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Farjallah A, Boubakri H, Barhoumi F, Brahmi R, Gandour M. Systematic analysis of Prx genes in the Brachypodium genus and their expression pattern under abiotic constraints. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:93-105. [PMID: 37991495 DOI: 10.1111/plb.13592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/24/2023] [Indexed: 11/23/2023]
Abstract
Peroxiredoxins (Prx) are ubiquitous peroxidases required for the removal of excess free radicals produced under stress conditions. Peroxiredoxin genes (Prx) in the Brachypodium genus were identified using bioinformatics tools and their expression profiles were determined under abiotic stress using RT-qPCR. The promoter regions of Prx genes contain several cis-acting elements related to stress response. In silico expression analysis showed that B. distachyon Prx genes (BdPrx) are tissue specific. RT-qPCR analysis revealed their differential expression when exposed to salt or PEG-induced dehydration stress. In addition, the upregulation of BdPrx genes was accompanied by accumulation of H2 O2 . Exogenous application of H2 O2 induced expression of almost all BdPrx genes. The identified molecular interaction network indicated that Prx proteins may contribute to abiotic stress tolerance by regulating key enzymes involved in lignin biosynthesis. Overall, our findings suggest the potential role of Prx genes in abiotic stress tolerance and lay the foundation for future functional analyses aiming to engineer genetically improved cereal lines.
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Affiliation(s)
- A Farjallah
- Laboratory of Extremophile Plants, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
- Faculty of Sciences and Technics of Sidi Bouzid, University of Kairouan, Kairouan, Tunisia
| | - H Boubakri
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - F Barhoumi
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - R Brahmi
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - M Gandour
- Laboratory of Extremophile Plants, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
- Faculty of Sciences and Technics of Sidi Bouzid, University of Kairouan, Kairouan, Tunisia
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Stritt C, Gimmi EL, Wyler M, Bakali AH, Skalska A, Hasterok R, Mur LAJ, Pecchioni N, Roulin AC. Migration without interbreeding: Evolutionary history of a highly selfing Mediterranean grass inferred from whole genomes. Mol Ecol 2022; 31:70-85. [PMID: 34601787 PMCID: PMC9298040 DOI: 10.1111/mec.16207] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 09/07/2021] [Accepted: 09/28/2021] [Indexed: 11/30/2022]
Abstract
Wild plant populations show extensive genetic subdivision and are far from the ideal of panmixia which permeates population genetic theory. Understanding the spatial and temporal scale of population structure is therefore fundamental for empirical population genetics - and of interest in itself, as it yields insights into the history and biology of a species. In this study we extend the genomic resources for the wild Mediterranean grass Brachypodium distachyon to investigate the scale of population structure and its underlying history at whole-genome resolution. A total of 86 accessions were sampled at local and regional scales in Italy and France, which closes a conspicuous gap in the collection for this model organism. The analysis of 196 accessions, spanning the Mediterranean from Spain to Iraq, suggests that the interplay of high selfing and seed dispersal rates has shaped genetic structure in B. distachyon. At the continental scale, the evolution in B. distachyon is characterized by the independent expansion of three lineages during the Upper Pleistocene. Today, these lineages may occur on the same meadow yet do not interbreed. At the regional scale, dispersal and selfing interact and maintain high genotypic diversity, thus challenging the textbook notion that selfing in finite populations implies reduced diversity. Our study extends the population genomic resources for B. distachyon and suggests that an important use of this wild plant model is to investigate how selfing and dispersal, two processes typically studied separately, interact in colonizing plant species.
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Affiliation(s)
- Christoph Stritt
- Institute for Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Elena L Gimmi
- Institute for Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Michele Wyler
- Institute for Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Abdelmonaim H Bakali
- National Institute of Agronomy, Regional Center of Errachidia, Errachidia, Morocco
| | - Aleksandra Skalska
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Robert Hasterok
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Luis A J Mur
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Wales, UK
| | - Nicola Pecchioni
- Research Centre for Cereal and Industrial Crops, CREA - Council for Agricultural Research and Economics, Foggia, Italy
| | - Anne C Roulin
- Institute for Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
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Monroe JG, Cai H, Des Marais DL. Diversity in nonlinear responses to soil moisture shapes evolutionary constraints in Brachypodium. G3 (BETHESDA, MD.) 2021; 11:jkab334. [PMID: 34570202 PMCID: PMC8664479 DOI: 10.1093/g3journal/jkab334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/15/2021] [Indexed: 12/03/2022]
Abstract
Water availability is perhaps the greatest environmental determinant of plant yield and fitness. However, our understanding of plant-water relations is limited because-like many studies of organism-environment interaction-it is primarily informed by experiments considering performance at two discrete levels-wet and dry-rather than as a continuously varying environmental gradient. Here, we used experimental and statistical methods based on function-valued traits to explore genetic variation in responses to a continuous soil moisture gradient in physiological and morphological traits among 10 genotypes across two species of the model grass genus Brachypodium. We find that most traits exhibit significant genetic variation and nonlinear responses to soil moisture variability. We also observe differences in the shape of these nonlinear responses between traits and genotypes. Emergent phenomena arise from this variation including changes in trait correlations and evolutionary constraints as a function of soil moisture. Our results point to the importance of considering diversity in nonlinear organism-environment relationships to understand plastic and evolutionary responses to changing climates.
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Affiliation(s)
- J Grey Monroe
- Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA
| | - Haoran Cai
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David L Des Marais
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Arnold Arboretum of Harvard University, Boston, MA 02130, USA
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Jiang M, Li P, Wang W. Comparative analysis of MAPK and MKK gene families reveals differential evolutionary patterns in Brachypodium distachyon inbred lines. PeerJ 2021; 9:e11238. [PMID: 33868831 PMCID: PMC8034371 DOI: 10.7717/peerj.11238] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 03/17/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Mitogen-activated protein kinase (MAPK) cascades are involved with signal transduction in almost every aspect of plant growth and development, as well as biotic and abiotic stress responses. The evolutionary analysis of MAPKs and MKKs in individual or entire plant species has been reported, but the evolutionary patterns in the diverse inbred lines of Brachypodium distachyon are still unclear. RESULTS We conducted the systematical molecular evolutionary analysis of B. distachyon. A total of 799 MAPKs and 618 MKKs were identified from 53 B. distachyon inbred lines. Remarkably, only three inbred lines had 16 MPKs and most of those inbred lines lacked MPK7-2 members, whereas 12 MKKs existed in almost all B. distachyon inbred lines. Phylogenetic analysis indicated that MAPKs and MKKs were divided into four groups as previously reported, grouping them in the same branch as corresponding members. MPK21-2 was the exception and fell into two groups, which may be due to their exon-intron patterns, especially the untranslated regions (UTRs). We also found that differential evolution patterns of MKK10 paralogues from ancient tandem duplicates may have undergone functional divergence. Expression analyses suggested that MAPKs and MKKs likely played different roles in different genetic contexts within various tissues and with abiotic stresses. CONCLUSION Our study revealed that UTRs affected the structure and evolution of MPK21-2 genes and the differential evolution of MKK10 paralogues with ancient tandem duplication might have functional divergences. Our findings provide new insights into the functional evolution of genes in closely inbred lines.
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Affiliation(s)
- Min Jiang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai Chenshan Botanical Garden, Shanghai, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Peng Li
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Wei Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai Chenshan Botanical Garden, Shanghai, China
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Genetic and Methylome Variation in Turkish Brachypodium Distachyon Accessions Differentiate Two Geographically Distinct Subpopulations. Int J Mol Sci 2020; 21:ijms21186700. [PMID: 32933168 PMCID: PMC7556024 DOI: 10.3390/ijms21186700] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 09/04/2020] [Accepted: 09/09/2020] [Indexed: 12/13/2022] Open
Abstract
Brachypodium distachyon (Brachypodium) is a non-domesticated model grass species that can be used to test if variation in genetic sequence or methylation are linked to environmental differences. To assess this, we collected seeds from 12 sites within five climatically distinct regions of Turkey. Seeds from each region were grown under standardized growth conditions in the UK to preserve methylated sequence variation. At six weeks following germination, leaves were sampled and assessed for genomic and DNA methylation variation. In a follow-up experiment, phenomic approaches were used to describe plant growth and drought responses. Genome sequencing and population structure analysis suggested three ancestral clusters across the Mediterranean, two of which were geographically separated in Turkey into coastal and central subpopulations. Phenotypic analyses showed that the coastal subpopulation tended to exhibit relatively delayed flowering and the central, increased drought tolerance as indicated by reduced yellowing. Genome-wide methylation analyses in GpC, CHG and CHH contexts also showed variation which aligned with the separation into coastal and central subpopulations. The climate niche modelling of both subpopulations showed a significant influence from the “Precipitation in the Driest Quarter” on the central subpopulation and “Temperature of the Coldest Month” on the coastal subpopulation. Our work demonstrates genetic diversity and variation in DNA methylation in Turkish accessions of Brachypodium that may be associated with climate variables and the molecular basis of which will feature in ongoing analyses.
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Nandety RS, Serrani‐Yarce JC, Gill US, Oh S, Lee H, Zhang X, Dai X, Zhang W, Krom N, Wen J, Zhao PX, Mysore KS. Insertional mutagenesis of Brachypodium distachyon using the Tnt1 retrotransposable element. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1924-1936. [PMID: 32410353 PMCID: PMC7496502 DOI: 10.1111/tpj.14813] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 04/29/2020] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
Brachypodium distachyon is an annual C3 grass used as a monocot model system in functional genomics research. Insertional mutagenesis is a powerful tool for both forward and reverse genetics studies. In this study, we explored the possibility of using the tobacco retrotransposon Tnt1 to create a transposon-based insertion mutant population in B. distachyon. We developed transgenic B. distachyon plants expressing Tnt1 (R0) and in the subsequent regenerants (R1) we observed that Tnt1 actively transposed during somatic embryogenesis, generating an average of 6.37 insertions per line in a population of 19 independent R1 regenerant plants analyzed. In seed-derived progeny of R1 plants, Tnt1 segregated in a Mendelian ratio of 3:1 and no new Tnt1 transposition was observed. A total of 126 flanking sequence tags (FSTs) were recovered from the analyzed R0 and R1 lines. Analysis of the FSTs showed a uniform pattern of insertion in all the chromosomes (1-5) without any preference for a particular chromosome region. Considering the average length of a gene transcript to be 3.37 kb, we estimated that 29 613 lines are required to achieve a 90% possibility of tagging a given gene in the B. distachyon genome using the Tnt1-based mutagenesis approach. Our results show the possibility of using Tnt1 to achieve near-saturation mutagenesis in B. distachyon, which will aid in functional genomics studies of other C3 grasses.
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Affiliation(s)
| | - Juan C. Serrani‐Yarce
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
- Present address:
Department of Biological SciencesUniversity of North TexasDentonTX76203USA
| | - Upinder S. Gill
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
- Present address:
Department of Plant PathologyNorth Dakota State UniversityFargoND58102USA
| | - Sunhee Oh
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
| | - Hee‐Kyung Lee
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
| | - Xinji Zhang
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
| | - Xinbin Dai
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
| | - Wenchao Zhang
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
| | - Nick Krom
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
| | - Jiangqi Wen
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
| | - Patrick X. Zhao
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
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Eichten SR, Srivastava A, Reddiex AJ, Ganguly DR, Heussler A, Streich JC, Wilson PB, Borevitz JO. Extending the Genotype in Brachypodium by Including DNA Methylation Reveals a Joint Contribution with Genetics on Adaptive Traits. G3 (BETHESDA, MD.) 2020; 10:1629-1637. [PMID: 32132166 PMCID: PMC7202021 DOI: 10.1534/g3.120.401189] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epigenomic changes have been considered a potential missing link underlying phenotypic variation in quantitative traits but is potentially confounded with the underlying DNA sequence variation. Although the concept of epigenetic inheritance has been discussed in depth, there have been few studies attempting to directly dissect the amount of epigenomic variation within inbred natural populations while also accounting for genetic diversity. By using known genetic relationships between Brachypodium lines, multiple sets of nearly identical accession families were selected for phenotypic studies and DNA methylome profiling to investigate the dual role of (epi)genetics under simulated natural seasonal climate conditions. Despite reduced genetic diversity, appreciable phenotypic variation was still observable in the measured traits (height, leaf width and length, tiller count, flowering time, ear count) between as well as within the inbred accessions. However, with reduced genetic diversity there was diminished variation in DNA methylation within families. Mixed-effects linear modeling revealed large genetic differences between families and a minor contribution of DNA methylation variation on phenotypic variation in select traits. Taken together, this analysis suggests a limited but significant contribution of DNA methylation toward heritable phenotypic variation relative to genetic differences.
