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Sample records for allopolyploid tragopogon miscellus

  1. On the road to diploidization? Homoeolog loss in independently formed populations of the allopolyploid Tragopogon miscellus (Asteraceae

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    Soltis Pamela S

    2009-06-01

    Full Text Available Abstract Background Polyploidy (whole-genome duplication is an important speciation mechanism, particularly in plants. Gene loss, silencing, and the formation of novel gene complexes are some of the consequences that the new polyploid genome may experience. Despite the recurrent nature of polyploidy, little is known about the genomic outcome of independent polyploidization events. Here, we analyze the fate of genes duplicated by polyploidy (homoeologs in multiple individuals from ten natural populations of Tragopogon miscellus (Asteraceae, all of which formed independently from T. dubius and T. pratensis less than 80 years ago. Results Of the 13 loci analyzed in 84 T. miscellus individuals, 11 showed loss of at least one parental homoeolog in the young allopolyploids. Two loci were retained in duplicate for all polyploid individuals included in this study. Nearly half (48% of the individuals examined lost a homoeolog of at least one locus, with several individuals showing loss at more than one locus. Patterns of loss were stochastic among individuals from the independently formed populations, except that the T. dubius copy was lost twice as often as T. pratensis. Conclusion This study represents the most extensive survey of the fate of genes duplicated by allopolyploidy in individuals from natural populations. Our results indicate that the road to genome downsizing and ultimate genetic diploidization may occur quickly through homoeolog loss, but with some genes consistently maintained as duplicates. Other genes consistently show evidence of homoeolog loss, suggesting repetitive aspects to polyploid genome evolution.

  2. Synthetic polyploids of Tragopogon miscellus and T. mirus (Asteraceae): 60 Years after Ownbey's discovery.

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    Tate, Jennifer A; Symonds, V Vaughan; Doust, Andrew N; Buggs, Richard J A; Mavrodiev, Evgeny; Majure, Lucas C; Soltis, Pamela S; Soltis, Douglas E

    2009-05-01

    In plants, polyploidy has been a significant evolutionary force on both recent and ancient time scales. In 1950, Ownbey reported two newly formed Tragopogon allopolyploids in the northwestern United States. We have made the first synthetic lines of T. mirus and T. miscellus using T. dubius, T. porrifolius, and T. pratensis as parents and colchicine treatment of F(1) hybrids. We also produced allotetraploids between T. porrifolius and T. pratensis, which are not known from nature. We report on the crossability between the diploids, as well as the inflorescence morphology, pollen size, meiotic behavior, and fertility of the synthetic polyploids. Morphologically, the synthetics resemble the natural polyploids with short- and long-liguled forms of T. miscellus resulting when T. pratensis and T. dubius are reciprocally crossed. Synthetic T. mirus was also formed reciprocally, but without any obvious morphological differences resulting from the direction of the cross. Of the 27 original crosses that yielded 171 hybrid individuals, 18 of these lineages have persisted to produce 386 S(1) progeny; each of these lineages has produced S(2) seed that are viable. The successful generation of these synthetic polyploids offers the opportunity for detailed comparative studies of natural and synthetic polyploids within a nonmodel system. PMID:21628250

  3. Rapid Concerted Evolution of Nuclear Ribosomal DNA in Two Tragopogon Allopolyploids of Recent and Recurrent Origin

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    Kovarik, A; Pires, J. C.; Leitch, A. R.; Lim, K. Y.; Sherwood, A M; Matyasek, R.; Rocca, J.; Soltis, D. E.; Soltis, P S

    2005-01-01

    We investigated concerted evolution of rRNA genes in multiple populations of Tragopogon mirus and T. miscellus, two allotetraploids that formed recurrently within the last 80 years following the introduction of three diploids (T. dubius, T. pratensis, and T. porrifolius) from Europe to North America. Using the earliest herbarium specimens of the allotetraploids (1949 and 1953) to represent the genomic condition near the time of polyploidization, we found that the parental rDNA repeats were in...

  4. Molecular cytogenetic analysis of recently evolved Tragopogon (Asteraceae) allopolyploids reveal a karyotype that is additive of the diploid progenitors

    Czech Academy of Sciences Publication Activity Database

    Pires, J. C.; Lim, K. Y.; Kovařík, Aleš; Matyášek, Roman; Boyd, A.; Leitch, A. R.; Leitch, I. J.; Bennet, M. D.; Soltis, P. S.; Soltis, D. E.

    2004-01-01

    Roč. 91, č. 7 (2004), s. 1022-1035. ISSN 0002-9122 R&D Projects: GA ČR GA204/01/0313; GA ČR GA521/01/0037 Institutional research plan: CEZ:AV0Z5004920 Keywords : centromere * chromosomal evolution * fluorescent in situ hybridization (FISH) Subject RIV: BO - Biophysics Impact factor: 2.438, year: 2004

  5. Hepatoprotective, Antioxidant, and Anticancer Effects of the Tragopogon porrifolius Methanolic Extract

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    Clara Tenkerian; Mirvat El-Sibai; Costantine F. Daher; Mohamad Mroueh

    2015-01-01

    Tragopogon porrifolius (Asteraceae), commonly referred to as white salsify, is an edible herb used in Lebanese folk medicine to treat cancer and liver dysfunction. In this study, we investigated the antioxidant activity of Tragopogon porrifolius methanolic extract, both in vitro and in vivo, in addition to its hepatoprotective and anticancer activities. Total phenolic and flavonoid contents were measured and found to be 37.0 ± 1.40 mg GAE/g and 16.6 ± 0.42 mg QE/g dry weight, respectively. In...

  6. Population-level study of ribosomal RNA genes expression in Tragopogon allotetraplopids of recent and recurrent origin

    Czech Academy of Sciences Publication Activity Database

    Kovařík, Aleš; Matyášek, Roman; Tate, J. A.; Šrubařová, Hana; Yoong, K.Y.; Leitch, A.R.; Soltis, D.E.; Soltis, P.E.

    Prague, 2006. [Groupe Cytogenetique et polyploidie. 05.04.2006-07.04.2006, Bordeaux] Institutional research plan: CEZ:AV0Z50040507 Keywords : RNA * Tragopogon * allotetraploids Subject RIV: BO - Biophysics

  7. Cytonuclear Evolution of Rubisco in Four Allopolyploid Lineages

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    Gong, Lei; Olson, Mischa; Wendel, Jonathan F.

    2014-01-01

    Allopolyploidization in plants entails the merger of two divergent nuclear genomes, typically with only one set (usually maternal) of parental plastidial and mitochondrial genomes and with an altered cytonuclear stoichiometry. Thus, we might expect cytonuclear coevolution to be an important dimension of allopolyploid evolution. Here, we investigate cytonuclear coordination for the key chloroplast protein rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase), which is composed of nuclear-e...

  8. Phenolic compounds from allium schoenoprasum, tragopogon pratensis and rumex acetosa and their antiproliferative effects

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    Petr Saha; Otakar Rop; Pavel Valasek; Petr Humpolicek; Jiri Mlcek; Zdenka Kucekova

    2011-01-01

    Experimental studies have shown that phenolic compounds have antiproliferative and tumour arresting effects. The aim of this original study was to investigate the content of phenolic compounds (PhC) in flowers of Allium schoenoprasum (chive), Tragopogon pratensis (meadow salsify) and Rumex acetosa (common sorrel) and their effect on proliferation of HaCaT cells. Antiproliferative effects were evaluated in vitro using the following concentrations of phenolic compounds in cultivation medium: 10...

  9. Standardization of Tragopogon graminifolius DC. Extract Based on Phenolic Compounds and Antioxidant Activity

    OpenAIRE

    2014-01-01

    Tragopogon graminifolius DC. (TG), Compositae family, is traditionally used for the treatment of various diseases like gastrointestinal and hepatic disorders. The aim of the present study is to standardize extracts from TG used for preparation of different dosage forms in traditional Iranian medicine (TIM) based on phenolic compounds. For this purpose, total phenolic content and some phenolic compounds were determined in ethanolic extracts from aerial part and root of TG by HPLC method. Furth...

  10. Epigenetic phenomena and the evolution of plant allopolyploids

    Institute of Scientific and Technical Information of China (English)

    BaoLiu; JonathanF.Wendel

    2005-01-01

    Allopolyploid speciation is widespread in plants, yet the molecular requirements for successful orchestration of coordinated gene expression for two divergent and reunited genomes are poorly understood. Recent studies in several plant systems have revealed that allopolyploid genesis under both synthetic and natural conditions often is accompanied by rapid and sometimes evolutionarily conserved epigeuetic changes, including alteration in cytosine methylation patterns, rapid silencing in ribosomal RNA and proteincoding genes, and de-repression of dormant transposable elements. These changes are inter-related and likely arise from chromatin remodeling and its effects on epigenetic codes during and subsequent to allopolyploid formation. Epigenetic modifications could produce adaptive epimutations and novel phenotypes, some of which may be evolutionarily stable for millions of years, thereby representing a vast reservoir of latent variation that may be episodically released and made visible to selection. This epigenetic variation may contribute to several important attributes of allopolyploidy, including functional diversification or subfunctionalization of duplicated genes, genetic and cytological diploidization, and quenching of incompatible inter-genomic interactions that are characteristic of allopolyploids. It is likely that the evolutionary success of allopolyploidy is in part attributatble to epigenetic phenomena that we are only just beginning to understand.

  11. The gene copy number and DNA methylation influence expression of ribosomal RNA loci in recently and recurrently formed Tragopogon allotetraploids

    Czech Academy of Sciences Publication Activity Database

    Kovařík, Aleš; Šrubařová, Hana; Lim, K.Y.; Leitch, A.R.; Soltis, D.E.; Soltis, P.S.; Matyášek, Roman

    Angers, 2008. s. 2. [Cytogénétique et Polyploidie, DGAP INRA - Technopole. 02.04.2008-04.04.2008, Angers] Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : epigenetic silencing * rDNA * Tragopogon allotetraploids Subject RIV: BO - Biophysics

  12. Genome Size in Diploids, Allopolyploids, and Autopolyploids of Mediterranean Triticeae

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    T. Eilam

    2010-01-01

    Full Text Available Nuclear DNA amount, determined by the flow cytometry method, in diploids, natural and synthetic allopolyploids, and natural and synthetic autopolyploids of the tribe Triticeae (Poaceae is reviewed here and discussed. In contrast to the very small and nonsignificant variation in nuclear DNA amount that was found at the intraspecific level, the variation at the interspecific level is very large. Evidently changes in genome size are either the cause or the result of speciation. Typical autopolyploids had the expected additive DNA amount of their diploid parents, whereas natural and synthetic cytologically diploidized autopolyploids and natural and synthetic allopolyploids had significantly less DNA than the sum of their parents. Thus, genome downsizing, occurring during or immediately after the formation of these polyploids, provides the physical basis for their cytological diploidization, that is, diploid-like meiotic behavior. Possible mechanisms that are involved in genome downsizing and the biological significance of this phenomenon are discussed.

  13. Gene expression dosage regulation in an allopolyploid fish.

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    I Matos

    Full Text Available How allopolyploids are able not only to cope but profit from their condition is a question that remains elusive, but is of great importance within the context of successful allopolyploid evolution. One outstanding example of successful allopolyploidy is the endemic Iberian cyprinid Squalius alburnoides. Previously, based on the evaluation of a few genes, it was reported that the transcription levels between diploid and triploid S. alburnoides were similar. If this phenomenon occurs on a full genomic scale, a wide functional ''diploidization'' could be related to the success of these polyploids. We generated RNA-seq data from whole juvenile fish and from adult livers, to perform the first comparative quantitative transcriptomic analysis between diploid and triploid individuals of a vertebrate allopolyploid. Together with an assay to estimate relative expression per cell, it was possible to infer the relative sizes of transcriptomes. This showed that diploid and triploid S. alburnoides hybrids have similar liver transcriptome sizes. This in turn made it valid to directly compare the S. alburnoides RNA-seq transcript data sets and obtain a profile of dosage responses across the S. alburnoides transcriptome. We found that 64% of transcripts in juveniles' samples and 44% in liver samples differed less than twofold between diploid and triploid hybrids (similar expression. Yet, respectively 29% and 15% of transcripts presented accurate dosage compensation (PAA/PA expression ratio of 1 instead of 1.5. Therefore, an exact functional diploidization of the triploid genome does not occur, but a significant down regulation of gene expression in triploids was observed. However, for those genes with similar expression levels between diploids and triploids, expression is not globally strictly proportional to gene dosage nor is it set to a perfect diploid level. This quantitative expression flexibility may be a strong contributor to overcome the genomic shock

  14. Hepatoprotective, Antioxidant, and Anticancer Effects of the Tragopogon porrifolius Methanolic Extract

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    Clara Tenkerian

    2015-01-01

    Full Text Available Tragopogon porrifolius (Asteraceae, commonly referred to as white salsify, is an edible herb used in Lebanese folk medicine to treat cancer and liver dysfunction. In this study, we investigated the antioxidant activity of Tragopogon porrifolius methanolic extract, both in vitro and in vivo, in addition to its hepatoprotective and anticancer activities. Total phenolic and flavonoid contents were measured and found to be 37.0±1.40 mg GAE/g and 16.6±0.42 mg QE/g dry weight, respectively. In vitro antioxidant assays revealed an FRAP value of 659±13.8 µmol Fe2+/g of extract and DPPH IC50 value 15.2 µg/mL. In rats subjected to CCl4-induced hepatotoxicity, significant increase in CAT, SOD, and GST levels was detected. The highest dose of the extract (250 mg/kg recorded a fold increase of 1.68 for SOD, 2.49 for GST, and 3.2 for CAT. The extract also showed substantial decrease in AST (57%, ALT (56%, and LDH (65% levels. Additionally, the extract caused a dose-dependent decrease in cell viability and proliferation. In conclusion, the methanolic extract of T. porrifolius displayed a relatively high antioxidant activity both in vitro and in vivo as well as hepatoprotective potential against liver toxicity in rats and anticancer effect on MDA-MB-231 and Caco-2 cells.

  15. Hepatoprotective, Antioxidant, and Anticancer Effects of the Tragopogon porrifolius Methanolic Extract.

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    Tenkerian, Clara; El-Sibai, Mirvat; Daher, Costantine F; Mroueh, Mohamad

    2015-01-01

    Tragopogon porrifolius (Asteraceae), commonly referred to as white salsify, is an edible herb used in Lebanese folk medicine to treat cancer and liver dysfunction. In this study, we investigated the antioxidant activity of Tragopogon porrifolius methanolic extract, both in vitro and in vivo, in addition to its hepatoprotective and anticancer activities. Total phenolic and flavonoid contents were measured and found to be 37.0 ± 1.40 mg GAE/g and 16.6 ± 0.42 mg QE/g dry weight, respectively. In vitro antioxidant assays revealed an FRAP value of 659 ± 13.8 µmol Fe(2+)/g of extract and DPPH IC50 value 15.2 µg/mL. In rats subjected to CCl4-induced hepatotoxicity, significant increase in CAT, SOD, and GST levels was detected. The highest dose of the extract (250 mg/kg) recorded a fold increase of 1.68 for SOD, 2.49 for GST, and 3.2 for CAT. The extract also showed substantial decrease in AST (57%), ALT (56%), and LDH (65%) levels. Additionally, the extract caused a dose-dependent decrease in cell viability and proliferation. In conclusion, the methanolic extract of T. porrifolius displayed a relatively high antioxidant activity both in vitro and in vivo as well as hepatoprotective potential against liver toxicity in rats and anticancer effect on MDA-MB-231 and Caco-2 cells. PMID:25694787

  16. Interpopulation hybridization generates meiotically stable rDNA epigenetic variants in allotetraploid Tragopogon mirus

    Czech Academy of Sciences Publication Activity Database

    Matyášek, Roman; Dobešová, Eva; Húska, Dalibor; Ježková, Ivana; Soltis, P. S.; Soltis, D.E.; Kovařík, Aleš

    2016-01-01

    Roč. 85, č. 3 (2016), s. 362-377. ISSN 0960-7412 R&D Projects: GA ČR(CZ) GA14-34632S; GA ČR GBP501/12/G090; GA ČR(CZ) GA13-10057S Institutional support: RVO:68081707 Keywords : allopolyploid * chromatin modification * epigenetic variants Subject RIV: BO - Biophysics Impact factor: 5.972, year: 2014

  17. Reproductive dynamics shapes genomotype composition in an allopolyploid complex.

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    Morgado-Santos, M; Carona, S; Magalhães, M F; Vicente, L; Collares-Pereira, M J

    2016-05-25

    Hybrid complexes are composed of organisms with multiple combinations of parental genomes (genomotypes) that interconnect through nets of crosses. Although several such complexes are well established without speciation or extinction, mechanisms shaping their dynamics remain poorly understood. In this study, we quantified the reproductive success of the allopolyploid Iberian fish Squalius alburnoides in experimental free-access and directional crosses involving the most common genomotypes. Specifically, we analysed the paternity of the offspring produced when females had free access to male genomotypes and quantified variations in egg allocation, fertilization rate, and offspring survival among crosses involving each male genomotype. The composition of the offspring produced from free-access crosses varied significantly from that expected from random mating, suggesting that offspring production and viability are not independent of parental male genomotype. Moreover, directional crosses producing the genomotype most commonly found in wild populations appeared to be the most successful, with females laying more eggs, and fertilization rate and offspring survival being the highest. These results suggest that reproductive dynamics plays a relevant role in structuring the genomotype composition of populations and opens a path to future research on the ecology and evolutionary biology of allopolyploids and their multiplicity of possible evolutionary pathways. PMID:27226473

  18. Environmental Regulation of Heterosis in the Allopolyploid Arabidopsis suecica1[OPEN

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    Solhaug, Erik M.; Ihinger, Jacie; Gamboa, Veronica; Bradford, Denise; Doerge, R.W.

    2016-01-01

    Allopolyploids are organisms possessing more than two complete sets of chromosomes from two or more species and are frequently more vigorous than their progenitors. To address the question why allopolyploids display hybrid vigor, we compared the natural allopolyploid Arabidopsis suecica to its progenitor species Arabidopsis thaliana and Arabidopsis arenosa. We measured chlorophyll content, CO2 assimilation, and carbohydrate production under varying light conditions and found that the allopolyploid assimilates more CO2 per unit chlorophyll than either of the two progenitor species in high intensity light. The increased carbon assimilation corresponds with greater starch accumulation, but only in strong light, suggesting that the strength of hybrid vigor is dependent on environmental conditions. In weaker light A. suecica tends to produce as much primary metabolites as the better progenitor. We found that gene expression of LIMIT DEXTRINASE1, a debranching enzyme that cleaves branch points within starch molecules, is at the same level in the allopolyploid as in the maternal progenitor A. thaliana and significantly more expressed than in the paternal progenitor A. arenosa. However, expression differences of β-amylases and GLUCAN-WATER DIKINASE1 were not statistically significantly elevated in the allopolyploid over progenitor expression levels. In contrast to allopolyploids, autopolyploid A. thaliana showed the same photosynthetic rate as diploids, indicating that polyploidization alone is likely not the reason for enhanced vigor in the allopolyploid. Taken together, our data suggest that the magnitude of heterosis in A. suecica is environmentally regulated, arises from more efficient photosynthesis, and, under specific conditions, leads to greater starch accumulation than in its progenitor species. PMID:26896394

  19. Antioxidant, mutagenic, and antimutagenic activities of Tragopogon longirostis var. longirostis, an edible wild plant in Turkey

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    Nurdan Sarac

    2015-01-01

    Full Text Available Objectives: The ethanolic extract of Tragopogon longirostis var. longirostis, a wild edible plant in Anatolia was isolated, and its antioxidant, mutagenic, and antimutagenic properties were investigated. Materials and Methods: The antioxidant activity (AA was determined by the inhibition of 2,2-diphenyl-1-picrylhydrazyl (DPPH radical, total AA, and phenolic compounds. The mutagenic and antimutagenic activities were investigated by Ames Salmonella/microsome mutagenicity test. Results: The IC 50 value for DPPH radicals was 7.84 ± 0.603 mg/mL. The total AA increased with an increase in the concentration of the extracts (1, 5, 10, 20, and 30 mg/mL, containing linoleic acid emulsion. The total phenolic content was 284.71 ± 5.6 mg gallic acid equivalent/g extract. The results showed that the ethanolic extract can be considered safe, because it does not have any mutagenic effect at the tested concentrations. As a result, the ethanolic extract of the leaves exhibited antimutagenic effects at 2.5, 0.25, and 0.025 mg/plate concentrations. Conclusions: To our knowledge, this is the first study of the antioxidant, mutagenic, and antimutagenic activities of T. longirostis var. longirostis. These activities are an important topic in the food industry, as well as in the medical field.

  20. Tragopogon porrifolius improves serum lipid profile and increases short-term satiety in rats.

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    Zeeni, Nadine; Daher, Costantine F; Saab, Lea; Mroueh, Mohamad

    2014-01-01

    Tragopogon porrifolius (white salsify) is an edible plant commonly used in folk medicine in Lebanon and neighbouring countries. This study investigates the effect of the aqueous extract of the aerial part of T. porrifolius on lipemia and appetite regulation using a rat model. Food intake, abdominal fat percentage, blood lipid profile, liver weight and liver enzymes were assessed following 4 weeks of extract intake via drinking water (50, 100, or 250 mg/kg body weight) in standard high-carbohydrate and high-fat dietary conditions. In a separate study, the short term effect of a preload of T. porrifolius extract on food intake was evaluated. Results showed that consumption of the plant extract for a period of four weeks resulted in a marked improvement of the lipid profile (triglycerides, total cholesterol, LDL and HDL cholesterol). Body weight, food intake and intra-abdominal fat were also lower in animals given the plant extract (100 and 250 mg/kg). In addition, T. porrifolius extract preload produced a dose dependent decrease in food intake observed over 24h. The intake of T. porrifolius aqueous extract therefore improved lipemia and increased satiety in rats with no visible adverse effects. PMID:24099703

  1. The cytonuclear dimension of allopolyploid evolution: an example from cotton using rubisco.

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    Gong, Lei; Salmon, Armel; Yoo, Mi-Jeong; Grupp, Kara K; Wang, Zining; Paterson, Andrew H; Wendel, Jonathan F

    2012-10-01

    During allopolyploid speciation, two divergent nuclear genomes merge, yet only one (usually the maternal) of the two sets of progenitor organellar genomes is maintained. Rubisco (1,5-bisphosphate carboxylase/oxygenase) is composed of nuclear-encoded small subunits (SSUs) and plastome-encoded large subunits (LSUs), providing an ideal system to explore the evolutionary process of cytonuclear accommodation. Here, we take initial steps in this direction, using Gossypium allopolyploids as our model. SSU copies from divergent (5-10 My) progenitor diploids ("A" and "D" genomes) were combined at the time of polyploid formation 1-2 Ma, with the LSU encoded by the maternal A-genome parent. LSU genes from A- and D-genome diploids and AD-genome allopolyploids were sequenced, revealing several nonsynonymous substitutions and suggesting the possibility of differential selection on the nuclear-encoded rbcS partner following allopolyploid formation. Sequence data for the rbcS gene family revealed nonreciprocal homoeologous recombination between A- and D-rbcS homoeologs in all polyploid species but not in a synthetic intergenomic F1 hybrid, demonstrating "gene conversion" during allopolyploid evolution. All progenitor rbcS genes are retained and expressed in the five extant allopolyploid species, but analysis of the leaf transcriptome showed that A-homoeologs are preferentially expressed in both the allopolyploid and hybrid, consistent with the maternal origin of rbcL. Although rbcS genes from both progenitor genomes are expressed, some appear to have experienced mutations that may represent cytonuclear coevolution. PMID:22490824

  2. Standardization of Tragopogon graminifolius DC. Extract Based on Phenolic Compounds and Antioxidant Activity

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    Mohammad Hosein Farzaei

    2014-01-01

    Full Text Available Tragopogon graminifolius DC. (TG, Compositae family, is traditionally used for the treatment of various diseases like gastrointestinal and hepatic disorders. The aim of the present study is to standardize extracts from TG used for preparation of different dosage forms in traditional Iranian medicine (TIM based on phenolic compounds. For this purpose, total phenolic content and some phenolic compounds were determined in ethanolic extracts from aerial part and root of TG by HPLC method. Furthermore, antioxidant activity was evaluated using DPPH-HPLC methods. Caffeic acid, gallic acid, ρ-coumaric acid, ferulic acid, and catechin were detected in root and aerial part of TG. ρ-Coumaric acid (6.357 ± 0.014 mg·g−1 was dominant phenolic compound in aerial part followed by ferulic acid (1.24 ± 0.018 mg·g−1. Also, ρ-coumaric acid (2.685 ± 0.031 mg·g−1 was highly abundant in root, followed by catechin (2.067 ± 0.021 mg·g−1. Antioxidant activity of root extract (460.45 ± 0.78 µg Vit.E.E·mL−1 was better than that of aerial part. Generally, phenolic compounds are one of the major constituents of TG and could be used as markers for standardization of dosage forms prepared from this plant. Also, TG demonstrated significant antioxidant activity using DPPH-HPLC method. Phenolic compounds of TG may be responsible for its marked antioxidant properties.

