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Abstract

The zebrafish, Danio rerio, has recently become the model system for the genetic analysis of vertebrate development. This paper reviews the advances in zebrafish cytogenetics, obtained through classical and molecular techniques, which will lead to the assignment of specific linkage groups to specific chromosome pairs in the zebrafish genome project. Several chromosome pairs of the 50-chromosome karyotype of D. rerio were differentially stained by classical staining techniques and additional information has been obtained by molecular cytogenetics. Indeed, the analysis of constitutive heterochromatin by C-banding and base-specific fluorochrome staining had suggested a differential composition of peri- and paracentromeric constitutive heterochromatin. The chromosome mapping of distinct AT- and GC-rich zebrafish satellite DNAs by means of PRINS (Primed in situ) and multicolor FISH (Fluorescence in situ Hybridization) has confirmed this hypothesis, which therefore provided the chromosome localization of 10% of the zebrafish genome. The analysis of nucleolus organizer regions (NORs) by silver staining and by FISH with 18S rDNA has also revealed the existence of variable and inactive NORs, in addition to those on the terminal regions of the long arms of the three NOR-bearing chromosome pairs. Other multicopy genes, such as minor ribosomal genes, or multicopy repeats, such as telomere specific sequences, have now been mapped on zebrafish chromosomes. The latest advancement in zebrafish molecular cytogenetics is the chromosome mapping of single locus genes. Single-copy genes from each of the 25 genetic linkage groups are now being mapped on zebrafish chromosomes by using PAC clones.

Gonad Morphogenesis in Vertebrates: Divergent Means to a Convergent End

“…In contrast to mammals and chickens, which have clearly heteromorphic sex chromosomes (XX/XY and ZZ/ZW), zebrafish do not have clearly identifiable sex chromosomes (Sola & Gornung 2001, Traut & Winking 2001). However, experiments indicate a genetic component to sex determination that is probably polygenic and complex.…”

Multiple Sex-Associated Regions and a Putative Sex Chromosome in Zebrafish Revealed by RAD Mapping and Population Genomics

“…First, chr-4q is the only arm in the zebrafish genome that is heterochromatic. Chr-4 (as designated at Ensembl and originally defined as Linkage Group-4 [60], [61]) is the third largest cytogenetic chromosome in zebrafish [18] and is used as a standard for cytogenetic comparisons because of its unique heterochromatic long (right) arm (chr-4q) [14]–[16], [64]. The heterochromatic region on chr-4 in genome assembly Zv9 begins at about 28 Mb and contains sar4 at about 61–62 Mb.…”

“…Subsequently, LGs were assigned to physical chromosomes [18] that cytogeneticists had previously numbered based on physical length [15], [16], [62]–[64]. In this paper, we use the designation ‘chr’ to mean ‘Linkage Group’ rather than cytogenetically identified physical chromosomes, in agreement with zebrafish nomenclature conventions.…”

Epistatic and allelic interactions control expression of ribosomal RNA gene clusters in Arabidopsis thaliana

“…The word “dominance” is used because one rDNA cluster apparently suppresses the activity of the other [18]. At the intraspecies level, many model organisms, such as humans, mice, zebrafish, wheat, and Arabidopsis thaliana have multiple rDNA clusters on different autosomes [19–23] and early cytogenetic studies have shown differential expression of such clusters in human cell types [24] and plants [25]. While attempts have been made to clone and sequence differentially expressed rRNA gene variants, it was not possible to assign them to a specific rDNA locus or cluster [26–28].…”