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Affiliation(s)
- Steven R Eichten
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Acton, Australian Capital Territory 2601, Australia
| | - Akanksha Srivastava
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Acton, Australian Capital Territory 2601, Australia
| | - Adam J Reddiex
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Acton, Australian Capital Territory 2601, Australia
| | - Diep R Ganguly
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Acton, Australian Capital Territory 2601, Australia
| | - Alison Heussler
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Acton, Australian Capital Territory 2601, Australia
| | - Jared C Streich
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Acton, Australian Capital Territory 2601, Australia
| | - Pip B Wilson
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Acton, Australian Capital Territory 2601, Australia
| | - Justin O Borevitz
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Acton, Australian Capital Territory 2601, Australia
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Shiposha V, Marques I, López-Alvarez D, Manzaneda AJ, Hernandez P, Olonova M, Catalán P. Multiple founder events explain the genetic diversity and structure of the model allopolyploid grass Brachypodium hybridum in the Iberian Peninsula hotspot. ANNALS OF BOTANY 2020; 125:625-638. [PMID: 31630169 PMCID: PMC7442330 DOI: 10.1093/aob/mcz169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 10/16/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND AND AIMS It is accepted that contemporary allopolyploid species have originated recurrently, but very few cases have been documented using multiple natural formations of the same species. To extend our knowledge, we have investigated the multiple origins, genetic variation and structure of the allotetraploid grass Brachypodium hybridum with respect to its progenitor diploid species B. distachyon (D genome) and B. stacei (S genome). For this, our primary focus is the Iberian Peninsula, an evolutionary hotspot for the genus Brachypodium. METHODS We analysed 342 B. hybridum individuals from 36 populations using ten nuclear SSR loci and two plastid loci. The B. hybridum genetic profiles were compared with those previously reported for B. stacei and B. distachyon. In addition, phylogenetic analysis of the plastid data was performed for a reduced subset of individuals. KEY RESULTS The nuclear simple sequence repeat (SSR) genetic analysis detected medium to high genetic diversity, with a strong south-to-north genetic structure cline, and a high selfing rate in B. hybridum. Comparative genetic analysis showed a close relatedness of current B. hybridum D allelic profiles with those of B. distachyon, but a lack of similarity with those of B. stacei, suggesting another B. stacei source for the B. hybridum S alleles. Plastid analysis detected three different bidirectional allopolyploidization events: two involved distinct B. distachyon-like ancestors and one involved a B. stacei-like ancestor. The south-eastern Iberian Peninsula B. hybridum populations were more genetically diverse and could have originated from at least two hybridization events whereas north-eastern/north-western Iberian Peninsula B. hybridum populations were less diverse and may have derived from at least one hybridization event. CONCLUSIONS The genetic and evolutionary evidence supports the plausible in situ origin of the south-eastern and northern Iberian Peninsula B. hybridum allopolyploids from their respective local B. distachyon and unknown B. stacei ancestors. The untapped multiple origins and genetic variation detected in these B. hybridum populations opens the way to future evolutionary analysis of allopolyploid formation and genomic dominance and expression in the B. hybridum-B. distachyon-B. stacei grass model complex.
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Affiliation(s)
- Valeriia Shiposha
- Departamento de Ciencias Agrarias y del Medio Natural, Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Ctra. Cuarte km 1, 22071 Huesca, Spain
- Department of Botany, Institute of Biology, Tomsk State University, Lenin Av. 36, Tomsk 634050, Russia
| | - Isabel Marques
- Departamento de Ciencias Agrarias y del Medio Natural, Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Ctra. Cuarte km 1, 22071 Huesca, Spain
- LEAF, School of Agriculture, Instituto Superior de Agronomia and cE3c-Centre for Ecology Evolution and Environmental Changes, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Diana López-Alvarez
- Departamento de Ciencias Agrarias y del Medio Natural, Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Ctra. Cuarte km 1, 22071 Huesca, Spain
| | - Antonio J Manzaneda
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Paraje Las Lagunillas s/n, 23071 Jaén, Spain
| | - Pilar Hernandez
- Instituto de Agricultura Sostenible (IAS-CSIC), Alameda del Obispo s/n, 14004 Córdoba, Spainand
| | - Marina Olonova
- Department of Botany, Institute of Biology, Tomsk State University, Lenin Av. 36, Tomsk 634050, Russia
| | - Pilar Catalán
- Departamento de Ciencias Agrarias y del Medio Natural, Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Ctra. Cuarte km 1, 22071 Huesca, Spain
- Department of Botany, Institute of Biology, Tomsk State University, Lenin Av. 36, Tomsk 634050, Russia
- Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza 50059, Spain
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Neji M, Kouas S, Gandour M, Aydi S, Abdelly C. Genetic variability of morpho-physiological response to phosphorus deficiency in Tunisian populations of Brachypodium hybridum. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 143:246-256. [PMID: 31525602 DOI: 10.1016/j.plaphy.2019.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/03/2019] [Accepted: 09/04/2019] [Indexed: 06/10/2023]
Abstract
Brachypodium hybridum (Poaceae) is widely distributed in the dry environments in Mediterranean basin, due to its high tolerance to drought. Investigating the natural variation of B. hybridum in response to environmental stresses is crucial for unraveling the genetic network of its stress tolerance. 79 B. hybridum lines from eight Tunisian populations were screened for their performance to low P availability using morpho-physiological parameters. ANOVA showed that treatment and population*treatment factors were the most contributors in the explained variance for the majority of parameters. A considerable population differentiation was detected in control and under P level (Qst = 0.77 vs Qst = 0.62). This suggests that B. hybridum exhibit an adaptive differential response to P deficiency related environmental conditions. Results revealed that Raouad and Sejnen lines were the most tolerant to P deficiency followed by Haouaria and Enfidha lines. The remaining populations were classified as sensitive. This pattern suggests that coastal populations were more tolerant to P deficiency than the inland ones. A slightly higher heritability was evidenced under low P level for most of traits, indicating that the direct selection under P deficiency is more reliable than an indirect one under optimal P supply.
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Affiliation(s)
- Mohamed Neji
- Laboratory of Extremophile Plants, Centre of Biotechnology of Borj Cedria, BP 901 Hammam Lif 2050, Tunisia; Department of Life Sciences, Faculty of Sciences of Gabès, University of Gabès, Cité Erriadh 6072 Zrig, Gabès, Tunisia; Unit of Evolutionary Biology & Ecology, Faculté des Sciences, Université Libre de Bruxelles, Av. F.D. Roosevelt, 50, CP 160/12, B-1050, Brussels, Belgium.
| | - Saber Kouas
- Laboratory of Extremophile Plants, Centre of Biotechnology of Borj Cedria, BP 901 Hammam Lif 2050, Tunisia; Department of Life Sciences, Faculty of Sciences of Gabès, University of Gabès, Cité Erriadh 6072 Zrig, Gabès, Tunisia; Plant Physiology and Functional Genomics Research Unit, Institute of Biotechnology, University of Sfax, BP 1175, 3038 Sfax, Tunisia
| | - Mhemmed Gandour
- Laboratory of Extremophile Plants, Centre of Biotechnology of Borj Cedria, BP 901 Hammam Lif 2050, Tunisia; Faculty of Sciences and Technology of Sidi Bouzid, 9100, Sidi Bouzid, Tunisia
| | - Samir Aydi
- Department of Life Sciences, Faculty of Sciences of Gabès, University of Gabès, Cité Erriadh 6072 Zrig, Gabès, Tunisia
| | - Chedly Abdelly
- Laboratory of Extremophile Plants, Centre of Biotechnology of Borj Cedria, BP 901 Hammam Lif 2050, Tunisia
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Brew-Appiah RAT, Peracchi LM, Sanguinet KA. Never the Two Shall Mix: Robust Indel Markers to Ensure the Fidelity of Two Pivotal and Closely-Related Accessions of Brachypodium distachyon. PLANTS 2019; 8:plants8060153. [PMID: 31174296 PMCID: PMC6630600 DOI: 10.3390/plants8060153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 05/30/2019] [Accepted: 06/05/2019] [Indexed: 11/25/2022]
Abstract
Brachypodium distachyon is an established model for monocotyledonous plants. Numerous markers intended for gene discovery and population genetics have been designed. However to date, very few indel markers with larger and easily scored length polymorphism differences, that distinguish between the two morphologically similar and highly utilized B. distachyon accessions, Bd21, the reference genome accession, and Bd21-3, the transformation-optimal accession, are publically available. In this study, 22 indel markers were designed and utilized to produce length polymorphism differences of 150 bp or more, for easy discrimination between Bd21 and Bd21-3. When tested on four other B. distachyon accessions, one case of multiallelism was observed. It was also shown that the markers could be used to determine homozygosity and heterozygosity at specific loci in a Bd21 x Bd3-1 F2 population. The work done in this study allows researchers to maintain the fidelity of Bd21 and Bd21-3 stocks for both transgenic and nontransgenic studies. It also provides markers that can be utilized in conjunction with others already available for further research on population genetics, gene discovery and gene characterization, all of which are necessary for the relevance of B. distachyon as a model species.
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Affiliation(s)
- Rhoda A T Brew-Appiah
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, USA.
| | - Luigi M Peracchi
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, USA.
| | - Karen A Sanguinet
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, USA.
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Onda Y, Inoue K, Sawada Y, Shimizu M, Takahagi K, Uehara-Yamaguchi Y, Hirai MY, Garvin DF, Mochida K. Genetic Variation for Seed Metabolite Levels in Brachypodium distachyon. Int J Mol Sci 2019; 20:ijms20092348. [PMID: 31083584 PMCID: PMC6540107 DOI: 10.3390/ijms20092348] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/26/2019] [Accepted: 04/27/2019] [Indexed: 12/27/2022] Open
Abstract
Metabolite composition and concentrations in seed grains are important traits of cereals. To identify the variation in the seed metabolotypes of a model grass, namely Brachypodium distachyon, we applied a widely targeted metabolome analysis to forty inbred lines of B. distachyon and examined the accumulation patterns of 183 compounds in the seeds. By comparing the metabolotypes with the population structure of these lines, we found signature metabolites that represent different accumulation patterns for each of the three B. distachyon subpopulations. Moreover, we found that thirty-seven metabolites exhibited significant differences in their accumulation between the lines Bd21 and Bd3-1. Using a recombinant inbred line (RIL) population from a cross between Bd3-1 and Bd21, we identified the quantitative trait loci (QTLs) linked with this variation in the accumulation of thirteen metabolites. Our metabolite QTL analysis illustrated that different genetic factors may presumably regulate the accumulation of 4-pyridoxate and pyridoxamine in vitamin B6 metabolism. Moreover, we found two QTLs on chromosomes 1 and 4 that affect the accumulation of an anthocyanin, chrysanthemin. These QTLs genetically interacted to regulate the accumulation of this compound. This study demonstrates the potential for metabolite QTL mapping in B. distachyon and provides new insights into the genetic dissection of metabolomic traits in temperate grasses.
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Affiliation(s)
- Yoshihiko Onda
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.
| | - Komaki Inoue
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Yuji Sawada
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Minami Shimizu
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Kotaro Takahagi
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Yukiko Uehara-Yamaguchi
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Masami Y Hirai
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - David F Garvin
- Plant Science Research Unit, United States Department of Agriculture, Agricultural Research Service, 1991 Upper Buford Circle, St. Paul, MN 55108, USA.
| | - Keiichi Mochida
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Institute of Plant Science and Resource, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan.
- Microalgae Production Control Technology Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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12
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Lenk I, Fisher LHC, Vickers M, Akinyemi A, Didion T, Swain M, Jensen CS, Mur LAJ, Bosch M. Transcriptional and Metabolomic Analyses Indicate that Cell Wall Properties are Associated with Drought Tolerance in Brachypodium distachyon. Int J Mol Sci 2019; 20:E1758. [PMID: 30974727 PMCID: PMC6479473 DOI: 10.3390/ijms20071758] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/03/2019] [Accepted: 04/08/2019] [Indexed: 01/07/2023] Open
Abstract
Brachypodium distachyon is an established model for drought tolerance. We previously identified accessions exhibiting high tolerance, susceptibility and intermediate tolerance to drought; respectively, ABR8, KOZ1 and ABR4. Transcriptomics and metabolomic approaches were used to define tolerance mechanisms. Transcriptional analyses suggested relatively few drought responsive genes in ABR8 compared to KOZ1. Linking these to gene ontology (GO) terms indicated enrichment for "regulated stress response", "plant cell wall" and "oxidative stress" associated genes. Further, tolerance correlated with pre-existing differences in cell wall-associated gene expression including glycoside hydrolases, pectin methylesterases, expansins and a pectin acetylesterase. Metabolomic assessments of the same samples also indicated few significant changes in ABR8 with drought. Instead, pre-existing differences in the cell wall-associated metabolites correlated with drought tolerance. Although other features, e.g., jasmonate signaling were suggested in our study, cell wall-focused events appeared to be predominant. Our data suggests two different modes through which the cell wall could confer drought tolerance: (i) An active response mode linked to stress induced changes in cell wall features, and (ii) an intrinsic mode where innate differences in cell wall composition and architecture are important. Both modes seem to contribute to ABR8 drought tolerance. Identification of the exact mechanisms through which the cell wall confers drought tolerance will be important in order to inform development of drought tolerant crops.
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Affiliation(s)
- Ingo Lenk
- DLF Seeds A/S, Højerupvej 31, 4660 Store Heddinge, Denmark.
| | - Lorraine H C Fisher
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3EE, UK.
| | - Martin Vickers
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3EE, UK.
| | - Aderemi Akinyemi
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3EE, UK.
| | - Thomas Didion
- DLF Seeds A/S, Højerupvej 31, 4660 Store Heddinge, Denmark.
| | - Martin Swain
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3EE, UK.
| | | | - Luis A J Mur
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3EE, UK.
| | - Maurice Bosch
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3EE, UK.
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13
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Handakumbura PP, Stanfill B, Rivas-Ubach A, Fortin D, Vogel JP, Jansson C. Metabotyping as a Stopover in Genome-to-Phenome Mapping. Sci Rep 2019; 9:1858. [PMID: 30755686 PMCID: PMC6372633 DOI: 10.1038/s41598-019-38483-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 12/21/2018] [Indexed: 01/01/2023] Open
Abstract
Predicting phenotypic expression from genomic and environmental information is arguably the greatest challenge in today's biology. Being able to survey genomic content, e.g., as single-nucleotide polymorphism data, within a diverse population and predict the phenotypes of external traits, represents the holy grail across genome-informed disciplines, from personal medicine and nutrition to plant breeding. In the present study, we propose a two-step procedure in bridging the genome to phenome gap where external phenotypes are viewed as emergent properties of internal phenotypes, such as molecular profiles, in interaction with the environment. Using biomass accumulation and shoot-root allometry as external traits in diverse genotypes of the model grass Brachypodium distachyon, we established correlative models between genotypes and metabolite profiles (metabotypes) as internal phenotypes, and between metabotypes and external phenotypes under two contrasting watering regimes. Our results demonstrate the potential for employing metabotypes as an integrator in predicting external phenotypes from genomic information.
