1
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Dou S, Zhang T, Wang L, Yang C, Quan C, Liang X, Ma C, Dai C. The self-compatibility is acquired after polyploidization: a case study of Brassica napus self-incompatible trilinear hybrid breeding system. THE NEW PHYTOLOGIST 2024; 241:1690-1707. [PMID: 38037276 DOI: 10.1111/nph.19451] [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: 05/22/2023] [Accepted: 11/07/2023] [Indexed: 12/02/2023]
Abstract
Self-incompatibility plays a vital role in angiosperms, by preventing inbreeding depression and maintaining genetic diversity within populations. Following polyploidization, many angiosperm species transition from self-incompatibility to self-compatibility. Here, we investigated the S-locus in Brassicaceae and identified distinct origins for the sRNA loci, SMI and SMI2 (SCR Methylation Inducer 1 and 2), within the S-locus. The SMI loci were found to be widespread in Cruciferae, whereas the SMI2 loci were exclusive to Brassica species. Additionally, we discovered four major S-haplotypes (BnS-1, BnS-6, BnS-7, and BnS-1300) in rapeseed. Overexpression of BnSMI-1 in self-incompatible Brassica napus ('S-70S1300S6 ') resulted in a significant increase in DNA methylation in the promoter regions of BnSCR-6 and BnSCR-1300, leading to self-compatibility. Conversely, by overexpressing a point mutation of BnSmi-1 in the 'S-70S1300S6 ' line, we observed lower levels of DNA methylation in BnSCR-6 and BnSCR-1300 promoters. Furthermore, the overexpression of BnSMI2-1300 in the 'SI-326S7S6 ' line inhibited the expression of BnSCR-7 through transcriptional repression of the Smi2 sRNA from the BnS-1300 haplotype. Our study demonstrates that the self-compatibility of rapeseed is determined by S-locus sRNA-mediated silencing of SCR after polyploidization, which helps to further breed self-incompatible or self-compatible rapeseed lines, thereby facilitating the utilization of heterosis.
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Affiliation(s)
- Shengwei Dou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Tong Zhang
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lulin Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Chuang Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Chengtao Quan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Xiaomei Liang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Cheng Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
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2
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Bramsiepe J, Krabberød AK, Bjerkan KN, Alling RM, Johannessen IM, Hornslien KS, Miller JR, Brysting AK, Grini PE. Structural evidence for MADS-box type I family expansion seen in new assemblies of Arabidopsis arenosa and A. lyrata. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:942-961. [PMID: 37517071 DOI: 10.1111/tpj.16401] [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: 01/22/2023] [Revised: 05/24/2023] [Accepted: 07/13/2023] [Indexed: 08/01/2023]
Abstract
Arabidopsis thaliana diverged from A. arenosa and A. lyrata at least 6 million years ago. The three species differ by genome-wide polymorphisms and morphological traits. The species are to a high degree reproductively isolated, but hybridization barriers are incomplete. A special type of hybridization barrier is based on the triploid endosperm of the seed, where embryo lethality is caused by endosperm failure to support the developing embryo. The MADS-box type I family of transcription factors is specifically expressed in the endosperm and has been proposed to play a role in endosperm-based hybridization barriers. The gene family is well known for its high evolutionary duplication rate, as well as being regulated by genomic imprinting. Here we address MADS-box type I gene family evolution and the role of type I genes in the context of hybridization. Using two de-novo assembled and annotated chromosome-level genomes of A. arenosa and A. lyrata ssp. petraea we analyzed the MADS-box type I gene family in Arabidopsis to predict orthologs, copy number, and structural genomic variation related to the type I loci. Our findings were compared to gene expression profiles sampled before and after the transition to endosperm cellularization in order to investigate the involvement of MADS-box type I loci in endosperm-based hybridization barriers. We observed substantial differences in type-I expression in the endosperm of A. arenosa and A. lyrata ssp. petraea, suggesting a genetic cause for the endosperm-based hybridization barrier between A. arenosa and A. lyrata ssp. petraea.
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Affiliation(s)
- Jonathan Bramsiepe
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
- CEES, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Anders K Krabberød
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Katrine N Bjerkan
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
- CEES, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Renate M Alling
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
- CEES, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Ida M Johannessen
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Karina S Hornslien
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Jason R Miller
- College of STEM, Shepherd University, Shepherdstown, West Virginia, 25443-5000, USA
| | - Anne K Brysting
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
- CEES, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Paul E Grini
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
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3
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Novikova PY, Kolesnikova UK, Scott AD. Ancestral self-compatibility facilitates the establishment of allopolyploids in Brassicaceae. PLANT REPRODUCTION 2023; 36:125-138. [PMID: 36282331 PMCID: PMC9957919 DOI: 10.1007/s00497-022-00451-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/20/2022] [Indexed: 05/15/2023]
Abstract
Self-incompatibility systems based on self-recognition evolved in hermaphroditic plants to maintain genetic variation of offspring and mitigate inbreeding depression. Despite these benefits in diploid plants, for polyploids who often face a scarcity of mating partners, self-incompatibility can thwart reproduction. In contrast, self-compatibility provides an immediate advantage: a route to reproductive viability. Thus, diploid selfing lineages may facilitate the formation of new allopolyploid species. Here, we describe the mechanism of establishment of at least four allopolyploid species in Brassicaceae (Arabidopsis suecica, Arabidopsis kamchatica, Capsella bursa-pastoris, and Brassica napus), in a manner dependent on the prior loss of the self-incompatibility mechanism in one of the ancestors. In each case, the degraded S-locus from one parental lineage was dominant over the functional S-locus of the outcrossing parental lineage. Such dominant loss-of-function mutations promote an immediate transition to selfing in allopolyploids and may facilitate their establishment.
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Affiliation(s)
- Polina Yu Novikova
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829, Cologne, Germany.
| | - Uliana K Kolesnikova
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829, Cologne, Germany
| | - Alison Dawn Scott
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829, Cologne, Germany
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4
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Borowska-Zuchowska N, Senderowicz M, Trunova D, Kolano B. Tracing the Evolution of the Angiosperm Genome from the Cytogenetic Point of View. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11060784. [PMID: 35336666 PMCID: PMC8953110 DOI: 10.3390/plants11060784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/14/2022] [Accepted: 03/14/2022] [Indexed: 05/05/2023]
Abstract
Cytogenetics constitutes a branch of genetics that is focused on the cellular components, especially chromosomes, in relation to heredity and genome structure, function and evolution. The use of modern cytogenetic approaches and the latest microscopes with image acquisition and processing systems enables the simultaneous two- or three-dimensional, multicolour visualisation of both single-copy and highly-repetitive sequences in the plant genome. The data that is gathered using the cytogenetic methods in the phylogenetic background enable tracing the evolution of the plant genome that involve changes in: (i) genome sizes; (ii) chromosome numbers and morphology; (iii) the content of repetitive sequences and (iv) ploidy level. Modern cytogenetic approaches such as FISH using chromosome- and genome-specific probes have been widely used in studies of the evolution of diploids and the consequences of polyploidy. Nowadays, modern cytogenetics complements analyses in other fields of cell biology and constitutes the linkage between genetics, molecular biology and genomics.
