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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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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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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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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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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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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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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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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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Matzrafi M, Gadri Y, Frenkel E, Rubin B, Peleg Z. Evolution of herbicide resistance mechanisms in grass weeds. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 229:43-52. [PMID: 25443832 DOI: 10.1016/j.plantsci.2014.08.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 08/14/2014] [Accepted: 08/21/2014] [Indexed: 05/27/2023]
Abstract
Herbicide resistant weeds are becoming increasingly common, threatening global food security. Here, we present BrIFAR: a new model system for the functional study of mechanisms of herbicide resistance in grass weeds. We have developed a large collection of Brachypodium accessions, the BrI collection, representing a wide range of habitats. Wide screening of the responses of the accessions to four major herbicide groups (PSII, ACCase, ALS/AHAS and EPSPS inhibitors) identified 28 herbicide-resistance candidate accessions. Target-site resistance to PSII inhibitors was found in accessions collected from habitats with a known history of herbicide applications. An amino acid substitution in the psbA gene (serine264 to glycine) conferred resistance and also significantly affected the flowering and shoot dry weight of the resistant accession, as compared to the sensitive accession. Non-target site resistance to ACCase inhibitors was found in accessions collected from habitats with a history of herbicide application and from a nature reserve. In-vitro enzyme activity tests and responses following pre-treatment with malathion (a cytochrome-P450 inhibitor) indicated sensitivity at the enzyme level, and give strong support to diclofop-methyl and pinoxaden enhanced detoxification as NTS resistance mechanism. BrIFAR can promote better understanding of the evolution of mechanisms of herbicide resistance and aid the implementation of integrative management approaches for sustainable agriculture.
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Affiliation(s)
- Maor Matzrafi
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, PO Box 12, Rehovot 7610001, Israel.
| | - Yaron Gadri
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, PO Box 12, Rehovot 7610001, Israel.
| | - Eyal Frenkel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, PO Box 12, Rehovot 7610001, Israel.
| | - Baruch Rubin
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, PO Box 12, Rehovot 7610001, Israel.
| | - Zvi Peleg
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, PO Box 12, Rehovot 7610001, Israel.
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Isozyme variation and differentiation of morphologically cryptic species in the Brachypodium distachyon complex. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.04.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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López-Alvarez D, López-Herranz ML, Betekhtin A, Catalán P. A DNA barcoding method to discriminate between the model plant Brachypodium distachyon and its close relatives B. stacei and B. hybridum (Poaceae). PLoS One 2012; 7:e51058. [PMID: 23240000 PMCID: PMC3519806 DOI: 10.1371/journal.pone.0051058] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 10/29/2012] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Brachypodium distachyon s. l. has been widely investigated across the world as a model plant for temperate cereals and biofuel grasses. However, this annual plant shows three cytotypes that have been recently recognized as three independent species, the diploids B. distachyon (2n = 10) and B. stacei (2n = 20) and their derived allotetraploid B. hybridum (2n = 30). METHODOLOGY/PRINCIPAL FINDINGS We propose a DNA barcoding approach that consists of a rapid, accurate and automatable species identification method using the standard DNA sequences of complementary plastid (trnLF) and nuclear (ITS, GI) loci. The highly homogenous but largely divergent B. distachyon and B. stacei diploids could be easily distinguished (100% identification success) using direct trnLF (2.4%), ITS (5.5%) or GI (3.8%) sequence divergence. By contrast, B. hybridum could only be unambiguously identified through the use of combined trnLF+ITS sequences (90% of identification success) or by cloned GI sequences (96.7%) that showed 5.4% (ITS) and 4% (GI) rate divergence between the two parental sequences found in the allopolyploid. CONCLUSION/SIGNIFICANCE Our data provide an unbiased and effective barcode to differentiate these three closely-related species from one another. This procedure overcomes the taxonomic uncertainty generated from methods based on morphology or flow cytometry identifications that have resulted in some misclassifications of the model plant and its allies. Our study also demonstrates that the allotetraploid B. hybridum has resulted from bi-directional crosses of B. distachyon and B. stacei plants acting either as maternal or paternal parents.
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Affiliation(s)
- Diana López-Alvarez
- Department of Agriculture and Environmental Sciences, University of Zaragoza, Huesca, Spain
| | | | - Alexander Betekhtin
- Department of Agriculture and Environmental Sciences, University of Zaragoza, Huesca, Spain
- Department of Plant Anatomy and Cytology, University of Silesia, Katowice, Poland
| | - Pilar Catalán
- Department of Agriculture and Environmental Sciences, University of Zaragoza, Huesca, Spain
- * E-mail:
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