Polymorphisms of the Leptin gene in Jabres cattle

Abstract

Abstract Many genes, including the leptin gene, control growth performance. Polymorphism or SNPs variant within the gene could change its expression in phenotypes. This study aimed to identify the SNP and haplotype variation of the leptin gene in Jabres cattle (n = 47 head). The SNPs variant was detected using the BioEdit version 7.0 program by sequence alignment. The HaploView program analyzed the haplotype pattern created from the SNP variants. As a result, 20 SNPs were found within the partial sequence of the leptin gene. Only 3 SNPs are located in the coding sequence (CDS) region, SNP g. 12215T>C, g.12237C>T, and g.12238G>A. For the haplotype analysis, we used only SNPs with HW p-value cutoff and minimum minor allele frequency (MAF) higher than 0.05 (Jabres = 12 SNPs). The result showed a distinctive haplotype pattern of SNPs. All the blocks of LD plot in Jabres cattle showed a high linked disequilibrium (LD) (R2 > 0.33, LOD > 2) except for the block containing SNP g.12238G>A (R2 < 0.33, LOD < 2). In conclusion, the polymorphism and haplotype pattern found in this study could be used for further association analysis to the phenotypes, and its utilization could be used as an effective marker selection tool.