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5
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Čertner M, Lučanová M, Sliwinska E, Kolář F, Loureiro J. Plant material selection, collection, preservation, and storage for nuclear DNA content estimation. Cytometry A 2021; 101:737-748. [PMID: 34254737 DOI: 10.1002/cyto.a.24482] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 01/23/2023]
Abstract
In theory, any plant tissue providing intact nuclei in sufficient quantity is suitable for nuclear DNA content estimation using flow cytometry (FCM). While this certainly opens a wide variety of possible applications of FCM, especially when compared to classical karyological techniques restricted to tissues with active cell division, tissue selection and quality may directly affect the precision (and sometimes even reliability) of FCM measurements. It is usually convenient to first consider the goals of the study to either aim for the highest possible accuracy of estimates (e.g., for inferring genome size, detecting homoploid intraspecific genome size variation, aneuploidy, among others), or to decide that histograms of reasonable resolution provide sufficient information (e.g., ploidy level screening within a single model species). Here, a set of best practices guidelines for selecting the optimal plant tissue for FCM analysis, sampling of material, and material preservation and storage are provided. In addition, factors potentially compromising the quality of FCM estimates of nuclear DNA content and data interpretation are discussed.
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Affiliation(s)
- Martin Čertner
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - Magdalena Lučanová
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic.,Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Elwira Sliwinska
- Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, UTP University of Science and Technology, Bydgoszcz, Poland
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - João Loureiro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
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6
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Zlonis KJ, Etterson JR. Constituents of a mixed-ploidy population of Solidago altissima differ in plasticity and predicted response to selection under simulated climate change. AMERICAN JOURNAL OF BOTANY 2019; 106:453-468. [PMID: 30901496 DOI: 10.1002/ajb2.1257] [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: 02/23/2018] [Accepted: 01/14/2019] [Indexed: 06/09/2023]
Abstract
PREMISE OF THE STUDY Polyploids possess unique attributes that influence their environmental tolerance and geographic distribution. It is often unknown, however, whether cytotypes within mixed-ploidy populations are also uniquely adapted and differ in their responses to environmental change. Here, we examine whether diploids and hexaploids from a single mixed-ploidy population of Solidago altissima differ in plasticity and potential response to natural selection under conditions simulating climate change. METHODS Clonal replicates of diploid and hexaploid genotypes were grown in a randomized split-plot design under two temperature (+1.9°C) and two watering treatments (-13% soil moisture) implemented with open-top passive chambers placed under rainout shelters. Physiological, phenological, morphological traits, and a fitness correlate, reproductive biomass, were measured and compared among treatments. KEY RESULTS Differences in traits suggest that diploids are currently better adapted to low- water availability than hexaploids. Both ploidy levels had adaptive plastic responses to treatments and are predicted to respond to selection, but often for different traits. Water availability generally had a stronger effect than temperature, but for some traits the effect of water depended on temperature. CONCLUSIONS Diploid and hexaploid S. altissima may maintain fitness in the short term through adaptive plasticity and evolution depending on which traits are important in a warmer, drier environment. Hexaploids may be at a disadvantage compared to diploids because fewer traits were heritable. Our results underscore the importance of studying combinations of climate variables that are predicted to change simultaneously.
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Affiliation(s)
- Katharine J Zlonis
- Department of Biology, University of Minnesota Duluth, 1035 Kirby Drive, Duluth, Minnesota, 55812, USA
| | - Julie R Etterson
- Department of Biology, University of Minnesota Duluth, 1035 Kirby Drive, Duluth, Minnesota, 55812, USA
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7
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Mable BK, Brysting AK, Jørgensen MH, Carbonell AKZ, Kiefer C, Ruiz-Duarte P, Lagesen K, Koch MA. Adding Complexity to Complexity: Gene Family Evolution in Polyploids. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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8
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Novikova PY, Hohmann N, Van de Peer Y. Polyploid Arabidopsis species originated around recent glaciation maxima. CURRENT OPINION IN PLANT BIOLOGY 2018; 42:8-15. [PMID: 29448159 DOI: 10.1016/j.pbi.2018.01.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/17/2018] [Indexed: 05/20/2023]
Abstract
Polyploidy may provide adaptive advantages and is considered to be important for evolution and speciation. Polyploidy events are found throughout the evolutionary history of plants, however they do not seem to be uniformly distributed along the time axis. For example, many of the detected ancient whole-genome duplications (WGDs) seem to cluster around the K/Pg boundary (∼66Mya), which corresponds to a drastic climate change event and a mass extinction. Here, we discuss more recent polyploidy events using Arabidopsis as the most developed plant model at the level of the entire genus. We review the history of the origin of allotetraploid species A. suecica and A. kamchatica, and tetraploid lineages of A. lyrata, A. arenosa and A. thaliana, and discuss potential adaptive advantages. Also, we highlight an association between recent glacial maxima and estimated times of origins of polyploidy in Arabidopsis. Such association might further support a link between polyploidy and environmental challenge, which has been observed now for different time-scales and for both ancient and recent polyploids.
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Affiliation(s)
- Polina Yu Novikova
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Nora Hohmann
- University of Basel, Department of Environmental Sciences, Basel, Switzerland
| | - Yves Van de Peer
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium; Department of Genetics, University of Pretoria, Pretoria, South Africa.
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9
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Kyriakidou M, Tai HH, Anglin NL, Ellis D, Strömvik MV. Current Strategies of Polyploid Plant Genome Sequence Assembly. FRONTIERS IN PLANT SCIENCE 2018; 9:1660. [PMID: 30519250 PMCID: PMC6258962 DOI: 10.3389/fpls.2018.01660] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 10/25/2018] [Indexed: 05/14/2023]
Abstract
Polyploidy or duplication of an entire genome occurs in the majority of angiosperms. The understanding of polyploid genomes is important for the improvement of those crops, which humans rely on for sustenance and basic nutrition. As climate change continues to pose a potential threat to agricultural production, there will increasingly be a demand for plant cultivars that can resist biotic and abiotic stresses and also provide needed and improved nutrition. In the past decade, Next Generation Sequencing (NGS) has fundamentally changed the genomics landscape by providing tools for the exploration of polyploid genomes. Here, we review the challenges of the assembly of polyploid plant genomes, and also present recent advances in genomic resources and functional tools in molecular genetics and breeding. As genomes of diploid and less heterozygous progenitor species are increasingly available, we discuss the lack of complexity of these currently available reference genomes as they relate to polyploid crops. Finally, we review recent approaches of haplotyping by phasing and the impact of third generation technologies on polyploid plant genome assembly.
