1
|
Ferreira LAI, de Oliveira RS, Constantin J, Brunharo C. Evolution of ACCase-inhibitor resistance in Chloris virgata is conferred by a Trp2027Cys mutation in the herbicide target site. PEST MANAGEMENT SCIENCE 2023; 79:5220-5229. [PMID: 37592752 DOI: 10.1002/ps.7723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/13/2023] [Accepted: 08/18/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND Chloris virgata is a troublesome weed in tropical regions. With the evolution of glyphosate resistance in key grass species, acetyl CoA carboxylase (ACCase) inhibitors have become a commonly used tool in soybean production areas in Brazil. We assessed if suspected resistant populations exhibited cross resistance to the different classes of ACCase inhibitors and investigated the resistance mechanisms in C. virgata. RESULTS Dose-response experiments revealed resistance to haloxyfop-methyl and pinoxaden, with 432- and 3-fold resistance, respectively, compared to susceptible populations. Due to the lack of genetic resources for C. virgata, we sequenced, assembled, and annotated the genome using short-read Illumina technology. The k-mer analysis estimated a genome size of approximately 336 Mbp, with BUSCO completeness of 97%, and over 36 000 gene models were annotated. We examined if ACCase copy number variation and increased gene expression were involved in the resistance phenotype and found no difference when compared to a susceptible population. A mutation was detected in ACCase that encodes for amino acid position 2027, resulting in a tryptophan-to-cysteine (Trp2027Cys) substitution. We found the resistant population absorbed 11.4% less herbicide and retained 21% more herbicide on the treated leaf compared to the susceptible population. We developed a genotyping assay targeting the resistance-endowing Trp2027Cys substitution for quick resistance diagnosis. CONCLUSION A Trp2027Cys amino acid substitution in ACCase confers resistance to haloxyfop and pinoxaden in C. virgata. We provide important insights into the evolutionary history of C. virgata and a draft genome as a useful resource to further our understanding of the biology in the genus Chloris. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
Collapse
Affiliation(s)
- Luiz Augusto Inojosa Ferreira
- Department of Agronomy, Center for Advanced Studies in Weed Science, State University of Maringá, Maringá, Brazil
- Department of Plant Science, Applied Weed Physiology Laboratory, The Pennsylvania State University, University Park, PA, USA
| | - Rubem Silvério de Oliveira
- Department of Agronomy, Center for Advanced Studies in Weed Science, State University of Maringá, Maringá, Brazil
| | - Jamil Constantin
- Department of Agronomy, Center for Advanced Studies in Weed Science, State University of Maringá, Maringá, Brazil
| | - Caio Brunharo
- Department of Plant Science, Applied Weed Physiology Laboratory, The Pennsylvania State University, University Park, PA, USA
| |
Collapse
|
2
|
Wang Y, Chen G, Zeng F, Han Z, Qiu CW, Zeng M, Yang Z, Xu F, Wu D, Deng F, Xu S, Chater C, Korol A, Shabala S, Wu F, Franks P, Nevo E, Chen ZH. Molecular evidence for adaptive evolution of drought tolerance in wild cereals. THE NEW PHYTOLOGIST 2023; 237:497-514. [PMID: 36266957 DOI: 10.1111/nph.18560] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
The considerable drought tolerance of wild cereal crop progenitors has diminished during domestication in the pursuit of higher productivity. Regaining this trait in cereal crops is essential for global food security but requires novel genetic insight. Here, we assessed the molecular evidence for natural variation of drought tolerance in wild barley (Hordeum spontaneum), wild emmer wheat (Triticum dicoccoides), and Brachypodium species collected from dry and moist habitats at Evolution Canyon, Israel (ECI). We report that prevailing moist vs dry conditions have differentially shaped the stomatal and photosynthetic traits of these wild cereals in their respective habitats. We present the genomic and transcriptomic evidence accounting for differences, including co-expression gene modules, correlated with physiological traits, and selective sweeps, driven by the xeric site conditions on the African Slope (AS) at ECI. Co-expression gene module 'circadian rhythm' was linked to significant drought-induced delay in flowering time in Brachypodium stacei genotypes. African Slope-specific differentially expressed genes are important in barley drought tolerance, verified by silencing Disease-Related Nonspecific Lipid Transfer 1 (DRN1), Nonphotochemical Quenching 4 (NPQ4), and Brassinosteroid-Responsive Ring-H1 (BRH1). Our results provide new genetic information for the breeding of resilient wheat and barley in a changing global climate with increasingly frequent drought events.
Collapse
Affiliation(s)
- Yuanyuan Wang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guang Chen
- Central Laboratory, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Fanrong Zeng
- Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Zhigang Han
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Cheng-Wei Qiu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Meng Zeng
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zujun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan, 611731, China
| | - Fei Xu
- Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Dezhi Wu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Fenglin Deng
- Central Laboratory, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Shengchun Xu
- Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Caspar Chater
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Abraham Korol
- Institute of Evolution, University of Haifa, Mount Carmel, 34988384, Haifa, Israel
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, 7004, Australia
- School of Biological Science, University of Western Australia, Crawley, WA, 6009, Australia
| | - Feibo Wu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Peter Franks
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Mount Carmel, 34988384, Haifa, Israel
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW, 2751, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
| |
Collapse
|
3
|
Mavrodi OV, McWilliams JR, Peter JO, Berim A, Hassan KA, Elbourne LDH, LeTourneau MK, Gang DR, Paulsen IT, Weller DM, Thomashow LS, Flynt AS, Mavrodi DV. Root Exudates Alter the Expression of Diverse Metabolic, Transport, Regulatory, and Stress Response Genes in Rhizosphere Pseudomonas. Front Microbiol 2021; 12:651282. [PMID: 33936009 PMCID: PMC8079746 DOI: 10.3389/fmicb.2021.651282] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/08/2021] [Indexed: 12/20/2022] Open
Abstract
Plants live in association with microorganisms that positively influence plant development, vigor, and fitness in response to pathogens and abiotic stressors. The bulk of the plant microbiome is concentrated belowground at the plant root-soil interface. Plant roots secrete carbon-rich rhizodeposits containing primary and secondary low molecular weight metabolites, lysates, and mucilages. These exudates provide nutrients for soil microorganisms and modulate their affinity to host plants, but molecular details of this process are largely unresolved. We addressed this gap by focusing on the molecular dialog between eight well-characterized beneficial strains of the Pseudomonas fluorescens group and Brachypodium distachyon, a model for economically important food, feed, forage, and biomass crops of the grass family. We collected and analyzed root exudates of B. distachyon and demonstrated the presence of multiple carbohydrates, amino acids, organic acids, and phenolic compounds. The subsequent screening of bacteria by Biolog Phenotype MicroArrays revealed that many of these metabolites provide carbon and energy for the Pseudomonas strains. RNA-seq profiling of bacterial cultures amended with root exudates revealed changes in the expression of genes encoding numerous catabolic and anabolic enzymes, transporters, transcriptional regulators, stress response, and conserved hypothetical proteins. Almost half of the differentially expressed genes mapped to the variable part of the strains’ pangenome, reflecting the importance of the variable gene content in the adaptation of P. fluorescens to the rhizosphere lifestyle. Our results collectively reveal the diversity of cellular pathways and physiological responses underlying the establishment of mutualistic interactions between these beneficial rhizobacteria and their plant hosts.
Collapse
Affiliation(s)
- Olga V Mavrodi
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Janiece R McWilliams
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Jacob O Peter
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Anna Berim
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Karl A Hassan
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | - Liam D H Elbourne
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Melissa K LeTourneau
- USDA Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - David R Gang
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Ian T Paulsen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - David M Weller
- USDA Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Linda S Thomashow
- USDA Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Alex S Flynt
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Dmitri V Mavrodi
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| |
Collapse
|
4
|
Wang X, Liu Y, Li Z, Gao X, Dong J, Yang M. Expression and evolution of the phospholipase C gene family in Brachypodium distachyon. Genes Genomics 2020; 42:1041-1053. [PMID: 32712839 DOI: 10.1007/s13258-020-00973-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/14/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Phospholipase C (PLC) is an enzyme that hydrolyzes phospholipids and plays an important role in plant growth and development. The Brachypodium distachyon is a model plant of Gramineae, but the research on PLC gene family of Brachypodium has not been reported. OBJECTIVE This study was performed to identify the PLC family gene in Brachypodium and to determine the expression profiles of PLCs under the abiotic stress. METHODS Complete genome sequences and transcriptomes of Brachypodium were downloaded from the PLAZA. The hidden Markov model-based profile of the conserved PLC domain was submitted as a query to identify all potential PLC domain sequences with HMMER software. Expression profiles of BdPLCs were obtained based on the qRT-PCR analysis. RESULTS There were 8 PLC genes in Brachypodium (BdPI-PLCs 1-4 and BdNPCs 1-4). All members of BdPI-PLC had three conserved domains of X, Y, and C2, and no EF-hand was found. All BdNPCs contained a phosphatase domain. BdPI-PLC genes were distributed on Chr1, Chr2 and Chr4, with different types and numbers of cis-regulatory elements in their respective gene promoters. Phylogenetic analysis showed that the genetic relationship between Brachypodium and rice was closer than Arabidopsis. The expression patterns of BdPI-PLC gene under abiotic stresses (drought, low temperature, high temperature and salt stress) were up-regulated, indicated their important roles in response to low temperature, high temperature, drought and salt stresses. CONCLUSIONS This study provides comprehensive information for the study of Brachypodium PLC gene family and lays a foundation for further research on the molecular mechanism of Brachypodium stress adaptation.
Collapse
Affiliation(s)
- Xianguo Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yang Liu
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zheng Li
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiang Gao
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Jian Dong
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Mingming Yang
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| |
Collapse
|
5
|
Głazowska S, Baldwin L, Mravec J, Bukh C, Fangel JU, Willats WG, Schjoerring JK. The source of inorganic nitrogen has distinct effects on cell wall composition in Brachypodium distachyon. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:6461-6473. [PMID: 31504748 PMCID: PMC6859728 DOI: 10.1093/jxb/erz388] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 08/19/2019] [Indexed: 05/22/2023]
Abstract
Plants have evolved different strategies to utilize various forms of nitrogen (N) from the environment. While regulation of plant growth and development in response to application of inorganic N forms has been characterized, our knowledge about the effect on cell wall structure and composition is quite limited. In this study, we analysed cell walls of Brachypodium distachyon supplied with three types of inorganic N (NH4NO3, NO3-, or NH4+). Cell wall profiles showed distinct alterations in both the quantity and structures of individual polymers. Nitrate stimulated cellulose, but inhibited lignin deposition at the heading growth stage. On the other hand, ammonium supply resulted in higher concentration of mixed linkage glucans. In addition, the chemical structure of pectins and hemicelluloses was strongly influenced by the form of N. Supply of only NO3- led to alteration in xylan substitution and to lower esterification of homogalacturonan. We conclude that the physiological response to absorption of different inorganic N forms includes pleotropic remodelling of type II cell walls.
