Research Note: Combined analysis of BSA-seq based mapping and RNA-seq reveals candidate genes associated with sub-Columbian plumage in H line chickens

Columbian coloration patterns in plum-age are widespread phenomena in several standard breeds of poultry, such as the Columbian Plymouth Rock chicken. H line chicken plumage is generally a pure white except in the hackle, wing, and tail plumage, which color-ation is very similar to the Columbian plumage pattern, but with the barring substituting for the black vertical striping. Thus, we refer to this plumage coloration as "sub-Columbian" pattern. However, the genetic basis of this phenotype remains unknown. Here, a F3 cross popu-lation between yellow plumage roosters and sub -Colum-bian plumage hens was constructed, for verifying sub -Columbian plumage was sex-linked dominant inheritance. To identify the candidate regions, F2 generation sub -Columbian plumage hens and yellow plumage hens with their parental lines were used for BSA-seq, and sub -Columbian plumage genes were mapped to a 10.46 Mb interval on chromosome Z. Remarkably, by transcriptome analysis of the neck and wing tip follicle tissues of the 2 plumage colors, we demonstrated that within the interval, only 1 gene, SLC45A2 expressed significant differently (P < 0.05). Through KASP, we identified L347M and A10331272T in solute carrier family 45 member 2 (SLC45A2), and B2 haplotype of cyclin-dependent kinase inhibitor 2A (CDKN2A), showed near complete association with the phenotype. Eventually, we designed a hybridization experiment for verifying the locus of sub -Columbian plumage, which is inherited through Z-linked dominant inheritance and is controlled by SLC45A2 and CDKN2A.