A Complex Genomic Structural Variation on Gallus gallus Chromosome 27 Lead to Ectopic Gene Expression Which Caused Beard in Chicken

Beard in Gallus gallus is a cluster of elongated feathers that grow on chin and cheeks compared to wild type. It is an excellent trait for studying feather formation and regional specificity. To study the genetic basis and molecular processes of the trait, we generated an F2 intercross population. In this research, we show that Beard is an autosomal dominant trait and is caused by a complex structural variation (SV) on chromosome 27 using GWAS, linkage analysis, array-CGH and resequencing. This variation involves three >14-kb-genomic-region duplicating and tandem inserting into the downstream of the first copy number variation region (CNVR). Continuous expression of genes located in these regions were demonstrated in both embryos and adults. Markedly ectopic expression of an excellent candidate gene, which plays an important role in feather development and shows region specific expression pattern, was identified during the critical period of beard morphogenesis. Our results first present that beard in chicken is caused by gene ectopic expression due to genomic structural variation. This also provides additional evidence that complex genomic structural variations produce prominent phenotypic alterations.