Collapse
Affiliation(s)
- Sylwia Głazowska
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Laetitia Baldwin
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Jozef Mravec
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Christian Bukh
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Jonathan U Fangel
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - William Gt Willats
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | | |
Collapse
|
6
|
Niu X, Chen S, Li J, Liu Y, Ji W, Li H. Genome-wide identification of GRAS genes in Brachypodium distachyon and functional characterization of BdSLR1 and BdSLRL1. BMC Genomics 2019; 20:635. [PMID: 31387534 PMCID: PMC6683515 DOI: 10.1186/s12864-019-5985-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 07/19/2019] [Indexed: 12/02/2022] Open
Abstract
Background As one of the most important transcription factor families, GRAS proteins are involved in numerous regulatory processes, especially plant growth and development. However, they have not been systematically analyzed in Brachypodium distachyon, a new model grass. Results In this study, 48 BdGRAS genes were identified. Duplicated genes account for 41.7% of them and contribute to the expansion of this gene family. 33, 39, 35 and 35 BdGRAS genes were identified by synteny with their orthologs in rice, sorghum, maize and wheat genome, respectively, indicating close relationships among these species. Based on their phylogenic relationships to GRAS genes in rice and maize, BdGRAS genes can be divided into ten subfamilies in which members of the same subfamily showed similar protein sequences, conserved motifs and gene structures, suggesting possible conserved functions. Although expression variation is high, some BdGRAS genes are tissue-specific, phytohormones- or abiotic stresses-responsive, and they may play key roles in development, signal transduction pathways and stress responses. In addition, DELLA genes BdSLR1 and BdSLRL1 were functionally characterized to play a role in plant growth via the GA signal pathway, consistent with GO annotations and KEGG pathway analyses. Conclusions Systematic analyses of BdGRAS genes indicated that members of the same subfamily may play similar roles. This was supported by the conserved functions of BdSLR1 and BdSLRL1 in GA pathway. These results laid a foundation for further functional elucidation of BdGRAS genes, especially, BdSLR1 and BdSLRL1. Electronic supplementary material The online version of this article (10.1186/s12864-019-5985-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Xin Niu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Shoukun Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Jiawei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Yue Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China.
| | - Haifeng Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China.
| |
Collapse
|
7
|
Zhu T, Xin F, Wei S, Liu Y, Han Y, Xie J, Ding Q, Ma L. Genome-wide identification, phylogeny and expression profiling of class III peroxidases gene family in Brachypodium distachyon. Gene 2019; 700:149-162. [DOI: 10.1016/j.gene.2019.02.103] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/04/2019] [Accepted: 02/21/2019] [Indexed: 11/16/2022]
|
8
|
Onda Y, Inoue K, Sawada Y, Shimizu M, Takahagi K, Uehara-Yamaguchi Y, Hirai MY, Garvin DF, Mochida K. Genetic Variation for Seed Metabolite Levels in Brachypodium distachyon. Int J Mol Sci 2019; 20:ijms20092348. [PMID: 31083584 PMCID: PMC6540107 DOI: 10.3390/ijms20092348] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/26/2019] [Accepted: 04/27/2019] [Indexed: 12/27/2022] Open
Abstract
Metabolite composition and concentrations in seed grains are important traits of cereals. To identify the variation in the seed metabolotypes of a model grass, namely Brachypodium distachyon, we applied a widely targeted metabolome analysis to forty inbred lines of B. distachyon and examined the accumulation patterns of 183 compounds in the seeds. By comparing the metabolotypes with the population structure of these lines, we found signature metabolites that represent different accumulation patterns for each of the three B. distachyon subpopulations. Moreover, we found that thirty-seven metabolites exhibited significant differences in their accumulation between the lines Bd21 and Bd3-1. Using a recombinant inbred line (RIL) population from a cross between Bd3-1 and Bd21, we identified the quantitative trait loci (QTLs) linked with this variation in the accumulation of thirteen metabolites. Our metabolite QTL analysis illustrated that different genetic factors may presumably regulate the accumulation of 4-pyridoxate and pyridoxamine in vitamin B6 metabolism. Moreover, we found two QTLs on chromosomes 1 and 4 that affect the accumulation of an anthocyanin, chrysanthemin. These QTLs genetically interacted to regulate the accumulation of this compound. This study demonstrates the potential for metabolite QTL mapping in B. distachyon and provides new insights into the genetic dissection of metabolomic traits in temperate grasses.
Collapse
Affiliation(s)
- Yoshihiko Onda
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.
| | - Komaki Inoue
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Yuji Sawada
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Minami Shimizu
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Kotaro Takahagi
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Yukiko Uehara-Yamaguchi
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Masami Y Hirai
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - David F Garvin
- Plant Science Research Unit, United States Department of Agriculture, Agricultural Research Service, 1991 Upper Buford Circle, St. Paul, MN 55108, USA.
| | - Keiichi Mochida
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Institute of Plant Science and Resource, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan.
- Microalgae Production Control Technology Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| |
Collapse
|
9
|
Bredow M, Tomalty HE, Smith L, Walker VK. Ice and anti-nucleating activities of an ice-binding protein from the annual grass, Brachypodium distachyon. PLANT, CELL & ENVIRONMENT 2018; 41:983-992. [PMID: 28035668 DOI: 10.1111/pce.12889] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/14/2016] [Accepted: 12/15/2016] [Indexed: 05/15/2023]
Abstract
Plants exposed to sub-zero temperatures face unique challenges that threaten their survival. The growth of ice crystals in the extracellular space can cause cellular dehydration, plasma membrane rupture and eventual cell death. Additionally, some pathogenic bacteria cause tissue damage by initiating ice crystal growth at high sub-zero temperatures through the use of ice-nucleating proteins (INPs), presumably to access nutrients from lysed cells. An annual species of brome grass, Brachypodium distachyon (Bd), produces an ice-binding protein (IBP) that shapes ice with a modest depression of the freezing point (~0.1 °C at 1 mg/mL), but high ice-recrystallization inhibition (IRI) activity, allowing ice crystals to remain small at near melting temperatures. This IBP, known as BdIRI, is unlike other characterized IBPs with a single ice-binding face, as mutational analysis indicates that BdIRI adsorbs to ice on two faces. BdIRI also dramatically attenuates the nucleation of ice by bacterial INPs (up to -2.26 °C). This 'anti-nucleating' activity is significantly higher than previously documented for any IBP.
Collapse
Affiliation(s)
- Melissa Bredow
- Department of Biology, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Heather E Tomalty
- Department of Biology, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Lindsay Smith
- Department of Biology, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Virginia K Walker
- Department of Biology, Queen's University, Kingston, Ontario, K7L 3N6, Canada
- Department of Biomedical and Molecular Sciences, and School of Environmental Studies, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| |
Collapse
|
10
|
Takahashi Y, Ono K, Akamine Y, Asano T, Ezaki M, Mouri I. Highly-expressed polyamine oxidases catalyze polyamine back conversion in Brachypodium distachyon. JOURNAL OF PLANT RESEARCH 2018; 131:341-348. [PMID: 29063977 DOI: 10.1007/s10265-017-0989-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/04/2017] [Indexed: 05/25/2023]
Abstract
To understand the polyamine (PA) catabolic pathways in Brachypodium distachyon, we focused on the flavin-containing polyamine oxidase enzymes (PAO), and characterized them at the molecular and biochemical levels. Five PAO isoforms were identified from database searches, and we named them BdPAO1 to BdPAO5. By gene expression analysis using above-ground tissues such as leaf, stem and inflorescence, it was revealed that BdPAO2 is the most abundant PAO gene in normal growth conditions, followed by BdPAO3 and BdPAO4. BdPAO1 and BdPAO5 were expressed at very low levels. All Arabidopsis thaliana and rice orthologs belonging to the same clade as BdPAO2, BdPAO3 and BdPAO4 have conserved peroxisome-targeting signal sequences at their C-termini. Amino acid sequences of BdPAO2 and BdPAO4 also showed such a sequence, but BdPAO3 did not. We selected the gene with the highest expression level (BdPAO2) and the peroxisome-targeting signal lacking PAO (BdPAO3) for biochemical analysis of substrate specificity and catabolic pathways. BdPAO2 catalyzed conversion of spermine (Spm) or thermospermine to spermidine (Spd), and Spd to putrescine, but its most-favored substrate was Spd. In contrast, BdPAO3 favored Spm as substrate and catalyzed conversion of tetraamines to Spd. These results indicated that the major PAOs in B. distachyon have back-conversion activity.
Collapse
Affiliation(s)
- Yoshihiro Takahashi
- Department of Applied Chemistry and Biochemistry, Faculty of Engineering, Kyushu Sangyo University, 2-3-1 Matsukadai Higashi-ku, Fukuoka, 813-8503, Japan.
| | - Kaede Ono
- Department of Applied Chemistry and Biochemistry, Faculty of Engineering, Kyushu Sangyo University, 2-3-1 Matsukadai Higashi-ku, Fukuoka, 813-8503, Japan
| | - Yuuta Akamine
- Department of Applied Chemistry and Biochemistry, Faculty of Engineering, Kyushu Sangyo University, 2-3-1 Matsukadai Higashi-ku, Fukuoka, 813-8503, Japan
| | - Takuya Asano
- Department of Applied Chemistry and Biochemistry, Faculty of Engineering, Kyushu Sangyo University, 2-3-1 Matsukadai Higashi-ku, Fukuoka, 813-8503, Japan
| | - Masatoshi Ezaki
- Department of Applied Chemistry and Biochemistry, Faculty of Engineering, Kyushu Sangyo University, 2-3-1 Matsukadai Higashi-ku, Fukuoka, 813-8503, Japan
| | - Itsupei Mouri
- Department of Applied Chemistry and Biochemistry, Faculty of Engineering, Kyushu Sangyo University, 2-3-1 Matsukadai Higashi-ku, Fukuoka, 813-8503, Japan
| |
Collapse
|
11
|
Zhao P, Wang L, Yin H. Transcriptional responses to phosphate starvation in Brachypodium distachyon roots. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 122:113-120. [PMID: 29216498 DOI: 10.1016/j.plaphy.2017.11.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 11/16/2017] [Accepted: 11/16/2017] [Indexed: 06/07/2023]
Abstract
Brachypodium distachyon is a model plant that has recently emerged in grass research. Although the growth and photochemical efficiency of this species respond strongly to phosphate (Pi) availability, its Pi starvation response mechanism, which controls the Pi homeostasis, remains largely unknown. This study presents the transcriptomic response profiles of Pi-deficient roots at growth stages during which the plants were starved but obvious growth defects were absent. The results identify several phosphate transporters (i.e., PHO1), purple acid phosphatases, and SYG1/PHO81/XPR1 (SPX) domain-containing proteins out of a total of 1740 differentially expressed genes (DEGs). In particular, the transcription factor ethylene response factor (ERF), basic helix-loop-helix (bHLH), and WRKY family genes were the three most abundant DEG groups and the latter was significantly enriched. Comparative transcriptome analysis of Brachypodium versus Arabidopsis and rice revealed the presence of several common components in response to Pi fluctuations. Most significantly, jasmonic acid (JA) signaling-related genes were overrepresented in gene ontology (GO) enrichment tests. The presence of a possible link between low Pi response, inositol polyphosphates, and JA signaling is therefore discussed.
Collapse
Affiliation(s)
- Pengshan Zhao
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China; Shapotou Desert Research & Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
| | - Lirong Wang
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
| | - Hengxia Yin
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China.
| |
Collapse
|
12
|
Onda Y, Takahagi K, Shimizu M, Inoue K, Mochida K. Multiplex PCR Targeted Amplicon Sequencing (MTA-Seq): Simple, Flexible, and Versatile SNP Genotyping by Highly Multiplexed PCR Amplicon Sequencing. FRONTIERS IN PLANT SCIENCE 2018; 9:201. [PMID: 29628929 PMCID: PMC5876661 DOI: 10.3389/fpls.2018.00201] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 02/02/2018] [Indexed: 05/20/2023]
Abstract
Next-generation sequencing (NGS) technologies have enabled genome re-sequencing for exploring genome-wide polymorphisms among individuals, as well as targeted re-sequencing for the rapid and simultaneous detection of polymorphisms in genes associated with various biological functions. Therefore, a simple and robust method for targeted re-sequencing should facilitate genotyping in a wide range of biological fields. In this study, we developed a simple, custom, targeted re-sequencing method, designated "multiplex PCR targeted amplicon sequencing (MTA-seq)," and applied it to the genotyping of the model grass Brachypodium distachyon. To assess the practical usability of MTA-seq, we applied it to the genotyping of genome-wide single-nucleotide polymorphisms (SNPs) identified in natural accessions (Bd1-1, Bd3-1, Bd21-3, Bd30-1, Koz-1, Koz-3, and Koz-4) by comparing the re-sequencing data with that of reference accession Bd21. Examination of SNP-genotyping accuracy in 443 amplicons from eight parental accessions and an F1 progeny derived by crossing of Bd21 and Bd3-1 revealed that ~95% of the SNPs were correctly called. The assessment suggested that the method provided an efficient framework for accurate and robust SNP genotyping. The method described here enables easy design of custom target SNP-marker panels in various organisms, facilitating a wide range of high-throughput genetic applications, such as genetic mapping, population analysis, molecular breeding, and genomic diagnostics.
