Whole-genome selective sweep analyses identifies the region and candidate gene associated with white earlobe color in Mediterranean chickens

We compared the genomes of multiple domestic chicken breeds with red and white earlobes to identify the differentiated regions between groups of breeds differing in earlobe color. This was done using a selective sweep mapping approach based on whole-genome sequence data. The most significant selective sweep was identified on chromosome 11, where the white earlobe chicken breeds originated from Mediterranean share a common haplotype, and where multiple candidate genes are located. The most plausible functional candidate gene is the Melanocor-tin 1 Receptor (MC1R), a receptor known to regulate pigmentation in the skin and hair, and it is also the gene with the strongest positional support from the haplotype-based analyses. It, however, still needs to be explored experimentally to identify effects also on chicken earlobe color variation. Our study is the first exploration of the genetic basis of white earlobe color in Mediterranean chickens using a selective sweep mapping method based on whole-genome sequencing data and shows its value for identifying likely func-tional genes mediating the pigmentation in earlobe. It also indicates a potential novel role of MC1R in birds and exemplifies how selection on fancy traits has influenced the genome during formation of the modern chicken breeds.

Automated summary

We compared the genomes of domestic chicken breeds with different earlobe colors and identified differentiated regions on chromosome 11. We found a significant selective sweep in white earlobe chicken breeds from the Mediterranean, where multiple candidate genes, including the Melanocor-tin 1 Receptor (MC1R), are located. MC1R is known to regulate pigmentation in the skin and hair and shows strong positional support from haplotype-based analyses. Further experimental exploration is needed to confirm its effects on chicken earlobe color variation. This study is the first to use whole-genome sequencing data and a selective sweep mapping method to explore the genetic basis of white earlobe color in Mediterranean chickens, demonstrating its value in identifying functional genes and suggesting a potential novel role of MC1R in birds. Selection for fancy traits has influenced the chicken genome during the formation of modern breeds.