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Painting the Chromosomes of Brachypodium—Current Status and Future Prospects Chromosoma (2011) 120:469–479 DOI 10.1007/s00412-011-0326-9 RESEARCH ARTICLE Painting the chromosomes of Brachypodium—current status and future prospects Dominika Idziak & Alexander Betekhtin & Elzbieta Wolny & Karolina Lesniewska & Jonathan Wright & Melanie Febrer & Michael W. Bevan & Glyn Jenkins & Robert Hasterok Received: 7 March 2011 /Revised: 23 May 2011 /Accepted: 25 May 2011 /Published online: 11 June 2011 # The Author(s) 2011. This article is published with open access at Springerlink.com Abstract Chromosome painting is one of the most power- containing relatively little repetitive genomic DNA enabled ful and spectacular tools of modern molecular cytogenetics, the first chromosome painting in dicotyledonous plants. enabling complex analyses of nuclear genome structure and Here, we show for the first time chromosome painting in evolution. For many years, this technique was restricted to three different cytotypes of a monocotyledonous plant—the the study of mammalian chromosomes, as it failed to work model grass, Brachypodium distachyon. Possible directions in plant genomes due mainly to the presence of large of further detailed studies are proposed, such as the amounts of repetitive DNA common to all the chromo- evolution of grass karyotypes, the behaviour of meiotic somes of the complement. The availability of ordered, chromosomes, and the analysis of chromosome distribution chromosome-specific BAC clones of Arabidopsis thaliana at interphase. Communicated by: I. Schubert Introduction Dominika Idziak and Alexander Betekhtin contributed equally to this work. : : : : Chromosome painting (CP), also known as chromosomal D. Idziak (*) A. Betekhtin E. Wolny K. Lesniewska in situ suppression, is one of the most powerful and R. Hasterok spectacular tools of molecular cytogenetics. It refers to the Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia, method of visualisation of specific chromosome regions or Jagiellonska 28, entire chromosomes using fluorescence in situ hybrid- 40-032 Katowice, Poland isation (FISH) with chromosome-specific DNA probes e-mail: [email protected] (Pinkel et al. 1988; Ried et al. 1998). For many years, this J. Wright : M. Febrer : M. W. Bevan technique was successfully applied only to studies of Department of Cell and Developmental Biology, animal chromosomes, giving unprecedented insight into John Innes Centre, the structural and functional compartmentalisation of the Colney Lane, nucleus (Cremer et al. 2008; Cremer et al. 1993; Kurz et Norwich NR4 7UH, UK al. 1996). It has also been widely used for molecular G. Jenkins cytotaxonomy, for example of primates (Muller et al. 1999; Institute of Biological, Environmental and Rural Sciences, Wienberg et al. 1990), mutagenicity testing (Marshall and Aberystwyth University, Obe 1998) and radiation biology (Gray et al. 1992). High Edward Llwyd Building, Penglais, Aberystwyth, Wales SY23 3DA( Ceredigion, UK resolution CP-based analyses have become especially important to pre-, neo- and postnatal clinical diagnostics Present Address:: of various chromosomal aberrations associated with J. Wright M. Febrer human diseases and malignancies (Gray and Pinkel 1992; The Genome Analysis Centre, Norwich Research Park, Popp et al. 1991; Tkachuk et al. 1991; Weise et al. 2003; Norwich NR4 7UH, UK Xu et al. 2010). 470 Chromosoma (2011) 120:469–479 For more than a decade, efforts to apply CP in plants Materials and methods failed to yield satisfactory results, which was attributed to the presence of vast amounts of ubiquitous repetitive DNA Plant material and chromosome preparations in most plant genomes (Schubert et al. 2001). The first true painting of plant chromosomes was achieved by Lysak et Three cytotypes of B. distachyon were used in this study. al. (2001) in the dicotyledonous model organism, Arabi- Detailed information on the plant material is provided in dopsis thaliana, whose nuclear genome had just been Table 1. Seeds were sown at high density in compost. All sequenced (Arabidopsis Genome Initiative 2000). The plants were grown as described in Jenkins and Hasterok availability of genome sequence and ordered libraries of (2007). The plants of cytotypes ABR114 and ABR113 did genomic DNA in BAC (Bacterial Artificial Chromosome) not require vernalisation and usually reached the generative vectors, along with some features of A. thaliana genome, stage of their life cycle within 1 month after sowing. such as its compactness, low amount of repetitive DNA and Mitotic chromosome preparations were made using the low number of chromosomes, were key prerequisites for methodology described by Hasterok et al. (2006). Preparation successful painting of its chromosomes. Initially restricted