Collapse
Affiliation(s)
- Yoshihiko Onda
- Cellulose Production Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Kotaro Takahagi
- Cellulose Production Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan
| | - Minami Shimizu
- Cellulose Production Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Komaki Inoue
- Cellulose Production Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Keiichi Mochida
- Cellulose Production Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- Institute of Plant Science and Resource, Okayama University, Okayama, Japan
- *Correspondence: Keiichi Mochida
| |
Collapse
|
13
|
Wu M, Liu H, Han G, Cai R, Pan F, Xiang Y. A moso bamboo WRKY gene PeWRKY83 confers salinity tolerance in transgenic Arabidopsis plants. Sci Rep 2017; 7:11721. [PMID: 28916739 PMCID: PMC5601430 DOI: 10.1038/s41598-017-10795-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 08/15/2017] [Indexed: 11/24/2022] Open
Abstract
The WRKY family are transcription factors, involved in plant development, and response to biotic and abiotic stresses. Moso bamboo is an important bamboo that has high ecological, economic and cultural value and is widely distributed in the south of China. In this study, we performed a genome-wide identification of WRKY members in moso bamboo and identified 89 members. By comparative analysis in six grass genomes, we found the WRKY gene family may have experienced or be experiencing purifying selection. Based on relative expression levels among WRKY IIc members under three abiotic stresses, PeWRKY83 functioned as a transcription factor and was selected for detailed analysis. The transgenic Arabidopsis of PeWRKY83 showed superior physiological properties compared with the WT under salt stress. Overexpression plants were less sensitive to ABA at both germination and postgermination stages and accumulated more endogenous ABA under salt stress conditions. Further studies demonstrated that overexpression of PeWRKY83 could regulate the expression of some ABA biosynthesis genes (AtAAO3, AtNCED2, AtNCED3), signaling genes (AtABI1, AtPP2CA) and responsive genes (AtRD29A, AtRD29B, AtABF1) under salt stress. Together, these results suggested that PeWRKY83 functions as a novel WRKY-related TF which plays a positive role in salt tolerance by regulating stress-induced ABA synthesis.
Collapse
Affiliation(s)
- Min Wu
- National Engineering Laboratory of Crop Stresses Resistance Breeding, Anhui Agricultural University, Hefei, 230036, China
| | - Huanlong Liu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Guomin Han
- National Engineering Laboratory of Crop Stresses Resistance Breeding, Anhui Agricultural University, Hefei, 230036, China
| | - Ronghao Cai
- National Engineering Laboratory of Crop Stresses Resistance Breeding, Anhui Agricultural University, Hefei, 230036, China
| | - Feng Pan
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Yan Xiang
- National Engineering Laboratory of Crop Stresses Resistance Breeding, Anhui Agricultural University, Hefei, 230036, China. xiangyanahau.@sina.com.,Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. xiangyanahau.@sina.com
| |
Collapse
|
14
|
Niu X, Guan Y, Chen S, Li H. Genome-wide analysis of basic helix-loop-helix (bHLH) transcription factors in Brachypodium distachyon. BMC Genomics 2017; 18:619. [PMID: 28810832 PMCID: PMC5558667 DOI: 10.1186/s12864-017-4044-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/09/2017] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND As a superfamily of transcription factors (TFs), the basic helix-loop-helix (bHLH) proteins have been characterized functionally in many plants with a vital role in the regulation of diverse biological processes including growth, development, response to various stresses, and so on. However, no systemic analysis of the bHLH TFs has been reported in Brachypodium distachyon, an emerging model plant in Poaceae. RESULTS A total of 146 bHLH TFs were identified in the Brachypodium distachyon genome and classified into 24 subfamilies. BdbHLHs in the same subfamily share similar protein motifs and gene structures. Gene duplication events showed a close relationship to rice, maize and sorghum, and segment duplications might play a key role in the expansion of this gene family. The amino acid sequence of the bHLH domains were quite conservative, especially Leu-27 and Leu-54. Based on the predicted binding activities, the BdbHLHs were divided into DNA binding and non-DNA binding types. According to the gene ontology (GO) analysis, BdbHLHs were speculated to function in homodimer or heterodimer manner. By integrating the available high throughput data in public database and results of quantitative RT-PCR, we found the expression profiles of BdbHLHs were different, implying their differentiated functions. CONCLUSION One hundred fourty-six BdbHLHs were identified and their conserved domains, sequence features, phylogenetic relationship, chromosomal distribution, GO annotations, gene structures, gene duplication and expression profiles were investigated. Our findings lay a foundation for further evolutionary and functional elucidation of BdbHLH genes.
Collapse
Affiliation(s)
- Xin Niu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Yuxiang Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Shoukun Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Haifeng Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
- Xinjiang Agricultural Vocational Technical College, Changji, China
| |
Collapse
|
15
|
Marques I, Shiposha V, López-Alvarez D, Manzaneda AJ, Hernandez P, Olonova M, Catalán P. Environmental isolation explains Iberian genetic diversity in the highly homozygous model grass Brachypodium distachyon. BMC Evol Biol 2017; 17:139. [PMID: 28619047 PMCID: PMC5472904 DOI: 10.1186/s12862-017-0996-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 06/08/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Brachypodium distachyon (Poaceae), an annual Mediterranean Aluminum (Al)-sensitive grass, is currently being used as a model species to provide new information on cereals and biofuel crops. The plant has a short life cycle and one of the smallest genomes in the grasses being well suited to experimental manipulation. Its genome has been fully sequenced and several genomic resources are being developed to elucidate key traits and gene functions. A reliable germplasm collection that reflects the natural diversity of this species is therefore needed for all these genomic resources. However, despite being a model plant, we still know very little about its genetic diversity. As a first step to overcome this gap, we used nuclear Simple Sequence Repeats (nSSR) to study the patterns of genetic diversity and population structure of B. distachyon in 14 populations sampled across the Iberian Peninsula (Spain), one of its best known areas. RESULTS We found very low levels of genetic diversity, allelic number and heterozygosity in B. distachyon, congruent with a highly selfing system. Our results indicate the existence of at least three genetic clusters providing additional evidence for the existence of a significant genetic structure in the Iberian Peninsula and supporting this geographical area as an important genetic reservoir. Several hotspots of genetic diversity were detected and populations growing on basic soils were significantly more diverse than those growing in acidic soils. A partial Mantel test confirmed a statistically significant Isolation-By-Distance (IBD) among all studied populations, as well as a statistically significant Isolation-By-Environment (IBE) revealing the presence of environmental-driven isolation as one explanation for the genetic patterns found in the Iberian Peninsula. CONCLUSIONS The finding of higher genetic diversity in eastern Iberian populations occurring in basic soils suggests that these populations can be better adapted than those occurring in western areas of the Iberian Peninsula where the soils are more acidic and accumulate toxic Al ions. This suggests that the western Iberian acidic soils might prevent the establishment of Al-sensitive B. distachyon populations, potentially causing the existence of more genetically depauperated individuals.
Collapse
Affiliation(s)
- Isabel Marques
- Departamento de Ciencias Agrarias y del Medio Natural, Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Ctra. Cuarte km 1, 22071, Huesca, Spain.
| | - Valeriia Shiposha
- Departamento de Ciencias Agrarias y del Medio Natural, Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Ctra. Cuarte km 1, 22071, Huesca, Spain
- Department of Botany, Institute of Biology, Tomsk State University, Lenin Av. 36, Tomsk, 634050, Russia
| | - Diana López-Alvarez
- Departamento de Ciencias Agrarias y del Medio Natural, Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Ctra. Cuarte km 1, 22071, Huesca, Spain
- Present address: Centro de Bioinformática y Biología Computacional de Colombia, BIOS, Parque los Yarumos, Manizales, Colombia
| | - Antonio J Manzaneda
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Paraje Las Lagunillas s⁄n, 23071, Jaén, Spain
| | - Pilar Hernandez
- Instituto de Agricultura Sostenible (IAS-CSIC), Alameda del Obispo s/n, 14004, Córdoba, Spain
| | - Marina Olonova
- Department of Botany, Institute of Biology, Tomsk State University, Lenin Av. 36, Tomsk, 634050, Russia
| | - Pilar Catalán
- Departamento de Ciencias Agrarias y del Medio Natural, Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Ctra. Cuarte km 1, 22071, Huesca, Spain
- Department of Botany, Institute of Biology, Tomsk State University, Lenin Av. 36, Tomsk, 634050, Russia
| |
Collapse
|
16
|
Comparative and Evolutionary Analysis of Grass Pollen Allergens Using Brachypodium distachyon as a Model System. PLoS One 2017; 12:e0169686. [PMID: 28103252 PMCID: PMC5245863 DOI: 10.1371/journal.pone.0169686] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/19/2016] [Indexed: 11/23/2022] Open
Abstract
Comparative genomics have facilitated the mining of biological information from a genome sequence, through the detection of similarities and differences with genomes of closely or more distantly related species. By using such comparative approaches, knowledge can be transferred from the model to non-model organisms and insights can be gained in the structural and evolutionary patterns of specific genes. In the absence of sequenced genomes for allergenic grasses, this study was aimed at understanding the structure, organisation and expression profiles of grass pollen allergens using the genomic data from Brachypodium distachyon as it is phylogenetically related to the allergenic grasses. Combining genomic data with the anther RNA-Seq dataset revealed 24 pollen allergen genes belonging to eight allergen groups mapping on the five chromosomes in B. distachyon. High levels of anther-specific expression profiles were observed for the 24 identified putative allergen-encoding genes in Brachypodium. The genomic evidence suggests that gene encoding the group 5 allergen, the most potent trigger of hay fever and allergic asthma originated as a pollen specific orphan gene in a common grass ancestor of Brachypodium and Triticiae clades. Gene structure analysis showed that the putative allergen-encoding genes in Brachypodium either lack or contain reduced number of introns. Promoter analysis of the identified Brachypodium genes revealed the presence of specific cis-regulatory sequences likely responsible for high anther/pollen-specific expression. With the identification of putative allergen-encoding genes in Brachypodium, this study has also described some important plant gene families (e.g. expansin superfamily, EF-Hand family, profilins etc) for the first time in the model plant Brachypodium. Altogether, the present study provides new insights into structural characterization and evolution of pollen allergens and will further serve as a base for their functional characterization in related grass species.
