Genomic Structural Variation and Transcriptomic Analyses Reveal Candidate Genes for Hybrid Sterility in Cattle-Yak_Supplementary Data

Yak females are crossed with taurine bull to produce cattle-yak that shows hybrid vigor. However, whereas the F1 hybrid females are fertile, the males exhibit complete sterility, therefore hinders the fixation of desired traits through hybridization. Currently, the genetic mechanisms associated with hybrid sterility have not been determined. We characterized the transcriptomes of yak and cattle-yak testes at several key developmental stages and examined the distribution of structural variants (SVs) among the differentially expressed genes (DEGs). We found that a proportion of the DEGs in cattle-yak at each stage contained SVs in their regulatory or coding regions, indicating the potential role of genetic variations in affecting gene expression; moreover, we selected the candidate genes <i>ESCO2</i> (establishment of sister chromatid cohesion N-acetyltransferase 2) and <i>BRDT</i> (bromodomain testis associated) for expression validation. The expression of X-linked genes was particularly dysregulated at different developmental stages, revealing the contribution of the X chromosome to hybrid sterility in large animals. Data from backcross generation (BC1) animals demonstrated that spermatogenic defects and dysregulated gene expression were partially recovered. Taken together, the findings of these experiments provide insights into the potential function of genetic structural variation in hybrid infertility.