Julio S. Masabanda

Molecular Cytogenetic Definition of the Chicken Genome: The First Complete Avian Karyotype

Chicken genome mapping is important for a range of scientific disciplines. The ability to distinguish chromosomes of the chicken and other birds is thus a priority. Here we describe the molecular cytogenetic characterization of each chicken chromosome using chromosome painting and mapping of individual clones by FISH. Where possible, we have assigned the chromosomes to known linkage groups. We propose, on the basis of size, that the NOR chromosome is approximately the size of chromosome 22; however, we suggest that its original assignment of 16 should be retained. We also suggest a definitive chromosome classification system and propose that the probes developed here will find wide utility in the fields of developmental biology, DT40 studies, agriculture, vertebrate genome organization, and comparative mapping of avian species.

Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution

BackgroundComparative genomics is a powerful means of establishing inter-specific relationships between gene function/location and allows insight into genomic rearrangements, conservation and evolutionary phylogeny. The availability of the complete sequence of the chicken genome has initiated the development of detailed genomic information in other birds including turkey, an agriculturally important species where mapping has hitherto focused on linkage with limited physical information. No molecular study has yet examined conservation of avian microchromosomes, nor differences in copy number variants (CNVs) between birds.ResultsWe present a detailed comparative cytogenetic map between chicken and turkey based on reciprocal chromosome painting and mapping of 338 chicken BACs to turkey metaphases. Two inter-chromosomal changes (both involving centromeres) and three pericentric inversions have been identified between chicken and turkey; and array CGH identified 16 inter-specific CNVs.ConclusionThis is the first study to combine the modalities of zoo-FISH and array CGH between different avian species. The first insight into the conservation of microchromosomes, the first comparative cytogenetic map of any bird and the first appraisal of CNVs between birds is provided. Results suggest that avian genomes have remained relatively stable during evolution compared to mammalian equivalents.

Comparative chromosome painting of chicken autosomal paints 1–9 in nine different bird species

In a Zoo-FISH study chicken autosomal chromosome paints 1 to 9 (GGA1–GGA9) were hybridized to metaphase spreads of nine diverse birds belonging to primitive and modern orders. This comparative approach allows tracing of chromosomal rearrangements that occurred during bird evolution. Striking homologies in the chromosomes of the different species were noted, indicating a high degree of evolutionary conservation in avian karyotypes. In two species, the quail and the goose, all chicken paints specifically labeled their corresponding chromosomes. In three pheasant species as well as in the American rhea and blackbird, GGA4 hybridized to chromosome 4 and additionally to a single pair of microchromosomes. Furthermore, in the pheasants fission of the ancestral galliform chromosome 2 could be documented. Hybridization of various chicken probes to two different chromosomes or to only the short or long chromosome arm of one chromosome pair in the species representing the orders Passeriformes, Strigiformes, and Columbiformes revealed translocations and chromosome fissions during species radiation. Thus comparative analysis with chicken chromosome-specific painting probes proves to be a rapid and comprehensive approach to elucidate the chromosomal relationships of the extant birds.

Karyotypic evolution in the Galliformes: an examination of the process of karyotypic evolution by comparison of the molecular cytogenetic findings with the molecular phylogeny

To define the process of karyotypic evolution in the Galliformes on a molecular basis, we conducted genome-wide comparative chromosome painting for eight species, i.e. silver pheasant (Lophura nycthemera), Lady Amherst’s pheasant (Chrysolophus amherstiae), ring-necked pheasant (Phasianus colchicus), turkey (Meleagris gallopavo), Western capercaillie (Tetrao urogallus), Chinese bamboo-partridge (Bambusicola thoracica) and common peafowl (Pavo cristatus) of the Phasianidae, and plain chachalaca (Ortalis vetula) of the Cracidae, with chicken DNA probes of chromosomes 1–9 and Z. Including our previous data from five other species, chicken (Gallus gallus), Japanese quail (Coturnix japonica) and blue-breasted quail (Coturnix chinensis) of the Phasianidae, guinea fowl (Numida meleagris) of the Numididae and California quail (Callipepla californica) of the Odontophoridae, we represented the evolutionary changes of karyotypes in the 13 species of the Galliformes. In addition, we compared the cytogenetic data with the molecular phylogeny of the 13 species constructed with the nucleotide sequences of the mitochondrial cytochrome b gene, and discussed the process of karyotypic evolution in the Galliformes. Comparative chromosome painting confirmed the previous data on chromosome rearrangements obtained by G-banding analysis, and identified several novel chromosome rearrangements. The process of the evolutionary changes of macrochromosomes in the 13 species was in good accordance with the molecular phylogeny, and the ancestral karyotype of the Galliformes is represented.

Identification of putative sex chromosomes in the blue tilapia, Oreochromis aureus, through synaptonemal complex and FISH analysis

Sex determination in the blue tilapia, Oreochromis aureus, is primarily a ZW female-ZZ male system. Here, by analysis of the pachytene meiotic chromosomes of O. aureus, we demonstrate the presence of two distinct regions of restricted pairing present only in heterogametic fish. The first, a subterminal region of the largest bivalent is located near to the region of unpairing found in the closely related species O. niloticus, while the second is in a small bivalent, most of which was unpaired. These results suggest that O. aureus has two separate pairs of sex chromosomes.

