From Gene Trees to a Dated Allopolyploid Network: Insights from the Angiosperm Genus Viola (Violaceae)

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Marcussen, Thomas; Heier, Lise; Brysting, Anne K.; Oxelman, Bengt; Jakobsen, Kjetill S.

2015-01-01

Allopolyploidization accounts for a significant fraction of speciation events in many eukaryotic lineages. However, existing phylogenetic and dating methods require tree-like topologies and are unable to handle the network-like phylogenetic relationships of lineages containing allopolyploids. No explicit framework has so far been established for evaluating competing network topologies, and few attempts have been made to date phylogenetic networks. We used a four-step approach to generate a dated polyploid species network for the cosmopolitan angiosperm genus Viola L. (Violaceae Batch.). The genus contains ca 600 species and both recent (neo-) and more ancient (meso-) polyploid lineages distributed over 16 sections. First, we obtained DNA sequences of three low-copy nuclear genes and one chloroplast region, from 42 species representing all 16 sections. Second, we obtained fossil-calibrated chronograms for each nuclear gene marker. Third, we determined the most parsimonious multilabeled genome tree and its corresponding network, resolved at the section (not the species) level. Reconstructing the “correct” network for a set of polyploids depends on recovering all homoeologs, i.e., all subgenomes, in these polyploids. Assuming the presence of Viola subgenome lineages that were not detected by the nuclear gene phylogenies (“ghost subgenome lineages”) significantly reduced the number of inferred polyploidization events. We identified the most parsimonious network topology from a set of five competing scenarios differing in the interpretation of homoeolog extinctions and lineage sorting, based on (i) fewest possible ghost subgenome lineages, (ii) fewest possible polyploidization events, and (iii) least possible deviation from expected ploidy as inferred from available chromosome counts of the involved polyploid taxa. Finally, we estimated the homoploid and polyploid speciation times of the most parsimonious network. Homoploid speciation times were estimated by

Evolutionary dynamics across discontinuous freshwater systems: Rapid expansions and repeated allopolyploid origins in the Palearctic white water-lilies (Nymphaea)

Czech Academy of Sciences Publication Activity Database

Volkova, P. A.; Trávníček, Pavel; Brochmann, C.

2010-01-01

Roč. 59, č. 2 (2010), s. 483-494 ISSN 0040-0262 R&D Projects: GA ČR GD206/08/H049 Institutional research plan: CEZ:AV0Z60050516 Keywords : AFLP * allopolyploid speciation * flow cytometry Subject RIV: EF - Botanics Impact factor: 2.364, year: 2010

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

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.

Mimulus peregrinus (Phrymaceae: A new British allopolyploid species

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Mario Vallejo-Marin

2012-07-01

Full Text Available Polyploidization plays an important role in species formation as chromosome doubling results in strong reproductive isolation between derivative and parental taxa. In this note I describe a new species, Mimulus peregrinus (Phrymaceae, which represents the first recorded instance of a new British polyploid species of Mimulus (2n = 6x = 92 that has arisen since the introduction of this genus into the United Kingdom in the 1800’s. M. peregrinus presents floral and vegetative characteristics intermediate between M. guttatus and M. luteus, but can be distinguished from all naturalized British Mimulus species and hybrids based on a combination of reproductive and vegetative traits. M. peregrinus displays high pollen and seed fertility as well as traits usually associated with genome doubling such as increased pollen and stomata size. The intermediate characteristics of M. peregrinus between M. guttatus (2n = 2x = 28 and M. luteus (2n = 4x = 60-62, and its close affinity with the highly sterile, triploid (2n = 3x = 44-45 hybrid taxon M. × robertsii (M. guttatus × M. luteus, suggests that M. peregrinus may constitute an example of recent allopolyploid speciation.

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

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

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

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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.

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

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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.

Three-genome mosses: complex double allopolyploid origins for triploid gametophytes in Sphagnum.

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Karlin, Eric F; Boles, S B; Ricca, M; Temsch, E M; Greilhuber, J; Shaw, A J

2009-04-01

This paper documents the occurrence of allotriploidy (having three differentiated genomes) in gametophytes of two Southern Hemisphere Sphagnum species (S. australe, S. falcatulum). The pattern of microsatellite alleles indicates that both species are composed of a complex of allodiploid and allotriploid gametophytes, with the latter resulting from two allopolyploidization events. No haploid (n = x) gametophytes were found for either species. The ploidal levels suggested by the pattern of microsatellite alleles were confirmed by flow cytometry and Feulgen DNA image densitometry. For both S. australe and S. falcatulum, the respective allodiploid plants (or their ancestors) are one of the parent species of the allotriploid plants. This is the first report of triploidy in Sphagnum gametophytes occurring in nature and also the first report of the presence of three differentiated genomes in any bryophyte. It is also the first report of intersectional allopolyploidy in Sphagnum, with S. australe appearing to have parental species from Sphagnum sections Rigida and Sphagnum, and S. falcatulum having parental species from Sphagnum sections Cuspidata and Subsecunda. In both species, the allotriploid cytotypes were the most prevalent cytotype on the South Island of New Zealand. The pattern of microsatellite alleles shows the presence of two genetically distinct populations of allodiploid S. australe, possibly indicating multiple origins of polyploidy for that allodiploid cytotype. Morphological evidence is also highly indicative of recurrent polyploidy in the allotriploid cytotype of S. falcatulum. Allopolyploidy has clearly played a major evolutionary role in these two Southern Hemisphere taxa. This study, in conjunction with other recent research, indicates that allopolyploidy is a common, if not the predominant, form of polyploidy in Sphagnum.

Digital gene expression analysis of gene expression differences within Brassica diploids and allopolyploids.

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Jiang, Jinjin; Wang, Yue; Zhu, Bao; Fang, Tingting; Fang, Yujie; Wang, Youping

2015-01-27

Brassica includes many successfully cultivated crop species of polyploid origin, either by ancestral genome triplication or by hybridization between two diploid progenitors, displaying complex repetitive sequences and transposons. The U's triangle, which consists of three diploids and three amphidiploids, is optimal for the analysis of complicated genomes after polyploidization. Next-generation sequencing enables the transcriptome profiling of polyploids on a global scale. We examined the gene expression patterns of three diploids (Brassica rapa, B. nigra, and B. oleracea) and three amphidiploids (B. napus, B. juncea, and B. carinata) via digital gene expression analysis. In total, the libraries generated between 5.7 and 6.1 million raw reads, and the clean tags of each library were mapped to 18547-21995 genes of B. rapa genome. The unambiguous tag-mapped genes in the libraries were compared. Moreover, the majority of differentially expressed genes (DEGs) were explored among diploids as well as between diploids and amphidiploids. Gene ontological analysis was performed to functionally categorize these DEGs into different classes. The Kyoto Encyclopedia of Genes and Genomes analysis was performed to assign these DEGs into approximately 120 pathways, among which the metabolic pathway, biosynthesis of secondary metabolites, and peroxisomal pathway were enriched. The non-additive genes in Brassica amphidiploids were analyzed, and the results indicated that orthologous genes in polyploids are frequently expressed in a non-additive pattern. Methyltransferase genes showed differential expression pattern in Brassica species. Our results provided an understanding of the transcriptome complexity of natural Brassica species. The gene expression changes in diploids and allopolyploids may help elucidate the morphological and physiological differences among Brassica species.

Evolution of rDNA in Nicotiana Allopolyploids: A Potential Link between rDNA Homogenization and Epigenetics

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Kovarik, Ales; Dadejova, Martina; Lim, Yoong K.; Chase, Mark W.; Clarkson, James J.; Knapp, Sandra; Leitch, Andrew R.

2008-01-01

Background The evolution and biology of rDNA have interested biologists for many years, in part, because of two intriguing processes: (1) nucleolar dominance and (2) sequence homogenization. We review patterns of evolution in rDNA in the angiosperm genus Nicotiana to determine consequences of allopolyploidy on these processes. Scope Allopolyploid species of Nicotiana are ideal for studying rDNA evolution because phylogenetic reconstruction of DNA sequences has revealed patterns of species divergence and their parents. From these studies we also know that polyploids formed over widely different timeframes (thousands to millions of years), enabling comparative and temporal studies of rDNA structure, activity and chromosomal distribution. In addition studies on synthetic polyploids enable the consequences of de novo polyploidy on rDNA activity to be determined. Conclusions We propose that rDNA epigenetic expression patterns established even in F1 hybrids have a material influence on the likely patterns of divergence of rDNA. It is the active rDNA units that are vulnerable to homogenization, which probably acts to reduce mutational load across the active array. Those rDNA units that are epigenetically silenced may be less vulnerable to sequence homogenization. Selection cannot act on these silenced genes, and they are likely to accumulate mutations and eventually be eliminated from the genome. It is likely that whole silenced arrays will be deleted in polyploids of 1 million years of age and older. PMID:18310159

The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres

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Yuan, Daojun; Tang, Zhonghui; Wang, Maojun; Gao, Wenhui; Tu, Lili; Jin, Xin; Chen, Lingling; He, Yonghui; Zhang, Lin; Zhu, Longfu; Li, Yang; Liang, Qiqi; Lin, Zhongxu; Yang, Xiyan; Liu, Nian; Jin, Shuangxia; Lei, Yang; Ding, Yuanhao; Li, Guoliang; Ruan, Xiaoan; Ruan, Yijun; Zhang, Xianlong

2015-01-01

Gossypium hirsutum contributes the most production of cotton fibre, but G. barbadense is valued for its better comprehensive resistance and superior fibre properties. However, the allotetraploid genome of G. barbadense has not been comprehensively analysed. Here we present a high-quality assembly of the 2.57 gigabase genome of G. barbadense, including 80,876 protein-coding genes. The double-sized genome of the A (or At) (1.50 Gb) against D (or Dt) (853 Mb) primarily resulted from the expansion of Gypsy elements, including Peabody and Retrosat2 subclades in the Del clade, and the Athila subclade in the Athila/Tat clade. Substantial gene expansion and contraction were observed and rich homoeologous gene pairs with biased expression patterns were identified, suggesting abundant gene sub-functionalization occurred by allopolyploidization. More specifically, the CesA gene family has adapted differentially temporal expression patterns, suggesting an integrated regulatory mechanism of CesA genes from At and Dt subgenomes for the primary and secondary cellulose biosynthesis of cotton fibre in a “relay race”-like fashion. We anticipate that the G. barbadense genome sequence will advance our understanding the mechanism of genome polyploidization and underpin genome-wide comparison research in this genus. PMID:26634818

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

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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

Ghasemi et al., Afr J Tradit Complement Altern Med. (2013) 10(2 ...

African Journals Online (AJOL)

AJTCAM

Perennial Stems, Leaves. Internal. Anti-calculus, anti-septic, kidney problems, urine tube infection and laxative (for baby). 5. Allium akaka Gmelin. Aliaceae or ..... Tragopogon graminifolius. DC. Asteraceae. Haplook. Shang. Salsify. H. Annual Root, Flowers. Internal/. External. Emollient, sore throat and wound healing. 111.

Wheat hybridization and polyploidization results in deregulation of small RNAs.

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Kenan-Eichler, Michal; Leshkowitz, Dena; Tal, Lior; Noor, Elad; Melamed-Bessudo, Cathy; Feldman, Moshe; Levy, Avraham A

2011-06-01

Speciation via interspecific or intergeneric hybridization and polyploidization triggers genomic responses involving genetic and epigenetic alterations. Such modifications may be induced by small RNAs, which affect key cellular processes, including gene expression, chromatin structure, cytosine methylation and transposable element (TE) activity. To date, the role of small RNAs in the context of wide hybridization and polyploidization has received little attention. In this work, we performed high-throughput sequencing of small RNAs of parental, intergeneric hybrid, and allopolyploid plants that mimic the genomic changes occurring during bread wheat speciation. We found that the percentage of small RNAs corresponding to miRNAs increased with ploidy level, while the percentage of siRNAs corresponding to TEs decreased. The abundance of most miRNA species was similar to midparent values in the hybrid, with some deviations, as seen in overrepresentation of miR168, in the allopolyploid. In contrast, the number of siRNAs corresponding to TEs strongly decreased upon allopolyploidization, but not upon hybridization. The reduction in corresponding siRNAs, together with decreased CpG methylation, as shown here for the Veju element, represent hallmarks of TE activation. TE-siRNA downregulation in the allopolyploid may contribute to genome destabilization at the initial stages of speciation. This phenomenon is reminiscent of hybrid dysgenesis in Drosophila.

Edible flowers - antioxidant activity and impact on cell viability

OpenAIRE

Kuceková, Zdenka; Mlček, Jiří; Humpolíček, Petr; Rop, Otakar

2013-01-01

The phenolic compound composition, antioxidant activity and impact on cell viability of edible flower extracts of Allium schoenoprasum; Bellis perennis; Cichorium intybus; Rumex acetosa; Salvia pratensis; Sambucus nigra; Taraxacum officinale; Tragopogon pratensis; Trifolium repens and Viola arvensis was examined for the first time. Total phenolic content of the flowers of these plants fell between 11.72 and 42.74 mg of tannin equivalents/kg of dry matter. Antioxidant activity ranged from 35.5...

Unraveling reticulate evolution in North American Dryopteris (Dryopteridaceae

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Sessa Emily B

2012-06-01

Full Text Available Abstract Background The thirteen species of Dryopteris in North America have long been suspected of having undergone a complicated history of reticulate evolution via allopolyploid hybridization. Various explanations for the origins of the allopolyploid taxa have been suggested, and though most lines of evidence have supported the so-called “semicristata” hypothesis, contention over the group’s history has continued in several recent, conflicting studies. Results Sequence data from nine plastid and two nuclear markers were collected from 73 accessions representing 35 species of Dryopteris. Sequences from each of the allopolyploids are most closely related to their progenitor species as predicted by the “semicristata” hypothesis. Allotetraploid D. campyloptera appears to be derived from a hybrid between diploid D. expansa and D. intermedia; D. celsa, from diploid D. ludoviciana x D. goldiana; and D. carthusiana and D. cristata, from diploid “D. semicristata” x D. intermedia and D. ludoviciana, respectively. Allohexaploid D. clintoniana appears to be derived from D. cristata x D.goldiana. The earliest estimated dates of formation of the allopolyploids, based on divergence time analyses, were within the last 6 Ma. We found no evidence for recurrent formation of any of the allopolyploids. The sexual allopolyploid taxa are derived from crosses between parents that show intermediate levels of genetic divergence relative to all pairs of potential progenitors. In addition, the four allotetraploids are transgressive with respect to geographic range relative to one or both of their parents (their ranges extend beyond those of the parents, suggesting that ecological advantages in novel habitats or regions may promote long-term regional coexistence of the hybrid taxa with their progenitors. Conclusions This study provides the first thorough evaluation of the North American complex of woodferns using extensive sampling of taxa and genetic

Allo-allo-triploid Sphagnum × falcatulum: single individuals contain most of the Holantarctic diversity for ancestrally indicative markers.

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Karlin, Eric F; Smouse, Peter E

2017-08-01

Allopolyploids exhibit both different levels and different patterns of genetic variation than are typical of diploids. However, scant attention has been given to the partitioning of allelic information and diversity in allopolyploids, particularly that among homeologous monoploid components of the hologenome. Sphagnum × falcatulum is a double allopolyploid peat moss that spans a considerable portion of the Holantarctic. With monoploid genomes from three ancestral species, this organism exhibits a complex evolutionary history involving serial inter-subgeneric allopolyploidizations. Studying populations from three disjunct regions [South Island (New Zealand); Tierra de Fuego archipelago (Chile, Argentina); Tasmania (Australia)], allelic information for five highly stable microsatellite markers that differed among the three (ancestral) monoploid genomes was examined. Using Shannon information and diversity measures, the holoploid information, as well as the information within and among the three component monoploid genomes, was partitioned into separate components for individuals within and among populations and regions, and those information components were then converted into corresponding diversity measures. The majority (76 %) of alleles detected across these five markers are most likely to have been captured by hybridization, but the information within each of the three monoploid genomes varied, suggesting a history of recurrent allopolyploidization between ancestral species containing different levels of genetic diversity. Information within individuals, equivalent to the information among monoploid genomes (for this dataset), was relatively stable, and represented 83 % of the grand total information across the Holantarctic, with both inter-regional and inter-population diversification each accounting for about 5 % of the total information. Sphagnum × falcatulum probably inherited the great majority of its genetic diversity at these markers by reticulation

Gene-Tree Reconciliation with MUL-Trees to Resolve Polyploidy Events.

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Gregg, W C Thomas; Ather, S Hussain; Hahn, Matthew W

2017-11-01

Polyploidy can have a huge impact on the evolution of species, and it is a common occurrence, especially in plants. The two types of polyploids-autopolyploids and allopolyploids-differ in the level of divergence between the genes that are brought together in the new polyploid lineage. Because allopolyploids are formed via hybridization, the homoeologous copies of genes within them are at least as divergent as orthologs in the parental species that came together to form them. This means that common methods for estimating the parental lineages of allopolyploidy events are not accurate, and can lead to incorrect inferences about the number of gene duplications and losses. Here, we have adapted an algorithm for topology-based gene-tree reconciliation to work with multi-labeled trees (MUL-trees). By definition, MUL-trees have some tips with identical labels, which makes them a natural representation of the genomes of polyploids. Using this new reconciliation algorithm we can: accurately place allopolyploidy events on a phylogeny, identify the parental lineages that hybridized to form allopolyploids, distinguish between allo-, auto-, and (in most cases) no polyploidy, and correctly count the number of duplications and losses in a set of gene trees. We validate our method using gene trees simulated with and without polyploidy, and revisit the history of polyploidy in data from the clades including both baker's yeast and bread wheat. Our re-analysis of the yeast data confirms the allopolyploid origin and parental lineages previously identified for this group. The method presented here should find wide use in the growing number of genomes from species with a history of polyploidy. [Polyploidy; reconciliation; whole-genome duplication.]. © The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Comparative proteomic study on Brassica hexaploid and its parents provides new insights into the effects of polyploidization.

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Shen, Yanyue; Zhang, Yu; Zou, Jun; Meng, Jinling; Wang, Jianbo

2015-01-01

Polyploidy has played an important role in promoting plant evolution through genomic merging and doubling. Although genomic and transcriptomic changes have been observed in polyploids, the effects of polyploidization on proteomic divergence are poorly understood. In this study, we reported quantitative analysis of proteomic changes in leaves of Brassica hexaploid and its parents using isobaric tags for relative and absolute quantitation (iTRAQ) coupled with mass spectrometry. A total of 2044 reproducible proteins were quantified by at least two unique peptides. We detected 452 proteins differentially expressed between Brassica hexaploid and its parents, and 100 proteins were non-additively expressed in Brassica hexaploid, which suggested a trend of non-additive protein regulation following genomic merger and doubling. Functional categories of cellular component biogenesis, immune system process, and response to stimulus, were significantly enriched in non-additive proteins, probably providing a driving force for variation and adaptation in allopolyploids. In particular, majority of the total 452 differentially expressed proteins showed expression level dominance of one parental expression, and there was an expression level dominance bias toward the tetraploid progenitor. In addition, the percentage of differentially expressed proteins that matched previously reported differentially genes were relatively low. This study aimed to get new insights into the effects of polyploidization on proteomic divergence. Using iTRAQ LC-MS/MS technology, we identified 452 differentially expressed proteins between allopolyploid and its parents which involved in response to stimulus, multi-organism process, and immune system process, much more than previous studies using 2-DE coupled with mass spectrometry technology. Therefore, our manuscript represents the most comprehensive analysis of protein profiles in allopolyploid and its parents, which will lead to a better understanding of

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

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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

Epigenomics: dissecting hybridization and polyploidization.

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Jackson, Scott A

2017-06-19

Epigenetic profiling in diploid, allopolyploid, and domesticated cotton shows that despite most DNA methylation being conserved and stably inherited, alterations likely due to hybridization and domestication affect gene expression.

Cytoplasmic and Genomic Effects on Meiotic Pairing in Brassica Hybrids and Allotetraploids from Pair Crosses of Three Cultivated Diploids

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Cui, Cheng; Ge, Xianhong; Gautam, Mayank; Kang, Lei; Li, Zaiyun

2012-01-01

Interspecific hybridization and allopolyploidization contribute to the origin of many important crops. Synthetic Brassica is a widely used model for the study of genetic recombination and “fixed heterosis” in allopolyploids. To investigate the effects of the cytoplasm and genome combinations on meiotic recombination, we produced digenomic diploid and triploid hybrids and trigenomic triploid hybrids from the reciprocal crosses of three Brassica diploids (B. rapa, AA; B. nigra, BB; B. oleracea, CC). The chromosomes in the resultant hybrids were doubled to obtain three allotetraploids (B. juncea, AA.BB; B. napus, AA.CC; B. carinata, BB.CC). Intra- and intergenomic chromosome pairings in these hybrids were quantified using genomic in situ hybridization and BAC-FISH. The level of intra- and intergenomic pairings varied significantly, depending on the genome combinations and the cytoplasmic background and/or their interaction. The extent of intragenomic pairing was less than that of intergenomic pairing within each genome. The extent of pairing variations within the B genome was less than that within the A and C genomes, each of which had a similar extent of pairing. Synthetic allotetraploids exhibited nondiploidized meiotic behavior, and their chromosomal instabilities were correlated with the relationship of the genomes and cytoplasmic background. Our results highlight the specific roles of the cytoplasm and genome to the chromosomal behaviors of hybrids and allopolyploids. PMID:22505621

Hybridization between invasive Spartina Densiflora (Poaceae) and native S. Foliosa in San Francisco Bay, California, USA

Science.gov (United States)

Rapid evolution in contemporary time can result when related species, brought together through human-aided introduction, hybridize. The evolutionary consequences of post introduction hybridization range from allopolyploid speciation to extinction of species through genetic amalg...

