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Loureiro I, Escorial MC, Chueca MC. Natural hybridization between wheat (Triticum aestivum L.) and its wild relatives Aegilops geniculata Roth and Aegilops triuncialis L. PEST MANAGEMENT SCIENCE 2023; 79:2247-2254. [PMID: 36785882 DOI: 10.1002/ps.7406] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Cultivated bread wheat (Triticum aestivum L.) spontaneously hybridizes with wild/weedy related Aegilops populations, but little is known about the actual rates at which this hybridization occurs under field conditions. It is very important to provide reliable empirical data on this phenomenon in order to assess the potential crop-wild introgression, especially in the context of conducting risk assessments for the commercialization of genetically modified (GM) wheat, as gene flow from wheat to Aegilops species could transfer into the wild species genes coding for traits such as resistance to herbicides, insects, diseases or environmental stresses. RESULTS The spontaneous hybridization rates between wheat and A. geniculata and A. triuncialis, which are very abundant in the Mediterranean area, have been estimated for the first time in the northern part of the Meseta Central, the great central plateau which includes the largest area of wheat cultivation in Spain. Hybridization rates averaged 0.12% and 0.008% for A. geniculata and A. triuncialis, respectively. Hybrids were found in 26% of A. geniculata and 5% of A. triuncialis populations, at rates that can be ≤3.6% for A. geniculata and 0.24% for A. triuncialis. CONCLUSION The detection of Aegilops spp.-wheat hybrids in Aegilops populations indicates that gene flow can occur, although wheat is considered a crop with a low-to-medium risk for transgene escape. These data on field hybridization rates are essential for GM wheat risk assessment purposes. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Iñigo Loureiro
- Plant Protection Department, Weed Science Group, Centro Nacional Instituto de Investigación y Tecnología Agraria y Alimentaria (INIA, CSIC), Madrid, Spain
| | - María Concepción Escorial
- Plant Protection Department, Weed Science Group, Centro Nacional Instituto de Investigación y Tecnología Agraria y Alimentaria (INIA, CSIC), Madrid, Spain
| | - María Cristina Chueca
- Plant Protection Department, Weed Science Group, Centro Nacional Instituto de Investigación y Tecnología Agraria y Alimentaria (INIA, CSIC), Madrid, Spain
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Premachandra T, Cauret CMS, Conradie W, Measey J, Evans BJ. Population genomics and subgenome evolution of the allotetraploid frog Xenopus laevis in southern Africa. G3 (BETHESDA, MD.) 2022; 13:6916838. [PMID: 36524354 PMCID: PMC9911082 DOI: 10.1093/g3journal/jkac325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/02/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022]
Abstract
Allotetraploid genomes have two distinct genomic components called subgenomes that are derived from separate diploid ancestral species. Many genomic characteristics such as gene function, expression, recombination, and transposable element mobility may differ significantly between subgenomes. To explore the possibility that subgenome population structure and gene flow may differ as well, we examined genetic variation in an allotetraploid frog-the African clawed frog (Xenopus laevis)-over the dynamic and varied habitat of its native range in southern Africa. Using reduced representation genome sequences from 91 samples from 12 localities, we found no strong evidence that population structure and gene flow differed substantially by subgenome. We then compared patterns of population structure in the nuclear genome to the mitochondrial genome using Sanger sequences from 455 samples from 183 localities. Our results provide further resolution to the geographic distribution of mitochondrial and nuclear diversity in this species and illustrate that population structure in both genomes corresponds roughly with variation in seasonal rainfall and with the topography of southern Africa.
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Affiliation(s)
- Tharindu Premachandra
- Department of Biology, McMaster University, Life Sciences Building Room 328, 1280 Main Street West, Hamilton, ON L8S4K1, Canada
| | - Caroline M S Cauret
- Department of Biology, McMaster University, Life Sciences Building Room 328, 1280 Main Street West, Hamilton, ON L8S4K1, Canada,Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Werner Conradie
- Port Elizabeth Museum (Bayworld), P.O. Box 13147, Humewood, Gqeberha 6013, South Africa,Department of Conservation Management, Natural Resource Science and Management Cluster, Faculty of Science, Nelson Mandela University, George Campus, George 6019, South Africa
| | - John Measey
- Corresponding author: Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa.
