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Ma G, Zhang W, Liu L, Chao WS, Gu YQ, Qi L, Xu SS, Cai X. Cloning and characterization of the homoeologous genes for the Rec8-like meiotic cohesin in polyploid wheat. BMC PLANT BIOLOGY 2018; 18:224. [PMID: 30305022 PMCID: PMC6180652 DOI: 10.1186/s12870-018-1442-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 09/27/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND Meiosis is a specialized cell division critical for gamete production in the sexual reproduction of eukaryotes. It ensures genome integrity and generates genetic variability as well. The Rec8-like cohesin is a cohesion protein essential for orderly chromosome segregation in meiotic cell division. The Rec8-like genes and cohesins have been cloned and characterized in diploid models, but not in polyploids. The present study aimed to clone the homoeologous genes (homoeoalleles) for Rec8-like cohesin in polyploid wheat, an important food crop for humans, and to characterize their structure and function under a polyploid condition. RESULTS We cloned two Rec8-like homoeoalleles from tetraploid wheat (TtRec8-A1 and TtRec8-B1) and one from hexaploid wheat (TaRec8-D1), and performed expression and functional analyses of the homoeoalleles. Also, we identified other two Rec8 homoeoalleles in hexaploid wheat (TaRec8-A1 and TaRec8-B1) and the one in Aegilops tauschii (AetRec8-D1) by referencing the DNA sequences of the Rec8 homoeoalleles cloned in this study. The coding DNA sequences (CDS) of these six Rec8 homoeoalleles are all 1,827 bp in length, encoding 608 amino acids. They differed from each other primarily in introns although single nucleotide polymorphisms were detected in CDS. Substantial difference was observed between the homoeoalleles from the subgenome B (TtRec8-B1 and TaRec8-B1) and those from the subgenomes A and D (TtRec8-A1, TaRec8-A1, and TaRec8-D1). TtRec8-A1 expressed dominantly over TtRec8-B1, but comparably to TaRec8-D1, in polyploid wheat. In addition, we developed the antibody against wheat Rec8 and used the antibody to detect Rec8 cohesin in the Western blotting and subcellular localization analyses. CONCLUSIONS The Rec8 homoeoalleles from the subgenomes A and D are transcriptionally more active than the one from the subgenome B in polyploid wheat. The structural variation and differential expression of the Rec8 homoeoalleles indicate a unique cross-genome coordination of the homoeologous genes in polyploid wheat, and imply the distinction of the wheat subgenome B from the subgenomes A and D in the origin and evolution.
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Affiliation(s)
- Guojia Ma
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108 USA
| | - Wei Zhang
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108 USA
| | - Liwang Liu
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108 USA
- Present address: National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 People’s Republic of China
| | - Wun S. Chao
- USDA-ARS, Red River Valley Agricultural Research Center, Fargo, ND 58102 USA
| | - Yong Qiang Gu
- USDA-ARS, Western Regional Research Center, Albany, CA 94710 USA
| | - Lili Qi
- USDA-ARS, Red River Valley Agricultural Research Center, Fargo, ND 58102 USA
| | - Steven S. Xu
- USDA-ARS, Red River Valley Agricultural Research Center, Fargo, ND 58102 USA
| | - Xiwen Cai
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108 USA
- North Dakota State University, NDSU Dept. 7670, P.O. Box 6050, Fargo, ND 58108 USA
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Kim DY, Hong MJ, Park CS, Seo YW. The effects of chronic radiation of gamma ray on protein expression and oxidative stress inBrachypodium distachyon. Int J Radiat Biol 2015; 91:407-19. [DOI: 10.3109/09553002.2015.1012307] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Przysiecka Ł, Książkiewicz M, Wolko B, Naganowska B. Structure, expression profile and phylogenetic inference of chalcone isomerase-like genes from the narrow-leafed lupin (Lupinus angustifolius L.) genome. FRONTIERS IN PLANT SCIENCE 2015; 6:268. [PMID: 25954293 PMCID: PMC4404975 DOI: 10.3389/fpls.2015.00268] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 04/03/2015] [Indexed: 05/20/2023]
Abstract
Lupins, like other legumes, have a unique biosynthesis scheme of 5-deoxy-type flavonoids and isoflavonoids. A key enzyme in this pathway is chalcone isomerase (CHI), a member of CHI-fold protein family, encompassing subfamilies of CHI1, CHI2, CHI-like (CHIL), and fatty acid-binding (FAP) proteins. Here, two Lupinus angustifolius (narrow-leafed lupin) CHILs, LangCHIL1 and LangCHIL2, were identified and characterized using DNA fingerprinting, cytogenetic and linkage mapping, sequencing and expression profiling. Clones carrying CHIL sequences were assembled into two contigs. Full gene sequences were obtained from these contigs, and mapped in two L. angustifolius linkage groups by gene-specific markers. Bacterial artificial chromosome fluorescence in situ hybridization approach confirmed the localization of two LangCHIL genes in distinct chromosomes. The expression profiles of both LangCHIL isoforms were very similar. The highest level of transcription was in the roots of the third week of plant growth; thereafter, expression declined. The expression of both LangCHIL genes in leaves and stems was similar and low. Comparative mapping to reference legume genome sequences revealed strong syntenic links; however, LangCHIL2 contig had a much more conserved structure than LangCHIL1. LangCHIL2 is assumed to be an ancestor gene, whereas LangCHIL1 probably appeared as a result of duplication. As both copies are transcriptionally active, questions arise concerning their hypothetical functional divergence. Screening of the narrow-leafed lupin genome and transcriptome with CHI-fold protein sequences, followed by Bayesian inference of phylogeny and cross-genera synteny survey, identified representatives of all but one (CHI1) main subfamilies. They are as follows: two copies of CHI2, FAPa2 and CHIL, and single copies of FAPb and FAPa1. Duplicated genes are remnants of whole genome duplication which is assumed to have occurred after the divergence of Lupinus, Arachis, and Glycine.
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Affiliation(s)
- Łucja Przysiecka
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of SciencesPoznań, Poland
- NanoBioMedical Centre, Adam Mickiewicz UniversityPoznań, Poland
| | - Michał Książkiewicz
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of SciencesPoznań, Poland
- *Correspondence: Michał Książkiewicz, Department of Genomics, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, Poznań 60-479, Poland
| | - Bogdan Wolko
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of SciencesPoznań, Poland
| | - Barbara Naganowska
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of SciencesPoznań, Poland
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Brutnell TP, Bennetzen JL, Vogel JP. Brachypodium distachyon and Setaria viridis: Model Genetic Systems for the Grasses. ANNUAL REVIEW OF PLANT BIOLOGY 2015; 66:465-85. [PMID: 25621515 DOI: 10.1146/annurev-arplant-042811-105528] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The family of grasses encompasses the world's most important food, feed, and bioenergy crops, yet we are only now beginning to develop the genetic resources to explore the diversity of form and function that underlies economically important traits. Two emerging model systems, Brachypodium distachyon and Setaria viridis, promise to greatly accelerate the process of gene discovery in the grasses and to serve as bridges in the exploration of panicoid and pooid grasses, arguably two of the most important clades of plants from a food security perspective. We provide both a historical view of the development of plant model systems and highlight several recent reports that are providing these developing communities with the tools for gene discovery and pathway engineering.
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Zeng Q, Yuan F, Xu X, Shi X, Nie X, Zhuang H, Chen X, Wang Z, Wang X, Huang L, Han D, Kang Z. Construction and characterization of a bacterial artificial chromosome library for the hexaploid wheat line 92R137. BIOMED RESEARCH INTERNATIONAL 2014; 2014:845806. [PMID: 24895618 PMCID: PMC4026951 DOI: 10.1155/2014/845806] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/26/2014] [Accepted: 04/18/2014] [Indexed: 11/18/2022]
Abstract
For map-based cloning of genes conferring important traits in the hexaploid wheat line 92R137, a bacterial artificial chromosome (BAC) library, including two sublibraries, was constructed using the genomic DNA of 92R137 digested with restriction enzymes HindIII and BamHI. The BAC library was composed of total 765,696 clones, of which 390,144 were from the HindIII digestion and 375,552 from the BamHI digestion. Through pulsed-field gel electrophoresis (PFGE) analysis of 453 clones randomly selected from the HindIII sublibrary and 573 clones from the BamHI sublibrary, the average insert sizes were estimated as 129 and 113 kb, respectively. Thus, the HindIII sublibrary was estimated to have a 3.01-fold coverage and the BamHI sublibrary a 2.53-fold coverage based on the estimated hexaploid wheat genome size of 16,700 Mb. The 765,696 clones were arrayed in 1,994 384-well plates. All clones were also arranged into plate pools and further arranged into 5-dimensional (5D) pools. The probability of identifying a clone corresponding to any wheat DNA sequence (such as gene Yr26 for stripe rust resistance) from the library was estimated to be more than 99.6%. Through polymerase chain reaction screening the 5D pools with Xwe173, a marker tightly linked to Yr26, six BAC clones were successfully obtained. These results demonstrate that the BAC library is a valuable genomic resource for positional cloning of Yr26 and other genes of interest.
