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Limborg MT, Seeb LW, Seeb JE. Sorting duplicated loci disentangles complexities of polyploid genomes masked by genotyping by sequencing. Mol Ecol 2016; 25:2117-29. [PMID: 26939067 DOI: 10.1111/mec.13601] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 02/19/2016] [Accepted: 02/24/2016] [Indexed: 01/04/2023]
Abstract
Many plants and animals of polyploid origin are currently enjoying a genomics explosion enabled by modern sequencing and genotyping technologies. However, routine filtering of duplicated loci in most studies using genotyping by sequencing introduces an unacceptable, but often overlooked, bias when detecting selection. Retained duplicates from ancient whole-genome duplications (WGDs) may be found throughout genomes, whereas retained duplicates from recent WGDs are concentrated at distal ends of some chromosome arms. Additionally, segmental duplicates can be found at distal ends or nearly anywhere in a genome. Evidence shows that these duplications facilitate adaptation through one of two pathways: neo-functionalization or increased gene expression. Filtering duplicates removes distal ends of some chromosomes, and distal ends are especially known to harbour adaptively important genes. Thus, filtering of duplicated loci impoverishes the interpretation of genomic data as signals from contiguous duplicated genes are ignored. We review existing strategies to genotype and map duplicated loci; we focus in detail on an overlooked strategy of using gynogenetic haploids (1N) as a part of new genotyping by sequencing studies. We provide guidelines on how to use this haploid strategy for studies on polyploid-origin vertebrates including how it can be used to screen duplicated loci in natural populations. We conclude by discussing areas of research that will benefit from better inclusion of polyploid loci; we particularly stress the sometimes overlooked fact that basing genomic studies on dense maps provides value added in the form of locating and annotating outlier loci or colocating outliers into islands of divergence.
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Affiliation(s)
- Morten T Limborg
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195, USA.,National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600 Silkeborg, Denmark
| | - Lisa W Seeb
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195, USA
| | - James E Seeb
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195, USA
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52
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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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53
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Blischak PD, Kubatko LS, Wolfe AD. Accounting for genotype uncertainty in the estimation of allele frequencies in autopolyploids. Mol Ecol Resour 2015; 16:742-54. [PMID: 26607217 DOI: 10.1111/1755-0998.12493] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 11/17/2015] [Accepted: 11/18/2015] [Indexed: 01/03/2023]
Abstract
Despite the increasing opportunity to collect large-scale data sets for population genomic analyses, the use of high-throughput sequencing to study populations of polyploids has seen little application. This is due in large part to problems associated with determining allele copy number in the genotypes of polyploid individuals (allelic dosage uncertainty-ADU), which complicates the calculation of important quantities such as allele frequencies. Here, we describe a statistical model to estimate biallelic SNP frequencies in a population of autopolyploids using high-throughput sequencing data in the form of read counts. We bridge the gap from data collection (using restriction enzyme based techniques [e.g. GBS, RADseq]) to allele frequency estimation in a unified inferential framework using a hierarchical Bayesian model to sum over genotype uncertainty. Simulated data sets were generated under various conditions for tetraploid, hexaploid and octoploid populations to evaluate the model's performance and to help guide the collection of empirical data. We also provide an implementation of our model in the R package polyfreqs and demonstrate its use with two example analyses that investigate (i) levels of expected and observed heterozygosity and (ii) model adequacy. Our simulations show that the number of individuals sampled from a population has a greater impact on estimation error than sequencing coverage. The example analyses also show that our model and software can be used to make inferences beyond the estimation of allele frequencies for autopolyploids by providing assessments of model adequacy and estimates of heterozygosity.
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Affiliation(s)
- Paul D Blischak
- Department of Evolution, Ecology and Organismal Biology, Ohio State University, 318 W. 12th Avenue, Columbus, OH, 43210, USA
| | - Laura S Kubatko
- Department of Evolution, Ecology and Organismal Biology, Ohio State University, 318 W. 12th Avenue, Columbus, OH, 43210, USA.,Department of Statistics, Ohio State University, 1958 Neil Avenue, Columbus, OH, 43210, USA
| | - Andrea D Wolfe
- Department of Evolution, Ecology and Organismal Biology, Ohio State University, 318 W. 12th Avenue, Columbus, OH, 43210, USA
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54
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The Double-Reduction Landscape in Tetraploid Potato as Revealed by a High-Density Linkage Map. Genetics 2015; 201:853-63. [PMID: 26377683 DOI: 10.1534/genetics.115.181008] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 09/09/2015] [Indexed: 01/27/2023] Open
Abstract
The creation of genetic linkage maps in polyploid species has been a long-standing problem for which various approaches have been proposed. In the case of autopolyploids, a commonly used simplification is that random bivalents form during meiosis. This leads to relatively straightforward estimation of recombination frequencies using maximum likelihood, from which a genetic map can be derived. However, autopolyploids such as tetraploid potato (Solanum tuberosum L.) may exhibit additional features, such as double reduction, not normally encountered in diploid or allopolyploid species. In this study, we produced a high-density linkage map of tetraploid potato and used it to identify regions of double reduction in a biparental mapping population. The frequency of multivalents required to produce this degree of double reduction was determined through simulation. We also determined the effect that multivalents or preferential pairing between homologous chromosomes has on linkage mapping. Low levels of multivalents or preferential pairing do not adversely affect map construction when highly informative marker types and phases are used. We reveal the double-reduction landscape in tetraploid potato, clearly showing that this phenomenon increases with distance from the centromeres.
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55
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High genetic diversity and population structure in the endangered Canarian endemic Ruta oreojasme (Rutaceae). Genetica 2015; 143:571-80. [DOI: 10.1007/s10709-015-9855-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 06/29/2015] [Indexed: 11/26/2022]
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56
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Hardy OJ. Population genetics of autopolyploids under a mixed mating model and the estimation of selfing rate. Mol Ecol Resour 2015; 16:103-17. [PMID: 25981126 DOI: 10.1111/1755-0998.12431] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 05/07/2015] [Accepted: 05/12/2015] [Indexed: 11/27/2022]
Abstract
Nowadays, the population genetics analysis of autopolyploid species faces many difficulties due to (i) limited development of population genetics tools under polysomic inheritance, (ii) difficulties to assess allelic dosage when genotyping individuals and (iii) a form of inbreeding resulting from the mechanism of 'double reduction'. Consequently, few data analysis computer programs are applicable to autopolyploids. To contribute bridging this gap, this article first derives theoretical expectations for the inbreeding and identity disequilibrium coefficients under polysomic inheritance in a mixed mating model. Moment estimators of these coefficients are proposed when exact genotypes or just markers phenotypes (i.e. allelic dosage unknown) are available. This led to the development of estimators of the selfing rate based on adult genotypes or phenotypes and applicable to any even-ploidy level. Their statistical performances and robustness were assessed by numerical simulations. Contrary to inbreeding-based estimators, the identity disequilibrium-based estimator using phenotypes is robust (absolute bias generally < 0.05), even in the presence of double reduction, null alleles or biparental inbreeding due to isolation by distance. A fairly good precision of the selfing rate estimates (root mean squared error < 0.1) is already achievable using a sample of 30-50 individuals phenotyped at 10 loci bearing 5-10 alleles each, conditions reachable using microsatellite markers. Diallelic markers (e.g. SNP) can also perform satisfactorily in diploids and tetraploids but more polymorphic markers are necessary for higher ploidy levels. The method is implemented in the software SPAGeDi and should contribute to reduce the lack of population genetics tools applicable to autopolyploids.