Evolutionary implications of permanent odd polyploidy in the stable sexual, pentaploid of Rosa canina L

Czech Academy of Sciences Publication Activity Database

Lim, K.Y.; Werlemark, G.; Matyášek, Roman; Bringloe, J.B.; Sieber, V.; El Mokadem, H.; Meynet, J.; Hemming, J.; Leitch, A.R.; Roberts, A.V.

2005-01-01

Roč. 94, č. 5 (2005), s. 501-506 ISSN 0018-067X Institutional research plan: CEZ:AV0Z50040507 Keywords : chromosome pairing * gynogenetic haploid * allopolyploid Subject RIV: BO - Biophysics Impact factor: 2.166, year: 2005

Polyphyly, gene-duplication and extensive allopolyploidy framed the evolution of the ephemeral Vulpia grasses and other fine-leaved Loliinae (Poaceae).

Science.gov (United States)

Díaz-Pérez, A J; Sharifi-Tehrani, M; Inda, L A; Catalán, P

2014-10-01

The fine-leaved Loliinae is one of the temperate grass lineages that is richest in number of evolutionary switches from perennial to annual life-cycle, and also shows one of the most complex reticulate patterns involving distinct diploid and allopolyploid lineages. Eight distinct annual lineages, that have traditionally been placed in the genus Vulpia and in other fine-leaved ephemeral genera, have apparently emerged from different perennial Festuca ancestors. The phenotypically similar Vulpia taxa have been reconstructed as polyphyletic, with polyploid lineages showing unclear relationships to their purported diploid relatives. Interspecific and intergeneric hybridization is, however, rampant across different lineages. An evolutionary analysis based on cloned nuclear low-copy GBSSI (Granule-Bound Starch Synthase I) and multicopy ITS (Internal Transcribed Spacer) sequences has been conducted on representatives of most Vulpia species and other fine-leaved lineages, using Bayesian consensus and agreement trees, networking split graphs and species tree-based approaches, to disentangle their phylogenetic relationships and to identify the parental genome donors of the allopolyploids. Both data sets were able to reconstruct a congruent phylogeny in which Vulpia was resolved as polyphyletic from at least three main ancestral diploid lineages. These, in turn, participated in the origin of the derived allopolyploid Vulpia lineages together with other Festuca-like, Psilurus-like and some unknown genome donors. Long-distance dispersal events were inferred to explain the polytopic origin of the Mediterranean and American Vulpia lineages. Copyright © 2014 Elsevier Inc. All rights reserved.

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

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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...

Meiotic homoeologous recombination-based alien gene introgression in the genomics era of wheat

Science.gov (United States)

Wheat (Triticum spp.) has a narrow genetic basis due to its allopolyploid origin. However, wheat has numerous wild relatives usable for expanding genetic variability of its genome through meiotic homoeologous recombination. Traditionally, laborious cytological analyses have been employed to detect h...

The effects of inheritance in tetraploids on genetic diversity and population divergence

NARCIS (Netherlands)

Meirmans, P.G.; van Tienderen, P.H.

2013-01-01

Polyploids are traditionally classified into allopolyploids and autopolyploids, based on their evolutionary origin and their disomic or multisomic mode of inheritance. Over the past decade it has become increasingly clear that there is a continuum between disomic and multisomic inheritance, with the

Evolution of allopolyploids in the genus Nicotiana

Czech Academy of Sciences Publication Activity Database

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

2007-01-01

Roč. 15, č. 2 (2007), s. 8 ISSN 0967-3849. [16th International Chromosome Conference. 25.08.2007-29.08.2007, Amsterdam] R&D Projects: GA ČR(CZ) GD204/05/H505; GA ČR(CZ) GA521/07/0116; GA ČR(CZ) GA204/05/0687 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : diploidisation * rDNA homogenisation * genome translocations Subject RIV: BO - Biophysics

DNA methylation alteration is a major consequence of genome doubling in autotetraploid Brassica rapa

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Xu Yanhao

2017-01-01

Full Text Available Polyploids are typically classified as autopolyploids or allopolyploids based on the origin of their chromosome sets. Autopolyploidy is much more common than traditionally believed. Allopolyploidization, accompanied by genomic and transcriptomic changes, has been well investigated. In this study, genetic, DNA methylation and gene expression changes in autotetraploid Brassica rapa were investigated. No genetic alteration was detected using an amplified fragment length polymorphism (AFLP approach. Using a cDNA-AFLP approach, approximately 0.58% of fragments showed changes in gene expression in autotetraploid B. rapa. The methylation-sensitive amplification polymorphism (MSAP analysis showed that approximately 1.7% of the fragments underwent DNA methylation changes upon genome doubling, with hypermethylation and demethylation changes equally affected. Fragments displaying changes in gene expression and methylation status were isolated and then sequenced and characterized, respectively. This study showed that variation in cytosine methylation is a major consequence of genome doubling in autotetraploid Brassica rapa.

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

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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.

Fulltext PDF

Indian Academy of Sciences (India)

State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, .... embryo rescue or hormone treatment was applied on the F1 seeds. ... genies of S1 plants, treated and fixed as described above, ..... Comai L. 2000 Genetic and epigenetic interactions in allopolyploid plants.

Taxonomy of Cyrtochilum-alliance (Orchidaceae) in the light of molecular and morphological data

Czech Academy of Sciences Publication Activity Database

Szlachetko, D. L.; Kolanowska, Marta; Naczk, A.; Gorniak, M.; Dudek, M.; Rutkowski, P.; Chiron, G.

2017-01-01

Roč. 58, JAN (2017), č. článku 8. ISSN 1999-3110 Institutional support: RVO:86652079 Keywords : ribosomal-rna genes * hybrid speciation * chloroplast dna * allopolyploid speciation * reconstructing patterns * phylogenetic inference * reticulate evolution * concerted evolution * horizontal transfer * sequence alignment * Cyrtochilum * Monophyly * New combinations * New species * Oncidiinae * Paraphyly * Taxonomy Subject RIV: EF - Botanics OBOR OECD: Plant sciences, botany Impact factor: 1.452, year: 2016

Untangling nucleotide diversity and evolution of the H genome in polyploid Hordeum and Elymus species based on the single copy of nuclear gene DMC1.

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Dongfa Sun

Full Text Available Numerous hybrid and polypoid species are found within the Triticeae. It has been suggested that the H subgenome of allopolyploid Elymus (wheatgrass species originated from diploid Hordeum (barley species, but the role of hybridization between polyploid Elymus and Hordeum has not been studied. It is not clear whether gene flow across polyploid Hordeum and Elymus species has occurred following polyploid speciation. Answering these questions will provide new insights into the formation of these polyploid species, and the potential role of gene flow among polyploid species during polyploid evolution. In order to address these questions, disrupted meiotic cDNA1 (DMC1 data from the allopolyploid StH Elymus are analyzed together with diploid and polyploid Hordeum species. Phylogenetic analysis revealed that the H copies of DMC1 sequence in some Elymus are very close to the H copies of DMC1 sequence in some polyploid Hordeum species, indicating either that the H genome in theses Elymus and polyploid Hordeum species originated from same diploid donor or that gene flow has occurred among them. Our analysis also suggested that the H genomes in Elymus species originated from limited gene pool, while H genomes in Hordeum polyploids have originated from broad gene pools. Nucleotide diversity (π of the DMC1 sequences on H genome from polyploid species (π = 0.02083 in Elymus, π = 0.01680 in polyploid Hordeum is higher than that in diploid Hordeum (π = 0.01488. The estimates of Tajima's D were significantly departure from the equilibrium neutral model at this locus in diploid Hordeum species (P<0.05, suggesting an excess of rare variants in diploid species which may not contribute to the origination of polyploids. Nucleotide diversity (π of the DMC1 sequences in Elymus polyploid species (π = 0.02083 is higher than that in polyploid Hordeum (π = 0.01680, suggesting that the degree of relationships between two parents of a polyploid might be a factor

Recombination between Homeologous Chromosomes in Lager Yeasts leads to Loss of Function of the Hybrid GPH1 Gene.

OpenAIRE

BOND, URSULA

2009-01-01

PUBLISHED Yeasts used in the production of lagers contain complex allopolyploid genomes, resulting from the fusion of two different yeast species closely related to Saccharomyces cerevisiae and Saccharomyces bayanus. Recombination between the homoeologous chromosomes has generated a number of hybrid chromosomes. These recombination events provide potential for adaptive evolution through the loss or gain of gene function. We have examined the genotypic and phenotypic effects of one of the c...

Candidate Gene Identification of Flowering Time Genes in Cotton

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Corrinne E. Grover

2015-07-01

Full Text Available Flowering time control is critically important to all sexually reproducing angiosperms in both natural ecological and agronomic settings. Accordingly, there is much interest in defining the genes involved in the complex flowering-time network and how these respond to natural and artificial selection, the latter often entailing transitions in day-length responses. Here we describe a candidate gene analysis in the cotton genus , which uses homologs from the well-described flowering network to bioinformatically and phylogenetically identify orthologs in the published genome sequence from Ulbr., one of the two model diploid progenitors of the commercially important allopolyploid cottons, L. and L. Presence and patterns of expression were evaluated from 13 aboveground tissues related to flowering for each of the candidate genes using allopolyploid as a model. Furthermore, we use a comparative context to determine copy number variability of each key gene family across 10 published angiosperm genomes. Data suggest a pattern of repeated loss of duplicates following ancient whole-genome doubling events in diverse lineages. The data presented here provide a foundation for understanding both the parallel evolution of day-length neutrality in domesticated cottons and the flowering-time network, in general, in this important crop plant.

Characterization and expression patterns of small RNAs in synthesized Brassica hexaploids.

Science.gov (United States)

Shen, Yanyue; Zhao, Qin; Zou, Jun; Wang, Wenliang; Gao, Yi; Meng, Jinling; Wang, Jianbo

2014-06-01

Polyploidy has played an important role in promoting plant evolution through genomic merging and doubling. We used high-throughput sequencing to compare miRNA expression profiles between Brassica hexaploid and its parents. A total of 613, 784 and 742 known miRNAs were identified in Brassica rapa, Brassica carinata, and Brassica hexaploid, respectively. We detected 618 miRNAs were differentially expressed (log(2)Ratio ≥ 1, P ≤ 0.05) between Brassica hexaploid and its parents, and 425 miRNAs were non-additively expressed in Brassica hexaploid, which suggest a trend of non-additive miRNA regulation following hybridization and polyploidization. Remarkably, majority of the non-additively expressed miRNAs in the Brassica hexaploid are repressed, and there was a bias toward repression of B. rapa miRNAs, which is consistent with the progenitor-biased gene repression in the synthetic allopolyploids. In addition, we identified 653 novel mature miRNAs in Brassica hexaploid and its parents. Finally, we found that almost all the non-additive accumulation of siRNA clusters exhibited a low-parent pattern in Brassica hexaploid. Non-additive small RNA regulation is involved in a range of biological pathways, probably providing a driving force for variation and adaptation in allopolyploids.

DNA methylation analysis of allotetraploid hybrids of red crucian carp (Carassius auratus red var. and common carp (Cyprinus carpio L..

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Jun Xiao

Full Text Available Hybridization and polyploidization may lead to divergence in adaptation and boost speciation in angiosperms and some lower animals. Epigenetic change plays a significant role in the formation and adaptation of polyploidy. Studies of the effects of methylation on genomic recombination and gene expression in allopolyploid plants have achieved good progress. However, relevant advances in polyploid animals have been relatively slower. In the present study, we used the bisexual, fertile, genetically stable allotetraploid generated by hybridization of Carassius auratus red var. and Cyprinus carpio L. to investigate cytosine methylation level using methylation-sensitive amplification polymorphism (MSAP analysis. We observed 38.31% of the methylation changes in the allotetraploid compared with the parents at 355 randomly selected CCGG sites. In terms of methylation status, these results indicate that the level of methylation modification in the allotetraploid may have increased relative to that in the parents. We also found that the major methylation changes were hypermethylation on some genomic fragments and genes related to metabolism or cell cycle regulation. These results provide circumstantial evidence that DNA methylation might be related to the gene expression and phenotype variation in allotetraploid hybrids. Our study partly fulfils the need for epigenetic research in polyploid animals, and provides evidence for the epigenetic regulation of allopolyploids.

The defence?associated transcriptome of hexaploid wheat displays homoeolog expression and induction bias

OpenAIRE

Powell, Jonathan J.; Fitzgerald, Timothy L.; Stiller, Jiri; Berkman, Paul J.; Gardiner, Donald M.; Manners, John M.; Henry, Robert J.; Kazan, Kemal

2016-01-01

Summary Bread wheat (Triticum aestivum L.) is an allopolyploid species containing three ancestral genomes. Therefore, three homoeologous copies exist for the majority of genes in the wheat genome. Whether different homoeologs are differentially expressed (homoeolog expression bias) in response to biotic and abiotic stresses is poorly understood. In this study, we applied a RNA?seq approach to analyse homoeolog?specific global gene expression patterns in wheat during infection by the fungal pa...

Recreating Stable Brachypodium hybridum Allotetraploids by Uniting the Divergent Genomes of B. distachyon and B. stacei

Science.gov (United States)

Dinh Thi, Vinh Ha; Coriton, Olivier; Le Clainche, Isabelle; Arnaud, Dominique; Gordon, Sean P.; Linc, Gabriella; Catalan, Pilar; Hasterok, Robert; Vogel, John P.; Jahier, Joseph; Chalhoub, Boulos

2016-01-01

Brachypodium hybridum (2n = 30) is a natural allopolyploid with highly divergent sub-genomes derived from two extant diploid species, B. distachyon (2n = 10) and B. stacei (2n = 20) that differ in chromosome evolution and number. We created synthetic B. hybridum allotetraploids by hybridizing various lines of B. distachyon and B. stacei. The initial amphihaploid F1 interspecific hybrids were obtained at low frequencies when B. distachyon was used as the maternal parent (0.15% or 0.245% depending on the line used) and were sterile. No hybrids were obtained from reciprocal crosses or when autotetraploids of the parental species were crossed. Colchicine treatment was used to double the genome of the F1 amphihaploid lines leading to allotetraploids. The genome-doubled F1 plants produced a few S1 (first selfed generation) seeds after self-pollination. S1 plants from one parental combination (Bd3-1×Bsta5) were fertile and gave rise to further generations whereas those of another parental combination (Bd21×ABR114) were sterile, illustrating the importance of the parental lineages crossed. The synthetic allotetraploids were stable and resembled the natural B. hybridum at the phenotypic, cytogenetic and genomic levels. The successful creation of synthetic B. hybridum offers the possibility to study changes in genome structure and regulation at the earliest stages of allopolyploid formation in comparison with the parental species and natural B. hybridum. PMID:27936041

Potential of Start Codon Targeted (SCoT) markers for DNA fingerprinting of newly synthesized tritordeums and their respective parents.

Science.gov (United States)

Cabo, Sandra; Ferreira, Luciana; Carvalho, Ana; Martins-Lopes, Paula; Martín, António; Lima-Brito, José Eduardo

2014-08-01

Hexaploid tritordeum (H(ch)H(ch)AABB; 2n = 42) results from the cross between Hordeum chilense (H(ch)H(ch); 2n = 14) and cultivated durum wheat (Triticum turgidum ssp. durum (AABB; 2n = 28). Morphologically, tritordeum resembles the wheat parent, showing promise for agriculture and wheat breeding. Start Codon Targeted (SCoT) polymorphism is a recently developed technique that generates gene-targeted markers. Thus, we considered it interesting to evaluate its potential for the DNA fingerprinting of newly synthesized hexaploid tritordeums and their respective parents. In this study, 60 SCoT primers were tested, and 18 and 19 of them revealed SCoT polymorphisms in the newly synthesized tritordeum lines HT27 and HT22, respectively, and their parents. An analysis of the presence/absence of bands among tritordeums and their parents revealed three types of polymorphic markers: (i) shared by tritordeums and one of their parents, (ii) exclusively amplified in tritordeums, and (iii) exclusively amplified in the parents. No polymorphism was detected among individuals of each parental species. Three SCoT markers were exclusively amplified in tritordeums of lines HT22 and HT27, being considered as polyploidization-induced rearrangements. About 70% of the SCoT markers of H. chilense origin were not transmitted to the allopolyploids of both lines, and most of the SCoTs scored in the newly synthesized allopolyploids originated from wheat, reinforcing the potential use of tritordeum as an alternative crop.

Origins, genetic structure, and systematics of the narrow endemic peatmosses (Sphagnum): S. guwassanense and S. triseriporum (Sphagnaceae).

Science.gov (United States)

Shaw, A Jonathan; Shaw, Blanka; Johnson, Matthew G; Higuchi, Masanobu; Arikawa, Tomotsugu; Ueno, Takeshi; Devos, Nicolas

2013-06-01

Sphagnum dominates vast expanses of wetland habitats throughout the northern hemisphere and species delimitation within the genus is important because floristic changes associated with a warming global climate may have measureable impacts on large-scale ecological processes. Most northern hemisphere peatmoss species (Sphagnum) have circumboreal ranges, but the Japanese species generally known as S. calymmatophyllum is endemic to Honshu Island. This prompted a population genetic and phylogenetic analysis to resolve the origin(s), population structure, and phylogenetic relationships of this morphologically variable species. • Sixty plants collected from Mt. Gassan and Mt. Hakkoda were genotyped for 12 microsatellite loci. Two plastid loci and three anonymous nuclear loci were sequenced in a subset of the plants, plus representatives from 10 closely related species. • Gametophytes exhibited fixed or nearly fixed heterozygosity at 9-10 of the 12 microsatellite loci. Two genetic groups were resolved by the microsatellite data, individuals showed no evidence of admixture, and the two groups of plants differ in morphology. They are heterozygous for different sets of alleles. The two taxa share plastid DNA sequences with two species that are common in Alaska. • Two taxa were distinguished: S. guwassanense and S. triseriporum. Both are allopolyploids; they originated independently from different but closely related progenitors. The maternal progenitor was likely either S. orientale or S. inexspectatum. The two allopolyploid taxa are heterozygous for (different) private microsatellite alleles, and one progenitor could be extinct.

Disentangling the origins of cultivated sweet potato (Ipomoea batatas (L.) Lam.).

Science.gov (United States)

Roullier, Caroline; Duputié, Anne; Wennekes, Paul; Benoit, Laure; Fernández Bringas, Víctor Manuel; Rossel, Genoveva; Tay, David; McKey, Doyle; Lebot, Vincent

2013-01-01

Sweet potato (Ipomoea batatas (L.) Lam., Convolvulaceae) counts among the most widely cultivated staple crops worldwide, yet the origins of its domestication remain unclear. This hexaploid species could have had either an autopolyploid origin, from the diploid I. trifida, or an allopolyploid origin, involving genomes of I. trifida and I. triloba. We generated molecular genetic data for a broad sample of cultivated sweet potatoes and its diploid and polyploid wild relatives, for noncoding chloroplast and nuclear ITS sequences, and nuclear SSRs. Our data did not support an allopolyploid origin for I. batatas, nor any contribution of I. triloba in the genome of domesticated sweet potato. I. trifida and I. batatas are closely related although they do not share haplotypes. Our data support an autopolyploid origin of sweet potato from the ancestor it shares with I. trifida, which might be similar to currently observed tetraploid wild Ipomoea accessions. Two I. batatas chloroplast lineages were identified. They show more divergence with each other than either does with I. trifida. We thus propose that cultivated I. batatas have multiple origins, and evolved from at least two distinct autopolyploidization events in polymorphic wild populations of a single progenitor species. Secondary contact between sweet potatoes domesticated in Central America and in South America, from differentiated wild I. batatas populations, would have led to the introgression of chloroplast haplotypes of each lineage into nuclear backgrounds of the other, and to a reduced divergence between nuclear gene pools as compared with chloroplast haplotypes.

Partial preferential chromosome pairing is genotype dependent in tetraploid rose.

Science.gov (United States)

Bourke, Peter M; Arens, Paul; Voorrips, Roeland E; Esselink, G Danny; Koning-Boucoiran, Carole F S; Van't Westende, Wendy P C; Santos Leonardo, Tiago; Wissink, Patrick; Zheng, Chaozhi; van Geest, Geert; Visser, Richard G F; Krens, Frans A; Smulders, Marinus J M; Maliepaard, Chris

2017-04-01

It has long been recognised that polyploid species do not always neatly fall into the categories of auto- or allopolyploid, leading to the term 'segmental allopolyploid' to describe everything in between. The meiotic behaviour of such intermediate species is not fully understood, nor is there consensus as to how to model their inheritance patterns. In this study we used a tetraploid cut rose (Rosa hybrida) population, genotyped using the 68K WagRhSNP array, to construct an ultra-high-density linkage map of all homologous chromosomes using methods previously developed for autotetraploids. Using the predicted bivalent configurations in this population we quantified differences in pairing behaviour among and along homologous chromosomes, leading us to correct our estimates of recombination frequency to account for this behaviour. This resulted in the re-mapping of 25 695 SNP markers across all homologues of the seven rose chromosomes, tailored to the pairing behaviour of each chromosome in each parent. We confirmed the inferred differences in pairing behaviour among chromosomes by examining repulsion-phase linkage estimates, which also carry information about preferential pairing and recombination. Currently, the closest sequenced relative to rose is Fragaria vesca. Aligning the integrated ultra-dense rose map with the strawberry genome sequence provided a detailed picture of the synteny, confirming overall co-linearity but also revealing new genomic rearrangements. Our results suggest that pairing affinities may vary along chromosome arms, which broadens our current understanding of segmental allopolyploidy. © 2017 The Authors The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.