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Affiliation(s)
- Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fengping Yuan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xin Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xue Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hua Zhuang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xianming Chen
- Wheat Genetics, Quality, Physiology, and Disease Research Unit, Agricultural Research Service, United States Department of Agriculture, and Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
| | - Zhonghua Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaojie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
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Wu J, Kong X, Shi C, Gu Y, Jin C, Gao L, Jia J. Dynamic evolution of rht-1 homologous regions in grass genomes. PLoS One 2013; 8:e75544. [PMID: 24086561 PMCID: PMC3782514 DOI: 10.1371/journal.pone.0075544] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 08/18/2013] [Indexed: 11/18/2022] Open
Abstract
Hexaploid bread wheat contains A, B, and D three subgenomes with its well-characterized ancestral genomes existed at diploid and tetraploid levels, making the wheat act as a good model species for studying evolutionary genomic dynamics. Here, we performed intra- and inter-species comparative analyses of wheat and related grass genomes to examine the dynamics of homologous regions surrounding Rht-1, a well-known "green revolution" gene. Our results showed that the divergence of the two A genomes in the Rht-1 region from the diploid and tetraploid species is greater than that from the tetraploid and hexaploid wheat. The divergence of D genome between diploid and hexaploid is lower than those of A genome, suggesting that D genome diverged latter than others. The divergence among the A, B and D subgenomes was larger than that among different ploidy levels for each subgenome which mainly resulted from genomic structural variation of insertions and, perhaps deletions, of the repetitive sequences. Meanwhile, the repetitive sequences caused genome expansion further after the divergence of the three subgenomes. However, several conserved non-coding sequences were identified to be shared among the three subgenomes of wheat, suggesting that they may have played an important role to maintain the homolog of three subgenomes. This is a pilot study on evolutionary dynamics across the wheat ploids, subgenomes and differently related grasses. Our results gained new insights into evolutionary dynamics of Rht-1 region at sequence level as well as the evolution of wheat during the plolyploidization process.
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Affiliation(s)
- Jing Wu
- Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiuying Kong
- Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chao Shi
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, China
| | - Yongqiang Gu
- United States Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, California, United States of America
| | - Cuiyun Jin
- Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lizhi Gao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, China
- * E-mail: (JJ); (LG)
| | - Jizeng Jia
- Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail: (JJ); (LG)
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Qi LL, Wu JJ, Friebe B, Qian C, Gu YQ, Fu DL, Gill BS. Sequence organization and evolutionary dynamics of Brachypodium-specific centromere retrotransposons. Chromosome Res 2013; 21:507-21. [PMID: 23955173 DOI: 10.1007/s10577-013-9378-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 07/30/2013] [Accepted: 07/30/2013] [Indexed: 12/18/2022]
Abstract
Brachypodium distachyon is a wild annual grass belonging to the Pooideae, more closely related to wheat, barley, and forage grasses than rice and maize. As an experimental model, the completed genome sequence of B. distachyon provides a unique opportunity to study centromere evolution during the speciation of grasses. Centromeric satellite sequences have been identified in B. distachyon, but little is known about centromeric retrotransposons in this species. In the present study, bacterial artificial chromosome (BAC)-fluorescence in situ hybridization was conducted in maize, rice, barley, wheat, and rye using B. distachyon (Bd) centromere-specific BAC clones. Eight Bd centromeric BAC clones gave no detectable fluorescence in situ hybridization (FISH) signals on the chromosomes of rice and maize, and three of them also did not yield any FISH signals in barley, wheat, and rye. In addition, four of five Triticeae centromeric BAC clones did not hybridize to the B. distachyon centromeres, implying certain unique features of Brachypodium centromeres. Analysis of Brachypodium centromeric BAC sequences identified a long terminal repeat (LTR)-centromere retrotransposon of B. distachyon (CRBd1). This element was found in high copy number accounting for 1.6 % of the B. distachyon genome, and is enriched in Brachypodium centromeric regions. CRBd1 accumulated in active centromeres, but was lost from inactive ones. The LTR of CRBd1 appears to be specific to B. distachyon centromeres. These results reveal different evolutionary events of this retrotransposon family across grass species.
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Affiliation(s)
- L L Qi
- Northern Crop Science Laboratory, USDA-ARS, 1605 Albrecht Blvd N, Fargo, ND 58102-2765, USA.
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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.
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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
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Bragg JN, Wu J, Gordon SP, Guttman ME, Thilmony R, Lazo GR, Gu YQ, Vogel JP. Generation and characterization of the Western Regional Research Center Brachypodium T-DNA insertional mutant collection. PLoS One 2012; 7:e41916. [PMID: 23028431 PMCID: PMC3444500 DOI: 10.1371/journal.pone.0041916] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 06/29/2012] [Indexed: 11/18/2022] Open
Abstract
The model grass Brachypodium distachyon (Brachypodium) is an excellent system for studying the basic biology underlying traits relevant to the use of grasses as food, forage and energy crops. To add to the growing collection of Brachypodium resources available to plant scientists, we further optimized our Agrobacterium tumefaciens-mediated high-efficiency transformation method and generated 8,491 Brachypodium T-DNA lines. We used inverse PCR to sequence the DNA flanking the insertion sites in the mutants. Using these flanking sequence tags (FSTs) we were able to assign 7,389 FSTs from 4,402 T-DNA mutants to 5,285 specific insertion sites (ISs) in the Brachypodium genome. More than 29% of the assigned ISs are supported by multiple FSTs. T-DNA insertions span the entire genome with an average of 19.3 insertions/Mb. The distribution of T-DNA insertions is non-uniform with a larger number of insertions at the distal ends compared to the centromeric regions of the chromosomes. Insertions are correlated with genic regions, but are biased toward UTRs and non-coding regions within 1 kb of genes over exons and intron regions. More than 1,300 unique genes have been tagged in this population. Information about the Western Regional Research Center Brachypodium insertional mutant population is available on a searchable website (http://brachypodium.pw.usda.gov) designed to provide researchers with a means to order T-DNA lines with mutations in genes of interest.
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Affiliation(s)
- Jennifer N. Bragg
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
- University of California Davis, Davis, California, United States of America
| | - Jiajie Wu
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
- University of California Davis, Davis, California, United States of America
| | - Sean P. Gordon
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
| | - Mara E. Guttman
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
| | - Roger Thilmony
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
| | - Gerard R. Lazo
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
| | - Yong Q. Gu
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
| | - John P. Vogel
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
- * E-mail:
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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.
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Affiliation(s)
- Prateek Tripathi
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA
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Cui Y, Lee MY, Huo N, Bragg J, Yan L, Yuan C, Li C, Holditch SJ, Xie J, Luo MC, Li D, Yu J, Martin J, Schackwitz W, Gu YQ, Vogel JP, Jackson AO, Liu Z, Garvin DF. Fine mapping of the Bsr1 barley stripe mosaic virus resistance gene in the model grass Brachypodium distachyon. PLoS One 2012; 7:e38333. [PMID: 22675544 PMCID: PMC3366947 DOI: 10.1371/journal.pone.0038333] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 05/03/2012] [Indexed: 11/18/2022] Open
Abstract
The ND18 strain of Barley stripe mosaic virus (BSMV) infects several lines of Brachypodium distachyon, a recently developed model system for genomics research in cereals. Among the inbred lines tested, Bd3-1 is highly resistant at 20 to 25°C, whereas Bd21 is susceptible and infection results in an intense mosaic phenotype accompanied by high levels of replicating virus. We generated an F6∶7 recombinant inbred line (RIL) population from a cross between Bd3-1 and Bd21 and used the RILs, and an F2 population of a second Bd21 × Bd3-1 cross to evaluate the inheritance of resistance. The results indicate that resistance segregates as expected for a single dominant gene, which we have designated Barley stripe mosaic virus resistance 1 (Bsr1). We constructed a genetic linkage map of the RIL population using SNP markers to map this gene to within 705 Kb of the distal end of the top of chromosome 3. Additional CAPS and Indel markers were used to fine map Bsr1 to a 23 Kb interval containing five putative genes. Our study demonstrates the power of using RILs to rapidly map the genetic determinants of BSMV resistance in Brachypodium. Moreover, the RILs and their associated genetic map, when combined with the complete genomic sequence of Brachypodium, provide new resources for genetic analyses of many other traits.
