots. As a dicotyledonous plant, Arabidopsis has an even more divergent root system that features a tap root system and cambia with secondary growth, both of which are lacking in the grasses. The major advantage of Brachypodium is its small stature that allows the adult grass root system to be readily phenotyped, unlike rice and maize. This will facilitate the identification of genes in adult roots that greatly influence yield by modulating water uptake during flowering and grain development. A summary of the advantages of Brachypodium for root studies is presented, including the adult root system architecture and root growth during grain development. Routes to translate discoveries from Brachypodium to wheat are also discussed.
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Barbieri M, Marcel TC, Niks RE, Francia E, Pasquariello M, Mazzamurro V, Garvin DF, Pecchioni N. QTLs for resistance to the false brome rust Puccinia brachypodii in the model grass Brachypodium distachyon L. Genome 2012; 55:152-63. [PMID: 22321152 DOI: 10.1139/g2012-001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The potential of the model grass Brachypodium distachyon L. (Brachypodium) for studying grass-pathogen interactions is still underexploited. We aimed to identify genomic regions in Brachypodium associated with quantitative resistance to the false brome rust fungus Puccinia brachypodii . The inbred lines Bd3-1 and Bd1-1, differing in their level of resistance to P. brachypodii, were crossed to develop an F(2) population. This was evaluated for reaction to a virulent isolate of P. brachypodii at both the seedling and advanced growth stages. To validate the results obtained on the F(2), resistance was quantified in F(2)-derived F(3) families in two experiments. Disease evaluations showed quantitative and transgressive segregation for resistance. A new AFLP-based Brachypodium linkage map consisting of 203 loci and spanning 812 cM was developed and anchored to the genome sequence with SSR and SNP markers. Three false brome rust resistance QTLs were identified on chromosomes 2, 3, and 4, and they were detected across experiments. This study is the first quantitative trait analysis in Brachypodium. Resistance to P. brachypodii was governed by a few QTLs: two acting at the seedling stage and one acting at both seedling and advanced growth stages. The results obtained offer perspectives to elucidate the molecular basis of quantitative resistance to rust fungi.
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Affiliation(s)
- Mirko Barbieri
- Dipartimento di Scienze Agrarie e degli Alimenti, Università di Modena e Reggio Emilia, Italy
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Manzaneda AJ, Rey PJ, Bastida JM, Weiss-Lehman C, Raskin E, Mitchell-Olds T. Environmental aridity is associated with cytotype segregation and polyploidy occurrence in Brachypodium distachyon (Poaceae). THE NEW PHYTOLOGIST 2012; 193:797-805. [PMID: 22150799 PMCID: PMC3257369 DOI: 10.1111/j.1469-8137.2011.03988.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
• The ecological and adaptive significance of plant polyploidization is not well understood and no clear pattern of association between polyploid frequency and environment has emerged. Climatic factors are expected to predict cytotype distribution. However, the relationship among climate, cytotype distribution and variation of abiotic stress tolerance traits has rarely been examined. • Here, we use flow cytometry and root-tip squashes to examine the cytotype distribution in the temperate annual grass Brachypodium distachyon in 57 natural populations distributed across an aridity gradient in the Iberian Peninsula. We further investigate the link between environmental aridity, ploidy, and variation of drought tolerance and drought avoidance (flowering time) traits. • Distribution of diploids (2n = 10) and allotetraploids (2n = 30) in this species is geographically structured throughout its range in the Iberian Peninsula, and is associated with aridity gradients. Importantly, after controlling for geographic and altitudinal effects, the link between aridity and polyploidization occurrence persisted. Water-use efficiency varied between ploidy levels, with tetraploids being more efficient in the use of water than diploids under water-restricted growing conditions. • Our results indicate that aridity is an important predictor of polyploid occurrence in B. distachyon, suggesting a possible adaptive origin of the cytotype segregation.
