Analysis of runs of homozygosity in Yeonsan Ogye chickens using 600K SNP arrays

Runs of homozygosity (ROHs) are caused by identical haplotypes inherited from ancestors. ROHs provide useful information regarding the inbreeding rate, demographics, and selection history. The Yeonsan Ogye (YO) breed is an indigenous chicken in Korea that is characterized by a completely black body. In this study, we investigated ROH in the YO genome to determine ROH-based inbreeding coefficients and their correlations with other inbreeding estimators, then analyzed their genetic characteristics. Using 600K single nucleotide polymorphism (SNP) chip information for 189 chickens, we found 20,339 ROHs in the YO population. The average number of ROHs was 107, the total average ROH length was 165 Mb, and the average ROH length was 1.542 Mb. Most ROHs were short (&lt; 8 Mb), suggesting a past population bottleneck. The average inbreeding coefficient (<strong><italic>F_ROH</italic></strong>) calculated based on ROHs was 0.184 and this was correlated with other inbreeding coefficients estimated using allele frequencies. 17 ROH islands were detected and these regions exceeded the threshold of the top 1% of SNPs among SNPs present in ROHs. In the ROH islands, 152 genes were annotated, some of which were genes associated with meat production traits and hyperpigmentation in chickens. A comparison of overlapping regions between ROH islands and quantitative trait loci (QTLs) indicated that most QTLs were related to color traits. These results will help to optimize conservation strategies for the YO breed.