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Baiakhmetov E, Nowak A, Gudkova PD, Nobis M. Morphological and genome-wide evidence for natural hybridisation within the genus Stipa (Poaceae). Sci Rep 2020; 10:13803. [PMID: 32796878 PMCID: PMC7427808 DOI: 10.1038/s41598-020-70582-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 07/31/2020] [Indexed: 11/17/2022] Open
Abstract
Hybridisation in the wild between closely related species is a common mechanism of speciation in the plant kingdom and, in particular, in the grass family. Here we explore the potential for natural hybridisation in Stipa (one of the largest genera in Poaceae) between genetically distant species at their distribution edges in Mountains of Central Asia using integrative taxonomy. Our research highlights the applicability of classical morphological and genome reduction approaches in studies on wild plant species. The obtained results revealed a new nothospecies, Stipa × lazkovii, which exhibits intermediate characters to S. krylovii and S. bungeana. A high-density DArTseq assay disclosed that S. × lazkovii is an F1 hybrid, and established that the plastid and mitochondrial DNA was inherited from S. bungeana. In addition, molecular markers detected a hybridisation event between morphologically and genetically distant species S. bungeana and probably S. glareosa. Moreover, our findings demonstrated an uncertainty on the taxonomic status of S. bungeana that currently belongs to the section Leiostipa, but it is genetically closer to S. breviflora from the section Barbatae. Finally, we noticed a discrepancy between the current molecular data with the previous findings on S. capillata and S. sareptana.
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Affiliation(s)
- Evgenii Baiakhmetov
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland. .,Research Laboratory 'Herbarium', National Research Tomsk State University, Lenin 36 Ave, 634050, Tomsk, Russia.
| | - Arkadiusz Nowak
- Botanical Garden-Centre for Biological Diversity Conservation, Polish Academy of Sciences, Prawdziwka 2, 02-973, Warszawa, Poland.,Institute of Biology, Opole University, Oleska 22, 45-052, Opole, Poland
| | - Polina D Gudkova
- Research Laboratory 'Herbarium', National Research Tomsk State University, Lenin 36 Ave, 634050, Tomsk, Russia.,Department of Biology, Altai State University, Lenin 61 Ave, 656049, Barnaul, Russia
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland.
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Huynh S, Marcussen T, Felber F, Parisod C. Hybridization preceded radiation in diploid wheats. Mol Phylogenet Evol 2019; 139:106554. [PMID: 31288105 DOI: 10.1016/j.ympev.2019.106554] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/03/2019] [Accepted: 07/03/2019] [Indexed: 01/06/2023]
Abstract
Evolutionary relationships among the Aegilops-Triticum relatives of cultivated wheats have been difficult to resolve owing to incomplete lineage sorting and reticulate evolution. Recent studies have suggested that the wheat D-genome lineage (progenitor of Ae. tauschii) originated through homoploid hybridization between the A-genome lineage (progenitor of Triticum s.str.) and the B-genome lineage (progenitor of Ae. speltoides). This scenario of reticulation has been debated, calling for adequate phylogenetic analyses based on comprehensive sampling. To reconstruct the evolution of Aegilops-Triticum diploids, we here combined high-throughput sequencing of 38 nuclear low-copy loci of multiple accessions of all 13 species with inferences of the species phylogeny using the full-parameterized MCMC_SEQ method. Phylogenies recovered a monophyletic Aegilops-Triticum lineage that began diversifying ~6.6 Ma ago and gave rise to four sublineages, i.e. the A- (2 species), B- (1 species), D- (9 species) and T- (Ae. mutica) genome lineage. Full-parameterized phylogenies as well as patterns of tree dilation and tree compression supported a hybrid origin of the D-genome lineage from A and B ~3.0-4.0 Ma ago, and did not indicate additional hybridization events. Conflicting ABBA-BABA tests suggestive of further reticulation were shown here to result from ancestral population structure rather than hybridization. This comprehensive and dated phylogeny of wheat relatives indicates that the origin of the hybrid D-genome was followed by intense diversification into the majority of extant diploid as well as allopolyploid wild wheats.
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Affiliation(s)
- Stella Huynh
- Institute of Biology, University of Neuchâtel, Switzerland
| | - Thomas Marcussen
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway
| | - François Felber
- Institute of Biology, University of Neuchâtel, Switzerland; Musée et Jardins botaniques cantonaux de Lausanne et Pont-de-Nant, Switzerland
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Schmickl R, Marburger S, Bray S, Yant L. Hybrids and horizontal transfer: introgression allows adaptive allele discovery. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5453-5470. [PMID: 29096001 DOI: 10.1093/jxb/erx297] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Evolution has devised countless remarkable solutions to diverse challenges. Understanding the mechanistic basis of these solutions provides insights into how biological systems can be subtly tweaked without maladaptive consequences. The knowledge gained from illuminating these mechanisms is equally important to our understanding of fundamental evolutionary mechanisms as it is to our hopes of developing truly rational plant breeding and synthetic biology. In particular, modern population genomic approaches are proving very powerful in the detection of candidate alleles for mediating consequential adaptations that can be tested functionally. Especially striking are signals gained from contexts involving genetic transfers between populations, closely related species, or indeed between kingdoms. Here we discuss two major classes of these scenarios, adaptive introgression and horizontal gene flow, illustrating discoveries made across kingdoms.