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Affiliation(s)
- Maria Kyriakidou
- Department of Plant Science, McGill University, Montreal, QC, Canada
| | - Helen H. Tai
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
| | | | | | - Martina V. Strömvik
- Department of Plant Science, McGill University, Montreal, QC, Canada
- *Correspondence: Martina V. Strömvik
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10
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Hohmann N, Koch MA. An Arabidopsis introgression zone studied at high spatio-temporal resolution: interglacial and multiple genetic contact exemplified using whole nuclear and plastid genomes. BMC Genomics 2017; 18:810. [PMID: 29058582 PMCID: PMC5651623 DOI: 10.1186/s12864-017-4220-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/16/2017] [Indexed: 12/30/2022] Open
Abstract
Background Gene flow between species, across ploidal levels, and even between evolutionary lineages is a common phenomenon in the genus Arabidopsis. However, apart from two genetically fully stabilized allotetraploid species that have been investigated in detail, the extent and temporal dynamics of hybridization are not well understood. An introgression zone, with tetraploid A. arenosa introgressing into A. lyrata subsp. petraea in the Eastern Austrian Forealps and subsequent expansion towards pannonical lowlands, was described previously based on morphological observations as well as molecular data using microsatellite and plastid DNA markers. Here we investigate the spatio-temporal context of this suture zone, making use of the potential of next-generation sequencing and whole-genome data. By utilizing a combination of nuclear and plastid genomic data, the extent, direction and temporal dynamics of gene flow are elucidated in detail and Late Pleistocene evolutionary processes are resolved. Results Analysis of nuclear genomic data significantly recognizes the clinal structure of the introgression zone, but also reveals that hybridization and introgression is more common and substantial than previously thought. Also tetraploid A. lyrata and A. arenosa subsp. borbasii from outside the previously defined suture zone show genomic signals of past introgression. A. lyrata is shown to serve usually as the maternal parent in these hybridizations, but one exception is identified from plastome-based phylogenetic reconstruction. Using plastid phylogenomics with secondary time calibration, the origin of A. lyrata and A. arenosa lineages is pre-dating the last three glaciation complexes (approx. 550,000 years ago). Hybridization and introgression followed during the last two glacial-interglacial periods (since approx. 300,000 years ago) with later secondary contact at the northern and southern border of the introgression zone during the Holocene. Conclusions Footprints of adaptive introgression in the Northeastern Forealps are older than expected and predate the Last Glaciation Maximum. This correlates well with high genetic diversity found within areas that served as refuge area multiple times. Our data also provide some first hints that early introgressed and presumably preadapted populations account for successful and rapid postglacial re-colonization and range expansion. Electronic supplementary material The online version of this article (doi: 10.1186/s12864-017-4220-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nora Hohmann
- Center for Organismal Studies (COS) Heidelberg/Botanic Garden and Herbarium Heidelberg (HEID), University of Heidelberg, Im Neuenheimer Feld 345, D-69120, Heidelberg, Germany.,Present address: Department of Environmental Sciences, Botany, University of Basel, Hebelstrasse 1, CH-4056, Basel, Switzerland
| | - Marcus A Koch
- Center for Organismal Studies (COS) Heidelberg/Botanic Garden and Herbarium Heidelberg (HEID), University of Heidelberg, Im Neuenheimer Feld 345, D-69120, Heidelberg, Germany.
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11
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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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12
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Lloyd A, Bomblies K. Meiosis in autopolyploid and allopolyploid Arabidopsis. CURRENT OPINION IN PLANT BIOLOGY 2016; 30:116-22. [PMID: 26950252 DOI: 10.1016/j.pbi.2016.02.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 02/05/2016] [Accepted: 02/08/2016] [Indexed: 05/20/2023]
Abstract
All newly formed polyploids face a challenge in meiotic chromosome segregation due to the presence of an additional set of chromosomes. Nevertheless, naturally occurring auto and allopolyploids are common and generally show high fertility, showing that evolution can find solutions. Exactly how meiosis is adapted in these cases, however, remains a mystery. The rise of Arabidopsis as a model genus for polyploid and meiosis research has seen several new studies begin to shed light on this long standing question.
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Affiliation(s)
- Andrew Lloyd
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA; Institut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026 Versailles Cedex, France.
| | - Kirsten Bomblies
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA; John Innes Centre, Department of Cell & Developmental Biology, Norwich, UK
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13
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Etterson JR, Toczydlowski RH, Winkler KJ, Kirschbaum JA, McAulay TS. Solidago altissima differs with respect to ploidy frequency and clinal variation across the prairie-forest biome border in Minnesota. AMERICAN JOURNAL OF BOTANY 2016; 103:22-32. [PMID: 26507110 DOI: 10.3732/ajb.1500146] [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: 04/02/2015] [Accepted: 06/30/2015] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Although our awareness of ploidy diversity has expanded with the application of flow cytometry, we still know little about the extent to which cytotypes within mixed-ploidy populations are genetically differentiated across environmental gradients. METHODS To address this issue, we reared 14 populations of Solidago altissima spanning the prairie-forest ecotone in Minnesota in a common garden with a watering treatment. We assessed ploidy frequencies and measured survival, flowering phenology, and plant architectural traits for 4 years. KEY RESULTS All populations harbored multiple cytotypes; prairie populations were dominated by tetraploids, forest populations by hexaploids. Diploids and polyploids differed significantly for 84% of the traits. Beyond average differences, the slope of trait values covaried with latitude and longitude, but this relationship was stronger for diploids than the other two polyploid cytotypes as indicated by numerous ploidy × latitude and ploidy × longitude interactions. For example, the timing of flowering of the cytotypes overlapped in populations sampled from the northeastern hemiboreal forest but differed significantly between cytotypes sampled from populations in the southwestern prairie. The watering treatments had weak effects, and there were no ploidy differences for phenotypic plasticity. CONCLUSIONS Our data show that diploids have diverged genetically to a greater extent than polyploids along the environmental clines sampled in this study. Moreover, different environments favor phenotypic convergence over divergence among cytotypes for some traits. Differences in ploidy frequency and phenotypic divergence among cytotypes across gradients of temperature and precipitation are important considerations for restoration in an age of climate change.
