A molecular cytogenetic analysis of chromosome behavior in Lilium ...

Chapter 1renewed interest in detecting chromosome rearrangements in recent years (Lim et al. 2008b;Pires and Hertweck 2008; Xie et al. 2010; Xiong et al. 2011). GISH, combined with FISH,allows the discrimination of alien chromosomes/segments and the identification of individualchromosomes in interspecific hybrids and backcrossing progenies (Barba-Gonzalez et al.2005b; Khan et al. 2009a; Lim et al. 2001b; Schwarzacher et al. 1992; Schwarzacher et al.1989; Stevenson et al. 1998; Zhou et al. 2008b). Since its successful application in detectingand analyzing intergenomic recombination between homoeologous genomes, the techniquehas been already used for detecting crossover events through analysis of anaphase I cells(Stevenson et al. 1998; Takahashi et al. 1997; Xie et al. 2010; Zhou et al. 2008a). Theparticular advantage of this system is that the two chromatids of each homoeologues have thesame labeling status, and therefore all crossover exchanges between non-sister chromatidswill be visible. As a result, it enables the accurate observation of homoeologous chromosomebehaviours during meiosis. As pointed in a previous publication (Xie et al. 2010), thenonreciprocal and reciprocal recombination both originated from a natural meiosis processchiasmataformation and crossing over between homoeologous chromatids, that is also thereason that the term “translocation” is not accurate in Brassica napus (Nicolas et al. 2007;Parkin et al. 1995; Sharpe et al. 1995; Udall et al. 2005); As a result, some genera, whichconsist of divergent genomes and large chromosomes, viz. Tulipa, Lilium, Alstroemeria andso on, are ideal for the GISH analysis. However, several disadvantages are also unavoidablefor detecting chromosome rearrangements using DNA in situ hybridization. the first one is itspoor resolution which made small recombinations invisible. Meanwhile, some kinds ofrearrangements like duplication and deletion are, however, very difficult to distinguish;another shortage is that GISH is very experimental demanding and labor-intensive. Besidethese, GISH can only detect chromosome variations between homoeologous andnonhomologous chromosomes. With their pros and cons of molecular markers and molecularcytogenetic techniques, there is a tendency that the combining of these two methods will leadto relatively accurate results, which has been used in several reports.With the development of modern molecular biology, some innovational methods, such aswhole genome sequencing and array comparative genomic hybridization (aCGH) which givedetailed and informative sequence information, have become available recently. Array-basedcomparative genomic hybridization allows high-resolution screening of copy numberabnormalities in the genome, and becomes an increasingly important tool to detect deletionsand duplications in the whole genome (Knijnenburg et al. 2005).6