Collapse
|
17
|
Luo N, Yu X, Nie G, Liu J, Jiang Y. Specific peroxidases differentiate Brachypodium distachyon accessions and are associated with drought tolerance traits. ANNALS OF BOTANY 2016; 118:259-70. [PMID: 27325900 PMCID: PMC4970367 DOI: 10.1093/aob/mcw104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 02/08/2016] [Accepted: 04/04/2016] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Brachypodium distachyon (Brachypodium) is a model system for studying cereal, bioenergy, forage and turf grasses. The genetic and evolutionary basis of the adaptation of this wild grass species to drought stress is largely unknown. Peroxidase (POD) may play a role in plant drought tolerance, but whether the allelic variations of genes encoding the specific POD isoenzymes are associated with plant response to drought stress is not well understood. The objectives of this study were to examine natural variation of POD isoenzyme patterns, to identify nucleotide diversity of POD genes and to relate the allelic variation of genes to drought tolerance traits of diverse Brachypodium accessions. METHODS Whole-plant drought tolerance and POD activity were examined in contrasting ecotypes. Non-denaturing PAGE and liquid chromatography-mass spectrometry were performed to detect distinct isozymes of POD in 34 accessions. Single nucleotide polymorphisms (SNPs) were identified by comparing DNA sequences of these accessions. Associations of POD genes encoding specific POD isoenzymes with drought tolerance traits were analysed using TASSEL software. KEY RESULTS Variations of POD isoenzymes were found among accessions with contrasting drought tolerance, while the most tolerant and susceptible accessions each had their own unique POD isoenzyme band. Eight POD genes were identified and a total of 90 SNPs were found among these genes across 34 accessions. After controlling population structure, significant associations of Bradi3g41340.1 and Bradi1g26870.1 with leaf water content or leaf wilting were identified. CONCLUSIONS Brachypodium ecotypes have distinct specific POD isozymes. This may contribute to natural variations of drought tolerance of this species. The role of specific POD genes in differentiating Brachypodium accessions with contrasting drought tolerance could be associated with the general fitness of Brachypodium during evolution.
Collapse
Affiliation(s)
- Na Luo
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xiaoqing Yu
- Department of Agronomy, Iowa State University, Ames IA 50011, USA
| | - Gang Nie
- Department of Grassland Science, Sichuan Agricultural University, Chengdu 611130, China
| | - Jianxiu Liu
- Institute of Botany, Jiangsu Province & Chinese Academy of Science, Nanjing 210014, China
| | - Yiwei Jiang
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
| |
Collapse
|
18
|
Onda Y, Hashimoto K, Yoshida T, Sakurai T, Sawada Y, Hirai MY, Toyooka K, Mochida K, Shinozaki K. Determination of growth stages and metabolic profiles in Brachypodium distachyon for comparison of developmental context with Triticeae crops. Proc Biol Sci 2016; 282:rspb.2015.0964. [PMID: 26156770 PMCID: PMC4528556 DOI: 10.1098/rspb.2015.0964] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Brachypodium distachyon is an emerging model plant for studying biological phenomena in temperate grasses. Study of the growth scale is essential to analyse spatio-temporal changes in molecular factors throughout the life cycle. For sensitive and robust staging based on morphology in B. distachyon, we demonstrated the utility of the BBCH (Biologische Bundesanstalt, Bundessortenamt and CHemical industry) scale, which is comparable to the Zadoks scale conventionally used for Triticeae crops. We compared the chronological progression of B. distachyon accessions Bd21 and Bd3-1, in addition to the progression of Chinese Spring wheat. The comparison of growth stages illustrates the morphological similarities and differences in the timing of life cycle events. Furthermore, we compared metabolite accumulation patterns across different growth stages and across different stress conditions using a widely targeted metabolome analysis. Metabolic profiling determined commonalities and specificities in chemical properties that were dependent on organisms, growth stages and/or stress conditions. Most metabolites accumulated equivalently in B. distachyon and wheat. This qualitative similarity indicated the superiority of B. distachyon as a model for Triticeae crops. The growth scale of B. distachyon should provide a conceptual framework for comparative analysis and for knowledge integration between this model grass and crops in the Pooideae subfamily.
Collapse
Affiliation(s)
- Yoshihiko Onda
- Cellulose Production Research Team, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan Kihara Institute for Biological Research, Yokohama City University, Kanagawa, Japan
| | - Kei Hashimoto
- Technology Platform Division, Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Takuhiro Yoshida
- Integrated Genome Informatics Research Unit, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Tetsuya Sakurai
- Integrated Genome Informatics Research Unit, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Yuji Sawada
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Masami Yokota Hirai
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Kiminori Toyooka
- Technology Platform Division, Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Keiichi Mochida
- Cellulose Production Research Team, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan Kihara Institute for Biological Research, Yokohama City University, Kanagawa, Japan
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan Biomass Research Platform Team, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| |
Collapse
|
19
|
Ho-Yue-Kuang S, Alvarado C, Antelme S, Bouchet B, Cézard L, Le Bris P, Legée F, Maia-Grondard A, Yoshinaga A, Saulnier L, Guillon F, Sibout R, Lapierre C, Chateigner-Boutin AL. Mutation in Brachypodium caffeic acid O-methyltransferase 6 alters stem and grain lignins and improves straw saccharification without deteriorating grain quality. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:227-37. [PMID: 26433202 PMCID: PMC4682429 DOI: 10.1093/jxb/erv446] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Cereal crop by-products are a promising source of renewable raw material for the production of biofuel from lignocellulose. However, their enzymatic conversion to fermentable sugars is detrimentally affected by lignins. Here the characterization of the Brachypodium Bd5139 mutant provided with a single nucleotide mutation in the caffeic acid O-methyltransferase BdCOMT6 gene is reported. This BdCOMT6-deficient mutant displayed a moderately altered lignification in mature stems. The lignin-related BdCOMT6 gene was also found to be expressed in grains, and the alterations of Bd5139 grain lignins were found to mirror nicely those evidenced in stem lignins. The Bd5139 grains displayed similar size and composition to the control. Complementation experiments carried out by introducing the mutated gene into the AtCOMT1-deficient Arabidopsis mutant demonstrated that the mutated BdCOMT6 protein was still functional. Such a moderate down-regulation of lignin-related COMT enzyme reduced the straw recalcitrance to saccharification, without compromising the vegetative or reproductive development of the plant.
Collapse
Affiliation(s)
- Séverine Ho-Yue-Kuang
- INRA-UR1268 Biopolymères, Interactions, Assemblages, F-44316 Nantes, France INRA-UMR1318, Institut Jean-Pierre Bourgin, F-78026 Versailles, France
| | - Camille Alvarado
- INRA-UR1268 Biopolymères, Interactions, Assemblages, F-44316 Nantes, France
| | - Sébastien Antelme
- INRA-UMR1318, Institut Jean-Pierre Bourgin, F-78026 Versailles, France
| | - Brigitte Bouchet
- INRA-UR1268 Biopolymères, Interactions, Assemblages, F-44316 Nantes, France
| | - Laurent Cézard
- INRA-UMR1318, Institut Jean-Pierre Bourgin, F-78026 Versailles, France
| | - Philippe Le Bris
- INRA-UMR1318, Institut Jean-Pierre Bourgin, F-78026 Versailles, France
| | - Frédéric Legée
- INRA-UMR1318, Institut Jean-Pierre Bourgin, F-78026 Versailles, France
| | | | - Arata Yoshinaga
- Laboratory of Tree Cell Biology, Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Luc Saulnier
- INRA-UR1268 Biopolymères, Interactions, Assemblages, F-44316 Nantes, France
| | - Fabienne Guillon
- INRA-UR1268 Biopolymères, Interactions, Assemblages, F-44316 Nantes, France
| | - Richard Sibout
- INRA-UMR1318, Institut Jean-Pierre Bourgin, F-78026 Versailles, France
| | | | | |
Collapse
|
20
|
|
21
|
Sharma A, Singh MB, Bhalla PL. Ultrastructure of microsporogenesis and microgametogenesis in Brachypodium distachyon. PROTOPLASMA 2015; 252:1575-86. [PMID: 25772681 DOI: 10.1007/s00709-015-0793-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 03/02/2015] [Indexed: 05/05/2023]
Abstract
Brachypodium distachyon has emerged as a model system for forage grass and cereal grain species. Here, we report B. distachyon pollen development at the ultrastructural level. The process of microsporogenesis and microgametogenesis in B. distachyon follows the typical angiosperm pollen development sequence. Pronounced evaginations of the nuclear envelope are observed prior to meiosis, indicating active nucleocytoplasmic exchange processes. The microspore mother cells undergo meiosis and subsequent cytokinesis, forming isobilateral tetrads. Following dissolution of the callose wall and release of free and vacuolated microspores, mitotic divisions lead to the formation of mature, three-celled pollen grains. In B. distachyon, pollen wall formation begins at the tetrad stage by the formation of the exine template (primexine). The exine is tectate-columellate, comprising a foot layer and endexine. Development of the tectum and the foot layer is complete by the free microspore stage of development, with the tectum formed discontinuously. The endexine initiates in the free microspore stage but becomes compressed in mature grains. The intine layer is deposited after mitosis and comprises three layers during the mature pollen stage of development. Pore development initiates during early free microspore development stage and Brachypodium pollen has a single germination pore consisting of a slightly raised annulus surrounding a central operculum. The tapetum is of the secretory type with loss of the tapetal cell walls beginning at about the time of microsporocyte meiosis. This is the first report on ultrastructure of microsporogenesis and microgametogenesis in B. distachyon. In general, Brachypodium microsporogenesis and microgametogenesis conform to a typical grass pollen development pattern.
Collapse
Affiliation(s)
- Akanksha Sharma
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
| | - Mohan B Singh
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
| | - Prem L Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia.
| |
Collapse
|
22
|
Zhu G, Chen G, Zhu J, Zhu Y, Lu X, Li X, Hu Y, Yan Y. Molecular Characterization and Expression Profiling of NAC Transcription Factors in Brachypodium distachyon L. PLoS One 2015; 10:e0139794. [PMID: 26444425 PMCID: PMC4596864 DOI: 10.1371/journal.pone.0139794] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 09/17/2015] [Indexed: 12/19/2022] Open
Abstract
NAC (NAM, ATAF1/2, CUC2) transcription factors are involved in regulating plant developmental processes and response to environmental stresses. Brachypodium distachyon is an emerging model system for cereals, temperate grasses and biofuel crops. In this study, a comprehensive investigation of the molecular characterizations, phylogenetics and expression profiles under various abiotic stresses of the NAC gene family in Brachypodium distachyon was performed. In total, 118 BNAC genes in B. distachyon were identified, of which 22 (18.64%) were tandemly duplicated and segmentally duplicated, respectively. The Bayesian phylogenetic inference using Markov Chain Monte Carlo (MCMC) algorithms showed that they were divided into two clades and fourteen subfamilies, supported by similar motif compositions within one subfamily. Some critical amino acids detected using DIVERGE v3.0 might contribute to functional divergence among subfamilies. The different exon-intron organizations among subfamilies revealed structural differentiation. Promoter sequence predictions showed that the BNAC genes were involved in various developmental processes and diverse stress responses. Three NAC domain-encoding genes (BNAC012, BNAC078 and BNAC108), orthologous of NAC1, were targeted by five miRNA164 (Bdi-miR164a-c, e, f), suggesting that they might function in lateral organ enlargement, floral development and the responses to abiotic stress. Eleven (~9.32%) BNAC proteins containing α-helical transmembrane motifs were identified. 23 representative BNAC genes were analyzed by quantitative real-time PCR, showing different expression patterns under various abiotic stresses, of which 18, 17 and 11 genes were up-regulated significantly under drought, H2O2 and salt stresses, respectively. Only four and two genes were up-regulated under cold and cadmium stresses, respectively. Dynamic transcriptional expression analysis revealed that six genes showed constitutive expression and period-specific expression. The current results provide novel insights into the structure and function of the plant NAC gene family.
