Standard Karyotypes and Nomenclature Systems as Prerequisites for Chromosome Mapping

Karyotypes represent arrangement of all the chromosomes from a cell on the basis of a universally agreed layout scheme that is specific for each species. In most cases chromosomes are classified into groups (e.g. meta-/submeta-centric and acrocentric) and then arranged based on their decreasing size within each group. Using banding techniques, homologous chromosomes are paired and presented together. Once a chromosome arrangement for a species is agreed upon by researchers around the world, it is referred to as a standard karyo-type. Such karyotypes are extremely important as global platforms for chromosome identification and numbering within a species. Standard karyotypes are generally supplemented with a universally accepted nomenclature system wherein individual regions and chromosome bands are numerically recognized. This markedly facilitates pinpointing specific regions on the chromosomes.

Chromosome mapping and standard kary-otype/nomenclature are closely connected. All gene mapping efforts will be in vain unless identified linkage or syntenic groups are assigned to specific chromosomes. Also, once a gene is mapped to a chromosome, it must be allocated to a specific region or band to indicate its position on the chromosome. Hence in species where genome analysis is carried out, each chromosome must: (i) bear a number; (ii) have a fixed position on the karyotype; and (iii) have an elaborate nomenclature system for individual regions and bands. This will enable every researcher around the world to associate a numbered chromosome of a species with a pre-determined size, structure, banding pattern and gene content.

Presently, standard karyotypes with nomenclature descriptions are available for ~15 species. Incidentally, all these species have strong to evolving gene mapping programmes. The most prominent among these is humans where several resolutions of banded standard kary-otypes and ideograms are available. The most commonly cited human standard is the ISCN 1985 (An International System for Human Cytogenetic Nomenclature, 1985). In view of rapid progress in cytogenetic analysis and gene mapping, this system was revised in 1991 and 1995 for higher resolution and for specific applications to gene mapping and cancer cyto-genetics (ISCN, 1991, 1995). To accommodate the growing need of computerized ideograms in genomic applications, Francke (1994) provided digitized and differentially shaded ideograms for individual human chromosomes.

Nomenclature systems are also available in mouse (Nesbitt and Francke, 1973), rat (Levan, 1974; Satoh et al., 1989), Chinese hamster (Ray and Mohandas, 1976), a range of livestock/farm species, i.e. cattle, sheep, goat (ISCNDB, 2000), river buffalo (Iannuzzi et al.,

1991), horse (ISCNH, 1997), dog (Reimann et al., 1996), Chinese raccoon dog (Pienkowska et al., 2002a), cat (Cho et al., 1997), donkey (Raudsepp et al., 2000) and rabbit (Hayes et al., 2002). Incidentally, other than rabbit, raccoon dog and donkey, genome projects are expanding rapidly among other mammals.

Genome programmes have also been initiated in some other mammalian species, e.g. American mink (Kuznetsov et al., 2003). However the scope of these programmes is limited. Either very few genes are mapped in these species or the genomes/chromosomes of these species are only compared by Zoo-FISH. For these species G-banded standard karyo-types are available. Though these karyotypes are useful for preliminary comparisons, they do not provide detailed information/nomenclature on individual chromosomes. Hence, before the launch of any expanded genome programme in these species, development of a comprehensive nomenclature will be essential.

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