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Affiliation(s)
- Yu Cui
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
- Department of Plant and Microbiology, University of California, Berkeley, California, United States of America
| | - Mi Yeon Lee
- Department of Plant and Microbiology, University of California, Berkeley, California, United States of America
| | - Naxin Huo
- USDA-ARS Western Regional Research Center, Albany, California, United States of America
| | - Jennifer Bragg
- USDA-ARS Western Regional Research Center, Albany, California, United States of America
| | - Lijie Yan
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Cheng Yuan
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Cui Li
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Sara J. Holditch
- Department of Plant and Microbiology, University of California, Berkeley, California, United States of America
| | - Jingzhong Xie
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Dawei Li
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Jialin Yu
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Joel Martin
- US DOE Joint Genome Institute, Walnut Creek, California, United States of America
| | - Wendy Schackwitz
- US DOE Joint Genome Institute, Walnut Creek, California, United States of America
| | - Yong Qiang Gu
- USDA-ARS Western Regional Research Center, Albany, California, United States of America
| | - John P. Vogel
- USDA-ARS Western Regional Research Center, Albany, California, United States of America
| | - Andrew O. Jackson
- Department of Plant and Microbiology, University of California, Berkeley, California, United States of America
- * E-mail: (AOJ); (ZL)
| | - Zhiyong Liu
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
- * E-mail: (AOJ); (ZL)
| | - David F. Garvin
- USDA-ARS Plant Science Research Unit and Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America
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Sharma MK, Sharma R, Cao P, Jenkins J, Bartley LE, Qualls M, Grimwood J, Schmutz J, Rokhsar D, Ronald PC. A genome-wide survey of switchgrass genome structure and organization. PLoS One 2012; 7:e33892. [PMID: 22511929 PMCID: PMC3325252 DOI: 10.1371/journal.pone.0033892] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 02/19/2012] [Indexed: 11/18/2022] Open
Abstract
The perennial grass, switchgrass (Panicum virgatum L.), is a promising bioenergy crop and the target of whole genome sequencing. We constructed two bacterial artificial chromosome (BAC) libraries from the AP13 clone of switchgrass to gain insight into the genome structure and organization, initiate functional and comparative genomic studies, and assist with genome assembly. Together representing 16 haploid genome equivalents of switchgrass, each library comprises 101,376 clones with average insert sizes of 144 (HindIII-generated) and 110 kb (BstYI-generated). A total of 330,297 high quality BAC-end sequences (BES) were generated, accounting for 263.2 Mbp (16.4%) of the switchgrass genome. Analysis of the BES identified 279,099 known repetitive elements, >50,000 SSRs, and 2,528 novel repeat elements, named switchgrass repetitive elements (SREs). Comparative mapping of 47 full-length BAC sequences and 330K BES revealed high levels of synteny with the grass genomes sorghum, rice, maize, and Brachypodium. Our data indicate that the sorghum genome has retained larger microsyntenous regions with switchgrass besides high gene order conservation with rice. The resources generated in this effort will be useful for a broad range of applications.
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Affiliation(s)
- Manoj K. Sharma
- Department of Plant Pathology, University of California Davis, Davis, California, United States of America
- Joint BioEnergy Institute, Emeryville, California, United States of America
| | - Rita Sharma
- Department of Plant Pathology, University of California Davis, Davis, California, United States of America
- Joint BioEnergy Institute, Emeryville, California, United States of America
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute, Zhengzhou, China
| | - Jerry Jenkins
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, United States of America
- United States Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Laura E. Bartley
- Department of Plant Pathology, University of California Davis, Davis, California, United States of America
- Joint BioEnergy Institute, Emeryville, California, United States of America
| | - Morgan Qualls
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, United States of America
- United States Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Jane Grimwood
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, United States of America
- United States Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, United States of America
- United States Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Daniel Rokhsar
- United States Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
- University of California, Berkeley, California, United States of America
| | - Pamela C. Ronald
- Department of Plant Pathology, University of California Davis, Davis, California, United States of America
- Joint BioEnergy Institute, Emeryville, California, United States of America
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Barbieri M, Marcel TC, Niks RE. Host Status of False Brome Grass to the Leaf Rust Fungus Puccinia brachypodii and the Stripe Rust Fungus P. striiformis. PLANT DISEASE 2011; 95:1339-1345. [PMID: 30731784 DOI: 10.1094/pdis-11-10-0825] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Purple false brome grass (Brachypodium distachyon) has recently emerged as a model system for temperate grasses and is also a potential model plant to investigate plant interactions with economically important pathogens such as rust fungi. We determined the host status of five Brachypodium species to three isolates of Puccinia brachypodii, the prevalent rust species on Brachypodium sylvaticum in nature, and to one isolate each of three formae speciales of the stripe rust fungus P. striiformis. Two P. striiformis isolates produced sporulating lesions, both in only one of the tested interactions, suggesting a marginal host status of B. distachyon. P. brachypodii formed sporulating uredinia on the five Brachypodium species tested, and a range of reactions was observed. Surprisingly, the B. sylvaticum-derived rust isolates were more frequently pathogenic to B. distachyon than to their original host species. The B. distachyon diploid inbred lines, developed and distributed as reference material to the Brachypodium research community, include susceptible and resistant genotypes to at least three of the four P. brachypodii isolates tested. This creates the opportunity to use B. distachyon/P. brachypodii as a model pathosystem. In one B. distachyon accession, heavy infection by the loose smut fungus Ustilago bromivora occurred. That pathogen could also serve as a model pathogen of Brachypodium.
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Affiliation(s)
- Mirko Barbieri
- Dipartimento di Scienze Agrarie e degli Alimenti, Università degli studi di Modena e Reggio Emilia, Via Amendola 2, Pad. Besta, 42100 Reggio Emilia, Italy
| | - Thierry C Marcel
- Laboratory of Plant Breeding, Graduate school for Experimental Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; INRA-AgroParisTech, UMR1290 BIOGER-CPP, Avenue Lucien Brétignières BP01, 78850 Thiverval-Grignon, France
| | - Rients E Niks
- Laboratory of Plant Breeding, Graduate school for Experimental Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Yordem BK, Conte SS, Ma JF, Yokosho K, Vasques KA, Gopalsamy SN, Walker EL. Brachypodium distachyon as a new model system for understanding iron homeostasis in grasses: phylogenetic and expression analysis of Yellow Stripe-Like (YSL) transporters. ANNALS OF BOTANY 2011; 108:821-33. [PMID: 21831857 PMCID: PMC3177677 DOI: 10.1093/aob/mcr200] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 06/10/2011] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Brachypodium distachyon is a temperate grass with a small stature, rapid life cycle and completely sequenced genome that has great promise as a model system to study grass-specific traits for crop improvement. Under iron (Fe)-deficient conditions, grasses synthesize and secrete Fe(III)-chelating agents called phytosiderophores (PS). In Zea mays, Yellow Stripe1 (ZmYS1) is the transporter responsible for the uptake of Fe(III)-PS complexes from the soil. Some members of the family of related proteins called Yellow Stripe-Like (YSL) have roles in internal Fe translocation of plants, while the function of other members remains uninvestigated. The aim of this study is to establish brachypodium as a model system to study Fe homeostasis in grasses, identify YSL proteins in brachypodium and maize, and analyse their expression profiles in brachypodium in response to Fe deficiency. METHODS The YSL family of proteins in brachypodium and maize were identified based on sequence similarity to ZmYS1. Expression patterns of the brachypodium YSL genes (BdYSL genes) were determined by quantitative RT-PCR under Fe-deficient and Fe-sufficient conditions. The types of PS secreted, and secretion pattern of PS in brachypodium were analysed by high-performance liquid chromatography. KEY RESULTS Eighteen YSL family members in maize and 19 members in brachypodium were identified. Phylogenetic analysis revealed that some YSLs group into a grass-specific clade. The Fe status of the plant can regulate expression of brachypodium YSL genes in both shoots and roots. 3-Hydroxy-2'-deoxymugineic acid (HDMA) is the dominant type of PS secreted by brachypodium, and its secretion is diurnally regulated. CONCLUSIONS PS secretion by brachypodium parallels that of related crop species such as barley and wheat. A single grass species-specific YSL clade is present, and expression of the BdYSL members of this clade could not be detected in shoots or roots, suggesting grass-specific functions in reproductive tissues. Finally, the Fe-responsive expression profiles of several YSLs suggest roles in Fe homeostasis.