Collapse
Affiliation(s)
- Gengrui Zhu
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Guanxing Chen
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Jiantang Zhu
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Yan Zhu
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Xiaobing Lu
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Xiaohui Li
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Yingkao Hu
- College of Life Science, Capital Normal University, Beijing, 100048, China
- * E-mail: (YH); (YY)
| | - Yueming Yan
- College of Life Science, Capital Normal University, Beijing, 100048, China
- * E-mail: (YH); (YY)
| |
Collapse
|
23
|
He SL, Yang Y, Morrell PL, Yi TS. Nucleotide Sequence Diversity and Linkage Disequilibrium of Four Nuclear Loci in Foxtail Millet (Setaria italica). PLoS One 2015; 10:e0137088. [PMID: 26325578 PMCID: PMC4556640 DOI: 10.1371/journal.pone.0137088] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 08/13/2015] [Indexed: 11/18/2022] Open
Abstract
Foxtail millet (Setaria italica (L.) Beauv) is one of the earliest domesticated grains, which has been cultivated in northern China by 8,700 years before present (YBP) and across Eurasia by 4,000 YBP. Owing to a small genome and diploid nature, foxtail millet is a tractable model crop for studying functional genomics of millets and bioenergy grasses. In this study, we examined nucleotide sequence diversity, geographic structure, and levels of linkage disequilibrium at four nuclear loci (ADH1, G3PDH, IGS1 and TPI1) in representative samples of 311 landrace accessions across its cultivated range. Higher levels of nucleotide sequence and haplotype diversity were observed in samples from China relative to other sampled regions. Genetic assignment analysis classified the accessions into seven clusters based on nucleotide sequence polymorphisms. Intralocus LD decayed rapidly to half the initial value within ~1.2 kb or less.
Collapse
Affiliation(s)
- Shui-lian He
- China Southwestern Germplasm Bank of Wild Species, the Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Landscape and Horticulture College, Yunnan Agriculture University, Kunming, Yunnan, China
| | - Yang Yang
- China Southwestern Germplasm Bank of Wild Species, the Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Peter L. Morrell
- Department of Agronomy & Plant genetics, 411 Borlaug Hall, 1991 Upper Buford Circle, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Ting-shuang Yi
- China Southwestern Germplasm Bank of Wild Species, the Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| |
Collapse
|
24
|
O'Driscoll A, Doohan F, Mullins E. Exploring the utility of Brachypodium distachyon as a model pathosystem for the wheat pathogen Zymoseptoria tritici. BMC Res Notes 2015; 8:132. [PMID: 25888730 PMCID: PMC4397700 DOI: 10.1186/s13104-015-1097-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 03/26/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Zymoseptoria tritici, the causative organism of Septoria tritici blotch disease is a prevalent biotic stressor of wheat production, exerting substantial economic constraints on farmers, requiring intensive chemical control to protect yields. A hemibiotrophic pathogen with a long asymptomless phase of up to 11 days post inoculation (dpi) before a rapid switch to necrotrophy; a deficit exists in our understanding of the events occurring within the host during the two phases of infection. Brachypodium distachyon has demonstrated its potential as a model species for the investigation of fungal disease resistance in cereal and grass species. The aim of this study was to assess the physical interaction between Z. tritici (strain IPO323) and B. distachyon and examine its potential as a model pathosystem for Z. tritici. RESULTS Septoria tritici blotch symptoms developed on the wheat cultivar Riband from 12 dpi with pycnidial formation abundant by 20 dpi. Symptoms on B. distachyon ecotype Bd21-1 were visible from 1 dpi: characteristic pale, water soaked lesions which developed into blotch-like lesions by 4 dpi. These lesions then became necrotic with chlorotic regions expanding up to 7 dpi. Sporulation on B. distachyon tissues was not observed and no evidence of fungal penetration could be obtained, indicating that Z. tritici was unable to complete its life cycle within B. distachyon ecotypes. However, observation of host responses to the Z. tritici strain IPO323 in five B. distachyon ecotypes revealed a variation in resistance responses, ranging from immunity to a chlorotic/necrotic phenotype. CONCLUSIONS The observed interactions suggest that B. distachyon is an incompatible host for Z. tritici infection, with STB symptom development on B. distachyon comparable to that observed during the early infection stages on the natural host, wheat. However first visible symptoms occurred more rapidly on B. distachyon; from 1 dpi in comparison to 12 dpi in wheat. Consequently, we propose that the interaction between B. distachyon and Z. tritici as observed in this study could serve as a suitable model pathosystem with which to investigate mechanisms underpinning an incompatible host response to Z. tritici.
Collapse
Affiliation(s)
- Aoife O'Driscoll
- Department of Crop Science, Teagasc Research Centre, Oak Park, Carlow, Ireland.
- UCD Earth Institute and UCD School of Biology and Environmental Sciences, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Fiona Doohan
- UCD Earth Institute and UCD School of Biology and Environmental Sciences, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Ewen Mullins
- Department of Crop Science, Teagasc Research Centre, Oak Park, Carlow, Ireland.
| |
Collapse
|
25
|
Sharma A, Singh MB, Bhalla PL. Anther ontogeny in Brachypodium distachyon. PROTOPLASMA 2015; 252:439-50. [PMID: 25149150 DOI: 10.1007/s00709-014-0689-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 08/13/2014] [Indexed: 05/07/2023]
Abstract
Brachypodium distachyon has emerged as a model plant for the improvement of grain crops such as wheat, barley and oats and for understanding basic biological processes to facilitate the development of grasses as superior energy crops. Brachypodium is also the first species of the grass subfamily Pooideae with a sequenced genome. For obtaining a better understanding of the mechanisms controlling male gametophyte development in B. distachyon, here we report the cellular changes during the stages of anther development, with special reference to the development of the anther wall. Brachypodium anthers are tetrasporangiate and follow the typical monocotyledonous-type anther wall formation pattern. Anther differentiation starts with the appearance of archesporial cells, which divide to generate primary parietal and primary sporogenous cells. The primary parietal cells form two secondary parietal layers. Later, the outer secondary parietal layer directly develops into the endothecium and the inner secondary parietal layer forms an outer middle layer and inner tapetum by periclinal division. The anther wall comprises an epidermis, endothecium, middle layer and the secretory-type tapetum. Major documented events of anther development include the degradation of a secretory-type tapetum and middle layer during the course of development and the rapid formation of U-shaped endothecial thickenings in the mature pollen grain stage. The tapetum undergoes degeneration at the tetrad stage and disintegrates completely at the bicellular stage of pollen development. The distribution of insoluble polysaccharides in the anther layers and connective tissue through progressive developmental stages suggests their role in the development of male gametophytes. Until sporogenous cell stage, the amount of insoluble polysaccharides in the anther wall was negligible. However, abundant levels of insoluble polysaccharides were observed during microspore mother cell and tetrad stages and gradually declined during the free microspore and vacuolated microspore stages to undetectable level at the mature stage. Thus, the cellular features in the development of anthers in B. distachyon share similarities with anther and pollen development of other members of Poaceae.
Collapse
Affiliation(s)
- Akanksha Sharma
- Plant Molecular Biology and Biotechnology Laboratory, Melbourne School of Land and Environment, University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
| | | | | |
Collapse
|
26
|
The Genus Brachypodium as a Model for Perenniality and Polyploidy. GENETICS AND GENOMICS OF BRACHYPODIUM 2015. [DOI: 10.1007/7397_2015_19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
27
|
Tanackovic V, Svensson JT, Jensen SL, Buléon A, Blennow A. The deposition and characterization of starch in Brachypodium distachyon. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5179-92. [PMID: 25056772 PMCID: PMC4157704 DOI: 10.1093/jxb/eru276] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 05/15/2014] [Accepted: 05/21/2014] [Indexed: 05/26/2023]
Abstract
Brachypodium distachyon is a non-domesticated cereal. Nonetheless, Brachypodium was recently introduced as a model plant for temperate cereals. This study compares grain starch metabolism in Brachypodium and barley (Hordeum vulgare). In Brachypodium, we identified and annotated 28 genes involved in starch metabolism and identified important motifs including transit peptides and putative carbohydrate-binding modules (CBMs) of the families CBM20, CBM45, CBM48, and CBM53. Starch content was markedly lower in Brachypodium grains (12%) compared to barley grains (47%). Brachypodium starch granules were doughnut shaped and bimodally distributed into distinct small B-type (2.5-10 µm) and very small C-type (0.5-2.5 µm) granules. Large A-type granules, typical of cereals, were absent. Starch-bound phosphate, important for starch degradation, was 2-fold lower in Brachypodium compared with barley indicating different requirements for starch mobilization. The amylopectin branch profiles were similar and the amylose content was only slightly higher compared with barley cv. Golden Promise. The crystallinity of Brachypodium starch granules was low (10%) compared to barley (20%) as determined by wide-angle X-ray scattering (WAXS) and molecular disorder was confirmed by differential scanning calorimetry (DSC). The expression profiles in grain for most genes were distinctly different for Brachypodium compared to barley, typically showing earlier decline during the course of development, which can explain the low starch content and differences in starch molecular structure and granule characteristics. High transitory starch levels were observed in leaves of Brachypodium (2.8% after 14h of light) compared to barley (1.9% after 14h of light). The data suggest important pre-domesticated features of cereals.
Collapse
Affiliation(s)
- Vanja Tanackovic
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, DK-1871, Denmark
| | - Jan T Svensson
- Nordic Genetic Resource Centre, P.O. Box 41, SE-230 53 Alnarp, Sweden
| | - Susanne L Jensen
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, DK-1871, Denmark
| | - Alain Buléon
- UR1268 Biopolymeres Interactions Assemblages, INRA, F-44300 Nantes, France
| | - Andreas Blennow
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, DK-1871, Denmark
| |
Collapse
|
28
|
Girin T, David LC, Chardin C, Sibout R, Krapp A, Ferrario-Méry S, Daniel-Vedele F. Brachypodium: a promising hub between model species and cereals. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5683-96. [PMID: 25262566 DOI: 10.1093/jxb/eru376] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Brachypodium distachyon was proposed as a model species for genetics and molecular genomics in cereals less than 10 years ago. It is now established as a standard for research on C3 cereals on a variety of topics, due to its close phylogenetic relationship with Triticeae crops such as wheat and barley, and to its simple genome, its minimal growth requirement, and its short life cycle. In this review, we first highlight the tools and resources for Brachypodium that are currently being developed and made available by the international community. We subsequently describe how this species has been used for comparative genomic studies together with cereal crops, before illustrating major research fields in which Brachypodium has been successfully used as a model: cell wall synthesis, plant-pathogen interactions, root architecture, and seed development. Finally, we discuss the usefulness of research on Brachypodium in order to improve nitrogen use efficiency in cereals, with the aim of reducing the amount of applied fertilizer while increasing the grain yield. Several paths are considered, namely an improvement of either nitrogen remobilization from the vegetative organs, nitrate uptake from the soil, or nitrate assimilation by the plant. Altogether, these examples position the research on Brachypodium as at an intermediate stage between basic research, carried out mainly in Arabidopsis, and applied research carried out on wheat and barley, enabling a complementarity of the studies and reciprocal benefits.