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Affiliation(s)
- Pubudu P Handakumbura
- The Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Washington, WA, 99352, USA.
| | - Bryan Stanfill
- Advanced Computing, Computing and Analytics Division, PNNL, Richland, WA, 99352, USA
| | - Albert Rivas-Ubach
- The Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Washington, WA, 99352, USA
| | - Dan Fortin
- Advanced Computing, Computing and Analytics Division, PNNL, Richland, WA, 99352, USA
| | - John P Vogel
- US Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA
| | - Christer Jansson
- The Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Washington, WA, 99352, USA.
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14
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Wilson PB, Streich JC, Murray KD, Eichten SR, Cheng R, Aitken NC, Spokas K, Warthmann N, Gordon SP, Vogel JP, Borevitz JO. Global Diversity of the Brachypodium Species Complex as a Resource for Genome-Wide Association Studies Demonstrated for Agronomic Traits in Response to Climate. Genetics 2019; 211:317-331. [PMID: 30446522 PMCID: PMC6325704 DOI: 10.1534/genetics.118.301589] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 11/08/2018] [Indexed: 01/29/2023] Open
Abstract
The development of model systems requires a detailed assessment of standing genetic variation across natural populations. The Brachypodium species complex has been promoted as a plant model for grass genomics with translation to small grain and biomass crops. To capture the genetic diversity within this species complex, thousands of Brachypodium accessions from around the globe were collected and genotyped by sequencing. Overall, 1897 samples were classified into two diploid or allopolyploid species, and then further grouped into distinct inbred genotypes. A core set of diverse B. distachyon diploid lines was selected for whole genome sequencing and high resolution phenotyping. Genome-wide association studies across simulated seasonal environments was used to identify candidate genes and pathways tied to key life history and agronomic traits under current and future climatic conditions. A total of 8, 22, and 47 QTL were identified for flowering time, early vigor, and energy traits, respectively. The results highlight the genomic structure of the Brachypodium species complex, and the diploid lines provided a resource that allows complex trait dissection within this grass model species.
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Affiliation(s)
- Pip B Wilson
- The ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 200, Australia
| | - Jared C Streich
- The ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 200, Australia
| | - Kevin D Murray
- The ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 200, Australia
| | - Steve R Eichten
- The ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 200, Australia
| | - Riyan Cheng
- The ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 200, Australia
- Department of Psychiatry, University of California San Diego, La Jolla, California 92093
| | - Nicola C Aitken
- The ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 200, Australia
- Ecogenomics and Bioinformatics Lab, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 200, Australia
| | - Kurt Spokas
- Soil and Water Management, Agricultural Research Service, United States Department of Agricutlture (USDA), St. Paul, Minnesota 55108
| | - Norman Warthmann
- The ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 200, Australia
| | - Sean P Gordon
- Department of Energy, Joint Genome Institute, Walnut Creek, California 94598
| | - John P Vogel
- Department of Energy, Joint Genome Institute, Walnut Creek, California 94598
| | - Justin O Borevitz
- The ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 200, Australia
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15
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Omidvar V, Dugyala S, Li F, Rottschaefer SM, Miller ME, Ayliffe M, Moscou MJ, Kianian SF, Figueroa M. Detection of Race-Specific Resistance Against Puccinia coronata f. sp. avenae in Brachypodium Species. PHYTOPATHOLOGY 2018; 108:1443-1454. [PMID: 29923800 DOI: 10.1094/phyto-03-18-0084-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Oat crown rust caused by Puccinia coronata f. sp. avenae is the most destructive foliar disease of cultivated oat. Characterization of genetic factors controlling resistance responses to Puccinia coronata f. sp. avenae in nonhost species could provide new resources for developing disease protection strategies in oat. We examined symptom development and fungal colonization levels of a collection of Brachypodium distachyon and B. hybridum accessions infected with three North American P. coronata f. sp. avenae isolates. Our results demonstrated that colonization phenotypes are dependent on both host and pathogen genotypes, indicating a role for race-specific responses in these interactions. These responses were independent of the accumulation of reactive oxygen species. Expression analysis of several defense-related genes suggested that salicylic acid and ethylene-mediated signaling but not jasmonic acid are components of resistance reaction to P. coronata f. sp. avenae. Our findings provide the basis to conduct a genetic inheritance study to examine whether effector-triggered immunity contributes to nonhost resistance to P. coronata f. sp. avenae in Brachypodium spp.
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Affiliation(s)
- Vahid Omidvar
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Sheshanka Dugyala
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Feng Li
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Susan M Rottschaefer
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Marisa E Miller
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Mick Ayliffe
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Matthew J Moscou
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Shahryar F Kianian
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Melania Figueroa
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
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16
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Stritt C, Gordon SP, Wicker T, Vogel JP, Roulin AC. Recent Activity in Expanding Populations and Purifying Selection Have Shaped Transposable Element Landscapes across Natural Accessions of the Mediterranean Grass Brachypodium distachyon. Genome Biol Evol 2018; 10:304-318. [PMID: 29281015 PMCID: PMC5786231 DOI: 10.1093/gbe/evx276] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2017] [Indexed: 01/05/2023] Open
Abstract
Transposable element (TE) activity has emerged as a major cause of variation in genome size and structure among species. To what extent TEs contribute to genetic variation and divergence within species, however, is much less clear, mainly because population genomic data have so far only been available for the classical model organisms. In this study, we use the annual Mediterranean grass Brachypodium distachyon to investigate TE dynamics in natural populations. Using whole-genome sequencing data for 53 natural accessions, we identified more than 5,400 TE polymorphisms across the studied genomes. We found, first, that while population bottlenecks and expansions have shaped genetic diversity in B. distachyon, these events did not lead to lineage-specific activations of TE families, as observed in other species. Instead, the same families have been active across the species range and TE activity is homogeneous across populations, indicating the presence of conserved regulatory mechanisms. Second, almost half of the TE insertion polymorphisms are accession-specific, most likely because of recent activity in expanding populations and the action of purifying selection. And finally, although TE insertion polymorphisms are underrepresented in and around genes, more than 1,000 of them occur in genic regions and could thus contribute to functional divergence. Our study shows that while TEs in B. distachyon are “well-behaved” compared with TEs in other species with larger genomes, they are an abundant source of lineage-specific genetic variation and may play an important role in population divergence and adaptation.
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Affiliation(s)
- Christoph Stritt
- Institute for Plant and Microbial Biology, University of Zurich, Switzerland
| | - Sean P Gordon
- DOE Joint Genome Institute, Walnut Creek, California
| | - Thomas Wicker
- Institute for Plant and Microbial Biology, University of Zurich, Switzerland
| | - John P Vogel
- DOE Joint Genome Institute, Walnut Creek, California
| | - Anne C Roulin
- Institute for Plant and Microbial Biology, University of Zurich, Switzerland
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17
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Gilbert B, Bettgenhaeuser J, Upadhyaya N, Soliveres M, Singh D, Park RF, Moscou MJ, Ayliffe M. Components of Brachypodium distachyon resistance to nonadapted wheat stripe rust pathogens are simply inherited. PLoS Genet 2018; 14:e1007636. [PMID: 30265668 PMCID: PMC6161853 DOI: 10.1371/journal.pgen.1007636] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 08/15/2018] [Indexed: 11/19/2022] Open
Abstract
Phytopathogens have a limited range of host plant species that they can successfully parasitise ie. that they are adapted for. Infection of plants by nonadapted pathogens often results in an active resistance response that is relatively poorly characterised because phenotypic variation in this response often does not exist within a plant species, or is too subtle for genetic dissection. In addition, complex polygenic inheritance often underlies these resistance phenotypes and mutagenesis often does not impact upon this resistance, presumably due to genetic or mechanistic redundancy. Here it is demonstrated that phenotypic differences in the resistance response of Brachypodium distachyon to the nonadapted wheat stripe rust pathogen Puccinia striiformis f. sp. tritici (Pst) are genetically tractable and simply inherited. Two dominant loci were identified on B. distachyon chromosome 4 that each reduce attempted Pst colonisation compared with sib and parent lines without these loci. One locus (Yrr1) is effective against diverse Australian Pst isolates and present in two B. distachyon mapping families as a conserved region that was reduced to 5 candidate genes by fine mapping. A second locus, Yrr2, shows Pst race-specificity and encodes a disease resistance gene family typically associated with host plant resistance. These data indicate that some components of resistance to nonadapted pathogens are genetically tractable in some instances and may mechanistically overlap with host plant resistance to avirulent adapted pathogens.
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Affiliation(s)
- Brian Gilbert
- CSIRO Agriculture and Food, Clunies Ross Drive, Canberra, ACT, Australia
| | - Jan Bettgenhaeuser
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Narayana Upadhyaya
- CSIRO Agriculture and Food, Clunies Ross Drive, Canberra, ACT, Australia
| | - Melanie Soliveres
- CSIRO Agriculture and Food, Clunies Ross Drive, Canberra, ACT, Australia
| | - Davinder Singh
- University of Sydney, Plant Breeding Institute, Cobbitty, NSW, Australia
| | - Robert F. Park
- University of Sydney, Plant Breeding Institute, Cobbitty, NSW, Australia
| | - Matthew J. Moscou
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
- University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Michael Ayliffe
- CSIRO Agriculture and Food, Clunies Ross Drive, Canberra, ACT, Australia
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18
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Shah T, Xu J, Zou X, Cheng Y, Nasir M, Zhang X. Omics Approaches for Engineering Wheat Production under Abiotic Stresses. Int J Mol Sci 2018; 19:E2390. [PMID: 30110906 PMCID: PMC6121627 DOI: 10.3390/ijms19082390] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 07/14/2018] [Accepted: 07/24/2018] [Indexed: 02/05/2023] Open
Abstract
Abiotic stresses greatly influenced wheat productivity executed by environmental factors such as drought, salt, water submergence and heavy metals. The effective management at the molecular level is mandatory for a thorough understanding of plant response to abiotic stress. Understanding the molecular mechanism of stress tolerance is complex and requires information at the omic level. In the areas of genomics, transcriptomics and proteomics enormous progress has been made in the omics field. The rising field of ionomics is also being utilized for examining abiotic stress resilience in wheat. Omic approaches produce a huge amount of data and sufficient developments in computational tools have been accomplished for efficient analysis. However, the integration of omic-scale information to address complex genetics and physiological questions is still a challenge. Though, the incorporation of omic-scale data to address complex genetic qualities and physiological inquiries is as yet a challenge. In this review, we have reported advances in omic tools in the perspective of conventional and present day approaches being utilized to dismember abiotic stress tolerance in wheat. Attention was given to methodologies, for example, quantitative trait loci (QTL), genome-wide association studies (GWAS) and genomic selection (GS). Comparative genomics and candidate genes methodologies are additionally talked about considering the identification of potential genomic loci, genes and biochemical pathways engaged with stress resilience in wheat. This review additionally gives an extensive list of accessible online omic assets for wheat and its effective use. We have additionally addressed the significance of genomics in the integrated approach and perceived high-throughput multi-dimensional phenotyping as a significant restricting component for the enhancement of abiotic stress resistance in wheat.
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Affiliation(s)
- Tariq Shah
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China.
| | - Jinsong Xu
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China.
| | - Xiling Zou
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China.
| | - Yong Cheng
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China.
| | - Mubasher Nasir
- College of Natural Resources and Environment, Northwest Agriculture and Forestry University, Yangling 712100, China.
| | - Xuekun Zhang
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China.
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19
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Scholthof KBG, Irigoyen S, Catalan P, Mandadi KK. Brachypodium: A Monocot Grass Model Genus for Plant Biology. THE PLANT CELL 2018; 30:1673-1694. [PMID: 29997238 PMCID: PMC6139682 DOI: 10.1105/tpc.18.00083] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/25/2018] [Accepted: 07/11/2018] [Indexed: 05/21/2023]
Abstract
The genus Brachypodium represents a model system that is advancing our knowledge of the biology of grasses, including small grains, in the postgenomics era. The most widely used species, Brachypodium distachyon, is a C3 plant that is distributed worldwide. B. distachyon has a small genome, short life cycle, and small stature and is amenable to genetic transformation. Due to the intensive and thoughtful development of this grass as a model organism, it is well-suited for laboratory and field experimentation. The intent of this review is to introduce this model system genus and describe some key outcomes of nearly a decade of research since the first draft genome sequence of the flagship species, B. distachyon, was completed. We discuss characteristics and features of B. distachyon and its congeners that make the genus a valuable model system for studies in ecology, evolution, genetics, and genomics in the grasses, review current hot topics in Brachypodium research, and highlight the potential for future analysis using this system in the coming years.