of anther tissue for meiotic chromosome squashes was to the chromosomes of A. thaliana (Pecinka et al. 2004), adopted from Jenkins and Hasterok (2007)withminor CP in later studies was also successfully applied to other modifications. In brief, immature inflorescences were collect- closely related members of the Brassicaceae. This comparative ed, fixed immediately in fresh 3:1 absolute methanol:glacial chromosome painting (CCP) allowed unprecedented analyses acetic acid mixture for 3×24 h at room temperature (RT) and of the evolution of the genomes of this group of plants at the stored at −20°C until required. Individual anthers were chromosomal level (Lysak et al. 2006; Lysak et al. 2010; isolated and washed in 10 mM citric acid–sodium citrate Mandakova and Lysak 2008). buffer and digested enzymatically for 2 h at 37°C in a mixture In contrast to the dicots, chromosome painting has not comprising 10% (v/v) pectinase (Sigma), 0.65% (w/v) been applied so far to any monocotyledonous plant. Despite cellulase Onozuka R-10 (Serva), 0.5% (w/v) cellulase the availability of its long-published genomic sequence (Calbiochem), 0.15% (w/v) cytohelicase and 0.15 % (w/v) (Goff et al. 2002), no chromosome painting has been pectolyase in 10 mM citrate buffer. Several anthers per slide performed in rice. Another species of Poaceae, Brachypo- were squashed in drops of 45% acetic acid, frozen, postfixed dium distachyon, emerged several years ago as a model in 4% formaldehyde for 10 min, washed briefly in distilled system for temperate cereals and grasses. Like A. thaliana, water and air dried. B. distachyon possesses numerous ‘model’ attributes, including inter alia a small (∼300 Mb) genome with a low Selection of BAC clones for chromosome painting (x=5) basic chromosome number, small physical stature, self-fertility, a short life cycle and undemanding growth BAC clones used for CP were selected from the five requirements (Draper et al. 2001; Garvin et al. 2008). The assemblies of FPCs (FingerPrinted Contigs) previously genome of B. distachyon has been extensively studied at aligned to the B. distachyon karyotype (Febrer et al. 2010; the chromosomal level using fluorescence in situ hybrid- International Brachypodium Initiative 2010). Clones from isation (FISH) with a wide range of DNA probes, which enabled unambiguous identification of all the chromosomes and their arms of the complement (Hasterok et al. 2004; Table 1 The original identities, sources, origins and chromosome Hasterok et al. 2006). numbers of the B. distachyon material used in this study The well-established cytogenetic platform, combined Species Accession no. Origin Source 2n with resources such as BAC DNA libraries and bioinfor- matic data from the recently completed genome sequencing B. distachyon Bd21 Iraq a 10 project (Febrer et al. 2010; Gu et al. 2009; International ‘B. distachyon’* ABR114 Spain b 20 Brachypodium Initiative 2010), opened up the possibility of ‘B. distachyon’* ABR113 Portugal b 30 painting for the first time the chromosomes of a monocot a US Department of Agriculture–National Plant Germplasm System, species. In this paper, we present the current status of CP in USA, b Institute of Biological, Environmental and Rural Sciences, B. distachyon, which allows reliable recognition and tracking Aberystwyth University, UK of individual chromosome regions during different stages of * According to our previous cytomolecular studies (Hasterok et al. meiosis. Additionally, we show that CCP with BAC 2004;Hasteroketal.2006) ABR114 and ABR113 represent, pools representing individual B. distachyon chromosomes respectively, a different unnamed diploid and an allotetraploid species can be used as an effective tool for studying karyotype within the Brachypodium genus. As their proposed taxonomical status is not yet officially accepted, we refer in this paper to ABR114 and evolution of its close relatives in the genus Brachypodium. ABR113 as the cytotypes of ‘B. distachyon’. The cytotype with 2n= Possible future prospects are also discussed. 10 chromosomes is referred to as B. distachyon without apostrophes Chromosoma (2011) 120:469–479 471 centromeric and pericentromeric regions were excluded experiment shown on Figs. 1f and 3. The list of BACs from the painting experiments as they were likely to contain comprising the pools for individual chromosomes may be large amounts of highly repetitive and dispersed DNA requested from the authors. sequences which might cause unspecific hybridisation The FISH procedure was carried out according to the signals. For the same reason, the BACs constituting the protocol of Jenkins and Hasterok (2007) with minor assemblies were examined for repetitive DNA content. Low modifications. The BAC DNAs were pooled, precipitated repeat BAC clones
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