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Affiliation(s)
- Antonio J. Manzaneda
- Departamento Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Paraje las Lagunillas s/n, 23071, Jaén, Spain
- Institute for Genome Sciences and Policy, Department of Biology, Duke University, PO Box 90338, Durham, North Carolina 27708, USA
| | - Pedro J. Rey
- Departamento Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Paraje las Lagunillas s/n, 23071, Jaén, Spain
| | - Jesús M. Bastida
- Departamento Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Paraje las Lagunillas s/n, 23071, Jaén, Spain
| | - Christopher Weiss-Lehman
- Institute for Genome Sciences and Policy, Department of Biology, Duke University, PO Box 90338, Durham, North Carolina 27708, USA
| | - Evan Raskin
- Institute for Genome Sciences and Policy, Department of Biology, Duke University, PO Box 90338, Durham, North Carolina 27708, USA
| | - Thomas Mitchell-Olds
- Institute for Genome Sciences and Policy, Department of Biology, Duke University, PO Box 90338, Durham, North Carolina 27708, USA
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77
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Catalán P, Müller J, Hasterok R, Jenkins G, Mur LAJ, Langdon T, Betekhtin A, Siwinska D, Pimentel M, López-Alvarez D. Evolution and taxonomic split of the model grass Brachypodium distachyon. ANNALS OF BOTANY 2012; 109:385-405. [PMID: 22213013 PMCID: PMC3268539 DOI: 10.1093/aob/mcr294] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 10/20/2011] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Brachypodium distachyon is being widely investigated across the world as a model plant for temperate cereals. This annual plant has three cytotypes (2n = 10, 20, 30) that are still regarded as part of a single species. Here, a multidisciplinary study has been conducted on a representative sampling of the three cytotypes to investigate their evolutionary relationships and origins, and to elucidate if they represent separate species. METHODS Statistical analyses of 15 selected phenotypic traits were conducted in individuals from 36 lines or populations. Cytogenetic analyses were performed through flow cytometry, fluorescence in situ hybridization (FISH) with genomic (GISH) and multiple DNA sequences as probes, and comparative chromosome painting (CCP). Phylogenetic analyses were based on two plastid (ndhF, trnLF) and five nuclear (ITS, ETS, CAL, DGAT, GI) genes from different Brachypodium lineages, whose divergence times and evolutionary rates were estimated. KEY RESULTS The phenotypic analyses detected significant differences between the three cytotypes and demonstrated stability of characters in natural populations. Genome size estimations, GISH, FISH and CCP confirmed that the 2n = 10 and 2n = 20 cytotypes represent two different diploid taxa, whereas the 2n = 30 cytotype represents the allotetraploid derived from them. Phylogenetic analysis demonstrated that the 2n = 20 and 2n = 10 cytotypes emerged from two independent lineages that were, respectively, the maternal and paternal genome donors of the 2n = 30 cytotype. The 2n = 20 lineage was older and mutated significantly faster than the 2n = 10 lineage and all the core perennial Brachypodium species. CONCLUSIONS The substantial phenotypic, cytogenetic and molecular differences detected among the three B. distachyon sensu lato cytotypes are indicative of major speciation processes within this complex that allow their taxonomic separation into three distinct species. We have kept the name B. distachyon for the 2n = 10 cytotype and have described two novel species as B. stacei and B. hybridum for, respectively, the 2n = 20 and 2n = 30 cytotypes.
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Affiliation(s)
- Pilar Catalán
- Department of Agriculture, High Polytechnic School of Huesca, University of Zaragoza, Spain.
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78
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Barrero JM, Jacobsen JV, Talbot MJ, White RG, Swain SM, Garvin DF, Gubler F. Grain dormancy and light quality effects on germination in the model grass Brachypodium distachyon. THE NEW PHYTOLOGIST 2012; 193:376-86. [PMID: 22039925 DOI: 10.1111/j.1469-8137.2011.03938.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
• Lack of grain dormancy in cereal crops such as barley and wheat is a common problem affecting farming areas around the world, causing losses in yield and quality because of preharvest sprouting. Control of seed or grain dormancy has been investigated extensively using various approaches in different species, including Arabidopsis and cereals. However, the use of a monocot model plant such as Brachypodium distachyon presents opportunities for the discovery of new genes related to grain dormancy that are not present in modern commercial crops. • In this work we present an anatomical description of the Brachypodium caryopsis, and we describe the dormancy behaviour of six common diploid Brachypodium inbred genotypes. We also study the effect of light quality (blue, red and far-red) on germination, and analyse changes in abscisic acid levels and gene expression between a dormant and a non-dormant Brachypodium genotype. • Our results indicate that different genotypes display high natural variability in grain dormancy and that the characteristics of dormancy and germination are similar to those found in other cereals. • We propose that Brachypodium is an ideal model for studies of grain dormancy in grasses and can be used to identify new strategies for increasing grain dormancy in crop species.
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Abstract
Brachypodium distachyon is an attractive genomics and biological model system for grass research. Recently, the complete annotated genome sequence of the diploid line Bd21 has been released. Genetic transformation technologies are critical for the discovery and validation of gene function in Brachypodium. Here, we describe an efficient procedure enabling the Agrobacterium-mediated transformation of a range of diploid and polyploid genotypes of Brachypodium. The procedure relies on the transformation of compact embryogenic calli derived from immature embryos using either chemical selection alone or a combination of chemical and visual screening of transformed tissues and plants. Transformation efficiencies of around 20% can routinely be achieved using this protocol. In the context of the BrachyTAG programme (BrachyTAG.org), this procedure made possible the mass production of Bd21T-DNA mutant plant lines.
