<div>Background: Marker assisted selection based strategies are essential to identify superior quality bulls at an early age for frozen semen production. The present study aims to determine the genetic variants in the Y-chromosome specific genes, sex determining region on Y-chromosome (SRY) and testis specific protein Y-encoded (TSPY) in association with semen production traits in Murrah buffalo bulls.&nbsp; 
 
Methods: The genomic DNA extracted from the blood samples of 70 Murrah buffalo bulls maintained under semen production in the frozen semen station were utilized for PCR amplification. The sequences of SRY and TSPY genes were screened for single nucleotide polymorphism using the seqman module of DNASTAR LASERGENE software. The single nucleotide variations in comparison with reference sequences and phylogenetic tree construct were obtained using Clustal W and MegAlign module.&nbsp; 
 
Result: The analysis revealed that the sequences of SRY and TSPY genes were monomorphic in nature, devoid of variations specifying that the sequences are highly conserved among the Murrah buffalo bulls studied. Hence, association studies with seminal traits could not be performed. However, the exon sequence of SRY gene of Murrah buffalo showed a single nucleotide variation at position 209 (G&lt;A) compared to the sequences of Nili-Ravi and Kundi buffaloes. Similarly, the TSPY gene exhibited a significant number of single nucleotide variations compared with Bos taurus sequences. The phylogenetic tree analysis evinced a close genetic relationship with less divergence between Murrah buffalo and other buffalo breeds and species in the bovinae family. Further extensive studies on SRY, TSPY and other Y-chromosome specific genes in a large, diverse population of Murrah buffalo bulls could help to discover a considerable number of SNP markers related to semen production for the early selection of breeding bulls.</div>

Identification of Genetic Variants in Y-Chromosome Specific Genes Associated with Seminal Production in Murrah Buffaloes