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

Chapter 6model for molecular cytogenetic research when studying the interaction of homoeologousgenomes in interspecific hybrids and allopolyploids. However, it should also be noticed thatsince the large genome, large probes (>2Kb) need to be used to get clear signals whenanalyzing lily with FISH.Chromosome rearrangements and its relevance to geneticmappingIn genetic mapping, normally two crossing parents are involved to produce a segregatingpopulation. These crossing materials, although related, should produce enough detectablesequence polymorphism throughout the genome. These populations, however, might givecomplicated maps because of parental chromosome structural differences (Chapter 3), whichis discussed in the following paragraph.Changes in chromosome composition have been considered as a cause of ambiguities ingenetic mapping with molecular markers. Such changes consists of translocations, deletions,duplications and inversions. Each of these events involves breakage of DNA double helices inthe genome at two different locations, followed by a reunion of the broken ends to produce anew chromosomal arrangement of genes, and causes gene order variation compared to theoriginal order. These alterations of gene order will have certain consequences in geneticmapping when parents with chromosome rearrangements are involved in crossing to generatesegregating populations. In general, structure variations cause reduced fertility in gametes,which lead to skewed populations (Fig. 6.1; Fig. 6.2). Different types of chromosomerearrangements give rise to various mapping problems. First, inversions, both pericentric andparacentric, lead to suppressed recombination between the inverted and non-inverted genomicregions (Loren H 2001; Noor et al. 2001; Rieseberg 2001a; Schaeffer and Anderson 2005).Molecular mapping studies have highlighted that loci within inversions can be in stronglinkage disequilibrium with each other for two reasons: a) chromosome pairing of the invertedregion is commonly hampered and an inversion loop is formed when the size of the invertedsegment is not big enough. b) even if inverted segments paired together and a single crossoverhappened in the inverted region, pericentric inversions would produce sterile gametes withduplication and deletion while paracentric inversions give rise to anaphase bridging, whichwould also result into unviable gametes (Fig. 6.1). Second, reciprocal translocations givepseudolinkage when progenies result from material with a reciprocal translocation is used forgenetic mapping. During meiosis of a plant with a reciprocal translocation, quadrivalents arenormally formed at metaphase I. Chiasma formation and crossing over will be suppressed inthe interstitial area (between centromere and translocation breakpoints) because suchexchanges between non-sister chromatids will lead to gametes with duplication and deletion(Fig. 6.2, see unviable gametes from alternate segregation).74