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Affiliation(s)
- Vera Thole
- Department of Crop Genetics, John Innes Centre, Norwich, UK
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80
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Wu J, Gu YQ, Hu Y, You FM, Dandekar AM, Leslie CA, Aradhya M, Dvorak J, Luo MC. Characterizing the walnut genome through analyses of BAC end sequences. PLANT MOLECULAR BIOLOGY 2012; 78:95-107. [PMID: 22101470 DOI: 10.1007/s11103-011-9849-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 10/29/2011] [Indexed: 05/31/2023]
Abstract
Persian walnut (Juglans regia L.) is an economically important tree for its nut crop and timber. To gain insight into the structure and evolution of the walnut genome, we constructed two bacterial artificial chromosome (BAC) libraries, containing a total of 129,024 clones, from in vitro-grown shoots of J. regia cv. Chandler using the HindIII and MboI cloning sites. A total of 48,218 high-quality BAC end sequences (BESs) were generated, with an accumulated sequence length of 31.2 Mb, representing approximately 5.1% of the walnut genome. Analysis of repeat DNA content in BESs revealed that approximately 15.42% of the genome consists of known repetitive DNA, while walnut-unique repetitive DNA identified in this study constitutes 13.5% of the genome. Among the walnut-unique repetitive DNA, Julia SINE and JrTRIM elements represent the first identified walnut short interspersed element (SINE) and terminal-repeat retrotransposon in miniature (TRIM) element, respectively; both types of elements are abundant in the genome. As in other species, these SINEs and TRIM elements could be exploited for developing repeat DNA-based molecular markers in walnut. Simple sequence repeats (SSR) from BESs were analyzed and found to be more abundant in BESs than in expressed sequence tags. The density of SSR in the walnut genome analyzed was also slightly higher than that in poplar and papaya. Sequence analysis of BESs indicated that approximately 11.5% of the walnut genome represents a coding sequence. This study is an initial characterization of the walnut genome and provides the largest genomic resource currently available; as such, it will be a valuable tool in studies aimed at genetically improving walnut.
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Affiliation(s)
- Jiajie Wu
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
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81
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Barbieri M, Marcel TC, Niks RE. Host Status of False Brome Grass to the Leaf Rust Fungus Puccinia brachypodii and the Stripe Rust Fungus P. striiformis. PLANT DISEASE 2011; 95:1339-1345. [PMID: 30731784 DOI: 10.1094/pdis-11-10-0825] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Purple false brome grass (Brachypodium distachyon) has recently emerged as a model system for temperate grasses and is also a potential model plant to investigate plant interactions with economically important pathogens such as rust fungi. We determined the host status of five Brachypodium species to three isolates of Puccinia brachypodii, the prevalent rust species on Brachypodium sylvaticum in nature, and to one isolate each of three formae speciales of the stripe rust fungus P. striiformis. Two P. striiformis isolates produced sporulating lesions, both in only one of the tested interactions, suggesting a marginal host status of B. distachyon. P. brachypodii formed sporulating uredinia on the five Brachypodium species tested, and a range of reactions was observed. Surprisingly, the B. sylvaticum-derived rust isolates were more frequently pathogenic to B. distachyon than to their original host species. The B. distachyon diploid inbred lines, developed and distributed as reference material to the Brachypodium research community, include susceptible and resistant genotypes to at least three of the four P. brachypodii isolates tested. This creates the opportunity to use B. distachyon/P. brachypodii as a model pathosystem. In one B. distachyon accession, heavy infection by the loose smut fungus Ustilago bromivora occurred. That pathogen could also serve as a model pathogen of Brachypodium.
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Affiliation(s)
- Mirko Barbieri
- Dipartimento di Scienze Agrarie e degli Alimenti, Università degli studi di Modena e Reggio Emilia, Via Amendola 2, Pad. Besta, 42100 Reggio Emilia, Italy
| | - Thierry C Marcel
- Laboratory of Plant Breeding, Graduate school for Experimental Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; INRA-AgroParisTech, UMR1290 BIOGER-CPP, Avenue Lucien Brétignières BP01, 78850 Thiverval-Grignon, France
| | - Rients E Niks
- Laboratory of Plant Breeding, Graduate school for Experimental Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Brkljacic J, Grotewold E, Scholl R, Mockler T, Garvin DF, Vain P, Brutnell T, Sibout R, Bevan M, Budak H, Caicedo AL, Gao C, Gu Y, Hazen SP, Holt BF, Hong SY, Jordan M, Manzaneda AJ, Mitchell-Olds T, Mochida K, Mur LA, Park CM, Sedbrook J, Watt M, Zheng SJ, Vogel JP. Brachypodium as a model for the grasses: today and the future. PLANT PHYSIOLOGY 2011; 157:3-13. [PMID: 21771916 PMCID: PMC3165879 DOI: 10.1104/pp.111.179531] [Citation(s) in RCA: 183] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 07/18/2011] [Indexed: 05/06/2023]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - John P. Vogel