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Affiliation(s)
- Olivier J Hardy
- Evolutionary Biology and Ecology-CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 Av. F. Roosevelt, 1050, Brussels, Belgium
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57
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Allendorf FW, Bassham S, Cresko WA, Limborg MT, Seeb LW, Seeb JE. Effects of crossovers between homeologs on inheritance and population genomics in polyploid-derived salmonid fishes. J Hered 2015; 106:217-27. [PMID: 25838153 DOI: 10.1093/jhered/esv015] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 02/19/2015] [Indexed: 01/24/2023] Open
Abstract
A whole genome duplication occurred in the ancestor of all salmonid fishes some 50-100 million years ago. Early inheritance studies with allozymes indicated that loci in the salmonid genome are inherited disomically in females. However, some pairs of duplicated loci showed patterns of inheritance in males indicating pairing and recombination between homeologous chromosomes. Nearly 20% of loci in the salmonid genome are duplicated and share the same alleles (isoloci), apparently due to homeologous recombination. Half-tetrad analysis revealed that isoloci tend to be telomeric. These results suggested that residual tetrasomic inheritance of isoloci results from homeologous recombination near chromosome ends and that continued disomic inheritance resulted from homologous pairing of centromeric regions. Many current genetic maps of salmonids are based on single nucleotide polymorphisms and microsatellites that are no longer duplicated. Therefore, long sections of chromosomes on these maps are poorly represented, especially telomeric regions. In addition, preferential multivalent pairing of homeologs from the same species in F1 hybrids results in an excess of nonparental gametes (so-called pseudolinkage). We consider how not including duplicated loci has affected our understanding of population and evolutionary genetics of salmonids, and we discuss how incorporating these loci will benefit our understanding of population genomics.
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Affiliation(s)
- Fred W Allendorf
- From the University of Montana, Division of Biological Sciences, Missoula, MT 59812 (Allendorf); University of Oregon, Institute of Ecology and Evolution, Eugene, OR (Bassham and Cresko); and University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA (Limborg, L. Seeb, and J. Seeb).
| | - Susan Bassham
- From the University of Montana, Division of Biological Sciences, Missoula, MT 59812 (Allendorf); University of Oregon, Institute of Ecology and Evolution, Eugene, OR (Bassham and Cresko); and University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA (Limborg, L. Seeb, and J. Seeb)
| | - William A Cresko
- From the University of Montana, Division of Biological Sciences, Missoula, MT 59812 (Allendorf); University of Oregon, Institute of Ecology and Evolution, Eugene, OR (Bassham and Cresko); and University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA (Limborg, L. Seeb, and J. Seeb)
| | - Morten T Limborg
- From the University of Montana, Division of Biological Sciences, Missoula, MT 59812 (Allendorf); University of Oregon, Institute of Ecology and Evolution, Eugene, OR (Bassham and Cresko); and University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA (Limborg, L. Seeb, and J. Seeb)
| | - Lisa W Seeb
- From the University of Montana, Division of Biological Sciences, Missoula, MT 59812 (Allendorf); University of Oregon, Institute of Ecology and Evolution, Eugene, OR (Bassham and Cresko); and University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA (Limborg, L. Seeb, and J. Seeb)
| | - James E Seeb
- From the University of Montana, Division of Biological Sciences, Missoula, MT 59812 (Allendorf); University of Oregon, Institute of Ecology and Evolution, Eugene, OR (Bassham and Cresko); and University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA (Limborg, L. Seeb, and J. Seeb)
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58
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Roux C, Pannell JR. Inferring the mode of origin of polyploid species from next-generation sequence data. Mol Ecol 2015; 24:1047-59. [DOI: 10.1111/mec.13078] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 01/06/2015] [Accepted: 01/08/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Camille Roux
- Department of Ecology and Evolution; University of Lausanne; Lausanne 1015 Switzerland
| | - John R. Pannell
- Department of Ecology and Evolution; University of Lausanne; Lausanne 1015 Switzerland
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59
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A maximum-likelihood estimation of pairwise relatedness for autopolyploids. Heredity (Edinb) 2014; 114:133-42. [PMID: 25370210 DOI: 10.1038/hdy.2014.88] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 07/13/2014] [Accepted: 08/12/2014] [Indexed: 11/08/2022] Open
Abstract
Relatedness between individuals is central to ecological genetics. Multiple methods are available to quantify relatedness from molecular data, including method-of-moment and maximum-likelihood estimators. We describe a maximum-likelihood estimator for autopolyploids, and quantify its statistical performance under a range of biologically relevant conditions. The statistical performances of five additional polyploid estimators of relatedness were also quantified under identical conditions. When comparing truncated estimators, the maximum-likelihood estimator exhibited lower root mean square error under some conditions and was more biased for non-relatives, especially when the number of alleles per loci was low. However, even under these conditions, this bias was reduced to be statistically insignificant with more robust genetic sampling. We also considered ambiguity in polyploid heterozygote genotyping and developed a weighting methodology for candidate genotypes. The statistical performances of three polyploid estimators under both ideal and actual conditions (including inbreeding and double reduction) were compared. The software package POLYRELATEDNESS is available to perform this estimation and supports a maximum ploidy of eight.
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60
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López-Caamal A, Tovar-Sánchez E. Genetic, morphological, and chemical patterns of plant hybridization. REVISTA CHILENA DE HISTORIA NATURAL 2014. [DOI: 10.1186/s40693-014-0016-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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61
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Rajkov J, Shao Z, Berrebi P. Evolution of Polyploidy and Functional Diploidization in Sturgeons: Microsatellite Analysis in 10 Sturgeon Species. J Hered 2014; 105:521-531. [DOI: 10.1093/jhered/esu027] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 03/21/2014] [Indexed: 11/13/2022] Open
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62
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Near-absent levels of segregational variation suggest limited opportunities for the introduction of genetic variation via homeologous chromosome pairing in synthetic neoallotetraploid Mimulus. G3-GENES GENOMES GENETICS 2014; 4:509-22. [PMID: 24470218 PMCID: PMC3962489 DOI: 10.1534/g3.113.008441] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Genetic variation is the fundamental medium of evolution. In allopolyploids, which are the product of hybridization and whole genome duplication, if homologous chromosomes always pair, then all descendants of a single diploid F1 hybrid lineage will be genetically identical. Contrarily, genetic variation among initially isogenic lineages is augmented when homeologous chromosomes pair; this added variation may contribute to phenotypic evolution. Mimulus sookensis is a naturally occurring, small-flowered allotetraploid derived from the large-flowered Mimulus guttatus and small-flowered Mimulus nasutus. Because diploid F1 hybrids between M. guttatus and M. nasutus have large flowers, phenotypic evolution post-polyploidization is implied in M. sookensis. Here, we present genetic and phenotypic analyses of synthetic neoallotetraploid Mimulus derived from a cross between M. guttatus and M. nasutus. Genetic marker data from S2 and BC1N progeny suggest that chromosomes regularly pair with their homologous counterpart. By measuring the phenotype of synthetic neoallotetraploids, we demonstrate that polyploidization per se does not induce the small flowers of M. sookensis. Moreover, phenotypic measurements of synthetic allotetraploid F2s and S4 families suggest that rare homeologous recombination events have a negligible phenotypic effect in the first few generations. In total, the results are consistent with either exceedingly rare homeologous pairing and recombination or spontaneous fragment loss. The low levels of fragment loss and phenotypic variation in neoallotetraploids suggest that homeologous recombination after polyploidization is not a major mechanism of phenotypic evolution in M. sookensis. Rather, it may be that spontaneous mutations or epigenetic changes after allopolyploidization have driven phenotypic evolution in M. sookensis.