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Affiliation(s)
- Julie R Etterson
- Department of Biology, University of Minnesota Duluth, 207A Swenson Science Building, Duluth, Minnesota 55812 USA
| | - Rachel H Toczydlowski
- Department of Biology, University of Minnesota Duluth, 207A Swenson Science Building, Duluth, Minnesota 55812 USA
| | - Katharine J Winkler
- Department of Biology, University of Minnesota Duluth, 207A Swenson Science Building, Duluth, Minnesota 55812 USA
| | - Jessica A Kirschbaum
- Department of Biology, University of Minnesota Duluth, 207A Swenson Science Building, Duluth, Minnesota 55812 USA
| | - Tim S McAulay
- Department of Biology, University of Minnesota Duluth, 207A Swenson Science Building, Duluth, Minnesota 55812 USA
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Enke N, Kunze R, Pustahija F, Glöckner G, Zimmermann J, Oberländer J, Kamari G, Siljak-Yakovlev S. Genome size shifts: karyotype evolution in Crepis section Neglectoides (Asteraceae). PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17:775-786. [PMID: 25683604 DOI: 10.1111/plb.12318] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 01/19/2015] [Indexed: 06/04/2023]
Abstract
Plant genome size evolution is a very dynamic process: the ancestral genome of angiosperms was initially most likely small, which led to a tendency towards genome increase during evolution. However, findings in several angiosperm lineages demonstrate mechanisms that also led to genome size contraction. Recent molecular investigations on the Asteraceae genus Crepis suggest that several genomic reduction events have occurred during the evolution of the genus. This study focuses on the Mediterranean Crepis sect. Neglectoides, which includes three species with some of the smallest genomes within the whole genus. Crepis neglecta has the largest genome in sect. Neglectoides, approximately twice the size of the two species Crepis cretica and Crepis hellenica. Whereas C. cretica and C. hellencia are more closely related to each other than to C. neglecta the karyotypes of the latter species and C. cretica are similar, while that of C. hellenica differs considerably. Here, the karyotypic organisation of the three species is investigated with fluorescence in-situ hybridisation and studied in a molecular phylogenetic framework based on the nuclear markers Actin, CHR12, CPN60B, GPCR1 and XTH23. Our findings further corroborate the occurrence of genome size contraction in Crepis, and suggest that the difference in genome size between C. neglecta and C. cretica is mostly due to elimination of dispersed repetitive elements, whereas chromosomal reorganisation was involved in the karyotype formation of C. hellenica.
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Affiliation(s)
- N Enke
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Berlin, Germany
- Dahlem Centre of Plant Sciences, Freie Universität Berlin, Berlin, Germany
| | - R Kunze
- Dahlem Centre of Plant Sciences, Freie Universität Berlin, Berlin, Germany
- Institut für Biologie - Angewandte Genetik, Freie Universität Berlin, Berlin, Germany
| | - F Pustahija
- CNRS, Laboratoire Ecologie, Systématique et Evolution, UMR 8079, Université Paris Sud, Orsay, France
- Faculty of Forestry, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - G Glöckner
- Institute for Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany
- Molecular Biology Group, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - J Zimmermann
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Berlin, Germany
- AG Spezielle Botanik, Justus-Liebig-Universität Giessen, Giessen, Germany
| | - J Oberländer
- Dahlem Centre of Plant Sciences, Freie Universität Berlin, Berlin, Germany
- Institut für Biologie - Angewandte Genetik, Freie Universität Berlin, Berlin, Germany
| | - G Kamari
- Department of Biology, Botanical Institute, University of Patras, Patras, Greece
| | - S Siljak-Yakovlev
- CNRS, Laboratoire Ecologie, Systématique et Evolution, UMR 8079, Université Paris Sud, Orsay, France
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Hohmann N, Schmickl R, Chiang TY, Lučanová M, Kolář F, Marhold K, Koch MA. Taming the wild: resolving the gene pools of non-model Arabidopsis lineages. BMC Evol Biol 2014; 14:224. [PMID: 25344686 PMCID: PMC4216345 DOI: 10.1186/s12862-014-0224-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 10/15/2014] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Wild relatives in the genus Arabidopsis are recognized as useful model systems to study traits and evolutionary processes in outcrossing species, which are often difficult or even impossible to investigate in the selfing and annual Arabidopsis thaliana. However, Arabidopsis as a genus is littered with sub-species and ecotypes which make realizing the potential of these non-model Arabidopsis lineages problematic. There are relatively few evolutionary studies which comprehensively characterize the gene pools across all of the Arabidopsis supra-groups and hypothesized evolutionary lineages and none include sampling at a world-wide scale. Here we explore the gene pools of these various taxa using various molecular markers and cytological analyses. RESULTS Based on ITS, microsatellite, chloroplast and nuclear DNA content data we demonstrate the presence of three major evolutionary groups broadly characterized as A. lyrata group, A. halleri group and A. arenosa group. All are composed of further species and sub-species forming larger aggregates. Depending on the resolution of the marker, a few closely related taxa such as A. pedemontana, A. cebennensis and A. croatica are also clearly distinct evolutionary lineages. ITS sequences and a population-based screen based on microsatellites were highly concordant. The major gene pools identified by ITS sequences were also significantly differentiated by their homoploid nuclear DNA content estimated by flow cytometry. The chloroplast genome provided less resolution than the nuclear data, and it remains unclear whether the extensive haplotype sharing apparent between taxa results from gene flow or incomplete lineage sorting in this relatively young group of species with Pleistocene origins. CONCLUSIONS Our study provides a comprehensive overview of the genetic variation within and among the various taxa of the genus Arabidopsis. The resolved gene pools and evolutionary lineages will set the framework for future comparative studies on genetic diversity. Extensive population-based phylogeographic studies will also be required, however, in particular for A. arenosa and their affiliated taxa and cytotypes.
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Affiliation(s)
- Nora Hohmann
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, 69120, Germany.
| | - Roswitha Schmickl
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, 69120, Germany.
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, CZ-25243, Czech Republic.
| | - Tzen-Yuh Chiang
- Department of Life Sciences, Cheng-Kung University, Tainan, Taiwan.
| | - Magdalena Lučanová
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, CZ-25243, Czech Republic.
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01, Czech Republic.
| | - Filip Kolář
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, CZ-25243, Czech Republic.
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01, Czech Republic.
| | - Karol Marhold
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, CZ-25243, Czech Republic.
- Institute of Botany Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava, SK-845 23, Slovakia.
| | - Marcus A Koch
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, 69120, Germany.
