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Reproduction of cattleyak was greatly restricted due to male infertility. Genomic sequencing indicated higher similarity between cattle and yak and studies were undertaken to investigate the mechanisms of spermatogenic arrest of cattleyak on the molecular level, while there was no information available on the genetic variants of testis transcriptomes between cattleyak and yak. To gain insight into molecular genetic characteristics of spermatogenesis for cattleyak and yak, we investigated genetic alterations for their testis transcriptomes using RNA-seq. The total number of novel transcript units identified from cattleyak was much lower than for yak. The total number of alternative splicing (AS) events identified from cattleyak was also lower than it was in yak, among which intron retention was the prevalent type of AS and it occurred on average in 40% of all AS events in cattleyak and at an average 37% in yak. The cattleyak exhibited lower transitions than yak. The transversions identified in cattleyak were also lower than in yak. The lower AS events in the testis transcriptome of cattleyak resulted in the deficiency of mRNA/protein isoforms and their critical roles in spermatogenesis, which would lead to the spermatogenic arrest. The lower genetic polymorphisms in cattleyak could be attributed to the stagnant spermatogenic differentiation in cattleyak compared to vigorous spermatogenic differentiation in yak. [ABSTRACT FROM AUTHOR]