  3. Genetic Basis for Spontaneous Hybrid Genome Doubling during Allopolyploid Speciation of Common Wheat Shown by Natural Variation Analyses of the Paternal Species

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    Yoshihiro Matsuoka; Shuhei Nasuda; Yasuyo Ashida; Miyuki Nitta; Hisashi Tsujimoto; Shigeo Takumi; Taihachi Kawahara

    2013-01-01

    The complex process of allopolyploid speciation includes various mechanisms ranging from species crosses and hybrid genome doubling to genome alterations and the establishment of new allopolyploids as persisting natural entities. Currently, little is known about the genetic mechanisms that underlie hybrid genome doubling, despite the fact that natural allopolyploid formation is highly dependent on this phenomenon. We examined the genetic basis for the spontaneous genome doubling of triploid F...

  4. Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd's purse (Capsella bursa-pastoris).

    Science.gov (United States)

    Cornille, A; Salcedo, A; Kryvokhyzha, D; Glémin, S; Holm, K; Wright, S I; Lascoux, M

    2016-01-01

    Polyploidization is a dominant feature of flowering plant evolution. However, detailed genomic analyses of the interpopulation diversification of polyploids following genome duplication are still in their infancy, mainly because of methodological limits, both in terms of sequencing and computational analyses. The shepherd's purse (Capsella bursa-pastoris) is one of the most common weed species in the world. It is highly self-fertilizing, and recent genomic data indicate that it is an allopolyploid, resulting from hybridization between the ancestors of the diploid species Capsella grandiflora and Capsella orientalis. Here, we investigated the genomic diversity of C. bursa-pastoris, its population structure and demographic history, following allopolyploidization in Eurasia. To that end, we genotyped 261 C. bursa-pastoris accessions spread across Europe, the Middle East and Asia, using genotyping-by-sequencing, leading to a total of 4274 SNPs after quality control. Bayesian clustering analyses revealed three distinct genetic clusters in Eurasia: one cluster grouping samples from Western Europe and Southeastern Siberia, the second one centred on Eastern Asia and the third one in the Middle East. Approximate Bayesian computation (ABC) supported the hypothesis that C. bursa-pastoris underwent a typical colonization history involving low gene flow among colonizing populations, likely starting from the Middle East towards Europe and followed by successive human-mediated expansions into Eastern Asia. Altogether, these findings bring new insights into the recent multistage colonization history of the allotetraploid C. bursa-pastoris and highlight ABC and genotyping-by-sequencing data as promising but still challenging tools to infer demographic histories of selfing allopolyploids. PMID:26607306

  5. Phylogeny of a genomically diverse group of elymus (poaceae allopolyploids reveals multiple levels of reticulation.

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    Roberta J Mason-Gamer

    Full Text Available The grass tribe Triticeae (=Hordeeae comprises only about 300 species, but it is well known for the economically important crop plants wheat, barley, and rye. The group is also recognized as a fascinating example of evolutionary complexity, with a history shaped by numerous events of auto- and allopolyploidy and apparent introgression involving diploids and polyploids. The genus Elymus comprises a heterogeneous collection of allopolyploid genome combinations, all of which include at least one set of homoeologs, designated St, derived from Pseudoroegneria. The current analysis includes a geographically and genomically diverse collection of 21 tetraploid Elymus species, and a single hexaploid species. Diploid and polyploid relationships were estimated using four molecular data sets, including one that combines two regions of the chloroplast genome, and three from unlinked nuclear genes: phosphoenolpyruvate carboxylase, β-amylase, and granule-bound starch synthase I. Four gene trees were generated using maximum likelihood, and the phylogenetic placement of the polyploid sequences reveals extensive reticulation beyond allopolyploidy alone. The trees were interpreted with reference to numerous phenomena known to complicate allopolyploid phylogenies, and introgression was identified as a major factor in their history. The work illustrates the interpretation of complicated phylogenetic results through the sequential consideration of numerous possible explanations, and the results highlight the value of careful inspection of multiple independent molecular phylogenetic estimates, with particular focus on the differences among them.

  6. Analysis of gene expression in resynthesized Brassica napus Allopolyploids using arabidopsis 70mer oligo microarrays.

    Directory of Open Access Journals (Sweden)

    Robert T Gaeta

    Full Text Available BACKGROUND: Studies in resynthesized Brassica napus allopolyploids indicate that homoeologous chromosome exchanges in advanced generations (S(5ratio6 alter gene expression through the loss and doubling of homoeologous genes within the rearrangements. Rearrangements may also indirectly affect global gene expression if homoeologous copies of gene regulators within rearrangements have differential affects on the transcription of genes in networks. METHODOLOGY/PRINCIPAL FINDINGS: We utilized Arabidopsis 70mer oligonucleotide microarrays for exploring gene expression in three resynthesized B. napus lineages at the S(0ratio1 and S(5ratio6 generations as well as their diploid progenitors B. rapa and B. oleracea. Differential gene expression between the progenitors and additive (midparent expression in the allopolyploids were tested. The S(5ratio6 lines differed in the number of genetic rearrangements, allowing us to test if the number of genes displaying nonadditive expression was related to the number of rearrangements. Estimates using per-gene and common variance ANOVA models indicated that 6-15% of 26,107 genes were differentially expressed between the progenitors. Individual allopolyploids showed nonadditive expression for 1.6-32% of all genes. Less than 0.3% of genes displayed nonadditive expression in all S(0ratio1 lines and 0.1-0.2% were nonadditive among all S(5ratio6 lines. Differentially expressed genes in the polyploids were over-represented by genes differential between the progenitors. The total number of differentially expressed genes was correlated with the number of genetic changes in S(5ratio6 lines under the common variance model; however, there was no relationship using a per-gene variance model, and many genes showed nonadditive expression in S(0ratio1 lines. CONCLUSIONS/SIGNIFICANCE: Few genes reproducibly demonstrated nonadditive expression among lineages, suggesting few changes resulted from a general response to polyploidization

  7. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome.

    Science.gov (United States)

    Chalhoub, Boulos; Denoeud, France; Liu, Shengyi; Parkin, Isobel A P; Tang, Haibao; Wang, Xiyin; Chiquet, Julien; Belcram, Harry; Tong, Chaobo; Samans, Birgit; Corréa, Margot; Da Silva, Corinne; Just, Jérémy; Falentin, Cyril; Koh, Chu Shin; Le Clainche, Isabelle; Bernard, Maria; Bento, Pascal; Noel, Benjamin; Labadie, Karine; Alberti, Adriana; Charles, Mathieu; Arnaud, Dominique; Guo, Hui; Daviaud, Christian; Alamery, Salman; Jabbari, Kamel; Zhao, Meixia; Edger, Patrick P; Chelaifa, Houda; Tack, David; Lassalle, Gilles; Mestiri, Imen; Schnel, Nicolas; Le Paslier, Marie-Christine; Fan, Guangyi; Renault, Victor; Bayer, Philippe E; Golicz, Agnieszka A; Manoli, Sahana; Lee, Tae-Ho; Thi, Vinh Ha Dinh; Chalabi, Smahane; Hu, Qiong; Fan, Chuchuan; Tollenaere, Reece; Lu, Yunhai; Battail, Christophe; Shen, Jinxiong; Sidebottom, Christine H D; Wang, Xinfa; Canaguier, Aurélie; Chauveau, Aurélie; Bérard, Aurélie; Deniot, Gwenaëlle; Guan, Mei; Liu, Zhongsong; Sun, Fengming; Lim, Yong Pyo; Lyons, Eric; Town, Christopher D; Bancroft, Ian; Wang, Xiaowu; Meng, Jinling; Ma, Jianxin; Pires, J Chris; King, Graham J; Brunel, Dominique; Delourme, Régine; Renard, Michel; Aury, Jean-Marc; Adams, Keith L; Batley, Jacqueline; Snowdon, Rod J; Tost, Jorg; Edwards, David; Zhou, Yongming; Hua, Wei; Sharpe, Andrew G; Paterson, Andrew H; Guan, Chunyun; Wincker, Patrick

    2014-08-22

    Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement. PMID:25146293

  8. Independent, rapid and targeted loss of highly repetitive DNA in natural and synthetic allopolyploids of Nicotiana tabacum

    Czech Academy of Sciences Publication Activity Database

    Renny-Byfield, S.; Kovařík, Aleš; Chester, M.; Nichols, R.A.; Macas, Jiří; Novák, Petr; Leitch, A.R.

    2012-01-01

    Roč. 7, č. 5 (2012), e36963. E-ISSN 1932-6203 R&D Projects: GA ČR(CZ) GAP501/10/0208; GA MŠk OC10037 Institutional research plan: CEZ:AV0Z50040702; CEZ:AV0Z50510513 Keywords : chromosome evolution * repetitive DNA * allopolyploid Subject RIV: BO - Biophysics; EB - Genetics ; Molecular Biology (BC-A) Impact factor: 3.730, year: 2012

  9. Karyotyping and identifying all of the chromosomes of allopolyploid Brassica juncea using multicolor FISH

    Directory of Open Access Journals (Sweden)

    Zhijun Xu

    2016-08-01

    Full Text Available Chromosome identification and karyotype using fluorescence in situ hybridization (FISH provides a technical platform for genome and cytogenetic studies. Brassica juncea (brown mustard, 2n = 4 × = 36; genome AABB is an allopolyploid species that originated from a spontaneous hybridization of Brassica rapa and Brassica nigra and contains many valuable traits. In this study, a multicolor FISH procedure allowing the identification of all 18 chromosomal pairs was developed by two-step hybridizations with probes on the same metaphase chromosomes. The distribution patterns and chromosomal localizations of six repeat sequences (satellite repeat pBrSTR, 5S rDNA, 45S rDNA, B genome-specific repeat pBNBH35, and centromeric satellite repeats CentBr1 and CentBr2 on B. juncea chromosomes were characterized. Comparative karyotype analyses showed that the genome is relatively stable in comparison with its diploid progenitor species and revealed intraspecific karyotypic diversity among three accessions of B. juncea. This study provides valuable information about the genome evolution of B. juncea and a toolkit that will be helpful for chromosome identification.

  10. Au Elements and Their Evolution in Some Allopolyploid Genomes of Aegilops

    Institute of Scientific and Technical Information of China (English)

    GONG Han-yu; WANG Jian-bo

    2006-01-01

    To study the sequences of short interspersed nuclear elements (SINEs) evolution in some allopolyploid genomes of Aegilops, 108 Au element fragments (a novel kind of plant SINE) were amplified and sequenced in 10 species of Aegilops,which were clustered into three different groups (A, B and C) based on their related genome types. The sequences of these Au element fragments were heterogonous in di-, tetra-, and hexa-ploids, and the dendrograms of Au element obtained from phylogenetic analysis were very complex in each group and could be clustered into 15, 15 and 22 families,respectively. In this study, three rules about Au elements evolution have been drawn from the results: i. Most families were composed of Au element members with different host species in three groups; ii. Family 1-6 in Group A, Family 1-6 in Group B, Family 1-4 and Family 6-13 in Group C contained only one, apparently highly degenerate Au element member (a single representative element); iii. Elements generally fell into clades that were species-specific with respect to their host species. The potential mechanisms of Au element evolution in Aegilops were discussed.

  11. Genetic architecture of adaptation to novel environmental conditions in a predominantly selfing allopolyploid plant.

    Science.gov (United States)

    Volis, S; Ormanbekova, D; Yermekbayev, K; Abugalieva, S; Turuspekov, Y; Shulgina, I

    2016-06-01

    Genetic architecture of adaptation is traditionally studied in the context of local adaptation, viz. spatially varying conditions experienced by the species. However, anthropogenic changes in the natural environment pose a new context to this issue, that is, adaptation to an environment that is new for the species. In this study, we used crossbreeding to analyze genetic architecture of adaptation to conditions not currently experienced by the species but with high probability of encounter in the near future due to global climate change. We performed targeted interpopulation crossing using genotypes from two core and two peripheral Triticum dicoccoides populations and raised the parents and three generations of hybrids in a greenhouse under simulated desert conditions to analyze the genetic architecture of adaptation to these conditions and an effect of gene flow from plants having different origin. The hybrid (F1) fitness did not differ from that of the parents in crosses where both plants originated from the species core, but in crosses involving one parent from the species core and another one from the species periphery the fitness of F1 was consistently higher than that of the periphery-originated parent. Plant fitness in the next two generations (F2 and F3) did not differ from the F1, suggesting that effects of epistatic interactions between recombining and segregating alleles of genes contributing to fitness were minor or absent. The observed low importance of epistatic gene interactions in allopolyploid T. dicoccoides and low probability of hybrid breakdown appear to be the result of permanent fixation of heterozygosity and lack of intergenomic recombination in this species. At the same time, predominant but not complete selfing combined with an advantage of bivalent pairing of homologous chromosomes appears to maintain high genetic variability in T. dicoccoides, greatly enhancing its adaptive ability. PMID:26837272

  12. Genetic and Epigenetic Changes in Oilseed Rape (Brassica napus L.) Extracted from Intergeneric Allopolyploid and Additions with Orychophragmus.

    Science.gov (United States)

    Gautam, Mayank; Dang, Yanwei; Ge, Xianhong; Shao, Yujiao; Li, Zaiyun

    2016-01-01

    Allopolyploidization with the merger of the genomes from different species has been shown to be associated with genetic and epigenetic changes. But the maintenance of such alterations related to one parental species after the genome is extracted from the allopolyploid remains to be detected. In this study, the genome of Brassica napus L. (2n = 38, genomes AACC) was extracted from its intergeneric allohexaploid (2n = 62, genomes AACCOO) with another crucifer Orychophragmus violaceus (2n = 24, genome OO), by backcrossing and development of alien addition lines. B. napus-type plants identified in the self-pollinated progenies of nine monosomic additions were analyzed by the methods of amplified fragment length polymorphism, sequence-specific amplified polymorphism, and methylation-sensitive amplified polymorphism. They showed modifications to certain extents in genomic components (loss and gain of DNA segments and transposons, introgression of alien DNA segments) and DNA methylation, compared with B. napus donor. The significant differences in the changes between the B. napus types extracted from these additions likely resulted from the different effects of individual alien chromosomes. Particularly, the additions which harbored the O. violaceus chromosome carrying dominant rRNA genes over those of B. napus tended to result in the development of plants which showed fewer changes, suggesting a role of the expression levels of alien rRNA genes in genomic stability. These results provided new cues for the genetic alterations in one parental genome that are maintained even after the genome becomes independent. PMID:27148282

  13. Genetic and epigenetic changes in oilseed rape (Brassica napus L. extracted from intergeneric allopolyploid and additions with Orychophragmus

    Directory of Open Access Journals (Sweden)

    Mayank eGautam

    2016-04-01

    Full Text Available ABSTRACT Allopolyploidization with the merger of the genomes from different species has been shown to be associated with genetic and epigenetic changes. But the maintenance of such alterations related to one parental species after the genome is extracted from the allopolyploid remains to be detected. In this study, the genome of Brassica napus L. (2n=38, genomes AACC was extracted from its intergeneric allohexaploid (2n=62, genomes AACCOO with another crucifer Orychophragmus violaceus (2n=24, genome OO, by backcrossing and development of alien addition lines. B. napus-type plants identified in the self-pollinated progenies of nine monosomic additions were analyzed by the methods of amplified fragment length polymorphism (AFLP, sequence-specific amplified polymorphism (SSAP, and methylation-sensitive amplified polymorphism (MSAP. They showed modifications to certain extents in genomic components (loss and gain of DNA segments and transposons, introgression of alien DNA segments and DNA methylation, compared with B. napus donor. The significant differences in the changes between the B. napus types extracted from these additions likely resulted from the different effects of individual alien chromosomes. Particularly, the additions which harbored the O. violaceus chromosome carrying dominant rRNA genes over those of B. napus tended to result in the development of plants which showed fewer changes, suggesting a role of the expression levels of alien rRNA genes in genomic stability. These results provided new cues for the genetic alterations in one parental genome that are maintained even after the genome becomes independent.

  14. Genetic and Epigenetic Changes in Oilseed Rape (Brassica napus L.) Extracted from Intergeneric Allopolyploid and Additions with Orychophragmus

    Science.gov (United States)

    Gautam, Mayank; Dang, Yanwei; Ge, Xianhong; Shao, Yujiao; Li, Zaiyun

    2016-01-01

    Allopolyploidization with the merger of the genomes from different species has been shown to be associated with genetic and epigenetic changes. But the maintenance of such alterations related to one parental species after the genome is extracted from the allopolyploid remains to be detected. In this study, the genome of Brassica napus L. (2n = 38, genomes AACC) was extracted from its intergeneric allohexaploid (2n = 62, genomes AACCOO) with another crucifer Orychophragmus violaceus (2n = 24, genome OO), by backcrossing and development of alien addition lines. B. napus-type plants identified in the self-pollinated progenies of nine monosomic additions were analyzed by the methods of amplified fragment length polymorphism, sequence-specific amplified polymorphism, and methylation-sensitive amplified polymorphism. They showed modifications to certain extents in genomic components (loss and gain of DNA segments and transposons, introgression of alien DNA segments) and DNA methylation, compared with B. napus donor. The significant differences in the changes between the B. napus types extracted from these additions likely resulted from the different effects of individual alien chromosomes. Particularly, the additions which harbored the O. violaceus chromosome carrying dominant rRNA genes over those of B. napus tended to result in the development of plants which showed fewer changes, suggesting a role of the expression levels of alien rRNA genes in genomic stability. These results provided new cues for the genetic alterations in one parental genome that are maintained even after the genome becomes independent. PMID:27148282

  15. Ploidy mosaicism and allele-specific gene expression differences in the allopolyploid Squalius alburnoides

    Directory of Open Access Journals (Sweden)

    Matos Isa

    2011-12-01

    Full Text Available Abstract Background Squalius alburnoides is an Iberian cyprinid fish resulting from an interspecific hybridisation between Squalius pyrenaicus females (P genome and males of an unknown Anaecypris hispanica-like species (A genome. S. alburnoides is an allopolyploid hybridogenetic complex, which makes it a likely candidate for ploidy mosaicism occurrence, and is also an interesting model to address questions about gene expression regulation and genomic interactions. Indeed, it was previously suggested that in S. alburnoides triploids (PAA composition silencing of one of the three alleles (mainly of the P allele occurs. However, not a whole haplome is inactivated but a more or less random inactivation of alleles varying between individuals and even between organs of the same fish was seen. In this work we intended to correlate expression differences between individuals and/or between organs to the occurrence of mosaicism, evaluating if mosaics could explain previous observations and its impact on the assessment of gene expression patterns. Results To achieve our goal, we developed flow cytometry and cell sorting protocols for this system generating more homogenous cellular and transcriptional samples. With this set-up we detected 10% ploidy mosaicism within the S. alburnoides complex, and determined the allelic expression profiles of ubiquitously expressed genes (rpl8; gapdh and β-actin in cells from liver and kidney of mosaic and non-mosaic individuals coming from different rivers over a wide geographic range. Conclusions Ploidy mosaicism occurs sporadically within the S. alburnoides complex, but in a frequency significantly higher than reported for other organisms. Moreover, we could exclude the influence of this phenomenon on the detection of variable allelic expression profiles of ubiquitously expressed genes (rpl8; gapdh and β-actin in cells from liver and kidney of triploid individuals. Finally, we determined that the expression patterns

  16. Capturing sequence variation among flowering-time regulatory gene homologs in the allopolyploid crop species Brassica napus.

    Science.gov (United States)

    Schiessl, Sarah; Samans, Birgit; Hüttel, Bruno; Reinhard, Richard; Snowdon, Rod J

    2014-01-01

    Flowering, the transition from the vegetative to the generative phase, is a decisive time point in the lifecycle of a plant. Flowering is controlled by a complex network of transcription factors, photoreceptors, enzymes and miRNAs. In recent years, several studies gave rise to the hypothesis that this network is also strongly involved in the regulation of other important lifecycle processes ranging from germination and seed development through to fundamental developmental and yield-related traits. In the allopolyploid crop species Brassica napus, (genome AACC), homoeologous copies of flowering time regulatory genes are implicated in major phenological variation within the species, however the extent and control of intraspecific and intergenomic variation among flowering-time regulators is still unclear. To investigate differences among B. napus morphotypes in relation to flowering-time gene variation, we performed targeted deep sequencing of 29 regulatory flowering-time genes in four genetically and phenologically diverse B. napus accessions. The genotype panel included a winter-type oilseed rape, a winter fodder rape, a spring-type oilseed rape (all B. napus ssp. napus) and a swede (B. napus ssp. napobrassica), which show extreme differences in winter-hardiness, vernalization requirement and flowering behavior. A broad range of genetic variation was detected in the targeted genes for the different morphotypes, including non-synonymous SNPs, copy number variation and presence-absence variation. The results suggest that this broad variation in vernalization, clock and signaling genes could be a key driver of morphological differentiation for flowering-related traits in this recent allopolyploid crop species. PMID:25202314

  17. Capturing sequence variation among flowering-time regulatory gene homologues in the allopolyploid crop species Brassica napus

    Directory of Open Access Journals (Sweden)

    Sarah eSchiessl

    2014-08-01

    Full Text Available Flowering, the transition from the vegetative to the generative phase, is a decisive time point in the lifecycle of a plant. Flowering is controlled by a complex network of transcription factors, photoreceptors, enzymes and miRNAs. In recent years, several studies gave rise to the hypothesis that this network is also strongly involved in the regulation of other important lifecycle processes ranging from germination and seed development through to fundamental developmental and yield-related traits. In the allopolyploid crop species Brassica napus, (genome AACC, homoeologous copies of flowering time regulatory genes are implicated in major phenological variation within the species, however the extent and control of intraspecific and intergenomic variation among flowering-time regulators is still unclear. To investigate differences among B. napus morphotypes in relation to flowering-time gene variation, we performed targeted deep sequencing of 29 regulatory flowering-time genes in four genetically and phenologically diverse B. napus accessions. The genotype panel included a winter-type oilseed rape, a winter fodder rape, a spring-type oilseed rape (all B. napus ssp. napus and a swede (B. napus ssp. napobrassica, which show extreme differences in winter-hardiness, vernalization requirement and flowering behaviour. A broad range of genetic variation was detected in the targeted genes for the different morphotypes, including non-synonymous SNPs, copy number variation and presence-absence variation. The results suggest that this broad variation in vernalisation, clock and signaling genes could be a key driver of morphological differentiation for flowering-related traits in this recent allopolyploid crop species.