Interploidal hybridization and mating patterns in the Sphagnum subsecundum complex.

Science.gov (United States)

Ricca, M; Szövényi, P; Temsch, E M; Johnson, M G; Shaw, A J

2011-08-01

Polyploidization is thought to result in instant sympatric speciation, but several cases of hybrid zones between one of the parental species and its polyploid derivative have been documented. Previous work showed that diploid Sphagnum lescurii is an allopolyploid derived from the haploids S. lescurii (maternal progenitor) and S. subsecundum (paternal progenitor). Here, we report the results from analyses of a population where allodiploid and haploid S. lescurii co-occur and produce sporophytes. We tested (i) whether haploids and diploids form hybrid triploid sporophytes; (ii) how hybrid and nonhybrid sporophytes compare in fitness; (iii) whether hybrid sporophytes form viable spores; (iv) the ploidy of any viable gametophyte offspring from hybrid sporophytes; (v) the relative viability of sporelings derived from hybrid and nonhybrid sporophytes; and (vi) if interploidal hybridization results in introgression between the allopolyploid and its haploid progenitor. We found that triploid hybrid sporophytes do occur and are larger than nonhybrid sporophytes, but exhibit very low germination percentages and produce sporelings that develop more slowly than those from nonhybrid sporophytes. All sporophytes attached to haploid gametophytes were triploid and were sired by diploid males, but all sporophytes attached to diploid gametophytes were tetraploid. This asymmetric pattern of interploidal hybridization is related to an absence of haploid male gametophytes in the population. Surprisingly, all sporelings from triploid sporophytes were triploid, yet were genetically variable, suggesting some form of aberrant meiosis that warrants further study. There was limited (but some) evidence of introgression between allodiploid and haploid S. lescurii. © 2011 Blackwell Publishing Ltd.

Disentangling the origins of cultivated sweet potato (Ipomoea batatas (L. Lam..

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Caroline Roullier

Full Text Available Sweet potato (Ipomoea batatas (L. Lam., Convolvulaceae counts among the most widely cultivated staple crops worldwide, yet the origins of its domestication remain unclear. This hexaploid species could have had either an autopolyploid origin, from the diploid I. trifida, or an allopolyploid origin, involving genomes of I. trifida and I. triloba. We generated molecular genetic data for a broad sample of cultivated sweet potatoes and its diploid and polyploid wild relatives, for noncoding chloroplast and nuclear ITS sequences, and nuclear SSRs. Our data did not support an allopolyploid origin for I. batatas, nor any contribution of I. triloba in the genome of domesticated sweet potato. I. trifida and I. batatas are closely related although they do not share haplotypes. Our data support an autopolyploid origin of sweet potato from the ancestor it shares with I. trifida, which might be similar to currently observed tetraploid wild Ipomoea accessions. Two I. batatas chloroplast lineages were identified. They show more divergence with each other than either does with I. trifida. We thus propose that cultivated I. batatas have multiple origins, and evolved from at least two distinct autopolyploidization events in polymorphic wild populations of a single progenitor species. Secondary contact between sweet potatoes domesticated in Central America and in South America, from differentiated wild I. batatas populations, would have led to the introgression of chloroplast haplotypes of each lineage into nuclear backgrounds of the other, and to a reduced divergence between nuclear gene pools as compared with chloroplast haplotypes.

Asymmetric evolution and domestication in allotetraploid cotton (Gossypium hirsutum L.

Directory of Open Access Journals (Sweden)

Lei Fang

2017-04-01

Full Text Available Polyploidy plays a major role in genome evolution, which corresponds to environmental changes over millions of years. The mechanisms of genome evolution, particularly during the process of domestication, are of broad interest in the fields of plant science and crop breeding. Upland cotton is derived from the hybridization and polyploidization of its ancient A and D diploid ancestors. As a result, cotton is a model for polyploid genome evolution and crop domestication. To explore the genomic mysteries of allopolyploid cotton, we investigated asymmetric evolution and domestication in the A and D subgenomes. Interestingly, more structural rearrangements have been characterized in the A subgenome than in the D subgenome. Correspondingly, more transposable elements, a greater number of lost and disrupted genes, and faster evolution have been identified in the A subgenome. In contrast, the centromeric retroelement (RT-domain related sequence of tetraploid cotton derived from the D subgenome progenitor was found to have invaded the A subgenome centromeres after allotetrapolyploid formation. Although there is no genome-wide expression bias between the subgenomes, as with expression-level alterations, gene expression bias of homoeologous gene pairs is widespread and varies from tissue to tissue. Further, there are more positively selected genes for fiber yield and quality in the A subgenome and more for stress tolerance in the D subgenome, indicating asymmetric domestication. This review highlights the asymmetric subgenomic evolution and domestication of allotetraploid cotton, providing valuable genomic resources for cotton research and enhancing our understanding of the basis of many other allopolyploids.

Species-Level Phylogeny and Polyploid Relationships in Hordeum (Poaceae) Inferred by Next-Generation Sequencing and In Silico Cloning of Multiple Nuclear Loci.

Science.gov (United States)

Brassac, Jonathan; Blattner, Frank R

2015-09-01

Polyploidization is an important speciation mechanism in the barley genus Hordeum. To analyze evolutionary changes after allopolyploidization, knowledge of parental relationships is essential. One chloroplast and 12 nuclear single-copy loci were amplified by polymerase chain reaction (PCR) in all Hordeum plus six out-group species. Amplicons from each of 96 individuals were pooled, sheared, labeled with individual-specific barcodes and sequenced in a single run on a 454 platform. Reference sequences were obtained by cloning and Sanger sequencing of all loci for nine supplementary individuals. The 454 reads were assembled into contigs representing the 13 loci and, for polyploids, also homoeologues. Phylogenetic analyses were conducted for all loci separately and for a concatenated data matrix of all loci. For diploid taxa, a Bayesian concordance analysis and a coalescent-based dated species tree was inferred from all gene trees. Chloroplast matK was used to determine the maternal parent in allopolyploid taxa. The relative performance of different multilocus analyses in the presence of incomplete lineage sorting and hybridization was also assessed. The resulting multilocus phylogeny reveals for the first time species phylogeny and progenitor-derivative relationships of all di- and polyploid Hordeum taxa within a single analysis. Our study proves that it is possible to obtain a multilocus species-level phylogeny for di- and polyploid taxa by combining PCR with next-generation sequencing, without cloning and without creating a heavy load of sequence data. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

ЧИСЛА ХРОМОСОМ НЕКОТОРЫХ ВИДОВ ДВУДОЛЬНЫХ РАСТЕНИЙ ЮЖНОЙ СИБИРИ И КАЗАХСТАНА

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T. V. An’kova

2015-04-01

Full Text Available Приведены числа хромосом (2n для девяти видов семейств Asteraceae, Caryophyllaceae, Fabaceae, Rosaceae и Scrophulariaceae. Впервые определены числа хромосом Silene cretacea (2n=20 и Oxytropis stenofoliola (2n=48. Впервые для Казахстана и Южной Сибири (Западный Саян, Новосибирская область определены числа хромосом у Jurinea arachnoidea, Tragopogon ruber, Astragalus brachylobus, A. cicer, A. danicus, Verbascum phoeniceum.

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.

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

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

Allopolyploid Origin of Chenopodium album s. str. (Chenopodiaceae): A Molecular and Cytogenetic Insight

Czech Academy of Sciences Publication Activity Database

Krak, Karol; Vít, Petr; Belyayev, Alexander; Douda, Jan; Hreusová, Lucia; Mandák, Bohumil

2016-01-01

Roč. 11, č. 8 (2016), s. 1-22, č. článku e0161063. E-ISSN 1932-6203 R&D Projects: GA ČR GA13-02290S Institutional support: RVO:67985939 Keywords : Chenopodium * allopolyploidy * evolution Subject RIV: EF - Botanics Impact factor: 2.806, year: 2016

Новые данные по числам хромосом некоторых сосудистых растений из Израиля и России

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M. N. Lomonosova

2015-07-01

Full Text Available Приведены числа хромосом для 10 видов из семейств Amaranthaceae s. str., Asteraceae, Caryophyllaceae, Chenopodiaceae и Frankeniaceae. Для Atriplex intracontinentalis Sukhor. (2n = 18, Corispermum filifolium C.A. Meyer ex Becker (2n = 18 и Frankenia tuvinica Lomon. (2n = 20 числа хромосом не были известны ранее. Впервые на материале из Израиля указаны числа хромосом для Amaranthus albus L. (2n = 32, Dyssodia tenuiloba (DC R.B. Rob. (2n = 24, Lactuca viminea (L. J. et C. Presl (2n = 18, Tragopogon coelesyriacus Boiss. (2n = 12, Chenopodium opulifolium Schrad. ex W.D.J. Koch et Ziz (2n = 54 и Chenopodium missouriense Aellen (2n = 54.

Formation of diploid and triploid hybrid groupers (hybridization of Epinephelus coioides ♀ × Epinephelus lanceolatus ♂) and their 5S gene analysis.

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Huang, Wen; Qin, Qinbo; Yang, Huirong; Li, Shuisheng; Hu, Chaoqun; Wang, Yude; Zhang, Yong; Liu, Shaojun; Lin, Haoran

2016-10-07

Interspecies hybridization is widely used to achieve heterosis or hybrid vigor, which has been observed and harnessed by breeders for centuries. Natural allopolyploid hybrids generally exhibit more superior heterosis than both the diploid progenies and their parental species. However, polyploid formation processes have been long ignored, the genetic basis of heterosis in polyploids remains elusive. In the present study, triploid hybrids had been demonstrated to contain two sets of chromosomes from mother species and one set from father species. Cellular polyploidization process in the embryos had been traced. The triploid hybrids might be formed by failure formation of the second polarized genome during the second meiosis stage. Four spindle centers were observed in anaphase stage of the first cell division. Three spindle centers were observed in side of cell plate after the first cell division. The 5S rDNA genes of four types of groupers were cloned and analyzed. The diploid and triploid hybrids had been proved to contain the tandem chimera structures which were recombined by maternal and paternal monomer units. The results indicated that genome re-fusion had occurred in the hybrid progenies. To further elucidate the genetic patterns of diploid and triploid hybrids, fluorescence chromosome location had been carried out, maternal 5S gene (M-386) were used as the probe. The triploid hybrids contained fewer fluorescence loci numbers than the maternal species. The results indicated that participation of paternal 5S gene in the triploid hybrid genome had degraded the match rates of M-386 probe. Our study is the first to investigate the cellular formation processes of natural allopolyploids in hybrid fish, the cellular polyploidization process may be caused by failure formation of the second polarized genome during the meiosis, and our results will provide the molecular basis of hybrid vigor in interspecies hybridization.

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.

Five nuclear loci resolve the polyploid history of switchgrass (Panicum virgatum L. and relatives.

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Jimmy K Triplett

Full Text Available Polyploidy poses challenges for phylogenetic reconstruction because of the need to identify and distinguish between homoeologous loci. This can be addressed by use of low copy nuclear markers. Panicum s.s. is a genus of about 100 species in the grass tribe Paniceae, subfamily Panicoideae, and is divided into five sections. Many of the species are known to be polyploids. The most well-known of the Panicum polyploids are switchgrass (Panicum virgatum and common or Proso millet (P. miliaceum. Switchgrass is in section Virgata, along with P. tricholaenoides, P. amarum, and P. amarulum, whereas P. miliaceum is in sect. Panicum. We have generated sequence data from five low copy nuclear loci and two chloroplast loci and have clarified the origin of P. virgatum. We find that all members of sects. Virgata and Urvilleana are the result of diversification after a single allopolyploidy event. The closest diploid relatives of switchgrass are in sect. Rudgeana, native to Central and South America. Within sections Virgata and Urvilleana, P. tricholaenoides is sister to the remaining species. Panicum racemosum and P. urvilleanum form a clade, which may be sister to P. chloroleucum. Panicum amarum, P. amarulum, and the lowland and upland ecotypes of P. virgatum together form a clade, within which relationships are complex. Hexaploid and octoploid plants are likely allopolyploids, with P. amarum and P. amarulum sharing genomes with P. virgatum. Octoploid P. virgatum plants are formed via hybridization between disparate tetraploids. We show that polyploidy precedes diversification in a complex set of polyploids; our data thus suggest that polyploidy could provide the raw material for diversification. In addition, we show two rounds of allopolyploidization in the ancestry of switchgrass, and identify additional species that may be part of its broader gene pool. This may be relevant for development of the crop for biofuels.

Gene capture from across the grass family in the allohexaploid Elymus repens (L.) Gould (Poaceae, Triticeae) as evidenced by ITS, GBSSI, and molecular cytogenetics.

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Mahelka, Václav; Kopecký, David

2010-06-01

Four accessions of hexaploid Elymus repens from its native Central European distribution area were analyzed using sequencing of multicopy (internal transcribed spacer, ITS) and single-copy (granule-bound starch synthase I, GBSSI) DNA in concert with genomic and fluorescent in situ hybridization (GISH and FISH) to disentangle its allopolyploid origin. Despite extensive ITS homogenization, nrDNA in E. repens allowed us to identify at least four distinct lineages. Apart from Pseudoroegneria and Hordeum, representing the major genome constituents, the presence of further unexpected alien genetic material, originating from species outside the Triticeae and close to Panicum (Paniceae) and Bromus (Bromeae), was revealed. GBSSI sequences provided information complementary to the ITS. Apart from Pseudoroegneria and Hordeum, two additional gene variants from within the Triticeae were discovered: One was Taeniatherum-like, but the other did not have a close relationship with any of the diploids sampled. GISH results were largely congruent with the sequence-based markers. GISH clearly confirmed Pseudoroegneria and Hordeum as major genome constituents and further showed the presence of a small chromosome segment corresponding to Panicum. It resided in the Hordeum subgenome and probably represents an old acquisition of a Hordeum progenitor. Spotty hybridization signals across all chromosomes after GISH with Taeniatherum and Bromus probes suggested that gene acquisition from these species is more likely due to common ancestry of the grasses or early introgression than to recent hybridization or allopolyploid origin of E. repens. Physical mapping of rDNA loci using FISH revealed that all rDNA loci except one minor were located on Pseudoroegneria-derived chromosomes, which suggests the loss of all Hordeum-derived loci but one. Because homogenization mechanisms seem to operate effectively among Pseudoroegneria-like copies in this species, incomplete ITS homogenization in our samples

Progenitor-derivative relationships of Hordeum polyploids (Poaceae, Triticeae inferred from sequences of TOPO6, a nuclear low-copy gene region.

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Jonathan Brassac

Full Text Available Polyploidization is a major mechanism of speciation in plants. Within the barley genus Hordeum, approximately half of the taxa are polyploids. While for diploid species a good hypothesis of phylogenetic relationships exists, there is little information available for the polyploids (4×, 6× of Hordeum. Relationships among all 33 diploid and polyploid Hordeum species were analyzed with the low-copy nuclear marker region TOPO6 for 341 Hordeum individuals and eight outgroup species. PCR products were either directly sequenced or cloned and on average 12 clones per individual were included in phylogenetic analyses. In most diploid Hordeum species TOPO6 is probably a single-copy locus. Most sequences found in polyploid individuals phylogenetically cluster together with sequences derived from diploid species and thus allow the identification of parental taxa of polyploids. Four groups of sequences occurring only in polyploid taxa are interpreted as footprints of extinct diploid taxa, which contributed to allopolyploid evolution. Our analysis identifies three key species involved in the evolution of the American polyploids of the genus. (i All but one of the American tetraploids have a TOPO6 copy originating from the Central Asian diploid H. roshevitzii, the second copy clustering with different American diploid species. (ii All hexaploid species from the New World have a copy of an extinct close relative of H. californicum and (iii possess the TOPO6 sequence pattern of tetraploid H. jubatum, each with an additional copy derived from different American diploids. Tetraploid H. bulbosum is an autopolyploid, while the assumed autopolyploid H. brevisubulatum (4×, 6× was identified as allopolyploid throughout most of its distribution area. The use of a proof-reading DNA polymerase in PCR reduced the proportion of chimerical sequences in polyploids in comparison to Taq polymerase.

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

Evolutionarily advanced ant farmers rear polyploid fungal crops

DEFF Research Database (Denmark)

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

2015-01-01

to be lowly and facultatively polyploid (just over two haplotypes on average), whereas Atta and Acromyrmex symbionts are highly and obligatorily polyploid (ca. 5-7 haplotypes on average). This stepwise transition appears analogous to ploidy variation in plants and fungi domesticated by humans and in fungi...... the number of nuclei per fungal cell for 42 symbionts reared by 14 species of Panamanian fungus-growing ants. This showed that domesticated symbionts of higher attine ants are polykaryotic with 7-17 nuclei per cell, whereas nonspecialized crops of lower attines are dikaryotic similar to most free...... 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....

New xenophytes from La Palma (Canary Islands, Spain, with emphasis on naturalized and (potentially invasive species

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R. Otto

2016-07-01

Full Text Available Many years of field work in La Palma (western Canary Islands yielded a number of interesting new records of non-native vascular plants. Amaranthus blitoides, A. deflexus, Aptenia cordifolia, Argemone ochroleuca, Begonia schmidtiana, Capsella rubella, Cardamine hamiltonii, Centratherum punctatum, Cerastium fontanum subsp. vulgare, Chasmanthe floribunda (widely confused with C. aethiopica and Crocosmia xcrocosmiiflora in Macaronesia, Chenopodium probstii, Commelina latifolia var. latifolia, Dichondra micrantha, Dysphania anthelmintica, Epilobium ciliatum, Erigeron sumatrensis, Erodium neuradifolium, Eucalyptus globulus, Euphorbia hypericifolia, E. maculata, Gamochaeta antillana, Geranium pyrenaicum, Hedychium coronarium, Hypochaeris radicata, Kalanchoe daigremontiana, K. delagoensis, K. xhoughtonii, Kickxia commutata subsp. graeca, K. spuria subsp. integrifolia, Lactuca viminea subsp. ramosissima, Landoltia punctata, Malvastrum coromandelianum subsp. capitatospicatum, Oenothera jamesii, Orobanche nana, Oxalis latifolia, Papaver hybridum, P. setigerum, Pilea microphylla, Podranea ricasoliana, Polygonum arenastrum, Portulaca granulatostellulata, P. nicaraguensis, P. nitida, P. papillatostellulata, Rumex crispus subsp. crispus, R. pulcher subsp. pulcher, R. xpratensis, Sechium edule, Sida spinosa var. angustifolia, Silene nocturna, Solanum abutiloides, S. alatum, S. decipiens, Sonchus tenerrimus, Spergularia marina, Stellaria pallida, Tragopogon porrifolius subsp. australis, Tribulus terrestris and Trifolium repens subsp. repens are naturalized or (potentially invasive xenophytes, reported for the first time from either the Canary Islands or from La Palma. 37 additional, presumably ephemeral taxa are reported for the first time from the Canary Islands, whereas 56 ephemeral taxa are new for La Palma..

Ancient tetraploidy and slow molecular evolution in Scaphiophryne: ecological correlates of speciation mode in Malagasy relict amphibians.

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Vences, Miguel; Aprea, Gennaro; Capriglione, Teresa; Andreone, Franco; Odierna, Gaetano

2002-01-01

Karyotypes of three microhylid frog species of the Malagasy relict genus Scaphiophryne were studied: Scaphiophryne gottlebei, S. madagascariensis and S. spinosa. The latter two showed a plesiomorphic ranoid karyotype of 2n = 26. In contrast, tetraploidy was demonstrated in S. gottlebei, which constitutes an exceptional state among Malagasy amphibians. A combination of different banding techniques and of rDNA-FISH provided evidence for allopolyploidy in the species and for a completed subsequent functional and structural diploidization. Phylogenetic analysis of mitochondrial 16S rDNA sequences revealed a significant deceleration of nucleotide substitution rates in Scaphiophryne. The tetraploidy of S. gottlebei probably occurred early in their radiation. Ecological and behavioural patterns of Scaphiophryne probably favoured intraspecific gene flow and hybridization events, thereby leading to slow molecular substitution rates and to allopolyploid chromosome speciation in S. gottlebei.

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

The northward shifting neophyte Tragopogon dubius is just as effective in forming mycorrhizal associations as the native T. pratensis.

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van Grunsven, R.; Yuwati, T.; Kowalchuk, George; van der Putten, W.H.; van Veenendaal, E.

2014-01-01

Background: As a consequence of climate warming, many organisms are shifting their range towards higher latitudes and altitudes. As not all do so at the same speed, this may disrupt biotic interaction. Release from natural enemies through range expansion can result in invasiveness, whereas loss of

Medicinal plants with hepatoprotective activity in Iranian folk medicine

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Majid Asadi-Samani

2015-02-01

Full Text Available 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 CC14 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, CC14, anti-inflammatory, and antihepatotoxic, hepatitis, alone or in combination. Allium hirtifolium Boiss., Apium graveolens L., Cynara scolymus, Berberis vulgaris L., Calendula officinalis, Nigella sativa L., Taraxacum officinale, Tragopogon porrifolius, Prangos ferulacea L., Allium sativum, Marrubium vulgare, Ammi majus L., Citrullus lanatus Thunb, Agrimonia eupatoria L. and Prunus 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, β-sitosterol, betalain, neoandrographolide, phyllanthin, andrographolide, curcumin, picroside, hypophyllanthin, 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.

