Painting the chromosomes of Brachypodium—current status and future prospects

Idziak, D.; Betekhtin, Alexander; Wolny, Elżbieta; Lesniewska, Karolina; Wright, Jonathan; Febrer, Melanie; Bevan, Michael W.; Jenkins, Glyn; Hasterok, Robert

doi:10.1007/s00412-011-0326-9

Cited by 53 publications

(68 citation statements)

References 47 publications

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“…The allopolyploid origin of B. hybridum is currently out of debate mainly based upon the strong cytogenetic evidences reported by Hasterok and co-workers (Hasterok et al 2004(Hasterok et al , 2006Idziak et al 2011). It has also been confirmed by the analysis of plastid and nuclear gene sequences (Catalán et al 2012) and prolamin storage protein profiles (Hammami et al 2011) on collections of B. distachyon (s.l.)…”

Section: Resultsmentioning

confidence: 93%

“…The existence of distinct cytotypes, with 2n values of 10, 20, and 30 chromosomes (Robertson 1981), was assumed to be a case of an autopolyploid series with x = 5. Nonetheless, solid experimental evidences support that B. hybridum derives from B. distachyon and B. stacei (Hasterok et al 2004(Hasterok et al , 2006Idziak et al 2011;Catalán et al 2012). Under the framework established by Catalán and co-workers, all newly collected or yet uncharacterized B. distachyon-type accession must be unambiguously assigned to the right species to be valuable for further research.…”

Section: Introductionmentioning

confidence: 99%

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Validation of microsatellite markers for cytotype discrimination in the model grass Brachypodium distachyon

Giraldo

Rodríguez-Quijano

Vázquez

et al. 2012

Genome

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Brachypodium distachyon (L.) P. Beauv. (2n = 2x = 10) is a small annual grass species where the existence of three different cytotypes (10, 20, and 30 chromosomes) has long been regarded as a case of autopolyploid series with x = 5. However, it has been demonstrated that the cytotypes assumed to be polyploids represent two separate Brachypodium species recently named as Brachypodium stacei (2n = 2x = 20) and Brachypodium hybridum (2n = 4x = 30). The aim of this study was to find a PCR-based alternative approach that could replace standard cytotyping methods (i.e., chromosome counting and flow cytometry) to characterize each of the three Brachypodium species. We have analyzed with four microsatellite (SSR) markers 83 B. distachyon-type lines from varied locations in Spain, including the Balearic and Canary Islands. Within this set of lines, 64, 4, and 15 had 10, 20, and 30 chromosomes, respectively. The surveyed markers produced cytotype-specific SSR profiles. So, a single amplification product was generated in the diploid samples, with nonoverlapping allelic ranges between the 2n = 10 and 2n = 20 cytotypes, whereas two bands, one in the size range of each of the diploid cytotypes, were amplified in the 2n = 30 lines. Furthermore, the remarkable size difference obtained with the SSR ALB165 allowed the identification of the Brachypodium species by simple agarose gel electrophoresis.Key words: Brachypodium distachyon, B. stacei, B. hybridum, cytotype-specific markers, SSR analysis.Résumé : Le Brachypodium distachyon (L.) P. Beauv. (2n = 2x = 10) est une petite graminée annuelle chez laquelle l'existence de trois cytotypes différents (à 10, 20 ou 30 chromosomes) a longtemps été considérée comme une série autopolyploïde avec x = 5. Cependant, il a été démontré que les cytotypes qui étaient présumés polyploïdes représentent en fait deux espèces distinctes du genre Brachypodium récemment nommées Brachypodium stacei (2n = 2x = 20) et Brachypodium hybridum (2n = 4x = 30). Le but de ce travail était de trouver une approche PCR permettant de remplacer les méthodes cytologiques (décomptes chromosomiques, cytométrie en flux) pour caractériser les trois espèces de Brachypodium. Les auteurs ont analysé 83 lignées de type B. distachyon provenant de différents sites en Espagne, incluant les Îles Baléares et Canaries, au moyen de quatre marqueurs microsatellites (SSR). Au sein de cette collection, 64, 4 et 15 lignées présentaient respectivement 10, 20 et 30 chromosomes. Les marqueurs examinés ont produit des profils spécifiques des cytotypes. Ainsi, un seul amplicon a été obtenu chez les échantillons diploïdes et les séries alléliques ne chevauchaient pas entre les cytotypes à 2n = 10 et 2n = 20, tandis que deux amplicons ont été obtenus chez les lignées à 2n = 30, chacun de ces amplicons logeant à l'intérieur des séries alléliques observées chez les cytotypes diploïdes. De plus, la différence de taille remarquable observée entre les amplicons du SSR ALB165 permettait l'identification des espèces de Brachypodium sur un ...