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63
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Silvestrini M, Pinto-Maglio CAF, Zucchi MI, dos Santos FAM. Cytogenetics and characterization of microsatellite loci for a South American pioneer tree species, Croton floribundus. Genome 2014; 56:743-51. [PMID: 24433210 DOI: 10.1139/gen-2013-0159] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Despite the recent advances in plant population genetic studies, the lack of information regarding pedigree, ploidy level, or mode of inheritance for many polyploids can compromise the analysis of the molecular data produced. The aim of this study was to examine both microsatellite and cytogenetic characteristics of the pioneer tree Croton floribundus Spreng. (Euphorbiaceae) to test for the occurrence of polyploidy in the species and to evaluate its implications for the appropriate use of SSR markers. Seven microsatellite markers were developed and screened for 62 individuals from a semi-deciduous tropical forest in Brazil. Chromosome number, meiotic behavior, and pollen viability were evaluated from male flower buds. All SSR loci were highly polymorphic. The number of bivalents observed in meiosis n = 56 (2n = 8× = 112) and the maximum number of alleles per individual (Ni = 8) demonstrated the occurrence of polyploidy in C. floribundus. The normal meiotic pairing and the high pollen viability suggested that C. floribundus is a regular and stable polyploid, most likely an allopolyploid. The combined SSR and cytogenetic data provided new evidence on the origin and evolution of the species as well as assured the accurate use of SSR loci for population genetic studies of the polyploid pioneer species.
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Affiliation(s)
- Milene Silvestrini
- a Programa de Pós-Graduação em Ecologia, Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Rua Monteiro Lobato, 970, P.O. Box 6109, 13083-862, Campinas, Brazil
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64
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Klie M, Schie S, Linde M, Debener T. The type of ploidy of chrysanthemum is not black or white: a comparison of a molecular approach to published cytological methods. FRONTIERS IN PLANT SCIENCE 2014; 5:479. [PMID: 25295046 PMCID: PMC4172100 DOI: 10.3389/fpls.2014.00479] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 08/30/2014] [Indexed: 05/18/2023]
Abstract
Polyploidy is a widespread phenomenon among higher plants and a major factor shaping the structure and evolution of plant genomes. The important ornamental chrysanthemum (Chrysanthemum indicum hybrid) possesses a hexaploid genome with 54 chromosomes and was classified based on its evolutionary origin and cytological methods as an allopolyploid. However, it is questionable whether cytological methods are sufficient to determine the type of ploidy, and there are more informative methods available based on molecular marker analyses. Therefore, we collected segregation data for 406 dominant molecular marker alleles [327 amplified fragment length polymorphism (AFLPs), 65 single-strand conformation polymorphism (SSCPs) and 14 microsatellites (EST-SSRs)] in a biparental F1 population of 160 individuals. We analyzed these data for the characteristics that differ between allopolyploids and autopolyploids, including the segregation ratio of each marker, the ratio of single-dose (SD) to multi-dose (MD) markers, the ratio of SD markers in coupling to those in repulsion and the banding patterns of the SSRs. Whereas the analysis of the segregation ratio of each polymorphic marker indicated disomic (13 markers) as well as hexasomic (eight markers) inheritance, the ratio of SD markers in coupling to those in repulsion was 1:0, which is characteristic of autopolyploids. The observed ratio of SD to MD markers was 0.67:0.33 which is significantly different to the expected segregation for auto- and allohexaploids. Furthermore, the three EST-SSR alleles were inherited in all possible combinations and were not independent of each other, as expected for fixed heterozygosity in allopolyploids. Combining our results with published cytological data indicates that cultivated chrysanthemums should be classified as segmental allohexaploids.
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Affiliation(s)
- Maik Klie
- Department of Molecular Plant Breeding, Institute for Plant Genetics, Leibniz Universität HannoverHannover, Germany
- Kleinwanzlebener Saatzucht AG formerly Rabbethge and GieseckeEinbeck, Germany
| | - Stephan Schie
- Department of Molecular Plant Breeding, Institute for Plant Genetics, Leibniz Universität HannoverHannover, Germany
- Saaten-Union Biotec GmbHLeopoldshöhe, Germany
| | - Marcus Linde
- Department of Molecular Plant Breeding, Institute for Plant Genetics, Leibniz Universität HannoverHannover, Germany
- *Correspondence: Marcus Linde and Thomas Debener, Department of Molecular Plant Breeding, Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Street 2, Hannover 30419, Germany e-mail: ;
| | - Thomas Debener
- Department of Molecular Plant Breeding, Institute for Plant Genetics, Leibniz Universität HannoverHannover, Germany
- *Correspondence: Marcus Linde and Thomas Debener, Department of Molecular Plant Breeding, Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Street 2, Hannover 30419, Germany e-mail: ;
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65
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Dufresne F, Stift M, Vergilino R, Mable BK. Recent progress and challenges in population genetics of polyploid organisms: an overview of current state-of-the-art molecular and statistical tools. Mol Ecol 2013; 23:40-69. [DOI: 10.1111/mec.12581] [Citation(s) in RCA: 248] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 10/29/2013] [Accepted: 10/30/2013] [Indexed: 12/19/2022]
Affiliation(s)
- France Dufresne
- Département de Biologie; Université du Québec à Rimouski; Québec QC Canada G5L 3A1
| | - Marc Stift
- Department of Biology; University of Konstanz; Konstanz D 78457 Germany
| | - Roland Vergilino
- Department of Integrative Biology; University of Guelph; Guelph ON Canada N1G 2W1
| | - Barbara K. Mable
- Institute of Biodiversity; Animal Health and Comparative Medicine; College of Medical, Veterinary and Life Sciences; University of Glasgow; Glasgow UK
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66
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Xu F, Lyu Y, Tong C, Wu W, Zhu X, Yin D, Yan Q, Zhang J, Pang X, Tobias CM, Wu R. A statistical model for QTL mapping in polysomic autotetraploids underlying double reduction. Brief Bioinform 2013; 15:1044-56. [DOI: 10.1093/bib/bbt073] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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67
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Xu F, Tong C, Lyu Y, Bo W, Pang X, Wu R. Allotetraploid and autotetraploid models of linkage analysis. Brief Bioinform 2013; 16:32-8. [DOI: 10.1093/bib/bbt075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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68
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Lepais O, Muller SD, Ben Saad-Limam S, Benslama M, Rhazi L, Belouahem-Abed D, Daoud-Bouattour A, Gammar AM, Ghrabi-Gammar Z, Bacles CFE. High genetic diversity and distinctiveness of rear-edge climate relicts maintained by ancient tetraploidisation for Alnus glutinosa. PLoS One 2013; 8:e75029. [PMID: 24098677 PMCID: PMC3787099 DOI: 10.1371/journal.pone.0075029] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 08/08/2013] [Indexed: 11/19/2022] Open
Abstract
Populations located at the rear-edge of a species' distribution may have disproportionate ecological and evolutionary importance for biodiversity conservation in a changing global environment. Yet genetic studies of such populations remain rare. This study investigates the evolutionary history of North-African low latitude marginal populations of Alnus glutinosa Gaertn., a European tree species that plays a significant ecological role as a keystone of riparian ecosystems. We genotyped 551 adults from 19 populations located across North Africa at 12 microsatellite loci and applied a coalescent-based simulation approach to reconstruct the demographic and evolutionary history of these populations. Surprisingly, Moroccan trees were tetraploids demonstrating a strong distinctiveness of these populations within a species otherwise known as diploid. Best-fitting models of demographic reconstruction revealed the relict nature of Moroccan populations that were found to have withstood past climate change events and to be much older than Algerian and Tunisian populations. This study highlights the complex demographic history that can be encountered in rear-edge distribution margins that here consist of both old stable climate relict and more recent populations, distinctively diverse genetically both quantitatively and qualitatively. We emphasize the high evolutionary and conservation value of marginal rear-edge populations of a keystone riparian species in the context of on-going climate change in the Mediterranean region.