Evolution of rDNA in Nicotiana allopolyploids: A potential link between rDNa homogenization and epigenetics

Czech Academy of Sciences Publication Activity Database

Kovařík, Aleš; Nešpor Dadejová, Martina; Lim, Y.K.; Chase, M.W.; Clarkson, J.J.; Knapp, S.; Leitch, A.R.

2008-01-01

Roč. 101, č. 6 (2008), s. 815-823 ISSN 0305-7364 R&D Projects: GA ČR(CZ) GA521/07/0116 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : rDNA * allopolyploidy * evolution-Nicotiana Subject RIV: BO - Biophysics Impact factor: 2.755, year: 2008

Persistence, dispersal and genetic evolution of recently formed Spartina homoploid hybrids and allopolyploids in Southern England

Czech Academy of Sciences Publication Activity Database

Húska, Dalibor; Leitch, I. J.; de Carvalho, J.F.; Leitch, A.R.; Salmon, A.; Ainouche, M.; Kovařík, Aleš

2016-01-01

Roč. 18, č. 8 (2016), s. 2137-2151 ISSN 1387-3547 R&D Projects: GA ČR(CZ) GA13-10057S Institutional support: RVO:68081707 Keywords : Spartina * Allopolyploidy * Cytotypes Subject RIV: BO - Biophysics Impact factor: 2.473, year: 2016

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

Gypsophila bermejoi G. López: A possible case of speciation repressed by bioclimatic factors.

Science.gov (United States)

de Luis, Miguel; Bartolomé, Carmen; García Cardo, Óscar; Álvarez-Jiménez, Julio

2018-01-01

Gypsophila bermejoi G. López is an allopolyploid species derived from the parental G. struthium L. subsp. struthium and G. tomentosa L. All these plants are gypsophytes endemic to the Iberian Peninsula of particular ecological, evolutionary and biochemical interest. In this study, we present evidence of a possible repression on the process of G. bermejoi speciation by climatic factors. We modelled the ecological niches of the three taxa considered here using a maximum entropy approach and employing a series of bioclimatic variables. Subsequently, we projected these models onto the geographical space of the Iberian Peninsula in the present age and at two past ages: the Last Glacial Maximum and the mid-Holocene period. Furthermore, we compared these niches using the statistical method devised by Warren to calculate their degree of overlap. We also evaluated the evolution of the bioclimatic habitat suitability at those sites were the soil favors the growth of these species. Both the maximum entropy model and the degree of overlap indicated that the ecological behavior of the hybrid differs notably from that of the parental species. During the Last Glacial Maximum, the two parental species appear to take refuge in the western coastal strip of the Peninsula, a region in which there are virtually no sites where G. bermejoi could potentially be found. However, in the mid-Holocene period the suitability of G. bermejoi to sites with favorable soils shifts from almost null to a strong adaptation, a clear change in this tendency. These results suggest that the ecological niches of hybrid allopolyploids can be considerably different to those of their parental species, which may have evolutionary and ecologically relevant consequences. The data obtained indicate that certain bioclimatic variables may possibly repress the processes by which new species are formed. The difference in the ecological niche of G. bermejoi with respect to its parental species prevented it from

Genome-wide SNP identification in multiple morphotypes of allohexaploid tall fescue (Festuca arundinacea Schreb

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Hand Melanie L

2012-06-01

Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs provide essential tools for the advancement of research in plant genomics, and the development of SNP resources for many species has been accelerated by the capabilities of second-generation sequencing technologies. The current study aimed to develop and use a novel bioinformatic pipeline to generate a comprehensive collection of SNP markers within the agriculturally important pasture grass tall fescue; an outbreeding allopolyploid species displaying three distinct morphotypes: Continental, Mediterranean and rhizomatous. Results A bioinformatic pipeline was developed that successfully identified SNPs within genotypes from distinct tall fescue morphotypes, following the sequencing of 414 polymerase chain reaction (PCR – generated amplicons using 454 GS FLX technology. Equivalent amplicon sets were derived from representative genotypes of each morphotype, including six Continental, five Mediterranean and one rhizomatous. A total of 8,584 and 2,292 SNPs were identified with high confidence within the Continental and Mediterranean morphotypes respectively. The success of the bioinformatic approach was demonstrated through validation (at a rate of 70% of a subset of 141 SNPs using both SNaPshot™ and GoldenGate™ assay chemistries. Furthermore, the quantitative genotyping capability of the GoldenGate™ assay revealed that approximately 30% of the putative SNPs were accessible to co-dominant scoring, despite the hexaploid genome structure. The sub-genome-specific origin of each SNP validated from Continental tall fescue was predicted using a phylogenetic approach based on comparison with orthologous sequences from predicted progenitor species. Conclusions Using the appropriate bioinformatic approach, amplicon resequencing based on 454 GS FLX technology is an effective method for the identification of polymorphic SNPs within the genomes of Continental and Mediterranean tall fescue. The

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: 6.090, year: 2015

Interspecific hybridization in the genus Hieracium (s. str.) – evidence for bidirectional gene flow and spontaneous allopolyploidization

Czech Academy of Sciences Publication Activity Database

Mráz, P.; Chrtek, Jindřich; Fehrer, Judith

2011-01-01

Roč. 293, 1-4 (2011), s. 237-245 ISSN 0378-2697 R&D Projects: GA ČR GAP506/10/1363 Institutional research plan: CEZ:AV0Z60050516 Keywords : additive polymorphism * hybridization * polyploidization Subject RIV: EF - Botanics Impact factor: 1.335, year: 2011

Chasing ghosts: allopolyploid origin of Oxyria sinensis (Polygonaceae) from its only diploid congener and an unknown ancestor.

Science.gov (United States)

Luo, Xin; Hu, Quanjun; Zhou, Pingping; Zhang, Dan; Wang, Qian; Abbott, Richard J; Liu, Jianquan

2017-06-01

Reconstructing the origin of a polyploid species is particularly challenging when an ancestor has become extinct. Under such circumstances, the extinct donor of a genome found in the polyploid may be treated as a 'ghost' species in that its prior existence is recognized through the presence of its genome in the polyploid. In this study, we aimed to determine the polyploid origin of Oxyria sinensis (2n = 40) for which only one congeneric species is known, that is diploid O. digyna (2n = 14). Genomic in situ hybridization (GISH), transcriptome, phylogenetic and demographic analyses, and ecological niche modelling were conducted for this purpose. GISH revealed that O. sinensis comprised 14 chromosomes from O. digyna and 26 chromosomes from an unknown ancestor. Transcriptome analysis indicated that following divergence from O. digyna, involving genome duplication around 12 million years ago (Ma), a second genome duplication occurred approximately 6 Ma to give rise to O. sinensis. Oxyria sinensis was shown to contain homologous gene sequences divergent from those present in O. digyna in addition to a set that clustered with those in O. digyna. Coalescent simulations indicated that O. sinensis expanded its distribution approximately 6-7 Ma, possibly following the second polyploidization event, whereas O. digyna expanded its range much later. It was also indicated that the distributions of both species contracted and re-expanded during the Pleistocene climatic oscillations. Ecological niche modelling similarly suggested that both species experienced changes in their distributional ranges in response to Quaternary climatic changes. The extinction of the unknown 'ghost' tetraploid species implicated in the origin of O. sinensis could have resulted from superior adaptation of O. sinensis to repeated climatic changes in the region where it now occurs. © 2017 John Wiley & Sons Ltd.

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

Patterns of seed proteins in Triticum monococcum (2n = 2x = 14 = AA), Aegilops ventricosa (2n = 4x = 28 = DDMVMV), and their synthetic amphiploid were studied. The distribution of proteins in the individual Osborne protein fractions of the amphiploid was characterized by a 14 per cent increase...

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: 3.801, year: 2015

Nuclear DNA content of the hybrid plant pathogen Phytophthora andina determined by flow cytometry.

Science.gov (United States)

Wang, Jianan; Presser, Jackson W; Goss, Erica M

2016-09-01

Phytophthora andina is a heterothallic plant pathogen of Andean solanaceous hosts and is an interspecific hybrid of P. infestans and an unknown Phytophthora species. The objective of this study was to estimate the nuclear DNA content of isolates in three clonal lineages of P. andina relative to P. infestans Twelve isolates of P. andina and six isolates of P. infestans were measured for nuclear DNA content by propidium iodide-stained flow cytometry. We found that the DNA content of P. andina was similar but slightly smaller, on average, than that of our sample of P. infestans isolates. This is consistent with P. andina being a homoploid hybrid rather than allopolyploid hybrid. Nuclear DNA content was more variable among a smaller sample of P. infestans isolates, including a putative triploid isolate from Mexico, but small differences in nuclear DNA content were also observed among P. andina isolates. Both species appear to be able to tolerate significant variation in genome size. © 2016 by The Mycological Society of America.

Evolutionary dynamics of 3D genome architecture following polyploidization in cotton.

Science.gov (United States)

Wang, Maojun; Wang, Pengcheng; Lin, Min; Ye, Zhengxiu; Li, Guoliang; Tu, Lili; Shen, Chao; Li, Jianying; Yang, Qingyong; Zhang, Xianlong

2018-02-01

The formation of polyploids significantly increases the complexity of transcriptional regulation, which is expected to be reflected in sophisticated higher-order chromatin structures. However, knowledge of three-dimensional (3D) genome structure and its dynamics during polyploidization remains poor. Here, we characterize 3D genome architectures for diploid and tetraploid cotton, and find the existence of A/B compartments and topologically associated domains (TADs). By comparing each subgenome in tetraploids with its extant diploid progenitor, we find that genome allopolyploidization has contributed to the switching of A/B compartments and the reorganization of TADs in both subgenomes. We also show that the formation of TAD boundaries during polyploidization preferentially occurs in open chromatin, coinciding with the deposition of active chromatin modification. Furthermore, analysis of inter-subgenomic chromatin interactions has revealed the spatial proximity of homoeologous genes, possibly associated with their coordinated expression. This study advances our understanding of chromatin organization in plants and sheds new light on the relationship between 3D genome evolution and transcriptional regulation.

Application of Genomic In Situ Hybridization in Horticultural Science

Directory of Open Access Journals (Sweden)

Fahad Ramzan

2017-01-01

Full Text Available Molecular cytogenetic techniques, such as in situ hybridization methods, are admirable tools to analyze the genomic structure and function, chromosome constituents, recombination patterns, alien gene introgression, genome evolution, aneuploidy, and polyploidy and also genome constitution visualization and chromosome discrimination from different genomes in allopolyploids of various horticultural crops. Using GISH advancement as multicolor detection is a significant approach to analyze the small and numerous chromosomes in fruit species, for example, Diospyros hybrids. This analytical technique has proved to be the most exact and effective way for hybrid status confirmation and helps remarkably to distinguish donor parental genomes in hybrids such as Clivia, Rhododendron, and Lycoris ornamental hybrids. The genome characterization facilitates in hybrid selection having potential desirable characteristics during the early hybridization breeding, as this technique expedites to detect introgressed sequence chromosomes. This review study epitomizes applications and advancements of genomic in situ hybridization (GISH techniques in horticultural plants.

Study of the repeatability of histone genes in the ploidy series of wheat and Aegilops

International Nuclear Information System (INIS)

Vakhitov, V.A.; Kulikov, A.M.

1986-01-01

The hDNA content and number of histone genes in the genomes of different wheat and Aegilops species have been determined by molecular hybridization of DNA with 125 I-histone DNA of Drosophila (L-repeat) on nitrocellulose filters. It has been demonstrated that the proportion of hDNA in the total DNA of diploid and polyploid wheat species is (1.3-7.7) x 10 -3 % (57-850 genes), and in the ploidy series of Aegilops species (2.0-8.0) x 10 -3 % (89-780 genes). The repeatability of the histone genes generally increases at each ploidy level in the species with higher DNA content. At the same time, it has been demonstrated that the DNA content is not the only factor determining repeatability of the histone genes, as some diploid and allopolyploid species have similar number of these genes. It has been concluded that genetic mechanisms are involved in the regulation of the number of histone genes

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

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

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

Science.gov (United States)

Zhang, Lianquan; Liu, Dengcai; Yan, Zehong; Zheng, Youliang

2005-10-01

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.

Saccharomyces pastorianus: genomic insights inspiring innovation for industry.

Science.gov (United States)

Gibson, Brian; Liti, Gianni

2015-01-01

A combination of biological and non-biological factors has led to the interspecific hybrid yeast species Saccharomyces pastorianus becoming one of the world's most important industrial organisms. This yeast is used in the production of lager-style beers, the fermentation of which requires very low temperatures compared to other industrial fermentation processes. This group of organisms has benefited from both the whole-genome duplication in its ancestral lineage and the subsequent hybridization event between S. cerevisiae and S. eubayanus, resulting in strong fermentative ability. The hybrid has key traits, such as cold tolerance and good maltose- and maltotriose-utilizing ability, inherited either from the parental species or originating from genetic interactions between the parent genomes. Instability in the nascent allopolyploid hybrid genome may have contributed to rapid evolution of the yeast to tolerate conditions prevalent in the brewing environment. The recent discovery of S. eubayanus has provided new insights into the evolutionary history of S. pastorianus and may offer new opportunities for generating novel industrially-beneficial lager yeast strains. Copyright © 2014 John Wiley & Sons, Ltd.

Concerted evolution of rDNA in recently formed Tragopogon allotetraploids is typically associated with an inverse correlation between gene copy number and expression

Czech Academy of Sciences Publication Activity Database

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

2007-01-01

Roč. 176, č. 4 (2007), s. 2509-2519 ISSN 0016-6731 R&D Projects: GA ČR(CZ) GA204/05/0687; GA ČR(CZ) GA521/07/0116; GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : rDNA silencing * nucleolar dominance * allopolyploidy Subject RIV: BO - Biophysics Impact factor: 4.001, year: 2007

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

Directory of Open Access Journals (Sweden)

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.

Determination of the number of copies of genes coding for 5s-rRNA and tRNA in the genomes of 43 species of wheat and Aegilops

International Nuclear Information System (INIS)

Vakhitov, V.A.; Gimalov, F.R.; Nikonorov, Yu.M.

1986-01-01

The number of 5s-rRNA and tRNA genes has been studied in 43 species of wheat and Aegilops differing in ploidy level, genomic composition and origin. It has been demonstrated that the repeatability of the 5s-rRNA and tRNA genes increases in wheat with increasing ploidy level, but not in proportion to the genome size. In Aegilops, in distinction from wheat, the relative as well as absolute number of 5s-RNA genes increases with increasing ploidy level. The proportion of the sequences coding for tRNA in the dipoloid and polyploid Aegilops species is practically similar, while the number of tRNA genes increases almost 2-3 times with increasing ploidy level. Large variability has been recorded between the species with similar genomic composition and ploidy level in respect of the number of the 5s-rRNA and tRNA genes. It has been demonstrated that integration of the initial genomes of the amphidiploids is accompanied by elimination of a particular part of these genomes. It has been concluded that the mechanisms of establishment and evolution of genomes in the intra- and intergeneric allopolyploids are not identical

Generation of amphidiploids from hybrids of wheat and related species from the genera Aegilops, Secale, Thinopyrum, and Triticum as a source of genetic variation for wheat improvement.

Science.gov (United States)

Nemeth, Csilla; Yang, Cai-yun; Kasprzak, Paul; Hubbart, Stella; Scholefield, Duncan; Mehra, Surbhi; Skipper, Emma; King, Ian; King, Julie

2015-02-01

We aim to improve diversity of domesticated wheat by transferring genetic variation for important target traits from related wild and cultivated grass species. The present study describes the development of F1 hybrids between wheat and related species from the genera Aegilops, Secale, Thinopyrum, and Triticum and production of new amphidiploids. Amphidiploid lines were produced from 20 different distant relatives. Both colchicine and caffeine were successfully used to double the chromosome numbers. The genomic constitution of the newly formed amphidiploids derived from seven distant relatives was determined using genomic in situ hybridization (GISH). Altogether, 42 different plants were analysed, 19 using multicolour GISH separating the chromosomes from the A, B, and D genomes of wheat, as well as the distant relative, and 23 using single colour GISH. Restructuring of the allopolyploid genome, both chromosome losses and aneuploidy, was detected in all the genomes contained by the amphidiploids. From the observed chromosome numbers there is an indication that in amphidiploids the B genome of wheat suffers chromosome losses less frequently than the other wheat genomes. Phenotyping to realize the full potential of the wheat-related grass germplasm is underway, linking the analyzed genotypes to agronomically important target traits.

A distributional and cytological survey of the presently recognized taxa of Hibiscus section Furcaria (Malvaceae.

Directory of Open Access Journals (Sweden)

F. Douglas Wilson

2006-01-01

Full Text Available Hibiscus section Furcaria is a natural group of plants that presently includes 109 recognized taxa. Taxa are found in subsaharan Africa, India, southeastern Asia, Malesia, Australia, islands of the Pacific basin, the Caribbean, North, Central, and South America. The basic chromosome number is x = 18. In nature, ploidy levels range from diploid to decaploid. The taxa exhibit a remarkable amount of genome diversity. At least 13 genomes have been identified, some distributed widely and others with more restricted distributions. No modern taxonomic monograph ofHibiscus section Furcaria exists, but a number of regional studies have appeared that are essentially global in extent. Also, a number of studies of chromosome numbers and genome relationships have been published. The present paper includes a census of all the presently accepted taxa, the geographical distribution of each taxon, and chromosome numbers and genome designations of the 49 taxa for which the information is available. Important mechanisms of speciation include genome divergence at the diploid level, followed by hybridization and allopolyploidy, significant species radiation at the tetraploid and hexaploid levels, and the development of even higher levels of allopolyploids.

Evolution in an autopolyploid group displaying predominantly bivalent pairing at meiosis: genomic similarity of diploid Vaccinium darrowi and autotetraploid V. corymbosum (Ericaceae).

Science.gov (United States)

Qu, L; Hancock, J; Whallon, J

1998-05-01

The genomic relationship between V. darrowi Camp (2n = 2x = 24) and V. corymbosum L. (2n = 4x = 48) was examined using an interspecific tetraploid hybrid, US 75, and representatives of the parental species. Two features in the background of US 75 led to the prediction that it was an allopolyploid: (1) the parental species are quite distinct morphologically and geographically, and (2) the diploid genome was incorporated into US 75 via an unreduced gamete. However, US 75 recently was shown to display tetrasomic inheritance using molecular markers. In the present cytological study, US 75 was found to have a lower than expected number of multivalents for an autopolyploid, although it had a significantly higher number of quadrivalents than its autotetraploid parent, V. corymbosum. Normal chromosome distributions were observed at anaphase I and II, and pollen viability was high. Our findings suggest that little genomic divergence has developed between the Vaccinium species and that the polyploids may freely exchange genes with sympatric diploid species via unreduced gametes. This pattern of hybridization could be an important component of evolution in all autopolyploid groups, making them much more dynamic than traditionally assumed.

Mate Choice Drives Evolutionary Stability in a Hybrid Complex.

Directory of Open Access Journals (Sweden)

Miguel Morgado-Santos

Full Text Available 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.

Inter- and interspecific serological relationships in Pellia epiphylla complex

Directory of Open Access Journals (Sweden)

Aleksandra Wojnicka-Półtorak

2014-01-01

Full Text Available Antigenic proteins were used as markers for the study of relationships between three liverwort species from P. epiphylla complex. It has recently been shown that the electrophoretic phenotypes of this species suggested an amphiploid origin of P. borealis. Two sibling species: P. epiphylla -species S and -species N could have probably represented the parental species for P. borealis. We examined three clones of P. borealis from different localities using immunodiffusion. Then we compared them with P. epiphylla species S and N as well as with the mixture of proteins of P. epiphylla S and N samples. The results indicate that polyploid P. borealis shows an identical immunological pattern to that of the mixture of proteins of putative parental species. Only in one case the result resembled much more the pattern of P. epiphylla S proteins. The sibling species P. epiphylla S and N showed antigenic difference but the nature of the differences requires further studies. Antigenic pro-perties of proteins from P. epiphylla S and N and of their allopolyploid - P. borealis, indicated some specifity of the protein spectrum in each of the parental species and intermediate character of proteins in the polyploid forms.

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

2016-01-04

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.

Re-exploration of U's Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences.

Science.gov (United States)

Kim, Chang-Kug; Seol, Young-Joo; Perumal, Sampath; Lee, Jonghoon; Waminal, Nomar Espinosa; Jayakodi, Murukarthick; Lee, Sang-Choon; Jin, Seungwoo; Choi, Beom-Soon; Yu, Yeisoo; Ko, Ho-Cheol; Choi, Ji-Weon; Ryu, Kyoung-Yul; Sohn, Seong-Han; Parkin, Isobel; Yang, Tae-Jin

2018-05-09

The concept of U's triangle, which revealed the importance of polyploidization in plant genome evolution, described natural allopolyploidization events in Brassica using three diploids [B. rapa (A genome), B. nigra (B), and B. oleracea (C)] and derived allotetraploids [B. juncea (AB genome), B. napus (AC), and B. carinata (BC)]. However, comprehensive understanding of Brassica genome evolution has not been fully achieved. Here, we performed low-coverage (2-6×) whole-genome sequencing of 28 accessions of Brassica as well as of Raphanus sativus [R genome] to explore the evolution of six Brassica species based on chloroplast genome and ribosomal DNA variations. Our phylogenomic analyses led to two main conclusions. (1) Intra-species-level chloroplast genome variations are low in the three allotetraploids (2~7 SNPs), but rich and variable in each diploid species (7~193 SNPs). (2) Three allotetraploids maintain two 45SnrDNA types derived from both ancestral species with maternal dominance. Furthermore, this study sheds light on the maternal origin of the AC chloroplast genome. Overall, this study clarifies the genetic relationships of U's triangle species based on a comprehensive genomics approach and provides important genomic resources for correlative and evolutionary studies.

