Cytogenetic localization of avian Z- and W-linked genes using large insert BAC clones

In all studied neognathous birds, the Z–W pair of sex chromosomes shows strictly localized recombination in a very short pseudoautosomal region. There are five published W-linked genes in this region that have homologs on the Z, reflecting their common origin from an ancestral homologous chromosome pairs: CHD1, HINT, SPIN, UBAP2, and ATP5A1. Using BAC-based FISH, we have investigated in detail the genes located on the chicken Z and W chromosomes, especially those in the pseudoautosomal region. For one of them, UBAP2Z, we identified its precise cytogenetic location on the Z chromosome and mapped its W-linked counterpart, UBAP2W. The fine FISH mapping of two more homologs, ATPA5A1Z and ATPA5A1W, has been completed. By screening two gridded genomic jungle fowl BAC libraries, TAMU 031-JF256-BI and CHORI-261, with labeled amplified gene fragments or overgos, we detected four and five specific clones, respectively. BAC clones TAM31-100C09, TAM31-099N01, TAM31-027P16 and TAM31-095L18 were assigned to GGAZ at Zp23-p22 site (Flpter, 0.12 ± 0.034 to 0.15 ± 0.033). Clones CH261-046G16, CH261-033F10 and CH261-064F22 were detected on GGAZ (Flpter, 0.12 ± 0.033 to 0.14 ± 0.033). They also co-localized on GGAW, along with the CH261-114G22 BAC clone containing the GGAW-specific UBAP2W DNA sequence. We cytogenetically mapped in the chicken genome the sixth, previously unknown pair of Z- and W-linked homologs, UBE2R2Z and UBE2R2W. Using a chicken UBE2R2W-specific overgo, a positive clone was identified in the California condor BAC library and is being used for FISH in this endangered species and other birds.