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Affiliation(s)
- Olivier Lepais
- Biological and Environmental Sciences, School of Natural Sciences, University of Stirling, Stirling, United Kingdom
- INRA, UMR 1224, Ecologie Comportementale et Biologie des Populations de Poissons, Saint Pée sur Nivelle, France
- Univ Pau & Pays Adour, UMR 1224, Ecologie Comportementale et Biologie des Populations de Poissons, Anglet, France
- * E-mail:
| | - Serge D. Muller
- Université Montpellier 2, CNRS, UMR 5554, Institut des Sciences de l’Evolution, Montpellier, France
| | - Samia Ben Saad-Limam
- Université de Tunis El Manar, Faculté des Sciences de Tunis, Département de Biologie, Tunis, Tunisie
- Université de Manouba, UR Biogéographie, Climatologie Appliquée et Dynamique Erosive, Faculté des Lettres des Arts et des Humanités de Manouba, Manouba, Tunisie
| | - Mohamed Benslama
- Laboratoire de Biologie Végétale et Environnement, Université Badji Mokhtar, Annaba, Algérie
| | - Laila Rhazi
- Université Hassan II Casablanca, Faculté des Sciences Aïn Chock, Laboratoire d’Ecologie Aquatique et Environnement, Casablanca, Maroc
| | | | - Amina Daoud-Bouattour
- Université de Tunis El Manar, Faculté des Sciences de Tunis, Département de Biologie, Tunis, Tunisie
- Université de Manouba, UR Biogéographie, Climatologie Appliquée et Dynamique Erosive, Faculté des Lettres des Arts et des Humanités de Manouba, Manouba, Tunisie
| | - Amor Mokhtar Gammar
- Université de Manouba, UR Biogéographie, Climatologie Appliquée et Dynamique Erosive, Faculté des Lettres des Arts et des Humanités de Manouba, Manouba, Tunisie
| | - Zeineb Ghrabi-Gammar
- Université de Manouba, UR Biogéographie, Climatologie Appliquée et Dynamique Erosive, Faculté des Lettres des Arts et des Humanités de Manouba, Manouba, Tunisie
- Université de Carthage, Institut National Agronomique de Tunisie, Tunis, Tunisie
| | - Cécile Fanny Emilie Bacles
- Biological and Environmental Sciences, School of Natural Sciences, University of Stirling, Stirling, United Kingdom
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69
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Tayalé A, Parisod C. Natural pathways to polyploidy in plants and consequences for genome reorganization. Cytogenet Genome Res 2013; 140:79-96. [PMID: 23751271 DOI: 10.1159/000351318] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The last decade highlighted polyploidy as a rampant evolutionary process that triggers drastic genome reorganization, but much remains to be understood about their causes and consequences in both autopolyploids and allopolyploids. Here, we provide an overview of the current knowledge on the pathways leading to different types of polyploids and patterns of polyploidy-induced genome restructuring and functional changes in plants. Available evidence leads to a tentative 'diverge, merge and diverge' model supporting polyploid speciation and stressing patterns of divergence between diploid progenitors as a suitable predictor of polyploid genome reorganization. The merging of genomes at the origin of a polyploid lineage may indeed reveal different kinds of incompatibilities (chromosomal, genic and transposable elements) that have accumulated in diverging progenitors and reduce the fitness of nascent polyploids. Accordingly, successful polyploids have to overcome these incompatibilities through non-Mendelian mechanisms, fostering polyploid genome reorganization in association with the establishment of new lineages. See also sister article focusing on animals by Collares-Pereira et al., in this themed issue.
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Affiliation(s)
- A Tayalé
- Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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70
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Meloni M, Reid A, Caujapé-Castells J, Marrero A, Fernández-Palacios JM, Mesa-Coelo RA, Conti E. Effects of clonality on the genetic variability of rare, insular species: the case of Ruta microcarpa from the Canary Islands. Ecol Evol 2013; 3:1569-79. [PMID: 23789068 PMCID: PMC3686192 DOI: 10.1002/ece3.571] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 03/14/2013] [Accepted: 03/15/2013] [Indexed: 11/08/2022] Open
Abstract
Many plant species combine sexual and clonal reproduction. Clonal propagation has ecological costs mainly related to inbreeding depression and pollen discounting; at the same time, species able to reproduce clonally have ecological and evolutionary advantages being able to persist when conditions are not favorable for sexual reproduction. The presence of clonality has profound consequences on the genetic structure of populations, especially when it represents the predominant reproductive strategy in a population. Theoretical studies suggest that high rate of clonal propagation should increase the effective number of alleles and heterozygosity in a population, while an opposite effect is expected on genetic differentiation among populations and on genotypic diversity. In this study, we ask how clonal propagation affects the genetic diversity of rare insular species, which are often characterized by low levels of genetic diversity, hence at risk of extinction. We used eight polymorphic microsatellite markers to study the genetic structure of the critically endangered insular endemic Ruta microcarpa. We found that clonality appears to positively affect the genetic diversity of R. microcarpa by increasing allelic diversity, polymorphism, and heterozygosity. Moreover, clonal propagation seems to be a more successful reproductive strategy in small, isolated population subjected to environmental stress. Our results suggest that clonal propagation may benefit rare species. However, the advantage of clonal growth may be only short-lived for prolonged clonal growth could ultimately lead to monoclonal populations. Some degree of sexual reproduction may be needed in a predominantly clonal species to ensure long-term viability.
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Affiliation(s)
- M Meloni
- Institute of Systematic Botany, University of Zurich Zollikerstrase 107, Zurich, 8008, Switzerland
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71
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The effects of inheritance in tetraploids on genetic diversity and population divergence. Heredity (Edinb) 2012; 110:131-7. [PMID: 23211786 DOI: 10.1038/hdy.2012.80] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Polyploids are traditionally classified into allopolyploids and autopolyploids, based on their evolutionary origin and their disomic or multisomic mode of inheritance. Over the past decade it has become increasingly clear that there is a continuum between disomic and multisomic inheritance, with the rate of tetrasomy differing among species and among chromosomes within species. Here, we use a simple population genetic model to study the impact of the mode of inheritance on the genetic diversity and population divergence of tetraploids. We found that under almost strict disomic inheritance the tetraploid genome is divided into two separate subgenomes, such as found in classical allopolyploids. In those cases, assuming full tetrasomy in the analysis of polyploid genetic data will lead to an important bias in estimates of genetic diversity and population divergence. However, we found that even a low rate of allele exchange between the two subgenomes, at about one event per generation, is sufficient to homogenise the allele frequencies over the subgenomes, and the estimates become essentially unbiased. The inbreeding coefficient F(IS) can then be used to detect whether the estimates of diversity and divergence will be biased when full multisomy is assumed. Finally, we found that different summary statistics for measuring the strength of population differentiation are differentially affected by a deviation from full tetrasomy. Our model results provide several useful guidelines for the analysis of polyploid data, helping researchers to determine when their inferences are biased and which summary statistics to use.
