Prediction of desirable genotype patterns in Baladi beef cattle and water buffalo by identification of new leptin gene SNPs

The leptin gene is considered to be an excellent candidate gene for predicting desirable economic traits in both beef and dairy cattle. Leptin gene polymorphism has been analyzed in different livestock species and the polymorphic pattern has been demonstrated to be associated with energy balance, milk production, live body weight and reproductive performance. The present study was designed to analyze genetic polymorphisms in the coding region of leptin gene in native beef cattle and water buffalo in comparison to Holstein cattle. A total number of 180 animals (60 animals of each breed) were used for blood sampling and DNA extraction. Target sites in leptin gene (first 94 bp fragment of exon 2 and 330 bp fragment including first part of exon 3) were amplified by polymerase chain reaction (PCR) using two specific primers pairs. Genotyping for R25C single nucleotide polymorphism (SNP) in exon 2 was carried out using the Kpn21-RFLP method. Variations in the exon 3 coding sequence were investigated by PCR-SSCP analysis. Two alleles (C and T) were observed in exon 2 giving rise to three R25C variants (CC, CT and TT). The highest frequency in all populations was the homozygote genotype (CC) where it recorded 91.6%, 98.3% and 100% for Baladi cattle, Holstein cattle and buffalo, respectively. Four alleles (A, B, C and D) and six genotypes (AA, AB, BB, CC, DD and CD) were identified in all studied breeds upon exon 3 analysis. Genotype AA was found to be the most dominant in all studied breeds followed by genotype CC in Holstein and Baladi cattle but followed by AB genotype in buffalo. All observed and expected genotypes were found to be statistically significant (P≤0.05) when subjected to chi-square analysis. Two point mutations have been identified in the first part of exon 3 coding sequence (a3033>t and c3051>t) of Baladi cattle samples. Polymorphisms that were detected in this study indicated that these breeds have high genetic variability in the leptin gene. These results implicate the prospective use of leptin gene polymorphisms for association studies with different productive and reproductive performances and marker assisted selection (MAS).