Comparative analysis of gene structure in 5-flanking region of MC1R gene in indigenous sheep breeds

Abstract

Motivations and aim

Currently, coat color scoring is of significant interest to researchers due to its effect on a sheep's ability to adapt to environmental heat stress, as well as its implications for the marketability of sheep products, such as wool and skin, which are vital to the textile industry. Additionally, coat color can indicate its breed and genetic characteristics. Former studies have demonstrated that some genetic variants are directly associated with coat color. The MC1R gene is one of the major genes associated with coat color in sheep. This study aimed to investigate the comparative analysis of MC1R gene among some Iranian sheep breeds for the first time.

Materials and methods

Ten blood samples were collected from each of the following sheep breeds: Zel, Romanov, Iran-Black, Naeini, Baluchi, and Kurdi. Following DNA isolation using the modified salting-out method, the 5-flanking region of the MC1R gene was amplified and subsequently analyzed using sanger sequencing. Then, the resulting sequences were assessed by bioinformatics software.

Results

Sequencing analysis of the 5′-UTR region of the gene revealed various motifs and transcription factor binding sites. A 26-nucleotide deletion/insertion mutation in this region was found in some breeds, such as Romanov, Zel, and Iran-Black. Additionally, a nucleotide substitution of −206G > A was observed in these breeds. Overall, the identified polymorphisms resulted in the loss and alteration of the number and type of motifs and transcription factor binding sites, such as MOK2 and Gamma_IRE_CS, which may influence the mechanism of gene expression.

Conclusion

The presence of A 26-nucleotide deletion/insertion mutation and a nucleotide substitution (−206G > A) among different sheep breeds and its effect on the coat color scoring confirm the 5′-UTR region of the MC1R gene as a functional candidate locus. The findings reveal significant mutations resulted in alterations to motifs and transcription factor binding sites, potentially affecting gene expression mechanisms and, consequently, coat color phenotypes.