- Plant Biotechnology Center and Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210 (J.B., E.G., R.S.); Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331 (T.M.); United States Department of Agriculture-Agricultural Research Service Plant Science Research Unit and Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 (D.F.G.); Crop Genetics Department (P.V.) and Cell and Developmental Biology Department (M.B.), John Innes Centre, Norwich NR4 7UJ, United Kingdom; Boyce Thompson Institute, Ithaca, New York 14853 (T.B.); Institut Jean-Pierre Bourgin, UMR1318 Institut National de la Recherche Agronomique-AgroParisTech, Versailles 78026, France (R.S.); Faculty of Engineering and Natural Science, Sabanci University, Istanbul 34956, Turkey (H.B.); Biology Department, University of Massachusetts, Amherst, Massachusetts 01003 (A.L.C., S.P.H.); State Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (C.G.); Genomics and Gene Discovery Research Unit, United States Department of Agriculture-Agricultural Research Service Western Regional Research Center, Albany, California 94710 (Y.G., J.P.V.); Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019 (B.F.H.); Department of Chemistry, Seoul National University, Seoul 151–742 Korea (S.-Y.H., C.-M.P.); Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, Manitoba, Canada R3T 2M9 (M.J.); Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaen 23071 Spain (A.J.M.); Institute for Genome Sciences and Policy, Department of Biology, Duke University, Durham, North Carolina 27708 (T.M.-O.); RIKEN Biomass Engineering Program, RIKEN Plant Science Center, Kanagawa 230–0045, Japan (K.M.); Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales SY23 3DA, United Kingdom (L.A.J.M.); School of Biological Sciences, Illinois State University and Department of Energy Great Lakes Bioenergy Research Center, Normal, Illinois 61790 (J.S.); CSIRO Plant Industry, Canberra, Australian Capital Territory 2601, Australia (M.W.); College of Life Sciences, Zhejiang University, Hangzhou 310058, China (S.J.Z.)
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Huo N, Garvin DF, You FM, McMahon S, Luo MC, Gu YQ, Lazo GR, Vogel JP. Comparison of a high-density genetic linkage map to genome features in the model grass Brachypodium distachyon. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:455-64. [PMID: 21597976 DOI: 10.1007/s00122-011-1598-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Accepted: 04/08/2011] [Indexed: 05/25/2023]
Abstract
The small annual grass Brachypodium distachyon (Brachypodium) is rapidly emerging as a powerful model system to study questions unique to the grasses. Many Brachypodium resources have been developed including a whole genome sequence, highly efficient transformation and a large germplasm collection. We developed a genetic linkage map of Brachypodium using single nucleotide polymorphism (SNP) markers and an F(2) mapping population of 476 individuals. SNPs were identified by targeted resequencing of single copy genomic sequences. Using the Illumina GoldenGate Genotyping platform we placed 558 markers into five linkage groups corresponding to the five chromosomes of Brachypodium. The unusually long total genetic map length, 1,598 centiMorgans (cM), indicates that the Brachypodium mapping population has a high recombination rate. By comparing the genetic map to genome features we found that the recombination rate was positively correlated with gene density and negatively correlated with repetitive regions and sites of ancestral chromosome fusions that retained centromeric repeat sequences. A comparison of adjacent genome regions with high versus low recombination rates revealed a positive correlation between interspecific synteny and recombination rate.
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Affiliation(s)
- Naxin Huo
- USDA-ARS Western Regional Research Center, Albany, CA, 94710, USA
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84
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Mochida K, Yoshida T, Sakurai T, Yamaguchi-Shinozaki K, Shinozaki K, Tran LSP. In silico analysis of transcription factor repertoires and prediction of stress-responsive transcription factors from six major gramineae plants. DNA Res 2011; 18:321-32. [PMID: 21729923 PMCID: PMC3190953 DOI: 10.1093/dnares/dsr019] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The interactions between transcription factors (TFs) and cis-regulatory DNA sequences control gene expression, constituting the essential functional linkages of gene regulatory networks. The aim of this study is to identify and integrate all putative TFs from six grass species: Brachypodium distachyon, maize, rice, sorghum, barley, and wheat with significant information into an integrative database (GramineaeTFDB) for comparative genomics and functional genomics. For each TF, sequence features, promoter regions, domain alignments, GO assignment, FL-cDNA information, if available, and cross-references to various public databases and genetic resources are provided. Additionally, GramineaeTFDB possesses a tool which aids the users to search for putative cis-elements located in the promoter regions of TFs and predict the functions of the TFs using cis-element-based functional prediction approach. We also supplied hyperlinks to expression profiles of those TF genes of maize, rice, and barley, for which data are available. Furthermore, information about the availability of FOX and Ds mutant lines for rice and maize TFs, respectively, are also accessible through hyperlinks. Our study provides an important user-friendly public resource for functional analyses and comparative genomics of grass TFs, and understanding of the architecture of transcriptional regulatory networks and evolution of the TFs in agriculturally important cereal crops.