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

TALEN-mediated targeted mutagenesis of fatty acid desaturase 2 (FAD2) in peanut (Arachis hypogaea L.) promotes the accumulation of oleic acid.

Science.gov (United States)

Wen, Shijie; Liu, Hao; Li, Xingyu; Chen, Xiaoping; Hong, Yanbin; Li, Haifen; Lu, Qing; Liang, Xuanqiang

2018-05-01

A first creation of high oleic acid peanut varieties by using transcription activator-like effecter nucleases (TALENs) mediated targeted mutagenesis of Fatty Acid Desaturase 2 (FAD2). Transcription activator like effector nucleases (TALENs), which allow the precise editing of DNA, have already been developed and applied for genome engineering in diverse organisms. However, they are scarcely used in higher plant study and crop improvement, especially in allopolyploid plants. In the present study, we aimed to create targeted mutagenesis by TALENs in peanut. Targeted mutations in the conserved coding sequence of Arachis hypogaea fatty acid desaturase 2 (AhFAD2) were created by TALENs. Genetic stability of AhFAD2 mutations was identified by DNA sequencing in up to 9.52 and 4.11% of the regeneration plants at two different targeted sites, respectively. Mutation frequencies among AhFAD2 mutant lines were significantly correlated to oleic acid accumulation. Genetically, stable individuals of positive mutant lines displayed a 0.5-2 fold increase in the oleic acid content compared with non-transgenic controls. This finding suggested that TALEN-mediated targeted mutagenesis could increase the oleic acid content in edible peanut oil. Furthermore, this was the first report on peanut genome editing event, and the obtained high oleic mutants could serve for peanut breeding project.

Gossypium barbadense genome sequence provides insight into the evolution of extra-long staple fiber and specialized metabolites.

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Liu, Xia; Zhao, Bo; Zheng, Hua-Jun; Hu, Yan; Lu, Gang; Yang, Chang-Qing; Chen, Jie-Dan; Chen, Jun-Jian; Chen, Dian-Yang; Zhang, Liang; Zhou, Yan; Wang, Ling-Jian; Guo, Wang-Zhen; Bai, Yu-Lin; Ruan, Ju-Xin; Shangguan, Xiao-Xia; Mao, Ying-Bo; Shan, Chun-Min; Jiang, Jian-Ping; Zhu, Yong-Qiang; Jin, Lei; Kang, Hui; Chen, Shu-Ting; He, Xu-Lin; Wang, Rui; Wang, Yue-Zhu; Chen, Jie; Wang, Li-Jun; Yu, Shu-Ting; Wang, Bi-Yun; Wei, Jia; Song, Si-Chao; Lu, Xin-Yan; Gao, Zheng-Chao; Gu, Wen-Yi; Deng, Xiao; Ma, Dan; Wang, Sen; Liang, Wen-Hua; Fang, Lei; Cai, Cai-Ping; Zhu, Xie-Fei; Zhou, Bao-Liang; Jeffrey Chen, Z; Xu, Shu-Hua; Zhang, Yu-Gao; Wang, Sheng-Yue; Zhang, Tian-Zhen; Zhao, Guo-Ping; Chen, Xiao-Ya

2015-09-30

Of the two cultivated species of allopolyploid cotton, Gossypium barbadense produces extra-long fibers for the production of superior textiles. We sequenced its genome (AD)2 and performed a comparative analysis. We identified three bursts of retrotransposons from 20 million years ago (Mya) and a genome-wide uneven pseudogenization peak at 11-20 Mya, which likely contributed to genomic divergences. Among the 2,483 genes preferentially expressed in fiber, a cell elongation regulator, PRE1, is strikingly At biased and fiber specific, echoing the A-genome origin of spinnable fiber. The expansion of the PRE members implies a genetic factor that underlies fiber elongation. Mature cotton fiber consists of nearly pure cellulose. G. barbadense and G. hirsutum contain 29 and 30 cellulose synthase (CesA) genes, respectively; whereas most of these genes (>25) are expressed in fiber, genes for secondary cell wall biosynthesis exhibited a delayed and higher degree of up-regulation in G. barbadense compared with G. hirsutum, conferring an extended elongation stage and highly active secondary wall deposition during extra-long fiber development. The rapid diversification of sesquiterpene synthase genes in the gossypol pathway exemplifies the chemical diversity of lineage-specific secondary metabolites. The G. barbadense genome advances our understanding of allopolyploidy, which will help improve cotton fiber quality.

Proteomics profiling of fiber development and domestication in upland cotton (Gossypium hirsutum L.).

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Hu, Guanjing; Koh, Jin; Yoo, Mi-Jeong; Pathak, Dharminder; Chen, Sixue; Wendel, Jonathan F

2014-12-01

Comparative proteomic analyses were performed to detail the evolutionary consequences of strong directional selection for enhanced fiber traits in modern upland cotton (Gossypium hirsutum L.). Using two complementary proteomic approaches, 2-DE and iTRAQ LC-MS/MS, fiber proteomes were examined for four representative stages of fiber development. Approximately 1,000 protein features were characterized using each strategy, collectively resulting in the identification and functional categorization of 1,223 proteins. Unequal contributions of homoeologous proteins were detected for over a third of the fiber proteome, but overall expression was balanced with respect to the genome-of-origin in the allopolyploid G. hirsutum. About 30% of the proteins were differentially expressed during fiber development within wild and domesticated cotton. Notably, domestication was accompanied by a doubling of protein developmental dynamics for the period between 10 and 20 days following pollination. Expression levels of 240 iTRAQ proteins and 293 2-DE spots were altered by domestication, collectively representing multiple cellular and metabolic processes, including metabolism, energy, protein synthesis and destination, defense and stress response. Analyses of homoeolog-specific expression indicate that duplicated gene products in cotton fibers can be differently regulated in response to selection. These results demonstrate the power of proteomics for the analysis of crop domestication and phenotypic evolution.

A Solution to the C-Value Paradox and the Function of Junk DNA: The Genome Balance Hypothesis.

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Freeling, Michael; Xu, Jie; Woodhouse, Margaret; Lisch, Damon

2015-06-01

The Genome Balance Hypothesis originated from a recent study that provided a mechanism for the phenomenon of genome dominance in ancient polyploids: unique 24nt RNA coverage near genes is greater in genes on the recessive subgenome irrespective of differences in gene expression. 24nt RNAs target transposons. Transposon position effects are now hypothesized to balance the expression of networked genes and provide spring-like tension between pericentromeric heterochromatin and microtubules. The balance (coordination) of gene expression and centromere movement is under selection. Our hypothesis states that this balance can be maintained by many or few transposons about equally well. We explain known balanced distributions of junk DNA within genomes and between subgenomes in allopolyploids (and our hypothesis passes "the onion test" for any so-called solution to the C-value paradox). Importantly, when the allotetraploid maize chromosomes delete redundant genes, their nearby transposons are also lost; this result is explained if transposons near genes function. The Genome Balance Hypothesis is hypothetical because the position effect mechanisms implicated are not proved to apply to all junk DNA, and the continuous nature of the centromeric and gene position effects have not yet been studied as a single phenomenon. Copyright © 2015 The Author. Published by Elsevier Inc. All rights reserved.

Transcriptome and metabolome of synthetic Solanum autotetraploids reveal key genomic stress events following polyploidization.

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Fasano, Carlo; Diretto, Gianfranco; Aversano, Riccardo; D'Agostino, Nunzio; Di Matteo, Antonio; Frusciante, Luigi; Giuliano, Giovanni; Carputo, Domenico

2016-06-01

Polyploids are generally classified as autopolyploids, derived from a single species, and allopolyploids, arising from interspecific hybridization. The former represent ideal materials with which to study the consequences of genome doubling and ascertain whether there are molecular and functional rules operating following polyploidization events. To investigate whether the effects of autopolyploidization are common to different species, or if species-specific or stochastic events are prevalent, we performed a comprehensive transcriptomic and metabolomic characterization of diploids and autotetraploids of Solanum commersonii and Solanum bulbocastanum. Autopolyploidization remodelled the transcriptome and the metabolome of both species. In S. commersonii, differentially expressed genes (DEGs) were highly enriched in pericentromeric regions. Most changes were stochastic, suggesting a strong genotypic response. However, a set of robustly regulated transcripts and metabolites was also detected, including purine bases and nucleosides, which are likely to underlie a common response to polyploidization. We hypothesize that autopolyploidization results in nucleotide pool imbalance, which in turn triggers a genomic shock responsible for the stochastic events observed. The more extensive genomic stress and the higher number of stochastic events observed in S. commersonii with respect to S. bulbocastanum could be the result of the higher nucleoside depletion observed in this species. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Origins of domestication and polyploidy in oca (Oxalis Tuberosa: Oxalidaceae). 2. Chloroplast-expressed glutamine synthetase data.

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Emshwiller, Eve; Doyle, Jeff J

2002-07-01

In continuing study of the origins of the octoploid tuber crop oca, Oxalis tuberosa Molina, we used phylogenetic analysis of DNA sequences of the chloroplast-active (nuclear encoded) isozyme of glutamine synthetase (ncpGS) from cultivated oca, its allies in the "Oxalis tuberosa alliance," and other Andean Oxalis. Multiple ncpGS sequences found within individuals of both the cultigen and a yet unnamed wild tuber-bearing taxon of Bolivia were separated by molecular cloning, but some cloned sequences appeared to be artifacts of polymerase chain reaction (PCR) recombination and/or Taq error. Nonetheless, three classes of nonrecombinant sequences each joined a different part of the O. tuberosa alliance clade on the ncpGS gene tree. Octoploid oca shares two sequence classes with the Bolivian tuber-bearing taxon (of unknown ploidy level). Fixed heterozygosity of these two sequence classes in all ocas sampled suggests that they represent homeologous loci and that oca is allopolyploid. A third sequence class, found in eight of nine oca plants sampled, might represent a third homeologous locus, suggesting that oca may be autoallopolyploid, and is shared with another wild tuber-bearing species, tetraploid O. picchensis of southern Peru. Thus, ncpGS data identify these two taxa as the best candidates as progenitors of cultivated oca.

A criticism of the value of midparent in polyploidization.

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Gianinetti, A

2013-11-01

The hypothesis of genetic additivity states that the effects of different alleles, or different genes, add up to produce the phenotype. When considering the F1 progeny of a cross, the hypothesis of additivity of the genetic dosages provided by the parents is tested against the mid-parent value (MPV), which is the average of parental phenotypes and represents the reference value for genetic additivity. Non-additive effects (genetic interactions) are typically measured as deviations from MPV. Recently, however, the use of MPV has been directly transposed to the study of genetic additivity in newly synthesized plant polyploids, assuming that they should as well display mid-parent expression patterns for additive traits. It is shown here that this direct transposition is incorrect. It is suggested that, in neo-polyploids, mid-parent expression has to be reconsidered in terms of reduced genetic additivity. Homeostatic mechanisms are deemed to be the obvious ones responsible for this effect. Genomes are therefore ruled by negative epistasis, and heterosis in allopolyploids is due to a decreased interaction of the parental repressive systems. It is contended that focalizing on the right perspective has relevant theoretical consequences and makes the studies of neo-polyploids very important for our understanding of how genomes work.

Haplotype-Based Genotyping in Polyploids

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Josh P. Clevenger

2018-04-01

Full Text Available Accurate identification of polymorphisms from sequence data is crucial to unlocking the potential of high throughput sequencing for genomics. Single nucleotide polymorphisms (SNPs are difficult to accurately identify in polyploid crops due to the duplicative nature of polyploid genomes leading to low confidence in the true alignment of short reads. Implementing a haplotype-based method in contrasting subgenome-specific sequences leads to higher accuracy of SNP identification in polyploids. To test this method, a large-scale 48K SNP array (Axiom Arachis2 was developed for Arachis hypogaea (peanut, an allotetraploid, in which 1,674 haplotype-based SNPs were included. Results of the array show that 74% of the haplotype-based SNP markers could be validated, which is considerably higher than previous methods used for peanut. The haplotype method has been implemented in a standalone program, HAPLOSWEEP, which takes as input bam files and a vcf file and identifies haplotype-based markers. Haplotype discovery can be made within single reads or span paired reads, and can leverage long read technology by targeting any length of haplotype. Haplotype-based genotyping is applicable in all allopolyploid genomes and provides confidence in marker identification and in silico-based genotyping for polyploid genomics.

Differential contributions to the transcriptome of duplicated genes in response to abiotic stresses in natural and synthetic polyploids.

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Dong, Shaowei; Adams, Keith L

2011-06-01

Polyploidy has occurred throughout plant evolution and can result in considerable changes to gene expression when it takes place and over evolutionary time. Little is known about the effects of abiotic stress conditions on duplicate gene expression patterns in polyploid plants. We examined the expression patterns of 60 duplicated genes in leaves, roots and cotyledons of allotetraploid Gossypium hirsutum in response to five abiotic stress treatments (heat, cold, drought, high salt and water submersion) using single-strand conformation polymorphism assays, and 20 genes in a synthetic allotetraploid. Over 70% of the genes showed stress-induced changes in the relative expression levels of the duplicates under one or more stress treatments with frequent variability among treatments. Twelve pairs showed opposite changes in expression levels in response to different abiotic stress treatments. Stress-induced expression changes occurred in the synthetic allopolyploid, but there was little correspondence in patterns between the natural and synthetic polyploids. Our results indicate that abiotic stress conditions can have considerable effects on duplicate gene expression in a polyploid, with the effects varying by gene, stress and organ type. Differential expression in response to environmental stresses may be a factor in the preservation of some duplicated genes in polyploids. © 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.

Application of genotyping by sequencing technology to a variety of crop breeding programs.

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Kim, Changsoo; Guo, Hui; Kong, Wenqian; Chandnani, Rahul; Shuang, Lan-Shuan; Paterson, Andrew H

2016-01-01

Since the Arabidopsis genome was completed, draft sequences or pseudomolecules have been published for more than 100 plant genomes including green algae, in large part due to advances in sequencing technologies. Advanced DNA sequencing technologies have also conferred new opportunities for high-throughput low-cost crop genotyping, based on single-nucleotide polymorphisms (SNPs). However, a recurring complication in crop genotyping that differs from other taxa is a higher level of DNA sequence duplication, noting that all angiosperms are thought to have polyploidy in their evolutionary history. In the current article, we briefly review current genotyping methods using next-generation sequencing (NGS) technologies. We also explore case studies of genotyping-by-sequencing (GBS) applications to several crops differing in genome size, organization and breeding system (paleopolyploids, neo-allopolyploids, neo-autopolyploids). GBS typically shows good results when it is applied to an inbred diploid species with a well-established reference genome. However, we have also made some progress toward GBS of outcrossing species lacking reference genomes and of polyploid populations, which still need much improvement. Regardless of some limitations, low-cost and multiplexed genotyping offered by GBS will be beneficial to breed superior cultivars in many crop species. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

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

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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. Copyright © 2016 Elsevier Inc. All rights reserved.

The narrow endemic Norwegian peat moss Sphagnum troendelagicum originated before the last glacial maximum.

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Stenøien, H K; Shaw, A J; Stengrundet, K; Flatberg, K I

2011-02-01

It is commonly found that individual hybrid, polyploid species originate recurrently and that many polyploid species originated relatively recently. It has been previously hypothesized that the extremely rare allopolyploid peat moss Sphagnum troendelagicum has originated multiple times, possibly after the last glacial maximum in Scandinavia. This conclusion was based on low linkage disequilibrium in anonymous genetic markers within natural populations, in which sexual reproduction has never been observed. Here we employ microsatellite markers and chloroplast DNA (cpDNA)-encoded trnG sequence data to test hypotheses concerning the origin and evolution of this species. We find that S. tenellum is the maternal progenitor and S. balticum is the paternal progenitor of S. troendelagicum. Using various Bayesian approaches, we estimate that S. troendelagicum originated before the Holocene but not before c. 80,000 years ago (median expected time since speciation 40 000 years before present). The observed lack of complete linkage disequilibrium in the genome of this species suggests cryptic sexual reproduction and recombination. Several lines of evidence suggest multiple origins for S. troendelagicum, but a single origin is supported by approximate Bayesian computation analyses. We hypothesize that S. troendelagicum originated in a peat-dominated refugium before last glacial maximum, and subsequently immigrated to central Norway by means of spore flow during the last thousands of years.

Proteomic profiling of developing cotton fibers from wild and domesticated Gossypium barbadense.

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Hu, Guanjing; Koh, Jin; Yoo, Mi-Jeong; Grupp, Kara; Chen, Sixue; Wendel, Jonathan F

2013-10-01

Pima cotton (Gossypium barbadense) is widely cultivated because of its long, strong seed trichomes ('fibers') used for premium textiles. These agronomically advanced fibers were derived following domestication and thousands of years of human-mediated crop improvement. To gain an insight into fiber development and evolution, we conducted comparative proteomic and transcriptomic profiling of developing fiber from an elite cultivar and a wild accession. Analyses using isobaric tag for relative and absolute quantification (iTRAQ) LC-MS/MS technology identified 1317 proteins in fiber. Of these, 205 were differentially expressed across developmental stages, and 190 showed differential expression between wild and cultivated forms, 14.4% of the proteome sampled. Human selection may have shifted the timing of developmental modules, such that some occur earlier in domesticated than in wild cotton. A novel approach was used to detect possible biased expression of homoeologous copies of proteins. Results indicate a significant partitioning of duplicate gene expression at the protein level, but an approximately equal degree of bias for each of the two constituent genomes of allopolyploid cotton. Our results demonstrate the power of complementary transcriptomic and proteomic approaches for the study of the domestication process. They also provide a rich database for mining for functional analyses of cotton improvement or evolution. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Differential transcriptome analysis between Populus and its synthesized allotriploids driven by second-division restitution.

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Cheng, Shiping; Huang, Zhen; Li, Yun; Liao, Ting; Suo, Yujing; Zhang, Pingdong; Wang, Jun; Kang, Xiangyang

2015-12-01

In this report, we compared transcriptomic differences between a synthetic Populus section Tacamahaca triploid driven by second-division restitution and its parents using a high-throughput RNA-seq method. A total of 4,080 genes were differentially expressed between the high-growth vigor allotriploids (SDR-H) and their parents, and 719 genes were non-additively expressed in SDR-H. Differences in gene expression between the allotriploid and male parent were more significant than those between the allotriploid and female parent, which may be caused by maternal effects. We observed 3,559 differentially expressed genes (DEGs) between the SDR-H and male parent. Notably, the genes were mainly involved in metabolic process, cell proliferation, DNA methylation, cell division, and meristem and developmental growth. Among the 1,056 DEGs between SDR-H and female parent, many genes were associated with metabolic process and carbon utilization. In addition, 1,789 DEGs between high- and low-growth vigor allotriploid were mainly associated with metabolic process, auxin poplar transport, and regulation of meristem growth. Our results indicated that the higher poplar ploidy level can generate extensive transcriptomic diversity compared with its parents. Overall, these results increased our understanding of the driving force for phenotypic variation and adaptation in allopolyploids driven by second-division restitution. © 2015 Institute of Botany, Chinese Academy of Sciences.

The narrow endemic Norwegian peat moss Sphagnum troendelagicum originated before the last glacial maximum

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Stenøien, H K; Shaw, A J; Stengrundet, K; Flatberg, K I

2011-01-01

It is commonly found that individual hybrid, polyploid species originate recurrently and that many polyploid species originated relatively recently. It has been previously hypothesized that the extremely rare allopolyploid peat moss Sphagnum troendelagicum has originated multiple times, possibly after the last glacial maximum in Scandinavia. This conclusion was based on low linkage disequilibrium in anonymous genetic markers within natural populations, in which sexual reproduction has never been observed. Here we employ microsatellite markers and chloroplast DNA (cpDNA)-encoded trnG sequence data to test hypotheses concerning the origin and evolution of this species. We find that S. tenellum is the maternal progenitor and S. balticum is the paternal progenitor of S. troendelagicum. Using various Bayesian approaches, we estimate that S. troendelagicum originated before the Holocene but not before c. 80 000 years ago (median expected time since speciation 40 000 years before present). The observed lack of complete linkage disequilibrium in the genome of this species suggests cryptic sexual reproduction and recombination. Several lines of evidence suggest multiple origins for S. troendelagicum, but a single origin is supported by approximate Bayesian computation analyses. We hypothesize that S. troendelagicum originated in a peat-dominated refugium before last glacial maximum, and subsequently immigrated to central Norway by means of spore flow during the last thousands of years. PMID:20717162

Sweet vernal grasses (Anthoxanthum) colonized African mountains along two fronts in the Late Pliocene, followed by secondary contact, polyploidization and local extinction in the Pleistocene.

