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We investigated means to improve the production of the indigenous Naked Neck chicken in Afghanistan. Specifically, we analyzed single nucleotide polymorphisms (SNPs) in the prolactin ( PRL ) (24 bp indel), growth hormone ( GH ) (T185G), and pituitary specific transcript factor 1 ( PIT-1 ) (intron 5) genes. Blood samples were collected from 52 birds and genomic DNA was extracted. Polymorphisms in the mentioned loci were analyzed by PCR, allele-specific PCR, and PCR-restriction fragment length polymorphism (RFLP) using Taq I and Msp I endonucleases. Cloning followed by DNA sequencing was performed to ascertain the accuracy of the PCR-RFLP analysis for PIT-1 .Two alleles were found for the PRL 24 bp indel, GH (T185G), and PIT-1/Taq I, with the following respective allelic frequencies: PRL-In 0.64 and PRL-Del 0.36, GH -T 0.91 and GH -G 0.09, and PIT-1 -A 0.64 and PIT-1 -B 0.36. Regarding the PIT-1/Msp I polymorphism, three novel Msp I recognition sites, as well as two reported Msp I recognition sites, were detected in intron 5. Moreover, during sequence screening, two novel SNPs were found that generated restriction sites for Mse I. Therefore, our results suggest that the PRL indel, GH T185G, and PIT-1/Taq I polymorphisms may be used as selection markers for Afghanistan Naked Neck chickens. Intron 5 of PIT-1 in the Afghani Naked Neck chicken was highly polymorphic compared to the reported Gallus gallus PIT-1 gene (GenBank accession no. NC_006088.4).

Determination of Polymorphisms in Pituitary Genes of the Native Afghani Naked Neck Chicken