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Affiliation(s)
- Keiichi Mochida
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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Mur LAJ, Allainguillaume J, Catalán P, Hasterok R, Jenkins G, Lesniewska K, Thomas I, Vogel J. Exploiting the Brachypodium Tool Box in cereal and grass research. THE NEW PHYTOLOGIST 2011; 191:334-347. [PMID: 21623796 DOI: 10.1111/j.1469-8137.2011.03748.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
It is now a decade since Brachypodium distachyon (Brachypodium) was suggested as a model species for temperate grasses and cereals. Since then transformation protocols, large expressed sequence tag (EST) databases, tools for forward and reverse genetic screens, highly refined cytogenetic probes, germplasm collections and, recently, a complete genome sequence have been generated. In this review, we will describe the current status of the Brachypodium Tool Box and how it is beginning to be applied to study a range of biological traits. Further, as genomic analysis of larger cereals and forage grasses genomes are becoming easier, we will re-evaluate Brachypodium as a model species. We suggest that there remains an urgent need to employ reverse genetic and functional genomic approaches to identify the functionality of key genetic elements, which could be employed subsequently in plant breeding programmes; and a requirement for a Pooideae reference genome to aid assembling large pooid genomes. Brachypodium is an ideal system for functional genomic studies, because of its easy growth requirements, small physical stature, and rapid life cycle, coupled with the resources offered by the Brachypodium Tool Box.
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Affiliation(s)
- Luis A J Mur
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth, Wales SY23 3DA, UK
| | - Joel Allainguillaume
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth, Wales SY23 3DA, UK
| | - Pilar Catalán
- Department of Agriculture, University of Zaragoza, High Polytechnic School of Huesca, Ctra. Cuarte km 1, ES-22071 Huesca, Spain
| | - Robert Hasterok
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia, PL-40-032 Katowice, Poland
| | - Glyn Jenkins
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth, Wales SY23 3DA, UK
| | - Karolina Lesniewska
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia, PL-40-032 Katowice, Poland
| | - Ianto Thomas
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth, Wales SY23 3DA, UK
| | - John Vogel
- USDA ARS Western Regional Research Center, Albany, CA 94710 USA
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Genome-wide distribution and organization of microsatellites in plants: an insight into marker development in Brachypodium. PLoS One 2011; 6:e21298. [PMID: 21713003 PMCID: PMC3119692 DOI: 10.1371/journal.pone.0021298] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 05/25/2011] [Indexed: 11/29/2022] Open
Abstract
Plant genomes are complex and contain large amounts of repetitive DNA including microsatellites that are distributed across entire genomes. Whole genome sequences of several monocot and dicot plants that are available in the public domain provide an opportunity to study the origin, distribution and evolution of microsatellites, and also facilitate the development of new molecular markers. In the present investigation, a genome-wide analysis of microsatellite distribution in monocots (Brachypodium, sorghum and rice) and dicots (Arabidopsis, Medicago and Populus) was performed. A total of 797,863 simple sequence repeats (SSRs) were identified in the whole genome sequences of six plant species. Characterization of these SSRs revealed that mono-nucleotide repeats were the most abundant repeats, and that the frequency of repeats decreased with increase in motif length both in monocots and dicots. However, the frequency of SSRs was higher in dicots than in monocots both for nuclear and chloroplast genomes. Interestingly, GC-rich repeats were the dominant repeats only in monocots, with the majority of them being present in the coding region. These coding GC-rich repeats were found to be involved in different biological processes, predominantly binding activities. In addition, a set of 22,879 SSR markers that were validated by e-PCR were developed and mapped on different chromosomes in Brachypodium for the first time, with a frequency of 101 SSR markers per Mb. Experimental validation of 55 markers showed successful amplification of 80% SSR markers in 16 Brachypodium accessions. An online database ‘BraMi’ (Brachypodium microsatellite markers) of these genome-wide SSR markers was developed and made available in the public domain. The observed differential patterns of SSR marker distribution would be useful for studying microsatellite evolution in a monocot–dicot system. SSR markers developed in this study would be helpful for genomic studies in Brachypodium and related grass species, especially for the map based cloning of the candidate gene(s).
