Copy Number Variation and Association Studies of PRAMEY in Cattle

The male-specific region (MSY) of the mammalian Y chromosome is enriched with multicopy genes that function predominantly in spermatogenesis and male fertility. Copy number variations (CNVs) of the MSY genes have been reported in humans and cattle. We have recently identified a lineage-specific gene family, termed PRAMEY (for preferentially expressed antigen in melanoma, Y-linked), in the bovine MSY. PRAMEY are expressed in testis and spermatozoa, and play a role in spermiogenesis. The objective of this study is to determine PRAMEY CNVs, and to study the association of CNVs with bull reproductive traits. We applied quantitative real-time PCR to determine the copy number of PRAMEY in 435 bulls from 15 cattle breeds. A single-copy Y-linked gene, DDX3Y, was used as the reference gene, and the super bull DNA sample (used for the Y chromosome sequencing project) was used as a calibrator. The results revealed that the copy number of PRAMEY varied from 2 to 30 among all individuals analyzed with a significant difference among breeds (p<0.05).  The median copy number of PRAMEY in taurine lineage (13 copies) is significantly lower than that of indicine lineage (17 copies). The lowest median copy number was observed in Holstein (12 copies), whereas the highest in Limous (24 copies). Association analysis with data from 261 Holstein A.I. bulls revealed that the CNVs were correlated negatively with the non-return rate (p<0.001), while positively with the semen quality index (p<0.05), suggesting that the CNV of PRAMEY may be a valuable genetic marker for bull fertility selection.