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Section: Resultsmentioning

confidence: 93%

Section: Introductionmentioning

confidence: 99%

Validation of microsatellite markers for cytotype discrimination in the model grass Brachypodium distachyon

Giraldo

Rodríguez-Quijano

Vázquez

et al. 2012

Genome

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“…More importantly, it relies on the fact that the A. thaliana genome is not only very small (125 Mb) (The Arabidopsis Genome Initiative 2000), but also largely euchromatic and that most of the selected BACs contain almost exclusively single-or low-copy sequences. This approach was also applied in another model plant, Brachypodium distachyon, and its related species (Idziak et al 2011;Betekhtin et al 2014). Similarly, B. distachyon has a relatively small genome (300 Mb) and ordered BAC contigs covering the entire genome are available.…”

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confidence: 99%

Chromosome-Specific Painting in Cucumis Species Using Bulked Oligonucleotides

et al. 2015

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Chromosome-specific painting is a powerful technique in molecular cytogenetic and genome research. We developed an oligonucleotide (oligo)-based chromosome painting technique in cucumber (Cucumis sativus) that will be applicable in any plant species with a sequenced genome. Oligos specific to a single chromosome of cucumber were identified using a newly developed bioinformatic pipeline and then massively synthesized de novo in parallel. The synthesized oligos were amplified and labeled with biotin or digoxigenin for use in fluorescence in situ hybridization (FISH). We developed three different probes with each containing 23,000-27,000 oligos. These probes spanned 8.3-17 Mb of DNA on targeted cucumber chromosomes and had the densities of 1.5-3.2 oligos per kilobases. These probes produced FISH signals on a single cucumber chromosome and were used to paint homeologous chromosomes in other Cucumis species diverged from cucumber for up to 12 million years. The bulked oligo probes allowed us to track a single chromosome in early stages during meiosis. We were able to precisely map the pairing between cucumber chromosome 7 and chromosome 1 of Cucumis hystrix in a F 1 hybrid. These two homeologous chromosomes paired in 71% of prophase I cells but only 25% of metaphase I cells, which may provide an explanation of the higher recombination rates compared to the chiasma frequencies between homeologous chromosomes reported in plant hybrids.

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“…In this way a library of different sequences multiplied in numerous probes is formed, tagged with compounds of different colour fluorescence (Sharma 2000). Idziak et al (2011) used the cloned sequences as molecular probes to identify the types of chromosomes in the karyotype of Brachypodium distachyon. In this way the chromosome of a given type was specifically painted with fluorescent staining after carrying out the in situ hybridization, due to the different molecular probes (the chromosome painting method).…”

Section: Some Advanced Molecular Methodsmentioning

confidence: 99%

Plant biosystematics with the help of cytology and cytogenetics

Ilnicki

2014

Caryologia

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The importance of cytological and cytogenetic information in the investigation of evolutionary history of species, i.e. biosystematics (cytotaxonomy) and cytogeography, is surveyed. The main issues considered are the numbers and morphology of the chromosomes, the distribution and amount of the different types of chromatin in chromosomes, nuclei at interphase stained with classical and molecular cytogenetic methods, e.g. fluorescence in situ hybridization (FISH), genomic in situ hybridization (GISH) and bacterial artificial chromosome (BAC), painting chromosomes, the isolation of large DNA segments using e.g. pulse-field gel electrophoresis, and chromosome disposition in the cell nucleus. A wide ranging biosystematic interest puts emphasis with the help of cytological and cytogenetic methods on getting to know chromosome variation within the family, genus and species connected with the phenomena of hybridization and polyploidization. Chromosome variation among taxa includes differences in the morphology and numbers of chromosomes, the amount of DNA, the sizes of chromosomes, inner chromosome structure, and DNA sequence, often shown in chromosome bands or various proportions of AT and GC pairs. On this basis we can track the course of evolution among taxa and determine reciprocal relationships. One of the main aims of our work, apart from getting to know evolutionary processes, is to create a taxonomic system of organisms.

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Painting the chromosomes of Brachypodium—current status and future prospects

Cited by 53 publications

References 47 publications

Validation of microsatellite markers for cytotype discrimination in the model grass Brachypodium distachyon

Validation of microsatellite markers for cytotype discrimination in the model grass Brachypodium distachyon

Chromosome-Specific Painting in Cucumis Species Using Bulked Oligonucleotides

Plant biosystematics with the help of cytology and cytogenetics

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