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Cao S, Siriwardana CL, Kumimoto RW, Holt BF. Construction of high quality Gateway™ entry libraries and their application to yeast two-hybrid for the monocot model plant Brachypodium distachyon. BMC Biotechnol 2011; 11:53. [PMID: 21595971 PMCID: PMC3239850 DOI: 10.1186/1472-6750-11-53] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2011] [Accepted: 05/19/2011] [Indexed: 11/25/2022] Open
Abstract
Background Monocots, especially the temperate grasses, represent some of the most agriculturally important crops for both current food needs and future biofuel development. Because most of the agriculturally important grass species are difficult to study (e.g., they often have large, repetitive genomes and can be difficult to grow in laboratory settings), developing genetically tractable model systems is essential. Brachypodium distachyon (hereafter Brachypodium) is an emerging model system for the temperate grasses. To fully realize the potential of this model system, publicly accessible discovery tools are essential. High quality cDNA libraries that can be readily adapted for multiple downstream purposes are a needed resource. Additionally, yeast two-hybrid (Y2H) libraries are an important discovery tool for protein-protein interactions and are not currently available for Brachypodium. Results We describe the creation of two high quality, publicly available Gateway™ cDNA entry libraries and their derived Y2H libraries for Brachypodium. The first entry library represents cloned cDNA populations from both short day (SD, 8/16-h light/dark) and long day (LD, 20/4-h light/dark) grown plants, while the second library was generated from hormone treated tissues. Both libraries have extensive genome coverage (~5 × 107 primary clones each) and average clone lengths of ~1.5 Kb. These entry libraries were then used to create two recombination-derived Y2H libraries. Initial proof-of-concept screens demonstrated that a protein with known interaction partners could readily re-isolate those partners, as well as novel interactors. Conclusions Accessible community resources are a hallmark of successful biological model systems. Brachypodium has the potential to be a broadly useful model system for the grasses, but still requires many of these resources. The Gateway™ compatible entry libraries created here will facilitate studies for multiple user-defined purposes and the derived Y2H libraries can be immediately applied to large scale screening and discovery of novel protein-protein interactions. All libraries are freely available for distribution to the research community.
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Affiliation(s)
- Shuanghe Cao
- Department of Botany and Microbiology, University of Oklahoma, 770 Van Vleet Oval, GLCH, Room 43, Norman, OK 73019, USA
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Kubik C, Honig J, Bonos SA. Characterization of 215 simple sequence repeat markers in creeping bentgrass (Agrostis stolonifera L.). Mol Ecol Resour 2011; 11:872-6. [PMID: 21843299 DOI: 10.1111/j.1755-0998.2011.03006.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Creeping bentgrass (Agrostis stolonifera L.) is a versatile, cross-pollinated, temperate and perennial turfgrass species. It occurs naturally in a wide variety of habitats and is also cultivated on golf courses, bowling greens and tennis courts worldwide. Isozymes and amplified fragment length polymorphisms (AFLPs) have been used to determine genetic diversity, and restriction fragment length polymorphisms (RFLPs) and random amplified polymorphic DNA (RAPDs) were used to construct a genetic linkage map of this species. In the current report, we developed and characterized 215 unique genomic simple sequence repeat (SSR) markers in creeping bentgrass. The SSRs reported here are the first available markers in creeping bentgrass to date. Eight hundred and eighteen alleles were amplified by 215 SSR loci, an average of 3.72 alleles per locus. Fifty-nine per cent of those alleles segregated in a 1:1 Mendelian fashion (P > 0.05). Twenty-two per cent had a distorted segregation ratio (P ≤ 0.05). These SSR markers will be useful for assessing genetic diversity in creeping bentgrass and will be important for the development of genetic linkage maps and identifying quantitative trait loci. These markers could enhance breeding programmes by improving the efficiency of selection techniques.
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Affiliation(s)
- Christine Kubik
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, 59 Dudley Rd., Foran Hall, New Brunswick, NJ 08901-8520, USA
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90
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Luo N, Liu J, Yu X, Jiang Y. Natural variation of drought response in Brachypodium distachyon. PHYSIOLOGIA PLANTARUM 2011; 141:19-29. [PMID: 20875057 DOI: 10.1111/j.1399-3054.2010.01413.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Brachypodium distachyon (Brachypodium) is a temperate wild grass species and is a powerful model system for studying grain, energy, forage and turf grasses. Exploring the natural variation in the drought response of Brachypodium provides an important basis for dissecting the genetic network of drought tolerance. Two experiments were conducted in a greenhouse to assess the drought tolerance of 57 natural populations of Brachypodium. Principle component analysis revealed that reductions in chlorophyll fluorescence (Fv/Fm) and leaf water content (LWC) under drought stress explained most of the phenotypic variation, which was used to classify the tolerant and susceptible accessions. Four groups of accessions differing in drought tolerance were identified, with 3 tolerant, 16 moderately tolerant, 32 susceptible and 6 most susceptible accessions. The tolerant group had little leaf wilting and fewer reductions in Fv/Fm and LWC, while the most susceptible groups showed severe leaf wilting and more reductions in Fv/Fm and LWC. Drought stress increased total water soluble sugar (WSS) concentration, but no differences in the increased WSS were found among different groups of accessions. The large phenotypic variation of Brachypodium in response to drought stress can be used to identify genes and alleles important for the complex trait of drought tolerance.