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Affiliation(s)
- Burcu K. Yordem
- Biology Department
- Plant Biology Graduate Program, University of Massachusetts Amherst, 611 North Pleasant St., Amherst, MA 01002, USA
| | | | - Jian Feng Ma
- Okayama University, Institute of Plant Science and Resources, Chuo 2-20-1, Kurashiki, 710-0046, Japan
| | - Kengo Yokosho
- Okayama University, Institute of Plant Science and Resources, Chuo 2-20-1, Kurashiki, 710-0046, Japan
| | - Kenneth A. Vasques
- Biology Department
- Plant Biology Graduate Program, University of Massachusetts Amherst, 611 North Pleasant St., Amherst, MA 01002, USA
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15
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Brkljacic J, Grotewold E, Scholl R, Mockler T, Garvin DF, Vain P, Brutnell T, Sibout R, Bevan M, Budak H, Caicedo AL, Gao C, Gu Y, Hazen SP, Holt BF, Hong SY, Jordan M, Manzaneda AJ, Mitchell-Olds T, Mochida K, Mur LA, Park CM, Sedbrook J, Watt M, Zheng SJ, Vogel JP. Brachypodium as a model for the grasses: today and the future. PLANT PHYSIOLOGY 2011; 157:3-13. [PMID: 21771916 PMCID: PMC3165879 DOI: 10.1104/pp.111.179531] [Citation(s) in RCA: 183] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 07/18/2011] [Indexed: 05/06/2023]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - John P. Vogel
- Plant Biotechnology Center and Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210 (J.B., E.G., R.S.); Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331 (T.M.); United States Department of Agriculture-Agricultural Research Service Plant Science Research Unit and Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 (D.F.G.); Crop Genetics Department (P.V.) and Cell and Developmental Biology Department (M.B.), John Innes Centre, Norwich NR4 7UJ, United Kingdom; Boyce Thompson Institute, Ithaca, New York 14853 (T.B.); Institut Jean-Pierre Bourgin, UMR1318 Institut National de la Recherche Agronomique-AgroParisTech, Versailles 78026, France (R.S.); Faculty of Engineering and Natural Science, Sabanci University, Istanbul 34956, Turkey (H.B.); Biology Department, University of Massachusetts, Amherst, Massachusetts 01003 (A.L.C., S.P.H.); State Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (C.G.); Genomics and Gene Discovery Research Unit, United States Department of Agriculture-Agricultural Research Service Western Regional Research Center, Albany, California 94710 (Y.G., J.P.V.); Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019 (B.F.H.); Department of Chemistry, Seoul National University, Seoul 151–742 Korea (S.-Y.H., C.-M.P.); Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, Manitoba, Canada R3T 2M9 (M.J.); Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaen 23071 Spain (A.J.M.); Institute for Genome Sciences and Policy, Department of Biology, Duke University, Durham, North Carolina 27708 (T.M.-O.); RIKEN Biomass Engineering Program, RIKEN Plant Science Center, Kanagawa 230–0045, Japan (K.M.); Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales SY23 3DA, United Kingdom (L.A.J.M.); School of Biological Sciences, Illinois State University and Department of Energy Great Lakes Bioenergy Research Center, Normal, Illinois 61790 (J.S.); CSIRO Plant Industry, Canberra, Australian Capital Territory 2601, Australia (M.W.); College of Life Sciences, Zhejiang University, Hangzhou 310058, China (S.J.Z.)
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16
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Huo N, Garvin DF, You FM, McMahon S, Luo MC, Gu YQ, Lazo GR, Vogel JP. Comparison of a high-density genetic linkage map to genome features in the model grass Brachypodium distachyon. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:455-64. [PMID: 21597976 DOI: 10.1007/s00122-011-1598-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Accepted: 04/08/2011] [Indexed: 05/25/2023]
Abstract
The small annual grass Brachypodium distachyon (Brachypodium) is rapidly emerging as a powerful model system to study questions unique to the grasses. Many Brachypodium resources have been developed including a whole genome sequence, highly efficient transformation and a large germplasm collection. We developed a genetic linkage map of Brachypodium using single nucleotide polymorphism (SNP) markers and an F(2) mapping population of 476 individuals. SNPs were identified by targeted resequencing of single copy genomic sequences. Using the Illumina GoldenGate Genotyping platform we placed 558 markers into five linkage groups corresponding to the five chromosomes of Brachypodium. The unusually long total genetic map length, 1,598 centiMorgans (cM), indicates that the Brachypodium mapping population has a high recombination rate. By comparing the genetic map to genome features we found that the recombination rate was positively correlated with gene density and negatively correlated with repetitive regions and sites of ancestral chromosome fusions that retained centromeric repeat sequences. A comparison of adjacent genome regions with high versus low recombination rates revealed a positive correlation between interspecific synteny and recombination rate.
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Affiliation(s)
- Naxin Huo
- USDA-ARS Western Regional Research Center, Albany, CA, 94710, USA
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17
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18
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Febrer M, Goicoechea JL, Wright J, McKenzie N, Song X, Lin J, Collura K, Wissotski M, Yu Y, Ammiraju JSS, Wolny E, Idziak D, Betekhtin A, Kudrna D, Hasterok R, Wing RA, Bevan MW. An integrated physical, genetic and cytogenetic map of Brachypodium distachyon, a model system for grass research. PLoS One 2010; 5:e13461. [PMID: 20976139 PMCID: PMC2956642 DOI: 10.1371/journal.pone.0013461] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Accepted: 08/27/2010] [Indexed: 11/18/2022] Open
Abstract
The pooid subfamily of grasses includes some of the most important crop, forage and turf species, such as wheat, barley and Lolium. Developing genomic resources, such as whole-genome physical maps, for analysing the large and complex genomes of these crops and for facilitating biological research in grasses is an important goal in plant biology. We describe a bacterial artificial chromosome (BAC)-based physical map of the wild pooid grass Brachypodium distachyon and integrate this with whole genome shotgun sequence (WGS) assemblies using BAC end sequences (BES). The resulting physical map contains 26 contigs spanning the 272 Mb genome. BES from the physical map were also used to integrate a genetic map. This provides an independent vaildation and confirmation of the published WGS assembly. Mapped BACs were used in Fluorescence In Situ Hybridisation (FISH) experiments to align the integrated physical map and sequence assemblies to chromosomes with high resolution. The physical, genetic and cytogenetic maps, integrated with whole genome shotgun sequence assemblies, enhance the accuracy and durability of this important genome sequence and will directly facilitate gene isolation.
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Affiliation(s)
| | - Jose Luis Goicoechea
- The Arizona Genomics Institute, School of Plant Sciences and the BIO5 Institute for Collaborative Research, The University of Arizona, Tucson, Arizona, United States of America
| | | | | | - Xiang Song
- The Arizona Genomics Institute, School of Plant Sciences and the BIO5 Institute for Collaborative Research, The University of Arizona, Tucson, Arizona, United States of America
| | - Jinke Lin
- The Arizona Genomics Institute, School of Plant Sciences and the BIO5 Institute for Collaborative Research, The University of Arizona, Tucson, Arizona, United States of America
| | - Kristi Collura
- The Arizona Genomics Institute, School of Plant Sciences and the BIO5 Institute for Collaborative Research, The University of Arizona, Tucson, Arizona, United States of America
| | - Marina Wissotski
- The Arizona Genomics Institute, School of Plant Sciences and the BIO5 Institute for Collaborative Research, The University of Arizona, Tucson, Arizona, United States of America
| | - Yeisoo Yu
- The Arizona Genomics Institute, School of Plant Sciences and the BIO5 Institute for Collaborative Research, The University of Arizona, Tucson, Arizona, United States of America
| | - Jetty S. S. Ammiraju
- The Arizona Genomics Institute, School of Plant Sciences and the BIO5 Institute for Collaborative Research, The University of Arizona, Tucson, Arizona, United States of America
| | - Elzbieta Wolny
- Department of Plant Anatomy and Cytology, University of Silesia, Katowice, Poland
| | - Dominika Idziak
- Department of Plant Anatomy and Cytology, University of Silesia, Katowice, Poland
| | - Alexander Betekhtin
- Department of Plant Anatomy and Cytology, University of Silesia, Katowice, Poland
| | - Dave Kudrna
- The Arizona Genomics Institute, School of Plant Sciences and the BIO5 Institute for Collaborative Research, The University of Arizona, Tucson, Arizona, United States of America
| | - Robert Hasterok
- Department of Plant Anatomy and Cytology, University of Silesia, Katowice, Poland
| | - Rod A. Wing
- The Arizona Genomics Institute, School of Plant Sciences and the BIO5 Institute for Collaborative Research, The University of Arizona, Tucson, Arizona, United States of America
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The compact Brachypodium genome conserves centromeric regions of a common ancestor with wheat and rice. Funct Integr Genomics 2010; 10:477-92. [DOI: 10.1007/s10142-010-0190-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Revised: 08/20/2010] [Accepted: 08/24/2010] [Indexed: 12/19/2022]
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Escobar JS, Cenci A, Bolognini J, Haudry A, Laurent S, David J, Glémin S. An integrative test of the dead-end hypothesis of selfing evolution in Triticeae (Poaceae). Evolution 2010; 64:2855-72. [PMID: 20500214 DOI: 10.1111/j.1558-5646.2010.01045.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Self-fertilization is hypothesized to be an evolutionary dead end because reversion to outcrossing can rarely happen, and selfing lineages are thought to rapidly become extinct because of limited potential for adaptation and/or accumulation of deleterious mutations. We tested these two assumptions by combining morphological characters and molecular-evolution analyses in a tribe of hermaphroditic grasses (Triticeae). First, we determined the mating system of the 19 studied species. Then, we sequenced 27 protein-coding loci and compared base composition and substitution patterns between selfers and outcrossers. We found that the evolution of the mating system is best described by a model including outcrossing-to-selfing transitions only. At the molecular level, we showed that regions of low recombination exhibit signatures of relaxed selection. However, we did not detect any evidence of accumulation of nonsynonymous substitutions in selfers compared to outcrossers. Additionally, we tested for the potential deleterious effects of GC-biased gene conversion in outcrossing species. We found that recombination and not the mating system affected substitution patterns and base composition. We suggest that, in Triticeae, although recombination patterns have remained stable, selfing lineages are of recent origin and inbreeding may have persisted for insufficient time for differences between the two mating systems to evolve.
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Affiliation(s)
- Juan S Escobar
- Institut National de la Recherche Agronomique, Centre de Montpellier, UMR Diversité et Adaptation des Plantes Cultivées, Domaine de Melgueil, Mauguio, France.