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Affiliation(s)
- Roswitha Schmickl
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, 252 43 Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague, Czech Republic
| | - Sarah Marburger
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Sian Bray
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Levi Yant
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
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Abstract
An interesting and possibly unique pattern of genome evolution following polyploidy can be observed among allopolyploids of the Triticum and Aegilops genera (wheat group). Most polyploids in this group are presumed to share a common unaltered (pivotal) subgenome (U, D, or A) together with one or two modified (differential) subgenomes, a status that has been referred to as 'pivotal-differential' genome evolution. In this review we discuss various mechanisms that could be responsible for this evolutionary pattern, as well as evidence for and against the putative evolutionary mechanisms involved. We suggest that, in light of recent advances in genome sequencing and related technologies in the wheat group, the time has come to reopen the investigation into pivotal-differential genome evolution.
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Affiliation(s)
- Ghader Mirzaghaderi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, PO Box 416, Sanandaj, Iran
| | - Annaliese S Mason
- Department of Plant Breeding, Justus Liebig University, Research Center for Biosystems, Land Use, and Nutrition (IFZ), Heinrich-Buff-Ring 26-32, Giessen 35392, Germany.
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Ostrowski MF, Prosperi JM, David J. Potential Implications of Climate Change on Aegilops Species Distribution: Sympatry of These Crop Wild Relatives with the Major European Crop Triticum aestivum and Conservation Issues. PLoS One 2016; 11:e0153974. [PMID: 27100790 PMCID: PMC4839726 DOI: 10.1371/journal.pone.0153974] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 04/06/2016] [Indexed: 11/23/2022] Open
Abstract
Gene flow from crop to wild relatives is a common phenomenon which can lead to reduced adaptation of the wild relatives to natural ecosystems and/or increased adaptation to agrosystems (weediness). With global warming, wild relative distributions will likely change, thus modifying the width and/or location of co-occurrence zones where crop-wild hybridization events could occur (sympatry). This study investigates current and 2050 projected changes in sympatry levels between cultivated wheat and six of the most common Aegilops species in Europe. Projections were generated using MaxEnt on presence-only data, bioclimatic variables, and considering two migration hypotheses and two 2050 climate scenarios (RCP4.5 and RCP8.5). Overall, a general decline in suitable climatic conditions for Aegilops species outside the European zone and a parallel increase in Europe were predicted. If no migration could occur, the decline was predicted to be more acute outside than within the European zone. The potential sympatry level in Europe by 2050 was predicted to increase at a higher rate than species richness, and most expansions were predicted to occur in three countries, which are currently among the top four wheat producers in Europe: Russia, France and Ukraine. The results are also discussed with regard to conservation issues of these crop wild relatives.
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Affiliation(s)
- Marie-France Ostrowski
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes, Montpellier Supagro, France
- Montpellier Supagro, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes, Montpellier Supagro, France
| | - Jean-Marie Prosperi
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes, Montpellier Supagro, France
| | - Jacques David
- Montpellier Supagro, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes, Montpellier Supagro, France
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Senerchia N, Felber F, North B, Sarr A, Guadagnuolo R, Parisod C. Differential introgression and reorganization of retrotransposons in hybrid zones between wild wheats. Mol Ecol 2016; 25:2518-28. [DOI: 10.1111/mec.13515] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/24/2015] [Accepted: 11/30/2015] [Indexed: 12/20/2022]
Affiliation(s)
- Natacha Senerchia
- Laboratory of Evolutionary Botany; Institute of Biology; University of Neuchâtel; 2000 Neuchâtel Switzerland
| | - François Felber
- Laboratory of Evolutionary Botany; Institute of Biology; University of Neuchâtel; 2000 Neuchâtel Switzerland
- Musée et Jardins Botaniques Cantonaux; 1007 Lausanne Switzerland
| | - Béatrice North
- Laboratory of Evolutionary Botany; Institute of Biology; University of Neuchâtel; 2000 Neuchâtel Switzerland