  18. Genetic basis for spontaneous hybrid genome doubling during allopolyploid speciation of common wheat shown by natural variation analyses of the paternal species.

    Directory of Open Access Journals (Sweden)

    Yoshihiro Matsuoka

    Full Text Available The complex process of allopolyploid speciation includes various mechanisms ranging from species crosses and hybrid genome doubling to genome alterations and the establishment of new allopolyploids as persisting natural entities. Currently, little is known about the genetic mechanisms that underlie hybrid genome doubling, despite the fact that natural allopolyploid formation is highly dependent on this phenomenon. We examined the genetic basis for the spontaneous genome doubling of triploid F1 hybrids between the direct ancestors of allohexaploid common wheat (Triticum aestivum L., AABBDD genome, namely Triticumturgidum L. (AABB genome and Aegilopstauschii Coss. (DD genome. An Ae. tauschii intraspecific lineage that is closely related to the D genome of common wheat was identified by population-based analysis. Two representative accessions, one that produces a high-genome-doubling-frequency hybrid when crossed with a T. turgidum cultivar and the other that produces a low-genome-doubling-frequency hybrid with the same cultivar, were chosen from that lineage for further analyses. A series of investigations including fertility analysis, immunostaining, and quantitative trait locus (QTL analysis showed that (1 production of functional unreduced gametes through nonreductional meiosis is an early step key to successful hybrid genome doubling, (2 first division restitution is one of the cytological mechanisms that cause meiotic nonreduction during the production of functional male unreduced gametes, and (3 six QTLs in the Ae. tauschii genome, most of which likely regulate nonreductional meiosis and its subsequent gamete production processes, are involved in hybrid genome doubling. Interlineage comparisons of Ae. tauschii's ability to cause hybrid genome doubling suggested an evolutionary model for the natural variation pattern of the trait in which non-deleterious mutations in six QTLs may have important roles. The findings of this study demonstrated

  19. Natural selection and neutral evolution jointly drive population divergence between alpine and lowland ecotypes of the allopolyploid plant Anemone multifida (Ranunculaceae.

    Directory of Open Access Journals (Sweden)

    Jamie R McEwen

    Full Text Available Population differentiation can be driven in large part by natural selection, but selectively neutral evolution can play a prominent role in shaping patters of population divergence. The decomposition of the evolutionary history of populations into the relative effects of natural selection and selectively neutral evolution enables an understanding of the causes of population divergence and adaptation. In this study, we examined heterogeneous genomic divergence between alpine and lowland ecotypes of the allopolyploid plant, Anemone multifida. Using peak height and dominant AFLP data, we quantified population differentiation at non-outlier (neutral and outlier loci to determine the potential contribution of natural selection and selectively neutral evolution to population divergence. We found 13 candidate loci, corresponding to 2.7% of loci, with signatures of divergent natural selection between alpine and lowland populations and between alpine populations (Fst  = 0.074-0.445 at outlier loci, but neutral population differentiation was also evident between alpine populations (FST  = 0.041-0.095 at neutral loci. By examining population structure at both neutral and outlier loci, we determined that the combined effects of selection and neutral evolution are associated with the divergence of alpine populations, which may be linked to extreme abiotic conditions and isolation between alpine sites. The presence of outlier levels of genetic variation in structured populations underscores the importance of separately analyzing neutral and outlier loci to infer the relative role of divergent natural selection and neutral evolution in population divergence.

  20. A rare case of a natural contact zone in Morocco between an autopolyploid and an allopolyploid of Centaurea aspera with sterile tetraploid hybrids.

    Science.gov (United States)

    Garmendia, A; Ferriol, M; Juarez, J; Zając, A; Kałużny, K; Merle, H

    2015-05-01

    A new contact zone between Centaurea aspera and Centaurea seridis was found in Morocco. Chromosome counts and flow cytometry showed that both taxa were tetraploid (4x = 44). A literature review and morphometric analysis established that C. aspera corresponds to the autopolyploid C. aspera subsp. gentilii and C. seridis corresponds to the allopolyploid C. seridis var. auriculata. This contact area was compared with the homologous contact zones in Spain formed by the diploid C. aspera subsp. stenophylla and the tetraploid C. seridis subsp. maritima. Natural hybrids between parental species were frequent in both areas. In Spain, hybrids were triploid (from reduced gametes A and gamete AB), highly sterile and exerted a 'triploid block'. In Morocco, cytometry showed that hybrids were tetraploid and, therefore, probably fertile, but all the capitula lacked achenes. It is likely that the resulting genome of the new tetraploid hybrid (AAAB), through the fusion of reduced gametes AA (from subsp. gentilii) and AB (from var. auriculata), could explain irregularities in meiosis through formation of aneuploid gametes and, therefore, infertility of the hybrid. Moroccan sterile tetraploid hybrids develop, but have the identical irregularities to Spanish triploids, probably due to the odd number of homologous chromosomes. The new hybrid is first described as C. x subdecurrens nothosubsp. paucispinus. In addition, distribution and ecological traits are analysed. PMID:25363815

  1. Evolution of allopolyploids in the genus Nicotiana

    Czech Academy of Sciences Publication Activity Database

    Leitch, A.; Lim, K.Y.; Kovařík, Aleš; Matyášek, Roman; Skalická, Kamila; Chase, M.W.; Clarkson, J.J.; Leitch, I.; Knapp, S.; Grandbastien, M.-A.

    Clermont-Ferrand, 2007. s. 1-1. [Réunion du Groupe de travail Cytogénétique & Polyploidie du DGAP. 18.04.2007-20.04.2007, Clermont-Ferrand] R&D Projects: GA ČR(CZ) GA521/07/0116; GA ČR(CZ) GA204/05/0687 Institutional research plan: CEZ:AV0Z50040507 Keywords : allopolyploidy * genome * evolution Subject RIV: BO - Biophysics

  2. Rapid chromosome evolution in recently formed polyploids in Tragopogon (Asteraceae)

    Czech Academy of Sciences Publication Activity Database

    Lim, K.Y.; Soltis, D.E.; Soltis, P.S.; Tate, J.; Matyášek, Roman; Šrubařová, Hana; Kovařík, Aleš; Pires, J.Ch.; Xiong, Z.; Leitch, A.R.

    2008-01-01

    Roč. 3, č. 10 (2008), s. 1-13. E-ISSN 1932-6203 R&D Projects: GA ČR(CZ) GA521/07/0116 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : allopolyploidy * chromosome s * evolution Subject RIV: BO - Biophysics

  3. Recent and recurrent polyploidy in Tragopogon (Asteraceae): cytogenetic, genomic and genetic comparisons

    Czech Academy of Sciences Publication Activity Database

    Soltis, D. E.; Soltis, P. S.; Pires, J. C.; Kovařík, Aleš; Tate, J. A.; Mavrodiev, E.

    2004-01-01

    Roč. 82, č. 4 (2004), s. 485-501. ISSN 0024-4066 R&D Projects: GA ČR GA204/01/0313; GA ČR GA521/01/0037 Grant ostatní: NSF/NATO Postgradual Fellowship(US) DGE-0000658; National Science Foundation(US) DEB-0083659; National Science Foundation(US) MCB-0346591; National Science Foundation(US) MCB-034659 Institutional research plan: CEZ:AV0Z5004920 Keywords : concerted evolution * gene expression * molecular cytogenetics Subject RIV: BO - Biophysics Impact factor: 1.935, year: 2004

  4. Similar patterns of rDNA evolution in synthetic and recently formed natural populations of Tragopogon (Asteraceae) allotetraploids

    Czech Academy of Sciences Publication Activity Database

    Malinská, Hana; Tate, J.A.; Matyášek, Roman; Leitch, A.R.; Soltis, D.E.; Soltis, P.S.; Kovařík, Aleš

    2010-01-01

    Roč. 10, č. 291 (2010), s. 1-17. ISSN 1471-2148 R&D Projects: GA ČR(CZ) GA206/09/1751; GA ČR(CZ) GD204/09/H002 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : polyploidy * nucleolar dominance * homogenization Subject RIV: BO - Biophysics Impact factor: 3.702, year: 2010

  5. Tragopogon porrifolius x T. pratensis: the present state of an old hybrid population in Central Bohemia, the Czech Republic

    Czech Academy of Sciences Publication Activity Database

    Krahulec, František; Kaplan, Zdeněk; Novák, J.

    2005-01-01

    Roč. 77, - (2005), s. 297-306. ISSN 0032-7786 R&D Projects: GA ČR(CZ) GA206/02/0582 Institutional research plan: CEZ:AV0Z60050516 Keywords : chromosome numbers * DNA content * distribution Subject RIV: EF - Botanics Impact factor: 1.545, year: 2005

  6. Identification, evolution, and expression partitioning of miRNAs in allopolyploid Brassica napus.

    Science.gov (United States)

    Shen, Enhui; Zou, Jun; Hubertus Behrens, Falk; Chen, Li; Ye, Chuyu; Dai, Shutao; Li, Ruiyan; Ni, Meng; Jiang, Xiaoxue; Qiu, Jie; Liu, Yang; Wang, Weidi; Zhu, Qian-Hao; Chalhoub, Boulos; Bancroft, Ian; Meng, Jinling; Cai, Daguang; Fan, Longjiang

    2015-12-01

    The recently published genome of Brassica napus offers for the first time the opportunity to gain insights into the genomic organization and the evolution of miRNAs in oilseed rape. In this study, 12 small RNA libraries from two B. napus cultivars (Tapidor and Ningyou7) and their four double-haploid lines were sequenced, employing the newly sequenced B. napus genome, together with genomes of its progenitors Brassica rapa and Brassica oleracea. A total of 645 miRNAs including 280 conserved and 365 novel miRNAs were identified. Comparative analysis revealed a high level of genomic conservation of MIRNAs (75.9%) between the subgenomes of B. napus and its two progenitors' genomes, and MIRNA lost/gain events (133) occurred in B. napus after its speciation. Furthermore, significant partitioning of miRNA expressions between the two subgenomes in B. napus was detected. The data of degradome sequencing, miRNA-mediated cleavage, and expression analyses support specific interactions between miRNAs and their targets in the modulation of diverse physiological processes in roots and leaves, as well as in biosynthesis of, for example, glucosinolates and lipids in oilseed rape. These data provide a first genome-wide view on the origin, evolution, and genomic organization of B. napus MIRNAs. PMID:26357884

  7. Fall and rise of satellite repeats in allopolyploids of Nicotiana over c. 5 million years

    Czech Academy of Sciences Publication Activity Database

    Koukalová, Blažena; Moraes, A.P.; Renny-Byfield, S.; Matyášek, Roman; Leitch, A.R.; Kovařík, Aleš

    2010-01-01

    Roč. 186, č. 1 (2010), s. 148-160. ISSN 0028-646X R&D Projects: GA ČR(CZ) GA521/07/0116 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : concerted evolution * interlocus homogenization * Nicotiana Subject RIV: BO - Biophysics Impact factor: 6.516, year: 2010

  8. Chalcone Synthase Gene Lineage Diversification confirms allopolyploid evolutionary relationships of European Rostrate Violets

    NARCIS (Netherlands)

    Hof, van den K.; Berg, van den R.G.; Gravendeel, B.

    2008-01-01

    Phylogenetic relationships among and within the subsections of the genus Viola are still far from resolved. We present the first organismal phylogeny of predominantly western European species of subsection Rostratae based on the plastid trnS¿trnG intron and intergenic spacer and the nuclear low-copy

  9. Possible genetic consequences of epigenetic interactions between ribosomal RNA loci in Nicotiana allopolyploids

    Czech Academy of Sciences Publication Activity Database

    Kovařík, Aleš; Nešpor Dadejová, Martina; Lim, K.Y.; Součková Skalická, Kamila; Matyášek, Roman; Grandbastien, M.-A.; Leitch, A.

    Clermont-Ferrand, 2007. s. 1-1. [Réunion du Groupe de travail Cytogénétique & Polyploidie du DGAP. 18.04.2007-20.04.2007, Clermont-Ferrand] R&D Projects: GA ČR(CZ) GA521/07/0116; GA ČR(CZ) GA204/05/0687 Institutional research plan: CEZ:AV0Z50040507 Keywords : allopolyploidy * epigenetic silencing * ribosomal RNA gene Subject RIV: BO - Biophysics

  10. Nuclear cytoplasmic interaction hypothesis and the role of translocations in Nicotiana allopolyploids

    Czech Academy of Sciences Publication Activity Database

    Leitch, A.R.; Lim, K.Y.; Skalická, Kamila; Kovařík, Aleš

    Springer, 2006 - (Cigna, A.; Durante, M.), s. 319-326 ISBN 978-1-4020-4647-6 Institutional research plan: CEZ:AV0Z50040507 Keywords : genome evolution * allopolyploidy * nucleocytoplasmic interaction Subject RIV: BO - Biophysics

  11. Recent natural hybridization between two allopolyploid wheatgrasses (Elytrigia, Poaceae): Ecological and evolutionary implications

    Czech Academy of Sciences Publication Activity Database

    Mahelka, Václav; Fehrer, Judith; Krahulec, František; Jarolímová, Vlasta

    2007-01-01

    Roč. 100, - (2007), s. 249-260. ISSN 0305-7364 R&D Projects: GA ČR GA206/05/0778; GA ČR(CZ) GD206/03/H137 Institutional research plan: CEZ:AV0Z60050516 Keywords : Triticeae * polyploidy * gene flow Subject RIV: EF - Botanics Impact factor: 2.939, year: 2007

  12. Silenced rRNA genes are activated and substitute for partially eliminated active homeologs in the recently formed allotetraploid, Tragopogon mirus (Asteraceae)

    Czech Academy of Sciences Publication Activity Database

    Dobešová, Eva; Malinská, Hana; Matyášek, Roman; Leitch, A. R.; Soltis, D. E.; Kovařík, Aleš

    2015-01-01

    Roč. 114, č. 3 (2015), s. 356-365. ISSN 0018-067X R&D Projects: GA ČR(CZ) GA14-34632S; GA ČR(CZ) GA13-10057S Institutional support: RVO:68081707 Keywords : NUCLEOLAR DOMINANCE * POLYPLOID PLANTS * POLYPLOID PLANTS Subject RIV: BO - Biophysics Impact factor: 3.805, year: 2014

  13. Morphological Convergence Between an Allopolyploid and One of its Parental Species Correlates with Biased Gene Expression and DNA Loss.

    Science.gov (United States)

    Alexander-Webber, Douglas; Abbott, Richard J; Chapman, Mark A

    2016-09-01

    The contribution of gene expression modulation to phenotypic evolution is of major importance to an understanding of the origin of divergent or convergent phenotypes during and following polyploid speciation. Here, we analyzed genome-wide gene expression in 2 subspecies of the allotetraploid species, Senecio mohavensis A. Gray, and its diploid parents S. flavus (Decne.) Sch. Bip. and S. glaucus L. The tetraploid is morphologically much more similar to S. flavus, leading to earlier confusion over its taxonomic status. By means of an analysis of transcriptomes of all 3 species, we show that gene expression divergence between the parent species is relatively low (ca. 14% of loci), whereas there is significant unequal expression between ca. 20-25% of the parental homoeologues (gene copies) in the tetraploid. The majority of the expression bias in the tetraploid is in favor of S. flavus homoeologues (ca. 65% of the differentially expressed loci), and overall expression of this parental species subgenome is higher than that of the S. glaucus subgenome. To determine whether absence of expression of a particular S. glaucus homoeologue in the allotetraploid could be due to loss of DNA, we carried out a PCR-based assay and confirmed that in 3 out of 10 loci the S. glaucus homoeologue appeared absent. Our results suggest that biased gene expression is one cause of the allotetraploid S. mohavensis being more similar in morphology to one of its parent, S. flavus, and that such bias could result, in part, from loss of S. glaucus homoeologues at some loci in the allotetraploid. PMID:27217580

  14. Inheritance of Protein Patterns in a Synthetic Allopolyploid of Triticum Monococcum (AA) and Aegilops Ventricosa (DDMvMv)

    DEFF Research Database (Denmark)

    Siddiqui, K. A.; Ingversen, J.; Køie, B.

    1972-01-01

    the main reserve-protein group — the gliadins, with a concomitant decrease in the salt-soluble proteins and the glutenins. Also the amino-acid composition, especially of the gliadins, was influenced by the amphiploidy. The gliadins from T. monococcum had higher contents of histidine, arginine...... species in the amphiploid. Similarities in the protein patterns of T. monococcum and Ae. ventricosa provided further evidence of homoeoallelism in the A, D, and MV genomes. In most instances, however, the amphiploid represented additiveness of the parental proteins, especially with regard to the gliadins....

  15. When fathers are instant losers: homogenization of rDNA loci in recently formed Cardamine X schulzii trigenomic allopolyploid

    Czech Academy of Sciences Publication Activity Database

    Zozomová-Lihová, J.; Mandáková, T.; Kovaříková, Alena; Muehlhausen, A.; Mummenhoff, K.; Lysák, M. A.; Kovařík, Aleš

    2014-01-01

    Roč. 203, č. 4 (2014), s. 1096-1108. ISSN 0028-646X R&D Projects: GA ČR(CZ) GBP501/12/G090 Institutional support: RVO:68081707 Keywords : Brassicaceae * concerted evolution * hybridization Subject RIV: BO - Biophysics Impact factor: 7.672, year: 2014

  16. Sequencing chromosome 5D of Aegilops tauschii and comparison with its allopolyploid descendant bread wheat (Triticum aestivum)

    Czech Academy of Sciences Publication Activity Database

    Akpinar, B. A.; Lucas, S. J.; Vrána, Jan; Doležel, Jaroslav; Budak, H.

    2015-01-01

    Roč. 13, č. 6 (2015), s. 740-752. ISSN 1467-7644 R&D Projects: GA ČR GBP501/12/G090; GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : D genome donor of wheat * chromosome 5D * comparative genomics Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.752, year: 2014

  17. Diploidization and genome size change in allopolyploids is associated with differential dynamics of low- and high-copy sequences

    Czech Academy of Sciences Publication Activity Database

    Renny-Byfield, S.; Kovařík, Aleš; Kelly, L.J.; Macas, Jiří; Novák, Petr; Chase, M.W. (ed.); Nichols, R. A.; Pancholi, M. R.; Grandbastien, M.-A.; Leitch, Andrew R.

    2013-01-01

    Roč. 74, č. 5 (2013), s. 829-839. ISSN 0960-7412 R&D Projects: GA ČR GA13-10057S; GA ČR(CZ) GBP501/12/G090 Institutional support: RVO:68081707 ; RVO:60077344 Keywords : ALLOTETRAPLOID TOBACCO * NICOTIANA SOLANACEAE * SEED PLANTS Subject RIV: BO - Biophysics; EB - Genetics ; Molecular Biology (BC-A) Impact factor: 6.815, year: 2013

  18. Development of genome-specific primers for homoeologous genes in allopolyploid species: the waxy and starch synthase II genes in allohexaploid wheat (Triticum aestivum L. as examples

    Directory of Open Access Journals (Sweden)

    Brûlé-Babel Anita

    2010-05-01

    Full Text Available Abstract Background In allopolypoid crops, homoeologous genes in different genomes exhibit a very high sequence similarity, especially in the coding regions of genes. This makes it difficult to design genome-specific primers to amplify individual genes from different genomes. Development of genome-specific primers for agronomically important genes in allopolypoid crops is very important and useful not only for the study of sequence diversity and association mapping of genes in natural populations, but also for the development of gene-based functional markers for marker-assisted breeding. Here we report on a useful approach for the development of genome-specific primers in allohexaploid wheat. Findings In the present study, three genome-specific primer sets for the waxy (Wx genes and four genome-specific primer sets for the starch synthase II (SSII genes were developed mainly from single nucleotide polymorphisms (SNPs and/or insertions or deletions (Indels in introns and intron-exon junctions. The size of a single PCR product ranged from 750 bp to 1657 bp. The total length of amplified PCR products by these genome-specific primer sets accounted for 72.6%-87.0% of the Wx genes and 59.5%-61.6% of the SSII genes. Five genome-specific primer sets for the Wx genes (one for Wx-7A, three for Wx-4A and one for Wx-7D could distinguish the wild type wheat and partial waxy wheat lines. These genome-specific primer sets for the Wx and SSII genes produced amplifications in hexaploid wheat, cultivated durum wheat, and Aegilops tauschii accessions, but failed to generate amplification in the majority of wild diploid and tetraploid accessions. Conclusions For the first time, we report on the development of genome-specific primers from three homoeologous Wx and SSII genes covering the majority of the genes in allohexaploid wheat. These genome-specific primers are being used for the study of sequence diversity and association mapping of the three homoeologous Wx and SSII genes in natural populations of both hexaploid wheat and cultivated tetraploid wheat. The strategies used in this paper can be used to develop genome-specific primers for homoeologous genes in any allopolypoid species. They may be also suitable for (i the development of gene-specific primers for duplicated paralogous genes in any diploid species, and (ii the development of allele-specific primers at the same gene locus.

  19. Standard Metabolic Rate (SMR) is inversely related to erythrocyte and genome size in allopolyploid fish of the Cobitis taenia hybrid complex

    Czech Academy of Sciences Publication Activity Database

    Maciak, S.; Janko, Karel; Kotusz, J.; Choleva, Lukáš; Boron, A.; Juchno, D.; Kujawa, R.; Kozlowski, J.; Konarzewski, M.

    2011-01-01

    Roč. 25, č. 5 (2011), s. 1072-1078. ISSN 0269-8463 R&D Projects: GA AV ČR KJB600450902; GA ČR GA206/09/1298 Institutional research plan: CEZ:AV0Z50450515 Keywords : CELL-SIZE * C-VALUE * PASSERINE BIRDS Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.567, year: 2011

  20. Využití kvantitativní PCR při studiu exprese homeologních rRNA genů u allotetraploidních druhů rodu Tragopogon

    Czech Academy of Sciences Publication Activity Database

    Matyášek, Roman

    Lyon, 2006 - (Nátr, L.). s. 78-78 ISSN 1213-6670. [4. Metodické dny. 01.10.2006-04.10.2006, Srní] R&D Projects: GA ČR(CZ) GA204/05/0687 Institutional research plan: CEZ:AV0Z50040507 Keywords : ITS1 * bidirectional rDNA silencing Subject RIV: BO - Biophysics

  1. Multiple Mechanisms and Challenges for the Application of Allopolyploidy in Plants

    Directory of Open Access Journals (Sweden)

    Ryo Fujimoto

    2012-07-01

    Full Text Available An allopolyploid is an individual having two or more complete sets of chromosomes derived from different species. Generation of allopolyploids might be rare because of the need to overcome limitations such as co-existing populations of parental lines, overcoming hybrid incompatibility, gametic non-reduction, and the requirement for chromosome doubling. However, allopolyploids are widely observed among plant species, so allopolyploids have succeeded in overcoming these limitations and may have a selective advantage. As techniques for making allopolyploids are developed, we can compare transcription, genome organization, and epigenetic modifications between synthesized allopolyploids and their direct parental lines or between several generations of allopolyploids. It has been suggested that divergence of transcription caused either genetically or epigenetically, which can contribute to plant phenotype, is important for the adaptation of allopolyploids.

