Genome-Wide Analysis Revealed Homozygosity and Demographic History of Five Chinese Sheep Breeds Adapted to Dierent Environments

Homozygosity of long sequence genotypes are a result of parents transmitting identical
haplotypes, which can be used to estimate their auto-zygosity. Therefore, we used high-density SNP
Chip data to characterize the auto-zygosity of each breed according to the occurrence and distribution
of runs of homozygosity (ROH). Subsequently, we identified the genomic regions with high runs of
homozygosity frequencies within individuals of each breed. We selected 96 sheep samples from five
local Chinese sheep breeds belonging to dierent geographical locations. We identified 3046 ROHs
within the study breed individuals, among which the longer segments (>1–5 Mb) were dominant.
On average, ROH segments covered about 12% of the genomes; the coverage rate of OAR20 was
the lowest and that of OAR2 was the highest. The distribution analysis of runs of homozygosity
showed that the detected ROH mainly distributed between >26 and 28 Mb. The Hetian and Hu
sheep showed the lowest ROH distribution. The estimation of homozygosity level reflects the
history of modern and ancient inbreeding, which may aect the genomes of Chinese indigenous
sheep breeds and indicate that some animals have experienced recent self-pollination events (Yabuyi,
Karakul and Wadi). In these sheep breeds, the genomic regions were assumed to be under selection
signatures frequently in line with long ROH. These regions included candidate genes associated with
disease resistance traits (5S_rRNA), the innate and adaptive immune response (HERC2 and CYFIP1),
digestion and metabolism (CENPJ), growth (SPP1), body size and developments (GJB2 and GJA3).
This study highlighted new insights into the ROH patterns and provides a basis for future breeding
and conservation strategies of Chinese sheep breeds.