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Affiliation(s)
- Karen-Beth G Scholthof
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843
| | - Sonia Irigoyen
- Texas A&M AgriLife Research and Extension Center, Weslaco, Texas 78596
| | - Pilar Catalan
- Universidad de Zaragoza-Escuela Politécnica Superior de Huesca, 22071 Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza E-50059, Spain
- Institute of Biology, Tomsk State University, Tomsk 634050, Russia
| | - Kranthi K Mandadi
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843
- Texas A&M AgriLife Research and Extension Center, Weslaco, Texas 78596
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Zhu T, Hu Z, Rodriguez JC, Deal KR, Dvorak J, Vogel JP, Liu Z, Luo MC. Analysis of Brachypodium genomes with genome-wide optical maps. Genome 2018; 61:559-565. [PMID: 29883550 DOI: 10.1139/gen-2018-0013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Brachypodium distachyon (n = 5) is a diploid and has been widely used as a genetic model. Brachypodium stacei (n = 10) and B. hybridum (n = 15) are species that are related to B. distachyon, leading to an hypothesis that they are part of a polyploid series based on x = 5. Several lines of evidence suggest that this hypothesis is incorrect and that the genomes of the three taxa may have evolved by a more complex process. We constructed an optical whole-genome BioNano genome (BNG) map for each species and did pairwise alignment of the BNG maps. The maps showed that B. distachyon and B. stacei are both diploid, in spite of B. stacei having twice as many chromosomes as B. distachyon, and that B. hybridum is an allopolyploid formed from hybridization between B. distachyon and B. stacei. This study also demonstrated the use of BNG maps in the detection and quantification of structural variants among the genomes.
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Affiliation(s)
- Tingting Zhu
- a Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Zhaorong Hu
- a Department of Plant Sciences, University of California, Davis, CA 95616, USA.,b State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Juan C Rodriguez
- a Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Karin R Deal
- a Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Jan Dvorak
- a Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - John P Vogel
- c DOE Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, CA 94598, USA
| | - Zhiyong Liu
- d State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ming-Cheng Luo
- a Department of Plant Sciences, University of California, Davis, CA 95616, USA
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Sancho R, Cantalapiedra CP, López-Alvarez D, Gordon SP, Vogel JP, Catalán P, Contreras-Moreira B. Comparative plastome genomics and phylogenomics of Brachypodium: flowering time signatures, introgression and recombination in recently diverged ecotypes. THE NEW PHYTOLOGIST 2018; 218:1631-1644. [PMID: 29206296 DOI: 10.1111/nph.14926] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 03/03/2017] [Indexed: 05/24/2023]
Abstract
Few pan-genomic studies have been conducted in plants, and none of them have focused on the intraspecific diversity and evolution of their plastid genomes. We address this issue in Brachypodium distachyon and its close relatives B. stacei and B. hybridum, for which a large genomic data set has been compiled. We analyze inter- and intraspecific plastid comparative genomics and phylogenomic relationships within a family-wide framework. Major indel differences were detected between Brachypodium plastomes. Within B. distachyon, we detected two main lineages, a mostly Extremely Delayed Flowering (EDF+) clade and a mostly Spanish (S+) - Turkish (T+) clade, plus nine chloroplast capture and two plastid DNA (ptDNA) introgression and micro-recombination events. Early Oligocene (30.9 million yr ago (Ma)) and Late Miocene (10.1 Ma) divergence times were inferred for the respective stem and crown nodes of Brachypodium and a very recent Mid-Pleistocene (0.9 Ma) time for the B. distachyon split. Flowering time variation is a main factor driving rapid intraspecific divergence in B. distachyon, although it is counterbalanced by repeated introgression between previously isolated lineages. Swapping of plastomes between the three different genomic groups, EDF+, T+, S+, probably resulted from random backcrossing followed by stabilization through selection pressure.
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Affiliation(s)
- Rubén Sancho
- Department of Agricultural and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Saragossa, Spain
| | - Carlos P Cantalapiedra
- Department of Genetics and Plant Breeding, Estación Experimental de Aula Dei-Consejo Superior de Investigaciones Científicas, Zaragoza, Spain
| | - Diana López-Alvarez
- Department of Agricultural and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza, Huesca, Spain
| | - Sean P Gordon
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - John P Vogel
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Pilar Catalán
- Department of Agricultural and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Saragossa, Spain
| | - Bruno Contreras-Moreira
- Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Saragossa, Spain
- Department of Genetics and Plant Breeding, Estación Experimental de Aula Dei-Consejo Superior de Investigaciones Científicas, Zaragoza, Spain
- Fundación ARAID, Zaragoza, Spain
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Metz J, Freundt H, Jeltsch F. Stable germination behavior but partly changing seed–seed interactions along a steep rainfall gradient. Basic Appl Ecol 2018. [DOI: 10.1016/j.baae.2018.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Onda Y, Takahagi K, Shimizu M, Inoue K, Mochida K. Multiplex PCR Targeted Amplicon Sequencing (MTA-Seq): Simple, Flexible, and Versatile SNP Genotyping by Highly Multiplexed PCR Amplicon Sequencing. FRONTIERS IN PLANT SCIENCE 2018; 9:201. [PMID: 29628929 PMCID: PMC5876661 DOI: 10.3389/fpls.2018.00201] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 02/02/2018] [Indexed: 05/20/2023]
Abstract
Next-generation sequencing (NGS) technologies have enabled genome re-sequencing for exploring genome-wide polymorphisms among individuals, as well as targeted re-sequencing for the rapid and simultaneous detection of polymorphisms in genes associated with various biological functions. Therefore, a simple and robust method for targeted re-sequencing should facilitate genotyping in a wide range of biological fields. In this study, we developed a simple, custom, targeted re-sequencing method, designated "multiplex PCR targeted amplicon sequencing (MTA-seq)," and applied it to the genotyping of the model grass Brachypodium distachyon. To assess the practical usability of MTA-seq, we applied it to the genotyping of genome-wide single-nucleotide polymorphisms (SNPs) identified in natural accessions (Bd1-1, Bd3-1, Bd21-3, Bd30-1, Koz-1, Koz-3, and Koz-4) by comparing the re-sequencing data with that of reference accession Bd21. Examination of SNP-genotyping accuracy in 443 amplicons from eight parental accessions and an F1 progeny derived by crossing of Bd21 and Bd3-1 revealed that ~95% of the SNPs were correctly called. The assessment suggested that the method provided an efficient framework for accurate and robust SNP genotyping. The method described here enables easy design of custom target SNP-marker panels in various organisms, facilitating a wide range of high-throughput genetic applications, such as genetic mapping, population analysis, molecular breeding, and genomic diagnostics.
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Affiliation(s)
- Yoshihiko Onda
- Cellulose Production Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Kotaro Takahagi
- Cellulose Production Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan
| | - Minami Shimizu
- Cellulose Production Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Komaki Inoue
- Cellulose Production Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Keiichi Mochida
- Cellulose Production Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- Institute of Plant Science and Resource, Okayama University, Okayama, Japan
- *Correspondence: Keiichi Mochida
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Kouzai Y, Kimura M, Watanabe M, Kusunoki K, Osaka D, Suzuki T, Matsui H, Yamamoto M, Ichinose Y, Toyoda K, Matsuura T, Mori IC, Hirayama T, Minami E, Nishizawa Y, Inoue K, Onda Y, Mochida K, Noutoshi Y. Salicylic acid-dependent immunity contributes to resistance against Rhizoctonia solani, a necrotrophic fungal agent of sheath blight, in rice and Brachypodium distachyon. THE NEW PHYTOLOGIST 2018; 217:771-783. [PMID: 29048113 PMCID: PMC5765516 DOI: 10.1111/nph.14849] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 09/13/2017] [Indexed: 05/20/2023]
Abstract
Rhizoctonia solani is a soil-borne fungus causing sheath blight. In consistent with its necrotrophic life style, no rice cultivars fully resistant to R. solani are known, and agrochemical plant defense activators used for rice blast, which upregulate a phytohormonal salicylic acid (SA)-dependent pathway, are ineffective towards this pathogen. As a result of the unavailability of genetics, the infection process of R. solani remains unclear. We used the model monocotyledonous plants Brachypodium distachyon and rice, and evaluated the effects of phytohormone-induced resistance to R. solani by pharmacological, genetic and microscopic approaches to understand fungal pathogenicity. Pretreatment with SA, but not with plant defense activators used in agriculture, can unexpectedly induce sheath blight resistance in plants. SA treatment inhibits the advancement of R. solani to the point in the infection process in which fungal biomass shows remarkable expansion and specific infection machinery is developed. The involvement of SA in R. solani resistance is demonstrated by SA-deficient NahG transgenic rice and the sheath blight-resistant B. distachyon accessions, Bd3-1 and Gaz-4, which activate SA-dependent signaling on inoculation. Our findings suggest a hemi-biotrophic nature of R. solani, which can be targeted by SA-dependent plant immunity. Furthermore, B. distachyon provides a genetic resource that can confer disease resistance against R. solani to plants.
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Affiliation(s)
- Yusuke Kouzai
- Graduate School of Environmental and Life Science, Okayama University, Kita-ku, Okayama, 700-8530, Japan
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, 230-0045, Japan
| | - Mamiko Kimura
- Graduate School of Environmental and Life Science, Okayama University, Kita-ku, Okayama, 700-8530, Japan
| | - Megumi Watanabe
- Graduate School of Environmental and Life Science, Okayama University, Kita-ku, Okayama, 700-8530, Japan
| | - Kazuki Kusunoki
- Graduate School of Environmental and Life Science, Okayama University, Kita-ku, Okayama, 700-8530, Japan
| | - Daiki Osaka
- Graduate School of Environmental and Life Science, Okayama University, Kita-ku, Okayama, 700-8530, Japan
| | - Tomoko Suzuki
- Department of Science, Japan Women's University, Mejirodai, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Hidenori Matsui
- Graduate School of Environmental and Life Science, Okayama University, Kita-ku, Okayama, 700-8530, Japan
| | - Mikihiro Yamamoto
- Graduate School of Environmental and Life Science, Okayama University, Kita-ku, Okayama, 700-8530, Japan
| | - Yuki Ichinose
- Graduate School of Environmental and Life Science, Okayama University, Kita-ku, Okayama, 700-8530, Japan
| | - Kazuhiro Toyoda
- Graduate School of Environmental and Life Science, Okayama University, Kita-ku, Okayama, 700-8530, Japan
| | - Takakazu Matsuura
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, 710-0046, Japan
| | - Izumi C Mori
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, 710-0046, Japan
| | - Takashi Hirayama
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, 710-0046, Japan
| | - Eiichi Minami
- Division of Plant and Microbial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, 305-8602, Japan
| | - Yoko Nishizawa
- Division of Plant and Microbial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, 305-8602, Japan
| | - Komaki Inoue
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, 230-0045, Japan
| | - Yoshihiko Onda
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, 230-0045, Japan
| | - Keiichi Mochida
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, 230-0045, Japan
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, 710-0046, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, 244-0813, Japan
| | - Yoshiteru Noutoshi
- Graduate School of Environmental and Life Science, Okayama University, Kita-ku, Okayama, 700-8530, Japan
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Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure. Nat Commun 2017; 8:2184. [PMID: 29259172 PMCID: PMC5736591 DOI: 10.1038/s41467-017-02292-8] [Citation(s) in RCA: 200] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 11/17/2017] [Indexed: 12/17/2022] Open
Abstract
While prokaryotic pan-genomes have been shown to contain many more genes than any individual organism, the prevalence and functional significance of differentially present genes in eukaryotes remains poorly understood. Whole-genome de novo assembly and annotation of 54 lines of the grass Brachypodium distachyon yield a pan-genome containing nearly twice the number of genes found in any individual genome. Genes present in all lines are enriched for essential biological functions, while genes present in only some lines are enriched for conditionally beneficial functions (e.g., defense and development), display faster evolutionary rates, lie closer to transposable elements and are less likely to be syntenic with orthologous genes in other grasses. Our data suggest that differentially present genes contribute substantially to phenotypic variation within a eukaryote species, these genes have a major influence in population genetics, and transposable elements play a key role in pan-genome evolution. The role of differential gene content in the evolution and function of eukaryotic genomes remains poorly explored. Here the authors assemble and annotate the Brachypodium distachyon pan-genome consisting of 54 diverse lines and reveal the differential present genes as a major driver of phenotypic variation.
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26
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Hussain B, Lucas SJ, Ozturk L, Budak H. Mapping QTLs conferring salt tolerance and micronutrient concentrations at seedling stagein wheat. Sci Rep 2017. [PMID: 29142238 DOI: 10.1038/s41598‐017‐15726‐6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Soil salinization and degradation is one of the consequences of climate change. Identification of major salt tolerance genes and marker assisted selection (MAS) can accelerate wheat breeding for this trait. We genotyped 154 wheat F2 lines derived from a cross between salt tolerant and susceptible cultivars using the Axiom Wheat Breeder's Genotyping Array. A high-density linkage map of 988 single nucleotide polymorphisms (SNPs) was constructed and utilized for quantitative trait loci (QTL) mapping for salt tolerance traits and mineral concentrations under salinity. Of 49 mapped QTLs, six were for Na+ exclusion (NAX) and two QTLs (qSNAX.2 A.1, qSNAX.2 A.2) on chromosome 2 A coincided with a reported major NAX QTL (Nax1 or HKT1;4). Two other major NAX QTLs were mapped on 7 A, which contributed 11.23 and 18.79% of the salt tolerance respectively. In addition to Ca+2 and Mg+2 QTLs, twenty-seven QTLs for tissue Phosphorus, Zinc, Iron, Manganese, Copper, Sulphur and Boron concentrations under salinity were also mapped. The 1293 segregating SNPs were annotated/located within genes for various ion channels, signalling pathways, transcription factors (TFs), metabolic pathways and 258 of them showed differential expression in silico under salinity. These findings will create new opportunities for salt tolerance breeding programs.
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Affiliation(s)
- Babar Hussain
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Stuart James Lucas
- SU Nanotechnology Research and Application Centre, Sabanci University, Istanbul, Turkey
| | - Levent Ozturk
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Hikmet Budak
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey. .,Cereal genomics Lab, Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA.