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72
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Jeridi M, Perrier X, Rodier-Goud M, Ferchichi A, D'Hont A, Bakry F. Cytogenetic evidence of mixed disomic and polysomic inheritance in an allotetraploid (AABB) Musa genotype. ANNALS OF BOTANY 2012; 110:1593-606. [PMID: 23087127 PMCID: PMC3503499 DOI: 10.1093/aob/mcs220] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 09/10/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Edible bananas originated mainly from two wild species, Musa acuminata Colla (AA) and Musa balbisiana Colla (BB), and triploid cultivars with an AAA, AAB or ABB genome are the most widely used. In the present study, chromosome pairing affinities are investigated in a sterile AB Indian variety and in its fertile colchicine-induced allotetraploid (AABB) derivative to determine the inheritance pattern of the tetraploid genotype. The potential implications of interspecific recombination and chromosomal composition of diploid gametes for Musa improvement are presented. METHODS The pairing of different chromosome sets at diploid and tetraploid levels was investigated through a combination of conventional cytogenetic and genomic in-situ hybridization (GISH) analyses of meiotic chromosomes, leading to a likelihood model of the pairing behaviour. GISH analysis of mitotic chromosomes was also conducted to reveal the chromosome constitution of hybrids derived from crosses involving the allotetraploid genotype. KEY RESULTS Analysis of chromosome associations at both ploidy levels suggested that the newly formed allotetraploid behaves as a 'segmental allotetraploid' with three chromosome sets in a tetrasomic pattern, three sets in a likely disomic pattern and the five remaining sets in an intermediate pattern. Balanced and unbalanced diploid gametes were detected in progenies, with the chromosome constitution appearing to be more homogenous in pollen than in ovules. CONCLUSIONS Colchicine-induced allotetraploids in Musa provide access to the genetic background of natural AB varieties. The segmental inheritance pattern exhibited by the AABB allotetraploid genotype implies chromosome exchanges between M. acuminata and M. balbisiana species and opens new horizons for reciprocal transfer of valuable alleles.
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Affiliation(s)
- Mouna Jeridi
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR AGAP, Avenue Agropolis, F-34398 Montpellier, France
- Institut des Régions Arides (IRA), 4119 Médenine, Tunisia
| | - Xavier Perrier
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR AGAP, Avenue Agropolis, F-34398 Montpellier, France
| | - Marguerite Rodier-Goud
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR AGAP, Avenue Agropolis, F-34398 Montpellier, France
| | - Ali Ferchichi
- Institut des Régions Arides (IRA), 4119 Médenine, Tunisia
| | - Angélique D'Hont
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR AGAP, Avenue Agropolis, F-34398 Montpellier, France
| | - Frédéric Bakry
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR AGAP, Avenue Agropolis, F-34398 Montpellier, France
- For correspondence. E-mail
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73
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Abstract
Hybridisation among taxa with different ploidy levels is often associated with hybrid sterility. Clonal reproduction can stabilise these hybrids, but pervasive clonality may have a profound impact on the distribution of genetic diversity in natural populations. Here we investigate a widespread triploid taxon resulting from hybridisation between diploid Mimulus guttatus and tetraploid Mimulus luteus, two species that were introduced into the United Kingdom (UK) in the nineteenth century. This hybrid, Mimulus x robertsii, is largely sterile but capable of prolific vegetative propagation and has been recorded in the wild since 1872. We surveyed 40 Mimulus populations from localities across the UK to examine the current incidence of hybrids, and selected seventeen populations for genetic analysis using codominant markers. Cluster analyses revealed two main groups of genetically distinct individuals, corresponding to either diploid (M. guttatus) or polyploid (M. luteus and M. x robertsii) samples. Triploid hybrids were found in around 50% of sampled sites, sometimes coexisting with one of the parental species (M. guttatus). The other parent, M. luteus, was restricted to a single locality. Individual populations of M. x robertsii were genetically variable, containing multiple, highly heterozygous clones, with the majority of genetic variation distributed among- rather than within populations. Our findings demonstrate that this largely sterile, clonal taxon can preserve non-negligible amounts of genetic variation. The presence of genetically variable hybrid populations may provide the material for the continued success of asexual taxa in diverse environments.
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74
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Voorrips RE, Maliepaard CA. The simulation of meiosis in diploid and tetraploid organisms using various genetic models. BMC Bioinformatics 2012; 13:248. [PMID: 23013469 PMCID: PMC3542247 DOI: 10.1186/1471-2105-13-248] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 09/18/2012] [Indexed: 11/17/2022] Open
Abstract
Background While the genetics of diploid inheritance are well studied and software for linkage mapping, haplotyping and QTL analysis are available, for tetraploids the available tools are limited. In order to develop such tools it would be helpful if simulated populations based on a variety of models of the tetraploid meiosis would be available. Results Here we present PedigreeSim, a software package that simulates meiosis in both diploid and tetraploid species and uses this to simulate pedigrees and cross populations. For tetraploids a variety of models can be used, including both bivalent and quadrivalent formation, varying degrees of preferential pairing of hom(oe)ologous chromosomes, different quadrivalent configurations and more. Simulation of quadrivalent meiosis results as expected in double reduction and recombination between more than two hom(oe)ologous chromosomes. The results are shown to match theoretical predictions. Conclusions This is the first simulation software that implements all features of meiosis in tetraploids. It allows to generate data for tetraploid and diploid populations, and to investigate different models of tetraploid meiosis. The software and manual are available from
http://www.plantbreeding.nl/UK/software_pedigreeSim.html and as Additional files
1,
2,
3 and
4 with this publication.
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Affiliation(s)
- Roeland E Voorrips
- Department of Plant Breeding, Wageningen University and Research Center, P,O, Box 16, 6700 AA, Wageningen, the Netherlands.
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75
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Lu Y, Yang X, Tong C, Li X, Feng S, Wang Z, Pang X, Wang Y, Wang N, Tobias CM, Wu R. A multivalent three-point linkage analysis model of autotetraploids. Brief Bioinform 2012; 14:460-8. [DOI: 10.1093/bib/bbs051] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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76
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Arnold B, Bomblies K, Wakeley J. Extending coalescent theory to autotetraploids. Genetics 2012; 192:195-204. [PMID: 22714411 PMCID: PMC3430536 DOI: 10.1534/genetics.112.140582] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 06/01/2012] [Indexed: 11/18/2022] Open
Abstract
We develop coalescent models for autotetraploid species with tetrasomic inheritance. We show that the ancestral genetic process in a large population without recombination may be approximated using Kingman's standard coalescent, with a coalescent effective population size 4N. Numerical results suggest that this approximation is accurate for population sizes on the order of hundreds of individuals. Therefore, existing coalescent simulation programs can be adapted to study population history in autotetraploids simply by interpreting the timescale in units of 4N generations. We also consider the possibility of double reduction, a phenomenon unique to polysomic inheritance, and show that its effects on gene genealogies are similar to partial self-fertilization.
