Genomic signatures of environmental adaptation in Danzhou chickens

Danzhou chicken (DZC) is a native chicken breed endemic to Hainan Island, which is renowned for its superior meat quality and strong disease resistance. Prolonged geographical isolation, coupled with natural and artificial selection events in response to the tropical environment, has significantly transformed the behavior, appearance, and economically important traits of DZC. However, the relatively small size of its conservation population has impeded research on the genetic mechanisms of specific traits and population genetics, exerting an adverse influence on resource conservation and commercial development. This study aims to investigate the formation mechanisms of environmental adaptability through a scanning analysis of population selection in DZC. The results of ROH (runs of homozygosity) analysis revealed a total of 59,217 ROH segments among 200 individuals, with short ROH segments constituting approximately 96% of the total count. The FROH method determined an average inbreeding coefficient of 0.068, indicating a low level of inbreeding in the DZC population. Furthermore, by employing the Wenchang chicken (WCC) population as a control group and utilizing within-group and between-group selection scan methods, we identified the genomic selection characteristics of the DZC population. Through multi-method analysis, a total of 160 potential candidate genes, including IL1RAPL1, RBFOX1, VSTM2A, CADM2, ANO5, PHF14, and BCO2, were identified. Gene annotation revealed the potential impacts of these genes on behavioral traits, immunity, neural development processes, lipid regulation, reproduction, and growth development. In summary, we used whole-genome resequencing data combined with SNPs detection data from other local varieties and four selection signal analysis methods to explore selection signatures. These discoveries contribute to the identification of genes associated with phenotypic traits in the DZC population and enhance our understanding of the biological processes underlying strong and sustained selective influences in populations. These findings provide crucial insights for conserving DZC genetic resources as well as driving advancements in breeding innovation and genetic improvement.