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Affiliation(s)
- Na Luo
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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91
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Garvin DF, McKenzie N, Vogel JP, Mockler TC, Blankenheim ZJ, Wright J, Cheema JJS, Dicks J, Huo N, Hayden DM, Gu Y, Tobias C, Chang JH, Chu A, Trick M, Michael TP, Bevan MW, Snape JW. An SSR-based genetic linkage map of the model grass Brachypodium distachyon. Genome 2010; 53:1-13. [PMID: 20130744 DOI: 10.1139/g09-079] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The grass species Brachypodium distachyon (hereafter, Brachypodium) has been adopted as a model system for grasses. Here, we describe the development of a genetic linkage map of Brachypodium. The genetic linkage map was developed with an F2 population from a cross between the diploid Brachypodium lines Bd3-1 and Bd21. The map was populated with polymorphic simple sequence repeat (SSR) markers from Brachypodium expressed sequence tag (EST) and bacterial artificial chromosome (BAC) end sequences and conserved orthologous sequence (COS) markers from other grass species. The map is 1386 cM in length and consists of 139 marker loci distributed across 20 linkage groups. Five of the linkage groups exceed 100 cM in length, with the largest being 231 cM long. Assessment of colinearity between the Brachypodium linkage map and the rice genome sequence revealed significant regions of macrosynteny between the two genomes, as well as rearrangements similar to those reported in other grass comparative structural genomics studies. The Brachypodium genetic linkage map described here will serve as a new tool to pursue a range of molecular genetic analyses and other applications in this new model plant system.
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Affiliation(s)
- David F Garvin
- USDA-ARS Plant Science Research Unit, 411 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN 55108, USA.
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92
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Bevan MW, Garvin DF, Vogel JP. Brachypodium distachyon genomics for sustainable food and fuel production. Curr Opin Biotechnol 2010; 21:211-7. [PMID: 20362425 DOI: 10.1016/j.copbio.2010.03.006] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Revised: 03/09/2010] [Accepted: 03/09/2010] [Indexed: 01/10/2023]
Abstract
Grass crops are the most important sources of human nutrition, and their improvement is centrally important for meeting the challenges of sustainable agriculture, for feeding the world's population and for developing renewable supplies of fuel and industrial products. We describe the complete sequence of the compact genome of Brachypodium distachyon (Brachypodium) the first pooid grass to be sequenced. We demonstrate the many favorable characteristics of Brachypodium as an experimental system and show how it can be used to navigate the large and complex genomes of closely related grasses. The functional genomics and other experimental resources that are being developed will provide a key resource for improving food and forage crops, in particular wheat, barley and forage grasses, and for establishing new grass crops for sustainable energy production.
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93
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Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 2010; 463:763-8. [PMID: 20148030 DOI: 10.1038/nature08747] [Citation(s) in RCA: 1210] [Impact Index Per Article: 86.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2009] [Accepted: 12/09/2009] [Indexed: 11/09/2022]
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94
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Watt M, Schneebeli K, Dong P, Wilson IW. The shoot and root growth of Brachypodium and its potential as a model for wheat and other cereal crops. FUNCTIONAL PLANT BIOLOGY : FPB 2009; 36:960-969. [PMID: 32688707 DOI: 10.1071/fp09214] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Accepted: 09/18/2009] [Indexed: 06/11/2023]
Abstract
The grass genetic model Brachypodium (Brachypodium distachyon (L.) Beauv., sequenced line Bd 21) was studied from germination to seed production to assess its potential as a phenotypic model for wheat (Triticum aestivum L.) and other cereal crops. Brachypodium and wheat shoot and root development and anatomy were highly similar. Main stem leaves and tillers (side shoots) emerged at the same time in both grasses in four temperature and light environments. Both developed primary and nodal axile roots at similar leaf stages with the same number and arrangement of vascular xylem tracheary elements (XTEs). Brachypodium, unlike wheat, had an elongated a mesocotyl above the seed and developed only one fine primary axile root from the base of the embryo, while wheat generally has three to five. Roots of both grasses could develop first, second and third order branches that emerged from phloem poles. Both developed up to two nodal axile roots from the coleoptile node at leaf 3, more than eight nodal axile roots from stem nodes after leaf 4, and most (97%) of the deepest roots at flowering were branches. In long days Brachypodium flowered 30 days after emergence, and root systems ceased descent 42 cm from the soil surface, such that mature roots can be studied readily in much smaller soil volumes than wheat. Brachypodium has the overwhelming advantage of a small size, fast life cycle and small genome, and is an excellent model to study cereal root system genetics and function, as well as genes for resource partitioning in whole plants.