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Wolf DE, Steets JA, Houliston GJ, Takebayashi N. Genome size variation and evolution in allotetraploid Arabidopsis kamchatica and its parents, Arabidopsis lyrata and Arabidopsis halleri. AOB PLANTS 2014; 6:plu025. [PMID: 24887004 PMCID: PMC4076644 DOI: 10.1093/aobpla/plu025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Polyploidization and subsequent changes in genome size are fundamental processes in evolution and diversification. Little is currently known about the extent of genome size variation within taxa and the evolutionary forces acting on this variation. Arabidopsis kamchatica has been reported to contain both diploid and tetraploid individuals. The aim of this study was to determine the genome size of A. kamchatica, whether there is variation in ploidy and/or genome size in A. kamchatica and to study how genome size has evolved. We used propidium iodide flow cytometry to measure 2C DNA content of 73 plants from 25 geographically diverse populations of the putative allotetraploid A. kamchatica and its parents, Arabidopsis lyrata and Arabidopsis halleri. All A. kamchatica plants appear to be tetraploids. The mean 2C DNA content of A. kamchatica was 1.034 pg (1011 Mbp), which is slightly smaller than the sum of its diploid parents (A. lyrata: 0.502 pg; A. halleri: 0.571 pg). Arabidopsis kamchatica appears to have lost ∼37.594 Mbp (3.6 %) of DNA from its 2C genome. Tetraploid A. lyrata from Germany and Austria appears to have lost ∼70.366 Mbp (7.2 %) of DNA from the 2C genome, possibly due to hybridization with A. arenosa, which has a smaller genome than A. lyrata. We did find genome size differences among A. kamchatica populations, which varied up to 7 %. Arabidopsis kamchatica ssp. kawasakiana from Japan appears to have a slightly larger genome than A. kamchatica ssp. kamchatica from North America, perhaps due to multiple allopolyploid origins or hybridization with A. halleri. However, the among-population coefficient of variation in 2C DNA content is lower in A. kamchatica than in other Arabidopsis taxa. Due to its close relationship to A. thaliana, A. kamchatica has the potential to be very useful in the study of polyploidy and genome evolution.
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Affiliation(s)
- Diana E Wolf
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, 311 Irving I, Fairbanks, AK 99775-7000, USA
| | - Janette A Steets
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, 311 Irving I, Fairbanks, AK 99775-7000, USA Present Address: Department of Botany, Oklahoma State University, 301 Physical Sciences, Stillwater, OK 74078-3013, USA
| | - Gary J Houliston
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, 311 Irving I, Fairbanks, AK 99775-7000, USA Present Address: Landcare Research, Gerald St, Lincoln 7608, New Zealand
| | - Naoki Takebayashi
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, 311 Irving I, Fairbanks, AK 99775-7000, USA
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18
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19
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Duncan TM, Rausher MD. Morphological and genetic differentiation and reproductive isolation among closely related taxa in the Ipomoea series Batatas. AMERICAN JOURNAL OF BOTANY 2013; 100:2183-2193. [PMID: 24169430 DOI: 10.3732/ajb.1200467] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
PREMISE OF THE STUDY Identifying recently diverged taxa can be useful for studying the process of speciation. Ipomoea lacunosa and I. cordatotriloba, along with a putative homoploid hybrid, I. ×leucantha, are closely related taxa, which are promising for investigating the early stages of speciation. The objectives of this investigation were to determine how distinct these purported taxa are morphologically and genetically, and to assess the magnitude of reproductive isolation among the taxa. METHODS We measured morphological characteristics and determined genotypes at four microsatellite loci in several populations of each of the taxa in North Carolina and South Carolina to quantify genetic and morphological differentiation. We also included a previously undescribed fourth taxon, which we term 'I. austinii'. KEY RESULTS Our study revealed that all four taxa had distinct but overlapping geographical ranges, and had significantly distinct morphologies. Patterns of microsatellite variation and the results of crosses indicate that I. ×leucantha and I. austinii are morphologically and genetically distinct taxa. Each exhibits substantial reproductive isolation from the other three taxa. By contrast, microsatellite markers indicate that I. lacunosa and I. cordatotriloba exhibit little differentiation at neutral markers, despite substantial morphological differentiation, and exhibit some reproductive isolation. CONCLUSION I. ×leucantha and I. austinii should be considered separate species. Our results provide no evidence that either species originated through homoploid hybrid speciation. I. cordatotriloba and I. lacunosa should be considered incipient species, but may be experiencing considerable reciprocal gene flow.
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Martin SL, Husband BC. ADAPTATION OF DIPLOID AND TETRAPLOIDCHAMERION ANGUSTIFOLIUMTO ELEVATION BUT NOT LOCAL ENVIRONMENT. Evolution 2013; 67:1780-91. [DOI: 10.1111/evo.12065] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 01/09/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Sara L. Martin
- Department of Integrative Biology, University of Guelph; Guelph N1G 2W1 Canada
| | - Brian C. Husband
- Department of Integrative Biology, University of Guelph; Guelph N1G 2W1 Canada
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21
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Modliszewski JL, Willis JH. Allotetraploid Mimulus sookensis are highly interfertile despite independent origins. Mol Ecol 2012; 21:5280-98. [PMID: 22831280 DOI: 10.1111/j.1365-294x.2012.05706.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polyploidy (whole-genome duplication) has contributed significantly to angiosperm evolution and diversification. To date, it has been found that most polyploids are the result of multiple formation events, which may contribute to genetic diversity and affect interfertility among polyploid lineages of independent origin. A recently discovered allotetraploid derivative of Mimulus guttatus and M. nasutus, Mimulus sookensis, is found throughout the valleys of western Oregon and Vancouver Island. Here, we analyse the patterns of nucleotide diversity at three chloroplast and six nuclear loci in M. guttatus, M. nasutus and M. sookensis, to gain insight into the formation of M. sookensis. By analysing the patterns of genetic variation seen in the diploid progenitors in comparison with the variation seen in M. sookensis, we are able to show that M. sookensis has recurrently formed. We also observed that most M. sookensis individuals are fixed heterozygotes at all of the nuclear loci examined, suggesting that duplicate gene loss is not extensive in M. sookensis. To assess the possibility that hybridization among M. sookensis has contributed to genetic diversity, we conducted crossing experiments within M. sookensis. We found that M. sookensis of independent origin are highly interfertile, suggesting that crossing barriers do not exist within M. sookensis, and that hybridization among M. sookensis may result in new recombinant genotypes. Together, the data suggest that although recurrent origins may be common, they can contribute to genetic diversity without contributing to reproductive isolation among independently arisen polyploid lineages.
