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

Guo Y, Rubin CJ, Rönneburg T, Wang S, Li H, Hu X, Carlborg Ö

Poult. Sci. 103 (1) 103232 [2024-01-00; online 2023-10-24]

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 Melanocortin 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 functional 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.

NGI Short read [Service]

NGI Uppsala (SNP&SEQ Technology Platform) [Service]

National Genomics Infrastructure [Service]

PubMed 37980749

DOI 10.1016/j.psj.2023.103232

Crossref 10.1016/j.psj.2023.103232

pmc: PMC10692716
pii: S0032-5791(23)00751-4

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