| | - Anouk Sarr
- Laboratory of Evolutionary Botany; Institute of Biology; University of Neuchâtel; 2000 Neuchâtel Switzerland
| | - Roberto Guadagnuolo
- Laboratory of Evolutionary Botany; Institute of Biology; University of Neuchâtel; 2000 Neuchâtel Switzerland
| | - Christian Parisod
- Laboratory of Evolutionary Botany; Institute of Biology; University of Neuchâtel; 2000 Neuchâtel Switzerland
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Senerchia N, Felber F, Parisod C. Genome reorganization in F1 hybrids uncovers the role of retrotransposons in reproductive isolation. Proc Biol Sci 2015; 282:20142874. [PMID: 25716787 DOI: 10.1098/rspb.2014.2874] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Interspecific hybridization leads to new interactions among divergent genomes, revealing the nature of genetic incompatibilities having accumulated during and after the origin of species. Conflicts associated with misregulation of transposable elements (TEs) in hybrids expectedly result in their activation and genome-wide changes that may be key to species boundaries. Repetitive genomes of wild wheats have diverged under differential dynamics of specific long terminal repeat retrotransposons (LTR-RTs), offering unparalleled opportunities to address the underpinnings of plant genome reorganization by selfish sequences. Using reciprocal F1 hybrids between three Aegilops species, restructuring and epigenetic repatterning was assessed at random and LTR-RT sequences with amplified fragment length polymorphism and sequence-specific amplified polymorphisms as well as their methylation-sensitive counterparts, respectively. Asymmetrical reorganization of LTR-RT families predicted to cause conflicting interactions matched differential survival of F1 hybrids. Consistent with the genome shock model, increasing divergence of merged LTR-RTs yielded higher levels of changes in corresponding genome fractions and lead to repeated reorganization of LTR-RT sequences in F1 hybrids. Such non-random reorganization of hybrid genomes is coherent with the necessary repression of incompatible TE loci in support of hybrid viability and indicates that TE-driven genomic conflicts may represent an overlooked factor supporting reproductive isolation.
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Affiliation(s)
- Natacha Senerchia
- Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, Rue Emile Argand 11, Neuchâtel 2000, Switzerland
| | - François Felber
- Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, Rue Emile Argand 11, Neuchâtel 2000, Switzerland Musée et Jardins Botaniques Cantonaux, Lausanne 1007, Switzerland
| | - Christian Parisod
- Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, Rue Emile Argand 11, Neuchâtel 2000, Switzerland
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Pajkovic M, Lappe S, Barman R, Parisod C, Neuenschwander S, Goudet J, Alvarez N, Guadagnuolo R, Felber F, Arrigo N. Wheat alleles introgress into selfing wild relatives: empirical estimates from approximate Bayesian computation inAegilops triuncialis. Mol Ecol 2014; 23:5089-101. [DOI: 10.1111/mec.12918] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 09/03/2014] [Accepted: 09/10/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Mila Pajkovic
- Department of Ecology and Evolution; University of Lausanne; Lausanne CH-1015 Switzerland
| | - Sylvain Lappe
- Laboratory of Evolutionary Botany; Institute of Biology; University of Neuchatel; Emile-Argand 11 Neuchatel CH-2001 Switzerland
| | - Rachel Barman
- Department of Ecology and Evolution; University of Lausanne; Lausanne CH-1015 Switzerland
| | - Christian Parisod
- Laboratory of Evolutionary Botany; Institute of Biology; University of Neuchatel; Emile-Argand 11 Neuchatel CH-2001 Switzerland
| | - Samuel Neuenschwander
- Department of Ecology and Evolution; University of Lausanne; Lausanne CH-1015 Switzerland
- Vital-IT; Swiss Institute of Bioinformatics; University of Lausanne; Lausanne Switzerland
| | - Jerome Goudet
- Department of Ecology and Evolution; University of Lausanne; Lausanne CH-1015 Switzerland
- Vital-IT; Swiss Institute of Bioinformatics; University of Lausanne; Lausanne Switzerland
| | - Nadir Alvarez
- Department of Ecology and Evolution; University of Lausanne; Lausanne CH-1015 Switzerland
| | - Roberto Guadagnuolo
- Laboratory of Evolutionary Botany; Institute of Biology; University of Neuchatel; Emile-Argand 11 Neuchatel CH-2001 Switzerland
| | - François Felber
- Musée et Jardins botaniques cantonaux vaudois; Lausanne CH-1007 Switzerland
| | - Nils Arrigo
- Department of Ecology and Evolution; University of Lausanne; Lausanne CH-1015 Switzerland
- Laboratory of Evolutionary Botany; Institute of Biology; University of Neuchatel; Emile-Argand 11 Neuchatel CH-2001 Switzerland
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