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Higashi H, Ikeda H, Setoguchi H. Population fragmentation causes randomly fixed genotypes in populations of Arabidopsis kamchatica in the Japanese Archipelago. JOURNAL OF PLANT RESEARCH 2012; 125:223-233. [PMID: 21618072 DOI: 10.1007/s10265-011-0436-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 05/08/2011] [Indexed: 05/30/2023]
Abstract
Populations of arctic alpine plants likely disappeared and re-colonised several times at the southern edge of their distributions during glacial and interglacial cycles throughout the Quaternary. Range shift and population fragmentation after a glacial period would affect the genetic structure of such plants in southernmost populations. We aimed to elucidate how climatic oscillations influenced the population subsistence of alpine plants in the Japanese Archipelago as one of the southernmost populations, by inferring the genetic structure of Arabidopsis kamchatica subsp. kamchatica and the intraspecific littoral taxon, subsp. kawasakiana. We identified genotypes based on the haplotypes of five nuclear genes and two chloroplast DNA spacers for 164 individuals from 24 populations. Most populations harboured only one private genotype, whereas few polymorphisms were found in each population. Two genetic genealogies were found, suggesting that northern Japanese populations of alpine subsp. kamchatica, subsp. kawasakiana and the northerly subsp. kamchatica in eastern Russia and Alaska clustered and differentiated from populations in central Honshu, western Japan and Taiwan. During climatic oscillations, the genetic structure of extant southernmost populations would have been shaped by strong genetic drift under population fragmentation and randomly fixed to a single genotype among their ancestral polymorphisms.
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Affiliation(s)
- Hiroyuki Higashi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, Japan.
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23
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Glycerol-treated nuclear suspensions—an efficient preservation method for flow cytometric analysis of plant samples. Chromosome Res 2012; 20:303-15. [DOI: 10.1007/s10577-012-9277-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2011] [Revised: 01/31/2012] [Accepted: 02/02/2012] [Indexed: 10/28/2022]
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Delaney JT, Baack EJ. Intraspecific Chromosome Number Variation and Prairie Restoration-A Case Study in Northeast Iowa, U.S.A. Restor Ecol 2011. [DOI: 10.1111/j.1526-100x.2011.00825.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Enke N, Fuchs J, Gemeinholzer B. Shrinking genomes? Evidence from genome size variation in Crepis (Compositae). PLANT BIOLOGY (STUTTGART, GERMANY) 2011; 13:185-193. [PMID: 21143740 DOI: 10.1111/j.1438-8677.2010.00341.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Large-scale surveys of genome size evolution in angiosperms show that the ancestral genome was most likely small, with a tendency towards an increase in DNA content during evolution. Due to polyploidisation and self-replicating DNA elements, angiosperm genomes were considered to have a 'one-way ticket to obesity' (Bennetzen & Kellogg 1997). New findings on how organisms can lose DNA challenged the hypotheses of unidirectional evolution of genome size. The present study is based on the classical work of Babcock (1947a) on karyotype evolution within Crepis and analyses karyotypic diversification within the genus in a phylogenetic context. Genome size of 21 Crepis species was estimated using flow cytometry. Additional data of 17 further species were taken from the literature. Within 30 diploid Crepis species there is a striking trend towards genome contraction. The direction of genome size evolution was analysed by reconstructing ancestral character states on a molecular phylogeny based on ITS sequence data. DNA content is correlated to distributional aspects as well as life form. Genome size is significantly higher in perennials than in annuals. Within sampled species, very small genomes are only present in Mediterranean or European species, whereas their Central and East Asian relatives have larger 1C values.
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Affiliation(s)
- N Enke
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Berlin, Germany.
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26
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Wang WK, Ho CW, Hung KH, Wang KH, Huang CC, Araki H, Hwang CC, Hsu TW, Osada N, Chiang TY. Multilocus analysis of genetic divergence between outcrossing Arabidopsis species: evidence of genome-wide admixture. THE NEW PHYTOLOGIST 2010; 188:488-500. [PMID: 20673288 DOI: 10.1111/j.1469-8137.2010.03383.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
• Outcrossing Arabidopsis species that diverged from their inbreeding relative Arabidopsis thaliana 5 million yr ago and display a biogeographical pattern of interspecific sympatry vs intraspecific allopatry provides an ideal model for studying impacts of gene introgression and polyploidization on species diversification. • Flow cytometry analyses detected ploidy polymorphisms of 2× and 4× in Arabidopsis lyrata ssp. kamchatica of Taiwan. Genomic divergence between species/subspecies was estimated based on 98 randomly chosen nuclear genes. Multilocus analyses revealed a mosaic genome in diploid A. l. kamchatica composed of Arabidopsis halleri-like and A. lyrata-like alleles. • Coalescent analyses suggest that the segregation of ancestral polymorphisms alone cannot explain the high inconsistency between gene trees across loci, and that gene introgression via diploid A. l. kamchatica likely distorts the molecular phylogenies of Arabidopsis species. However, not all genes migrated across species freely. Gene ontology analyses suggested that some nonmigrating genes were constrained by natural selection. • High levels of estimated ancestral polymorphisms between A. halleri and A. lyrata suggest that gene flow between these species has not completely ceased since their initial isolation. Polymorphism data of extant populations also imply recent gene flow between the species. Our study reveals that interspecific gene flow affects the genome evolution in Arabidopsis.
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Affiliation(s)
- Wei-Kuang Wang
- Department of Life Sciences, National Cheng-Kung University, Tainan, Taiwan
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Maherali H, Walden AE, Husband BC. Genome duplication and the evolution of physiological responses to water stress. THE NEW PHYTOLOGIST 2009; 184:721-731. [PMID: 19703115 DOI: 10.1111/j.1469-8137.2009.02997.x] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Whole-genome multiplication, or polyploidy, is common in angiosperms and many species consist of multiple cytotypes that have different physiological tolerances. However, the relative importance of genome duplication vs post-duplication evolutionary change in causing differentiation between cytotypes is not known. We examined the water relations of Chamerion angustifolium, a herbaceous perennial in which diploid and tetraploid cytotypes occupy different niches. To differentiate between the effects of genome duplication and evolutionary changes that followed polyploidization, we compared extant diploids and tetraploids with experimentally synthesized neotetraploids. Tetraploids had 32% higher xylem hydraulic conductivity (K(H)) than neotetraploids and 87% higher K(H) than diploids, but vulnerability to water stress induced cavitation and gas exchange sensitivity to water potential did not differ among cytotypes. Nevertheless, tetraploids took 22% and 30% longer to wilt than neotetraploids and diploids. A simple hydraulic model suggested that tetraploids deplete soil moisture to a greater degree than neotetraploids and diploids before reaching leaf water potentials that cause stomatal closure. We conclude that the different physiological tolerances and distribution of diploid and tetraploid C. angustifolium are unlikely to be caused solely by genome duplication. The enhanced ability of tetraploids to survive water stress likely evolved after polyploidization.