Molecular-cytogenetic analysis reveals sequence differences between the sex chromosomes of Oreochromis niloticus: evidence for an early stage of sex-chromosome differentiation

Sex determination in the Nile tilapia, Oreochromis niloticus, is primarily genetic, with XX females and XY males. A candidate sex-determining region in the terminal region of the largest chromosome pair has been identified by analysis of meiotic chromosomes. This region shows an inhibition of pairing and synapsis in the XY genotype, but not in XX or YY genotypes, suggesting that recombination is inhibited. Here we show that chromosome microdissection and subsequent amplification by degenerate oligonucleotide-primed PCR (DOP-PCR) can be used to produce in situ hybridization probes to this largest pair of O. niloticus chromosomes. Furthermore, analysis of the comparative hybridization of X and Y chromosome-derived probes to different genotypes provides the first demonstration that sequence differences exist between the sex chromosomes of O. niloticus. This provides further support for the theory that this chromosome pair is related to sex determination and further suggests that the sex chromosomes are at a very early stage of divergence.

Chromosome rearrangements between chicken and guinea fowl defined by comparative chromosome painting and FISH mapping of DNA clones.

Chromosome homology between chicken (Gallus gallus) and guinea fowl (Numida meleagris) was investigated by comparative chromosome painting with chicken whole chromosome paints for chromosomes 1–9 and Z and by comparative mapping of 38 macrochromosome-specific (chromosomes 1–8 and Z) and 30 microchromosome-specific chicken cosmid DNA clones. The comparative chromosome analysis revealed that the homology of macrochromosomes is highly conserved between the two species except for two inter-chromosomal rearrangements. Guinea fowl chromosome 4 represented the centric fusion of chicken chromosome 9 with the q arm of chicken chromosome 4. Guinea fowl chromosome 5 resulted from the fusion of chicken chromosomes 6 and 7. A pericentric inversion was found in guinea fowl chromosome 7, which corresponded to chicken chromosome 8. All the chicken microchromosome-specific DNA clones were also localized to microchromosomes of guinea fowl except for several clones localized to the short arm of chromosome 4. These results suggest that the cytogenetic genome organization is highly conserved between chicken and guinea fowl.

A comparative karyological study of the blue-breasted quail (Coturnix chinensis, Phasianidae) and California quail (Callipepla californica, Odontophoridae)

We conducted comparative chromosome painting and chromosome mapping with chicken DNA probes against the blue-breasted quail (Coturnix chinensis, CCH) and California quail (Callipepla californica, CCA), which are classified into the Old World quail and the New World quail, respectively. Each chicken probe of chromosomes 1–9 and Z painted a pair of chromosomes in the blue-breasted quail. In California quail, chicken chromosome 2 probe painted chromosomes 3 and 6, and chicken chromosome 4 probe painted chromosomes 4 and a pair of microchromosomes. Comparison of the cytogenetic maps of the two quail species with those of chicken and Japanese quail revealed that there are several intrachromosomal rearrangements, pericentric and/or paracentric inversions, in chromosomes 1, 2 and 4 between chicken and the Old World quail. In addition, a pericentric inversion was found in chromosome 8 between chicken and the three quail species. Ordering of the Z-linked DNA clones revealed the presence of multiple rearrangements in the Z chromosomes of the three quail species. Comparing these results with the molecular phylogeny of Galliformes species, it was also cytogenetically supported that the New World quail is classified into a different clade from the lineage containing chicken and the Old World quail.

Chromosome assignment of eight SOX family genes in chicken.

Chromosome locations of the eight SOX family genes, SOX1, SOX2, SOX3, SOX5, SOX9, SOX10, SOX14 and SOX21, were determined in the chicken by fluorescence in situ hybridization. The SOX1 and SOX21 genes were localized to chicken chromosome 1q3.1→q3.2, SOX5 to chromosome 1p1.6→p1.4, SOX10 to chromosome 1p1.6, and SOX3 to chromosome 4p1.2→p1.1. The SOX2 and SOX14 genes were shown to be linked to chromosome 9 using two-colored FISH and chromosome painting, and the SOX9 gene was assigned to a pair of microchromosomes. These results suggest that these SOX genes form at least three clusters on chicken chromosomes. The seven SOX genes, SOX1, SOX2, SOX3, SOX5, SOX10, SOX14 and SOX21 were localized to chromosome segments with homologies to human chromosomes, indicating that the chromosome locations of SOX family genes are highly conserved between chicken and human.

High-resolution comparative chromosome painting in the Arizona collared peccary (Pecari tajacu, Tayassuidae): a comparison with the karyotype of pig and sheep

We used chromosome painting with chromosome-specific probes derived from domestic sheep and pig for a high-resolution cytogenetic comparison with the karyotype of collared peccary (Pecari tajacu sonoriensis). A reorganization of the karyotype involving at least 62–66 conserved segments were observed between the sheep and collared peccary. This is an extremely high number compared with other members of the same mammalian order (Cetartiodactyla). The comparison between pig and collared peccary, both belonging to the Suiformes, however, revealed various changes in the gross organization of both karyotypes that may have already occurred in a common ancestor of both species suggesting a monophyletic origin of Suidae/Tayassuidae. The sheep probes, however, also revealed several rearrangements between the two Suidae/Tayassuidae, indicating that these probes represent a useful tool for a more detailed analysis of the evolutionary history of Suiformes. Our sample of the collared peccary from North America (Arizona, USA) showed distinct differences to those already described from South America. The chromosome painting results defined a complex translocation that involves chromosomes including about one-quarter of the entire collared peccary karyotype. This considerable rearrangement indicates subspecies or even species status of both peccary populations, as it should present a significant barrier for their hybridization.