Collapse
Affiliation(s)
- Thomas Girin
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Laure C David
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Camille Chardin
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Richard Sibout
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Anne Krapp
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Sylvie Ferrario-Méry
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Françoise Daniel-Vedele
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| |
Collapse
|
29
|
Meineke T, Manisseri C, Voigt CA. Phylogeny in defining model plants for lignocellulosic ethanol production: a comparative study of Brachypodium distachyon, wheat, maize, and Miscanthus x giganteus leaf and stem biomass. PLoS One 2014; 9:e103580. [PMID: 25133818 PMCID: PMC4136770 DOI: 10.1371/journal.pone.0103580] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 07/04/2014] [Indexed: 12/26/2022] Open
Abstract
The production of ethanol from pretreated plant biomass during fermentation is a strategy to mitigate climate change by substituting fossil fuels. However, biomass conversion is mainly limited by the recalcitrant nature of the plant cell wall. To overcome recalcitrance, the optimization of the plant cell wall for subsequent processing is a promising approach. Based on their phylogenetic proximity to existing and emerging energy crops, model plants have been proposed to study bioenergy-related cell wall biochemistry. One example is Brachypodium distachyon, which has been considered as a general model plant for cell wall analysis in grasses. To test whether relative phylogenetic proximity would be sufficient to qualify as a model plant not only for cell wall composition but also for the complete process leading to bioethanol production, we compared the processing of leaf and stem biomass from the C3 grasses B. distachyon and Triticum aestivum (wheat) with the C4 grasses Zea mays (maize) and Miscanthus x giganteus, a perennial energy crop. Lambda scanning with a confocal laser-scanning microscope allowed a rapid qualitative analysis of biomass saccharification. A maximum of 108-117 mg ethanol·g(-1) dry biomass was yielded from thermo-chemically and enzymatically pretreated stem biomass of the tested plant species. Principal component analysis revealed that a relatively strong correlation between similarities in lignocellulosic ethanol production and phylogenetic relation was only given for stem and leaf biomass of the two tested C4 grasses. Our results suggest that suitability of B. distachyon as a model plant for biomass conversion of energy crops has to be specifically tested based on applied processing parameters and biomass tissue type.
Collapse
Affiliation(s)
- Till Meineke
- Phytopathology & Biochemistry, Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
| | - Chithra Manisseri
- Phytopathology & Biochemistry, Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
| | - Christian A. Voigt
- Phytopathology & Biochemistry, Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
| |
Collapse
|
30
|
Wen F, Zhu H, Li P, Jiang M, Mao W, Ong C, Chu Z. Genome-wide evolutionary characterization and expression analyses of WRKY family genes in Brachypodium distachyon. DNA Res 2014; 21:327-39. [PMID: 24453041 PMCID: PMC4060952 DOI: 10.1093/dnares/dst060] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Members of plant WRKY gene family are ancient transcription factors that function in plant growth and development and respond to biotic and abiotic stresses. In our present study, we have investigated WRKY family genes in Brachypodium distachyon, a new model plant of family Poaceae. We identified a total of 86 WRKY genes from B. distachyon and explored their chromosomal distribution and evolution, domain alignment, promoter cis-elements, and expression profiles. Combining the analysis of phylogenetic tree of BdWRKY genes and the result of expression profiling, results showed that most of clustered gene pairs had higher similarities in the WRKY domain, suggesting that they might be functionally redundant. Neighbour-joining analysis of 301 WRKY domains from Oryza sativa, Arabidopsis thaliana, and B. distachyon suggested that BdWRKY domains are evolutionarily more closely related to O. sativa WRKY domains than those of A. thaliana. Moreover, tissue-specific expression profile of BdWRKY genes and their responses to phytohormones and several biotic or abiotic stresses were analysed by quantitative real-time PCR. The results showed that the expression of BdWRKY genes was rapidly regulated by stresses and phytohormones, and there was a strong correlation between promoter cis-elements and the phytohormones-induced BdWRKY gene expression.
Collapse
Affiliation(s)
- Feng Wen
- Shanghai Chenshan Plant Science Research Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai Chenshan Botanic Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China
| | - Hong Zhu
- Shanghai Chenshan Plant Science Research Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai Chenshan Botanic Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China
| | - Peng Li
- Shanghai Chenshan Plant Science Research Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai Chenshan Botanic Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China
| | - Min Jiang
- Shanghai Chenshan Plant Science Research Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai Chenshan Botanic Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China
| | - Wenqing Mao
- Shanghai Chenshan Plant Science Research Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai Chenshan Botanic Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China
| | - Chermaine Ong
- Shanghai Chenshan Plant Science Research Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai Chenshan Botanic Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China
| | - Zhaoqing Chu
- Shanghai Chenshan Plant Science Research Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai Chenshan Botanic Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China
| |
Collapse
|
31
|
Ryu JY, Hong SY, Jo SH, Woo JC, Lee S, Park CM. Molecular and functional characterization of cold-responsive C-repeat binding factors from Brachypodium distachyon. BMC PLANT BIOLOGY 2014; 14:15. [PMID: 24405987 PMCID: PMC3898008 DOI: 10.1186/1471-2229-14-15] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 01/08/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Adverse environmental conditions severely influence various aspects of plant growth and developmental processes, causing worldwide reduction of crop yields. The C-repeat binding factors (CBFs) are critical transcription factors constituting the gene regulatory network that mediates the acclimation process to low temperatures. They regulate a large number of cold-responsive genes, including COLD-REGULATED (COR) genes, via the CBF-COR regulon. Recent studies have shown that the CBF transcription factors also play a role in plant responses to drought and salt stresses. Putative CBF gene homologues and their downstream genes are also present in the genome of Brachypodium distachyon, which is perceived as a monocot model in recent years. However, they have not been functionally characterized at the molecular level. RESULTS Three CBF genes that are responsive to cold were identified from Brachypodium, designated BdCBF1, BdCBF2, and BdCBF3, and they were functionally characterized by molecular biological and transgenic approaches in Brachypodium and Arabidopsis thaliana. Our results demonstrate that the BdCBF genes contribute to the tolerance response of Brachypodium to cold, drought, and salt stresses by regulating downstream targets, such as DEHYDRIN5.1 (Dhn5.1) and COR genes. The BdCBF genes are induced under the environmental stress conditions. The BdCBF proteins possess transcriptional activation activity and bind directly to the promoters of the target genes. Transgenic Brachypodium plants overexpressing the BdCBF genes exhibited enhanced resistance to drought and salt stresses as well as low temperatures, and accordingly endogenous contents of proline and soluble sugars were significantly elevated in the transgenic plants. The BdCBF transcription factors are also functional in the heterologous system Arabidopsis. Transgenic Arabidopsis plants overexpressing the BdCBF genes were also tolerant to freezing, drought, and salt stresses, and a set of stress-responsive genes was upregulated in the transgenic Arabidopsis plants. CONCLUSIONS Taken together, our results strongly support that the BdCBF transcription factors are key regulators of cold stress responses in Brachypodium and the CBF-mediated cold stress signaling pathway is conserved in this plant species. We believe that this study would confer great impact on stress biology in monocot species and could be applied to engineer abiotic stress tolerance of bioenergy grass species.
Collapse
Affiliation(s)
- Jae Yong Ryu
- Department of Chemistry, Seoul National University, Seoul 151-742, Korea
| | - Shin-Young Hong
- Department of Chemistry, Seoul National University, Seoul 151-742, Korea
| | - Sin-Hye Jo
- Department of Chemistry, Seoul National University, Seoul 151-742, Korea
| | - Je-Chang Woo
- Department of Biological Science, Mokpo National University, Jeonnam 534-729, Korea
| | - Sangmin Lee
- Department of Chemistry, Seoul National University, Seoul 151-742, Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul 151-742, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-742, Korea
| |
Collapse
|
32
|
Venglat P, Xiang D, Wang E, Datla R. Genomics of seed development: Challenges and opportunities for genetic improvement of seed traits in crop plants. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2014. [DOI: 10.1016/j.bcab.2013.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
33
|
Mochida K, Shinozaki K. Unlocking Triticeae genomics to sustainably feed the future. PLANT & CELL PHYSIOLOGY 2013; 54:1931-50. [PMID: 24204022 PMCID: PMC3856857 DOI: 10.1093/pcp/pct163] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 11/04/2013] [Indexed: 05/23/2023]
Abstract
The tribe Triticeae includes the major crops wheat and barley. Within the last few years, the whole genomes of four Triticeae species-barley, wheat, Tausch's goatgrass (Aegilops tauschii) and wild einkorn wheat (Triticum urartu)-have been sequenced. The availability of these genomic resources for Triticeae plants and innovative analytical applications using next-generation sequencing technologies are helping to revitalize our approaches in genetic work and to accelerate improvement of the Triticeae crops. Comparative genomics and integration of genomic resources from Triticeae plants and the model grass Brachypodium distachyon are aiding the discovery of new genes and functional analyses of genes in Triticeae crops. Innovative approaches and tools such as analysis of next-generation populations, evolutionary genomics and systems approaches with mathematical modeling are new strategies that will help us discover alleles for adaptive traits to future agronomic environments. In this review, we provide an update on genomic tools for use with Triticeae plants and Brachypodium and describe emerging approaches toward crop improvements in Triticeae.
Collapse
Affiliation(s)
- Keiichi Mochida
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 230-0045 Japan
| | - Kazuo Shinozaki
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
| |
Collapse
|
34
|
Mochida K, Uehara-Yamaguchi Y, Takahashi F, Yoshida T, Sakurai T, Shinozaki K. Large-scale collection and analysis of full-length cDNAs from Brachypodium distachyon and integration with Pooideae sequence resources. PLoS One 2013; 8:e75265. [PMID: 24130698 PMCID: PMC3793998 DOI: 10.1371/journal.pone.0075265] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 08/14/2013] [Indexed: 01/09/2023] Open
Abstract
A comprehensive collection of full-length cDNAs is essential for correct structural gene annotation and functional analyses of genes. We constructed a mixed full-length cDNA library from 21 different tissues of Brachypodium distachyon Bd21, and obtained 78,163 high quality expressed sequence tags (ESTs) from both ends of ca. 40,000 clones (including 16,079 contigs). We updated gene structure annotations of Brachypodium genes based on full-length cDNA sequences in comparison with the latest publicly available annotations. About 10,000 non-redundant gene models were supported by full-length cDNAs; ca. 6,000 showed some transcription unit modifications. We also found ca. 580 novel gene models, including 362 newly identified in Bd21. Using the updated transcription start sites, we searched a total of 580 plant cis-motifs in the −3 kb promoter regions and determined a genome-wide Brachypodium promoter architecture. Furthermore, we integrated the Brachypodium full-length cDNAs and updated gene structures with available sequence resources in wheat and barley in a web-accessible database, the RIKEN Brachypodium FL cDNA database. The database represents a “one-stop” information resource for all genomic information in the Pooideae, facilitating functional analysis of genes in this model grass plant and seamless knowledge transfer to the Triticeae crops.
Collapse
Affiliation(s)
- Keiichi Mochida
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, Kanagawa, Japan
- * E-mail:
| | - Yukiko Uehara-Yamaguchi
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Fuminori Takahashi
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Takuhiro Yoshida
- Integrated Genome Informatics Research Unit, RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Tetsuya Sakurai
- Integrated Genome Informatics Research Unit, RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Kazuo Shinozaki
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
| |
Collapse
|
35
|
Walters B, Lum G, Sablok G, Min XJ. Genome-wide landscape of alternative splicing events in Brachypodium distachyon. DNA Res 2013; 20:163-71. [PMID: 23297300 PMCID: PMC3628446 DOI: 10.1093/dnares/dss041] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 12/12/2012] [Indexed: 01/23/2023] Open
Abstract
Recently, Brachypodium distachyon has emerged as a model plant for studying monocot grasses and cereal crops. Using assembled expressed transcript sequences and subsequent mapping to the corresponding genome, we identified 1219 alternative splicing (AS) events spanning across 2021 putatively assembled transcripts generated from 941 genes. Approximately, 6.3% of expressed genes are alternatively spliced in B. distachyon. We observed that a majority of the identified AS events were related to retained introns (55.5%), followed by alternative acceptor sites (16.7%). We also observed a low percentage of exon skipping (5.0%) and alternative donor site events (8.8%). The 'complex event' that consists of a combination of two or more basic splicing events accounted for ∼14.0%. Comparative AS transcript analysis revealed 163 and 39 homologous pairs between B. distachyon and Oryza sativa and between B. distachyon and Arabidopsis thaliana, respectively. In all, we found 16 AS transcripts to be conserved in all 3 species. AS events and related putative assembled transcripts annotation can be systematically browsed at Plant Alternative Splicing Database (http://proteomics.ysu.edu/altsplice/plant/).
