Analysis of homozygous regions in the genome of chinese silkie chickens to identify genes affecting adaptive properties

Homozygous regions in the genome serve as markers of areas under selective pressure. These regions likely harbor genes responsible for key production traits targeted in breeding programs. For this study, we performed whole-genome genotyping at 30×coverage on DNA extracted from blood samples of Chinese Silkie chickens (n=20) maintained at the Center for Genetic Collections of Rare and Endangered Chicken Breeds (Pushkin, St. Petersburg, Russia). Our aim was to identify runs of homozygosity (ROH) in this population and pinpoint genes within them that relate to adaptive traits and immune resilience. After quality filtering, we analyzed 10,593,367 SNPs. We detected ROH on chromosomes 1, 3, 4, 7, and 9, encompassing nine regions that collectively contain 40 genes. Of these, we annotated 25 genes; here, we focus on those that directly or indirectly influence adaptive capacity and immune responses in chickens: HAAO gene on chromosome 3, and ATP5G3, ATF2, WIPF1, SCRN3, CIR1, and OLA1 genes on chromosome 7. Functional annotation links these genes to adaptive and physiological processes in chickens. The HAAO gene contributes to multiple roles, including the heat stress response. Meanwhile, ATF2, ATP5G3, OLA1, WIPF1, SCRN3, and CIR1 form a cluster associated with stress reactivity, immune function, mitochondrial activity, and cellular homeostasis. Together, they modulate energy metabolism, oxidative stress, inflammatory signaling, tissue repair, and intercellular communication. This gene set underscores the importance of metabolic robustness, immune defense, and stress adaptation to the distinctive phenotype of the Chinese Silkie population. We posit that homozygosity at these loci enhances the breed's hardiness and adaptability across diverse rearing conditions.

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