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21
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Garvin DF, McKenzie N, Vogel JP, Mockler TC, Blankenheim ZJ, Wright J, Cheema JJS, Dicks J, Huo N, Hayden DM, Gu Y, Tobias C, Chang JH, Chu A, Trick M, Michael TP, Bevan MW, Snape JW. An SSR-based genetic linkage map of the model grass Brachypodium distachyon. Genome 2010; 53:1-13. [PMID: 20130744 DOI: 10.1139/g09-079] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The grass species Brachypodium distachyon (hereafter, Brachypodium) has been adopted as a model system for grasses. Here, we describe the development of a genetic linkage map of Brachypodium. The genetic linkage map was developed with an F2 population from a cross between the diploid Brachypodium lines Bd3-1 and Bd21. The map was populated with polymorphic simple sequence repeat (SSR) markers from Brachypodium expressed sequence tag (EST) and bacterial artificial chromosome (BAC) end sequences and conserved orthologous sequence (COS) markers from other grass species. The map is 1386 cM in length and consists of 139 marker loci distributed across 20 linkage groups. Five of the linkage groups exceed 100 cM in length, with the largest being 231 cM long. Assessment of colinearity between the Brachypodium linkage map and the rice genome sequence revealed significant regions of macrosynteny between the two genomes, as well as rearrangements similar to those reported in other grass comparative structural genomics studies. The Brachypodium genetic linkage map described here will serve as a new tool to pursue a range of molecular genetic analyses and other applications in this new model plant system.
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Affiliation(s)
- David F Garvin
- USDA-ARS Plant Science Research Unit, 411 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN 55108, USA.
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22
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Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 2010; 463:763-8. [PMID: 20148030 DOI: 10.1038/nature08747] [Citation(s) in RCA: 1210] [Impact Index Per Article: 86.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2009] [Accepted: 12/09/2009] [Indexed: 11/09/2022]
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23
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Gu YQ, Ma Y, Huo N, Vogel JP, You FM, Lazo GR, Nelson WM, Soderlund C, Dvorak J, Anderson OD, Luo MC. A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat. BMC Genomics 2009; 10:496. [PMID: 19860896 PMCID: PMC2774330 DOI: 10.1186/1471-2164-10-496] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Accepted: 10/27/2009] [Indexed: 11/13/2022] Open
Abstract
Background Brachypodium distachyon (Brachypodium) has been recognized as a new model species for comparative and functional genomics of cereal and bioenergy crops because it possesses many biological attributes desirable in a model, such as a small genome size, short stature, self-pollinating habit, and short generation cycle. To maximize the utility of Brachypodium as a model for basic and applied research it is necessary to develop genomic resources for it. A BAC-based physical map is one of them. A physical map will facilitate analysis of genome structure, comparative genomics, and assembly of the entire genome sequence. Results A total of 67,151 Brachypodium BAC clones were fingerprinted with the SNaPshot HICF fingerprinting method and a genome-wide physical map of the Brachypodium genome was constructed. The map consisted of 671 contigs and 2,161 clones remained as singletons. The contigs and singletons spanned 414 Mb. A total of 13,970 gene-related sequences were detected in the BAC end sequences (BES). These gene tags aligned 345 contigs with 336 Mb of rice genome sequence, showing that Brachypodium and rice genomes are generally highly colinear. Divergent regions were mainly in the rice centromeric regions. A dot-plot of Brachypodium contigs against the rice genome sequences revealed remnants of the whole-genome duplication caused by paleotetraploidy, which were previously found in rice and sorghum. Brachypodium contigs were anchored to the wheat deletion bin maps with the BES gene-tags, opening the door to Brachypodium-Triticeae comparative genomics. Conclusion The construction of the Brachypodium physical map, and its comparison with the rice genome sequence demonstrated the utility of the SNaPshot-HICF method in the construction of BAC-based physical maps. The map represents an important genomic resource for the completion of Brachypodium genome sequence and grass comparative genomics. A draft of the physical map and its comparisons with rice and wheat are available at .
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Affiliation(s)
- Yong Q Gu
- 1Genomics and Gene Discovery Research Unit, USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710,USA.
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Faricelli ME, Valárik M, Dubcovsky J. Control of flowering time and spike development in cereals: the earliness per se Eps-1 region in wheat, rice, and Brachypodium. Funct Integr Genomics 2009; 10:293-306. [PMID: 19851796 PMCID: PMC2862174 DOI: 10.1007/s10142-009-0146-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Revised: 09/22/2009] [Accepted: 09/26/2009] [Indexed: 05/25/2023]
Abstract
The earliness per se gene Eps-Am1 from diploid wheat Triticum monococcum affects heading time, spike development, and spikelet number. In this study, the Eps1 orthologous regions from rice, Aegilops tauschii, and Brachypodium distachyon were compared as part of current efforts to clone this gene. A single Brachypodium BAC clone spanned the Eps-Am1 region, but a gap was detected in the A. tauschii physical map. Sequencing of the Brachypodium and A. tauschii BAC clones revealed three genes shared by the three species, which showed higher identity between wheat and Brachypodium than between them and rice. However, most of the structural changes were detected in the wheat lineage. These included an inversion encompassing the wg241-VatpC region and the presence of six unique genes. In contrast, only one unique gene (and one pseudogene) was found in Brachypodium and none in rice. Three genes were present in both Brachypodium and wheat but were absent in rice. Two of these genes, Mot1 and FtsH4, were completely linked to the earliness per se phenotype in the T. monococcum high-density genetic map and are candidates for Eps-Am1. Both genes were expressed in apices and developing spikes, as expected for Eps-Am1 candidates. The predicted MOT1 protein showed amino acid differences between the parental T. monococcum lines, but its effect is difficult to predict. Future steps to clone the Eps-Am1 gene include the generation of mot1 and ftsh4 mutants and the completion of the T. monococcum physical map to test for the presence of additional candidate genes.
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Affiliation(s)
- Maria E Faricelli
- Department of Plant Sciences, University of California, Mail Stop 1, One Shields Avenue, Davis, CA 95616-8780, USA
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Wolny E, Hasterok R. Comparative cytogenetic analysis of the genomes of the model grass Brachypodium distachyon and its close relatives. ANNALS OF BOTANY 2009; 104:873-81. [PMID: 19633311 PMCID: PMC2749528 DOI: 10.1093/aob/mcp179] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Revised: 05/29/2009] [Accepted: 06/12/2009] [Indexed: 05/06/2023]
Abstract
BACKGROUND AND AIMS Brachypodium is a small genus of temperate grasses that comprises 12-15 species. Brachypodium distachyon is now well established as a model species for temperate cereals and forage grasses. In contrast to B. distachyon, other members of the genus have been poorly investigated at the chromosome level or not at all. METHODS Twenty accessions comprising six species and two subspecies of Brachypodium were analysed cytogenetically. Measurements of nuclear genome size were made by flow cytometry. Chromosomal localization of 18-5.8-25S rDNA and 5S rDNA loci was performed by dual-colour fluorescence in situ hybridization (FISH) on enzymatically digested root-tip meristematic cells. For comparative phylogenetic analyses genomic in situ hybridization (GISH) applied to somatic chromosome preparations was used. KEY RESULTS All Brachypodium species examined have rather small genomes and chromosomes. Their chromosome numbers and genome sizes vary from 2n = 10 and 0.631 pg/2C in B. distachyon to 2n = 38 and 2.57 pg/2C in B. retusum, respectively. Genotypes with 18 and 28 chromosomes were found among B. pinnatum accessions. GISH analysis revealed that B. pinnatum with 28 chromosomes is most likely an interspecific hybrid between B. distachyon (2n = 10) and B. pinnatum (2n = 18). Two other species, B. phoenicoides and B. retusum, are also allopolyploids and B. distachyon or a close relative seems to be one of their putative ancestral species. In chromosomes of all species examined the 45S rDNA loci are distally distributed whereas loci for 5S rDNA are pericentromeric. CONCLUSIONS The increasing significance of B. distachyon as a model grass emphasizes the need to understand the evolutionary relationships in the genus Brachypodium and to ensure consistency in the biological nomenclature of its species. Modern molecular cytogenetic techniques such as FISH and GISH are suitable for comparative phylogenetic analyses and may provide informative chromosome- and/or genome-specific landmarks.
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Affiliation(s)
| | - Robert Hasterok
- Department of Plant Anatomy and Cytology, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
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Filiz E, Ozdemir BS, Budak F, Vogel JP, Tuna M, Budak H. Molecular, morphological, and cytological analysis of diverse Brachypodium distachyon inbred lines. Genome 2009; 52:876-90. [DOI: 10.1139/g09-062] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Brachypodium distachyon (brachypodium) is a small grass with the biological and genomic attributes necessary to serve as a model system for all grasses including small grains and grasses being developed as energy crops (e.g., switchgrass and Miscanthus ). To add natural variation to the toolkit available to plant biologists using brachypodium as a model system, it is imperative to establish extensive, well-characterized germplasm collections. The objectives of this study were to collect brachypodium accessions from throughout Turkey and then characterize the molecular (nuclear and organelle genome), morphological, and cytological variation within the collection. We collected 164 lines from 45 diverse geographic regions of Turkey and created 146 inbred lines. The majority of this material (116 of 146 inbred lines) was diploid. The similarity matrix for the diploid lines based on AFLP analysis indicated extensive diversity, with genetic distances ranging from 0.05 to 0.78. Organelle genome diversity, on the other hand, was low both among and within the lines used in this study. The geographic distribution of genotypes was not significantly correlated with either nuclear or organelle genome variation for the genotypes studied. Phenotypic characterization of the lines showed extensive variation in flowering time (7–22 weeks), seed production (4–193 seeds/plant), and biomass (15–77 g). Chromosome morphology of the collected brachypodium accessions varied from submetacentric to metacentric, except for chromosome 5, which was acrocentric. The diverse brachypodium lines developed in this study will allow experimental approaches dependent upon natural variation to be applied to this new model grass. These results will also help efforts to have a better understanding of complex large genomes (i.e., wheat, barley, and switchgrass).