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Affiliation(s)
- B Arnold
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
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77
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Koning-Boucoiran CFS, Gitonga VW, Yan Z, Dolstra O, van der Linden CG, van der Schoot J, Uenk GE, Verlinden K, Smulders MJM, Krens FA, Maliepaard C. The mode of inheritance in tetraploid cut roses. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:591-607. [PMID: 22526522 PMCID: PMC3397129 DOI: 10.1007/s00122-012-1855-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 03/21/2012] [Indexed: 05/18/2023]
Abstract
Tetraploid hybrid tea roses (Rosa hybrida) represent most of the commercial cultivars of cut roses and form the basis for breeding programmes. Due to intensive interspecific hybridizations, modern cut roses are complex tetraploids for which the mode of inheritance is not exactly known. The segregation patterns of molecular markers in a tetraploid mapping population of 184 genotypes, an F(1) progeny from a cross of two heterozygous parents, were investigated for disomic and tetrasomic inheritance. The possible occurrence of double reduction was studied as well. We can exclude disomic inheritance, but while our observations are more in line with a tetrasomic inheritance, we cannot exclude that there is a mixture of both inheritance modes. Two novel parental tetraploid linkage maps were constructed using markers known from literature, combined with newly generated markers. Comparison with the integrated consensus diploid map (ICM) of Spiller et al. (Theor Appl Genet 122:489-500, 2010) allowed assigning numbers to each of the linkage groups of both maps and including small linkage groups. So far, the possibility of using marker-assisted selection in breeding of tetraploid cut roses and of other species with a tetrasomic or partly tetrasomic inheritance, is still limited due to the difficulties in establishing marker-trait associations. We used these tetraploid linkage maps to determine associations between markers, two morphological traits and powdery mildew resistance. The knowledge on inheritance and marker-trait associations in tetraploid cut roses will be of direct use to cut rose breeding.
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Affiliation(s)
- C F S Koning-Boucoiran
- Wageningen University and Research Centre, Plant Breeding, P.O. Box 16, 6700 AA, Wageningen, The Netherlands.
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78
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Aguirre AA, Wollenweber B, Frei UK, Lübberstedt T. PollenCALC: software for estimation of pollen compatibility of self-incompatible allo- and autotetraploid species. BMC Bioinformatics 2012; 13:125. [PMID: 22676372 PMCID: PMC3439690 DOI: 10.1186/1471-2105-13-125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 06/07/2012] [Indexed: 11/30/2022] Open
Abstract
Background Self-incompatibility (SI) is a biological mechanism to avoid inbreeding in allogamous plants. In grasses, this mechanism is controlled by a two-locus system (S-Z). Calculation of male and female gamete frequencies is complex for tetraploid species. We are not aware of any software available for predicting pollen haplotype frequencies and pollen compatibility in tetraploid species. Results PollenCALC is a software tool written in C++ programming language that can predict pollen compatibility percentages for polyploid species with a two-locus (S, Z) self-incompatibility system. The program predicts pollen genotypes and frequencies based on defined meiotic parameters for allo- or autotetraploid species with a gametophytic S-Z SI system. These predictions can be used to obtain expected values for for diploid and for (allo- or autotetraploidy SI grasses. Conclusion The information provided by this calculator can be used to predict compatibility of pair-crosses in plant breeding applications, to analyze segregation distortion for S and Z genes, as well as linked markers in mapping populations, hypothesis testing of the number of S and Z alleles in a pair cross, and the underlying genetic model.
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79
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Jørgensen MH, Ehrich D, Schmickl R, Koch MA, Brysting AK. Interspecific and interploidal gene flow in Central European Arabidopsis (Brassicaceae). BMC Evol Biol 2011; 11:346. [PMID: 22126410 PMCID: PMC3247304 DOI: 10.1186/1471-2148-11-346] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 11/29/2011] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Effects of polyploidisation on gene flow between natural populations are little known. Central European diploid and tetraploid populations of Arabidopsis arenosa and A. lyrata are here used to study interspecific and interploidal gene flow, using a combination of nuclear and plastid markers. RESULTS Ploidal levels were confirmed by flow cytometry. Network analyses clearly separated diploids according to species. Tetraploids and diploids were highly intermingled within species, and some tetraploids intermingled with the other species, as well. Isolation with migration analyses suggested interspecific introgression from tetraploid A. arenosa to tetraploid A. lyrata and vice versa, and some interploidal gene flow, which was unidirectional from diploid to tetraploid in A. arenosa and bidirectional in A. lyrata. CONCLUSIONS Interspecific genetic isolation at diploid level combined with introgression at tetraploid level indicates that polyploidy may buffer against negative consequences of interspecific hybridisation. The role of introgression in polyploid systems may, however, differ between plant species, and even within the small genus Arabidopsis, we find very different evolutionary fates when it comes to introgression.
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Affiliation(s)
- Marte H Jørgensen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, P.O. Box 1066 Blindern, NO-0316 Oslo, Norway
| | - Dorothee Ehrich
- Institute for Arctic and Marine Biology, University of Tromsø, NO-9037 Tromsø, Norway
| | - Roswitha Schmickl
- Centre for Organismal Studies (COS) Heidelberg, Department of Biodiversity and Plant Systematics, University of Heidelberg, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - Marcus A Koch
- Centre for Organismal Studies (COS) Heidelberg, Department of Biodiversity and Plant Systematics, University of Heidelberg, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - Anne K Brysting
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, P.O. Box 1066 Blindern, NO-0316 Oslo, Norway
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80
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Trapnell DW, Hamrick JL, Parker KC, Braungart KW, Glenn TC. Evaluating the utility of microsatellites for investigations of autopolyploid taxa. J Hered 2011; 102:473-8. [PMID: 21670174 DOI: 10.1093/jhered/esr045] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Autopolyploid taxa present numerous challenges for population genetic analyses due to difficulties determining allele dosage. Dosage ambiguity hinders accurate assessment of allele frequencies, multilocus genotypes (MLGTs), as well as levels and patterns of clonality. The pervasiveness of polyploidy in the evolutionary history of plant taxa makes this a recurring problem. Whereas diploidization of loci may occur over time, duplication of at least some loci is still frequently evident. Fortunately, with high-quality allozyme gels, it is possible to accurately infer allele dosage and, thus, determine exact MLGTs. However, accurately assessing dosage of microsatellite peaks is nearly impossible when studying wild populations with a large number of alleles per locus. Even if precise knowledge of genotypes is not required, for comparable numbers of alleles per locus and loci, the number of "phenotypes" is always lower with microsatellites than allozymes due to the inability to assess allele dosage. Microsatellite loci typically have more alleles per locus relative to allozymes although fewer loci are generally employed. Here, we present a mathematical model for comparing the relative utility of simple sequence repeat (SSR) versus allozyme markers to discriminate MLGTs. For example, the average plant allozyme study (2.6 alleles per locus, 10 polymorphic loci) has better discriminating power than SSR markers with 10 alleles at each of 3 loci, 9 alleles at 4 loci, 6 alleles at 5 loci, 5 alleles at 6 loci, and 4 alleles at 8 loci, demonstrating the value of assessing the relative discriminating power of these markers.
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Affiliation(s)
- Dorset W Trapnell
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.