Collapse
Affiliation(s)
- Braden Walters
- Department of Computer Science and Information Systems, Youngstown State University, Youngstown, OH 44555, USA
| | - Gengkon Lum
- Department of Computer Science and Information Systems, Youngstown State University, Youngstown, OH 44555, USA
| | - Gaurav Sablok
- Sustainable Agro-ecosystems and Bioresources Department, IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele all'Adige, Trentino 38010, Italy
| | - Xiang Jia Min
- Center for Applied Chemical Biology, Department of Biological Sciences, Youngstown State University, Youngstown, OH 44555, USA
| |
Collapse
|
36
|
Bouvier d'Yvoire M, Bouchabke-Coussa O, Voorend W, Antelme S, Cézard L, Legée F, Lebris P, Legay S, Whitehead C, McQueen-Mason SJ, Gomez LD, Jouanin L, Lapierre C, Sibout R. Disrupting the cinnamyl alcohol dehydrogenase 1 gene (BdCAD1) leads to altered lignification and improved saccharification in Brachypodium distachyon. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 73:496-508. [PMID: 23078216 DOI: 10.1111/tpj.12053] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 10/09/2012] [Accepted: 10/12/2012] [Indexed: 05/17/2023]
Abstract
Brachypodium distachyon (Brachypodium) has been proposed as a model for grasses, but there is limited knowledge regarding its lignins and no data on lignin-related mutants. The cinnamyl alcohol dehydrogenase (CAD) genes involved in lignification are promising targets to improve the cellulose-to-ethanol conversion process. Down-regulation of CAD often induces a reddish coloration of lignified tissues. Based on this observation, we screened a chemically induced population of Brachypodium mutants (Bd21-3 background) for red culm coloration. We identified two mutants (Bd4179 and Bd7591), with mutations in the BdCAD1 gene. The mature stems of these mutants displayed reduced CAD activity and lower lignin content. Their lignins were enriched in 8-O-4- and 4-O-5-coupled sinapaldehyde units, as well as resistant inter-unit bonds and free phenolic groups. By contrast, there was no increase in coniferaldehyde end groups. Moreover, the amount of sinapic acid ester-linked to cell walls was measured for the first time in a lignin-related CAD grass mutant. Functional complementation of the Bd4179 mutant with the wild-type BdCAD1 allele restored the wild-type phenotype and lignification. Saccharification assays revealed that Bd4179 and Bd7591 lines were more susceptible to enzymatic hydrolysis than wild-type plants. Here, we have demonstrated that BdCAD1 is involved in lignification of Brachypodium. We have shown that a single nucleotide change in BdCAD1 reduces the lignin level and increases the degree of branching of lignins through incorporation of sinapaldehyde. These changes make saccharification of cells walls pre-treated with alkaline easier without compromising plant growth.
Collapse
Affiliation(s)
- Madeleine Bouvier d'Yvoire
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 INRA-AgroParisTech, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, Route de St Cyr (RD10), 78026, Versailles, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Mandadi KK, Scholthof KBG. Characterization of a viral synergism in the monocot Brachypodium distachyon reveals distinctly altered host molecular processes associated with disease. PLANT PHYSIOLOGY 2012; 160:1432-52. [PMID: 22961132 PMCID: PMC3490591 DOI: 10.1104/pp.112.204362] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 08/30/2012] [Indexed: 05/05/2023]
Abstract
Panicum mosaic virus (PMV) and its satellite virus (SPMV) together infect several small grain crops, biofuel, and forage and turf grasses. Here, we establish the emerging monocot model Brachypodium (Brachypodium distachyon) as an alternate host to study PMV- and SPMV-host interactions and viral synergism. Infection of Brachypodium with PMV+SPMV induced chlorosis and necrosis of leaves, reduced seed set, caused stunting, and lowered biomass, more than PMV alone. Toward gaining a molecular understanding of PMV- and SPMV-affected host processes, we used a custom-designed microarray and analyzed global changes in gene expression of PMV- and PMV+SPMV-infected plants. PMV infection by itself modulated expression of putative genes functioning in carbon metabolism, photosynthesis, metabolite transport, protein modification, cell wall remodeling, and cell death. Many of these genes were additively altered in a coinfection with PMV+SPMV and correlated to the exacerbated symptoms of PMV+SPMV coinfected plants. PMV+SPMV coinfection also uniquely altered expression of certain genes, including transcription and splicing factors. Among the host defenses commonly affected in PMV and PMV+SPMV coinfections, expression of an antiviral RNA silencing component, SILENCING DEFECTIVE3, was suppressed. Several salicylic acid signaling components, such as pathogenesis-related genes and WRKY transcription factors, were up-regulated. By contrast, several genes in jasmonic acid and ethylene responses were down-regulated. Strikingly, numerous protein kinases, including several classes of receptor-like kinases, were misexpressed. Taken together, our results identified distinctly altered immune responses in monocot antiviral defenses and provide insights into monocot viral synergism.
Collapse
Affiliation(s)
- Kranthi K. Mandadi
- Department of Plant Pathology and Microbiology, Texas A&M University, 2132 TAMU, College Station, Texas 77843
| | - Karen-Beth G. Scholthof
- Department of Plant Pathology and Microbiology, Texas A&M University, 2132 TAMU, College Station, Texas 77843
| |
Collapse
|
38
|
Chen L, Hu W, Tan S, Wang M, Ma Z, Zhou S, Deng X, Zhang Y, Huang C, Yang G, He G. Genome-wide identification and analysis of MAPK and MAPKK gene families in Brachypodium distachyon. PLoS One 2012; 7:e46744. [PMID: 23082129 PMCID: PMC3474763 DOI: 10.1371/journal.pone.0046744] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 09/04/2012] [Indexed: 01/31/2023] Open
Abstract
MAPK cascades are universal signal transduction modules and play important roles in plant growth, development and in response to a variety of biotic and abiotic stresses. Although MAPKs and MAPKKs have been systematically investigated in several plant species including Arabidopsis, rice and poplar, no systematic analysis has been conducted in the emerging monocot model plant Brachypodium distachyon. In the present study, a total of 16 MAPK genes and 12 MAPKK genes were identified from B. distachyon. An analysis of the genomic evolution showed that both tandem and segment duplications contributed significantly to the expansion of MAPK and MAPKK families. Evolutionary relationships within subfamilies were supported by exon-intron organizations and the architectures of conserved protein motifs. Synteny analysis between B. distachyon and the other two plant species of rice and Arabidopsis showed that only one homolog of B. distachyon MAPKs was found in the corresponding syntenic blocks of Arabidopsis, while 13 homologs of B. distachyon MAPKs and MAPKKs were found in that of rice, which was consistent with the speciation process of the three species. In addition, several interactive protein pairs between the two families in B. distachyon were found through yeast two hybrid assay, whereas their orthologs of a pair in Arabidopsis and other plant species were not found to interact with each other. Finally, expression studies of closely related family members among B. distachyon, Arabidopsis and rice showed that even recently duplicated representatives may fulfill different functions and be involved in different signal pathways. Taken together, our data would provide a foundation for evolutionary and functional characterization of MAPK and MAPKK gene families in B. distachyon and other plant species to unravel their biological roles.
Collapse
Affiliation(s)
- Lihong Chen
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, College of Life Science and Technology, Huazhong University of Science & Technology (HUST), Wuhan, China
| | - Wei Hu
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, College of Life Science and Technology, Huazhong University of Science & Technology (HUST), Wuhan, China
| | - Shenglong Tan
- Services Computing Technology and System Laboratory, Cluster and Grid Computing Laboratory, School of Computer Science and Technology, Huazhong University of Science & Technology (HUST), Wuhan, China
| | - Min Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, College of Life Science and Technology, Huazhong University of Science & Technology (HUST), Wuhan, China
| | - Zhanbing Ma
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, College of Life Science and Technology, Huazhong University of Science & Technology (HUST), Wuhan, China
| | - Shiyi Zhou
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, College of Life Science and Technology, Huazhong University of Science & Technology (HUST), Wuhan, China
| | - Xiaomin Deng
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, College of Life Science and Technology, Huazhong University of Science & Technology (HUST), Wuhan, China
| | - Yang Zhang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, College of Life Science and Technology, Huazhong University of Science & Technology (HUST), Wuhan, China
| | - Chao Huang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, College of Life Science and Technology, Huazhong University of Science & Technology (HUST), Wuhan, China
| | - Guangxiao Yang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, College of Life Science and Technology, Huazhong University of Science & Technology (HUST), Wuhan, China
- * E-mail: (GY); (GH)
| | - Guangyuan He
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, College of Life Science and Technology, Huazhong University of Science & Technology (HUST), Wuhan, China
- * E-mail: (GY); (GH)
| |
Collapse
|
39
|
Hands P, Kourmpetli S, Sharples D, Harris RG, Drea S. Analysis of grain characters in temperate grasses reveals distinctive patterns of endosperm organization associated with grain shape. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:6253-66. [PMID: 23081982 PMCID: PMC3481217 DOI: 10.1093/jxb/ers281] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Members of the core pooids represent the most important crops in temperate zones including wheat, barley, and oats. Their importance as crops is largely due to the grain, particularly the storage capabilities of the endosperm. In this study, a comprehensive survey of grain morphology and endosperm organization in representatives of wild and cultivated species throughout the core pooids was performed. As sister to the core pooid tribes Poeae, Aveneae, Triticeae, and Bromeae within the Pooideae subfamily, Brachypodium provides a taxonomically relevant reference point. Using macroscopic, histological, and molecular analyses distinct patterns of grain tissue organization in these species, focusing on the peripheral and modified aleurone, are described. The results indicate that aleurone organization is correlated with conventional grain quality characters such as grain shape and starch content. In addition to morphological and organizational variation, expression patterns of candidate gene markers underpinning this variation were examined. Features commonly associated with grains are largely defined by analyses on lineages within the Triticeae and knowledge of grain structure may be skewed as a result of the focus on wheat and barley. Specifically, the data suggest that the modified aleurone is largely restricted to species in the Triticeae tribe.
Collapse
Affiliation(s)
- Philip Hands
- Biology Department, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Sofia Kourmpetli
- Biology Department, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Donna Sharples
- Biology Department, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Robert G. Harris
- Biology Department, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Sinéad Drea
- To whom correspondence should be addressed. E-mail:
| |
Collapse
|
40
|
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.
Collapse
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:
| |
Collapse
|
41
|
Hong JJ, Park YS, Bravo A, Bhattarai KK, Daniels DA, Harrison MJ. Diversity of morphology and function in arbuscular mycorrhizal symbioses in Brachypodium distachyon. PLANTA 2012; 236:851-865. [PMID: 22711284 DOI: 10.1007/s00425-012-1677-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 05/25/2012] [Indexed: 05/28/2023]
Abstract
Brachypodium distachyon is a grass species that serves as a useful model for wheat and also for many of the grass species proposed as feedstocks for bioenergy production. Here, we monitored B. distachyon symbioses with five different arbuscular mycorrhizal (AM) fungi and identified symbioses that vary functionally with respect to plant performance. Three symbioses promoted significant increases in shoot phosphorus (P) content and shoot growth of Brachypodium, while two associations were neutral. The Brachypodium/Glomus candidum symbiosis showed a classic 'Paris-type' morphology. In the other four AM symbioses, hyphal growth was exclusively intracellular and linear; hyphal coils were not observed and arbuscules were abundant. Expression of the Brachypodium ortholog of the symbiosis-specific phosphate (Pi) transporter MtPT4 did not differ significantly in these five interactions indicating that the lack of apparent functionality did not result from a failure to express this gene or several other AM symbiosis-associated genes. Analysis of the expression patterns of the complete PHT1 Pi transporter gene family and AMT2 gene family in B. distachyon/G. intraradices mycorrhizal roots identified additional family members induced during symbiosis and again, transcript levels were similar in the different Brachypodium AM symbioses. This initial morphological, molecular and functional characterization provides a framework for future studies of functional diversity in AM symbiosis in B. distachyon.