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Affiliation(s)
- E. Filiz
- Sabanci University, Biological Science and Bioengineering Program, 34956, Tuzla, Istanbul, Turkey
- Igdir University, Department of Crops Science, Igdir, Turkey
- USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
- Namik Kemal University, Department of Crop Science, Tekirdag, Turkey
| | - B. S. Ozdemir
- Sabanci University, Biological Science and Bioengineering Program, 34956, Tuzla, Istanbul, Turkey
- Igdir University, Department of Crops Science, Igdir, Turkey
- USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
- Namik Kemal University, Department of Crop Science, Tekirdag, Turkey
| | - F. Budak
- Sabanci University, Biological Science and Bioengineering Program, 34956, Tuzla, Istanbul, Turkey
- Igdir University, Department of Crops Science, Igdir, Turkey
- USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
- Namik Kemal University, Department of Crop Science, Tekirdag, Turkey
| | - J. P. Vogel
- Sabanci University, Biological Science and Bioengineering Program, 34956, Tuzla, Istanbul, Turkey
- Igdir University, Department of Crops Science, Igdir, Turkey
- USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
- Namik Kemal University, Department of Crop Science, Tekirdag, Turkey
| | - M. Tuna
- Sabanci University, Biological Science and Bioengineering Program, 34956, Tuzla, Istanbul, Turkey
- Igdir University, Department of Crops Science, Igdir, Turkey
- USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
- Namik Kemal University, Department of Crop Science, Tekirdag, Turkey
| | - H. Budak
- Sabanci University, Biological Science and Bioengineering Program, 34956, Tuzla, Istanbul, Turkey
- Igdir University, Department of Crops Science, Igdir, Turkey
- USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
- Namik Kemal University, Department of Crop Science, Tekirdag, Turkey
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Wanjugi H, Coleman-Derr D, Huo N, Kianian SF, Luo MC, Wu J, Anderson O, Gu YQ. Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat. Genome 2009; 52:576-87. [PMID: 19483776 DOI: 10.1139/g09-033] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In hexaploid wheat (Triticum aestivum L.) (AABBDD, C=17 000 Mb), repeat DNA accounts for approximately 90% of the genome, of which transposable elements (TEs) constitute 60%-80%. Despite the dynamic evolution of TEs, our previous study indicated that the majority of TEs are conserved and collinear between the homologous wheat genomes, based on identical insertion patterns. In this study, we exploited the unique and abundant TE insertion junction regions identified from diploid Aegilops tauschii to develop genome-specific repeat DNA junction markers (RJM) for use in hexaploid wheat. In this study, both BAC end and random shotgun sequences were used to search for RJM. Of the 300 RJM primer pairs tested, 269 (90%) amplified single bands from diploid Ae. tauschii. Of these 269 primer pairs, 260 (97%) amplified hexaploid wheat and 9 (3%) amplified Ae. tauschii only. Among the RJM primers that amplified hexaploid wheat, 88% were successfully assigned to individual chromosomes of the hexaploid D genome. Among the 38 RJM primers mapped on chromosome 6D, 31 (82%) were unambiguously mapped to delineated bins of the chromosome using various wheat deletion lines. Our results suggest that the unique RJM derived from the diploid D genome could facilitate genetic, physical, and radiation mapping of the hexaploid wheat D genome.
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Affiliation(s)
- Humphrey Wanjugi
- Genomics and Gene Discovery Unit, USDA/ARS Western Regional Research Center, Albany, CA 94710, USA
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Vogel JP, Tuna M, Budak H, Huo N, Gu YQ, Steinwand MA. Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon. BMC PLANT BIOLOGY 2009; 9:88. [PMID: 19594938 PMCID: PMC2719641 DOI: 10.1186/1471-2229-9-88] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Accepted: 07/13/2009] [Indexed: 05/19/2023]
Abstract
BACKGROUND Brachypodium distachyon (Brachypodium) is rapidly emerging as a powerful model system to facilitate research aimed at improving grass crops for grain, forage and energy production. To characterize the natural diversity of Brachypodium and provide a valuable new tool to the growing list of resources available to Brachypodium researchers, we created and characterized a large, diverse collection of inbred lines. RESULTS We developed 84 inbred lines from eight locations in Turkey. To enable genotypic characterization of this collection, we created 398 SSR markers from BAC end and EST sequences. An analysis of 187 diploid lines from 56 locations with 43 SSR markers showed considerable genotypic diversity. There was some correlation between SSR genotypes and broad geographic regions, but there was also a high level of genotypic diversity at individual locations. Phenotypic analysis of this new germplasm resource revealed considerable variation in flowering time, seed size, and plant architecture. The inbreeding nature of Brachypodium was confirmed by an extremely high level of homozygosity in wild plants and a lack of cross-pollination under laboratory conditions. CONCLUSION Taken together, the inbreeding nature and genotypic diversity observed at individual locations suggest a significant amount of long-distance seed dispersal. The resources developed in this study are freely available to the research community and will facilitate experimental applications based on natural diversity.
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Affiliation(s)
- John P Vogel
- USDA-ARS, Western Regional Research Center, Albany, CA, USA
| | - Metin Tuna
- Namik Kemal University, Department of Field Crops, Tekirdag, Turkey
| | - Hikmet Budak
- Sabanci University, Biological Science and Bioengineering Program, Istanbul, Turkey
| | - Naxin Huo
- USDA-ARS, Western Regional Research Center, Albany, CA, USA
| | - Yong Q Gu
- USDA-ARS, Western Regional Research Center, Albany, CA, USA
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Kumar S, Mohan A, Balyan HS, Gupta PK. Orthology between genomes of Brachypodium, wheat and rice. BMC Res Notes 2009; 2:93. [PMID: 19470185 PMCID: PMC2695472 DOI: 10.1186/1756-0500-2-93] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2009] [Accepted: 05/27/2009] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND In the past, rice genome served as a good model for studies involving comparative genomics of grass species. More recently, however, Brachypodium distachyon genome has emerged as a better model system for genomes of temperate cereals including wheat. During the present study, Brachypodium EST contigs were utilized to resolve orthologous relationships among the genomes of Brachypodium, wheat and rice. FINDINGS Comparative sequence analysis of 3,818 Brachypodium EST (bEST) contigs and 3,792 physically mapped wheat EST (wEST) contigs revealed that as many as 449 bEST contigs were orthologous to 1,154 wEST loci that were bin-mapped on all the 21 wheat chromosomes. Similarly 743 bEST contigs were orthologous to specific rice genome sequences distributed on all the 12 rice chromosomes. As many as 183 bEST contigs were orthologous to both wheat and rice genome sequences, which harbored as many as 17 SSRs conserved across the three species. Primers developed for 12 of these 17 conserved SSRs were used for a wet-lab experiment, which resolved relatively high level of conservation among the genomes of Brachypodium, wheat and rice. CONCLUSION The present study confirmed that Brachypodium is a better model than rice for analysis of the genomes of temperate cereals like wheat and barley. The whole genome sequence of Brachypodium, which should become available in the near future, will further facilitate greatly the studies involving comparative genomics of cereals.
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Affiliation(s)
- Sachin Kumar
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding Ch. Charan Singh University, Meerut-250 004, India
| | - Amita Mohan
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding Ch. Charan Singh University, Meerut-250 004, India
| | - Harindra S Balyan
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding Ch. Charan Singh University, Meerut-250 004, India
| | - Pushpendra K Gupta
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding Ch. Charan Singh University, Meerut-250 004, India
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Bakker EG, Montgomery B, Nguyen T, Eide K, Chang J, Mockler TC, Liston A, Seabloom EW, Borer ET. Strong population structure characterizes weediness gene evolution in the invasive grass species Brachypodium distachyon. Mol Ecol 2009; 18:2588-601. [PMID: 19457186 DOI: 10.1111/j.1365-294x.2009.04225.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mediterranean annual grasses have invaded California and have replaced vast areas of native grassland. One of these invasive grasses is Brachypodium distachyon, a new model species for the grasses with extensive genomic resources and a nearly completed genome sequence. This study shows that the level of genetic variation in invaded California grasslands is lower compared to the native range in Eurasia. The invaded regions are characterized by highly differentiated populations of B. distachyon isolated by distance, most likely as a result of founder effects and a dearth of outcrossing events. EXP6 and EXP10 encoding alpha-expansins responsible for rapid growth, and AGL11 and AGL13 encoding proteins involved in vegetative phase regulation, appear to be under purifying selection with no evidence for local adaptation. Our data show that B. distachyon has diverged only recently from related Brachypodium species and that tetraploidization might have been as recent as a few thousand years ago. Observed low genetic variation in EXP10 and AGL13 appears to have been present in Eurasia before tetraploidization, potentially as a result of strong selective pressures on advantageous mutations, which are most likely responsible for its fast growth and rapid completion of its life cycle.
