Genome-wide candidate signatures of divergent selection between broody Silkie and White Leghorn chickens revealed by high-density SNP genotyping.

1. In this study, genome-wide population structure, genetic differentiation and homozygosity patterns were investigated between Silkie (SLK) and White Leghorn (WLH) chickens, using high-density autosomal SNP genotypes. These breeds were selected as they have markedly different breed histories and productive performances.2. Principal component analysis revealed complete genetic separation between the two breeds, explaining 75.82% of total genomic variance and indicating strong divergence. Genome-wide differentiation showed heterogeneous patterns across autosomes. The top 1% of windows (FST ≥ 0.7467) were used as an empirical threshold for prioritising regions showing elevated differentiation.3. The study identified 20 protein-coding positional candidate genes, including TRHDE, GABBR2, SEMA3A, SEMA5A, IGF1, SOCS2, AR and NLGN4, which have roles in neuroendocrine, behavioural, growth and reproduction.4. Breed-specific runs of homozygosity (ROH) revealed marked differences in autozygosity, with Silkie chickens showing substantially higher genomic inbreeding coefficients (F) of ROH (mean FROH = 0.396) than White Leghorns (mean FROH = 0.175). Island analysis identified 30 islands in Silkie and 19 in White Leghorn chickens, predominantly located on macrochromosomes. There were breed-specific and partially overlapping differentiated genomic intervals, highlighting concurrent differentiation and homozygosity in the two breeds.5. The results showed substantial genome-wide differentiation between Silkie and White Leghorn chickens. This provided a population-genomic framework for prioritising candidate regions for maternal behaviour, reproductive physiology and egg production.