Abstract：The Wenshang Barred chicken (Gallus gallus) is the only barred-feather breed in China as an indigenous breeds of chicken. This study aimed to investigate the genetic diversity and genetic structure, detect the genomic selection signals and explore the important germplasm characteristic genes of Wenshang Barred chicken population from the genomic level. According to multiple factors such as geographical distribution and genetic background, the Wenshang Barred chicken and 23 other indigenous chicken breeds as well as 3 introduced chicken breeds were selected as the research objects. The genomic SNPs were identified using restriction-site associated DNA sequencing (RAD-seq), which was used to compare the genetic differences between Wenshang Luhua chicken and other chicken populations, and annotate the selected genes in the process of evolution. The results showed that 300 543 SNP markers were detected in Wenshang Barred chicken population, and 14 breed-specific SNPs as well as 5 genes were identified. In terms of genetic structure, Wenshang Barred chicken and Yuanbao chicken, Tianjin monkey chicken, Langya chicken and Langshan Chicken as separate branches on the evolutionary tree. Functional analysis showed that the selected genes were mainly involved in physiological functions such as hormone regulation, nervous system development, amino acid metabolism and germ cell differentiation. This study can provide crucial reference information and theoretical basis for germplasm conservation and genetic diversity evaluation of Wenshang Barred chicken population.
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