Meiotic pairing of X and Y chromosomes in male Lucilia cuprina was studied by cytological observation of normal, rearranged and deficient sex chromosome karyotypes in spermatogenesis. Two X-Y pairing regions located distally in each arm of the X and Y chromosomes were defined. Contrasting with findings in Drosophila melanogaster, these pairing regions show specific recognition of their partners. By studying rearranged sex chromosomes short arm pairing was localised to their distal ends, closely associated with secondary constrictions containing nucleolar organisers in both sex chromosomes. Short arm pairing is very tight and not greatly disrupted by chromosome rearrangement, deficiency for the Y chromosome long arm or the presence of supernumerary X chromosomes. The pairing region of the long arms could not be precisely localised but probably also occurs at their distal ends. Pairing between the long arm sites is much weaker and is easily disrupted by chromosome rearrangement, failing completely in flies deficient for the Y chromosome short arm. No cytologically visible pairing was seen between X chromosomes and the remainder of the Y. In males with an extra X chromosome, the ends of both X chromosomes pair to form multivalents with normal and rearranged Y chromosomes provided the Y short arm is present, otherwise an independent X chromosome bivalent is formed. The mechanism of pairing in male Lucilia sex chromosomes thus seems to depend on specific loci of distinctive structure within the X and Y heterochromatin. Comparison of cytological and genetic data shows that increasing cytological pairing failure is matched by higher genetic X-Y nondisjunction but that the former occurs at much higher levels. In some karyotypes cytologically observed X-Y pairing failure is not matched by high frequencies of nondisjunction presumably because weak pairing associations are disrupted during slide preparation.
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