  2. Instability of chromosome number and DNA methylation variation induced by hybridization and amphidiploid formation between Raphanus sativus L. and Brassica alboglabra Bailey

    OpenAIRE

    Wang Yanjie; Wei Lihua; Chen Honggao; Li Xiangsong; Wang Bing; Guo Weiwei; Li Xuanli; Wu Jiangsheng; Long Hong

    2010-01-01

    Abstract Background Distant hybridization can result genome duplication and allopolyploid formation which may play a significant role in the origin and evolution of many plant species. It is unclear how the two or more divergent genomes coordinate in one nucleus with a single parental cytoplasm within allopolyploids. We used cytological and molecular methods to investigate the genetic and epigenetic instabilities associated with the process of distant hybridization and allopolyploid formation...

  3. Microsatellite Mutation Rate during Allohexaploidization of Newly Resynthesized Wheat

    OpenAIRE

    Huaigang Zhang; Yang Yen; Dengcai Liu; Youliang Zheng; Jixiang Chen; Lianquan Zhang; Zhongwei Yuan; Zehong Yan; Li Zhang; Ming Hao; Jiangtao Luo

    2012-01-01

    Simple sequence repeats (SSRs, also known as microsatellites) are known to be mutational hotspots in genomes. DNA rearrangements have also been reported to accompany allopolyploidization. A study of the effect of allopolyploidization on SSR mutation is therefore important for understanding the origin and evolutionary dynamics of SSRs in allopolyploids. Three synthesized double haploid (SynDH) populations were made from 241 interspecific F1 haploid hybrids between Triticum turgidum L. and Aegi...

  4. Genomes Behave as Social Entities: Alien Chromatin Minorities Evolve Through Specificities Reduction

    Science.gov (United States)

    Hybridization and chromosome doubling entailed by allopolyploidization requires genetic and epigenetic modifications, resulting in the adjustment of different genomes to the same nuclear environment. Recently, the main role of retrotransposon/microsatellite-rich regions of the genome in DNA sequenc...

  5. Genomic legacies of the progenitors and the evolutionary consequences of allopolyploidy.

    Science.gov (United States)

    Steige, Kim A; Slotte, Tanja

    2016-04-01

    The formation of an allopolyploid species involves the merger of genomes with separate evolutionary histories and thereby different genomic legacies. Contrary to expectations from theory, genes from one are often lost preferentially in allopolyploids - there is biased fractionation. Here, we provide an overview of two ways in which the genomic legacies of the progenitors may impact the fate of duplicated genes in allopolyploids. Specifically, we discuss the role of homeolog expression biases in setting the stage for biased fractionation, and the evidence for transposable element silencing as a possible mechanism for homeolog expression biases. Finally, we highlight how differences between the progenitors with respect to accumulation of deleterious variation may affect trajectories of duplicate gene evolution in allopolyploids. PMID:26943938

  6. Cytotoxic effect of some medicinal plants from Asteraceae family on J-45.01 leukemic cell line--pilot study.

    Science.gov (United States)

    Wegiera, Magdalena; Smolarz, Helena D; Jedruch, Marcin; Korczak, Magdalena; Koproń, Kamila

    2012-01-01

    In this study the in vitro cytotoxic properties of ethanol extracts from the herbs, inflorescents and roots of selected Asteraceae species: Arctium lappa, Artemisia absinthium, Calendula officinalis, Centaurea cyanus, Tanacetum vulgare and Tragopogon pratensis on J-45.01 human acute T leukemia cell line was examined. All tested samples possess antileukemic properties and induce cells death via apoptosis. The correlation between antileukemic activity and total polyphenol content was determined. PMID:22568040

  7. Bemerkenswerte floristische Funde im Landkreis Emsland (1. Fortsetzung)

    OpenAIRE

    Feder, Jürgen

    2010-01-01

    Neue Fundorte seltener Gefäßpflanzen aus dem Emsland (Niedersachsen) werden aufgeführt als Ergänzung zur Flora vonWeber (1995). Siewurden vomAutor in den Jahren 1998 und 1999 ermittelt. Hierbei wurden 26 teilweise neuerdings eingeschleppte Arten erstmalig imEmsland gefunden, beispielsweise Allium vineale, Amaranthus powellii, Anthriscus caucalis, Bromus carinatus, Chaerophyllum bulbosum, Coronilla varia, Erucastrum gallicum, Papaver argemone, Sisymbrium loeselii und Tragopogon dubius. Davon s...

  8. Polyploid formation in cotton is not accompanied by rapid genomic changes.

    Science.gov (United States)

    Liu, B; Brubaker, C L; Mergeai, G; Cronn, R C; Wendel, J F

    2001-06-01

    Recent work has demonstrated that allopolyploid speciation in plants may be associated with non-Mendelian genomic changes in the early generations following polyploid synthesis. To address the question of whether rapid genomic changes also occur in allopolyploid cotton (Gossypium) species, amplified fragment length polymorphism (AFLP) analysis was performed to evaluate nine sets of newly synthesized allotetraploid and allohexaploid plants, their parents, and the selfed progeny from colchicine-doubled synthetics. Using both methylation-sensitive and methylation-insensitive enzymes, the extent of fragment additivity in newly combined genomes was ascertained for a total of approximately 22,000 genomic loci. Fragment additivity was observed in nearly all cases, with the few exceptions most likely reflecting parental heterozygosity or experimental error. In addition, genomic Southern analysis on six sets of synthetic allopolyploids probed with five retrotransposons also revealed complete additivity. Because no alterations were observed using methylation-sensitive isoschizomers, epigenetic changes following polyploid synthesis were also minimal. These indications of genomic additivity and epigenetic stasis during allopolyploid formation provide a contrast to recent evidence from several model plant allopolyploids, most notably wheat and Brassica, where rapid and unexplained genomic changes have been reported. In addition, the data contrast with evidence from repetitive DNAs in Gossypium, some of which are subject to non-Mendelian molecular evolutionary phenomena in extant polyploids. These contrasts indicate polyploid speciation in plants is accompanied by a diverse array of molecular evolutionary phenomena, which will vary among both genomic constituents and taxa. PMID:11444689

  9. Assembly and sorting of homologous BAC contigs in allotetraploid cotton genomes

    Science.gov (United States)

    Upland cotton (G. hirsutum) is a diploidized allopolyploid species containing At and Dt sub-genomes that have partial homology. Assembly and sorting of homologous BAC contigs into their subgenomes and further to individual chromosomes are of both great interest and great challenge for genome-wide i...

  10. Analysis of the allohexaploid bread wheat genome (Triticum aestivum) using comparative whole genome shotgun sequencing

    Science.gov (United States)

    The large 17 Gb allopolyploid genome of bread wheat is a major challenge for genome analysis because it is composed of three closely- related and independently maintained genomes, with genes dispersed as small “islands” separated by vast tracts of repetitive DNA. We used a novel comparative genomi...

  11. Molecular Evolution of Clustered MIC-3 (Meloidogyne Induced Cotton -3) Multigene Family of Gossypium Species

    Science.gov (United States)

    Uniqueness, content, localization, and defense-related features of the root-knot nematode resistance-associated MIC-3 multigene cluster in the genus Gossypium are all of interest for molecular evolutionary studies of duplicate genes in allopolyploids. Here we report molecular evolutionary rates of t...

  12. A whole-genome, radiation hybrid map of wheat

    Science.gov (United States)

    Generating a reference sequence of bread wheat (Triticum aestivum L.) is a challenging task because of its large, highly repetitive and allopolyploid genome. Ordering of BAC- and NGS-based contigs in ongoing wheat genome-sequencing projects primarily uses recombination and comparative genomics-base...

  13. Floral Reversion in Arabidopsis suecica Is Correlated with the Onset of Flowering and Meristem Transitioning.

    Directory of Open Access Journals (Sweden)

    Amelia Asbe

    Full Text Available Angiosperm flowers are usually determinate structures that may produce seeds. In some species, flowers can revert from committed flower development back to an earlier developmental phase in a process called floral reversion. The allopolyploid Arabidopsis suecica displays photoperiod-dependent floral reversion in a subset of its flowers, yet little is known about the environmental conditions enhancing this phenotype, or the morphological processes leading to reversion. We have used light and electron microscopy to further describe this phenomenon. Additionally, we have further studied the phenology of flowering and floral reversion in A. suecica. In this study we confirm and expand upon our previous findings that floral reversion in the allopolyploid A. suecica is photoperiod-dependent, and show that its frequency is correlated with the timing for the onset of flowering. Our results also suggest that floral reversion in A. suecica displays natural variation in its penetrance between geographic populations of A. suecica.

  14. A cytogeneticist's view of plant domestication

    International Nuclear Information System (INIS)

    The role of cytogenetics in plant domestication is not as direct as that of plant breeding, agronomy or crop botany. Five major areas of cytogenetic interest in plant domestication are distinguished: analysis of the genetic structure of the species and its relation with other species, including genome analysis; monitoring of chromosomal, including meiotic, consequences of drastic genetic alterations such as artificial mutations (including somaclonal variation) and interspecific hybridization (including complete and partial protoplast fusion); induction, monitoring and adjustment of auto- and allopolyploidy; introduction of alien chromosome segments by meiotic manipulation and translocation; adjustment of the genetic transmission system, such as the construction of systems for hybrid varieties, allopolyploidization of (partial) autopolyploids or non-functional allopolyploids and permanent complex translocation heterozygotes. It is concluded that the last three areas are of interest only in the context of large programmes with sufficient and guaranteed input and continuity. (author). 23 refs

  15. Instability of chromosome number and DNA methylation variation induced by hybridization and amphidiploid formation between Raphanus sativus L. and Brassica alboglabra Bailey

    Directory of Open Access Journals (Sweden)

    Wang Yanjie

    2010-09-01

    Full Text Available Abstract Background Distant hybridization can result genome duplication and allopolyploid formation which may play a significant role in the origin and evolution of many plant species. It is unclear how the two or more divergent genomes coordinate in one nucleus with a single parental cytoplasm within allopolyploids. We used cytological and molecular methods to investigate the genetic and epigenetic instabilities associated with the process of distant hybridization and allopolyploid formation, measuring changes in chromosome number and DNA methylation across multiple generations. Results F1 plants from intergeneric hybridization between Raphanus sativus L. (2n = 18, RR and Brassica alboglabra Bailey (2n = 18, CC were obtained by hand crosses and subsequent embryo rescue. Random amplification of polymorphic DNA (RAPD markers were used to identify the F1 hybrid plants. The RAPD data indicated that the hybrids produced specific bands similar to those of parents and new bands that were not present in either parent. Chromosome number variation of somatic cells from allotetraploids in the F4 to F10 generations showed that intensive genetic changes occurred in the early generations of distant hybridization, leading to the formation of mixopolyploids with different chromosome numbers. DNA methylation variation was revealed using MSAP (methylation-sensitive amplification polymorphism, which showed that cytosine methylation patterns changed markedly in the process of hybridization and amphidiploid formation. Differences in cytosine methylation levels demonstrated an epigenetic instability of the allopolyploid of Raphanobrassica between the genetically stable and unstable generations. Conclusions Our results showed that chromosome instability occurred in the early generations of allopolyploidy and then the plants were reverted to largely euploidy in later generations. During this process, DNA methylation changed markedly. These results suggest that

  16. Interspecific hybridization, polyploidization, and backcross of Brassica oleracea var. alboglabra with B. rapa var. purpurea morphologically recapitulate the evolution of Brassica vegetables

    OpenAIRE

    Xiaohui Zhang; Tongjin Liu; Xixiang Li; Mengmeng Duan; Jinglei Wang; Yang Qiu; Haiping Wang; Jiangping Song; Di Shen

    2016-01-01

    Brassica oleracea and B. rapa are two important vegetable crops. Both are composed of dozens of subspecies encompassing hundreds of varieties and cultivars. Synthetic B. napus with these two plants has been used extensively as a research model for the investigation of allopolyploid evolution. However, the mechanism underlying the explosive evolution of hundreds of varieties of B. oleracea and B. rapa within a short period is poorly understood. In the present study, interspecific hybridization...

  17. QTug.sau-3B Is a Major Quantitative Trait Locus for Wheat Hexaploidization

    OpenAIRE

    Zeng, Deying; Zhang, Li; Ning, Shunzong; Yuan, Zhongwei; Yan, ZeHong; Zhang, Huaigang; Zheng, Youliang; Feuillet, Catherine; Choulet, Frédéric; Yen, Yang; Zhang, Lianquan; Liu, Dengcai

    2014-01-01

    Meiotic nonreduction resulting in unreduced gametes is thought to be the predominant mechanism underlying allopolyploid formation in plants. Until now, however, its genetic base was largely unknown. The allohexaploid crop common wheat (Triticum aestivum L.), which originated from hybrids of T. turgidum L. with Aegilops tauschii Cosson, provides a model to address this issue. Our observations of meiosis in pollen mother cells from T. turgidum×Ae. tauschii hybrids indicated that first division ...

  18. Evolutionarily advanced ant farmers rear polyploid fungal crops

    DEFF Research Database (Denmark)

    Kooij, Pepijn Wilhelmus; Aanen, D.K.; Schiøtt, Morten;

    2015-01-01

    Innovative evolutionary developments are often related to gene or genome duplications. The crop fungi of attine fungus-growing ants are suspected to have enhanced genetic variation reminiscent of polyploidy, but this has never been quantified with cytological data and genetic markers. We estimate...... in fungi domesticated by termites and plants, where gene or genome duplications were typically associated with selection for higher productivity, but allopolyploid chimerism was incompatible with sexual reproduction....

  19. CenH3 evolution in diploids and polyploids of three angiosperm genera

    OpenAIRE

    Masonbrink, Rick E.; Gallagher, Joseph P.; Jareczek, Josef J; Renny-Byfield, Simon; Grover, Corrinne E.; Gong, Lei; Wendel, Jonathan F.

    2014-01-01

    Background Centromeric DNA sequences alone are neither necessary nor sufficient for centromere specification. The centromere specific histone, CenH3, evolves rapidly in many species, perhaps as a coevolutionary response to rapidly evolving centromeric DNA. To gain insight into CenH3 evolution, we characterized patterns of nucleotide and protein diversity among diploids and allopolyploids within three diverse angiosperm genera, Brassica, Oryza, and Gossypium (cotton), with a focus on evidence ...

  20. Comparison of genome-wide gene expression patterns in the seedlings of nascent allohexaploid wheats produced by two combinations of hybrids.

    Science.gov (United States)

    Jung, Yeonju; Kawaura, Kanako; Kishii, Masahiro; Sakuma, Shun; Ogihara, Yasunari

    2015-01-01

    Allopolyploidization in plants is an important event that enhances heterosis and environmental adaptation. Common wheat, Triticum aestivum (AABBDD), which is an allohexaploid that evolved from an allopolyploidization event between T. turgidum (AABB) and Aegilops tauschii (DD), shows more growth vigor and wider adaptation than tetraploid wheats. To better understand the molecular basis for the heterosis of hexaploid wheat, we systematically analyzed the genome-wide gene expression patterns of two combinations of newly hybridized triploids (ABD), their chromosome-doubled hexaploids (AABBDD), stable synthetic hexaploids (AABBDD) and natural hexaploids, in addition to their parents, T. turgidum (AABB) and Ae. tauschii (DD), using a microarray to reconstruct the events of allopolyploidization and genome stabilization. Overall comparisons of gene expression profiles showed that the newly generated hexaploids exhibited gene expression patterns similar to those of their maternal tetraploids, irrespective of hybrid combination. With successive generations, the gene expression profiles of nascent hexaploids became less similar to the maternal profiles, and belonged to a separate cluster from the natural hexaploids. Triploids revealed characteristic expression patterns, suggesting endosperm effects. In the newly hybridized triploids (ABD) of two independent synthetic lines, approximately one-fifth of expressed genes displayed non-additive expression; the number of these genes decreased with polyploidization and genome stabilization. Approximately 20% of the non-additively expressed genes were transmitted across generations throughout allopolyploidization and successive self-pollinations, and 43 genes overlapped between the two combinations, indicating that shared gene expression patterns can be seen during allohexaploidization. Furthermore, four of these 43 genes were involved in starch and sucrose metabolism, suggesting that these metabolic events play key roles in the

  1. Accelerated Senescence and Enhanced Disease Resistance in Hybrid Chlorosis Lines Derived from Interspecific Crosses between Tetraploid Wheat and Aegilops tauschii

    OpenAIRE

    Hiroki Nakano; Nobuyuki Mizuno; Yukio Tosa; Kentaro Yoshida; Pyoyun Park; Shigeo Takumi

    2015-01-01

    Hybrid chlorosis, a type of hybrid incompatibility, has frequently been reported in inter- and intraspecific crosses of allopolyploid wheat. In a previous study, we reported some types of growth abnormalities such as hybrid necrosis and observed hybrid chlorosis with mild or severe abnormalities in wheat triploids obtained in crosses between tetraploid wheat cultivar Langdon and four Ae. tauschii accessions and in their derived synthetic hexaploids. However, the molecular mechanisms underlyin...

  2. Molecular mechanisms of polyploidy and hybrid vigor

    OpenAIRE

    Chen, Z. Jeffrey

    2010-01-01

    Hybrids such as maize (Zea mays) or domestic dog (Canis lupus familiaris) grow bigger and stronger than their parents. This is also true for allopolyploids such as wheat (Triticum spp.) or frog (i.e. Xenopus and Silurana) that contain two or more sets of chromosomes from different species. The phenomenon, known as hybrid vigor or heterosis, was systematically characterized by Charles Darwin (1876). The rediscovery of heterosis in maize a century ago has revolutionized plant and animal breedin...

  3. Microsatellite Mutation Rate during Allohexaploidization of Newly Resynthesized Wheat

    Science.gov (United States)

    Luo, Jiangtao; Hao, Ming; Zhang, Li; Chen, Jixiang; Zhang, Lianquan; Yuan, Zhongwei; Yan, Zehong; Zheng, Youliang; Zhang, Huaigang; Yen, Yang; Liu, Dengcai

    2012-01-01

    Simple sequence repeats (SSRs, also known as microsatellites) are known to be mutational hotspots in genomes. DNA rearrangements have also been reported to accompany allopolyploidization. A study of the effect of allopolyploidization on SSR mutation is therefore important for understanding the origin and evolutionary dynamics of SSRs in allopolyploids. Three synthesized double haploid (SynDH) populations were made from 241 interspecific F1 haploid hybrids between Triticum turgidum L. and Aegilops tauschii (Coss.) through spontaneous chromosome doubling via unreduced gametes. Mutation events were studied at 160 SSR loci in the S1 generation (the first generation after chromosome doubling) of the three SynDH populations. Of the 148260 SSR alleles investigated in S1 generation, only one mutation (changed number of repeats) was confirmed with a mutation rate of 6.74 × 10−6. This mutation most likely occurred in the respective F1 hybrid. In comparison with previously reported data, our results suggested that allohexaploidization of wheat did not increase SSR mutation rate. PMID:23202911

  4. Microsatellite Mutation Rate during Allohexaploidization of Newly Resynthesized Wheat

    Directory of Open Access Journals (Sweden)

    Huaigang Zhang

    2012-10-01

    Full Text Available Simple sequence repeats (SSRs, also known as microsatellites are known to be mutational hotspots in genomes. DNA rearrangements have also been reported to accompany allopolyploidization. A study of the effect of allopolyploidization on SSR mutation is therefore important for understanding the origin and evolutionary dynamics of SSRs in allopolyploids. Three synthesized double haploid (SynDH populations were made from 241 interspecific F1 haploid hybrids between Triticum turgidum L. and Aegilops tauschii (Coss. through spontaneous chromosome doubling via unreduced gametes. Mutation events were studied at 160 SSR loci in the S1 generation (the first generation after chromosome doubling of the three SynDH populations. Of the 148260 SSR alleles investigated in S1 generation, only one mutation (changed number of repeats was confirmed with a mutation rate of 6.74 × 10−6. This mutation most likely occurred in the respective F1 hybrid. In comparison with previously reported data, our results suggested that allohexaploidization of wheat did not increase SSR mutation rate.

  5. Chromosomal engineering and crop improvement in bread wheat

    International Nuclear Information System (INIS)

    Bread wheat is not only the world's most important food crop but is also an excellent model system for genetic analysis of allopolyploid plants. Diploid nuclear and cytoplasm donors are now known for polyploid wheats. The origin of disomic allopolyploid species can be traced back to a single plant. Establishment of nucleocytoplasmic compatibility is critical in allopolyploid speciation. Polyploid wheats show disomic inheritance that is genetically controlled. Genetic expression arises from interactive and dosage dependent effects. Apart form polyploidy, the basic wheat genome (1n = 1x = 7) is also huge (5.3 x 109 bp). Because of the availability of a large number of cytogenic stocks, target mapping is possible. It shows that the gene rich, recombinogenic regions are restricted to the distal ends of the chromosome arms and gene cloning by chromosome landing is feasible. Because of polyploidy, the wheat genome is highly buffered and transfer of chromosome segments of large linkage blocks is more important than single genes. There are spectacular examples of alien chromosome segments transferred to wheat, either by physical means (irradiation) or by genetic manipulation, which have immensely improved productivity. Therefore, enhancing the efficiency of chromosome engineering protocols is a worthwhile goal in wheat improvement. (author). 15 refs, 3 figs, 1 tab

  6. Variation in Copy Number of Ty3/Gypsy Centromeric Retrotransposons in the Genomes of Thinopyrum intermedium and Its Diploid Progenitors

    Science.gov (United States)

    Divashuk, Mikhail G.; Khuat, Thi Mai L.; Kroupin, Pavel Yu.; Kirov, Ilya V.; Romanov, Dmitry V.; Kiseleva, Anna V.; Khrustaleva, Ludmila I.; Alexeev, Dmitry G.; Zelenin, Alexandr S.; Klimushina, Marina V.; Razumova, Olga V.; Karlov, Gennady I.

    2016-01-01

    Speciation and allopolyploidization in cereals may be accompanied by dramatic changes in abundance of centromeric repeated transposable elements. Here we demonstrate that the reverse transcriptase part of Ty3/gypsy centromeric retrotransposon (RT-CR) is highly conservative in the segmental hexaploid Thinopyrum intermedium (JrJvsSt) and its possible diploid progenitors Th. bessarabicum (Jb), Pseudoroegneria spicata (St) and Dasypyrum villosum (V) but the abundance of the repeats varied to a large extent. Fluorescence in situ hybridization (FISH) showed hybridization signals in centromeric region of all chromosomes in the studied species, although the intensity of the signals drastically differed. In Th. intermedium, the strongest signal of RT-CR probe was detected on the chromosomes of Jv, intermediate on Jr and faint on Js and St subgenome suggesting different abundance of RT-CR on the individual chromosomes rather than the sequence specificity of RT-CRs of the subgenomes. RT-CR quantification using real-time PCR revealed that its content per genome in Th. bessarabicum is ~ 2 times and P. spicata is ~ 1,5 times higher than in genome of D. villosum. The possible burst of Ty3/gypsy centromeric retrotransposon in Th. intermedium during allopolyploidization and its role in proper mitotic and meiotic chromosome behavior in a nascent allopolyploid is discussed. PMID:27119343

  7. Insight into the karyotype evolution of brachypodium species using comparative chromosome barcoding.

    Science.gov (United States)

    Idziak, Dominika; Hazuka, Iwona; Poliwczak, Beata; Wiszynska, Anna; Wolny, Elzbieta; Hasterok, Robert

    2014-01-01

    Paleogenomic studies based on bioinformatic analyses of DNA sequences have enabled unprecedented insight into the evolution of grass genomes. They have revealed that nested chromosome fusions played an important role in the divergence of modern grasses. Nowadays, studies on karyotype evolution based on the sequence analysis can also be effectively complemented by the fine-scale cytomolecular approach. In this work, we studied the karyotype evolution of small genome grasses using BAC-FISH based comparative chromosome barcoding in four Brachypodium species: diploid B. distachyon (2n = 10) and B. sylvaticum (2n = 18), diploid (2n = 18) and allopolyploid (2n = 28) B. pinnatum as well as B. phoenicoides (2n = 28). Using BAC clones derived from the B. distachyon genomic libraries for the chromosomes Bd2 and Bd3, we identified the descending dysploidy events that were common for diploids with x = 9 and B. distachyon as well as two nested chromosome fusions that were specific only for B. distachyon. We suggest that dysploidy events that are shared by different lineages of the genus had already appeared in their common ancestor. We also show that additional structural rearrangements, such as translocations and duplications, contributed to increasing genome diversification in the species analysed. No chromosomes structured exactly like Bd2 and Bd3 were found in B. pinnatum (2n = 28) and B. phoenicoides. The structure of Bd2 and Bd3 homeologues belonging to the two genomes in the allopolyploids resembled the structure of their counterparts in the 2n = 18 diploids. These findings reinforce the hypothesis which excludes B. distachyon as a potential parent for Eurasian perennial Brachypodium allopolyploids. Our cytomolecular data elucidate some mechanisms of the descending dysploidy in monocots and enable reconstructions of the evolutionary events which shaped the extant karyotypes in both the genus Brachypodium and in grasses as a whole. PMID:24675822

  8. Nonadditive changes to cytosine methylation as a consequence of hybridization and genome duplication in Senecio (Asteraceae).