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27
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Mapping QTLs conferring salt tolerance and micronutrient concentrations at seedling stagein wheat. Sci Rep 2017; 7:15662. [PMID: 29142238 PMCID: PMC5688110 DOI: 10.1038/s41598-017-15726-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 11/01/2017] [Indexed: 11/16/2022] Open
Abstract
Soil salinization and degradation is one of the consequences of climate change. Identification of major salt tolerance genes and marker assisted selection (MAS) can accelerate wheat breeding for this trait. We genotyped 154 wheat F2 lines derived from a cross between salt tolerant and susceptible cultivars using the Axiom Wheat Breeder’s Genotyping Array. A high-density linkage map of 988 single nucleotide polymorphisms (SNPs) was constructed and utilized for quantitative trait loci (QTL) mapping for salt tolerance traits and mineral concentrations under salinity. Of 49 mapped QTLs, six were for Na+ exclusion (NAX) and two QTLs (qSNAX.2 A.1, qSNAX.2 A.2) on chromosome 2 A coincided with a reported major NAX QTL (Nax1 or HKT1;4). Two other major NAX QTLs were mapped on 7 A, which contributed 11.23 and 18.79% of the salt tolerance respectively. In addition to Ca+2 and Mg+2 QTLs, twenty-seven QTLs for tissue Phosphorus, Zinc, Iron, Manganese, Copper, Sulphur and Boron concentrations under salinity were also mapped. The 1293 segregating SNPs were annotated/located within genes for various ion channels, signalling pathways, transcription factors (TFs), metabolic pathways and 258 of them showed differential expression in silico under salinity. These findings will create new opportunities for salt tolerance breeding programs.
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28
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Contreras R, Figueiras AM, Gallego FJ, Benavente E, Manzaneda AJ, Benito C. Neutral molecular markers support common origin of aluminium tolerance in three congeneric grass species growing in acidic soils. AOB PLANTS 2017; 9:plx060. [PMID: 29302302 PMCID: PMC5739048 DOI: 10.1093/aobpla/plx060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 10/27/2017] [Indexed: 06/07/2023]
Abstract
Aluminium (Al) toxicity is the main abiotic stress limiting plant productivity in acidic soils that are widely distributed among arable lands. Plant species differ in the level of Al resistance showing intraspecific and interspecific variation in many crop species. However, the origin of Al-tolerance is not well known. Three annual species, difficult to distinguish phenotypically and that were until recently misinterpreted as a single complex species under Brachypodium distachyon, have been recently separated into three distinct species: the diploids B. distachyon (2n = 10) and B. stacei (2n = 20), and B. hybridum (2n = 30), the allotetraploid derived from the two diploid species. The aims of this work were to know the origin of Al-tolerance in acidic soil conditions within these three Brachypodium species and to develop new DNA markers for species discrimination. Two multiplex SSR-PCRs allowed to genotype a group of 94 accessions for 17 pentanucleotide microsatellite (SSRs) loci. The variability for 139 inter-microsatellite (ISSRs) markers was also examined. The genetic relationships obtained using those neutral molecular markers (SSRs and ISSRs) support that all Al-tolerant allotetraploid accessions of B. hybridum have a common origin that is related with both geographic location and acidic soils. The possibility that the adaptation to acidic soils caused the isolation of the tolerant B. hybridum populations from the others is discussed. We finally describe a new, easy, DNA barcoding method based in the upstream-intron 1 region of the ALMT1 gene, a tool that is 100 % effective to distinguish among these three Brachypodium species.
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Affiliation(s)
- Roberto Contreras
- Departamento de Genética, Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain
| | - Ana M Figueiras
- Departamento de Genética, Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain
| | - F Javier Gallego
- Departamento de Genética, Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain
| | - Elena Benavente
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Madrid, Spain
| | - Antonio J Manzaneda
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Paraje Las Lagunillas s⁄n, Jaén, Spain
| | - César Benito
- Departamento de Genética, Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain
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29
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Transcriptional and Posttranscriptional Regulation of Drought Stress Treatments in Brachypodium Leaves. Methods Mol Biol 2017. [PMID: 29039000 DOI: 10.1007/978-1-4939-7278-4_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Plant sensing drought stress conditions activate complex molecular networks leading to a rapid reprogramming of plant physiology and metabolism, in order to survive in suboptimal conditions.Here, we describe a standardized in vivo soil drought assay to investigate the effects of drought stress on leaf growth. Since it is now clear that stress responses can be specific to developmental stages and cell types, we describe a procedure to dissect the leaf in three distinct areas in order to study transcriptional and posttranscriptional gene regulation on both organ and cellular levels. Noncoding RNAs, both small RNAs and long noncoding RNAs, are emerging to be deeply involved in abiotic stress responses, acting as molecular switches, interconnecting different response pathways. Here, we illustrate the methodology that has been used to identify miRNAs involved in drought response and to analyze the modulation of expression of their putative targets, in order to gain a complete picture of transcriptional and posttranscriptional regulation driven by noncoding RNAs.
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30
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De Quattro C, Pè ME, Bertolini E. Long noncoding RNAs in the model species Brachypodium distachyon. Sci Rep 2017; 7:11252. [PMID: 28900227 PMCID: PMC5595811 DOI: 10.1038/s41598-017-11206-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 08/21/2017] [Indexed: 02/06/2023] Open
Abstract
Eukaryotic genomes are pervasively transcribed and only a small portion of the transcribed sequences belongs to protein coding genes. High-throughput sequencing technology contributed to consolidate this perspective, allowing the identification of numerous noncoding RNAs with key roles in biological processes. Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nt with limited phylogenetic conservation, expressed at low levels and characterized by tissue/organ specific expression profiles. Although a large set of lncRNAs has been identified, the functional roles of lncRNAs are only beginning to be recognized and the molecular mechanism of lncRNA-mediated gene regulation remains largely unexplored, particularly in plants where their annotation and characterization are still incomplete. Using public and proprietary poly-(A)+ RNA-seq data as well as a collection of full length ESTs from several organs, developmental stages and stress conditions in three Brachypodium distachyon inbred lines, we describe the identification and the main features of thousands lncRNAs. Here we provide a genome-wide characterization of lncRNAs, highlighting their intraspecies conservation and describing their expression patterns among several organs/tissues and stress conditions. This work represents a fundamental resource to deepen our knowledge on long noncoding RNAs in C3 cereals, allowing the Brachypodium community to exploit these results in future research programs.
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Affiliation(s)
- Concetta De Quattro
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy
| | - Mario Enrico Pè
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy
| | - Edoardo Bertolini
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA.
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Rey PJ, Manzaneda AJ, Alcántara JM. The interplay between aridity and competition determines colonization ability, exclusion and ecological segregation in the heteroploid Brachypodium distachyon species complex. THE NEW PHYTOLOGIST 2017; 215:85-96. [PMID: 28436561 DOI: 10.1111/nph.14574] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 03/15/2017] [Indexed: 06/07/2023]
Abstract
A higher competitive advantage of polyploid plants compared with their parental diploids is frequently invoked to explain their establishment success, colonization of novel environments and cytotypic ecological segregation, yet there is scarce experimental evidence supporting such hypotheses. Here, we investigated whether differential competitive ability of species of the Brachypodium distachyon (Poaceae) species complex, a model system for genomic, ecological and evolutionary studies of temperate grasses, contributes to explaining their ecological segregation as well as their coexistence in diploid/allotetraploid contact zones. We conducted two field experiments in dry and humid localities to evaluate the tolerance to competition of diploids and allotetraploids in densely occupied environments, and to parameterize models of intra- and intercytotype competition as a mechanism for species exclusion/coexistence. We provide experimental evidence supporting the hypothesis that, under natural field conditions, allotetraploids have superior ecological success compared with one of their parental diploids in terms of both colonizing competitive habitats and intercytotypic competition, with the balance of intra/intercytotype competition favoring polyploid population establishment. These findings, together with previous data on ecogeographic segregation and adaptive response to water stress, suggest that the interplay between aridity and competitive outcome determines the ability to colonize competitive environments, the exclusion of diploids, especially in arid localities, and species geographic segregation.
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Affiliation(s)
- Pedro J Rey
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaén, E 23071, Spain
| | - Antonio J Manzaneda
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaén, E 23071, Spain
| | - Julio M Alcántara
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaén, E 23071, Spain
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Marques I, Shiposha V, López-Alvarez D, Manzaneda AJ, Hernandez P, Olonova M, Catalán P. Environmental isolation explains Iberian genetic diversity in the highly homozygous model grass Brachypodium distachyon. BMC Evol Biol 2017; 17:139. [PMID: 28619047 PMCID: PMC5472904 DOI: 10.1186/s12862-017-0996-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 06/08/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Brachypodium distachyon (Poaceae), an annual Mediterranean Aluminum (Al)-sensitive grass, is currently being used as a model species to provide new information on cereals and biofuel crops. The plant has a short life cycle and one of the smallest genomes in the grasses being well suited to experimental manipulation. Its genome has been fully sequenced and several genomic resources are being developed to elucidate key traits and gene functions. A reliable germplasm collection that reflects the natural diversity of this species is therefore needed for all these genomic resources. However, despite being a model plant, we still know very little about its genetic diversity. As a first step to overcome this gap, we used nuclear Simple Sequence Repeats (nSSR) to study the patterns of genetic diversity and population structure of B. distachyon in 14 populations sampled across the Iberian Peninsula (Spain), one of its best known areas. RESULTS We found very low levels of genetic diversity, allelic number and heterozygosity in B. distachyon, congruent with a highly selfing system. Our results indicate the existence of at least three genetic clusters providing additional evidence for the existence of a significant genetic structure in the Iberian Peninsula and supporting this geographical area as an important genetic reservoir. Several hotspots of genetic diversity were detected and populations growing on basic soils were significantly more diverse than those growing in acidic soils. A partial Mantel test confirmed a statistically significant Isolation-By-Distance (IBD) among all studied populations, as well as a statistically significant Isolation-By-Environment (IBE) revealing the presence of environmental-driven isolation as one explanation for the genetic patterns found in the Iberian Peninsula. CONCLUSIONS The finding of higher genetic diversity in eastern Iberian populations occurring in basic soils suggests that these populations can be better adapted than those occurring in western areas of the Iberian Peninsula where the soils are more acidic and accumulate toxic Al ions. This suggests that the western Iberian acidic soils might prevent the establishment of Al-sensitive B. distachyon populations, potentially causing the existence of more genetically depauperated individuals.
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Affiliation(s)
- Isabel Marques
- Departamento de Ciencias Agrarias y del Medio Natural, Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Ctra. Cuarte km 1, 22071, Huesca, Spain.
| | - Valeriia Shiposha
- Departamento de Ciencias Agrarias y del Medio Natural, Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Ctra. Cuarte km 1, 22071, Huesca, Spain
- Department of Botany, Institute of Biology, Tomsk State University, Lenin Av. 36, Tomsk, 634050, Russia
| | - Diana López-Alvarez
- Departamento de Ciencias Agrarias y del Medio Natural, Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Ctra. Cuarte km 1, 22071, Huesca, Spain
- Present address: Centro de Bioinformática y Biología Computacional de Colombia, BIOS, Parque los Yarumos, Manizales, Colombia
| | - Antonio J Manzaneda
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Paraje Las Lagunillas s⁄n, 23071, Jaén, Spain
| | - Pilar Hernandez
- Instituto de Agricultura Sostenible (IAS-CSIC), Alameda del Obispo s/n, 14004, Córdoba, Spain
| | - Marina Olonova
- Department of Botany, Institute of Biology, Tomsk State University, Lenin Av. 36, Tomsk, 634050, Russia
| | - Pilar Catalán
- Departamento de Ciencias Agrarias y del Medio Natural, Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Ctra. Cuarte km 1, 22071, Huesca, Spain
- Department of Botany, Institute of Biology, Tomsk State University, Lenin Av. 36, Tomsk, 634050, Russia
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Des Marais DL, Lasky JR, Verslues PE, Chang TZ, Juenger TE. Interactive effects of water limitation and elevated temperature on the physiology, development and fitness of diverse accessions of Brachypodium distachyon. THE NEW PHYTOLOGIST 2017; 214:132-144. [PMID: 27864966 DOI: 10.1111/nph.14316] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 10/03/2016] [Indexed: 05/21/2023]
Abstract
An enduring question in plant physiology and evolution is how single genotypes of plants optimize performance in diverse, often highly variable, environments. We grew 35 natural accessions of the grass Brachypodium distachyon in four environments in the glasshouse, contrasting soil water deficit, elevated temperature and their interaction. We modeled treatment, genotype and interactive effects on leaf-level and whole-plant traits, including fecundity. We also assessed the relationship between glasshouse-measured traits and parameters related to climate at the place of origin. We found abundant genetic variation in both constitutive and induced traits related to plant-water relations. Most traits showed strong interaction between temperature and water availability, and we observed genotype-by-environment interaction for several traits. Notably, leaf free proline abundance showed a strong effect of genotype × temperature × water. We found strong associations between phenology, biomass and water use efficiency (WUE) with parameters describing climate of origin. Plants respond to multiple stressors in ways not directly predictable from single stressors, underscoring the complex and trait-specific mechanisms of environmental response. Climate-trait correlations support a role for WUE and phenology in local adaptation to climate in B. distachyon.
