Detection and Visualization of Heterozygosity-Rich Regions and Runs of Homozygosity in Worldwide Sheep Populations

Abstract

In this study, we chose 17 worldwide sheep populations of eight breeds, which were intensively selected for different purposes (meat, milk, or wool), or locally-adapted breeds, in order to identify and characterize factors impacting the detection of runs of homozygosity (ROH) and heterozygosity-rich regions (HRRs) in sheep. We also applied a business intelligence (BI) tool to integrate and visualize outputs from complementary analyses. We observed a prevalence of short ROH, and a clear distinction between the ROH profiles across populations. The visualizations showed a fragmentation of medium and long ROH segments. Furthermore, we tested different scenarios for the detection of HRR and evaluated the impact of the detection parameters used. Our findings suggest that HRRs are small and frequent in the sheep genome; however, further studies with higher density SNP chips and different detection methods are suggested for future research. We also defined ROH and HRR islands and identified common regions across the populations, where genes related to a variety of traits were reported, such as body size, muscle development, and brain functions. These results indicate that such regions are associated with many traits, and thus were under selective pressure in sheep breeds raised for different purposes. Interestingly, many candidate genes detected within the HRR islands were associated with brain integrity. We also observed a strong association of high linkage disequilibrium pattern with ROH compared with HRR, despite the fact that many regions in linkage disequilibrium were not located in ROH regions.

The SNP-Based Profiling of Montecristo Feral Goat Populations Reveals a History of Isolation, Bottlenecks, and the Effects of Management

“…These findings are in line with expectations, considering the geographical isolation and the repeated bottleneck events that have characterised the demographic history of the insular population, at least from the 18th century. They also agree with previous studies on insular populations, i.e., goats from the Mediterranean basin [ 35 ] and Soay sheep from the Scottish island of Hirta [ 36 , 37 ]. In all cases, insular populations had increased levels of inbreeding and a reduced variability compared to the nearby mainland populations.…”

Genomic population structure and inbreeding history of Lake Superior caribou

“…The lowest diversity levels correspond to caribou from the Slate Islands with high ROH estimates; however, our results indicated relatively high diversity has been maintained outside of ROH (Figure 5). This suggests genetic diversity may be maintained by natural selection in genomic regions where variation is important (Hedrick & Garcia‐Dorado, 2016; Selli et al, 2021).…”

Genome‐wide population structure, homozygosity, and heterozygosity patterns of Nero Siciliano pig in the framework of Italian and cosmopolitan breeds

“…Sliding window and consecutive runs are the methods of choice to detect stretches of consecutive ROH and ROHet in livestock species (e.g. Bizarria Dos Santos et al, 2021; Dixit et al, 2020; Mulim et al, 2022; Selli et al, 2021). Here, we investigated both approaches (Bizarria Dos Santos et al, 2021) and then outlined the results of the overlapping regions in order to identify and characterise the ROHet and ROH patterns, as well as to reveal the related fixed islands harbouring the candidate genes linked to specific traits.…”