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Affiliation(s)
- Erica G Bakker
- Department of Horticulture, 4017 Agriculture and Life Sciences Bldg., Oregon State University, Corvallis, OR 97331, USA.
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Yu GT, Cai X, Harris MO, Gu YQ, Luo MC, Xu SS. Saturation and comparative mapping of the genomic region harboring Hessian fly resistance gene H26 in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 118:1589-1599. [PMID: 19322558 DOI: 10.1007/s00122-009-1006-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Accepted: 03/08/2009] [Indexed: 05/27/2023]
Abstract
Resistance gene H26, derived from Aegilops tauschii Coss., is one of the most effective R genes against the Hessian fly [Mayetiola destructor (Say)], an important pest of wheat (Triticum aestivum L.). Using a limited number of PCR-based molecular markers a previous study mapped H26 to the wheat chromosomal deletion bin 3DL3-0.81-1.00. The objectives of this study were to saturate the chromosomal region harboring H26 with newly developed PCR-based markers and to investigate the collinearity of this wheat chromosomal region with rice (Oryza sativa L.) and Brachypodium distachyon genome. A population of 96 F(2) individuals segregating at the H26 gene locus was used for saturation mapping. All wheat ESTs assigned to the deletion bin 3DL3-0.81-1.00 were used to design STS (sequence tagged site) primers. The wheat ESTs mapped near H26 were further used to BLAST rice and B. distachyon genomic sequences for comparative mapping. To date, 26 newly developed STS markers have been mapped to the chromosomal region spanning the H26 locus. Two of them were mapped 1.0 cM away from the H26 locus. Comparative analysis identified genomic regions on rice chromosome 1 and Brachypodium Super contig 13 which are collinear with the genomic region spanning the H26 locus within the distal region of 3DL. The newly developed STS markers closely linked to H26 will be useful for mapped-based cloning of H26 and marker-assisted selection of this gene in wheat breeding. The results will also enhance understanding of this chromosomal region which contains several other Hessian fly resistance genes.
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Affiliation(s)
- Guo Tai Yu
- Department of Entomology, North Dakota State University, Fargo, ND 58105, USA
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Bortiri E, Coleman-Derr D, Lazo GR, Anderson OD, Gu YQ. The complete chloroplast genome sequence of Brachypodium distachyon: sequence comparison and phylogenetic analysis of eight grass plastomes. BMC Res Notes 2008; 1:61. [PMID: 18710514 PMCID: PMC2527572 DOI: 10.1186/1756-0500-1-61] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2008] [Accepted: 07/31/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Wheat, barley, and rye, of tribe Triticeae in the Poaceae, are among the most important crops worldwide but they present many challenges to genomics-aided crop improvement. Brachypodium distachyon, a close relative of those cereals has recently emerged as a model for grass functional genomics. Sequencing of the nuclear and organelle genomes of Brachypodium is one of the first steps towards making this species available as a tool for researchers interested in cereals biology. FINDINGS The chloroplast genome of Brachypodium distachyon was sequenced by a combinational approach using BAC end and shotgun sequences derived from a selected BAC containing the entire chloroplast genome. Comparative analysis indicated that the chloroplast genome is conserved in gene number and organization with respect to those of other cereals. However, several Brachypodium genes evolve at a faster rate than those in other grasses. Sequence analysis reveals that rice and wheat have a ~2.1 kb deletion in their plastid genomes and this deletion must have occurred independently in both species. CONCLUSION We demonstrate that BAC libraries can be used to sequence plastid, and likely other organellar, genomes. As expected, the Brachypodium chloroplast genome is very similar to those of other sequenced grasses. The phylogenetic analyses and the pattern of insertions and deletions in the chloroplast genome confirmed that Brachypodium is a close relative of the tribe Triticeae. Nevertheless, we show that some large indels can arise multiple times and may confound phylogenetic reconstruction.
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Affiliation(s)
- Esteban Bortiri
- Genomics and Gene Discovery Research Unit, USDA-Agriculture Research Service, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA.
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YE XG, TAO LL. Research Outline on Some Characteristics of Brachypodium distachyon as a New Model Plant Species. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/s1875-2780(08)60032-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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You FM, Huo N, Gu YQ, Luo MC, Ma Y, Hane D, Lazo GR, Dvorak J, Anderson OD. BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinformatics 2008; 9:253. [PMID: 18510760 PMCID: PMC2438325 DOI: 10.1186/1471-2105-9-253] [Citation(s) in RCA: 487] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2007] [Accepted: 05/29/2008] [Indexed: 01/25/2023] Open
Abstract
Background Microsatellite (simple sequence repeat – SSR) and single nucleotide polymorphism (SNP) markers are two types of important genetic markers useful in genetic mapping and genotyping. Often, large-scale genomic research projects require high-throughput computer-assisted primer design. Numerous such web-based or standard-alone programs for PCR primer design are available but vary in quality and functionality. In particular, most programs lack batch primer design capability. Such a high-throughput software tool for designing SSR flanking primers and SNP genotyping primers is increasingly demanded. Results A new web primer design program, BatchPrimer3, is developed based on Primer3. BatchPrimer3 adopted the Primer3 core program as a major primer design engine to choose the best primer pairs. A new score-based primer picking module is incorporated into BatchPrimer3 and used to pick position-restricted primers. BatchPrimer3 v1.0 implements several types of primer designs including generic primers, SSR primers together with SSR detection, and SNP genotyping primers (including single-base extension primers, allele-specific primers, and tetra-primers for tetra-primer ARMS PCR), as well as DNA sequencing primers. DNA sequences in FASTA format can be batch read into the program. The basic information of input sequences, as a reference of parameter setting of primer design, can be obtained by pre-analysis of sequences. The input sequences can be pre-processed and masked to exclude and/or include specific regions, or set targets for different primer design purposes as in Primer3Web and primer3Plus. A tab-delimited or Excel-formatted primer output also greatly facilitates the subsequent primer-ordering process. Thousands of primers, including wheat conserved intron-flanking primers, wheat genome-specific SNP genotyping primers, and Brachypodium SSR flanking primers in several genome projects have been designed using the program and validated in several laboratories. Conclusion BatchPrimer3 is a comprehensive web primer design program to develop different types of primers in a high-throughput manner. Additional methods of primer design can be easily integrated into future versions of BatchPrimer3. The program with source code and thousands of PCR and sequencing primers designed for wheat and Brachypodium are accessible at .
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Affiliation(s)
- Frank M You
- Department of Plant Sciences, University of California, CA 95616, USA.
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35
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You FM, Huo N, Gu YQ, Luo MC, Ma Y, Hane D, Lazo GR, Dvorak J, Anderson OD. BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinformatics 2008. [PMID: 18510760 DOI: 10.1186/1471‐2105‐9‐253] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Microsatellite (simple sequence repeat - SSR) and single nucleotide polymorphism (SNP) markers are two types of important genetic markers useful in genetic mapping and genotyping. Often, large-scale genomic research projects require high-throughput computer-assisted primer design. Numerous such web-based or standard-alone programs for PCR primer design are available but vary in quality and functionality. In particular, most programs lack batch primer design capability. Such a high-throughput software tool for designing SSR flanking primers and SNP genotyping primers is increasingly demanded. RESULTS A new web primer design program, BatchPrimer3, is developed based on Primer3. BatchPrimer3 adopted the Primer3 core program as a major primer design engine to choose the best primer pairs. A new score-based primer picking module is incorporated into BatchPrimer3 and used to pick position-restricted primers. BatchPrimer3 v1.0 implements several types of primer designs including generic primers, SSR primers together with SSR detection, and SNP genotyping primers (including single-base extension primers, allele-specific primers, and tetra-primers for tetra-primer ARMS PCR), as well as DNA sequencing primers. DNA sequences in FASTA format can be batch read into the program. The basic information of input sequences, as a reference of parameter setting of primer design, can be obtained by pre-analysis of sequences. The input sequences can be pre-processed and masked to exclude and/or include specific regions, or set targets for different primer design purposes as in Primer3Web and primer3Plus. A tab-delimited or Excel-formatted primer output also greatly facilitates the subsequent primer-ordering process. Thousands of primers, including wheat conserved intron-flanking primers, wheat genome-specific SNP genotyping primers, and Brachypodium SSR flanking primers in several genome projects have been designed using the program and validated in several laboratories. CONCLUSION BatchPrimer3 is a comprehensive web primer design program to develop different types of primers in a high-throughput manner. Additional methods of primer design can be easily integrated into future versions of BatchPrimer3. The program with source code and thousands of PCR and sequencing primers designed for wheat and Brachypodium are accessible at http://wheat.pw.usda.gov/demos/BatchPrimer3/.
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Affiliation(s)
- Frank M You
- Department of Plant Sciences, University of California, CA 95616, USA.