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Affiliation(s)
- David L Des Marais
- Department of Integrative Biology and Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Paul E Verslues
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Trent Z Chang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Thomas E Juenger
- Department of Integrative Biology and Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA
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López-Álvarez D, Zubair H, Beckmann M, Draper J, Catalán P. Diversity and association of phenotypic and metabolomic traits in the close model grasses Brachypodium distachyon, B. stacei and B. hybridum. ANNALS OF BOTANY 2017; 119:545-561. [PMID: 28040672 PMCID: PMC5458712 DOI: 10.1093/aob/mcw239] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/25/2016] [Accepted: 10/12/2016] [Indexed: 05/30/2023]
Abstract
BACKGROUND AND AIMS Morphological traits in combination with metabolite fingerprinting were used to investigate inter- and intraspecies diversity within the model annual grasses Brachypodium distachyon, Brachypodium stacei and Brachypodium hybridum . METHODS Phenotypic variation of 15 morphological characters and 2219 nominal mass ( m / z ) signals generated using flow infusion electrospray ionization-mass spectrometry (FIE-MS) were evaluated in individuals from a total of 174 wild populations and six inbred lines, and 12 lines, of the three species, respectively. Basic statistics and multivariate principal component analysis and discriminant analysis were used to differentiate inter- and intraspecific variability of the two types of variable, and their association was assayed with the rcorr function. KEY RESULTS Basic statistics and analysis of variance detected eight phenotypic characters [(stomata) leaf guard cell length, pollen grain length, (plant) height, second leaf width, inflorescence length, number of spikelets per inflorescence, lemma length, awn length] and 434 tentatively annotated metabolite signals that significantly discriminated the three species. Three phenotypic traits (pollen grain length, spikelet length, number of flowers per inflorescence) might be genetically fixed. The three species showed different metabolomic profiles. Discriminant analysis significantly discriminated the three taxa with both morphometric and metabolome traits and the intraspecific phenotypic diversity within B. distachyon and B. stacei . The populations of B. hybridum were considerably less differentiated. CONCLUSIONS Highly explanatory metabolite signals together with morphological characters revealed concordant patterns of differentiation of the three taxa. Intraspecific phenotypic diversity was observed between northern and southern Iberian populations of B. distachyon and between eastern Mediterranean/south-western Asian and western Mediterranean populations of B. stacei . Significant association was found for pollen grain length and lemma length and ten and six metabolomic signals, respectively. These results would guide the selection of new germplasm lines of the three model grasses in ongoing genome-wide association studies.
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Affiliation(s)
- Diana López-Álvarez
- Department of Agriculture and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza, Ctra. Cuarte Km 1, 22071 Huesca, Spain
| | - Hassan Zubair
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth SY23 3EB, UK
| | - Manfred Beckmann
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth SY23 3EB, UK
| | - John Draper
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth SY23 3EB, UK
| | - Pilar Catalán
- Department of Agriculture and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza, Ctra. Cuarte Km 1, 22071 Huesca, Spain
- Department of Botany, Institute of Biology, Tomsk State University, Lenin Av. 36, Tomsk 634050, Russia
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Jensen JK, Wilkerson CG. Brachypodium as an experimental system for the study of stem parenchyma biology in grasses. PLoS One 2017; 12:e0173095. [PMID: 28248997 PMCID: PMC5332097 DOI: 10.1371/journal.pone.0173095] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 02/15/2017] [Indexed: 11/19/2022] Open
Abstract
Stem parenchyma is a major cell type that serves key metabolic functions for the plant especially in large grasses, such as sugarcane and sweet sorghum, where it serves to store sucrose or other products of photosynthesis. It is therefore desirable to understand the metabolism of this cell type as well as the mechanisms by which it provides its function for the rest of the plant. Ultimately, this information can be used to selectively manipulate this cell type in a controlled manner to achieve crop improvement. In this study, we show that Brachypodium distachyon is a useful model system for stem pith parenchyma biology. Brachypodium can be grown under condition where it resembles the growth patterns of important crops in that it produces large amounts of stem material with the lower leaves senescing and with significant stores of photosynthate located in the stem parenchyma cell types. We further characterize stem plastid morphology as a function of tissue types, as this organelle is central for a number of metabolic pathways, and quantify gene expression for the four main classes of starch biosynthetic genes. Notably, we find several of these genes differentially regulated between stem and leaf. These studies show, consistent with other grasses, that the stem functions as a specialized storage compartment in Brachypodium.
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Affiliation(s)
- Jacob Krüger Jensen
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States of America.,DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, United States of America
| | - Curtis Gene Wilkerson
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States of America.,DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, United States of America.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States of America
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36
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Woods DP, Bednarek R, Bouché F, Gordon SP, Vogel JP, Garvin DF, Amasino RM. Genetic Architecture of Flowering-Time Variation in Brachypodium distachyon. PLANT PHYSIOLOGY 2017; 173:269-279. [PMID: 27742753 PMCID: PMC5210718 DOI: 10.1104/pp.16.01178] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/10/2016] [Indexed: 05/03/2023]
Abstract
The transition to reproductive development is a crucial step in the plant life cycle, and the timing of this transition is an important factor in crop yields. Here, we report new insights into the genetic control of natural variation in flowering time in Brachypodium distachyon, a nondomesticated pooid grass closely related to cereals such as wheat (Triticum spp.) and barley (Hordeum vulgare L.). A recombinant inbred line population derived from a cross between the rapid-flowering accession Bd21 and the delayed-flowering accession Bd1-1 were grown in a variety of environmental conditions to enable exploration of the genetic architecture of flowering time. A genotyping-by-sequencing approach was used to develop SNP markers for genetic map construction, and quantitative trait loci (QTLs) that control differences in flowering time were identified. Many of the flowering-time QTLs are detected across a range of photoperiod and vernalization conditions, suggesting that the genetic control of flowering within this population is robust. The two major QTLs identified in undomesticated B. distachyon colocalize with VERNALIZATION1/PHYTOCHROME C and VERNALIZATION2, loci identified as flowering regulators in the domesticated crops wheat and barley. This suggests that variation in flowering time is controlled in part by a set of genes broadly conserved within pooid grasses.
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Affiliation(s)
- Daniel P Woods
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.M.A.)
- United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.M.A.)
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.B., F.B., R.M.A.)
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598 (S.P.G., J.P.V.); and
- USDA-ARS Plant Science Research Unit, University of Minnesota, Department of Agronomy and Plant Genetics, St. Paul, Minnesota 55108 (D.F.G.)
| | - Ryland Bednarek
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.M.A.)
- United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.M.A.)
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.B., F.B., R.M.A.)
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598 (S.P.G., J.P.V.); and
- USDA-ARS Plant Science Research Unit, University of Minnesota, Department of Agronomy and Plant Genetics, St. Paul, Minnesota 55108 (D.F.G.)
| | - Frédéric Bouché
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.M.A.)
- United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.M.A.)
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.B., F.B., R.M.A.)
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598 (S.P.G., J.P.V.); and
- USDA-ARS Plant Science Research Unit, University of Minnesota, Department of Agronomy and Plant Genetics, St. Paul, Minnesota 55108 (D.F.G.)
| | - Sean P Gordon
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.M.A.)
- United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.M.A.)
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.B., F.B., R.M.A.)
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598 (S.P.G., J.P.V.); and
- USDA-ARS Plant Science Research Unit, University of Minnesota, Department of Agronomy and Plant Genetics, St. Paul, Minnesota 55108 (D.F.G.)
| | - John P Vogel
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.M.A.)
- United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.M.A.)
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.B., F.B., R.M.A.)
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598 (S.P.G., J.P.V.); and
- USDA-ARS Plant Science Research Unit, University of Minnesota, Department of Agronomy and Plant Genetics, St. Paul, Minnesota 55108 (D.F.G.)
| | - David F Garvin
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.M.A.)
- United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.M.A.)
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.B., F.B., R.M.A.)
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598 (S.P.G., J.P.V.); and
- USDA-ARS Plant Science Research Unit, University of Minnesota, Department of Agronomy and Plant Genetics, St. Paul, Minnesota 55108 (D.F.G.)
| | - Richard M Amasino
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.M.A.);
- United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.M.A.);
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.B., F.B., R.M.A.);
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598 (S.P.G., J.P.V.); and
- USDA-ARS Plant Science Research Unit, University of Minnesota, Department of Agronomy and Plant Genetics, St. Paul, Minnesota 55108 (D.F.G.)
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Dinh Thi VH, Coriton O, Le Clainche I, Arnaud D, Gordon SP, Linc G, Catalan P, Hasterok R, Vogel JP, Jahier J, Chalhoub B. Recreating Stable Brachypodium hybridum Allotetraploids by Uniting the Divergent Genomes of B. distachyon and B. stacei. PLoS One 2016; 11:e0167171. [PMID: 27936041 PMCID: PMC5147888 DOI: 10.1371/journal.pone.0167171] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 11/09/2016] [Indexed: 11/19/2022] Open
Abstract
Brachypodium hybridum (2n = 30) is a natural allopolyploid with highly divergent sub-genomes derived from two extant diploid species, B. distachyon (2n = 10) and B. stacei (2n = 20) that differ in chromosome evolution and number. We created synthetic B. hybridum allotetraploids by hybridizing various lines of B. distachyon and B. stacei. The initial amphihaploid F1 interspecific hybrids were obtained at low frequencies when B. distachyon was used as the maternal parent (0.15% or 0.245% depending on the line used) and were sterile. No hybrids were obtained from reciprocal crosses or when autotetraploids of the parental species were crossed. Colchicine treatment was used to double the genome of the F1 amphihaploid lines leading to allotetraploids. The genome-doubled F1 plants produced a few S1 (first selfed generation) seeds after self-pollination. S1 plants from one parental combination (Bd3-1×Bsta5) were fertile and gave rise to further generations whereas those of another parental combination (Bd21×ABR114) were sterile, illustrating the importance of the parental lineages crossed. The synthetic allotetraploids were stable and resembled the natural B. hybridum at the phenotypic, cytogenetic and genomic levels. The successful creation of synthetic B. hybridum offers the possibility to study changes in genome structure and regulation at the earliest stages of allopolyploid formation in comparison with the parental species and natural B. hybridum.
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Affiliation(s)
- Vinh Ha Dinh Thi
- Organization and evolution of complex genomes, Institut National de la Recherche agronomique, Université d’Evry Val d’Essonne, Evry, France
| | - Olivier Coriton
- Unité Mixte de Recherches INRA, Agrocampus Rennes—Université Rennes 1, Institut de Génétique, Environnement et Protection des Plantes, Le Rheu, France
| | - Isabelle Le Clainche
- Organization and evolution of complex genomes, Institut National de la Recherche agronomique, Université d’Evry Val d’Essonne, Evry, France
| | - Dominique Arnaud
- Organization and evolution of complex genomes, Institut National de la Recherche agronomique, Université d’Evry Val d’Essonne, Evry, France
| | - Sean P. Gordon
- DOE Joint Genome Institute, Walnut Creek, United States of America
| | - Gabriella Linc
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences,Martonvásár, Brunszvik u 2, Hungary
| | - Pilar Catalan
- Department of Agriculture and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza, Huesca, Spain
- Department of Botany, Institute of Biology, Tomsk State University, Tomsk, Russia
| | - Robert Hasterok
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia,Katowice, Poland
| | - John P. Vogel
- DOE Joint Genome Institute, Walnut Creek, United States of America
- Department of Plant and Microbial Biology, University of California, Berkeley, United States of America
| | - Joseph Jahier
- Unité Mixte de Recherches INRA, Agrocampus Rennes—Université Rennes 1, Institut de Génétique, Environnement et Protection des Plantes, Le Rheu, France
| | - Boulos Chalhoub
- Organization and evolution of complex genomes, Institut National de la Recherche agronomique, Université d’Evry Val d’Essonne, Evry, France
- Institute of System and Synthetic Biology, Genopole, Centre National de la Recherche Scientifique, Université d’Evry Val d’Essonne, Université Paris-Saclay, Evry, France
- * E-mail:
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Rabe F, Bosch J, Stirnberg A, Guse T, Bauer L, Seitner D, Rabanal FA, Czedik-Eysenberg A, Uhse S, Bindics J, Genenncher B, Navarrete F, Kellner R, Ekker H, Kumlehn J, Vogel JP, Gordon SP, Marcel TC, Münsterkötter M, Walter MC, Sieber CMK, Mannhaupt G, Güldener U, Kahmann R, Djamei A. A complete toolset for the study of Ustilago bromivora and Brachypodium sp. as a fungal-temperate grass pathosystem. eLife 2016; 5:e20522. [PMID: 27835569 PMCID: PMC5106213 DOI: 10.7554/elife.20522] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/12/2016] [Indexed: 11/18/2022] Open
Abstract
Due to their economic relevance, the study of plant pathogen interactions is of importance. However, elucidating these interactions and their underlying molecular mechanisms remains challenging since both host and pathogen need to be fully genetically accessible organisms. Here we present milestones in the establishment of a new biotrophic model pathosystem: Ustilago bromivora and Brachypodium sp. We provide a complete toolset, including an annotated fungal genome and methods for genetic manipulation of the fungus and its host plant. This toolset will enable researchers to easily study biotrophic interactions at the molecular level on both the pathogen and the host side. Moreover, our research on the fungal life cycle revealed a mating type bias phenomenon. U. bromivora harbors a haplo-lethal allele that is linked to one mating type region. As a result, the identified mating type bias strongly promotes inbreeding, which we consider to be a potential speciation driver.
