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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

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

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Author(s):
Selli, Alana [1] ; Ventura, Ricardo V. [1] ; Fonseca, Pablo A. S. [2] ; Buzanskas, Marcos E. [3] ; Andrietta, Lucas T. [1] ; Balieiro, Julio C. C. [1] ; Brito, Luiz F. [4]
Total Authors: 7
Affiliation:
[1] Univ Sao Paulo, Sch Vet Med & Anim Sci FMVZ, Dept Nutr & Anim Prod, Pirassununga 13635-900, Sao Paulo - Brazil
[2] Univ Guelph, Ctr Genet Improvement Livestock, Dept Anim Biosci, Guelph, ON N1G 2W1 - Canada
[3] Univ Fed Paraiba, Dept Anim Sci, BR-58051900 Joao Pessoa, Paraiba - Brazil
[4] Purdue Univ, Dept Anim Sci, W Lafayette, IN 47907 - USA
Total Affiliations: 4
Document type: Journal article
Source: ANIMALS; v. 11, n. 9 SEP 2021.
Web of Science Citations: 0
Abstract

Simple Summary Heterozygosity-rich regions (HRRs) are regions of high heterozygosity, which can harbor important genes associated with key functional traits such as immune response and disease resilience. Runs of homozygosity (ROH) are contiguous homozygous segments of the genome, which can be informative of the population's history, structure, demography events, and overall genetic diversity. We first detected factors impacting the identification of ROH and HRR in worldwide sheep populations, which were artificially selected for specific purposes or under natural conditions. We also identified common regions of high homozygosity or heterozygosity among these populations, where a diversity of candidate genes with distinct functions might indicate differential selection pressure on these regions in breeds with different trait expression. Moreover, we evaluated a tool commonly used in the corporate environment, making use of the business intelligence (BI) concept to support managers in the decision-making process, which allowed us to combine results from multiple analyses and create visualization schemes integrating different information. Our findings and proposed tools contribute to the development of more efficient breeding strategies and conservation of genetic resources in sheep and other livestock species. 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. (AU)

FAPESP's process: 16/19514-2 - Development of a genomic database for Nellore cattle and computational tools for implementing large-scale studies
Grantee:Ricardo Vieira Ventura
Support Opportunities: Research Grants - Young Investigators Grants
FAPESP's process: 20/04461-6 - Applications of machine learning and genomic data to improve economic traits in dairy cattle
Grantee:Lucas Tassoni Andrietta
Support Opportunities: Scholarships in Brazil - Master