Single Nucleotide Polymorphism and Restriction Enzyme Analysis of Chicken’s Prolactin Gene based on Genbank Sequences

Abstract

Abstract The prolactin gene (PRL) has a role in controlling broodiness and egg production in chickens. This study aimed to identify Single Nucleotide Polymorphism (SNP) in the chicken PRL gene sequences and analyzed the possible restriction enzymes to conduct the PCR-RFLP as a preliminary study. Four sequences of the PRL gene were collected from GenBank and aligned. Primers were designed for the simulation of restriction enzyme analysis. Virtual PCR-RFLP gel electrophoresis was generated specifically for SNPs located in exon regions. As a result, there were 6 SNPs found in the exon regions. Restriction enzyme analysis revealed there were two SNPs (g.5806C/T and g.5856T/A) that cannot recognized by any restriction enzyme. The SNP g.5878C/T was only perceived by the TaqI enzyme. Three restriction enzymes could be used to recognize the SNP g.1621G/C (BsmAI, BsaI, and BcoDI) and g.5753G/C (SfaNI, HphI, and MslI). The BsrI, BmrI, BsMFI, and Hpy188I enzymes could be used to recognize SNP g.5781G/C. The SfaNI, HphI, and TaqI match the criteria for detection of the SNP g.5753 G/C and g.5878C/T using the PCR-RFLP method. In conclusion, the SfaNI, HphI, and TaqI enzymes can be used for conventional analysis using the PCR-RFLP method.