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81
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Kamiri M, Stift M, Srairi I, Costantino G, El Moussadik A, Hmyene A, Bakry F, Ollitrault P, Froelicher Y. Evidence for non-disomic inheritance in a Citrus interspecific tetraploid somatic hybrid between C. reticulata and C. limon using SSR markers and cytogenetic analysis. PLANT CELL REPORTS 2011; 30:1415-25. [PMID: 21409551 DOI: 10.1007/s00299-011-1050-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2010] [Revised: 02/14/2011] [Accepted: 03/02/2011] [Indexed: 05/18/2023]
Abstract
Artificial tetraploid somatic hybrids have been developed for sterile triploid citrus breeding by sexual hybridization between diploid and tetraploid somatic hybrids. The genetic structure of diploid gametes produced by tetraploid genotypes depends on the mode of chromosome association at meiosis. In order to evaluate tetraploid inheritance in a tetraploid interspecific somatic hybrid between mandarin and lemon, we performed segregation studies using cytogenetic and single sequence repeat molecular markers. Cytogenetic analysis of meiosis in the somatic hybrid revealed 11% tetravalents and 76% bivalents. Inheritance of the tetraploid hybrid was analyzed by genotyping the triploid progeny derived from a cross between a diploid pummelo and the tetraploid somatic hybrid, in order to derive genotypes of the meiospores produced by the tetraploid. A likelihood-based approach was used to distinguish between disomic, tetrasomic, and intermediate inheritance models and to estimate the double reduction rate. In agreement with expectations based the cytogenetic data, marker segregation was largely compatible with tetrasomic and inheritance intermediate between disomic and tetrasomic, with some evidence for preferential pairing of homoeologous chromosomes. This has important implications for the design of breeding programs that involve tetraploid hybrids, and underscores the need to consider inheritance models that are intermediate between disomic and tetrasomic.
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Affiliation(s)
- Mourad Kamiri
- Unité de Recherche Multiplication végétative, CIRAD, San Giuliano, 20230, France
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82
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Li J, Das K, Fu G, Tong C, Li Y, Tobias C, Wu R. Em algorithm for mapping quantitative trait Loci in multivalent tetraploids. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2011; 2010:216547. [PMID: 21317976 PMCID: PMC3022269 DOI: 10.1155/2010/216547] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 11/16/2010] [Indexed: 05/25/2023]
Abstract
Multivalent tetraploids that include many plant species, such as potato, sugarcane, and rose, are of paramount importance to agricultural production and biological research. Quantitative trait locus (QTL) mapping in multivalent tetraploids is challenged by their unique cytogenetic properties, such as double reduction. We develop a statistical method for mapping multivalent tetraploid QTLs by considering these cytogenetic properties. This method is built in the mixture model-based framework and implemented with the EM algorithm. The method allows the simultaneous estimation of QTL positions, QTL effects, the chromosomal pairing factor, and the degree of double reduction as well as the assessment of the estimation precision of these parameters. We used simulated data to examine the statistical properties of the method and validate its utilization. The new method and its software will provide a useful tool for QTL mapping in multivalent tetraploids that undergo double reduction.
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Affiliation(s)
- Jiahan Li
- Center for Statistical Genetics, Pennsylvania State University, Hershey, PA 17033, USA
| | - Kiranmoy Das
- Center for Statistical Genetics, Pennsylvania State University, Hershey, PA 17033, USA
| | - Guifang Fu
- Center for Statistical Genetics, Pennsylvania State University, Hershey, PA 17033, USA
| | - Chunfa Tong
- Center for Statistical Genetics, Pennsylvania State University, Hershey, PA 17033, USA
| | - Yao Li
- Department of Statistics, West Virginia University, Morgantown, WV 26506, USA
| | - Christian Tobias
- Genomics and Gene Discovery Research Unit, USDA-ARS Western Regional Research Center, Albany, CA 94710, USA
| | - Rongling Wu
- Center for Statistical Genetics, Pennsylvania State University, Hershey, PA 17033, USA
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83
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Stift M, Bregman R, Oostermeijer JGB, van Tienderen PH. Other tetraploid species and conspecific diploids as sources of genetic variation for an autotetraploid. AMERICAN JOURNAL OF BOTANY 2010; 97:1858-1866. [PMID: 21616824 DOI: 10.3732/ajb.1000048] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
PREMISE OF THE STUDY Most plants are polyploid and have more than two copies of the genome. The evolutionary success of polyploids is often attributed to their potential to harbor increased genetic variation, but it is poorly understood how polyploids can attain such variation. Because of their formation bottleneck, newly formed tetraploids start out with little variation. Tetraploids may attain genetic variation through a combination of new mutations, recurrent formation, and gene exchange with diploid ancestors or related tetraploid species. We explore the role of gene exchange and introgression in autotetraploid Rorippa amphibia, a species that harbors more genetic variation than its diploid ancestors. • METHODS We crossed autotetraploid R. amphibia to diploid conspecifics and tetraploid R. sylvestris and backcrossed resulting F(1) hybrids. We used flow cytometry to determine the ploidy of all progeny. • KEY RESULTS Tetraploids of R. amphibia and R. sylvestris were interfertile; F(1) hybrids were fertile and could backcross. Crosses between diploids and tetraploids yielded a small number of viable, often tetraploid progeny. This indicates that unreduced gametes can facilitate gene flow from diploids to tetraploids. We detected a frequency of unreduced gametes of around 2.7 per 1000, which was comparable between diploids and tetraploids. • CONCLUSIONS Introgression from tetraploid R. sylvestris provides a realistic source of variation in autotetraploid R. amphibia. Only in a scenario where other compatible partners are absent, for example immediately after tetraploidization, gene flow through unreduced gametes from diploids could be an important source of genetic variation for tetraploids.
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Affiliation(s)
- Marc Stift
- Division of Ecology and Evolutionary Biology, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
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84
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Stift M, Reeve R, van Tienderen PH. Inheritance in tetraploid yeast revisited: segregation patterns and statistical power under different inheritance models. J Evol Biol 2010; 23:1570-8. [PMID: 20524952 DOI: 10.1111/j.1420-9101.2010.02012.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In their recent article, Albertin et al. (2009) suggest an autotetraploid origin of 10 tetraploid strains of baker's yeast (Saccharomyces cerevisiae), supported by the frequent observation of double reduction meiospores. However, the presented inheritance results were puzzling and seemed to contradict the authors' interpretation that segregation ratios support a tetrasomic model of inheritance. Here, we provide an overview of the expected segregation ratios at the tetrad and meiospore level given scenarios of strict disomic and tetrasomic inheritance, for cases with and without recombination between locus and centromere. We also use a power analysis to derive adequate sample sizes to distinguish alternative models. Closer inspection of the Albertin et al. data reveals that strict disomy can be rejected in most cases. However, disomic inheritance with strong but imperfect preferential pairing could not be excluded with the sample sizes used. The possibility of tetrad analysis in tetraploid yeast offers a valuable opportunity to improve our understanding of meiosis and inheritance of tetraploids.
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Affiliation(s)
- M Stift
- Division of Ecology and Evolutionary Biology, University of Glasgow, Glasgow G12 8QQ, UK.
