Runs of Homozygosity as Footprints of Selection in the Norik of Muran Horse Genome

Abstract

The aim of this study was to analyse the genome-wide distribution of runs of homozygosity (ROH) segments in the genome of Norik of Muran horse and to identify the regions under strong selection pressure. Overall, 25 animals genotyped by the GGP Equine70k chip were included in the study. After SNP pruning, 54479 SNPs (75.72%) covering 2.25 Gb of the autosomal genome were retained for scan of ROH segments distribution. The ROHs were present in the genome of all animals and covered in average 13.17% (295.29 Mb) of autosomal genome expressed by the SNP loci. The highest number of ROHs was identified on autosome 1 (404), while the lowest proportion of autosome residing in ROH showed ECA31 (38). The footprints of selection, characterized by SNPs with extreme frequency in ROHs across specific genomic regions, were defined by the top 0.01 percentile of signals. Overall, nine genomic regions located on seven autosomes (3, 6, 9, 11, 15, 23) were identified. The strongest signal of selection showed three autosomes ECA3, ECA9 and ECA11. The protein-coding genes located within these regions suggested that the identified footprints of selection are most likely consequences of intensive breeding for traits of interest during the grading-up process of the Norik of Muran horse.

Genetic Variability in the Italian Heavy Draught Horse from Pedigree Data and Genomic Information

“…These two ROH islands overlapped also with QTLs for two disease-related traits: the insect bite hypersensitivity and the guttural pouch tympani; therefore, we cannot rule out the hypothesis that those regions might be under selection due to their association with disease resistance. In addition, those two regions highly overlapped with the potential selection signatures found in two other draught horse breeds: the Noriker horse breed [46] and the Muran horse breed [67]. Therefore, we can suggest that some of the genes located in those two regions might have an important function for draught horse.…”

“…A possible explanation might be related to the multiple aims currently present in the IHDH breeding program, including meat production and several types of leisure activities. The lack of significant differences from the ROH island analysis based on the two subpopulations suggested that the difference found from the population structure analyses is mainly due to ancestors' effects rather than different breeding purposes [46,67]. A further use of high-density SNP panels (600 K), with a 10-fold number of SNPs, or a different marker panel that is more appropriate for this breed could maybe allow identifying additional ROH, if present.…”

Genetic Diversity and Signatures of Selection in a Native Italian Horse Breed Based on SNP Data

“…Since directional artificial selection reduces genomic variability, ROH islands are thought to be potential signs of selection around a target locus [ 16 , 24 , 25 ]. Several recent examples of ROH and population structure analyses applied to European horse breeds show key aspects of history and selection pressure [ 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 ]. However, few studies were conducted in the framework of European small native horse breeds [ 29 , 31 , 32 , 34 ] and, to the best of our knowledge, none of them specifically analyzed Italian autochthonous horse breeds.…”

“…Several recent examples of ROH and population structure analyses applied to European horse breeds show key aspects of history and selection pressure [ 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 ]. However, few studies were conducted in the framework of European small native horse breeds [ 29 , 31 , 32 , 34 ] and, to the best of our knowledge, none of them specifically analyzed Italian autochthonous horse breeds. Therefore, based on a medium-density single nucleotide polymorphism (SNP) genotype panel, we aimed to investigate genomic diversity in the Bardigiano breed as an example of the reservoir of Italian native breeds.…”