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Affiliation(s)
- Hafiz Maherali
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Alison E Walden
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Brian C Husband
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
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Shimizu-Inatsugi R, Lihová J, Iwanaga H, Kudoh H, Marhold K, Savolainen O, Watanabe K, Yakubov VV, Shimizu KK. The allopolyploid Arabidopsis kamchatica originated from multiple individuals of Arabidopsis lyrata and Arabidopsis halleri. Mol Ecol 2009; 18:4024-48. [PMID: 19754506 DOI: 10.1111/j.1365-294x.2009.04329.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polyploidization, or genome duplication, has played a critical role in the diversification of animals, fungi and plants. Little is known about the population structure and multiple origins of polyploid species because of the difficulty in identifying multiple homeologous nuclear genes. The allotetraploid species Arabidopsis kamchatica is closely related to the model species Arabidopsis thaliana and is distributed in a broader climatic niche than its parental species. Here, we performed direct sequencing of homeologous pairs of the low-copy nuclear genes WER and CHS by designing homeolog-specific primers, and obtained also chloroplast and ribosomal internal transcribed spacer sequences. Phylogenetic analysis showed that 50 individuals covering the distribution range including North America are allopolyploids derived from Arabidopsis lyrata and Arabidopsis halleri. Three major clusters within A. kamchatica were detected using Bayesian clustering. One cluster has widespread distribution. The other two are restricted to the southern part of the distribution range including Japan, where the parent A. lyrata is not currently distributed. This suggests that the mountains in Central Honshu and surrounding areas in Japan served as refugia during glacial-interglacial cycles and retained this diversity. We also found that multiple haplotypes of nuclear and chloroplast sequences of A. kamchatica are identical to those of their parental species. This indicates that multiple diploid individuals contributed to the origin of A. kamchatica. The haplotypes of low-copy nuclear genes in Japan suggest independent polyploidization events rather than introgression. Our findings suggest that self-compatibility and gene silencing occurred independently in different origins.
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Hersch-Green EI, Cronn R. Tangled trios?: Characterizing a hybrid zone in Castilleja (Orobanchaceae). AMERICAN JOURNAL OF BOTANY 2009; 96:1519-1531. [PMID: 21628297 DOI: 10.3732/ajb.0800357] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Hybridization and polyploidization are exceedingly important processes because both influence the ecological envelope and evolutionary trajectory of land plants. These processes are frequently invoked for Castilleja (Indian paintbrushes) as contributors to morphological and genetic novelty and as complicating factors in species delimitations. Here, we provide a detailed analysis of morphological and genetic evidence for hybridization in a well-characterized hybrid swarm involving three broadly sympatric species (C. miniata, C. rhexiifolia, C. sulphurea) in western Colorado. Field-classified hybrids are present at high frequencies at these sites and show morphological intermediacy to and segregate for chloroplast DNA haplotypes with C. rhexiifolia and C. sulphurea. Contrarily, DNA content and AFLP variation show that field-classified hybrids are not recent hybrids but a distinctive fourth taxon. Actual hybrids (plants showing admixture ≥10% for two genotypic groups) comprised 13% of our sample, with most admixture involving C. rhexiifolia, C. sulphurea, and the unknown taxon. The identity of the field-classified "hybrids" remains unknown; they either represent a stabilized hybrid species or a species with uncharacteristically high diversity for color alleles. This study highlights the importance of examining concordance and discordance between morphology, cytology, and genetic criteria to understand the complex evolutionary history of diverse groups such as Castilleja.
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Affiliation(s)
- Erika I Hersch-Green
- Department of Biology, Northern Arizona University, S. Beaver St. Box 5640 Flagstaff, Arizona 86011 USA
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Sugisaka J, Kudoh H. Breeding system of the annual Cruciferae, Arabidopsis kamchatica subsp. kawasakiana. JOURNAL OF PLANT RESEARCH 2008; 121:65-68. [PMID: 17982712 DOI: 10.1007/s10265-007-0119-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2007] [Accepted: 09/19/2007] [Indexed: 05/25/2023]
Abstract
The breeding system of an annual Cruciferae, Arabidopsis kamchatica subsp. kawasakiana, was studied in three natural populations. We applied four experimental treatments, open pollination, bagging, emasculation + bagging, and emasculation + hand-pollination + bagging. None of the emasculated flowers with bags produced fruits but we observed high fruit sets in the other three treatments. The results confirmed that A. kamchatica subsp. kawasakiana is a self-compatible, non-apomictic species that can produce seeds through auto-pollination. Considering the life cycle as an annual, increased reproductive assurance through auto-pollination should be critical for the maintenance of populations of A. kamchatica subsp. kawasakiana.
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Affiliation(s)
- Jiro Sugisaka
- Division of Life Science, Graduate School of Science and Technology, Kobe University, Nada-ku, Kobe 657-8501, Japan.
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Suda J, Trávníček P. Estimation of Relative Nuclear DNA Content in Dehydrated Plant Tissues by Flow Cytometry. ACTA ACUST UNITED AC 2006; Chapter 7:Unit7.30. [DOI: 10.1002/0471142956.cy0730s38] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jan Suda
- Charles University in Prague and Academy of Sciences of the Czech Republic Prague Czech Republic
| | - Pavel Trávníček
- Charles University in Prague and Academy of Sciences of the Czech Republic Prague Czech Republic
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Kennedy BF, Sabara HA, Haydon D, Husband BC. Pollinator-mediated assortative mating in mixed ploidy populations of Chamerion angustifolium (Onagraceae). Oecologia 2006; 150:398-408. [PMID: 17024387 DOI: 10.1007/s00442-006-0536-7] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2006] [Accepted: 08/03/2006] [Indexed: 10/24/2022]
Abstract
Establishment of polyploid individuals within diploid populations is theoretically unlikely unless polyploids are reproductively isolated, pre-zygotically, through assortative pollination. Here, we quantify the contribution of pollinator diversity and foraging behaviour to assortative pollen deposition in three mixed-ploidy populations of Chamerion angustifolium (Onagraceae). Diploids and tetraploids were not differentiated with respect to composition of insect visitors. However, foraging patterns of the three most common insect visitors (all bees) reinforced assortative pollination. Bees visited tetraploids disproportionately often and exhibited higher constancy on tetraploids in all three populations. In total, 73% of all bee flights were between flowers of the same ploidy (2x-2x, 4x-4x); 58% of all flights to diploids and 83% to tetraploids originated from diploid and tetraploid plants, respectively. Patterns of pollen deposition on stigmas mirrored pollinator foraging behaviour; 73% of all pollen on stigmas (70 and 75% of pollen on diploid and tetraploid stigmas, respectively) came from within-ploidy pollinations. These results indicate that pollinators contribute to high rates of pre-zygotic reproductive isolation. If patterns of fertilization track pollen deposition, pollinator-plant interactions may help explain the persistence and spread of tetraploids in mixed-ploidy populations.