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Affiliation(s)
- Michelle Watt
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
| | | | - Pan Dong
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Iain W Wilson
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
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95
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Filiz E, Ozdemir BS, Budak F, Vogel JP, Tuna M, Budak H. Molecular, morphological, and cytological analysis of diverse Brachypodium distachyon inbred lines. Genome 2009; 52:876-90. [DOI: 10.1139/g09-062] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Brachypodium distachyon (brachypodium) is a small grass with the biological and genomic attributes necessary to serve as a model system for all grasses including small grains and grasses being developed as energy crops (e.g., switchgrass and Miscanthus ). To add natural variation to the toolkit available to plant biologists using brachypodium as a model system, it is imperative to establish extensive, well-characterized germplasm collections. The objectives of this study were to collect brachypodium accessions from throughout Turkey and then characterize the molecular (nuclear and organelle genome), morphological, and cytological variation within the collection. We collected 164 lines from 45 diverse geographic regions of Turkey and created 146 inbred lines. The majority of this material (116 of 146 inbred lines) was diploid. The similarity matrix for the diploid lines based on AFLP analysis indicated extensive diversity, with genetic distances ranging from 0.05 to 0.78. Organelle genome diversity, on the other hand, was low both among and within the lines used in this study. The geographic distribution of genotypes was not significantly correlated with either nuclear or organelle genome variation for the genotypes studied. Phenotypic characterization of the lines showed extensive variation in flowering time (7–22 weeks), seed production (4–193 seeds/plant), and biomass (15–77 g). Chromosome morphology of the collected brachypodium accessions varied from submetacentric to metacentric, except for chromosome 5, which was acrocentric. The diverse brachypodium lines developed in this study will allow experimental approaches dependent upon natural variation to be applied to this new model grass. These results will also help efforts to have a better understanding of complex large genomes (i.e., wheat, barley, and switchgrass).
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Affiliation(s)
- E. Filiz
- Sabanci University, Biological Science and Bioengineering Program, 34956, Tuzla, Istanbul, Turkey
- Igdir University, Department of Crops Science, Igdir, Turkey
- USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
- Namik Kemal University, Department of Crop Science, Tekirdag, Turkey
| | - B. S. Ozdemir
- Sabanci University, Biological Science and Bioengineering Program, 34956, Tuzla, Istanbul, Turkey
- Igdir University, Department of Crops Science, Igdir, Turkey
- USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
- Namik Kemal University, Department of Crop Science, Tekirdag, Turkey
| | - F. Budak
- Sabanci University, Biological Science and Bioengineering Program, 34956, Tuzla, Istanbul, Turkey
- Igdir University, Department of Crops Science, Igdir, Turkey
- USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
- Namik Kemal University, Department of Crop Science, Tekirdag, Turkey
| | - J. P. Vogel
- Sabanci University, Biological Science and Bioengineering Program, 34956, Tuzla, Istanbul, Turkey
- Igdir University, Department of Crops Science, Igdir, Turkey
- USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
- Namik Kemal University, Department of Crop Science, Tekirdag, Turkey
| | - M. Tuna
- Sabanci University, Biological Science and Bioengineering Program, 34956, Tuzla, Istanbul, Turkey
- Igdir University, Department of Crops Science, Igdir, Turkey
- USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
- Namik Kemal University, Department of Crop Science, Tekirdag, Turkey
| | - H. Budak
- Sabanci University, Biological Science and Bioengineering Program, 34956, Tuzla, Istanbul, Turkey
- Igdir University, Department of Crops Science, Igdir, Turkey
- USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
- Namik Kemal University, Department of Crop Science, Tekirdag, Turkey
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96
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Gu YQ, Wanjugi H, Coleman-Derr D, Kong X, Anderson OD. Conserved globulin gene across eight grass genomes identify fundamental units of the loci encoding seed storage proteins. Funct Integr Genomics 2009; 10:111-22. [PMID: 19707805 DOI: 10.1007/s10142-009-0135-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Revised: 08/06/2009] [Accepted: 08/08/2009] [Indexed: 12/30/2022]
Abstract
The wheat high molecular weight (HMW) glutenins are important seed storage proteins that determine bread-making quality in hexaploid wheat (Triticum aestivum). In this study, detailed comparative sequence analyses of large orthologous HMW glutenin genomic regions from eight grass species, representing a wide evolutionary history of grass genomes, reveal a number of lineage-specific sequence changes. These lineage-specific changes, which resulted in duplications, insertions, and deletions of genes, are the major forces disrupting gene colinearity among grass genomes. Our results indicate that the presence of the HMW glutenin gene in Triticeae genomes was caused by lineage-specific duplication of a globulin gene. This tandem duplication event is shared by Brachypodium and Triticeae genomes, but is absent in rice, maize, and sorghum, suggesting the duplication occurred after Brachypodium and Triticeae genomes diverged from the other grasses ~35 Ma ago. Aside from their physical location in tandem, the sequence similarity, expression pattern, and conserved cis-acting elements responsible for endosperm-specific expression further support the paralogous relationship between the HMW glutenin and globulin genes. While the duplicated copy in Brachypodium has apparently become nonfunctional, the duplicated copy in wheat has evolved to become the HMW glutenin gene by gaining a central prolamin repetitive domain.
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Affiliation(s)
- Yong Qiang Gu
- Western Regional Research Center, United States Department of Agricultural-Agricultural Research Service, Albany, CA 94710, USA.
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