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Tusiime, Felly Mugizi; Gizaw, Abel; Wondimu, Tigist; Masao, Catherine Aloyce; Abdi, Ahmed Abdikadir; Muwanika, Vincent; Trávníček, Pavel; Nemomissa, Sileshi; Popp, Magnus; Eilu, Gerald; Brochmann, Christian; Pimentel, Manuel

2017-07-01

High tropical mountains harbour remarkable and fragmented biodiversity thought to a large degree to have been shaped by multiple dispersals of cold-adapted lineages from remote areas. Few dated phylogenetic/phylogeographic analyses are however available. Here, we address the hypotheses that the sub-Saharan African sweet vernal grasses have a dual colonization history and that lineages of independent origins have established secondary contact. We carried out rangewide sampling across the eastern African high mountains, inferred dated phylogenies from nuclear ribosomal and plastid DNA using Bayesian methods, and performed flow cytometry and AFLP (amplified fragment length polymorphism) analyses. We inferred a single Late Pliocene western Eurasian origin of the eastern African taxa, whose high-ploid populations in one mountain group formed a distinct phylogeographic group and carried plastids that diverged from those of the currently allopatric southern African lineage in the Mid- to Late Pleistocene. We show that Anthoxanthum has an intriguing history in sub-Saharan Africa, including Late Pliocene colonization from southeast and north, followed by secondary contact, hybridization, allopolyploidization and local extinction during one of the last glacial cycles. Our results add to a growing body of evidence showing that isolated tropical high mountain habitats have a dynamic recent history involving niche conservatism and recruitment from remote sources, repeated dispersals, diversification, hybridization and local extinction. © 2017 John Wiley & Sons Ltd.

Asymmetric epigenetic modification and elimination of rDNA sequences by polyploidization in wheat.

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Guo, Xiang; Han, Fangpu

2014-11-01

rRNA genes consist of long tandem repeats clustered on chromosomes, and their products are important functional components of the ribosome. In common wheat (Triticum aestivum), rDNA loci from the A and D genomes were largely lost during the evolutionary process. This biased DNA elimination may be related to asymmetric transcription and epigenetic modifications caused by the polyploid formation. Here, we observed both sets of parental nucleolus organizing regions (NORs) were expressed after hybridization, but asymmetric silencing of one parental NOR was immediately induced by chromosome doubling, and reversing the ploidy status could not reactivate silenced NORs. Furthermore, increased CHG and CHH DNA methylation on promoters was accompanied by asymmetric silencing of NORs. Enrichment of H3K27me3 and H3K9me2 modifications was also observed to be a direct response to increased DNA methylation and transcriptional inactivation of NOR loci. Both A and D genome NOR loci with these modifications started to disappear in the S4 generation and were completely eliminated by the S7 generation in synthetic tetraploid wheat. Our results indicated that asymmetric epigenetic modification and elimination of rDNA sequences between different donor genomes may lead to stable allopolyploid wheat with increased differentiation and diversity. © 2014 American Society of Plant Biologists. All rights reserved.

Evolution of finger millet: evidence from random amplified polymorphic DNA.

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Hilu, K W

1995-04-01

Finger millet (Eleusine coracana ssp. coracana) is an annual tetraploid member of a predominantly African genus. The crop is believed to have been domesticated from the tetraploid E. coracana ssp. africana. Cytogenetic and isozyme data point to the allopolyploid nature of the species and molecular information has shown E. indica to be one of the genomic donors. A recent isozyme study questioned the proposed phylogenetic relationship between finger millet and its direct ancestor subspecies africana. An approach using random amplified polymorphic DNA (RAPD) was employed in this study to examine genetic diversity and to evaluate hypotheses concerning the evolution of domesticated and wild annual species of Eleusine. Unlike previous molecular approaches, the RAPD study revealed genetic diversity in the crop. The pattern of genetic variation was loosely correlated to geographic distribution. The allotetraploid nature of the crop was confirmed and molecular markers that can possibly identify the other genomic donor were proposed. Genotypes of subspecies africana did not group closely with those of the crop but showed higher affinities to E. indica, reflecting the pattern of similarity revealed by the isozyme study. The multiple origin of subspecies africana could explain the discrepancy between the isozyme-RAPD evidence and previous information. The RAPD study showed the close genetic affinity of E. tristachya to the E. coracana--E. indica group and understood the distinctness of E. multiflora.

Meiotic behaviour and its implication on species inter-relationship in the genus Curcuma (Linnaeus, 1753 (Zingiberaceae

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Judith Mary Lamo

2017-10-01

Full Text Available In this paper, detailed meiotic analysis was investigated in seven species of Curcuma (Linnaeus, 1753 which can contribute significantly to our understanding about species inter-relationship, speciation and evolution. The species were divided into two groups viz., Group I having 2n = 42 (C. comosa Roxburgh, 1810, C. haritha Mangaly & M.Sabu, 1993, C. mangga Valeton & Zijp, 1917, and C. motana Roxburgh, 1800 and Group II with 2n = 63 (C. caesia Roxburgh, 1810, C. longa Linnaeus, 1753 and C. sylvatica Valeton, 1918. Both groups display varying degree of chromosome associations. Group I species showed the prevalence of bivalents, however occasional quadrivalents besides univalents were also encountered. About 48% of the PMCs analyzed in C. mangga showed 21 bivalents (II meiotic configurations, 32% in C. comosa and 16% in C. haritha. Group II species as expected showed the presence of trivalents besides bivalents, univalents and quadrivalents. About 32% of the PMCs analyzed at MI in C. sylvatica showed 21 trivalents (III meiotic configurations, 24% in C. longa and 8% in C. caesia. Overall, low frequency of multivalent associations as compared to bivalents indicates that Curcuma is an allopolyploid complex. Moreover, x = 21 is too high a basic number, therefore, we suggest that the genus Curcuma has evolved by hybridization of species with different chromosome numbers of 2n = 24 and 18, resulting in a dibasic amphidiploid species.

A New Perspective on Polyploid Fragaria (Strawberry) Genome Composition Based on Large-Scale, Multi-Locus Phylogenetic Analysis.

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Yang, Yilong; Davis, Thomas M

2017-12-01

The subgenomic compositions of the octoploid (2n = 8× = 56) strawberry (Fragaria) species, including the economically important cultivated species Fragaria x ananassa, have been a topic of long-standing interest. Phylogenomic approaches utilizing next-generation sequencing technologies offer a new window into species relationships and the subgenomic compositions of polyploids. We have conducted a large-scale phylogenetic analysis of Fragaria (strawberry) species using the Fluidigm Access Array system and 454 sequencing platform. About 24 single-copy or low-copy nuclear genes distributed across the genome were amplified and sequenced from 96 genomic DNA samples representing 16 Fragaria species from diploid (2×) to decaploid (10×), including the most extensive sampling of octoploid taxa yet reported. Individual gene trees were constructed by different tree-building methods. Mosaic genomic structures of diploid Fragaria species consisting of sequences at different phylogenetic positions were observed. Our findings support the presence in octoploid species of genetic signatures from at least five diploid ancestors (F. vesca, F. iinumae, F. bucharica, F. viridis, and at least one additional allele contributor of unknown identity), and questions the extent to which distinct subgenomes are preserved over evolutionary time in the allopolyploid Fragaria species. In addition, our data support divergence between the two wild octoploid species, F. virginiana and F. chiloensis. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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

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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

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.

Centromere separation and association in the nuclei of an interspecific hybrid between Torenia fournieri and T. baillonii (Scrophulariaceae) during mitosis and meiosis.

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Kikuchi, Shinji; Tanaka, Hiroyuki; Wako, Toshiyuki; Tsujimoto, Hisashi

2007-10-01

In the nuclei of some interspecific hybrid and allopolyploid plant species, each genome occupies a separate spatial domain. To analyze this phenomenon, we studied localization of the centromeres in the nuclei of a hybrid between Torenia fournieri and T. baillonii during mitosis and meiosis using three-dimensional fluorescence in situ hybridization (3D-FISH) probed with species-specific centromere repeats. Centromeres of each genome were located separately in undifferentiated cells but not differentiated cells, suggesting that cell division might be the possible force causing centromere separation. However, no remarkable difference of dividing distance was detected between chromatids with different centromeres in anaphase and telophase, indicating that tension of the spindle fiber attached to each chromatid is not the cause of centromere separation in Torenia. In differentiated cells, centromeres in both genomes were not often observed for the expected chromosome number, indicating centromere association. In addition, association of centromeres from the same genome was observed at a higher frequency than between different genomes. This finding suggests that centromeres within one genome are spatially separated from those within the other. This close position may increase possibility of association between centromeres of the same genome. In meiotic prophase, all centromeres irrespective of the genome were associated in a certain portion of the nucleus. Since centromere association in the interspecific hybrid and amphiploid was tighter than that in the diploid parents, it is possible that this phenomenon may be involved in sorting and pairing of homologous chromosomes.

Saccharomyces cerevisiae Differential Functionalization of Presumed ScALT1 and ScALT2 Alanine Transaminases Has Been Driven by Diversification of Pyridoxal Phosphate Interactions

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Erendira Rojas-Ortega

2018-05-01

Full Text Available Saccharomyces cerevisiae arose from an interspecies hybridization (allopolyploidiza-tion, followed by Whole Genome Duplication. Diversification analysis of ScAlt1/ScAlt2 indicated that while ScAlt1 is an alanine transaminase, ScAlt2 lost this activity, constituting an example in which one of the members of the gene pair lacks the apparent ancestral physiological role. This paper analyzes structural organization and pyridoxal phosphate (PLP binding properties of ScAlt1 and ScAlt2 indicating functional diversification could have determined loss of ScAlt2 alanine transaminase activity and thus its role in alanine metabolism. It was found that ScAlt1 and ScAlt2 are dimeric enzymes harboring 67% identity and intact conservation of the catalytic residues, with very similar structures. However, tertiary structure analysis indicated that ScAlt2 has a more open conformation than that of ScAlt1 so that under physiological conditions, while PLP interaction with ScAlt1 allows the formation of two tautomeric PLP isomers (enolimine and ketoenamine ScAlt2 preferentially forms the ketoenamine PLP tautomer, indicating a modified polarity of the active sites which affect the interaction of PLP with these proteins, that could result in lack of alanine transaminase activity in ScAlt2. The fact that ScAlt2 forms a catalytically active Schiff base with PLP and its position in an independent clade in “sensu strictu” yeasts suggests this protein has a yet undiscovered physiological function.

Evolutionary History of the Genus Capsella (Brassicaceae - Capsella orientalis , New for Mongolia

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Barbara Neuffer

2014-12-01

Full Text Available To elucidate the evolutionary history of the genus Capsella , we included the hitherto poorly known species C. orientalis and C. thracica into our studies together with C. grandifl ora , C. rubella , and C. bursa-pastoris . We sequenced the ITS, and four loci of noncoding cpDNA regions (trnL – F, rps16, trnH – psbA, trnQ – rps16. In common garden fi eld experiments C. orientalis turned out as early fl owering with a specifi c leaf type. The crossing ability of the species was tested in pollen germination experiments. Capsella orientalis (self-compatible, SC; 2n = 16 forms a clade (eastern lineage with C . bursa-pastoris (SC; 2n = 32, which is a sister clade (western lineage to C. grandifl ora (self-incompatible, SI; 2n = 16 and C. rubella (SC; 2n = 16. Capsella bursa-pastoris is an autopolyploid species of multiple origin, whereas the Bulgarian endemic C. thracica (SC; 2n = 32 is allopolyploid and emerged from interspecifi c hybridisation between C. bursa-pastoris and C. grandifl ora . The common ancestor of the two lineages was diploid and SI, and its distribution ranged from eastern Europe to central Asia, predominantly confi ned to steppe like habitats. Biogeographic dynamics during the Pleistocene caused geographic and genetic subdivisions within the common ancestor giving rise to the two extant lineages. Capsella orientalis is verifi ed at several positions in western Mongolia.

A Novel Complementation Assay for Quick and Specific Screen of Genes Encoding Glycerol-3-Phosphate Acyltransferases

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Jie Lei

2018-03-01

Full Text Available The initial step in glycerolipid biosynthesis, especially in diverse allopolyploid crop species, is poorly understood, mainly due to the lack of an effective and convenient method for functional characterization of genes encoding glycerol-3-phosphate acyltransferases (GPATs catalyzing this reaction. Here we present a novel complementation assay for quick and specific characterization of GPAT-encoding genes. Its key design involves rational construction of yeast conditional lethal gat1Δgat2Δ double mutant bearing the heterologous Arabidopsis AtGPAT1 gene whose leaky expression under repressed conditions does not support any non-specific growth, thereby circumventing the false positive problem encountered with the system based on the gat1Δgat2Δ mutant harboring the native episomal GAT1 gene whose leaky expression appears to be sufficient for generating enough GPAT activities for the non-specific restoration of the mutant growth. A complementation assay developed based on this novel mutant enables quick phenotypic screen of GPAT sequences. A high degree of specificity of our assay was exemplified by its ability to differentiate effectively GPAT-encoding genes from those of other fatty acyltransferases and lipid-related sequences. Using this assay, we show that Arabidopsis AtGPAT1, AtGPAT5, and AtGPAT7 can complement the phosphatidate biosynthetic defect in the double mutants. Collectively, our assay provides a powerful tool for rapid screening, validation and optimization of GPAT sequences, aiding future engineering of the initial step of the triacylglycerol biosynthesis in oilseeds.

Saccharomyces cerevisiae Differential Functionalization of Presumed ScALT1 and ScALT2 Alanine Transaminases Has Been Driven by Diversification of Pyridoxal Phosphate Interactions

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Rojas-Ortega, Erendira; Aguirre-López, Beatriz; Reyes-Vivas, Horacio; González-Andrade, Martín; Campero-Basaldúa, Jose C.; Pardo, Juan P.; González, Alicia

2018-01-01

Saccharomyces cerevisiae arose from an interspecies hybridization (allopolyploidiza-tion), followed by Whole Genome Duplication. Diversification analysis of ScAlt1/ScAlt2 indicated that while ScAlt1 is an alanine transaminase, ScAlt2 lost this activity, constituting an example in which one of the members of the gene pair lacks the apparent ancestral physiological role. This paper analyzes structural organization and pyridoxal phosphate (PLP) binding properties of ScAlt1 and ScAlt2 indicating functional diversification could have determined loss of ScAlt2 alanine transaminase activity and thus its role in alanine metabolism. It was found that ScAlt1 and ScAlt2 are dimeric enzymes harboring 67% identity and intact conservation of the catalytic residues, with very similar structures. However, tertiary structure analysis indicated that ScAlt2 has a more open conformation than that of ScAlt1 so that under physiological conditions, while PLP interaction with ScAlt1 allows the formation of two tautomeric PLP isomers (enolimine and ketoenamine) ScAlt2 preferentially forms the ketoenamine PLP tautomer, indicating a modified polarity of the active sites which affect the interaction of PLP with these proteins, that could result in lack of alanine transaminase activity in ScAlt2. The fact that ScAlt2 forms a catalytically active Schiff base with PLP and its position in an independent clade in “sensu strictu” yeasts suggests this protein has a yet undiscovered physiological function. PMID:29867852

The Evolutionary History Of The White-Rayed Species Of Melampodium (Asteraceae) Involved Multiple Cycles Of Hybridization And Polyploidization1

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Rebernig, Carolin A.; Weiss-Schneeweiss, Hanna; Blöch, Cordula; Turner, Barbara; Stuessy, Tod F.; Obermayer, Renate; Villaseñor, Jose L.; Schneeweiss, Gerald M.

2014-01-01

Premise of the study Polyploidy plays an important role in race differentiation and eventually speciation. Underlying mechanisms include chromosomal and genomic changes facilitating reproductive isolation and/or stabilization of hybrids. A prerequisite for studying these processes is a sound knowledge on the origin of polyploids. A well-suited group for studying polyploid evolution consists of the three species of Melampodium ser. Leucantha (Asteraceae): M. argophyllum, M. cinereum, and M. leucanthum. Methods The origin of polyploids was inferred using network and tree-based phylogenetic analyses of several plastid and nuclear DNA sequences and of fingerprint data (AFLP). Genome evolution was assessed via genome size measurements, karyotype analysis, and in situ hybridization of ribosomal DNA. Key results Tetraploid cytotypes of the phylogenetically distinct M. cinereum and M. leucanthum had, compared to the diploid cytotypes, doubled genome sizes and no evidence of gross chromosomal rearrangements. Hexaploid M. argophyllum constituted a separate lineage with limited intermixing with the other species, except in analyses from nuclear ITS. Its genome size was lower than expected if M. cinereum and/or M. leucanthum were involved in its origin, and no chromosomal rearrangements were evident. Conclusions Polyploids in M. cinereum and M. leucanthum are of recent autopolyploid origin in line with the lack of significant genomic changes. Hexaploid M. argophyllum also appears to be of autopolyploid origin against the previous hypothesis of an allopolyploid origin involving the other two species, but some gene flow with the other species in early phases of differentiation cannot be excluded. PMID:22645096

Transgene-induced gene silencing is not affected by a change in ploidy level.

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Daniela Pignatta

Full Text Available BACKGROUND: Whole genome duplication, which results in polyploidy, is a common feature of plant populations and a recurring event in the evolution of flowering plants. Polyploidy can result in changes to gene expression and epigenetic instability. Several epigenetic phenomena, occurring at the transcriptional or post-transcriptional level, have been documented in allopolyploids (polyploids derived from species hybrids of Arabidopsis thaliana, yet findings in autopolyploids (polyploids derived from the duplication of the genome of a single species are limited. Here, we tested the hypothesis that an increase in ploidy enhances transgene-induced post-transcriptional gene silencing using autopolyploids of A. thaliana. METHODOLOGY/PRINCIPAL FINDINGS: Diploid and tetraploid individuals of four independent homozygous transgenic lines of A. thaliana transformed with chalcone synthase (CHS inverted repeat (hairpin constructs were generated. For each line diploids and tetraploids were compared for efficiency in post-transcriptional silencing of the endogenous CHS gene. The four lines differed substantially in their silencing efficiency. Yet, diploid and tetraploid plants derived from these plants and containing therefore identical transgene insertions showed no difference in the efficiency silencing CHS as assayed by visual scoring, anthocyanin assays and quantification of CHS mRNA. CONCLUSIONS/SIGNIFICANCE: Our results in A. thaliana indicated that there is no effect of ploidy level on transgene-induced post-transcriptional gene silencing. Our findings that post-transcriptional mechanisms were equally effective in diploids and tetraploids supports the use of transgene-driven post-transcriptional gene silencing as a useful mechanism to modify gene expression in polyploid species.

Molecular cytogenetic and genomic analyses reveal new insights into the origin of the wheat B genome.

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Zhang, Wei; Zhang, Mingyi; Zhu, Xianwen; Cao, Yaping; Sun, Qing; Ma, Guojia; Chao, Shiaoman; Yan, Changhui; Xu, Steven S; Cai, Xiwen

2018-02-01

This work pinpointed the goatgrass chromosomal segment in the wheat B genome using modern cytogenetic and genomic technologies, and provided novel insights into the origin of the wheat B genome. Wheat is a typical allopolyploid with three homoeologous subgenomes (A, B, and D). The donors of the subgenomes A and D had been identified, but not for the subgenome B. The goatgrass Aegilops speltoides (genome SS) has been controversially considered a possible candidate for the donor of the wheat B genome. However, the relationship of the Ae. speltoides S genome with the wheat B genome remains largely obscure. The present study assessed the homology of the B and S genomes using an integrative cytogenetic and genomic approach, and revealed the contribution of Ae. speltoides to the origin of the wheat B genome. We discovered noticeable homology between wheat chromosome 1B and Ae. speltoides chromosome 1S, but not between other chromosomes in the B and S genomes. An Ae. speltoides-originated segment spanning a genomic region of approximately 10.46 Mb was detected on the long arm of wheat chromosome 1B (1BL). The Ae. speltoides-originated segment on 1BL was found to co-evolve with the rest of the B genome. Evidently, Ae. speltoides had been involved in the origin of the wheat B genome, but should not be considered an exclusive donor of this genome. The wheat B genome might have a polyphyletic origin with multiple ancestors involved, including Ae. speltoides. These novel findings will facilitate genome studies in wheat and other polyploids.

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

Host Adaptation and Speciation through Hybridization and Polyploidy in Phytophthora

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Bertier, Lien; Leus, Leen; D’hondt, Liesbet; de Cock, Arthur W. A. M.; Höfte, Monica

2013-01-01

It is becoming increasingly evident that interspecific hybridization is a common event in phytophthora evolution. Yet, the fundamental processes underlying interspecific hybridization and the consequences for its ecological fitness and distribution are not well understood. We studied hybridization events in phytophthora clade 8b. This is a cold-tolerant group of plant pathogenic oomycetes in which six host-specific species have been described that mostly attack winter-grown vegetables. Hybrid characterization was done by sequencing and cloning of two nuclear (ITS and Ypt1) and two mitochondrial loci (Cox1 and Nadh1) combined with DNA content estimation using flow cytometry. Three different mtDNA haplotypes were recovered among the presumed hybrid isolates, dividing the hybrids into three types, with different parental species involved. In the nuclear genes, additivity, i.e. the presence of two alleles coming from different parents, was detected. Hybrid isolates showed large variations in DNA content, which was positively correlated with the additivity in nuclear loci, indicating allopolyploid hybridization followed by a process of diploidization. Moreover, indications of homeologous recombination were found in the hybrids by cloning ITS products. The hybrid isolates have been isolated from a range of hosts that have not been reported previously for clade 8b species, indicating that they have novel pathogenic potential. Next to this, DNA content measurements of the non-hybrid clade 8b species suggest that polyploidy is a common feature of this clade. We hypothesize that interspecific hybridization and polyploidy are two linked phenomena in phytophthora, and that these processes might play an important and ongoing role in the evolution of this genus. PMID:24386473

Production of a high-efficiency TILLING population through polyploidization.

