Assessment and Distribution of Runs of Homozygosity in Horse Breeds Representing Different Utility Types

Tomasz Szmatoła; Artur Gurgul; Igor Jasielczuk; Ewa Oclon; Katarzyna Ropka-Molik; Monika Stefaniuk-Szmukier; Grazyna Polak; Iwona Tomczyk-Wrona; Monika Bugno-Poniewierska

doi:10.3390/ani12233293

Assessment and Distribution of Runs of Homozygosity in Horse Breeds Representing Different Utility Types

Animals (Basel). 2022 Nov 25;12(23):3293. doi: 10.3390/ani12233293.

Authors

Tomasz Szmatoła^{1

2}, Artur Gurgul¹, Igor Jasielczuk¹, Ewa Oclon¹, Katarzyna Ropka-Molik², Monika Stefaniuk-Szmukier², Grazyna Polak³, Iwona Tomczyk-Wrona⁴, Monika Bugno-Poniewierska⁵

Affiliations

¹ Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1c, 30-248 Kraków, Poland.
² Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland.
³ Office of the Director for Scientific Affairs, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland.
⁴ Department of Horse Breeding, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland.
⁵ Department of Animal Reproduction, Anatomy and Genomics, University of Agriculture in Kraków, al. Mickiewicza 24/28, 30-059 Kraków, Poland.

Abstract

The present study reports runs of homozygosity (ROH) distribution in the genomes of six horse breeds (571 horses in total) representing three horse types (primitive, light, and draft horses) based on the 65k Equine BeadChip assay. Of major interest was the length, quantity, and frequency of ROH characteristics, as well as differences between horse breeds and types. Noticeable differences in the number, length and distribution of ROH between breeds were observed, as well as in genomic inbreeding coefficients. We also identified regions of the genome characterized by high ROH coverage, known as ROH islands, which may be signals of recent selection events. Eight to fourteen ROH islands were identified per breed, which spanned multiple genes. Many were involved in important horse breed characteristics, including WFIKNN2, CACNA1G, STXBP4, NOG, FAM184B, QDPR, LCORL, and the zinc finger protein family. Regions of the genome with zero ROH occurrences were also of major interest in specific populations. Depending on the breed, we detected between 2 to 57 no-ROH regions and identified 27 genes in these regions that were common for five breeds. These genes were involved in, e.g., muscle contractility (CACNA1A) and muscle development (miR-23, miR-24, miR-27). To sum up, the obtained results can be furthered analyzed in the topic of identification of markers unique for specific horse breed characteristics.

Keywords: ROH; autozygosity; inbreeding; microarray.

Grants and funding

The study was financed from funds of the project: “Directions for use and conservation of livestock genetic resources in sustainable development” co-financed by the National Research and Development Center (Poland) under the Strategic Research and Development Program: “Environment, Agriculture and Forestry”—BIOSTRATEG, the decision number BIOSTRATEG2/297267/14/NCBR/2016. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.