    Science.gov (United States)

    Hegarty, Matthew J; Batstone, Tom; Barker, Gary L; Edwards, Keith J; Abbott, Richard J; Hiscock, Simon J

    2011-01-01

    The merger of two or more divergent genomes within an allopolyploid nucleus can facilitate speciation and adaptive evolution in flowering plants. Widespread changes to gene expression have been shown to result from interspecific hybridisation and polyploidy in a number of plant species, and attention has now shifted to determining the epigenetic processes that drive these changes. We present here an analysis of cytosine methylation patterns in triploid F(1) Senecio (ragwort) hybrids and their allohexaploid derivatives. We observe that, in common with similar studies in Arabidopsis, Spartina and Triticum, a small but significant proportion of loci display nonadditive methylation in the hybrids, largely resulting from interspecific hybridisation. Despite this, genome duplication results in a secondary effect on methylation, with reversion to additivity at some loci and novel methylation status at others. We also observe differences in methylation state between different allopolyploid generations, predominantly in cases of additive methylation with regard to which parental methylation state is dominant. These changes to methylation state in both F(1) triploids and their allohexaploid derivatives largely mirror the overall patterns of nonadditive gene expression observed in our previous microarray analyses and may play a causative role in generating those expression changes. These similar global changes to DNA methylation resulting from hybridisation and genome duplication may serve as a source of epigenetic variation in natural populations, facilitating adaptive evolution. Our observations that methylation state can also vary between different generations of polyploid hybrids suggests that newly formed allopolyploid species may display a high degree of epigenetic diversity upon which natural selection can act. PMID:21073590

  9. Genome Sizes in Hepatica Mill: (Ranunculaceae Show a Loss of DNA, Not a Gain, in Polyploids

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    B. J. M. Zonneveld

    2010-01-01

    , and a possible pentaploid. The somatic nuclear DNA contents (2C-value, as measured by flow cytometry with propidium iodide, were shown to range from 33 to 80 pg. The Asiatic and American species, often considered subspecies of H. nobilis, could be clearly distinguished from European H. nobilis. DNA content confirmed the close relationships in the Asiatic species, and these are here considered as subspecies of H. asiatica. Parents for the allotetraploid species could be suggested based on their nuclear DNA content. Contrary to the increase in genome size suggested earlier for Hepatica, a significant (6%–14% loss of nuclear DNA in the natural allopolyploids was found.

  10. Polyploid evolution and Pleistocene glacial cycles: A case study from the alpine primrose Primula marginata (Primulaceae

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    Casazza Gabriele

    2012-04-01

    Full Text Available Abstract Background Recent studies highlighted the role of Pleistocene climatic cycles in polyploid speciation and of southern Alpine refugia as reservoirs of diversity during glacial maxima. The polyploid Primula marginata, endemic to the southwestern Alps, includes both hexaploid and dodecaploid cytotypes that show no ecological or morphological differences. We used flow cytometry to determine variation and geographic distribution of cytotypes within and between populations and analyses of chloroplast (cp and nuclear ribosomal (nr DNA sequences from the Internal Transcribed Spacer (ITS region to infer the evolutionary history of the two cytotypes and the auto- vs. allopolyploid origin of dodecaploid populations. Results We did not detect any intermediate cytotypes or variation of ploidy levels within populations. Hexaploids occur in the western and dodecaploids in the eastern part of the distributional range, respectively. The cpDNA and nrDNA topologies are in conflict, for the former supports shared ancestry between P. marginata and P. latifolia, while the latter implies common origins between at least some ITS clones of P. marginata and P. allionii. Conclusions Our results suggest an initial episode of chloroplast capture involving ancestral lineages of P. latifolia and P. marginata, followed by polyploidization between P. marginata-like and P. allionii-like lineages in a southern refugium of the Maritime Alps. The higher proportion of ITS polymorphisms in dodecaploid than in hexaploid accessions of P. marginata and higher total nucleotide diversity of ITS clones in dodecaploid vs. hexaploid individuals sequences are congruent with the allopolyploid hypothesis of dodecaploid origin.

  11. Identifying parental chromosomes and genomic rearrangements in animal hybrid complexes of species with small genome size using Genomic In Situ Hybridization (GISH

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    Massimiliano Rampin

    2012-09-01

    Full Text Available Genomic In Situ Hybridization (GISH, a powerful tool to identify and to quantify genomic constituents in allopolyploids, has been widely used in plants but not in animals mainly due to technical problems in obtaining informative results. Using the allopolyploid Squalius alburnoides fish complex as a model system, we succeeded in overcoming methodological constraints when dealing with parental species with a small genome size. This hybridogenetic complex has biotypes with different genome compositions and ploidy levels, but parental chromosomes are small, morphologically very similar and therefore cannot be distinguished by conventional cytogenetic approaches. Specimens have a small genome (C-value = 1.2 pg with a low level of highly and moderate repetitive sequences, mainly located at pericentromeric chromosome regions. Since it is well known that probe annealing depends on probe concentration and hybridization time to obtain uniform hybridization signals along the chromosome arms, we progressively increased the amount of labeled probes from 100ng up to 1µg per slide and the incubation time from overnight up to 72 h, among other minor improvements. Results showed a clear enhancement of signals with respect to previous data, allowing an accurate and reproducible assignment of the parental genomes in both diploid and triploid fish. It was thus evidenced that high probes’ concentrations and long incubation time are the key to obtain, without extra image editing, uniform and reliable hybridization signals in metaphase chromosomes of hybrid fish even involving parental species with small genome size.

  12. Prevalence of gene expression additivity in genetically stable wheat allohexaploids.

    Science.gov (United States)

    Chelaifa, Houda; Chagué, Véronique; Chalabi, Smahane; Mestiri, Imen; Arnaud, Dominique; Deffains, Denise; Lu, Yunhai; Belcram, Harry; Huteau, Virginie; Chiquet, Julien; Coriton, Olivier; Just, Jérémy; Jahier, Joseph; Chalhoub, Boulos

    2013-02-01

    The reprogramming of gene expression appears as the major trend in synthetic and natural allopolyploids where expression of an important proportion of genes was shown to deviate from that of the parents or the average of the parents. In this study, we analyzed gene expression changes in previously reported, highly stable synthetic wheat allohexaploids that combine the D genome of Aegilops tauschii and the AB genome extracted from the natural hexaploid wheat Triticum aestivum. A comprehensive genome-wide analysis of transcriptional changes using the Affymetrix GeneChip Wheat Genome Array was conducted. Prevalence of gene expression additivity was observed where expression does not deviate from the average of the parents for 99.3% of 34,820 expressed transcripts. Moreover, nearly similar expression was observed (for 99.5% of genes) when comparing these synthetic and natural wheat allohexaploids. Such near-complete additivity has never been reported for other allopolyploids and, more interestingly, for other synthetic wheat allohexaploids that differ from the ones studied here by having the natural tetraploid Triticum turgidum as the AB genome progenitor. Our study gave insights into the dynamics of additive gene expression in the highly stable wheat allohexaploids. PMID:23278496

  13. Expression and inheritance of sporophytic self-incompatibility in synthetic allohexaploid Senecio cambrensis (Asteraceae).

    Science.gov (United States)

    Brennan, Adrian C; Hiscock, Simon J

    2010-04-01

    Allopolyploid speciation is common in plants and is frequently associated with shifts from outcrossing, for example self-incompatibility, to inbreeding (i.e. selfing). Senecio cambrensis is a recently evolved allohexaploid species that formed following hybridization between diploid self-incompatible S. squalidus and tetraploid self-compatible S. vulgaris. Studies of reproduction in wild populations of S. cambrensis have concluded that it is self-compatible. Here, we investigated self-compatibility in synthetic lines of S. cambrensis generated via hybridization and colchicine-induced polyploidization and wild S. cambrensis using controlled crossing experiments. Synthetic F(1)S. cambrensis individuals were all self-compatible but, in F(2) and later generations, self-incompatible individuals were identified at frequencies of 6.7-9.2%. Self-incompatibility was also detected in wild sampled individuals at a frequency of 12.2%. The mechanism and genetics of self-incompatibility were tested in synthetic S. cambrensis and found to be similar to those of its paternal parent S. squalidus (i.e. sporophytic). These results show, for the first time, that functional sporophytic self-incompatibility can be inherited and expressed in allopolyploids as early as the second (F(2)) generation. Wild S. cambrensis should therefore be considered as possessing a mixed mating system with the potential for evolution towards either inbreeding or outcrossing. PMID:19895670

  14. Differential regulation of gene products in newly synthesized Brassica napus allotetraploids is not related to protein function nor subcellular localization

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    Valot Benoît

    2007-02-01

    Full Text Available Abstract Background Allopolyploidy is a preeminent process in plant evolution that results from the merger of distinct genomes in a common nucleus via inter-specific hybridization. Allopolyploid formation is usually related to genome-wide structural and functional changes though the underlying mechanisms operating during this "genomic shock" still remain poorly known. The aim of the present study was to investigate the modifications occurring at the proteomic level following an allopolyploidization event and to determine whether these changes are related to functional properties of the proteins. In a previous report, we applied comparative proteomics to synthetic amphiploids of Brassica napus and to its diploid progenitors B. rapa and B. oleracea. Although several hundred polypeptides displayed additivity (i.e. mid-parent values in the amphiploids, many of them showed non-additivity. Here, we report the in silico functional characterization of the "non-additive" proteins (the ones with a non-additive pattern of regulation in synthetic B. napus. Results The complete set of non-additive proteins (335 in the stem and 205 in the root, as well as a subset of additive polypeptides (200 per organ, was identified by mass spectrometry. Several protein isoforms were found, and most of them (~55% displayed "different" or "opposite" patterns of regulation in the amphiploids, i.e. isoforms of the same protein showing both up-regulation and down-regulation in the synthetic B. napus compared to the mid-parent value. Components of protein complexes were identified of which ~50% also displayed "different" or "opposite" patterns of regulation in the allotetraploids. In silico functional categorization of the identified proteins was carried out, and showed that neither functional category nor metabolic pathway were systematically affected by non-additivity in the synthetic amphiploids. In addition, no subcellular compartment was found to be over- or under

  15. Synthesizing double haploid hexaploid wheat populations based on a spontaneous alloploidization process.

    Science.gov (United States)

    Zhang, Lianquan; Zhang, Li; Luo, Jiangtao; Chen, Wenjie; Hao, Ming; Liu, Baolong; Yan, Zehong; Zhang, Bo; Zhang, Huaigang; Zheng, Youliang; Liu, Dengcai; Yen, Yang

    2011-02-01

    Doubled haploid (DH) populations are useful to scientists and breeders in both crop improvement and basic research. Current methods of producing DHs usually need in vitro culture for extracting haploids and chemical treatment for chromosome doubling. This report describes a simple method for synthesizing DHs (SynDH) especially for allopolyploid species by utilizing meiotic restitution genes. The method involves three steps: hybridization to induce recombination, interspecific hybridization to extract haploids, and spontaneous chromosome doubling by selfing the interspecific F(1)s. DHs produced in this way contain recombinant chromosomes in the genome(s) of interest in a homogeneous background. No special equipment or treatments are involved in the DH production and it can be easily applied in any breeding and/or genetic program. Triticum turgidum L. and Aegilops tauschii Coss, the two ancestral species of common wheat (Triticum aestivum L.) and molecular markers were used to demonstrate the SynDH method. PMID:21356528

  16. Large SNP arrays for genotyping in crop plants

    Indian Academy of Sciences (India)

    Martin W Ganal; Andreas Polley; Eva-Maria Graner; Joerg Plieske; Ralf Wieseke; Hartmut Luerssen; Gregor Durstewitz

    2012-11-01

    Genotyping with large numbers of molecular markers is now an indispensable tool within plant genetics and breeding. Especially through the identification of large numbers of single nucleotide polymorphism (SNP) markers using the novel high-throughput sequencing technologies, it is now possible to reliably identify many thousands of SNPs at many different loci in a given plant genome. For a number of important crop plants, SNP markers are now being used to design genotyping arrays containing thousands of markers spread over the entire genome and to analyse large numbers of samples. In this article, we discuss aspects that should be considered during the design of such large genotyping arrays and the analysis of individuals. The fact that crop plants are also often autopolyploid or allopolyploid is given due consideration. Furthermore, we outline some potential applications of large genotyping arrays including high-density genetic mapping, characterization (fingerprinting) of genetic material and breeding-related aspects such as association studies and genomic selection.

  17. Medicinal plants with hepatoprotective activity in Iranian folk medicine

    Institute of Scientific and Technical Information of China (English)

    Majid; Asadi-Samani; Najme; Kafash-Farkhad; Nafiseh; Azimi; Ali; Fasihi; Ebrahim; Alinia-Ahandani; Mahmoud; Rafieian-Kopaei

    2015-01-01

    There are a number of medicinal combinations in the Iranian traditional medicine which are commonly used as tonic for liver.In this review,we have introduced some medicinal plants that are used mainly for the treatment of liver disorders in Iranian folk medicine,with focus on their hepatoprotective effects particularly against CCI4 agent.In this study,online databases including Web of Science.PubMed.Scopus,and Science Direct were searched for papers published from January 1970 to December 2013.Search terms consisted of medicinal plants,traditional medicine,folk medicine,hepatoprotective.Iran,liver,therapeutic uses,compounds,antioxidant.CCI4.anti-inflammatory,and antihepatotoxic,hepatitis,alone or in combination.Allium hirtifolium Boiss..Apium graveolens L..Cynara scolyinus.Berberis vulgaris L..,Calendula officinalis,Nigella sativa L..Taraxacum officinale.Tragopogon porrifolius.Prangos ferulacea L..Allium sativum,Marribium vulgare,Ammi majus L..Citrullus lanatus Thunb.Agrimonia eupatoria L.and Primus armeniaca L.are some of the medicinal plants that have been used for the treatment of liver disorders in Iranian folk medicine.Out of several leads obtained from plants containing potential hepatoprotective agents,silymarin,P-sitosterol,betalain,neoandrographolide.phyllanthin.andrographolide.curcumin.picroside.hypophyllanlhin.kutkoside,and glycyrrhizin have been demonstrated to have potent hepatoprotective properties.Despite encouraging data on possibility of new discoveries in the near future,the evidence on treating viral hepatitis or other chronic liver diseases by herbal medications is not adequate.

  18. Phytoremediation Opportunities with Alimurgic Species in Metal-Contaminated Environments

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    Marianna Bandiera

    2016-04-01

    Full Text Available Alimurgic species are edible wild plants growing spontaneously as invasive weeds in natural grassland and farmed fields. Growing interest in biodiversity conservation projects suggests deeper study of the multifunctional roles they can play in metal uptake for phytoremediation and their food safety when cultivated in polluted land. In this study, the responses of the tap-rooted perennial species Cichorium intybus L., Sonchus oleracerus L., Taraxacum officinale Web., Tragopogon porrifolius L. and Rumex acetosa L. were studied in artificially-highly Cd-Co-Cu-Pb-Zn-contaminated soil in a pot-scale trial, and those of T. officinale and R. acetosa in critical open environments (i.e., landfill, ditch sediments, and sides of highly-trafficked roads. Germination was not inhibited, and all species showed appreciable growth, despite considerable increases in tissue metal rates. Substantial growth impairments were observed in C. intybus, T. officinale and T. porrifolius; R. acetosa and S. oleracerus were only marginally affected. Zn was generally well translocated and reached a high leaf concentration, especially in T. officinale (~600 mg·kg−1·dry weight, DW, a result which can be exploited for phytoremediation purposes. The elevated Cd translocation also suggested applications to phytoextraction, particularly with C. intybus, in which leaf Cd reached ~16 mg·kg−1·DW. The generally high root retention of Pb and Cu may allow their phytostabilisation in the medium-term in no-tillage systems, together with significant reductions in metal leaching compared with bare soil. In open systems, critical soil Pb and Zn were associated with heavily trafficked roadsides, although this was only seldom reflected in shoot metal accumulation. It is concluded that a community of alimurgic species can serve to establish an efficient, long-lasting vegetation cover applied for phytoremediation and reduction of soil metal movements in degraded environments. However

  19. CHARACTERISATION OF INULIN FROM CHICORY AND SALSIFY CULTIVATED IN PORTUGAL

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    M. L. BEIRÃO-DA-COSTA

    2009-03-01

    Full Text Available

    Inulin and fructooligosaccharides (FOS are important ingredients used in the food industry because of their diverse nutritional and functional properties. Among the sources of these compounds, chicory (Cichorium intybus L. is one of the most important, due to its high content of inulin, which shows a high F/G ratio. As in several European countries, chicory is grown in Portugal where is used traditionally as a coffee substitute. However, studies have been carried out concerning the evaluation of the characteristics of the carbohydrate fraction of Portuguese chicory, to investigate its industrial potential as a raw material for the production of inulin, FOS and fructose. Salsify (Tragopogon porrifolius L., another plant generally regarded as an inulin source, is also cultivated in the same regions of our country where it is used as a cooked vegetable. Carbohydrate constituents of chicory and salsify roots, mainly inulin and FOS, were submitted to a physical-chemical analysis by HPLC and DSC (Differential Scanning Calorimetry. The viscosities of the gels produced from both inulins were also evaluated. From HPLC results it was apparent that great differences exist between the inulin sources, mainly in degree of polymerisation which was higher in chicory. Endotherms showed that both peak temperature and enthalpy values of the transition were different, the latter being much higher for salsify. KEYWORDS: Physical-chemical analysis of inulin; chicory; salsify.

  20. Colchicum autumnale - Control strategies and their impact on vegetation composition of species-rich grasslands

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    Seither, Melanie

    2014-02-01

    Full Text Available The meadow saffron Colchicum autumnale occurs on agricultural land predominantly in extensively managed grassland, often underlying nature preservation regulations. Due to its high toxicity if fresh or conserved (hay and silage, there is a need of control measures to ensure the future management and sward utilization of sites with occurrence of C. autumnale. Until now it is unclear, to what extent common management recommendations affect the vegetation composition of species-rich grassland. In this study, the effect of different management measures (late hay cut with or without rolling, early hay cut, late mulching in May, early mulching in April, herbicide application with or without reseeding on the number of C. autumnale and the vegetation composition of a moderately species-rich Dauco-Arrhenatheretum elatioris (31 ± 4 species per m², mean ± standard deviation was examined since 2006. The number of C. autumnale was first significantly reduced three years after the start of the experiment in the early and late mulching treatments; in the next three experimental years treatment differences in C. autumnale reduction did not increase significantly. With respect to vegetation composition, herbicide application had the overriding effect, as it decreased the plant species number and proportions of forbs significantly. The late hay cut preserved the original plant diversity, no negative effect of rolling or the early hay cut was observed. Early mulching resulted in an increase in Dactylis glomerata and Trisetum flavescens and in the decrease of Crepis biennis, Vicia sepium, Tragopogon pratense and Trifolium pratense; it had no negative effect on the total proportion of high nature value (HNV species. Late mulching resulted in a significantly lower yield proportion of high nature value species in 2012 and less similar in vegetation composition compared to the late hay cut treatment than early mulching; therefore it seems not to be a suitable

  1. Heterosis as investigated in terms of polyploidy and genetic diversity using designed Brassica juncea amphiploid and its progenitor diploid species.

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    Payal Bansal

    Full Text Available Fixed heterosis resulting from favorable interactions between the genes on their homoeologous genomes in an allopolyploid is considered analogous to classical heterosis accruing from interactions between homologous chromosomes in heterozygous plants of a diploid species. It has been hypothesized that fixed heterosis may be one of the causes of low classical heterosis in allopolyploids. We used Indian mustard (Brassica juncea, 2n = 36; AABB as a model system to analyze this hypothesis due to ease of its resynthesis from its diploid progenitors, B. rapa (2n = 20; AA and B. nigra (2n = 16; BB. Both forms of heterosis were investigated in terms of ploidy level, gene action and genetic diversity. To facilitate this, eleven B. juncea genotypes were resynthesized by hybridizing ten near inbred lines of B. rapa and nine of B. nigra. Three half diallel combinations involving resynthesized B. juncea (11×11 and the corresponding progenitor genotypes of B. rapa (10×10 and B. nigra (9×9 were evaluated. Genetic diversity was estimated based on DNA polymorphism generated by SSR primers. Heterosis and genetic diversity in parental diploid species appeared not to predict heterosis and genetic diversity at alloploid level. There was also no association between combining ability, genetic diversity and heterosis across ploidy. Though a large proportion (0.47 of combinations showed positive values, the average fixed heterosis was low for seed yield but high for biomass yield. The genetic diversity was a significant contributor to fixed heterosis for biomass yield, due possibly to adaptive advantage it may confer on de novo alloploids during evolution. Good general/specific combiners at diploid level did not necessarily produce good general/specific combiners at amphiploid level. It was also concluded that polyploidy impacts classical heterosis indirectly due to the negative association between fixed heterosis and classical heterosis.

  2. Cytoplasmic and genomic effects on non-meiosis-driven genetic changes in Brassica hybrids and allotetraploids from pairwise crosses of three cultivated diploids.

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    Cheng Cui

    Full Text Available Nuclear-cytoplasmic interactions are predicted to be important in shaping the genetic changes in early stage of allopolyploidization. Our previous study shows the specific role of genome and cytoplasm affecting the chromosome pairing in Brassica hybrids and allotetraploids from pairwise crosses between three cultivated diploids with A, B and C genomes, respectively. Herein, to address how parental genomes and cytoplasm affects genomic, epigenetic and gene expression changes prior to meiosis in these hybrids and allopolyploids, their patterns of AFLP (Amplified fragment length polymorphism, mAFLP (Methylation AFLP and cDNA-AFLP were compared with the progenitors, revealing the major absent bands within each genome. These changes varied under various cytoplasm backgrounds and genome combinations, following the significant order of AFLP> mAFLP> cDNA -AFLP. The frequencies of AFLP bands lost were positively correlated with the divergence degrees of parental genomes, but not obvious for those of mAFLP and cDNA-AFLP absent bands, and methylation change showed least variations among hybrids and within each genome. These changes within each genome followed the A>B>C hierarchy, except the highest rate of cDNA loss in B genome. Among three changes, only overall AFLP bands were significantly correlated with cDNA-AFLP, and their correlations varied within each genome. These changes in allotetraploids were mainly caused by genome merger rather than doubling. Parental genomes altered differently at three levels, responded to the types of cytoplasm and genome and their interaction or divergence. The result provides new clues for instant non-meiosis-driven genome restructuring following genome merger and duplication.