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85
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Abstract
Autopolyploidy is more common in plants than traditionally assumed, but has received little attention compared with allopolyploidy. Hence, the advantages and disadvantages of genome doubling per se compared with genome doubling coupled with hybridizations in allopolyploids remain unclear. Autopolyploids are characterized by genomic redundancy and polysomic inheritance, increasing effective population size. To shed light on the evolutionary consequences of autopolyploidy, we review a broad range of studies focusing on both synthetic and natural autopolyploids encompassing levels of biological organization from genes to evolutionary lineages. The limited evidence currently available suggests that autopolyploids neither experience strong genome restructuring nor wide reorganization of gene expression during the first generations following genome doubling, but that these processes may become more important in the longer term. Biogeographic and ecological surveys point to an association between the formation of autopolyploid lineages and environmental change. We thus hypothesize that polysomic inheritance may provide a short-term evolutionary advantage for autopolyploids compared to diploid relatives when environmental change enforces range shifts. In addition, autopolyploids should possess increased genome flexibility, allowing them to adapt and persist across heterogeneous landscapes in the long run.
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Affiliation(s)
- Christian Parisod
- National Centre for Biosystematics, University of Oslo, 0318 Oslo, Norway.
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86
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Korbecka G, Rymer PD, Harris SA, Pannell JR. Solving the Problem of Ambiguous Paralogy for Marker Loci: Microsatellite Markers with Diploid Inheritance in Allohexaploid Mercurialis annua (Euphorbiaceae). J Hered 2010; 101:504-11. [DOI: 10.1093/jhered/esq026] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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87
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Albertin W, Marullo P, Aigle M, Bourgais A, Bely M, Dillmann C, DE Vienne D, Sicard D. Evidence for autotetraploidy associated with reproductive isolation in Saccharomyces cerevisiae: towards a new domesticated species. J Evol Biol 2009; 22:2157-70. [PMID: 19765175 DOI: 10.1111/j.1420-9101.2009.01828.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Partial or whole-genome duplications have played a major role in the evolution of new species. We have investigated the variation of ploidy level in a panel of domesticated strains of Saccharomyces cerevisiae coming from different geographical origins. Segregation studies and crosses with tester strains of different ploidy levels showed that part of the strains were well-balanced autotetraploids displaying tetrasomic inheritance. The presence of up to four different alleles for various loci is consistent with a polyploidization mechanism relying on the fusion of two nonreduced meiospores coming from two S. cerevisiae strains. Autotetraploidy was also in accordance with karyotype and flow cytometry analyses. Interestingly, most bakery strains were tetraploids, suggesting a link between ploidy level and human use. The null or drastically reduced fertility of the hybrids between tetraploid and diploid strains indicated that domesticated S. cerevisiae strains are composed of two groups isolated by post-zygotic reproductive barriers.
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Affiliation(s)
- W Albertin
- CNRS, UMR 0320/UMR 8120 Génétique Végétale, Gif-sur-Yvette, France
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88
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Larsen AS, Vaillant A, Verhaegen D, Kjær ED. Eighteen SSR-primers for tetraploid Adansonia digitata and its relatives. CONSERV GENET RESOUR 2009. [DOI: 10.1007/s12686-009-9075-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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89
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VAN Puyvelde K, VAN Geert A, Triest L. atetra, a new software program to analyse tetraploid microsatellite data: comparison with tetra and tetrasat. Mol Ecol Resour 2009; 10:331-4. [PMID: 21565028 DOI: 10.1111/j.1755-0998.2009.02748.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite the importance of tetraploid species, most population genetic studies deal with diploid ones because of difficulties in analysing codominant microsatellite data in tetraploid species. We developed a new software program-atetra-which combines both the rigorous method of enumeration for small data sets and Monte Carlo simulations for large ones. We discuss the added value of atetra by comparing its precision, stability and calculation time for different population sizes with those obtained from previous software programs tetrasat and tetra. The influence of the number of simulations on the calculation stability is also investigated. atetra and tetrasat proved to be more precise when compared with tetra, which, however, remains faster. atetra has the same precision than tetrasat, but is much faster, can handle an infinite number of partial heterozygotes and calculates more genetic variables. The more user-friendly interface of atetra reduces possible mistakes.
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Affiliation(s)
- K VAN Puyvelde
- Vrije Universiteit Brussel, Plant Biology and Nature Management (APNA), Pleinlaan 2, B-1050 Brussels, Belgium
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90
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Abstract
The importance of hybridization in plant speciation and evolution has been debated for decades, with opposing views of hybridization as either a creative evolutionary force or evolutionary noise. Hybrid speciation may occur at either the homoploid (i.e., between two species of the same ploidy) or the polyploid level, each with its attendant genetic and evolutionary consequences. Whereas allopolyploidy (i.e., resulting from hybridization and genome doubling) has long been recognized as an important mode of plant speciation, the implications of genome duplication have typically not been taken into account in most fields of plant biology. Recent developments in genomics are revolutionizing our views of angiosperm genomes, demonstrating that perhaps all angiosperms have likely undergone at least one round of polyploidization and that hybridization has been an important force in generating angiosperm species diversity. Hybridization and polyploid formation continue to generate species diversity, with several new allopolyploids having originated just within the past century or so. The origins of polyploid species-whether via hybridization between species or between genetically differentiated populations of a single species-and the immediate genetic consequences of polyploid formation are therefore receiving enthusiastic attention. The time is therefore right for a review of the role of hybridization in plant speciation.
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Affiliation(s)
- Pamela S Soltis
- The Genetics Institute, Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611, USA.
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91
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Stift M, Luttikhuizen PC, Visser EJW, Van Tienderen PH. Different flooding responses in Rorippa amphibia and Rorippa sylvestris, and their modes of expression in F1 hybrids. THE NEW PHYTOLOGIST 2008; 180:229-239. [PMID: 18631292 DOI: 10.1111/j.1469-8137.2008.02547.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The river floodplain species Rorippa amphibia, Rorippa sylvestris, and their hybrid Rorippa x anceps were studied here, with the aim of identifying potential species differences with respect to flooding tolerance, and of assessing their expression in F1 hybrids. Parents and their F1 hybrids were subjected to three flooding treatments mimicking natural conditions, and growth-related and leaf morphological traits were compared. In contrast to R. sylvestris, R. amphibia responded to waterlogging by forming specialized roots, and its growth was not reduced. These traits were dominantly expressed in hybrids. Both species and the hybrids established shoot growth over 2 wk of complete submergence. Only in R. sylvestris was this not at the expense of root biomass, suggesting that R. sylvestris can photosynthesize underwater. Rorippa sylvestris also showed a hyponastic response. Hybrids were intermediate to the parents in this respect. This study shows that phenotypic expression of parental traits in F1 hybrids is mostly additive, but can also be dominant. This suggests that a large overlap in habitat use of parents and hybrids is likely. If such an overlap occurs, the main evolutionary consequences of hybridization in Rorippa will be the introgression of genes, as the hybrids are fully fertile.
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Affiliation(s)
- Marc Stift
- Institute for Biodiversity and Ecosystem Dynamics, Experimental Plant Systematics, Universiteit van Amsterdam, P.O. Box 94062, 1090 GB Amsterdam, the Netherlands
- Present address: Division of Environmental & Evolutionary Biology, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, UK
| | - Pieternella C Luttikhuizen
- Institute for Biodiversity and Ecosystem Dynamics, Experimental Plant Systematics, Universiteit van Amsterdam, P.O. Box 94062, 1090 GB Amsterdam, the Netherlands
| | - Eric J W Visser
- Department of Experimental Plant Ecology, Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, the Netherlands
| | - Peter H Van Tienderen
- Institute for Biodiversity and Ecosystem Dynamics, Experimental Plant Systematics, Universiteit van Amsterdam, P.O. Box 94062, 1090 GB Amsterdam, the Netherlands
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