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Affiliation(s)
- Brad F Kennedy
- Department of Integrative Biology, University of Guelph, ON, Guelph, Canada
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Suda J, Trávnícek P. Reliable DNA ploidy determination in dehydrated tissues of vascular plants by DAPI flow cytometry—new prospects for plant research. Cytometry A 2006; 69:273-80. [PMID: 16528735 DOI: 10.1002/cyto.a.20253] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Only fresh plant material is generally used for rapid DNA ploidy estimation by flow cytometry (FCM). This requirement, however, substantially limits convenient FCM application in plant biosystematics, population biology, and ecology. As desiccation is a routine way for sample preservation in field botany, potential utilization of dehydrated tissues of vascular plants in FCM research was examined. METHODS Standard DAPI protocol was employed to evaluate the performance of 60 air-dried species, spanning more than 100-fold range of nuclear DNA amounts. Multiploid Vaccinium subg. Oxycoccus was selected as model taxon for detailed investigation and cytotype comparison. RESULTS A majority of analyzed plants yielded distinct peaks with reasonable coefficients of variation after several months of storage at room temperature. Fluorescence intensity of nuclei isolated from desiccated tissues was highly comparable with that for fresh material, allowing reliable DNA ploidy estimation. Deep-freezer preservation substantially extended Vaccinium samples lifetime (at least to 3 years) and maintained high histogram resolution. CONCLUSIONS The introduced approach eliminates the need for fresh material in many vascular plants and thus opens new prospects for plant FCM. Convenient cytotype investigation in field research and retrospective ploidy determination in already herbarized samples are among the principal advantages.
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Affiliation(s)
- Jan Suda
- Department of Botany, Charles University, Benátská 2, Prague, Czech Republic.
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Yeung K, Miller JS, Savage AE, Husband BC, Igic B, Kohn JR. ASSOCIATION OF PLOIDY AND SEXUAL SYSTEM IN LYCIUM CALIFORNICUM (SOLANACEAE). Evolution 2005. [DOI: 10.1111/j.0014-3820.2005.tb01073.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Yogeeswaran K, Frary A, York TL, Amenta A, Lesser AH, Nasrallah JB, Tanksley SD, Nasrallah ME. Comparative genome analyses of Arabidopsis spp.: inferring chromosomal rearrangement events in the evolutionary history of A. thaliana. Genome Res 2005; 15:505-15. [PMID: 15805492 PMCID: PMC1074365 DOI: 10.1101/gr.3436305] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Comparative genome analysis is a powerful tool that can facilitate the reconstruction of the evolutionary history of the genomes of modern-day species. The model plant Arabidopsis thaliana with its n = 5 genome is thought to be derived from an ancestral n = 8 genome. Pairwise comparative genome analyses of A. thaliana with polyploid and diploid Brassicaceae species have suggested that rapid genome evolution, manifested by chromosomal rearrangements and duplications, characterizes the polyploid, but not the diploid, lineages of this family. In this study, we constructed a low-density genetic linkage map of Arabidopsis lyrata ssp. lyrata (A. l. lyrata; n = 8, diploid), the closest known relative of A. thaliana (MRCA approximately 5 Mya), using A. thaliana-specific markers that resolve into the expected eight linkage groups. We then performed comparative Bayesian analyses using raw mapping data from this study and from a Capsella study to infer the number and nature of rearrangements that distinguish the n = 8 genomes of A. l. lyrata and Capsella from the n = 5 genome of A. thaliana. We conclude that there is strong statistical support in favor of the parsimony scenarios of 10 major chromosomal rearrangements separating these n = 8 genomes from A. thaliana. These chromosomal rearrangement events contribute to a rate of chromosomal evolution higher than previously reported in this lineage. We infer that at least seven of these events, common to both sets of data, are responsible for the change in karyotype and underlie genome reduction in A. thaliana.
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Mable BK, Beland J, Di Berardo C. Inheritance and dominance of self-incompatibility alleles in polyploid Arabidopsis lyrata. Heredity (Edinb) 2005; 93:476-86. [PMID: 15266298 DOI: 10.1038/sj.hdy.6800526] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Natural populations of diploid Arabidopsis lyrata exhibit the sporophytic type of self-incompatibility system characteristic of Brassicaceae, in which complicated dominance interactions among alleles in the diploid parent determine self-recognition phenotypes of both pollen and stigma. The purpose of this study was to investigate how polyploidy affects this already complex system. One tetraploid population (Arabidopsis lyrata ssp kawasakiana from Japan) showed complete self-compatibility and produced viable selfed progeny for at least three generations subsequent to field collection. In contrast, individuals from a second tetraploid population (A. lyrata ssp petraea from Austria) were strongly self-incompatible (SI). Segregation of SI genotypes in this population followed Mendelian patterns based on a tetrasomic model of inheritance, with two to four alleles per individual, independent segregation of alleles, and little evidence of dosage effects of alleles found in multiple copies. Similar to results from diploids, anomalous compatibility patterns involving particular combinations of individuals occurred at a low frequency in the tetraploids, suggesting altered dominance in certain genetic backgrounds that could be due to the influence of a modifier locus. Overall, dominance relationships among S-alleles in self-incompatible tetraploid families were remarkably similar to those in related diploids, suggesting that this very important and complicated locus has not undergone extensive modification subsequent to polyploidization.
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Affiliation(s)
- B K Mable
- Department of Botany, University of Guelph, Guelph, Ontario, Canada N1G 2W1.
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Hoffmann MH. EVOLUTION OF THE REALIZED CLIMATIC NICHE IN THE GENUS ARABIDOPSIS (BRASSICACEAE). Evolution 2005. [DOI: 10.1554/05-033] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Yeung K, Miller JS, Savage AE, Husband BC, Igic B, Kohn JR. ASSOCIATION OF PLOIDY AND SEXUAL SYSTEM IN LYCIUM CALIFORNICUM (SOLANACEAE). Evolution 2005. [DOI: 10.1554/05-354.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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