ZNF280AY: a pseudogene on the ovine Y chromosome and its copy number variation associated with testicular size in Hu sheep.

Y-chromosome gene copy number variations (CNV) are closely associated with testicular development and male fertility. ZNF280AY, originating from the transposition of the ZNF280A gene, has been identified as a multicopy gene in the male-specific region of the Y chromosome within the Bovidae family. However, the genomic structure of ZNF280AY and its impact on male fertility through CNV remain poorly characterized. Our study revealed that ZNF280AY exhibits pseudogene characteristics in sheep, as evidenced by disrupted coding sequences and the absence of mRNA expression across 7 somatic tissues (heart, liver, spleen, lung, kidney, testes, muscle) at 6 mo of age. The absence of expression was further found at various developmental stages (0 to 12 mo). Comparative genomic analysis confirmed sequence homology (>88%) with bovine orthologs, while structural divergence supports its pseudogenization trajectory. Large-scale qPCR analysis of 723 rams from 8 breeds revealed substantial CNV (15 to 122 copies, median = 42), with significant negative correlations between ZNF280AY copy number and testicular morphometric parameters (left testicular length: r = - 0.096, P = 0.044; left testicular width: r = - 0.112, P = 0.020; right testicular length: r = - 0.136, P = 0.005). These findings establish ZNF280AY CNV as a novel molecular marker for ram testicular development evaluation, providing critical insights for marker-assisted selection in sheep breeding programs.