A novel USP9Y polymorphism allowing a rapid and unambiguous classification of Bos taurus Y chromosomes into haplogroups

A new sequence-tagged site (STS) was identified within intron 26 of the bovine USP9Y gene, showing an 81-base pair insertion (g.76439_76440ins81 in sequence with GenBank accession FJ195366) able to distinguish Y2 and Y3 Bos Y haplogroups from Y1. Moreover, four Y3-specific sequence variants allow a distinction from haplogroup Y2. The typing of a Bison bison Y chromosome indicates that the ancestral allele for the USP9Y 81-bp insertion is the short Y1 version. The results from typing the new STS in 1230 cattle Y chromosomes are fully consistent with their classification through standard methods. Thanks to the newly identified STS, it is now possible to assign cattle Y chromosomes to the currently known haplogroups using a single marker.