Nig. J. Anim. Prod. 2019, 46(5):81 - 87 Nigerian Society for Animal Production Nigerian Journal of Animal Production © Abstract In-silico amplification of randomly selected male - specific region – Y (MSY) genes as candidate genes for the selection of fertile indigenous bulls for artificial insemination 1,4 1 5 1 1,2 Sikiru, A. B., Egena, S. S. A., Akinsola, O. M., Alemede, I. C., Makinde, J. O. 3 and Lawal, S. O. 1 Department of Animal Production, Federal University of Technology, Minna. 2 Department of Animal Sciences, Federal University, Gashua. 3 Department of Animal Science, University of Abuja. 4 Reproductive Physiology Laboratory, National Institute of Animal Nutrition and Physiology, India. 5 Department of Veterinary Theriogenology and Production, University of Jos, Nigeria. Corresponding author: akeembaba01@gmail.com; +2348160942976 Molecular markers-based selection is a novel tool for unbundling complexities associated with the selection of animals for breeding improvement programmes because these markers could contribute to full exploitation of animal potential prior to enrollment for improvement programmes. This study examined in-silico polymerase chain reaction amplification of some selected Male Specific region Y (MSY) genes in genome assemblies including Bos_taurus_UMD_3.1.1/bosTau8 and ARS-UCD 1.2/bosTau9; BaylorBtau_4.6.1/bosTau7, Bos_taurus_UMD_3.1/bosTau6, and Baylor4.0/bosTau4. The results of the amplification showed that 12 out of the selected 30 genes were expressed at an average primer melting o temperature of 61.78 C; while salt and annealing oligo concentrations were 50 mM and 50 nM per reaction, respectively. Out of expressed genes; 6, 5 and 1 genes were expressed in genome assemblies Bos_taurus_UMD_3.1.1/bosTau8, ARS-UCD1.2/bosTau9, and BaylorBtau_4.6. 1/bosTau7, respectively. The study concluded that the expressed genes are potential markers for selection of fertile bulls and the primers used are suitable for in-vivo annotation of the genes in the prospective bull selection process for breeding programmes. Keywords: Male-specific region-Y genes (MSY); molecular markers; bulls and in-silico Introduction The best reproductive technology with excellent potential for increasing herd level productivity in cattle is artificial insemination because semen from a single bull can sire multiple calves far and wide within and outside a given geographical location; but selection and recruitment of highly fertile bull is key to successful implementation of artificial insemination programmes especially in the tropical resources poor countries such as Nigeria. Challenges including inadequate record- keeping and poor implementation of deliberate improvement and breeding programme are limiting factors against identification of highly fertile indigenous bulls in the tropics such as Nigeria. Meanwhile, identifying these bulls in highly desirable; therefore, the need for field-level molecular fertility markers is a worthy application of molecular biology for increasing livestock productivity as a way of fighting food insecurity in a country like Nigeria where population is currently growing at an alarming rate. Expression profiling of MSY genes are potential molecular markers of bull fertility but their mechanisms of action are relatively unexplored; hence, the need to investigate them becomes highly imperative for the purpose of establishing relationships 81