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Opanowicz M, Vain P, Draper J, Parker D, Doonan JH. Brachypodium distachyon: making hay with a wild grass. TRENDS IN PLANT SCIENCE 2008; 13:172-7. [PMID: 18343709 DOI: 10.1016/j.tplants.2008.01.007] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Revised: 01/22/2008] [Accepted: 01/22/2008] [Indexed: 05/22/2023]
Abstract
Brachypodium distachyon is a wild grass with a short life cycle. Although it is related to small grain cereals such as wheat, its genome is only a fraction of the size. A draft genome sequence is currently available, and molecular and genetic tools have been developed for transformation, mutagenesis and gene mapping. Accessions collected from across its ancestral range show a surprising degree of phenotypic variation in many traits, including those implicated in domestication of the cereals. Thus, given its rapid cycling time and ease of cultivation, Brachypodium will be a useful model for investigating problems in grass biology.
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Vogel J, Hill T. High-efficiency Agrobacterium-mediated transformation of Brachypodium distachyon inbred line Bd21-3. PLANT CELL REPORTS 2008; 27:471-8. [PMID: 17999063 DOI: 10.1007/s00299-007-0472-y] [Citation(s) in RCA: 183] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2007] [Revised: 10/17/2007] [Accepted: 10/20/2007] [Indexed: 05/18/2023]
Abstract
Brachypodium distachyon (Brachypodium) is a small grass with biological attributes (rapid generation time, small genome, diploid accessions, small stature and simple growth requirements) that make it suitable for use as a model system. In addition, a growing list of genomic resources have been developed or are currently under development including: cDNA libraries, BAC libraries, EST sequences, BAC end sequences, a physical map, genetic markers, a linkage map and, most importantly, the complete genome sequence. To maximize the utility of Brachypodium as a model grass it is necessary to develop an efficient Agrobacterium-mediated transformation system. In this report we describe the identification of a transformable inbred diploid line, Bd21-3, and the development of a transformation method with transformation efficiencies as high as 41% of co-cultivated calluses producing transgenic plants. Conducting the co-cultivation step under desiccating conditions produced the greatest improvement in transformation efficiency.
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Affiliation(s)
- John Vogel
- USDA Western Regional Research Center, Albany, CA 94710, USA.
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Salse J, Bolot S, Throude M, Jouffe V, Piegu B, Quraishi UM, Calcagno T, Cooke R, Delseny M, Feuillet C. Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution. THE PLANT CELL 2008; 20:11-24. [PMID: 18178768 PMCID: PMC2254919 DOI: 10.1105/tpc.107.056309] [Citation(s) in RCA: 258] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Revised: 11/21/2007] [Accepted: 12/12/2007] [Indexed: 05/17/2023]
Abstract
The grass family comprises the most important cereal crops and is a good system for studying, with comparative genomics, mechanisms of evolution, speciation, and domestication. Here, we identified and characterized the evolution of shared duplications in the rice (Oryza sativa) and wheat (Triticum aestivum) genomes by comparing 42,654 rice gene sequences with 6426 mapped wheat ESTs using improved sequence alignment criteria and statistical analysis. Intraspecific comparisons identified 29 interchromosomal duplications covering 72% of the rice genome and 10 duplication blocks covering 67.5% of the wheat genome. Using the same methodology, we assessed orthologous relationships between the two genomes and detected 13 blocks of colinearity that represent 83.1 and 90.4% of the rice and wheat genomes, respectively. Integration of the intraspecific duplications data with colinearity relationships revealed seven duplicated segments conserved at orthologous positions. A detailed analysis of the length, composition, and divergence time of these duplications and comparisons with sorghum (Sorghum bicolor) and maize (Zea mays) indicated common and lineage-specific patterns of conservation between the different genomes. This allowed us to propose a model in which the grass genomes have evolved from a common ancestor with a basic number of five chromosomes through a series of whole genome and segmental duplications, chromosome fusions, and translocations.
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Affiliation(s)
- Jérôme Salse
- Institut National de la Recherche Agronomique/Université Blaise Pascal Unité Mixte de Recherche 1095, Amélioration et Santé des Plantes, 63100 Clermont-Ferrand, France
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Ozdemir BS, Hernandez P, Filiz E, Budak H. Brachypodium genomics. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2008; 2008:536104. [PMID: 18309367 PMCID: PMC2246064 DOI: 10.1155/2008/536104] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Accepted: 11/25/2007] [Indexed: 05/18/2023]
Abstract
Brachypodium distachyon (L.) Beauv. is a temperate wild grass species; its morphological and genomic characteristics make it a model system when compared to many other grass species. It has a small genome, short growth cycle, self-fertility, many diploid accessions, and simple growth requirements. In addition, it is phylogenetically close to economically important crops, like wheat and barley, and several potential biofuel grasses. It exhibits agricultural traits similar to those of these target crops. For cereal genomes, it is a better model than Arabidopsis thaliana and Oryza sativa (rice), the former used as a model for all flowering plants and the latter hitherto used as model for genomes of all temperate grass species including major cereals like barley and wheat. Increasing interest in this species has resulted in the development of a series of genomics resources, including nuclear sequences and BAC/EST libraries, together with the collection and characterization of other genetic resources. It is expected that the use of this model will allow rapid advances in generation of genomics information for the improvement of all temperate crops, particularly the cereals.
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Affiliation(s)
- Bahar Sogutmaz Ozdemir
- Biological Science and Bioengineering Program,
Faculty of Engineering and Natural Sciences,
Sabanci University Orhanli, 34956 Tuzla-Istanbul,
Turkey
| | - Pilar Hernandez
- Institute for Sustainable Agriculture (IAS),
Spanish National Research Council (CSIC),
Alameda del Obispo s/n,
Apartado 4084,
14080 Cordoba ,
Spain
| | - Ertugrul Filiz
- Biological Science and Bioengineering Program,
Faculty of Engineering and Natural Sciences,
Sabanci University Orhanli, 34956 Tuzla-Istanbul,
Turkey
| | - Hikmet Budak
- Biological Science and Bioengineering Program,
Faculty of Engineering and Natural Sciences,
Sabanci University Orhanli, 34956 Tuzla-Istanbul,
Turkey
- *Hikmet Budak:
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Huo N, Lazo GR, Vogel JP, You FM, Ma Y, Hayden DM, Coleman-Derr D, Hill TA, Dvorak J, Anderson OD, Luo MC, Gu YQ. The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences. Funct Integr Genomics 2007; 8:135-47. [PMID: 17985162 DOI: 10.1007/s10142-007-0062-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Revised: 10/04/2007] [Accepted: 10/06/2007] [Indexed: 10/22/2022]
Abstract
Due in part to its small genome (approximately 350 Mb), Brachypodium distachyon is emerging as a model system for temperate grasses, including important crops like wheat and barley. We present the analysis of 10.9% of the Brachypodium genome based on 64,696 bacterial artificial chromosome (BAC) end sequences (BES). Analysis of repeat DNA content in BES revealed that approximately 11.0% of the genome consists of known repetitive DNA. The vast majority of the Brachypodium repetitive elements are LTR retrotransposons. While Bare-1 retrotransposons are common to wheat and barley, Brachypodium repetitive element sequence-1 (BRES-1), closely related to Bare-1, is also abundant in Brachypodium. Moreover, unique Brachypodium repetitive element sequences identified constitute approximately 7.4% of its genome. Simple sequence repeats from BES were analyzed, and flanking primer sequences for SSR detection potentially useful for genetic mapping are available at http://brachypodium.pw.usda.gov . Sequence analyses of BES indicated that approximately 21.2% of the Brachypodium genome represents coding sequence. Furthermore, Brachypodium BES have more significant matches to ESTs from wheat than rice or maize, although these species have similar sizes of EST collections. A phylogenetic analysis based on 335 sequences shared among seven grass species further revealed a closer relationship between Brachypodium and Triticeae than Brachypodium and rice or maize.
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Affiliation(s)
- Naxin Huo
- Genomics and Gene Discovery Research Unit, USDA-ARS Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
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Farrar K, Donnison IS. Construction and screening of BAC libraries made from Brachypodium genomic DNA. Nat Protoc 2007; 2:1661-74. [PMID: 17641631 DOI: 10.1038/nprot.2007.204] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacterial artificial chromosome (BAC) libraries are the large DNA insert libraries of choice and valuable tools for the map-based cloning of target quantitative trait loci, physical mapping, molecular cytogenetics and comparative genomics. The protocol reported here is a simplified method used to produce and screen BAC libraries from Brachypodium species and other related grasses. Intact nuclei, containing high molecular weight (HMW) DNA, are isolated and embedded in agarose plugs. The HMW DNA is digested using an appropriate restriction enzyme and size-fractionated using pulsed-field gel electrophoresis. The DNA is isolated by dialysis, ligated into pre-prepared vector and electroporated into competent Escherichia coli cells. A PCR-based method for screening the library is also described. The entire protocol takes at least 6 weeks to complete.
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Affiliation(s)
- Kerrie Farrar
- Institute of Grassland and Environmental Research, Plas Gogerddan, Aberystwyth SY23 4AR, UK
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