Collapse
Affiliation(s)
- Jeon J Hong
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY 14853, USA
| | | | | | | | | | | |
Collapse
|
42
|
|
43
|
Fursova O, Pogorelko G, Zabotina OA. An efficient method for transient gene expression in monocots applied to modify the Brachypodium distachyon cell wall. ANNALS OF BOTANY 2012; 110:47-56. [PMID: 22589326 PMCID: PMC3380599 DOI: 10.1093/aob/mcs103] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 03/26/2012] [Indexed: 05/28/2023]
Abstract
BACKGROUND Agrobacterium-mediated transformation is widely used to produce insertions into plant genomes. There are a number of well-developed Agrobacterium-mediated transformation methods for dicotyledonous plants, but there are few for monocotyledonous plants. METHODS Three hydrolase genes were transiently expressed in Brachypodium distachyon plants using specially designed vectors that express the gene product of interest and target it to the plant cell wall. Expression of functional hydrolases in genotyped plants was confirmed using western blotting, activity assays, cell wall compositional analysis and digestibility tests. KEY RESULTS An efficient, new, Agrobacterium-mediated approach was developed for transient gene expression in the grass B. distachyon, using co-cultivation of mature seeds with bacterial cells. This method allows transformed tissues to be obtained rapidly, within 3-4 weeks after co-cultivation. Also, the plants carried transgenic tissue and maintained transgenic protein expression throughout plant maturation. The efficiency of transformation was estimated at around 5 % of initially co-cultivated seeds. Application of this approach to express three Aspergillus nidulans hydrolases in the Brachypodium cell wall successfully confirmed its utility and resulted in the expected expression of active microbial proteins and alterations of cell wall composition. Cell wall modifications caused by expression of A. nidulans α-arabinofuranosidase and α-galactosidase increased the biodegradability of plant biomass. CONCLUSIONS This newly developed approach is a quick and efficient technique for expressing genes of interest in Brachypodium plants, which express the gene product throughout development. In the future, this could be used for broad functional genomics studies of monocots and for biotechnological applications, such as plant biomass modification for biofuel production.
Collapse
|
44
|
Tripathi P, Rabara RC, Langum TJ, Boken AK, Rushton DL, Boomsma DD, Rinerson CI, Rabara J, Reese RN, Chen X, Rohila JS, Rushton PJ. The WRKY transcription factor family in Brachypodium distachyon. BMC Genomics 2012; 13:270. [PMID: 22726208 PMCID: PMC3583182 DOI: 10.1186/1471-2164-13-270] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Accepted: 05/29/2012] [Indexed: 11/12/2022] Open
Abstract
Background A complete assembled genome sequence of wheat is not yet available. Therefore, model plant systems for wheat are very valuable. Brachypodium distachyon (Brachypodium) is such a system. The WRKY family of transcription factors is one of the most important families of plant transcriptional regulators with members regulating important agronomic traits. Studies of WRKY transcription factors in Brachypodium and wheat therefore promise to lead to new strategies for wheat improvement. Results We have identified and manually curated the WRKY transcription factor family from Brachypodium using a pipeline designed to identify all potential WRKY genes. 86 WRKY transcription factors were found, a total higher than all other current databases. We therefore propose that our numbering system (BdWRKY1-BdWRKY86) becomes the standard nomenclature. In the JGI v1.0 assembly of Brachypodium with the MIPS/JGI v1.0 annotation, nine of the transcription factors have no gene model and eleven gene models are probably incorrectly predicted. In total, twenty WRKY transcription factors (23.3%) do not appear to have accurate gene models. To facilitate use of our data, we have produced The Database of Brachypodium distachyon WRKY Transcription Factors. Each WRKY transcription factor has a gene page that includes predicted protein domains from MEME analyses. These conserved protein domains reflect possible input and output domains in signaling. The database also contains a BLAST search function where a large dataset of WRKY transcription factors, published genes, and an extensive set of wheat ESTs can be searched. We also produced a phylogram containing the WRKY transcription factor families from Brachypodium, rice, Arabidopsis, soybean, and Physcomitrella patens, together with published WRKY transcription factors from wheat. This phylogenetic tree provides evidence for orthologues, co-orthologues, and paralogues of Brachypodium WRKY transcription factors. Conclusions The description of the WRKY transcription factor family in Brachypodium that we report here provides a framework for functional genomics studies in an important model system. Our database is a resource for both Brachypodium and wheat studies and ultimately projects aimed at improving wheat through manipulation of WRKY transcription factors.
Collapse
Affiliation(s)
- Prateek Tripathi
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
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.
Collapse
Affiliation(s)
| | - Christian S. Hardtke
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| |
Collapse
|
46
|
Ingram PA, Zhu J, Shariff A, Davis IW, Benfey PN, Elich T. High-throughput imaging and analysis of root system architecture in Brachypodium distachyon under differential nutrient availability. Philos Trans R Soc Lond B Biol Sci 2012; 367:1559-69. [PMID: 22527399 PMCID: PMC3321691 DOI: 10.1098/rstb.2011.0241] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Nitrogen (N) and phosphorus (P) deficiency are primary constraints for plant productivity, and root system architecture (RSA) plays a vital role in the acquisition of these nutrients. The genetic determinants of RSA are poorly understood, primarily owing to the complexity of crop genomes and the lack of sufficient RSA phenotyping methods. The objective of this study was to characterize the RSA of two Brachypodium distachyon accessions under different nutrient availability. To do so, we used a high-throughput plant growth and imaging platform, and developed software that quantified 19 different RSA traits. We found significant differences in RSA between two Brachypodium accessions grown on nutrient-rich, low-N and low-P conditions. More specifically, one accession maintained axile root growth under low N, while the other accession maintained lateral root growth under low P. These traits resemble the RSA of crops adapted to low-N and -P conditions, respectively. Furthermore, we found that a number of these traits were highly heritable. This work lays the foundation for future identification of important genetic components of RSA traits under nutrient limitation using a mapping population derived from these two accessions.
Collapse
Affiliation(s)
| | | | | | | | - Philip N. Benfey
- GrassRoots Biotechnology, Durham, NC, USA
- Department of Biology and Center for Systems Biology, Duke University, Durham, NC, USA
| | - Tedd Elich
- GrassRoots Biotechnology, Durham, NC, USA
| |
Collapse
|
47
|
Tan S, Wu S. Genome Wide Analysis of Nucleotide-Binding Site Disease Resistance Genes in Brachypodium distachyon. Comp Funct Genomics 2012; 2012:418208. [PMID: 22693425 PMCID: PMC3368180 DOI: 10.1155/2012/418208] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 02/20/2012] [Accepted: 02/27/2012] [Indexed: 02/07/2023] Open
Abstract
Nucleotide-binding site (NBS) disease resistance genes play an important role in defending plants from a variety of pathogens and insect pests. Many R-genes have been identified in various plant species. However, little is known about the NBS-encoding genes in Brachypodium distachyon. In this study, using computational analysis of the B. distachyon genome, we identified 126 regular NBS-encoding genes and characterized them on the bases of structural diversity, conserved protein motifs, chromosomal locations, gene duplications, promoter region, and phylogenetic relationships. EST hits and full-length cDNA sequences (from Brachypodium database) of 126 R-like candidates supported their existence. Based on the occurrence of conserved protein motifs such as coiled-coil (CC), NBS, leucine-rich repeat (LRR), these regular NBS-LRR genes were classified into four subgroups: CC-NBS-LRR, NBS-LRR, CC-NBS, and X-NBS. Further expression analysis of the regular NBS-encoding genes in Brachypodium database revealed that these genes are expressed in a wide range of libraries, including those constructed from various developmental stages, tissue types, and drought challenged or nonchallenged tissue.
Collapse
Affiliation(s)
- Shenglong Tan
- Services Computing Technology and System Laboratory, Cluster and Grid Computing Laboratory, School of Computer Science and Technology, Huazhong University of Science & Technology (HUST), Luoyu Road 1037, Wuhan 430074, China
- School of Information Management, Hubei University of Economics, Wuhan 430205, China
| | - Song Wu
- Services Computing Technology and System Laboratory, Cluster and Grid Computing Laboratory, School of Computer Science and Technology, Huazhong University of Science & Technology (HUST), Luoyu Road 1037, Wuhan 430074, China
| |
Collapse
|
48
|
Li C, Rudi H, Stockinger EJ, Cheng H, Cao M, Fox SE, Mockler TC, Westereng B, Fjellheim S, Rognli OA, Sandve SR. Comparative analyses reveal potential uses of Brachypodium distachyon as a model for cold stress responses in temperate grasses. BMC PLANT BIOLOGY 2012; 12:65. [PMID: 22569006 PMCID: PMC3487962 DOI: 10.1186/1471-2229-12-65] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 04/27/2012] [Indexed: 05/02/2023]
Abstract
BACKGROUND Little is known about the potential of Brachypodium distachyon as a model for low temperature stress responses in Pooideae. The ice recrystallization inhibition protein (IRIP) genes, fructosyltransferase (FST) genes, and many C-repeat binding factor (CBF) genes are Pooideae specific and important in low temperature responses. Here we used comparative analyses to study conservation and evolution of these gene families in B. distachyon to better understand its potential as a model species for agriculturally important temperate grasses. RESULTS Brachypodium distachyon contains cold responsive IRIP genes which have evolved through Brachypodium specific gene family expansions. A large cold responsive CBF3 subfamily was identified in B. distachyon, while CBF4 homologs are absent from the genome. No B. distachyon FST gene homologs encode typical core Pooideae FST-motifs and low temperature induced fructan accumulation was dramatically different in B. distachyon compared to core Pooideae species. CONCLUSIONS We conclude that B. distachyon can serve as an interesting model for specific molecular mechanisms involved in low temperature responses in core Pooideae species. However, the evolutionary history of key genes involved in low temperature responses has been different in Brachypodium and core Pooideae species. These differences limit the use of B. distachyon as a model for holistic studies relevant for agricultural core Pooideae species.
Collapse
Affiliation(s)
- Chuan Li
- Maize Research Institute, Sichuan Agricultural University, Sichuan, China
- Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, ÅS, Norway
| | - Heidi Rudi
- Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, ÅS, Norway
| | - Eric J Stockinger
- Department of Horticulture and Crop Science, The Ohio State University/OARDC, Wooster, OH, 44691, USA
| | - Hongmei Cheng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Moju Cao
- Maize Research Institute, Sichuan Agricultural University, Sichuan, China
| | - Samuel E Fox
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA
| | - Todd C Mockler
- Donald Danforth Plant Science Center, Saint Louis, MO, 63132, USA
| | - Bjørge Westereng
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Siri Fjellheim
- Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, ÅS, Norway
| | - Odd Arne Rognli
- Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, ÅS, Norway
| | - Simen R Sandve
- Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, ÅS, Norway
| |
Collapse
|
49
|
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.
Collapse
Affiliation(s)
- Mirko Barbieri
- Dipartimento di Scienze Agrarie e degli Alimenti, Università di Modena e Reggio Emilia, Italy
| | | | | | | | | | | | | | | |
Collapse
|
50
|
Lee MB, Jeon WB, Kim DY, Bold O, Hong MJ, Lee YJ, Park JH, Seo YW. Agrobacterium-mediated transformation of Brachypodium distachyon inbred line Bd21 with two binary vectors containing hygromycin resistance and GUS reporter genes. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s12892-011-0080-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|