  3. The Festuco-Brometea Grasslands on Sandstone and Marl-Clay-Sandstone Substrata in Tuscany (Northern-Central Italy

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    Foggi Bruno

    2014-06-01

    Full Text Available Travišča v katerih prevladujeta vrsti Bromus erectus in/ali Brachypodium rupestre pokrivajo velike površine na podlagi iz peščenjaka in laporasto-glinastega peščenjaka (apnenec je izključen na Apeninih in območju pred njimi med provincama Pistoia in Arezzo (Toskana, srednja Italija. Naša raziskava je bila osredotočena na 71 neobjavljenih in 45 objavljenih vegetacijskih popisov iz Toskane in sosednjih območij. Originalni popisi opisujejo asociacije Astragalo monspessulani-Brometum erecti, Centaureo bracteatae-Brometum erecti in Ononido masquillerii-Brometum erecti. Popise smo obdelali z multivariatno analizo s katero smo zaznali 9 skupin. Konsistenstnost skupin smo preverili s povprečjem NMDS proti Ellenberg/Pignatti indikatorskim vrednostim in CCA proti horotipom in rastnim oblikam. Diagnostične vrste posameznih skupin smo določili z navezanostjo vrst, ki temelji na φ koeficientu asociacije. Z analizo smo podatkovni niz razdelili na dva klastra; prvi (A vključuje nekaj popisov termofilne cenoze z nižje nadmorske višine, ki jih opišemo kot prehod med submediteranskim aspektom razreda Festuco-Brometea in drugih mediteranskih zeliščnih in grmiščnih razredov; drugi klaster (B pa vključuje večino podatkovnega niza in ga lahko členimo na pionirske, mezokserofilne (skupini B1 in B2a in mezofilne združbe (skupina B2b. Popise klastrov B1 in B2a uvrščamo v asociacijo Coronillo minimae-Astragaletum monspessulanii in tri druge skupine: združba Plantago argentea-Carex caryophyllea, združba Tragopogon samaritani-Bromus erectus in Festuco trachyphyllae-Brometum erecti ass. nova. Mezofilna skupina (B2b vključuje popise asociacij Centaureo bracteatae-Brometum erecti in Ononido masquillerii- Brometum erecti, skupaj z delno spremenjeno združbo. Zaradi majhnih razlik v florističnem, ekološkem in horološkem pogledu med temi traviščnimi tipi predlagamo, da jih obravnavamo kot tri subasociacije Centaureo bracteatae

  4. Loss of foundation species increases population growth of exotic forbs in sagebrush steppe.

    Science.gov (United States)

    Prevéy, Janet S; Germino, Matthew J; Huntly, Nancy J

    2010-10-01

    The invasion and spread of exotic plants following land disturbance threatens semiarid ecosystems. In sagebrush steppe, soil water is scarce and is partitioned between deep-rooted perennial shrubs and shallower-rooted native forbs and grasses. Disturbances commonly remove shrubs, leaving grass-dominated communities, and may allow for the exploitation of water resources by the many species of invasive, tap-rooted forbs that are increasingly successful in this habitat. We hypothesized that exotic forb populations would benefit from increased soil water made available by removal of sagebrush, a foundation species capable of deep-rooting, in semiarid shrub-steppe ecosystems. To test this hypothesis, we used periodic matrix models to examine effects of experimental manipulations of soil water on population growth of two exotic forb species, Tragopogon dubius and Lactuca serriola, in sagebrush steppe of southern Idaho, USA. We used elasticity analyses to examine which stages in the life cycle of T. dubius and L. serriola had the largest relative influence on population growth. We studied the demography of T. dubius and L. serriola in three treatments: (1) control, in which vegetation was not disturbed, (2) shrubs removed, or (3) shrubs removed but winter-spring recharge of deep-soil water blocked by rainout shelters. The short-term population growth rate (Lambda) of T. dubius in the shrub-removal treatment was more than double that of T. dubius in either sheltered or control treatments, both of which had limited soil water. All L. serriola individuals that emerged in undisturbed sagebrush plots died, whereas Lambda of L. serriola was high (Lambda > 2.5) in all shrub-removal plots, whether they had rainout shelters or not. Population growth of both forbs in all treatments was most responsive to flowering and seed production, which are life stages that should be particularly reliant on deep-soil water, as well as seedling establishment, which is important to most plant

  5. Production of viable male unreduced gametes in Brassica interspecific hybrids is genotype specific and stimulated by cold temperatures

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    Cowling Wallace A

    2011-06-01

    Full Text Available Abstract Background Unreduced gametes (gametes with the somatic chromosome number may provide a pathway for evolutionary speciation via allopolyploid formation. We evaluated the effect of genotype and temperature on male unreduced gamete formation in Brassica allotetraploids and their interspecific hybrids. The frequency of unreduced gametes post-meiosis was estimated in sporads from the frequency of dyads or giant tetrads, and in pollen from the frequency of viable giant pollen compared with viable normal pollen. Giant tetrads were twice the volume of normal tetrads, and presumably resulted from pre-meiotic doubling of chromosome number. Giant pollen was defined as pollen with more than 1.5 × normal diameter, under the assumption that the doubling of DNA content in unreduced gametes would approximately double the pollen cell volume. The effect of genotype was assessed in five B. napus, two B. carinata and one B. juncea parents and in 13 interspecific hybrid combinations. The effect of temperature was assessed in a subset of genotypes in hot (day/night 30°C/20°C, warm (25°C/15°C, cool (18°C/13°C and cold (10°C/5°C treatments. Results Based on estimates at the sporad stage, some interspecific hybrid genotypes produced unreduced gametes (range 0.06 to 3.29% at more than an order of magnitude higher frequency than in the parents (range 0.00% to 0.11%. In nine hybrids that produced viable mature pollen, the frequency of viable giant pollen (range 0.2% to 33.5% was much greater than in the parents (range 0.0% to 0.4%. Giant pollen, most likely formed from unreduced gametes, was more viable than normal pollen in hybrids. Two B. napus × B. carinata hybrids produced 9% and 23% unreduced gametes based on post-meiotic sporad observations in the cold temperature treatment, which was more than two orders of magnitude higher than in the parents. Conclusions These results demonstrate that sources of unreduced gametes, required for the triploid

  6. The evolutionary history of the Arabidopsis lyrata complex: a hybrid in the amphi-Beringian area closes a large distribution gap and builds up a genetic barrier

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    Koch Marcus A

    2010-04-01

    Full Text Available Abstract Background The genomes of higher plants are, on the majority, polyploid, and hybridisation is more frequent in plants than in animals. Both polyploidisation and hybridisation contribute to increased variability within species, and may transfer adaptations between species in a changing environment. Studying these aspects of evolution within a diversified species complex could help to clarify overall spatial and temporal patterns of plant speciation. The Arabidopsis lyrata complex, which is closely related to the model plant Arabidopsis thaliana, is a perennial, outcrossing, herbaceous species complex with a circumpolar distribution in the Northern Hemisphere as well as a disjunct Central European distribution in relictual habitats. This species complex comprises three species and four subspecies, mainly diploids but also several tetraploids, including one natural hybrid. The complex is ecologically, but not fully geographically, separated from members of the closely related species complex of Arabidopsis halleri, and the evolutionary histories of both species compexes have largely been influenced by Pleistocene climate oscillations. Results Using DNA sequence data from the nuclear encoded cytosolic phosphoglucoisomerase and Internal Transcribed Spacers 1 and 2 of the ribosomal DNA, as well as the trnL/F region from the chloroplast genome, we unravelled the phylogeography of the various taxonomic units of the A. lyrata complex. We demonstrate the existence of two major gene pools in Central Europe and Northern America. These two major gene pools are constructed from different taxonomic units. We also confirmed that A. kamchatica is the allotetraploid hybrid between A. lyrata and A. halleri, occupying the amphi-Beringian area in Eastern Asia and Northern America. This species closes the large distribution gap of the various other A. lyrata segregates. Furthermore, we revealed a threefold independent allopolyploid origin of this hybrid

  7. REARRANGEMENT IN THE B-GENOME FROM DIPLOID PROGENITOR TO WHEAT ALLOPOLYPOLID

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    Salina E.A.

    2012-08-01

    particular, Ph1, critical for correct mitosis and meiosis in the allopolyploid nucleus; Kr1, controlling interspecific incompatibility; the genes controlling hybrid necrosis and response to vernalization, Ne1 and Vrn-B1; and genes controlling resistance to various pathogens and bread-making quality. The translocations and inversions of chromosome 5B/5S, which could have taken place in the evolution of Ae. speltoides and allopolyploid wheats, yet has not been detected so far. On the other hand, the changes in chromosome 5B that had brought forth the locus Ph1 took place due to certain yet unknown mechanisms. Construction of the physical map for chromosome 5B and determination of its primary structure are in progress now.

  8. Alien DNA introgression and wheat DNA rearrangements in a stable wheat line derived from the early generation of distant hybridization

    Institute of Scientific and Technical Information of China (English)

    ZHANG; Lianquan; LIU; Dengcai; YAN; Zehong; ZHENG; Youlia

    2005-01-01

    Polyploidy has been found to be common in plants. Bread or common wheat (Triticum aestivum L., 2n = 42) is a good example of allopolyploid made up of three diploid genomes A, B and D. In recent years, by the study of mimicking the origination of common wheat, it was found that changes of DNA sequence and gene expression occurred at the early stages of artificial allohexaploid between tetraploid wheat and Aegilops tauschii, which was probably favorable to genetic diploidization of new synthetic hexaploid wheat. Common wheat 99L2 is a new line stable in genetic, which was derived from the early self-pollinated generation of wide hybrids between common wheat and rye. In this study, it was found that at least two rye DNA segments had been introgressed into 99L2. This result suggested that a mechanism of alien DNA introgression may exist, which was different from the traditional mechanism of chromosome pairing and DNA recombination between wheat and alien species. Meanwhile, during the introgression process of alien rye DNA segments, the changes in DNA sequences of wheat itself occurred.

  9. QTug.sau-3B Is a Major Quantitative Trait Locus for Wheat Hexaploidization

    Science.gov (United States)

    Hao, Ming; Luo, Jiangtao; Zeng, Deying; Zhang, Li; Ning, Shunzong; Yuan, Zhongwei; Yan, Zehong; Zhang, Huaigang; Zheng, Youliang; Feuillet, Catherine; Choulet, Frédéric; Yen, Yang; Zhang, Lianquan; Liu, Dengcai

    2014-01-01

    Meiotic nonreduction resulting in unreduced gametes is thought to be the predominant mechanism underlying allopolyploid formation in plants. Until now, however, its genetic base was largely unknown. The allohexaploid crop common wheat (Triticum aestivum L.), which originated from hybrids of T. turgidum L. with Aegilops tauschii Cosson, provides a model to address this issue. Our observations of meiosis in pollen mother cells from T. turgidum×Ae. tauschii hybrids indicated that first division restitution, which exhibited prolonged cell division during meiosis I, was responsible for unreduced gamete formation. A major quantitative trait locus (QTL) for this trait, named QTug.sau-3B, was detected on chromosome 3B in two T. turgidum×Ae. tauschii haploid populations. This QTL is situated between markers Xgwm285 and Xcfp1012 and covered a genetic distance of 1 cM in one population. QTug.sau-3B is a haploid-dependent QTL because it was not detected in doubled haploid populations. Comparative genome analysis indicated that this QTL was close to Ttam-3B, a collinear homolog of tam in wheat. Although the relationship between QTug.sau-3B and Ttam requires further study, high frequencies of unreduced gametes may be related to reduced expression of Ttam in wheat. PMID:25128436

  10. Epigenetic regulation of subgenome dominance following whole genome triplication in Brassica rapa.

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    Cheng, Feng; Sun, Chao; Wu, Jian; Schnable, James; Woodhouse, Margaret R; Liang, Jianli; Cai, Chengcheng; Freeling, Michael; Wang, Xiaowu

    2016-07-01

    Subgenome dominance is an important phenomenon observed in allopolyploids after whole genome duplication, in which one subgenome retains more genes as well as contributes more to the higher expressing gene copy of paralogous genes. To dissect the mechanism of subgenome dominance, we systematically investigated the relationships of gene expression, transposable element (TE) distribution and small RNA targeting, relating to the multicopy paralogous genes generated from whole genome triplication in Brassica rapa. The subgenome dominance was found to be regulated by a relatively stable factor established previously, then inherited by and shared among B. rapa varieties. In addition, we found a biased distribution of TEs between flanking regions of paralogous genes. Furthermore, the 24-nt small RNAs target TEs and are negatively correlated to the dominant expression of individual paralogous gene pairs. The biased distribution of TEs among subgenomes and the targeting of 24-nt small RNAs together produce the dominant expression phenomenon at a subgenome scale. Based on these findings, we propose a bucket hypothesis to illustrate subgenome dominance and hybrid vigor. Our findings and hypothesis are valuable for the evolutionary study of polyploids, and may shed light on studies of hybrid vigor, which is common to most species. PMID:26871271

  11. Interspecific hybridization, polyploidization, and backcross of Brassica oleracea var. alboglabra with B. rapa var. purpurea morphologically recapitulate the evolution of Brassica vegetables.

    Science.gov (United States)

    Zhang, Xiaohui; Liu, Tongjin; Li, Xixiang; Duan, Mengmeng; Wang, Jinglei; Qiu, Yang; Wang, Haiping; Song, Jiangping; Shen, Di

    2016-01-01

    Brassica oleracea and B. rapa are two important vegetable crops. Both are composed of dozens of subspecies encompassing hundreds of varieties and cultivars. Synthetic B. napus with these two plants has been used extensively as a research model for the investigation of allopolyploid evolution. However, the mechanism underlying the explosive evolution of hundreds of varieties of B. oleracea and B. rapa within a short period is poorly understood. In the present study, interspecific hybridization between B. oleracea var. alboglabra and B. rapa var. purpurea was performed. The backcross progeny displayed extensive morphological variation, including some individuals that phenocopied subspecies other than their progenitors. Numerous interesting novel phenotypes and mutants were identified among the backcross progeny. The chromosomal recombination between the A and C genomes and the chromosomal asymmetric segregation were revealed using Simple Sequence Repeats (SSR) markers. These findings provide direct evidence in support of the hypothesis that interspecific hybridization and backcrossing have played roles in the evolution of the vast variety of vegetables among these species and suggest that combination of interspecific hybridization and backcrossing may facilitate the development of new mutants and novel phenotypes for both basic research and the breeding of new vegetable crops. PMID:26727246

  12. Independent Domestication of Two Old World Cotton Species.

    Science.gov (United States)

    Renny-Byfield, Simon; Page, Justin T; Udall, Joshua A; Sanders, William S; Peterson, Daniel G; Arick, Mark A; Grover, Corrinne E; Wendel, Jonathan F

    2016-01-01

    Domesticated cotton species provide raw material for the majority of the world's textile industry. Two independent domestication events have been identified in allopolyploid cotton, one in Upland cotton (Gossypium hirsutum L.) and the other to Egyptian cotton (Gossypium barbadense L.). However, two diploid cotton species, Gossypium arboreum L. and Gossypium herbaceum L., have been cultivated for several millennia, but their status as independent domesticates has long been in question. Using genome resequencing data, we estimated the global abundance of various repetitive DNAs. We demonstrate that, despite negligible divergence in genome size, the two domesticated diploid cotton species contain different, but compensatory, repeat content and have thus experienced cryptic alterations in repeat abundance despite equivalence in genome size. Evidence of independent origin is bolstered by estimates of divergence times based on molecular evolutionary analysis of f7,000 orthologous genes, for which synonymous substitution rates suggest that G. arboreum and G. herbaceum last shared a common ancestor approximately 0.4-2.5 Ma. These data are incompatible with a shared domestication history during the emergence of agriculture and lead to the conclusion that G. arboreum and G. herbaceum were each domesticated independently. PMID:27289095

  13. Peptidomic analysis of the extensive array of host-defense peptides in skin secretions of the dodecaploid frog Xenopus ruwenzoriensis (Pipidae).

    Science.gov (United States)

    Coquet, Laurent; Kolodziejek, Jolanta; Jouenne, Thierry; Nowotny, Norbert; King, Jay D; Conlon, J Michael

    2016-09-01

    The Uganda clawed frog Xenopus ruwenzoriensis with a karyotype of 2n=108 is one of the very few vertebrates with dodecaploid status. Peptidomic analysis of norepinephrine-stimulated skin secretions from this species led to the isolation and structural characterization of 23 host-defense peptides belonging to the following families: magainin (3 peptides), peptide glycine-leucine-amide (PGLa; 6 peptides), xenopsin precursor fragment (XPF; 3 peptides), caerulein precursor fragment (CPF; 8 peptides), and caerulein precursor fragment-related peptide (CPF-RP; 3 peptides). In addition, the secretions contained caerulein, identical to the peptide from Xenopus laevis, and two peptides that were identified as members of the trefoil factor family (TFF). The data indicate that silencing of the host-defense peptide genes following polyploidization has been appreciable and non-uniform. Consistent with data derived from comparison of nucleotide sequences of mitochrondrial and nuclear genes, cladistic analyses based upon the primary structures of the host-defense peptides provide support for an evolutionary scenario in which X. ruwenzoriensis arose from an allopolyploidization event involving an octoploid ancestor of the present-day frogs belonging to the Xenopus amieti species group and a tetraploid ancestor of Xenopus pygmaeus. PMID:27290612

  14. Molecular and cytogenetic evidence for an allotetraploid origin of Chenopodium quinoa and C. berlandieri (Amaranthaceae).

    Science.gov (United States)

    Kolano, Bozena; McCann, Jamie; Orzechowska, Maja; Siwinska, Dorota; Temsch, Eva; Weiss-Schneeweiss, Hanna

    2016-07-01

    Most of the cultivated chenopods are polyploids, but their origin and evolutionary history are still poorly understood. Phylogenetic analyses of DNA sequences of four plastid regions, nrITS and nuclear 5S rDNA spacer region (NTS) of two tetraploid chenopods (2n=4x=36), Andean C. quinoa and North American C. berlandieri, and their diploid relatives allowed inferences of their origin. The phylogenetic analyses confirmed allotetraploid origin of both tetraploids involving diploids of two different genomic groups (genomes A and B) and suggested that these two might share very similar parentage. The hypotheses on the origin of the two allopolyploid species were further tested using genomic in situ hybridization (GISH). Several diploid Chenopodium species belonging to the two lineages, genome A and B, suggested by phylogenetic analyses, were tested as putative parental taxa. GISH differentiated two sets of parental chromosomes in both tetraploids and further corroborated their allotetraploid origin. Putative diploid parental taxa have been suggested by GISH for C. quinoa and C. berlandieri. Genome sizes of the analyzed allotetraploids fit nearly perfectly the expected additive values of the putative parental taxa. Directional and uniparental loss of rDNA loci of the maternal A-subgenome was revealed for both C. berlandieri and C. quinoa. PMID:27063253

  15. Making the Bread: Insights from Newly Synthesized Allohexaploid Wheat.

    Science.gov (United States)

    Li, Ai-li; Geng, Shuai-Feng; Zhang, Lian-quan; Liu, Deng-cai; Mao, Long

    2015-06-01

    Bread wheat (or common wheat, Triticum aestivum) is an allohexaploid (AABBDD, 2n = 6x = 42) that arose by hybridization between a cultivated tetraploid wheat T. turgidum (AABB, 2n = 4x = 28) and the wild goatgrass Aegilops tauschii (DD, 2n = 2x = 14). Polyploidization provided niches for rigorous genome modification at cytogenetic, genetic, and epigenetic levels, rendering a broader spread than its progenitors. This review summarizes the latest advances in understanding gene regulation mechanisms in newly synthesized allohexaploid wheat and possible correlation with polyploid growth vigor and adaptation. Cytogenetic studies reveal persistent association of whole-chromosome aneuploidy with nascent allopolyploids, in contrast to the genetic stability in common wheat. Transcriptome analysis of the euploid wheat shows that small RNAs are driving forces for homoeo-allele expression regulation via genetic and epigenetic mechanisms. The ensuing non-additively expressed genes and those with expression level dominance to the respective progenitor may play distinct functions in growth vigor and adaptation in nascent allohexaploid wheat. Further genetic diploidization of allohexaploid wheat is not random. Regional asymmetrical gene distribution, rather than subgenome dominance, is observed in both synthetic and natural allohexaploid wheats. The combinatorial effects of diverged genomes, subsequent selection of specific gene categories, and subgenome-specific traits are essential for the successful establishment of common wheat. PMID:25747845

  16. Cryptic sex? Estimates of genome exchange in unisexual mole salamanders (Ambystoma sp.).

    Science.gov (United States)

    Gibbs, H Lisle; Denton, Robert D

    2016-06-01

    Cryptic sex has been argued to explain the exceptional longevity of certain parthenogenetic vertebrate lineages, yet direct measurements of genetic exchange between sexual and apparently parthenogenetic forms are rare. Female unisexual mole salamanders (Ambystoma sp.) are the oldest known unisexual vertebrate lineage (~5 million years), and one hypothesis for their persistence is that allopolyploid female unisexuals periodically exchange haploid genomes 'genome exchange' during gynogenetic reproduction with males from sympatric sexual species. We test this hypothesis by using genome-specific microsatellite DNA markers to estimate the rates of genome exchange between sexual males and unisexual females in two ponds in NE Ohio. We also test the prediction that levels of gene flow should be higher for 'sympatric' (sexual males present) genomes in unisexuals compared to 'allopatric' (sexual males absent) unisexual genomes. We used a model testing framework in the coalescent-based program MIGRATE-N to compare models where unidirectional gene flow is present and absent between sexual species and unisexuals. As predicted, our results show higher levels of gene flow between sexuals and sympatric unisexual genomes compared to lower (likely artefactual) levels of gene flow between sexuals and allopatric unisexual genomes. Our results provide direct evidence that genome exchange between sexual and unisexual Ambystoma occurs and demonstrate that the magnitude depends on which sexual species are present. The relatively high levels of gene flow suggest that unisexuals must be at a selective advantage over sexual forms so as to avoid extinction due to genetic swamping through genome exchange. PMID:27100619

  17. The chloroplast genome of the hexaploid Spartina maritima (Poaceae, Chloridoideae): Comparative analyses and molecular dating.