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Tsai, Helen; Missirian, Victor; Ngo, Kathie J; Tran, Robert K; Chan, Simon R; Sundaresan, Venkatesan; Comai, Luca

2013-04-01

Targeting Induced Local Lesions in Genomes (TILLING) provides a nontransgenic method for reverse genetics that is widely applicable, even in species where other functional resources are missing or expensive to build. The efficiency of TILLING, however, is greatly facilitated by high mutation density. Species vary in the number of mutations induced by comparable mutagenic treatments, suggesting that genetic background may affect the response. Allopolyploid species have often yielded higher mutation density than diploids. To examine the effect of ploidy, we autotetraploidized the Arabidopsis (Arabidopsis thaliana) ecotype Columbia, whose diploid has been used for TILLING extensively, and mutagenized it with 50 mm ethylmethane sulfonate. While the same treatment sterilized diploid Columbia, the tetraploid M1 plants produced good seed. To determine the mutation density, we searched 528 individuals for induced mutations in 15 genes for which few or no knockout alleles were previously available. We constructed tridimensional pools from the genomic DNA of M2 plants, amplified target DNA, and subjected them to Illumina sequencing. The results were analyzed with an improved version of the mutation detection software CAMBa that accepts any pooling scheme. This small population provided a rich resource with approximately 25 mutations per queried 1.5-kb fragment, including on average four severe missense and 1.3 truncation mutations. The overall mutation density of 19.4 mutations Mb(-1) is 4 times that achieved in the corresponding diploid accession, indicating that genomic redundancy engenders tolerance to high mutation density. Polyploidization of diploids will allow the production of small populations, such as less than 2,000, that provide allelic series from knockout to mild loss of function for virtually all genes.

Reconstruction of phylogenetic relationships in a highly reticulate group with deep coalescence and recent speciation (Hieracium, Asteraceae).

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Krak, K; Caklová, P; Chrtek, J; Fehrer, J

2013-02-01

Phylogeny reconstruction based on multiple unlinked markers is often hampered by incongruent gene trees, especially in closely related species complexes with high degrees of hybridization and polyploidy. To investigate the particular strengths and limitations of chloroplast DNA (cpDNA), low-copy nuclear and multicopy nuclear markers for elucidating the evolutionary history of such groups, we focus on Hieracium s.str., a predominantly apomictic genus combining the above-mentioned features. Sequences of the trnV-ndhC and trnT-trnL intergenic spacers were combined for phylogenetic analyses of cpDNA. Part of the highly variable gene for squalene synthase (sqs) was applied as a low-copy nuclear marker. Both gene trees were compared with previous results based on the multicopy external transcribed spacer (ETS) of the nuclear ribosomal DNA. The power of the different markers to detect hybridization varied, but they largely agreed on particular hybrid and allopolyploid origins. The same crown groups of species were recognizable in each dataset, but basal relationships were strongly incongruent among cpDNA, sqs and ETS trees. The ETS tree was considered as the best approximation of the species tree. Both cpDNA and sqs trees showed basal polytomies as well as merging or splitting of species groups of non-hybrid taxa. These patterns can be best explained by a rapid diversification of the genus with ancestral polymorphism and incomplete lineage sorting. A hypothetical scenario of Hieracium speciation based on all available (including non-molecular) evidence is depicted. Incorporation of seemingly contradictory information helped to better understand species origins and evolutionary patterns in this notoriously difficult agamic complex.

Genome-wide analysis of short interspersed nuclear elements SINES revealed high sequence conservation, gene association and retrotranspositional activity in wheat.

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Ben-David, Smadar; Yaakov, Beery; Kashkush, Khalil

2013-10-01

Short interspersed nuclear elements (SINEs) are non-autonomous non-LTR retroelements that are present in most eukaryotic species. While SINEs have been intensively investigated in humans and other animal systems, they are poorly studied in plants, especially in wheat (Triticum aestivum). We used quantitative PCR of various wheat species to determine the copy number of a wheat SINE family, termed Au SINE, combined with computer-assisted analyses of the publicly available 454 pyrosequencing database of T. aestivum. In addition, we utilized site-specific PCR on 57 Au SINE insertions, transposon methylation display and transposon display on newly formed wheat polyploids to assess retrotranspositional activity, epigenetic status and genetic rearrangements in Au SINE, respectively. We retrieved 3706 different insertions of Au SINE from the 454 pyrosequencing database of T. aestivum, and found that most of the elements are inserted in A/T-rich regions, while approximately 38% of the insertions are associated with transcribed regions, including known wheat genes. We observed typical retrotransposition of Au SINE in the second generation of a newly formed wheat allohexaploid, and massive hypermethylation in CCGG sites surrounding Au SINE in the third generation. Finally, we observed huge differences in the copy numbers in diploid Triticum and Aegilops species, and a significant increase in the copy numbers in natural wheat polyploids, but no significant increase in the copy number of Au SINE in the first four generations for two of three newly formed allopolyploid species used in this study. Our data indicate that SINEs may play a prominent role in the genomic evolution of wheat through stress-induced activation. © 2013 Ben-Gurion University The Plant Journal © 2013 John Wiley & Sons Ltd.

Cytomolecular analysis of ribosomal DNA evolution in a natural allotetraploid Brachypodium hybridum and its putative ancestors – dissecting complex repetitive structure of intergenic spacers

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Natalia Borowska-Zuchowska

2016-10-01

Full Text Available Nucleolar dominance is an epigenetic phenomenon associated with nuclear 35S rRNA genes and consists in selective suppression of gene loci inherited from one of the progenitors in the allopolyploid. Our understanding of the exact mechanisms that determine this process is still fragmentary, especially in case of the grass species. This study aimed to shed some light on the molecular basis of this genome-specific inactivation of 35S rDNA loci in an allotetraploid Brachypodium hybridum (2n=30, which arose from the interspecific hybridization between two diploid ancestors that were very similar to modern B. distachyon (2n=10 and B. stacei (2n=20. Using fluorescence in situ hybridization with 25S rDNA and chromosome-specific BAC clones as probes we revealed that the nucleolar dominance is present not only in meristematic root-tip cells but also in differentiated cell fraction of B. hybridum. Additionally, the intergenic spacers (IGSs from both of the putative ancestors and the allotetraploid were sequenced and analyzed. The presumptive transcription initiation sites, spacer promoters and repeated elements were identified within the IGSs. Two different length variants, 2.3 kb and 3.5 kb, of IGSs were identified in B. distachyon and B. stacei, respectively, however only the IGS that had originated from B. distachyon-like ancestor was present in the allotetraploid. The amplification pattern of B. hybridum IGSs suggests that some genetic changes occurred in inactive B. stacei-like rDNA loci during the evolution of the allotetraploid. We hypothesize that their preferential silencing is an effect of structural changes in the sequence rather than just the result of the sole inactivation at the epigenetic level.

Adaptation of the Pivotal-Differential Genome Pattern for the Induction of Intergenomic Chromosome Recombination in Hybrids of Synthetic Amphidiploids within Triticeae Tribe

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Michal T. Kwiatek

2017-07-01

Full Text Available A pivotal-differential evolution pattern is when two allopolyploids share a common genome, which is called pivotal, and differ with respect to the other genome or genomes, called differential. This feature induces the intergenomic recombination between chromosomes of differential genomes, which can lead to speciation. Our study is a cytomolecular insight into this mechanism which was adapted for the induction of intergenomic chromosome recombination in hybrids of synthetic amphidiploids Aegilops biuncialis × S. cereale (UUMMRR and triticale (AABBRR where R-genome was pivotal. We observed chromosome recombination events which were induced by both: (1 random chromosome fragmentation and non-homologous chromosome end joining at mitosis of root meristem cells and (2 intergenomic chromosome associations at meiosis of pollen mother cells (PMCs of F1 hybrids. Reciprocal chromosome translocations were identified in six F1 plants and 15 plants of F2 generation using fluorescence in situ hybridization (FISH with DNA clones (pTa-86, pTa-k374, pTa-465, pTa-535, pTa-k566, and pTa-713. We observed signals of pTa-86, pTa-535, and pTa-k566 probes in several chromosome breakpoints. The comparison of the DNA clone sequences distinguished a number of common motifs, which can be considered as characteristics of chromosome breakpoint loci. Immunodetection of synaptonemal complex proteins and genomic in situ hybridization analysis at meiosis of PMCs of F1 hybrids showed, that the homologous pairing of pivotal R—genome chromosomes is crucial for the fertility of F1 hybrids, however, these chromosomes can be also involved in the intergeneric recombination.

Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes.

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Romain Blanc-Mathieu

2017-06-01

their TE-rich composite genomes, resulting from allopolyploidization events, and promoting plasticity and functional divergence between gene copies in the absence of sex and meiosis.

Genetic and genomic interactions of animals with different ploidy levels.

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Bogart, J P; Bi, K

2013-01-01

Polyploid animals have independently evolved from diploids in diverse taxa across the tree of life. We review a few polyploid animal species or biotypes where recently developed molecular and cytogenetic methods have significantly improved our understanding of their genetics, reproduction and evolution. Mitochondrial sequences that target the maternal ancestor of a polyploid show that polyploids may have single (e.g. unisexual salamanders in the genus Ambystoma) or multiple (e.g. parthenogenetic polyploid lizards in the genus Aspidoscelis) origins. Microsatellites are nuclear markers that can be used to analyze genetic recombinations, reproductive modes (e.g. Ambystoma) and recombination events (e.g. polyploid frogs such as Pelophylax esculentus). Hom(e)ologous chromosomes and rare intergenomic exchanges in allopolyploids have been distinguished by applying genome-specific fluorescent probes to chromosome spreads. Polyploids arise, and are maintained, through perturbations of the 'normal' meiotic program that would include pre-meiotic chromosome replication and genomic integrity of homologs. When possible, asexual, unisexual and bisexual polyploid species or biotypes interact with diploid relatives, and genes are passed from diploid to polyploid gene pools, which increase genetic diversity and ultimately evolutionary flexibility in the polyploid. When diploid relatives do not exist, polyploids can interact with another polyploid (e.g. species of African Clawed Frogs in the genus Xenopus). Some polyploid fish (e.g. salmonids) and frogs (Xenopus) represent independent lineages whose ancestors experienced whole genome duplication events. Some tetraploid frogs (P. esculentus) and fish (Squaliusalburnoides) may be in the process of becoming independent species, but diploid and triploid forms of these 'species' continue to genetically interact with the comparatively few tetraploid populations. Genetic and genomic interaction between polyploids and diploids is a complex

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

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

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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.

Polyploidisation and geographic differentiation drive diversification in a European High Mountain Plant Group (Doronicum clusii Aggregate, Asteraceae).

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Pachschwöll, Clemens; Escobar García, Pedro; Winkler, Manuela; Schneeweiss, Gerald M; Schönswetter, Peter

2015-01-01

Range shifts (especially during the Pleistocene), polyploidisation and hybridization are major factors affecting high-mountain biodiversity. A good system to study their role in the European high mountains is the Doronicum clusii aggregate (Asteraceae), whose four taxa (D. clusii s.s., D. stiriacum, D. glaciale subsp. glaciale and D. glaciale subsp. calcareum) are differentiated geographically, ecologically (basiphilous versus silicicolous) and/or via their ploidy levels (diploid versus tetraploid). Here, we use DNA sequences (three plastid and one nuclear spacer) and AFLP fingerprinting data generated for 58 populations to infer phylogenetic relationships, origin of polyploids-whose ploidy level was confirmed by chromosomally calibrated DNA ploidy level estimates-and phylogeographic history. Taxonomic conclusions were informed, among others, by a Gaussian clustering method for species delimitation using dominant multilocus data. Based on molecular data we identified three lineages: (i) silicicolous diploid D. clusii s.s. in the Alps, (ii) silicicolous tetraploid D. stiriacum in the eastern Alps (outside the range of D. clusii s.s.) and the Carpathians and (iii) the basiphilous diploids D. glaciale subsp. glaciale (eastern Alps) and D. glaciale subsp. calcareum (northeastern Alps); each taxon was identified as distinct by the Gaussian clustering, but the separation of D. glaciale subsp. calcareum and D. glaciale subsp. glaciale was not stable, supporting their taxonomic treatment as subspecies. Carpathian and Alpine populations of D. stiriacum were genetically differentiated suggesting phases of vicariance, probably during the Pleistocene. The origin (autopolyploid versus allopolyploid) of D. stiriacum remained unclear. Doronicum glaciale subsp. calcareum was genetically and morphologically weakly separated from D. glaciale subsp. glaciale but exhibited significantly higher genetic diversity and rarity. This suggests that the more widespread D. glaciale subsp

Polyploidisation and geographic differentiation drive diversification in a European High Mountain Plant Group (Doronicum clusii Aggregate, Asteraceae.

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Clemens Pachschwöll

Full Text Available Range shifts (especially during the Pleistocene, polyploidisation and hybridization are major factors affecting high-mountain biodiversity. A good system to study their role in the European high mountains is the Doronicum clusii aggregate (Asteraceae, whose four taxa (D. clusii s.s., D. stiriacum, D. glaciale subsp. glaciale and D. glaciale subsp. calcareum are differentiated geographically, ecologically (basiphilous versus silicicolous and/or via their ploidy levels (diploid versus tetraploid. Here, we use DNA sequences (three plastid and one nuclear spacer and AFLP fingerprinting data generated for 58 populations to infer phylogenetic relationships, origin of polyploids-whose ploidy level was confirmed by chromosomally calibrated DNA ploidy level estimates-and phylogeographic history. Taxonomic conclusions were informed, among others, by a Gaussian clustering method for species delimitation using dominant multilocus data. Based on molecular data we identified three lineages: (i silicicolous diploid D. clusii s.s. in the Alps, (ii silicicolous tetraploid D. stiriacum in the eastern Alps (outside the range of D. clusii s.s. and the Carpathians and (iii the basiphilous diploids D. glaciale subsp. glaciale (eastern Alps and D. glaciale subsp. calcareum (northeastern Alps; each taxon was identified as distinct by the Gaussian clustering, but the separation of D. glaciale subsp. calcareum and D. glaciale subsp. glaciale was not stable, supporting their taxonomic treatment as subspecies. Carpathian and Alpine populations of D. stiriacum were genetically differentiated suggesting phases of vicariance, probably during the Pleistocene. The origin (autopolyploid versus allopolyploid of D. stiriacum remained unclear. Doronicum glaciale subsp. calcareum was genetically and morphologically weakly separated from D. glaciale subsp. glaciale but exhibited significantly higher genetic diversity and rarity. This suggests that the more widespread D. glaciale

Genome-Wide Gene Expression Disturbance by Single A1/C1 Chromosome Substitution in Brassica rapa Restituted From Natural B. napus

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Bin Zhu

2018-03-01

Full Text Available Alien chromosome substitution (CS lines are treated as vital germplasms for breeding and genetic mapping. Previously, a whole set of nine Brassica rapa-oleracea monosonic alien addition lines (MAALs, C1-C9 was established in the background of natural B. napus genotype “Oro,” after the restituted B. rapa (RBR for Oro was realized. Herein, a monosomic substitution line with one alien C1 chromosome (Cs1 in the RBR complement was selected in the progenies of MAAL C1 and RBR, by the PCR amplification of specific gene markers and fluorescence in situ hybridization. Cs1 exhibited the whole plant morphology similar to RBR except for the defective stamens without fertile pollen grains, but it produced some seeds and progeny plants carrying the C1 chromosome at high rate besides those without the alien chromosome after pollinated by RBR. The viability of the substitution and its progeny for the RBR diploid further elucidated the functional compensation between the chromosome pairs with high homoeology. To reveal the impact of such aneuploidy on genome-wide gene expression, the transcriptomes of MAAL C1, Cs1 and euploid RBR were analyzed. Compared to RBR, Cs1 had sharply reduced gene expression level across chromosome A1, demonstrating the loss of one copy of A1 chromosome. Both additional chromosome C1 in MAAL and substitutional chromosome C1 in Cs1 caused not only cis-effect but also prevalent trans-effect differentially expressed genes. A dominant gene dosage effects prevailed among low expressed genes across chromosome A1 in Cs1, and moreover, dosage effects for some genes potentially contributed to the phenotype deviations. Our results provided novel insights into the transcriptomic perturbation and gene dosage effects on phenotype in CS related to one naturally evolved allopolyploid.

Tracing the Transcriptomic Changes in Synthetic Trigenomic allohexaploids of Brassica Using an RNA-Seq Approach

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Zhao, Qin; Zou, Jun; Meng, Jinling; Mei, Shiyong; Wang, Jianbo

2013-01-01

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 Brassica rapa , Brassica carinata , 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

Decomposing Additive Genetic Variance Revealed Novel Insights into Trait Evolution in Synthetic Hexaploid Wheat

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Abdulqader Jighly

2018-02-01

Full Text Available Whole genome duplication (WGD is an evolutionary phenomenon, which causes significant changes to genomic structure and trait architecture. In recent years, a number of studies decomposed the additive genetic variance explained by different sets of variants. However, they investigated diploid populations only and none of the studies examined any polyploid organism. In this research, we extended the application of this approach to polyploids, to differentiate the additive variance explained by the three subgenomes and seven sets of homoeologous chromosomes in synthetic allohexaploid wheat (SHW to gain a better understanding of trait evolution after WGD. Our SHW population was generated by crossing improved durum parents (Triticum turgidum; 2n = 4x = 28, AABB subgenomes with the progenitor species Aegilops tauschii (syn Ae. squarrosa, T. tauschii; 2n = 2x = 14, DD subgenome. The population was phenotyped for 10 fungal/nematode resistance traits as well as two abiotic stresses. We showed that the wild D subgenome dominated the additive effect and this dominance affected the A more than the B subgenome. We provide evidence that this dominance was not inflated by population structure, relatedness among individuals or by longer linkage disequilibrium blocks observed in the D subgenome within the population used for this study. The cumulative size of the three homoeologs of the seven chromosomal groups showed a weak but significant positive correlation with their cumulative explained additive variance. Furthermore, an average of 69% for each chromosomal group's cumulative additive variance came from one homoeolog that had the highest explained variance within the group across all 12 traits. We hypothesize that structural and functional changes during diploidization may explain chromosomal group relations as allopolyploids keep balanced dosage for many genes. Our results contribute to a better understanding of trait evolution mechanisms in polyploidy

Polyploidisation and Geographic Differentiation Drive Diversification in a European High Mountain Plant Group (Doronicum clusii Aggregate, Asteraceae)

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Pachschwöll, Clemens; Escobar García, Pedro; Winkler, Manuela; Schneeweiss, Gerald M.; Schönswetter, Peter

2015-01-01

Range shifts (especially during the Pleistocene), polyploidisation and hybridization are major factors affecting high-mountain biodiversity. A good system to study their role in the European high mountains is the Doronicum clusii aggregate (Asteraceae), whose four taxa (D. clusii s.s., D. stiriacum, D. glaciale subsp. glaciale and D. glaciale subsp. calcareum) are differentiated geographically, ecologically (basiphilous versus silicicolous) and/or via their ploidy levels (diploid versus tetraploid). Here, we use DNA sequences (three plastid and one nuclear spacer) and AFLP fingerprinting data generated for 58 populations to infer phylogenetic relationships, origin of polyploids—whose ploidy level was confirmed by chromosomally calibrated DNA ploidy level estimates—and phylogeographic history. Taxonomic conclusions were informed, among others, by a Gaussian clustering method for species delimitation using dominant multilocus data. Based on molecular data we identified three lineages: (i) silicicolous diploid D. clusii s.s. in the Alps, (ii) silicicolous tetraploid D. stiriacum in the eastern Alps (outside the range of D. clusii s.s.) and the Carpathians and (iii) the basiphilous diploids D. glaciale subsp. glaciale (eastern Alps) and D. glaciale subsp. calcareum (northeastern Alps); each taxon was identified as distinct by the Gaussian clustering, but the separation of D. glaciale subsp. calcareum and D. glaciale subsp. glaciale was not stable, supporting their taxonomic treatment as subspecies. Carpathian and Alpine populations of D. stiriacum were genetically differentiated suggesting phases of vicariance, probably during the Pleistocene. The origin (autopolyploid versus allopolyploid) of D. stiriacum remained unclear. Doronicum glaciale subsp. calcareum was genetically and morphologically weakly separated from D. glaciale subsp. glaciale but exhibited significantly higher genetic diversity and rarity. This suggests that the more widespread D. glaciale subsp

Complex Ancestries of Lager-Brewing Hybrids Were Shaped by Standing Variation in the Wild Yeast Saccharomyces eubayanus.