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Affiliation(s)
- Franziska Rabe
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jason Bosch
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Alexandra Stirnberg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Tilo Guse
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Lisa Bauer
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Denise Seitner
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Fernando A Rabanal
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | | | - Simon Uhse
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Janos Bindics
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Bianca Genenncher
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Fernando Navarrete
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Ronny Kellner
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Heinz Ekker
- Vienna Biocenter Core Facilities GmbH, Vienna, Austria
| | - Jochen Kumlehn
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, Gatersleben, Germany
| | - John P Vogel
- DOE Joint Genome Institute, California, United States
| | - Sean P Gordon
- DOE Joint Genome Institute, California, United States
| | - Thierry C Marcel
- INRA UMR BIOGER, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Martin Münsterkötter
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Mathias C Walter
- Department of Genome-oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
| | - Christian MK Sieber
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Gertrud Mannhaupt
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Ulrich Güldener
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Genome-oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
| | - Regine Kahmann
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Armin Djamei
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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Eichten SR, Stuart T, Srivastava A, Lister R, Borevitz JO. DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity. Genome Res 2016; 26:1520-1531. [PMID: 27613611 PMCID: PMC5088594 DOI: 10.1101/gr.205468.116] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 08/25/2016] [Indexed: 12/13/2022]
Abstract
DNA methylation, a common modification of genomic DNA, is known to influence the expression of transposable elements as well as some genes. Although commonly viewed as an epigenetic mark, evidence has shown that underlying genetic variation, such as transposable element polymorphisms, often associate with differential DNA methylation states. To investigate the role of DNA methylation variation, transposable element polymorphism, and genomic diversity, whole-genome bisulfite sequencing was performed on genetically diverse lines of the model cereal Brachypodium distachyon. Although DNA methylation profiles are broadly similar, thousands of differentially methylated regions are observed between lines. An analysis of novel transposable element indel variation highlighted hundreds of new polymorphisms not seen in the reference sequence. DNA methylation and transposable element variation is correlated with the genome-wide amount of genetic variation present between samples. However, there was minimal evidence that novel transposon insertions or deletions are associated with nearby differential methylation. This study highlights unique relationships between genetic variation and DNA methylation variation within Brachypodium and provides a valuable map of DNA methylation across diverse resequenced accessions of this model cereal species.
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Affiliation(s)
- Steven R Eichten
- ARC Centre of Excellence in Plant Energy Biology, The Australian National University, Canberra, Australia, 2601
| | - Tim Stuart
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Perth, Australia, 6009
| | - Akanksha Srivastava
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Perth, Australia, 6009
| | - Ryan Lister
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Perth, Australia, 6009
| | - Justin O Borevitz
- ARC Centre of Excellence in Plant Energy Biology, The Australian National University, Canberra, Australia, 2601
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Shiposha V, Catalán P, Olonova M, Marques I. Genetic structure and diversity of the selfing model grass Brachypodium stacei (Poaceae) in Western Mediterranean: out of the Iberian Peninsula and into the islands. PeerJ 2016; 4:e2407. [PMID: 27651993 PMCID: PMC5018678 DOI: 10.7717/peerj.2407] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 08/04/2016] [Indexed: 12/29/2022] Open
Abstract
Annual Mediterranean species of the genus Brachypodium are promising model plants for energy crops since their selfing nature and short-life cycles are an advantage in breeding programs. The false brome, B. distachyon, has already been sequenced and new genomic initiatives have triggered the de-novo genome sequencing of its close relatives such as B. stacei, a species that was until recently mistaken for B. distachyon. However, the success of these initiatives hinges on detailed knowledge about the distribution of genetic variation within and among populations for the effective use of germplasm in a breeding program. Understanding population genetic diversity and genetic structure is also an important prerequisite for designing effective experimental populations for genomic wide studies. However, population genetic data are still limited in B. stacei. We therefore selected and amplified 10 nuclear microsatellite markers to depict patterns of population structure and genetic variation among 181 individuals from 19 populations of B. stacei occurring in its predominant range, the western Mediterranean area: mainland Iberian Peninsula, continental Balearic Islands and oceanic Canary Islands. Our genetic results support the occurrence of a predominant selfing system with extremely high levels of homozygosity across the analyzed populations. Despite the low level of genetic variation found, two different genetic clusters were retrieved, one clustering all SE Iberian mainland populations and the island of Minorca and another one grouping all S Iberian mainland populations, the Canary Islands and all Majorcan populations except one that clustered with the former group. These results, together with a high sharing of alleles (89%) suggest different colonization routes from the mainland Iberian Peninsula into the islands. A recent colonization scenario could explain the relatively low levels of genetic diversity and low number of alleles found in the Canary Islands populations while older colonization events are hypothesized to explain the high genetic diversity values found in the Majorcan populations. Our study provides widely applicable information about geographical patterns of genetic variation in B. stacei. Among others, the genetic pattern and the existence of local alleles will need to be adequately reflected in the germplasm collection of B. stacei for efficient genome wide association studies.
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Affiliation(s)
- Valeriia Shiposha
- Department of Agriculture and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza, Huesca, Spain; Department of Botany, Institute of Biology, Tomsk State University, Tomsk, Russia
| | - Pilar Catalán
- Department of Agriculture and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza, Huesca, Spain; Department of Botany, Institute of Biology, Tomsk State University, Tomsk, Russia
| | - Marina Olonova
- Department of Botany, Institute of Biology, Tomsk State University , Tomsk , Russia
| | - Isabel Marques
- Department of Agriculture and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza , Huesca , Spain
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Luo N, Yu X, Nie G, Liu J, Jiang Y. Specific peroxidases differentiate Brachypodium distachyon accessions and are associated with drought tolerance traits. ANNALS OF BOTANY 2016; 118:259-70. [PMID: 27325900 PMCID: PMC4970367 DOI: 10.1093/aob/mcw104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 02/08/2016] [Accepted: 04/04/2016] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Brachypodium distachyon (Brachypodium) is a model system for studying cereal, bioenergy, forage and turf grasses. The genetic and evolutionary basis of the adaptation of this wild grass species to drought stress is largely unknown. Peroxidase (POD) may play a role in plant drought tolerance, but whether the allelic variations of genes encoding the specific POD isoenzymes are associated with plant response to drought stress is not well understood. The objectives of this study were to examine natural variation of POD isoenzyme patterns, to identify nucleotide diversity of POD genes and to relate the allelic variation of genes to drought tolerance traits of diverse Brachypodium accessions. METHODS Whole-plant drought tolerance and POD activity were examined in contrasting ecotypes. Non-denaturing PAGE and liquid chromatography-mass spectrometry were performed to detect distinct isozymes of POD in 34 accessions. Single nucleotide polymorphisms (SNPs) were identified by comparing DNA sequences of these accessions. Associations of POD genes encoding specific POD isoenzymes with drought tolerance traits were analysed using TASSEL software. KEY RESULTS Variations of POD isoenzymes were found among accessions with contrasting drought tolerance, while the most tolerant and susceptible accessions each had their own unique POD isoenzyme band. Eight POD genes were identified and a total of 90 SNPs were found among these genes across 34 accessions. After controlling population structure, significant associations of Bradi3g41340.1 and Bradi1g26870.1 with leaf water content or leaf wilting were identified. CONCLUSIONS Brachypodium ecotypes have distinct specific POD isozymes. This may contribute to natural variations of drought tolerance of this species. The role of specific POD genes in differentiating Brachypodium accessions with contrasting drought tolerance could be associated with the general fitness of Brachypodium during evolution.
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Affiliation(s)
- Na Luo
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xiaoqing Yu
- Department of Agronomy, Iowa State University, Ames IA 50011, USA
| | - Gang Nie
- Department of Grassland Science, Sichuan Agricultural University, Chengdu 611130, China
| | - Jianxiu Liu
- Institute of Botany, Jiangsu Province & Chinese Academy of Science, Nanjing 210014, China
| | - Yiwei Jiang
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
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Willis JD, Mazarei M, Stewart CN. Transgenic Plant-Produced Hydrolytic Enzymes and the Potential of Insect Gut-Derived Hydrolases for Biofuels. FRONTIERS IN PLANT SCIENCE 2016; 7:675. [PMID: 27303411 PMCID: PMC4885837 DOI: 10.3389/fpls.2016.00675] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 05/02/2016] [Indexed: 05/25/2023]
Abstract
Various perennial C4 grass species have tremendous potential for use as lignocellulosic biofuel feedstocks. Currently available grasses require costly pre-treatment and exogenous hydrolytic enzyme application to break down complex cell wall polymers into sugars that can then be fermented into ethanol. It has long been hypothesized that engineered feedstock production of cell wall degrading (CWD) enzymes would be an efficient production platform for of exogenous hydrolytic enzymes. Most research has focused on plant overexpression of CWD enzyme-coding genes from free-living bacteria and fungi that naturally break down plant cell walls. Recently, it has been found that insect digestive tracts harbor novel sources of lignocellulolytic biocatalysts that might be exploited for biofuel production. These CWD enzyme genes can be located in the insect genomes or in symbiotic microbes. When CWD genes are transformed into plants, negative pleiotropic effects are possible such as unintended cell wall digestion. The use of codon optimization along with organelle and tissue specific targeting improves CWD enzyme yields. The literature teaches several important lessons on strategic deployment of CWD genes in transgenic plants, which is the focus of this review.
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Affiliation(s)
- Jonathan D. Willis
- Department of Plant Sciences, University of TennesseeKnoxville, TN, USA
- Oak Ridge National Laboratory, BioEnergy Science CenterOak Ridge, TN, USA
| | - Mitra Mazarei
- Department of Plant Sciences, University of TennesseeKnoxville, TN, USA
- Oak Ridge National Laboratory, BioEnergy Science CenterOak Ridge, TN, USA
| | - C. Neal Stewart
- Department of Plant Sciences, University of TennesseeKnoxville, TN, USA
- Oak Ridge National Laboratory, BioEnergy Science CenterOak Ridge, TN, USA
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Onda Y, Hashimoto K, Yoshida T, Sakurai T, Sawada Y, Hirai MY, Toyooka K, Mochida K, Shinozaki K. Determination of growth stages and metabolic profiles in Brachypodium distachyon for comparison of developmental context with Triticeae crops. Proc Biol Sci 2016; 282:rspb.2015.0964. [PMID: 26156770 PMCID: PMC4528556 DOI: 10.1098/rspb.2015.0964] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Brachypodium distachyon is an emerging model plant for studying biological phenomena in temperate grasses. Study of the growth scale is essential to analyse spatio-temporal changes in molecular factors throughout the life cycle. For sensitive and robust staging based on morphology in B. distachyon, we demonstrated the utility of the BBCH (Biologische Bundesanstalt, Bundessortenamt and CHemical industry) scale, which is comparable to the Zadoks scale conventionally used for Triticeae crops. We compared the chronological progression of B. distachyon accessions Bd21 and Bd3-1, in addition to the progression of Chinese Spring wheat. The comparison of growth stages illustrates the morphological similarities and differences in the timing of life cycle events. Furthermore, we compared metabolite accumulation patterns across different growth stages and across different stress conditions using a widely targeted metabolome analysis. Metabolic profiling determined commonalities and specificities in chemical properties that were dependent on organisms, growth stages and/or stress conditions. Most metabolites accumulated equivalently in B. distachyon and wheat. This qualitative similarity indicated the superiority of B. distachyon as a model for Triticeae crops. The growth scale of B. distachyon should provide a conceptual framework for comparative analysis and for knowledge integration between this model grass and crops in the Pooideae subfamily.
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Affiliation(s)
- Yoshihiko Onda
- Cellulose Production Research Team, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan Kihara Institute for Biological Research, Yokohama City University, Kanagawa, Japan
| | - Kei Hashimoto
- Technology Platform Division, Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Takuhiro Yoshida
- Integrated Genome Informatics Research Unit, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Tetsuya Sakurai
- Integrated Genome Informatics Research Unit, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Yuji Sawada
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Masami Yokota Hirai
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Kiminori Toyooka
- Technology Platform Division, Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Keiichi Mochida
- Cellulose Production Research Team, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan Kihara Institute for Biological Research, Yokohama City University, Kanagawa, Japan
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan Biomass Research Platform Team, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
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Schneebeli K, Mathesius U, Zwart AB, Bragg JN, Vogel JP, Watt M. Brachypodium distachyon genotypes vary in resistance to Rhizoctonia solani AG8. FUNCTIONAL PLANT BIOLOGY : FPB 2016; 43:189-198. [PMID: 32480452 DOI: 10.1071/fp15244] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/12/2015] [Indexed: 06/11/2023]
Abstract
Brachypodium distachyon (L.)P.Beauv. (Bd) has previously been developed as a pathosystem model for the wheat root rot pathogen Rhizoctonia solani Kühn anastomosis group 8 (AG8). Here we explore variation in resistance to R. solani AG8 in Bd, to determine whether genomic tools could be used to find Bd genes involved in the grass defence response, with the aim of using this information for the improvement of Rhizoctonia root rot resistance in wheat. We looked for variation in resistance to R. solani AG8 in a diverse Bd natural accession collection and in Bd T-DNA insertion lines selected based on putative mechanisms reported for tagged genes. All lines were susceptible to the pathogen. Repeatable and significant variation in resistance was measured in both groups, with greater variation in resistance found across the natural accessions than in the T-DNA lines. The widest and most repeatable variation in resistance was between lines Koz-3 and BdTR 13a. The ratio of R. solani AG8-inoculated to uninoculated root length for line Koz-3 was 33% greater than the same ratio for line BdTR 13a. The increased resistance of Koz-3 was associated with nodal root initiation in response to the pathogen. A negative correlation between seedling vigour and resistance was observed, but found not to be the sole source of variation in resistance to R. solani AG8. The only T-DNA line with significantly greater resistance to R. solani AG8 than the reference line had an insertion in a putative galactosyltransferase gene; however, this result needs further confirmation. Genetic resistance to Rhizoctonia root rot is not available in wheat cultivars and only a few instances of quantitative resistance to the pathogen have been described within close relatives of wheat. Brachypodium distachyon offers potential for further investigation to find genes associated with quantitative resistance and mechanisms of tolerance to R. solani AG8.