    Science.gov (United States)

    Rousseau-Gueutin, M; Bellot, S; Martin, G E; Boutte, J; Chelaifa, H; Lima, O; Michon-Coudouel, S; Naquin, D; Salmon, A; Ainouche, K; Ainouche, M

    2015-12-01

    The history of many plant lineages is complicated by reticulate evolution with cases of hybridization often followed by genome duplication (allopolyploidy). In such a context, the inference of phylogenetic relationships and biogeographic scenarios based on molecular data is easier using haploid markers like chloroplast genome sequences. Hybridization and polyploidization occurred recurrently in the genus Spartina (Poaceae, Chloridoideae), as illustrated by the recent formation of the invasive allododecaploid S. anglica during the 19th century in Europe. Until now, only a few plastid markers were available to explore the history of this genus and their low variability limited the resolution of species relationships. We sequenced the complete chloroplast genome (plastome) of S. maritima, the native European parent of S. anglica, and compared it to the plastomes of other Poaceae. Our analysis revealed the presence of fast-evolving regions of potential taxonomic, phylogeographic and phylogenetic utility at various levels within the Poaceae family. Using secondary calibrations, we show that the tetraploid and hexaploid lineages of Spartina diverged 6-10 my ago, and that the two parents of the invasive allopolyploid S. anglica separated 2-4 my ago via long distance dispersal of the ancestor of S. maritima over the Atlantic Ocean. Finally, we discuss the meaning of divergence times between chloroplast genomes in the context of reticulate evolution. PMID:26182838

  18. Phylogenetic analysis of Elymus (Poaceae) in western China.

    Science.gov (United States)

    Song, H; Nan, Z B; Tian, P

    2015-01-01

    Elymus L. is often planted in temperate and subtropical regions as forage. Species in the genus have 5 allopolyploid genomes that are found in the grass tribe Triticeae. To determine the phylogenetic relationships in Elymus species from western China, we estimated phylogenetic trees using sequences from the nuclear ribosomal internal transcribed spacer and non-coding chloroplast DNA sequences from 56 accessions (871 samples) of 9 polyploid Elymus species and 42 accessions from GenBank. Tetraploid and hexaploid Elymus species from western China had independent origins, and Elymus species from the same area or neighboring geographic regions were the most closely related. Based on the phylogenetic tree topology, the St- and Y-genomes were not derived from the same donor and Y-genome likely originated from the H-genome of Hordeum species, or they shared the same origin or underwent introgression. The maternal genome of tetraploid and hexaploid Elymus species originated from species of Hordeum or Pseudoroegneria. Additionally, Elymus species in western China began diverging 17-8.5 million years ago, during a period of increased aridification as a consequence of the Messinian salinity crisis. Elymus species adapted to drought and high salinity may have developed based on the environmental conditions during this period. Elymus evolution in western China may have been affected by the uplift of the Qinghai-Tibetan Plateau (5 million years ago), when Elymus seeds were dispersed by gravity or wind into a newly heterogeneous habitat, resulting in isolation. PMID:26505371

  19. Inferring polyploid phylogenies from multiply-labeled gene trees

    Directory of Open Access Journals (Sweden)

    Petri Anna

    2009-08-01

    Full Text Available Abstract Background Gene trees that arise in the context of reconstructing the evolutionary history of polyploid species are often multiply-labeled, that is, the same leaf label can occur several times in a single tree. This property considerably complicates the task of forming a consensus of a collection of such trees compared to usual phylogenetic trees. Results We present a method for computing a consensus tree of multiply-labeled trees. As with the well-known greedy consensus tree approach for phylogenetic trees, our method first breaks the given collection of gene trees into a set of clusters. It then aims to insert these clusters one at a time into a tree, starting with the clusters that are supported by most of the gene trees. As the problem to decide whether a cluster can be inserted into a multiply-labeled tree is computationally hard, we have developed a heuristic method for solving this problem. Conclusion We illustrate the applicability of our method using two collections of trees for plants of the genus Silene, that involve several allopolyploids at different levels.

  20. Mate Choice Drives Evolutionary Stability in a Hybrid Complex

    Science.gov (United States)

    Morgado-Santos, Miguel; Pereira, Henrique Miguel

    2015-01-01

    Previous studies have shown that assortative mating acts as a driver of speciation by countering hybridization between two populations of the same species (pre-zygotic isolation) or through mate choice among the hybrids (hybrid speciation). In both speciation types, assortative mating promotes speciation over a transient hybridization stage. We studied mate choice in a hybrid vertebrate complex, the allopolyploid fish Squalius alburnoides. This complex is composed by several genomotypes connected by an intricate reproductive dynamics. We developed a model that predicts the hybrid complex can persist when females exhibit particular mate choice patterns. Our model is able to reproduce the diversity of population dynamic outcomes found in nature, namely the dominance of the triploids and the dominance of the tetraploids, depending on female mate choice patterns and frequency of the parental species. Experimental mate choice trials showed that females exhibit the preferences predicted by the model. Thus, despite the known role of assortative mating in driving speciation, our findings suggest that certain mate choice patterns can instead hinder speciation and support the persistence of hybrids over time without speciation or extinction. PMID:26181664

  1. Accelerated senescence and enhanced disease resistance in hybrid chlorosis lines derived from interspecific crosses between tetraploid wheat and Aegilops tauschii.

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    Hiroki Nakano

    Full Text Available Hybrid chlorosis, a type of hybrid incompatibility, has frequently been reported in inter- and intraspecific crosses of allopolyploid wheat. In a previous study, we reported some types of growth abnormalities such as hybrid necrosis and observed hybrid chlorosis with mild or severe abnormalities in wheat triploids obtained in crosses between tetraploid wheat cultivar Langdon and four Ae. tauschii accessions and in their derived synthetic hexaploids. However, the molecular mechanisms underlying hybrid chlorosis are not well understood. Here, we compared cytology and gene expression in leaves to characterize the abnormal growth in wheat synthetics showing mild and severe chlorosis. In addition, we compared disease resistance to wheat blast fungus. In total 55 and 105 genes related to carbohydrate metabolism and 53 and 89 genes for defense responses were markedly up-regulated in the mild and severe chlorosis lines, respectively. Abnormal chloroplasts formed in the mesophyll cells before the leaves yellowed in the hybrid chlorosis lines. The plants with mild chlorosis showed increased resistance to wheat blast and powdery mildew fungi, although significant differences only in two, third internode length and maturation time, out of the examined agricultural traits were found between the wild type and plants showing mild chlorosis. These observations suggest that senescence might be accelerated in hybrid chlorosis lines of wheat synthetics. Moreover, in wheat synthetics showing mild chlorosis, the negative effects on biomass can be minimized, and they may show substantial fitness under pathogen-polluted conditions.

  2. Spontaneous and divergent hexaploid triticales derived from common wheat × rye by complete elimination of D-genome chromosomes.

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    Hao Li

    Full Text Available Hexaploid triticale could be either synthesized by crossing tetraploid wheat with rye, or developed by crossing hexaploid wheat with a hexaploid triticale or an octoploid triticale.Here two hexaploid triticales with great morphologic divergence derived from common wheat cultivar M8003 (Triticum aestivum L. × Austrian rye (Secale cereale L. were reported, exhibiting high resistance for powdery mildew and stripe rust and potential for wheat improvement. Sequential fluorescence in situ hybridization (FISH and genomic in situ hybridization (GISH karyotyping revealed that D-genome chromosomes were completely eliminated and the whole A-genome, B-genome and R-genome chromosomes were retained in both lines. Furthermore, plentiful alterations of wheat chromosomes including 5A and 7B were detected in both triticales and additionally altered 5B, 7A chromosome and restructured chromosome 2A was assayed in N9116H and N9116M, respectively, even after selfing for several decades. Besides, meiotic asynchrony was displayed and a variety of storage protein variations were assayed, especially in the HMW/LMW-GS region and secalins region in both triticales.This study confirms that whole D-genome chromosomes could be preferentially eliminated in the hybrid of common wheat × rye, "genome shock" was accompanying the allopolyploidization of nascent triticales, and great morphologic divergence might result from the genetic variations. Moreover, new hexaploid triticale lines contributing potential resistance resources for wheat improvement were produced.

  3. Accelerated senescence and enhanced disease resistance in hybrid chlorosis lines derived from interspecific crosses between tetraploid wheat and Aegilops tauschii.

    Science.gov (United States)

    Nakano, Hiroki; Mizuno, Nobuyuki; Tosa, Yukio; Yoshida, Kentaro; Park, Pyoyun; Takumi, Shigeo

    2015-01-01

    Hybrid chlorosis, a type of hybrid incompatibility, has frequently been reported in inter- and intraspecific crosses of allopolyploid wheat. In a previous study, we reported some types of growth abnormalities such as hybrid necrosis and observed hybrid chlorosis with mild or severe abnormalities in wheat triploids obtained in crosses between tetraploid wheat cultivar Langdon and four Ae. tauschii accessions and in their derived synthetic hexaploids. However, the molecular mechanisms underlying hybrid chlorosis are not well understood. Here, we compared cytology and gene expression in leaves to characterize the abnormal growth in wheat synthetics showing mild and severe chlorosis. In addition, we compared disease resistance to wheat blast fungus. In total 55 and 105 genes related to carbohydrate metabolism and 53 and 89 genes for defense responses were markedly up-regulated in the mild and severe chlorosis lines, respectively. Abnormal chloroplasts formed in the mesophyll cells before the leaves yellowed in the hybrid chlorosis lines. The plants with mild chlorosis showed increased resistance to wheat blast and powdery mildew fungi, although significant differences only in two, third internode length and maturation time, out of the examined agricultural traits were found between the wild type and plants showing mild chlorosis. These observations suggest that senescence might be accelerated in hybrid chlorosis lines of wheat synthetics. Moreover, in wheat synthetics showing mild chlorosis, the negative effects on biomass can be minimized, and they may show substantial fitness under pathogen-polluted conditions. PMID:25806790

  4. Backcrossing to increase meiotic stability in triticale.

    Science.gov (United States)

    Giacomin, R M; Assis, R; Brammer, S P; Nascimento Junior, A; Da-Silva, P R

    2015-01-01

    Triticale (X Triticosecale Wittmack) is an intergeneric hybrid derived from a cross between wheat and rye. As a newly created allopolyploid, the plant shows instabilities during the meiotic process, which may result in the loss of fertility. This genomic instability has hindered the success of triticale-breeding programs. Therefore, strategies should be developed to obtain stable triticale lines for use in breeding. In some species, backcrossing has been effective in increasing the meiotic stability of lineages. To assess whether backcrossing has the same effect in triticale, indices of meiotic abnormalities, meiotic index, and pollen viability were determined in genotypes from multiple generations of triticale (P1, P2, F1, F2, BC1a, and BC1b). All analyzed genotypes exhibited instability during meiosis, and their meiotic index values were all lower than normal. However, the backcrosses BC1a and BC1b showed the lowest mean meiotic abnormalities and the highest meiotic indices, demonstrating higher stability. All genotypes showed a high rate of pollen viability, with the backcrosses BC1a and BC1b again exhibiting the best values. Statistical analyses confirmed that backcrossing positively affects the meiotic stability of triticale. Our results show that backcrossing should be considered by breeders aiming to obtain triticale lines with improved genomic stability. PMID:26400358

  5. Evolutionary History of the Chaetognaths Inferred from Actin and 18S-28S rRNA Paralogous Genes

    Directory of Open Access Journals (Sweden)

    J.P. Casanova

    2006-01-01

    Full Text Available The chaetognaths constitute a small and enigmatic phylum of marine invertebrates whose phylogenetic affinities remain uncertain. Our phylogenetical investigations inferred from partial paralogous 18S-28S rRNA genes suggest that the event resulting in the presence of two classes of rRNA genes would have occurred at approximately 300-400 million years and prior to the radiation of extant chaetognath, whereas the taxon, according to both molecular and paleontological data, would be dated from at least the Early Cambrian. These divergent rRNA genes could be the result of a whole ribosomal cluster duplication or of an allopolyploid event during a crisis period, since, the fossil are lacking posterioly to the post-Carboniferous period (c.a., 300 million years. In addition, actin phylogeny evidenced that the cytoplasmic chaetognath actin clustered with the cytoplasmic insect actins, while the muscular chaetognath actins are placed basal to all muscular vertebrate actins. The present study suggests that the gene conversion mechanisms could be inefficient in this taxon; this could explain the conservation of extremely divergent paralogous sequences in the chaetognath genomes which could be correlated to the difficulties to identify a sister group between chaetognaths and other taxa among metazoans.

  6. Reconstructing reticulation history in a phylogenetic framework and the potential of allopatric speciation driven by polyploidy in an agamic complex in Crataegus (Rosaceae).

    Science.gov (United States)

    Lo, Eugenia Y Y; Stefanović, Saša; Dickinson, Timothy A

    2010-12-01

    Polyploidy plays a prominent role in the speciation process in plants. Many species are known to be part of agamic complexes comprising sexual diploids and more or less exclusively asexual polyploids. However, polyploid formation has been studied in very few cases, primarily because of the challenges in examining these cases phylogenetically. In this study, we demonstrate the use of a variety of phylogenetic approaches to unravel origins and infer reticulation history in a diploid-polyploid complex of black-fruited Crataegus. The tree approaches are shown to be useful in testing alternative hypotheses and in revealing genealogies of nuclear genes, particularly in polyploid organisms that may contain multiple copies. Compared to trees, network approaches provide a better indication of reticulate relationships among recently diverged taxa. Taken together, our data point to both the autopolyploid and allopolyploid origins of triploids in natural populations of Crataegus suksdorfii, whereas tetraploids are formed via a triploid bridge, involving the backcross of allotriploid offspring with their diploid C. suksdorfii parent, followed by gene introgression from sympatric C. douglasii. Our findings provide empirical evidence for different pathways of polyploid formation that are all likely to occur within natural populations and the allopatric establishment of neopolyploids subsequent to their formation. PMID:20561052

  7. Mitosis and Interphase of the Highly Polyploid Palm Voanioalagerardii (2n = 606 ± 3).

    Science.gov (United States)

    Röser, Martin

    2015-01-01

    The endemic, highly polyploid, monotypic Madagascan palm genus Voanioala (2n ≈ 606) was studied with regard to mitotic stages and interphase. Features of the cell cycle, morphology and sizes of metaphase chromosomes, fluorochrome banding patterns, and silver staining of NORs of such an extremely high polyploid organism are reported for the first time. On a whole, karyokinesis appears to be stable and efficient. A comparison with closely related palm taxa reveals that V. gerardii is 38-ploid, and comparison with the closely related genera Butia, Cocos (coconut) and Jubaea shows that Voanioala has lost ∼35% of its DNA amount subsequent to polyploidization and has suppressed between 74 and 88% of the original nucleolar organizers. About 10 active NORs are present in the nuclei. An auto- or allopolyploid origin of Voanioala is discussed with respect to currently available nuclear gene data. The biogeographic relations to Jubaeopsis, a closely related, monotypic, apparently likewise relict palm genus from eastern mainland South Africa are discussed. From a cytogenetic point of view, a common polyploid ancestor of both genera is most likely, but the available molecular phylogenetic data are not univocal. PMID:26594788

  8. Cytotaxonomical analysis of Momordica L. (Cucurbitaceae) species of Indian occurrence

    Indian Academy of Sciences (India)

    L. K. Bharathi; A. D. Munshi; Vinod; Shanti Chandrashekaran; T. K. Behera; A. B. Das; K. Joseph John; Vishalnath

    2011-04-01

    Somatic chromosome number and detailed karyotype analysis were carried out in six Indian Momordica species viz. M. balsamina, M. charantia, M. cochinchinensis, M. dioica, M. sahyadrica and M. cymbalaria (syn. Luffa cymbalaria; a taxon of controversial taxonomic identity). The somatic chromosome number $2n = 22$ was reconfirmed in monoecious species (M. balsamina and M. charantia). Out of four dioecious species, the chromosome number was reconfirmed in M. cochinchinensis $(2n = 28)$, M. dioica $(2n = 28)$ and M. subangulata subsp. renigera $(2n = 56)$, while in M. sahyadrica $(2n = 28)$ somatic chromosome number was reported for the first time. A new chromosome number of $2n = 18$ was reported in M. cymbalaria against its previous reports of $2n = 16$, 22. The karyotype analysis of all the species revealed significant numerical and structural variations of chromosomes. It was possible to distinguish chromosomes of M. cymbalaria from other Momordica species and also between monoecious and dioecious taxa of the genus. Morphology and crossability among the dioecious species was also studied. Evidence from morphology, crossability, pollen viability and chromosome synapsis suggests a segmental allopolyploid origin for M. subangulata subsp. renigera. The taxonomic status of the controversial taxon M. cymbalaria was also discussed using morphological, karyological and crossability data.

  9. Molecular cytogenetics of lymegrass and wheat x lymegrass hybrids

    International Nuclear Information System (INIS)

    The genus Leymus (lymegrass) comprises about thirty polyploid perennial grass species in the tribe Triticeae (Poaceae). Leymus has its main distribution in the temperate regions of Eurasia and North America. Its natural habitats range from coastal to inland areas, including diverse soil types and climatic conditions. Lymegrass is a pioneer plant in an open or disturbed habitat, due to the ability of its extensive rhizome system to bind soil/sand and the plant's tolerance to extreme environmental stresses such as salinity and drought. The soil binding quality together with its perennial habit, large seeds and tolerance to diverse environmental conditions, makes lymegrass attractive as a potential crop for farming in marginal habitats or in a sustainable, multi-species, and perennial system of future agriculture. Amphiploids have been developed from crosses between wheat and lymegrass (Triticum x Leymus) with an aim to increase agronomic quality and yield, thus making Triticoleymus a viable, perennial grain crop for sub-arctic regions. Numerous Triticoleymus genotypes have been generated. Intergenomic translocations and various chromosomal rearrangements have been identified. The objective of this study is to characterize these materials, in order to prepare for more targeted breeding strategies. While wheat chromosomes are well characterized and mapped, lymegrass chromosomes are still relatively unknown. The polyploid genus Leymus has only recently been confirmed as being auto- or segmental allopolyploid consisting of the basic Ns genome. In this context, the genus Leymus is extended to include Ns species from other Triticeae genera, i.e. Psathyrostachys, Hordelymus and Hystrix. Isolation and characterization of Ns genome specific DNA sequences will be presented, as well as molecular cytogenetic mapping of these sequences on chromosomes of lymegrass species of geographically different origins. Novel repetitive sequences that can be used to identify intragenomic

  10. Tracing the transcriptomic changes in synthetic Trigenomic allohexaploids of Brassica using an RNA-Seq approach.

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    Qin Zhao

    Full Text Available Polyploidization has played an important role in plant evolution and speciation, and newly formed allopolyploids have experienced rapid transcriptomic changes. Here, we compared the transcriptomic differences between a synthetic Brassica allohexaploid and its parents using a high-throughput RNA-Seq method. A total of 35,644,409 sequence reads were generated, and 32,642 genes were aligned from the data. Totals of 29,260, 29,060, and 29,697 genes were identified in Brassicarapa, Brassicacarinata, and Brassica allohexaploid, respectively. We compared 7,397 differentially expressed genes (DEGs between Brassica hexaploid and its parents, as well as 2,545 nonadditive genes of Brassica hexaploid. We hypothesized that the higher ploidy level as well as secondary polyploidy might have influenced these changes. The majority of the 3,184 DEGs between Brassica hexaploid and its paternal parent, B. rapa, were involved in the biosynthesis of secondary metabolites, plant-pathogen interactions, photosynthesis, and circadian rhythm. Among the 2,233 DEGs between Brassica hexaploid and its maternal parent, B. carinata, several played roles in plant-pathogen interactions, plant hormone signal transduction, ribosomes, limonene and pinene degradation, photosynthesis, and biosynthesis of secondary metabolites. There were more significant differences in gene expression between the allohexaploid and its paternal parent than between it and its maternal parent, possibly partly because of cytoplasmic and maternal effects. Specific functional categories were enriched among the 2,545 nonadditive genes of Brassica hexaploid compared with the additive genes; the categories included response to stimulus, immune system process, cellular process, metabolic process, rhythmic process, and pigmentation. Many transcription factor genes, methyltransferases, and methylation genes showed differential expression between Brassica hexaploid and its parents. Our results demonstrate that the

  11. Characterization of two CENH3 genes and their roles in wheat evolution.

    Science.gov (United States)

    Yuan, Jing; Guo, Xiang; Hu, Jing; Lv, Zhenling; Han, Fangpu

    2015-04-01

    Wheat evolution is complex as a result of successive rounds of allopolyploidization and continuous selection during domestication. Diploid and tetraploid wheat species (Triticum spp.) were used as model systems in which to study the role of centromere-specific histone H3 variant (CENH3) in wheat evolution. We characterized two types of CENH3 genes, named αCENH3 and βCENH3, each of which has three slightly different copies derived from the AA, BB and DD genomes. Specific antibodies were raised against the two CENH3 proteins and were co-localized to centromeres with subtle differences. In most tetraploid wheat species, CENH3 genes are more highly expressed from the AA genome. In wild tetraploids, βCENH3 has a much lower expression level than αCENH3, while in cultivated tetraploids βCENH3 transcripts are enhanced to near αCENH3 levels. Comparison of the CENH3 proteins in wild and cultivated tetraploids revealed that the histone folding domain (HFD) of only βCENH3 is under positive selection, especially in the region responsible for targeting of CENH3 to the centromere. Taken together, positive selection of βCENH3 and its increased expression in tetraploid cultivars are indicative of adaptive evolution. Furthermore, the differences in localization between αCENH3 and βCENH3 observed using fiber fluorescence in situ hybridization (FISH) and immunodetection and in developmental phenotypes resulting from virus-reduced gene silencing imply their functional diversification during wheat evolution. PMID:25557089

  12. Los cariotipos de Cologania grandiflora y Erythrina americana (Leguminosae- Papilionoideae-Phaseoleae de la Reserva Ecológica del Pedregal de San Ángel, México Karyotypes of Cologania grandiflora and Erythrina americana (Leguminosae-Papilionoideae- Phaseoleae of Reserva Ecológica del Pedregal de San Ángel, Mexico

    Directory of Open Access Journals (Sweden)

    Fernando Tapia-Pastrana

    2011-09-01

    Full Text Available Se analizaron citogenéticamente células provenientes de meristemos radiculares de 2 leguminosas, Cologania grandiflora y Erythrina americana, que en la actualidad están incluidas en la flora de la Reserva Ecológica del Pedregal de San Ángel, México, D. F., mediante una técnica de extendido en superficie y secado al aire para determinar los números cromosómicos somáticos. Por vez primera se obtuvieron la morfología cromosómica y otras características cuantitativas de los cariotipos en C. grandiflora (2n= 44= 26m +18sm y en E. americana (2n= 42= 36m + 4sm +2st sat, primeras también en ambos géneros. Cologania y Erythrina se reconocen como poliploides estabilizados y el hallazgo de un único par de cromosomas con satélites (dominancia nucleolar en las especies estudiadas aquí, favorece la opinión de un origen alopoliploide para estos taxa.Meristematic root cells from Cologania grandiflora and Erythrina americana from Reserva Ecológica del Pedregal de San Ángel, Distrito Federal, Mexico, were analyzed cytogenenetically using a surface-spreading and air-drying method. The somatic chromosome numbers were determined. Chromosome morphology and others quantitative features of the karyotypes obtained for first time in C. grandiflora (2n= 44= 26m + 18sm and E. americana (2n= 42= 36m + 4sm + 2st sat and also the first in both genera. Cologania and Erythrina are recognized as stabilized polyploids and the finding of just one pair of chromosomes with satellites (nucleolar dominance in the species analyzed here supports the view of allopolyploid origin of these taxa.

  13. Phylogeny of Crocus (Iridaceae) based on one chloroplast and two nuclear loci: ancient hybridization and chromosome number evolution.