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Peris, David; Langdon, Quinn K; Moriarty, Ryan V; Sylvester, Kayla; Bontrager, Martin; Charron, Guillaume; Leducq, Jean-Baptiste; Landry, Christian R; Libkind, Diego; Hittinger, Chris Todd

2016-07-01

Lager-style beers constitute the vast majority of the beer market, and yet, the genetic origin of the yeast strains that brew them has been shrouded in mystery and controversy. Unlike ale-style beers, which are generally brewed with Saccharomyces cerevisiae, lagers are brewed at colder temperatures with allopolyploid hybrids of Saccharomyces eubayanus x S. cerevisiae. Since the discovery of S. eubayanus in 2011, additional strains have been isolated from South America, North America, Australasia, and Asia, but only interspecies hybrids have been isolated in Europe. Here, using genome sequence data, we examine the relationships of these wild S. eubayanus strains to each other and to domesticated lager strains. Our results support the existence of a relatively low-diversity (π = 0.00197) lineage of S. eubayanus whose distribution stretches across the Holarctic ecozone and includes wild isolates from Tibet, new wild isolates from North America, and the S. eubayanus parents of lager yeasts. This Holarctic lineage is closely related to a population with higher diversity (π = 0.00275) that has been found primarily in South America but includes some widely distributed isolates. A second diverse South American population (π = 0.00354) and two early-diverging Asian subspecies are more distantly related. We further show that no single wild strain from the Holarctic lineage is the sole closest relative of lager yeasts. Instead, different parts of the genome portray different phylogenetic signals and ancestry, likely due to outcrossing and incomplete lineage sorting. Indeed, standing genetic variation within this wild Holarctic lineage of S. eubayanus is responsible for genetic variation still segregating among modern lager-brewing hybrids. We conclude that the relationships among wild strains of S. eubayanus and their domesticated hybrids reflect complex biogeographical and genetic processes.

Tools for Genetic Studies in Experimental Populations of Polyploids

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Peter M. Bourke

2018-04-01

Full Text Available Polyploid organisms carry more than two copies of each chromosome, a condition rarely tolerated in animals but which occurs relatively frequently in the plant kingdom. One of the principal challenges faced by polyploid organisms is to evolve stable meiotic mechanisms to faithfully transmit genetic information to the next generation upon which the study of inheritance is based. In this review we look at the tools available to the research community to better understand polyploid inheritance, many of which have only recently been developed. Most of these tools are intended for experimental populations (rather than natural populations, facilitating genomics-assisted crop improvement and plant breeding. This is hardly surprising given that a large proportion of domesticated plant species are polyploid. We focus on three main areas: (1 polyploid genotyping; (2 genetic and physical mapping; and (3 quantitative trait analysis and genomic selection. We also briefly review some miscellaneous topics such as the mode of inheritance and the availability of polyploid simulation software. The current polyploid analytic toolbox includes software for assigning marker genotypes (and in particular, estimating the dosage of marker alleles in the heterozygous condition, establishing chromosome-scale linkage phase among marker alleles, constructing (short-range haplotypes, generating linkage maps, performing genome-wide association studies (GWAS and quantitative trait locus (QTL analyses, and simulating polyploid populations. These tools can also help elucidate the mode of inheritance (disomic, polysomic or a mixture of both as in segmental allopolyploids or reveal whether double reduction and multivalent chromosomal pairing occur. An increasing number of polyploids (or associated diploids are being sequenced, leading to publicly available reference genome assemblies. Much work remains in order to keep pace with developments in genomic technologies. However, such

Tools for Genetic Studies in Experimental Populations of Polyploids.

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Bourke, Peter M; Voorrips, Roeland E; Visser, Richard G F; Maliepaard, Chris

2018-01-01

Polyploid organisms carry more than two copies of each chromosome, a condition rarely tolerated in animals but which occurs relatively frequently in the plant kingdom. One of the principal challenges faced by polyploid organisms is to evolve stable meiotic mechanisms to faithfully transmit genetic information to the next generation upon which the study of inheritance is based. In this review we look at the tools available to the research community to better understand polyploid inheritance, many of which have only recently been developed. Most of these tools are intended for experimental populations (rather than natural populations), facilitating genomics-assisted crop improvement and plant breeding. This is hardly surprising given that a large proportion of domesticated plant species are polyploid. We focus on three main areas: (1) polyploid genotyping; (2) genetic and physical mapping; and (3) quantitative trait analysis and genomic selection. We also briefly review some miscellaneous topics such as the mode of inheritance and the availability of polyploid simulation software. The current polyploid analytic toolbox includes software for assigning marker genotypes (and in particular, estimating the dosage of marker alleles in the heterozygous condition), establishing chromosome-scale linkage phase among marker alleles, constructing (short-range) haplotypes, generating linkage maps, performing genome-wide association studies (GWAS) and quantitative trait locus (QTL) analyses, and simulating polyploid populations. These tools can also help elucidate the mode of inheritance (disomic, polysomic or a mixture of both as in segmental allopolyploids) or reveal whether double reduction and multivalent chromosomal pairing occur. An increasing number of polyploids (or associated diploids) are being sequenced, leading to publicly available reference genome assemblies. Much work remains in order to keep pace with developments in genomic technologies. However, such technologies

Immediate Genetic and Epigenetic Changes in F1 Hybrids Parented by Species with Divergent Genomes in the Rice Genus (Oryza.

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Ying Wu

Full Text Available Inter-specific hybridization occurs frequently in higher plants, and represents a driving force of evolution and speciation. Inter-specific hybridization often induces genetic and epigenetic instabilities in the resultant homoploid hybrids or allopolyploids, a phenomenon known as genome shock. Although genetic and epigenetic consequences of hybridizations between rice subspecies (e.g., japonica and indica and closely related species sharing the same AA genome have been extensively investigated, those of inter-specific hybridizations between more remote species with different genomes in the rice genus, Oryza, remain largely unknown.We investigated the immediate chromosomal and molecular genetic/epigenetic instability of three triploid F1 hybrids produced by inter-specific crossing between species with divergent genomes of Oryza by genomic in situ hybridization (GISH and molecular marker analysis. Transcriptional and transpositional activity of several transposable elements (TEs and methylation stability of their flanking regions were also assessed. We made the following principle findings: (i all three triploid hybrids are stable in both chromosome number and gross structure; (ii stochastic changes in both DNA sequence and methylation occurred in individual plants of all three triploid hybrids, but in general methylation changes occurred at lower frequencies than genetic changes; (iii alteration in DNA methylation occurred to a greater extent in genomic loci flanking potentially active TEs than in randomly sampled loci; (iv transcriptional activation of several TEs commonly occurred in all three hybrids but transpositional events were detected in a genetic context-dependent manner.Artificially constructed inter-specific hybrids of remotely related species with divergent genomes in genus Oryza are chromosomally stable but show immediate and highly stochastic genetic and epigenetic instabilities at the molecular level. These novel hybrids might

Levels of Intra-specific AFLP Diversity in Tuber-Bearing Potato Species with Different Breeding Systems and Ploidy Levels

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Glenn J. Bryan

2017-09-01

Full Text Available DNA-based marker analysis of plant genebank material has become a useful tool in the evaluation of levels of genetic diversity and for the informed use and maintenance of germplasm. In this study, we quantify levels of amplified fragment length polymorphism (AFLP in representative accessions of wild and cultivated potato species of differing geographic origin, ploidy, and breeding system. We generated 449 polymorphic AFLP fragments in 619 plants, representing multiple plants (16–23 from 17 accessions of 14 potato taxa as well as single plants sampled from available accessions (from 3 to 56 of the same 14 taxa. Intra-accession diversities were compared to those of a synthetic ‘taxon-wide’ population comprising a single individual from a variable number of available accessions of each sampled taxon. Results confirm the expected considerably lower levels of polymorphism within accessions of self-compatible as compared to self-incompatible taxa. We observed broadly similar levels of ‘taxon-wide’ polymorphism among self-compatible and self-incompatible species, with self-compatible taxa showing only slightly lower rates of polymorphism. The most diverse accessions were the two cultivated potato accessions examined, the least diverse being the Mexican allohexaploids Solanum demissum and S. iopetalum. Generally allopolyploid self-compatible accessions exhibited lower levels of diversity. Some purported self-incompatible accessions showed relatively low levels of marker diversity, similar to the more diverse self-compatible material surveyed. Our data indicate that for self-compatible species a single plant is highly representative of a genebank accession. The situation for self-incompatible taxa is less clear, and sampling strategies used will depend on the type of investigation. These results have important implications for those seeking novel trait variation (e.g., disease resistance in gene banks as well as for the selection of individuals

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

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Bianca B Z Vigna

Full Text Available 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

Phylogeny and evolutionary history of Leymus (Triticeae; Poaceae based on a single-copy nuclear gene encoding plastid acetyl-CoA carboxylase

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Ding Cun-Bang

2009-10-01

Full Text Available Abstract Background Single- and low- copy genes are less likely subject to concerted evolution, thus making themselves ideal tools for studying the origin and evolution of polyploid taxa. Leymus is a polyploid genus with a diverse array of morphology, ecology and distribution in Triticeae. The genomic constitution of Leymus was assigned as NsXm, where Ns was presumed to be originated from Psathyrostachys, while Xm represented a genome of unknown origin. In addition, little is known about the evolutionary history of Leymus. Here, we investigate the phylogenetic relationship, genome donor, and evolutionary history of Leymus based on a single-copy nuclear Acc1 gene. Results Two homoeologues of the Acc1 gene were isolated from nearly all the sampled Leymus species using allele-specific primer and were analyzed with those from 35 diploid taxa representing 18 basic genomes in Triticeae. Sequence diversity patterns and genealogical analysis suggested that (1 Leymus is closely related to Psathyrostachys, Agropyron, and Eremopyrum; (2 Psathyrostachys juncea is an ancestral Ns-genome donor of Leymus species; (3 the Xm genome in Leymus may be originated from an ancestral lineage of Agropyron and Eremopyrum triticeum; (4 the Acc1 sequences of Leymus species from the Qinghai-Tibetan plateau are evolutionarily distinct; (5 North America Leymus species might originate from colonization via the Bering land bridge; (6 Leymus originated about 11-12MYA in Eurasia, and adaptive radiation might have occurred in Leymus during the period of 3.7-4.3 MYA and 1.7-2.1 MYA. Conclusion Leymus species have allopolyploid origin. It is hypothesized that the adaptive radiation of Leymus species might have been triggered by the recent upliftings of the Qinghai-Tibetan plateau and subsequent climatic oscillations. Adaptive radiation may have promoted the rapid speciation, as well as the fixation of unique morphological characters in Leymus. Our results shed new light on our

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

Cytological and morphological analysis of hybrids between Brassicoraphanus, and Brassica napus for introgression of clubroot resistant trait into Brassica napus L.

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Zhan, Zongxiang; Nwafor, Chinedu Charles; Hou, Zhaoke; Gong, Jianfang; Zhu, Bin; Jiang, Yingfen; Zhou, Yongming; Wu, Jiangsheng; Piao, Zhongyun; Tong, Yue; Liu, Chao; Zhang, Chunyu

2017-01-01

Interspecific hybridization is a powerful tool for improvement of crop species, it has the potential to broaden the genetic base and create new plant forms for breeding programs. Synthetic allopolyploid is a widely-used model for the study of genetic recombination and fixed heterosis in Brassica. In Brassica napus breeding, identification and introgression of new sources of clubroot resistance trait from wild or related species into it by hybridization is a long-term crop management strategy for clubroot disease. Radish (Raphanus sativus L.) is a close relative of the Brassica and most radish accessions are immune to the clubroot disease. A synthesized allotetraploid Brassicoraphanus (RRCC, 2n = 36) between R. sativus cv. HQ-04 (2n = 18, RR) and Brassica oleracea var. alboglabra (L.H Bailey) (2n = 18, CC) proved resistant of multiple clubroot disease pathogen P. brassicae. To predict the possibility to transfer the clubroot resistance trait from the RR subgenome of allotetraploid Brassicoraphanus (RRCC, 2n = 36) into Brassica napus (AACC, 2n = 38), we analyzed the frequency of chromosome pairings in the F1 hybrids produced from a cross between B. napus cv. HS5 and the allotetraploid, characterize the genomic composition of some backcrossed progeny (BC1) using GISH, BAC-FISH and AFLP techniques. The level of intergenomic pairing between A and R genomes in the F1 hybrid was high, allosyndetic bivalents formed in 73.53% PMCs indicative of significant level of homeologous recombination between two genomes and high probability of incorporating chromosomal segments/genes from R-genome into A/C-genomes. The BC1 plants inherited variant extra R chromosomes or fragments from allotetraploid as revealed by GISH and AFLP analysis. 13.51% BC2 individuals were resistant to clubroot disease, and several resistance lines had high pollen fertility, Overall, the genetic material presented in this work represents a potential new genetic resource for practical use in breeding B. napus

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

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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

The reticulate evolutionary history of the polyploid NW Iberian Leucanthemum pluriflorum clan (Compositae, Anthemideae) as inferred from nrDNA ETS sequence diversity and eco-climatological niche-modelling.

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Oberprieler, Christoph; Greiner, Roland; Konowalik, Kamil; Vogt, Robert

2014-01-01

The genus Leucanthemum Mill. is a species-rich polyploid complex of southern and central Europe, comprising 41 species with ploidy levels ranging from 2x to 22x. The Leucanthemum pluriflorum clan, a geographically isolated species group of the NW Iberian Peninsula, comprises the diploid L. pluriflorum, the tetraploids Leucanthemumircutianum subsp. pseudosylvaticum and Leucanthemum×corunnense (being a putative hybrid taxon based on a cross between L. pluriflorum and Leucanthemummerinoi), and the two hexaploids Leucanthemumsylvaticum and L. merinoi. In order to reconstruct the evolutionary history of this species group, we analysed sequence variation at the external transcribed spacer region of the nuclear ribosomal repeat (nrDNA ETS) for its members and for a number of other diploid species of Leucanthemum. Our results indicate that there are two major ETS ribotypes present in Leucanthemum, with some of the diploid species fixed for either of the two types and several species (among them L. pluriflorum) exhibiting both types. This polymorphism at the nrDNA ETS locus suggests either gene flow among some of the diploid species (possibly via polyploids) or a homoploid hybrid origin of some of those diploids. Additionally, patterns of ETS ribotype sharing among populations of the four species of the L. pluriflorum clan suggest that the tetraploid L. ircutianum subsp. pseudosylvaticum and the hexaploids L. sylvaticum and L. merinoi have an allopolyploid origin with L. pluriflorum as the maternal parent. Eco-climatological modelling of present and past (last glacial maximum, LGM) distribution areas of the members of the L. pluriflorum clan indicates that the diploid L. pluriflorum may have undergone geographical differentiation into northern (Galician) and southern (central Portuguese) coastal lineages that could account for the two chloroplast haplotype groups observable in the tetra- and hexaploids. Later climatic changes in the Holocene could then have led to the

Diversification of Scrophularia (Scrophulariaceae) in the Western Mediterranean and Macaronesia--phylogenetic relationships, reticulate evolution and biogeographic patterns.

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Scheunert, Agnes; Heubl, Günther

2014-01-01

The flora of the Mediterranean region and Macaronesia is characterized by high levels of species diversity and endemism. We examined phylogenetic relationships of Scrophularia within one of its secondary centers of diversity located in the Iberian Peninsula and adjacent Macaronesia. In total, 65 ingroup accessions from 45 species, representing an almost complete sampling of the region, were analyzed using sequences from the internal transcribed spacer region (ITS) and the plastid trnQ-rps16 intergenic spacer. Phylogenetic relationships were inferred using Bayesian inference, maximum likelihood and statistical parsimony networking. Incongruence between datasets was assessed with statistical tests and displayed by split networks. Biogeographic inferences incorporating information from both markers (despite low resolution in some parts of the trees) and all incongruent taxa were accomplished with a novel combination of methods, using trees generated with the taxon duplication approach as input for Bayesian binary MCMC (BBM) analysis as implemented in RASP. Nuclear and chloroplast markers support a clade which comprises the majority of Iberian and Macaronesian species and consists of three subclades. Analyses of the substantial incongruence observed among markers indicate reticulate evolution and suggest that Scrophularia species diversity in this region is largely attributable to hybridization; a combination of both polyploidy and dysploidy in the karyotypic evolution of Western Mediterranean Scrophularia taxa is proposed. Our results provide support for an ancient hybridization event between two widespread lineages, which resulted in an allopolyploid ancestor of the Iberian - Macaronesian group with 2n=58 chromosomes. The ancestor then diverged into the three main lineages present in the Iberian Peninsula, Northern Africa and Macaronesia today. Subsequent interspecific hybridizations at different ploidy levels additionally generated new species. Presumably

Molecular characterization of a rice mutator-phenotype derived from an incompatible cross-pollination reveals transgenerational mobilization of multiple transposable elements and extensive epigenetic instability

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Xu Chunming

2009-05-01

Full Text Available Abstract Background Inter-specific hybridization occurs frequently in plants, which may induce genetic and epigenetic instabilities in the resultant hybrids, allopolyploids and introgressants. It remains unclear however whether pollination by alien pollens of an incompatible species may impose a "biological stress" even in the absence of genome-merger or genetic introgression, whereby genetic and/or epigenetic instability of the maternal recipient genome might be provoked. Results We report here the identification of a rice mutator-phenotype from a set of rice plants derived from a crossing experiment involving two remote and apparently incompatible species, Oryza sativa L. and Oenothera biennis L. The mutator-phenotype (named Tong211-LP showed distinct alteration in several traits, with the most striking being substantially enlarged panicles. Expectably, gel-blotting by total genomic DNA of the pollen-donor showed no evidence for introgression. Characterization of Tong211-LP (S0 and its selfed progenies (S1 ruled out contamination (via seed or pollen or polyploidy as a cause for its dramatic phenotypic changes, but revealed transgenerational mobilization of several previously characterized transposable elements (TEs, including a MITE (mPing, and three LTR retrotransposons (Osr7, Osr23 and Tos17. AFLP and MSAP fingerprinting revealed extensive, transgenerational alterations in cytosine methylation and to a less extent also genetic variation in Tong211-LP and its immediate progenies. mPing mobility was found to correlate with cytosine methylation alteration detected by MSAP but not with genetic variation detected by AFLP. Assay by q-RT-PCR of the steady-state transcript abundance of a set of genes encoding for the various putative DNA methyltransferases, 5-methylcytosine DNA glycosylases, and small interference RNA (siRNA pathway-related proteins showed that, relative to the rice parental line, heritable perturbation in expression of 12 out of

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

Evolutionary Diversification of Alanine Transaminases in Yeast: Catabolic Specialization and Biosynthetic Redundancy

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Ximena Escalera-Fanjul

2017-06-01

Full Text Available Gene duplication is one of the major evolutionary mechanisms providing raw material for the generation of genes with new or modified functions. The yeast Saccharomyces cerevisiae originated after an allopolyploidization event, which involved mating between two different ancestral yeast species. ScALT1 and ScALT2 codify proteins with 65% identity, which were proposed to be paralogous alanine transaminases. Further analysis of their physiological role showed that while ScALT1 encodes an alanine transaminase which constitutes the main pathway for alanine biosynthesis and the sole pathway for alanine catabolism, ScAlt2 does not display alanine transaminase activity and is not involved in alanine metabolism. Moreover, phylogenetic studies have suggested that ScALT1 and ScALT2 come from each one of the two parental strains which gave rise to the ancestral hybrid. The present work has been aimed to the understanding of the properties of the ancestral type Lacchancea kluyveri LkALT1 and Kluyveromyces lactis KlALT1, alanine transaminases in order to better understand the ScALT1 and ScALT2 evolutionary history. These ancestral -type species were chosen since they harbor ALT1 genes, which are related to ScALT2. Presented results show that, although LkALT1 and KlALT1 constitute ScALT1 orthologous genes, encoding alanine transaminases, both yeasts display LkAlt1 and KlAlt1 independent alanine transaminase activity and additional unidentified alanine biosynthetic and catabolic pathway(s. Furthermore, phenotypic analysis of null mutants uncovered the fact that KlAlt1 and LkAlt1 have an additional role, not related to alanine metabolism but is necessary to achieve wild type growth rate. Our study shows that the ancestral alanine transaminase function has been retained by the ScALT1 encoded enzyme, which has specialized its catabolic character, while losing the alanine independent role observed in the ancestral type enzymes. The fact that ScAlt2 conserves 64

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.

Effect of Time and Burial Depth on Breaking Seed dormancy and Germination of Weed Seeds

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marzie mazhari

2016-02-01

order to evaluate the effects of time and burial depth on breaking seed dormancy and percentage of germination of 27 dominants weed in Shahrekord region, an experiment was conducted at the research field at Shahrekord University in 2013. The experimental design set as factorial based on completely randomized design with three replications. Treatments consisted of three burial time levels (1, 2 and 3 months and 4 burial depth (0, 5, 15 and 25 cm from surface soil layer after 1, 2 and 3 months of burial. Results and Discussion: Results showed that the time and the depth of burial treatments had significant effect on breaking seed dormancy and germination percentage. Seeds retrieved from the soil surface showed highest dormancy percentage and breaking dormancy with increasing the depth and time of seed burial. The results showed that the effects of three burial times, burial depth and interaction of burial time and burial depth had significant effects on dormancy breaking and germination of weed seeds. The bitter herbs of expression and parsnip, the highest percentage of seed dormancy breaking. Germination of Geobelia alopecuoides and Anthriscus sylvestris was observed from seed burial depth of 15 cm. However, the germination percentage, between two and three seed burial months, did not show any significant difference. In this study, Convolvulus arvensies, Rumex acetisella and, Avena fatua in the highest depth (25 cm had the maximum seed germination. Tillage would bury weed seeds and may help to preserve some seeds, because the seeds on the soil surface or near it, are prone to hunting or decay that eventually, their number is reduced in the soil seed bank. Weed seeds of Centurea cyanus, Geobelia alopecuoides, Turgeniala tifolia, Tragopogon collinus, Bromus dantoniae and Anthriscus sylvestris had more germination percentage with increasing depth to 15 cm, but beyond this depth due to the negative impacts of increased depth, seed germination declined sharply. In fact, the

Mutation induction for domestication of Cuphea: Effects of gamma rays

International Nuclear Information System (INIS)

Campbell, T.A.

1989-01-01

(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)