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Affiliation(s)
| | - Ulrike Mathesius
- Division of Plant Science, Research School of Biology, 134 Linnaeus Way, Australian National University, Canberra, ACT 2601, Australia
| | - Alexander B Zwart
- CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Jennifer N Bragg
- Joint BioEnergy Institute, 5885 Hollis St. ESE 4th Floor, Emeryville, CA 94608, USA
| | - John P Vogel
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Michelle Watt
- CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia
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Cass CL, Lavell AA, Santoro N, Foster CE, Karlen SD, Smith RA, Ralph J, Garvin DF, Sedbrook JC. Cell Wall Composition and Biomass Recalcitrance Differences Within a Genotypically Diverse Set of Brachypodium distachyon Inbred Lines. FRONTIERS IN PLANT SCIENCE 2016; 7:708. [PMID: 27303415 PMCID: PMC4880586 DOI: 10.3389/fpls.2016.00708] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 05/09/2016] [Indexed: 05/09/2023]
Abstract
Brachypodium distachyon (Brachypodium) has emerged as a useful model system for studying traits unique to graminaceous species including bioenergy crop grasses owing to its amenability to laboratory experimentation and the availability of extensive genetic and germplasm resources. Considerable natural variation has been uncovered for a variety of traits including flowering time, vernalization responsiveness, and above-ground growth characteristics. However, cell wall composition differences remain underexplored. Therefore, we assessed cell wall-related traits relevant to biomass conversion to biofuels in seven Brachypodium inbred lines that were chosen based on their high level of genotypic diversity as well as available genome sequences and recombinant inbred line (RIL) populations. Senesced stems plus leaf sheaths from these lines exhibited significant differences in acetyl bromide soluble lignin (ABSL), cell wall polysaccharide-derived sugars, hydroxycinnamates content, and syringyl:guaiacyl:p-hydroxyphenyl (S:G:H) lignin ratios. Free glucose, sucrose, and starch content also differed significantly in senesced stems, as did the amounts of sugars released from cell wall polysaccharides (digestibility) upon exposure to a panel of thermochemical pretreatments followed by hydrolytic enzymatic digestion. Correlations were identified between inbred line lignin compositions and plant growth characteristics such as biomass accumulation and heading date (HD), and between amounts of cell wall polysaccharides and biomass digestibility. Finally, stem cell wall p-coumarate and ferulate contents and free-sugars content changed significantly with increased duration of vernalization for some inbred lines. Taken together, these results show that Brachypodium displays substantial phenotypic variation with respect to cell wall composition and biomass digestibility, with some compositional differences correlating with growth characteristics. Moreover, besides influencing HD and biomass accumulation, vernalization was found to affect cell wall composition and free sugars accumulation in some Brachypodium inbred lines, suggesting genetic differences in how vernalization affects carbon flux to polysaccharides. The availability of related RIL populations will allow for the genetic and molecular dissection of this natural variation, the knowledge of which may inform ways to genetically improve bioenergy crop grasses.
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Affiliation(s)
- Cynthia L. Cass
- School of Biological Sciences, Illinois State University, NormalIL, USA
- U.S. Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, MadisonWI, USA
| | - Anastasiya A. Lavell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. PaulMN, USA
- Plant Science Research Unit, United States Department of Agriculture, Agricultural Research Service, St. PaulMN, USA
| | - Nicholas Santoro
- U.S. Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East LansingMI, USA
| | - Cliff E. Foster
- U.S. Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East LansingMI, USA
| | - Steven D. Karlen
- U.S. Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, MadisonWI, USA
| | - Rebecca A. Smith
- U.S. Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, MadisonWI, USA
| | - John Ralph
- U.S. Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, MadisonWI, USA
- Department of Biochemistry, University of Wisconsin-Madison, MadisonWI, USA
| | - David F. Garvin
- Department of Agronomy and Plant Genetics, University of Minnesota, St. PaulMN, USA
- Plant Science Research Unit, United States Department of Agriculture, Agricultural Research Service, St. PaulMN, USA
| | - John C. Sedbrook
- School of Biological Sciences, Illinois State University, NormalIL, USA
- U.S. Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, MadisonWI, USA
- *Correspondence: John C. Sedbrook,
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Subburaj S, Luo N, Lu X, Li X, Cao H, Hu Y, Li J, Yan Y. Molecular characterization and evolutionary origins of farinin genes in Brachypodium distachyon L. J Appl Genet 2015; 57:287-303. [PMID: 26519166 DOI: 10.1007/s13353-015-0316-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 08/29/2015] [Accepted: 09/01/2015] [Indexed: 10/22/2022]
Abstract
Farinins are one of the oldest members of the gluten family in wheat and Aegilops species, and they influence dough properties. Here, we performed the first detailed molecular genetic study on farinin genes in Brachypodium distachyon L., the model species for Triticum aestivum. A total of 51 b-type farinin genes were cloned and characterized, including 27 functional and 24 non-functional pseudogenes from 14 different B. distachyon accessions. All genes were highly similar to those previously reported from wheat and Aegilops species. The identification of deduced amino acid sequences showed that b-type farinins across Triticeae genomes could be classified as b1-, b2-, b3-, and b4-type farinins; however, B. distachyon had only b3- and b4-type farinins. Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) revealed that farinin genes are transcribed into mRNA in B. distachyon at much lower levels than in Triticeae, despite the presence of cis-acting elements in promoter regions. Phylogenetic analysis suggested that Brachypodium farinins may have closer relationships with common wheat and further confirmed four different types of b-type farinins in Triticeae and Brachypodium genomes, corresponding to b1, b2, b3 (group 1), and b4 (group 2). A putative evolutionary origin model of farinin genes in Brachypodium, Triticum, and the related species suggests that all b-type farinins diverged from their common ancestor ~3.2 million years ago (MYA). The b3 and b4 types could be considered older in the farinin family. The results explain the loss of b1- and b2-type farinin alleles in Brachypodium.
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Affiliation(s)
| | - Nana Luo
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Xiaobing Lu
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Xiaohui Li
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Hui Cao
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Yingkao Hu
- College of Life Science, Capital Normal University, Beijing, 100048, China.
| | - Jiarui Li
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Yueming Yan
- College of Life Science, Capital Normal University, Beijing, 100048, China. .,Hubei Collaborative Innovation Center for Grain Industry (HCICGI), 434025, Jingzhou, China.
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Manzaneda AJ, Rey PJ, Anderson JT, Raskin E, Weiss-Lehman C, Mitchell-Olds T. Natural variation, differentiation, and genetic trade-offs of ecophysiological traits in response to water limitation in Brachypodium distachyon and its descendent allotetraploid B. hybridum (Poaceae). Evolution 2015; 69:2689-704. [PMID: 26377138 DOI: 10.1111/evo.12776] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 07/02/2015] [Accepted: 08/25/2015] [Indexed: 11/30/2022]
Abstract
Differences in tolerance to water stress may underlie ecological divergence of closely related ploidy lineages. However, the mechanistic basis of physiological variation governing ecogeographical cytotype segregation is not well understood. Here, using Brachypodium distachyon and its derived allotetraploid B. hybridum as model, we test the hypothesis that, for heteroploid annuals, ecological divergence of polyploids in drier environments is based on trait differentiation enabling drought escape. We demonstrate that under water limitation allotetraploids maintain higher photosynthesis and stomatal conductance and show earlier flowering than diploids, concordant with a drought-escape strategy to cope with water stress. Increased heterozygosity and greater genetic variability and plasticity of polyploids could confer a superior adaptive capability. Consistent with these predictions, we document (1) greater standing within-population genetic variation in water-use efficiency (WUE) and flowering time in allotetraploids, and (2) the existence of (nonlinear) environmental clines in physiology across allotetraploid populations. Increased gas exchange and diminished WUE occurred at the driest end of the gradient, consistent with a drought-escape strategy. Finally, we found that allotetraploids showed weaker genetic correlations than diploids congruous with the expectation of relaxed pleiotropic constraints in polyploids. Our results suggest evolutionary divergence of ecophysiological traits in each ploidy lineage.
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Affiliation(s)
- Antonio J Manzaneda
- Departamento Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Paraje las Lagunillas s/n, 23071, Jaén, Spain. .,Institute for Genome Sciences and Policy, Department of Biology, Duke University, P.O. Box 90338, Durham, North Carolina, 27708.
| | - Pedro J Rey
- Departamento Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Paraje las Lagunillas s/n, 23071, Jaén, Spain
| | - Jill T Anderson
- Department of Genetics, University of Georgia, Athens, Georgia, 30602
| | - Evan Raskin
- Institute for Genome Sciences and Policy, Department of Biology, Duke University, P.O. Box 90338, Durham, North Carolina, 27708
| | - Christopher Weiss-Lehman
- Department of Ecology and Evolutionary Biology, Biofrontiers Institute, University of Colorado, Boulder, Colarado, 80309
| | - Thomas Mitchell-Olds
- Institute for Genome Sciences and Policy, Department of Biology, Duke University, P.O. Box 90338, Durham, North Carolina, 27708
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Figueroa M, Castell-Miller CV, Li F, Hulbert SH, Bradeen JM. Pushing the boundaries of resistance: insights from Brachypodium-rust interactions. FRONTIERS IN PLANT SCIENCE 2015; 6:558. [PMID: 26284085 PMCID: PMC4519692 DOI: 10.3389/fpls.2015.00558] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/07/2015] [Indexed: 05/20/2023]
Abstract
The implications of global population growth urge transformation of current food and bioenergy production systems to sustainability. Members of the family Poaceae are of particular importance both in food security and for their applications as biofuel substrates. For centuries, rust fungi have threatened the production of valuable crops such as wheat, barley, oat, and other small grains; similarly, biofuel crops can also be susceptible to these pathogens. Emerging rust pathogenic races with increased virulence and recurrent rust epidemics around the world point out the vulnerability of monocultures. Basic research in plant immunity, especially in model plants, can make contributions to understanding plant resistance mechanisms and improve disease management strategies. The development of the grass Brachypodium distachyon as a genetically tractable model for monocots, especially temperate cereals and grasses, offers the possibility to overcome the experimental challenges presented by the genetic and genomic complexities of economically valuable crop plants. The numerous resources and tools available in Brachypodium have opened new doors to investigate the underlying molecular and genetic bases of plant-microbe interactions in grasses and evidence demonstrating the applicability and advantages of working with B. distachyon is increasing. Importantly, several interactions between B. distachyon and devastating plant pathogens, such rust fungi, have been examined in the context of non-host resistance. Here, we discuss the use of B. distachyon in these various pathosystems. Exploiting B. distachyon to understand the mechanisms underpinning disease resistance to non-adapted rust fungi may provide effective and durable approaches to fend off these pathogens. The close phylogenetic relationship among Brachypodium spp. and grasses with industrial and agronomic value support harnessing this model plant to improve cropping systems and encourage its use in translational research.
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Affiliation(s)
- Melania Figueroa
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
| | - Claudia V. Castell-Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
| | - Feng Li
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
| | - Scot H. Hulbert
- Department of Plant Pathology, Washington State University, Pullman, WA, USA
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - James M. Bradeen
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
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Chochois V, Vogel JP, Rebetzke GJ, Watt M. Variation in Adult Plant Phenotypes and Partitioning among Seed and Stem-Borne Roots across Brachypodium distachyon Accessions to Exploit in Breeding Cereals for Well-Watered and Drought Environments. PLANT PHYSIOLOGY 2015; 168:953-67. [PMID: 25975834 PMCID: PMC4741322 DOI: 10.1104/pp.15.00095] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 05/11/2015] [Indexed: 05/08/2023]
Abstract
Seedling roots enable plant establishment. Their small phenotypes are measured routinely. Adult root systems are relevant to yield and efficiency, but phenotyping is challenging. Root length exceeds the volume of most pots. Field studies measure partial adult root systems through coring or use seedling roots as adult surrogates. Here, we phenotyped 79 diverse lines of the small grass model Brachypodium distachyon to adults in 50-cm-long tubes of soil with irrigation; a subset of 16 lines was droughted. Variation was large (total biomass, ×8; total root length [TRL], ×10; and root mass ratio, ×6), repeatable, and attributable to genetic factors (heritabilities ranged from approximately 50% for root growth to 82% for partitioning phenotypes). Lines were dissected into seed-borne tissues (stem and primary seminal axile roots) and stem-borne tissues (tillers and coleoptile and leaf node axile roots) plus branch roots. All lines developed one seminal root that varied, with branch roots, from 31% to 90% of TRL in the well-watered condition. With drought, 100% of TRL was seminal, regardless of line because nodal roots were almost always inhibited in drying topsoil. Irrigation stimulated nodal roots depending on genotype. Shoot size and tillers correlated positively with roots with irrigation, but partitioning depended on genotype and was plastic with drought. Adult root systems of B. distachyon have genetic variation to exploit to increase cereal yields through genes associated with partitioning among roots and their responsiveness to irrigation. Whole-plant phenotypes could enhance gain for droughted environments because root and shoot traits are coselected.
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Affiliation(s)
- Vincent Chochois
- Commonwealth Scientific and Industrial Research Organisation Agriculture Flagship, Canberra, Australian Capital Territory 2601, Australia (V.C., G.J.R., M.W.); andUnited States Department of Energy Joint Genome Institute, Walnut Creek, California 94598 (J.P.V.)
| | - John P Vogel
- Commonwealth Scientific and Industrial Research Organisation Agriculture Flagship, Canberra, Australian Capital Territory 2601, Australia (V.C., G.J.R., M.W.); andUnited States Department of Energy Joint Genome Institute, Walnut Creek, California 94598 (J.P.V.)
| | - Gregory J Rebetzke
- Commonwealth Scientific and Industrial Research Organisation Agriculture Flagship, Canberra, Australian Capital Territory 2601, Australia (V.C., G.J.R., M.W.); andUnited States Department of Energy Joint Genome Institute, Walnut Creek, California 94598 (J.P.V.)
| | - Michelle Watt
- Commonwealth Scientific and Industrial Research Organisation Agriculture Flagship, Canberra, Australian Capital Territory 2601, Australia (V.C., G.J.R., M.W.); andUnited States Department of Energy Joint Genome Institute, Walnut Creek, California 94598 (J.P.V.)
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