    Science.gov (United States)

    Harpke, Dörte; Meng, Shuchun; Rutten, Twan; Kerndorff, Helmut; Blattner, Frank R

    2013-03-01

    Crocus consists of about 100 species distributed from western Europe and northern Africa to western China, with the center of diversity on the Balkan Peninsula and in Asia Minor. Our study focuses on clarifying phylogenetic relationships and chromosome number evolution within the genus using sequences of the chloroplast trnL-F region, the nuclear ribosomal DNA internal transcribed spacer (ITS) region, and a part of the nuclear single-copy gene pCOSAt103. In a combined dataset of ITS and trnL-F sequences, 115 individuals representing 110 taxa from both subgenera and all sections and series of Crocus were analyzed with Bayesian phylogenetic inference. For pCOSAt103 79 individuals representing 74 Crocus taxa were included, and for the majority of them PCR amplicons were cloned and up to eight clones per individual were sequenced to detect allopolyploidization events. Romulea species were included as outgroup in both analyses. Characteristics of seed surface structures were evaluated by scanning electron microscopy. Phylogenetic analysis of ITS/trnL-F data resulted in a monophyletic genus Crocus, probably monophyletic sections Crocus and Nudiscapus, and inferred monophyly for eight of the 15 series of the genus. The C. biflorus aggregate, thought to be consisting of closely related subspecies, was found to be polyphyletic, the taxa occurring within three major clades in the phylogenetic tree. Cloning of pCOSAt103 resulted in the detection of homoeologous copies in about one third of the taxa of section Nudiscapus, indicating an allotetraploid origin of this section. Reconstruction of chromosome number evolution along the phylogenetic tree using a probabilistic and a parsimony approach arrived at partly contradictory results. Both analyses agreed however on the occurrence of multiple polyploidization and dysploidy events. B chromosomes evolved at least five times independently within the genus, preferentially in clades characterized by karyotype changes. PMID:23123733

  14. A whole-genome, radiation hybrid mapping resource of hexaploid wheat.

    Science.gov (United States)

    Tiwari, Vijay K; Heesacker, Adam; Riera-Lizarazu, Oscar; Gunn, Hilary; Wang, Shichen; Wang, Yi; Gu, Young Q; Paux, Etienne; Koo, Dal-Hoe; Kumar, Ajay; Luo, Ming-Cheng; Lazo, Gerard; Zemetra, Robert; Akhunov, Eduard; Friebe, Bernd; Poland, Jesse; Gill, Bikram S; Kianian, Shahryar; Leonard, Jeffrey M

    2016-04-01

    Generating a contiguous, ordered reference sequence of a complex genome such as hexaploid wheat (2n = 6x = 42; approximately 17 GB) is a challenging task due to its large, highly repetitive, and allopolyploid genome. In wheat, ordering of whole-genome or hierarchical shotgun sequencing contigs is primarily based on recombination and comparative genomics-based approaches. However, comparative genomics approaches are limited to syntenic inference and recombination is suppressed within the pericentromeric regions of wheat chromosomes, thus, precise ordering of physical maps and sequenced contigs across the whole-genome using these approaches is nearly impossible. We developed a whole-genome radiation hybrid (WGRH) resource and tested it by genotyping a set of 115 randomly selected lines on a high-density single nucleotide polymorphism (SNP) array. At the whole-genome level, 26 299 SNP markers were mapped on the RH panel and provided an average mapping resolution of approximately 248 Kb/cR1500 with a total map length of 6866 cR1500 . The 7296 unique mapping bins provided a five- to eight-fold higher resolution than genetic maps used in similar studies. Most strikingly, the RH map had uniform bin resolution across the entire chromosome(s), including pericentromeric regions. Our research provides a valuable and low-cost resource for anchoring and ordering sequenced BAC and next generation sequencing (NGS) contigs. The WGRH developed for reference wheat line Chinese Spring (CS-WGRH), will be useful for anchoring and ordering sequenced BAC and NGS based contigs for assembling a high-quality, reference sequence of hexaploid wheat. Additionally, this study provides an excellent model for developing similar resources for other polyploid species. PMID:26945524

  15. DNA barcodes from four loci provide poor resolution of taxonomic groups in the genus Crataegus.

    Science.gov (United States)

    Zarrei, Mehdi; Talent, Nadia; Kuzmina, Maria; Lee, Jeanette; Lund, Jensen; Shipley, Paul R; Stefanović, Saša; Dickinson, Timothy A

    2015-01-01

    DNA barcodes can facilitate identification of organisms especially when morphological characters are limited or unobservable. To what extent this potential is realized in specific groups of plants remains to be determined. Libraries of barcode sequences from well-studied authoritatively identified plants represented by herbarium voucher specimens are needed in order for DNA barcodes to serve their intended purpose, where this is possible, and to understand the reasons behind their failure to do so, when this occurs. We evaluated four loci, widely regarded as universal DNA barcodes for plants, for their utility in hawthorn species identification. Three plastid regions, matK, rbcLa and psbA-trnH, and the internal transcribed spacer 2 (ITS2) of nuclear ribosomal DNA discriminate only some of the species of Crataegus that can be recognized on the basis of their morphology etc. This is, in part, because in Rosaceae tribe Maleae most individual plastid loci yield relatively little taxonomic resolution and, in part, because the effects of allopolyploidization have not been eliminated by concerted evolution of the ITS regions. Although individual plastid markers provided generally poor resolution of taxonomic groups in Crataegus, a few species were notable exceptions. In contrast, analyses of concatenated sequences of the 3 plastid barcode loci plus 11 additional plastid loci gave a well-resolved maternal phylogeny. In the ITS2 tree, different individuals of some species formed groups with taxonomically unrelated species. This is a sign of lineage sorting due to incomplete concerted evolution in ITS2. Incongruence between the ITS2 and plastid trees is best explained by hybridization between different lineages within the genus. In aggregate, limited between-species variation in plastid loci, hybridization and a lack of concerted evolution in ITS2 all combine to limit the utility of standard barcoding markers in Crataegus. These results have implications for authentication

  16. Evolution of the beta-amylase gene in the temperate grasses: Non-purifying selection, recombination, semiparalogy, homeology and phylogenetic signal.

    Science.gov (United States)

    Minaya, Miguel; Díaz-Pérez, Antonio; Mason-Gamer, Roberta; Pimentel, Manuel; Catalán, Pilar

    2015-10-01

    Low-copy nuclear genes (LCNGs) have complex genetic architectures and evolutionary dynamics. However, unlike multicopy nuclear genes, LCNGs are rarely subject to gene conversion or concerted evolution, and they have higher mutation rates than organellar or nuclear ribosomal DNA markers, so they have great potential for improving the robustness of phylogenetic reconstructions at all taxonomic levels. In this study, our first objective is to evaluate the evolutionary dynamics of the LCNG β-amylase by testing for potential pseudogenization, paralogy, homeology, recombination, and phylogenetic incongruence within a broad representation of the main Pooideae lineages. Our second objective is to determine whether β-amylase shows sufficient phylogenetic signal to reconstruct the evolutionary history of the Pooid grasses. A multigenic (ITS, matK, ndhF, trnTL, and trnLF) tree of the study group provided a framework for assessing the β-amylase phylogeny. Eight accessions showed complete absence of selection, suggesting putative pseudogenic copies or other relaxed selection pressures; resolution of Vulpia alopecuros 2x clones indicated its potential (semi) paralogy; and homeologous copies of allopolyploid species Festuca simensis, F. fenas, and F. arundinacea tracked their Mediterranean origin. Two recombination events were found within early-diverged Pooideae lineages, and five within the PACCMAD clade. The unexpected phylogenetic relationships of 37 grass species (26% of the sampled species) highlight the frequent occurrence of non-treelike evolutionary events, so this LCNG should be used with caution as a phylogenetic marker. However, once the pitfalls are identified and removed, the phylogenetic reconstruction of the grasses based on the β-amylase exon+intron positions is optimal at all taxonomic levels. PMID:26032971

  17. Untangling reticulate evolutionary relationships among New World and Hawaiian mints (Stachydeae, Lamiaceae).

    Science.gov (United States)

    Roy, Tilottama; Cole, Logan W; Chang, Tien-Hao; Lindqvist, Charlotte

    2015-08-01

    The phenomenon of polyploidy and hybridization usually results in novel genetic combinations, leading to complex, reticulate evolution and incongruence among gene trees, which in turn may show different phylogenetic histories than the inherent species tree. The largest tribe within the subfamily Lamioideae (Lamiaceae), Stachydeae, which includes the globally distributed Stachys, and one of the largest Hawaiian angiosperm radiations, the endemic mints, is a widespread and taxonomically challenging lineage displaying a wide spectrum of morphological and chromosomal diversity. Previous molecular phylogenetic studies have showed that while the Hawaiian mints group with Mexican-South American Stachys based on chloroplast DNA sequence data, nuclear ribosomal DNA (nrDNA) sequences suggest that they are most closely related to temperate North American Stachys. Here, we have utilized five independently inherited, low-copy nuclear loci, and a variety of phylogenetic methods, including multi-locus coalescence-based tree reconstructions, to provide insight into the complex origins and evolutionary relationships between the New World Stachys and the Hawaiian mints. Our results demonstrate incongruence between individual gene trees, grouping the Hawaiian mints with both temperate North American and Meso-South American Stachys clades. However, our multi-locus coalescence tree is concurrent with previous nrDNA results placing them within the temperate North American Stachys clade. Our results point toward a possible allopolyploid hybrid origin of the Hawaiian mints arising from temperate North American and Meso-South American ancestors, as well as a reticulate origin for South American Stachys. As such, our study is another significant step toward further understanding the putative parentage and the potential influence of hybridization and incomplete lineage sorting in giving rise to this insular plant lineage, which following colonization underwent rapid morphological and

  18. Evidence of Allopolyploidy in Urochloa humidicola Based on Cytological Analysis and Genetic Linkage Mapping.

    Science.gov (United States)

    Vigna, Bianca B Z; Santos, Jean C S; Jungmann, Leticia; do Valle, Cacilda B; Mollinari, Marcelo; Pastina, Maria M; Pagliarini, Maria Suely; Garcia, Antonio A F; Souza, Anete P

    2016-01-01

    The African species Urochloa humidicola (Rendle) Morrone & Zuloaga (syn. Brachiaria humidicola (Rendle) Schweick.) is an important perennial forage grass found throughout the tropics. This species is polyploid, ranging from tetra to nonaploid, and apomictic, which makes genetic studies challenging; therefore, the number of currently available genetic resources is limited. The genomic architecture and evolution of U. humidicola and the molecular markers linked to apomixis were investigated in a full-sib F1 population obtained by crossing the sexual accession H031 and the apomictic cultivar U. humidicola cv. BRS Tupi, both of which are hexaploid. A simple sequence repeat (SSR)-based linkage map was constructed for the species from 102 polymorphic and specific SSR markers based on simplex and double-simplex markers. The map consisted of 49 linkage groups (LGs) and had a total length of 1702.82 cM, with 89 microsatellite loci and an average map density of 10.6 cM. Eight homology groups (HGs) were formed, comprising 22 LGs, and the other LGs remained ungrouped. The locus that controls apospory (apo-locus) was mapped in LG02 and was located 19.4 cM from the locus Bh027.c.D2. In the cytological analyses of some hybrids, bi- to hexavalents at diakinesis were observed, as well as two nucleoli in some meiocytes, smaller chromosomes with preferential allocation within the first metaphase plate and asynchronous chromosome migration to the poles during anaphase. The linkage map and the meiocyte analyses confirm previous reports of hybridization and suggest an allopolyploid origin of the hexaploid U. humidicola. This is the first linkage map of an Urochloa species, and it will be useful for future quantitative trait locus (QTL) analysis after saturation of the map and for genome assembly and evolutionary studies in Urochloa spp. Moreover, the results of the apomixis mapping are consistent with previous reports and confirm the need for additional studies to search for a co

  19. Assessment of adaptive evolution between wheat and rice as deduced from full-length common wheat cDNA sequence data and expression patterns

    Directory of Open Access Journals (Sweden)

    Hayashizaki Yoshihide

    2009-06-01

    Full Text Available Abstract Background Wheat is an allopolyploid plant that harbors a huge, complex genome. Therefore, accumulation of expressed sequence tags (ESTs for wheat is becoming particularly important for functional genomics and molecular breeding. We prepared a comprehensive collection of ESTs from the various tissues that develop during the wheat life cycle and from tissues subjected to stress. We also examined their expression profiles in silico. As full-length cDNAs are indispensable to certify the collected ESTs and annotate the genes in the wheat genome, we performed a systematic survey and sequencing of the full-length cDNA clones. This sequence information is a valuable genetic resource for functional genomics and will enable carrying out comparative genomics in cereals. Results As part of the functional genomics and development of genomic wheat resources, we have generated a collection of full-length cDNAs from common wheat. By grouping the ESTs of recombinant clones randomly selected from the full-length cDNA library, we were able to sequence 6,162 independent clones with high accuracy. About 10% of the clones were wheat-unique genes, without any counterparts within the DNA database. Wheat clones that showed high homology to those of rice were selected in order to investigate their expression patterns in various tissues throughout the wheat life cycle and in response to abiotic-stress treatments. To assess the variability of genes that have evolved differently in wheat and rice, we calculated the substitution rate (Ka/Ks of the counterparts in wheat and rice. Genes that were preferentially expressed in certain tissues or treatments had higher Ka/Ks values than those in other tissues and treatments, which suggests that the genes with the higher variability expressed in these tissues is under adaptive selection. Conclusion We have generated a high-quality full-length cDNA resource for common wheat, which is essential for continuation of the

  20. Dating and functional characterization of duplicated genes in the apple (Malus domestica Borkh. by analyzing EST data

    Directory of Open Access Journals (Sweden)

    Sanzol Javier

    2010-05-01

    Full Text Available Abstract Background Gene duplication is central to genome evolution. In plants, genes can be duplicated through small-scale events and large-scale duplications often involving polyploidy. The apple belongs to the subtribe Pyrinae (Rosaceae, a diverse lineage that originated via allopolyploidization. Both small-scale duplications and polyploidy may have been important mechanisms shaping the genome of this species. Results This study evaluates the gene duplication and polyploidy history of the apple by characterizing duplicated genes in this species using EST data. Overall, 68% of the apple genes were clustered into families with a mean copy-number of 4.6. Analysis of the age distribution of gene duplications supported a continuous mode of small-scale duplications, plus two episodes of large-scale duplicates of vastly different ages. The youngest was consistent with the polyploid origin of the Pyrinae 37-48 MYBP, whereas the older may be related to γ-triplication; an ancient hexapolyploidization previously characterized in the four sequenced eurosid genomes and basal to the eurosid-asterid divergence. Duplicated genes were studied for functional diversification with an emphasis on young paralogs; those originated during or after the formation of the Pyrinae lineage. Unequal assignment of single-copy genes and gene families to Gene Ontology categories suggested functional bias in the pattern of gene retention of paralogs. Young paralogs related to signal transduction, metabolism, and energy pathways have been preferentially retained. Non-random retention of duplicated genes seems to have mediated the expansion of gene families, some of which may have substantially increased their members after the origin of the Pyrinae. The joint analysis of over-duplicated functional categories and phylogenies, allowed evaluation of the role of both polyploidy and small-scale duplications during this process. Finally, gene expression analysis indicated that 82

  1. Global transgenerational gene expression dynamics in two newly synthesized allohexaploid wheat (Triticum aestivum lines

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    Qi Bao

    2012-01-01

    Full Text Available Abstract Background Alteration in gene expression resulting from allopolyploidization is a prominent feature in plants, but its spectrum and extent are not fully known. Common wheat (Triticum aestivum was formed via allohexaploidization about 10,000 years ago, and became the most important crop plant. To gain further insights into the genome-wide transcriptional dynamics associated with the onset of common wheat formation, we conducted microarray-based genome-wide gene expression analysis on two newly synthesized allohexaploid wheat lines with chromosomal stability and a genome constitution analogous to that of the present-day common wheat. Results Multi-color GISH (genomic in situ hybridization was used to identify individual plants from two nascent allohexaploid wheat lines between Triticum turgidum (2n = 4x = 28; genome BBAA and Aegilops tauschii (2n = 2x = 14; genome DD, which had a stable chromosomal constitution analogous to that of common wheat (2n = 6x = 42; genome BBAADD. Genome-wide analysis of gene expression was performed for these allohexaploid lines along with their parental plants from T. turgidum and Ae. tauschii, using the Affymetrix Gene Chip Wheat Genome-Array. Comparison with the parental plants coupled with inclusion of empirical mid-parent values (MPVs revealed that whereas the great majority of genes showed the expected parental additivity, two major patterns of alteration in gene expression in the allohexaploid lines were identified: parental dominance expression and non-additive expression. Genes involved in each of the two altered expression patterns could be classified into three distinct groups, stochastic, heritable and persistent, based on their transgenerational heritability and inter-line conservation. Strikingly, whereas both altered patterns of gene expression showed a propensity of inheritance, identity of the involved genes was highly stochastic, consistent with the involvement of diverse Gene Ontology (GO

  2. A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses

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    Robin Charles

    2011-03-01

    Full Text Available Abstract Background Polyploidy is important from a phylogenetic perspective because of its immense past impact on evolution and its potential future impact on diversification, survival and adaptation, especially in plants. Molecular population genetics studies of polyploid organisms have been difficult because of problems in sequencing multiple-copy nuclear genes using Sanger sequencing. This paper describes a method for sequencing a barcoded mixture of targeted gene regions using next-generation sequencing methods to overcome these problems. Results Using 64 3-bp barcodes, we successfully sequenced three chloroplast and two nuclear gene regions (each of which contained two gene copies with up to two alleles per individual in a total of 60 individuals across 11 species of Australian Poa grasses. This method had high replicability, a low sequencing error rate (after appropriate quality control and a low rate of missing data. Eighty-eight percent of the 320 gene/individual combinations produced sequence reads, and >80% of individuals produced sufficient reads to detect all four possible nuclear alleles of the homeologous nuclear loci with 95% probability. We applied this method to a group of sympatric Australian alpine Poa species, which we discovered to share an allopolyploid ancestor with a group of American Poa species. All markers revealed extensive allele sharing among the Australian species and so we recommend that the current taxonomy be re-examined. We also detected hypermutation in the trnH-psbA marker, suggesting it should not be used as a land plant barcode region. Some markers indicated differentiation between Tasmanian and mainland samples. Significant positive spatial genetic structure was detected at Conclusions Our results demonstrate that 454 sequencing of barcoded amplicon mixtures can be used to reliably sample all alleles of homeologous loci in polyploid species and successfully investigate phylogenetic relationships among

  3. Mutation induction for domestication of Cuphea: Effects of gamma rays

    International Nuclear Information System (INIS)

    (n=22) would be more promising candidates than C. aperta for domestication: Both are characterized by erect growth, a high number of fruits which are generally borne on the upper portion of the plant, surplus space in the fruits (enhancing the chances of developing a non-shattering type), and lauric acid yields (as a percentage of total seed fatty acids) of 63.3 and 53.9%, respectively. C. tolucana is a diploid whereas C. wrightii may be an allopolyploid. Therefore, in a new series of experiments, dry seeds (2% moisture) of Cuphea tolucana and C. wrightii were exposed to 0 to 30 kR of gamma radiation. After irradiation the seeds were hydrated in oxygenated water. Responses of both species were curvilinear but C. tolucana was considerably more sensitive to gamma radiation than C. wrightii. The range of exposure causing 40 to 60% plant height reduction was approximately 5 to 8 kR in C. tolucana and 9 to 17 kR in C. wrightii. In a second experiment under the same conditions, C. tolucana was exposed to levels of 0 to 12.8 kR and C. wrightii to levels of 0 to 60 kR. A 50% plant height reduction was caused by 10-12 kR in C. tolucana, and between 11 to 18 kR in C. wrightii. Results of both experiments are consistent with the experience that chromosome number and tolerance to radiation are positively correlated. For large scale mutation breeding work, the appropriate gamma ray doses should be 8-12 kR for C. tolucana, and between 11 to 18 kR for C. wrightii. (author)

  4. RBCS1 expression in coffee: Coffea orthologs, Coffea arabica homeologs, and expression variability between genotypes and under drought stress

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    Vieira Luiz GE

    2011-05-01

    Full Text Available Abstract Background In higher plants, the inhibition of photosynthetic capacity under drought is attributable to stomatal and non-stomatal (i.e., photochemical and biochemical effects. In particular, a disruption of photosynthetic metabolism and Rubisco regulation can be observed. Several studies reported reduced expression of the RBCS genes, which encode the Rubisco small subunit, under water stress. Results Expression of the RBCS1 gene was analysed in the allopolyploid context of C. arabica, which originates from a natural cross between the C. canephora and C. eugenioides species. Our study revealed the existence of two homeologous RBCS1 genes in C. arabica: one carried by the C. canephora sub-genome (called CaCc and the other carried by the C. eugenioides sub-genome (called CaCe. Using specific primer pairs for each homeolog, expression studies revealed that CaCe was expressed in C. eugenioides and C. arabica but was undetectable in C. canephora. On the other hand, CaCc was expressed in C. canephora but almost completely silenced in non-introgressed ("pure" genotypes of C. arabica. However, enhanced CaCc expression was observed in most C. arabica cultivars with introgressed C. canephora genome. In addition, total RBCS1 expression was higher for C. arabica cultivars that had recently introgressed C. canephora genome than for "pure" cultivars. For both species, water stress led to an important decrease in the abundance of RBCS1 transcripts. This was observed for plants grown in either greenhouse or field conditions under severe or moderate drought. However, this reduction of RBCS1 gene expression was not accompanied by a decrease in the corresponding protein in the leaves of C. canephora subjected to water withdrawal. In that case, the amount of RBCS1 was even higher under drought than under unstressed (irrigated conditions, which suggests great stability of RBCS1 under adverse water conditions. On the other hand, for C. arabica, high nocturnal

  5. Melhoramento do cafeeiro: V - Melhoramento por hibridação

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    C. A. Krug

    1952-06-01

    genetic factors of one species in the genetic background of other coffee species. About 2500 inter-varietal and inter-specific artificial hybridization have been made in Campinas during the last 20 years. The economic value of some of these hybrids has been stressed in this paper and special attention has been called to the inter-specific hybrids involving the tetraploid C. arabica and other known diploid species as C. canephora, C. Dewevrei and C. congensis. After chromosome doubling of these triploid hybrids, the resulting allopolyploids may be of economic value.

  6. 新疆春小麦4个地方品种5S rRNA基因变异分析%The 5S rRNA Gene Sequence Variation of Four Local Variety in Xinjiang Spring Wheat

    Institute of Scientific and Technical Information of China (English)

    布热比艳木·吾布力卡斯木; 吾甫尔·米吉提; 米日古丽·马木提; 维尼拉·吾甫尔; 祖路皮亚·载买尔

    2015-01-01

    -and intra-specific sequence, the 5S rDNA multigene family has proven to be a useful tool to characterize genome composition in genomes. We have cloned and sequenced 128 repeat units of the 5S rRNA gene from germplasm resources in Xinjiang spring wheat, Sequence analysis revealed that each accession has two size classes, the short class with sequences 326~422 bp long, and the long class with sequences 481~491 bp long. Sequences were assorted into six unit classes by sequence alignment, Blast searching and cladistic analysis.Accessions ZM5291 and ZM52300 both contain Short A2, Short D1, Short G1, Long A1, Long D1 and Long{S1 unit classes, but accessions ZM5306 and ZM5343 only contain Short A2, Short D1, Short G1 and Long{S1 unit classes, the Long A1 and Long D1 unit class were missing. According to the others previous study on diploid species of Aegilops and Tritic um and in allopolyploid species of Tritic um formed from them, we characterize the four accession has AABBDD genome, and confirm they were Triticum aestivum. For the first time, we found six different unit classes in Triticum aestivum. According to the distribution of the six unit class in this four germplasm resources, we presume that this four germplasm resources from different origin may have formed at the different time, and accessions ZM5291 and ZM5300 may have abundant genetic resources from their progenitors than ZM5306 and ZM5343. These results provide new evidence for characterize genome composition of Xinjiang spring wheat, and parent selection for breeding work.