Population Networks Associated with Runs of Homozygosity Reveal New Insights into the Breeding History of the Haflinger Horse

Abstract

Within the scope of current genetic diversity analyses, population structure and homozygosity measures are independently analyzed and interpreted. To enhance analytical power, we combined the visualization of recently described high-resolution population networks with runs of homozygosity (ROH). In this study, we demonstrate that this approach enabled us to reveal important aspects of the breeding history of the Haflinger horse. We collected high-density genotype information of 531 horses originating from 7 populations which were involved in the formation of the Haflinger, namely 32 Italian Haflingers, 78 Austrian Haflingers, 190 Noriker, 23 Bosnian Mountain Horses, 20 Gidran, 33 Shagya Arabians, and 155 Purebred Arabians. Model-based cluster analysis identified substructures within Purebred Arabian, Haflinger, and Noriker that reflected distinct genealogy (Purebred Arabian), geographic origin (Haflinger), and coat color patterns (Noriker). Analysis of ROH revealed that the 2 Arabian populations (Purebred and Shagya Arabians), Gidran and the Bosnian Mountain Horse had the highest genome proportion covered by ROH segments (306-397 Mb). The Noriker and the Austrian Haflinger showed the lowest ROH coverage (228, 282 Mb). Our combined visualization approach made it feasible to clearly identify outbred (admixture) and inbred (ROH segments) horses. Genomic inbreeding coefficients (FROH) ranged from 10.1% (Noriker) to 17.7% (Purebred Arabian). Finally it could be demonstrated, that the Austrian Haflinger sample has a lack of longer ROH segments and a deviating ROH spectrum, which is associated with past bottleneck events and the recent mating strategy favoring out-crosses within the breed.

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

“…The ROHs detected in this study covered 13.17% (295.29 Mb) of the autosomal genome expressed by the SNP loci. The total genome length covered by ROHs is comparable with study of Grilz-Seger et al (2018) and Druml et al (2018) that showed across various breeds the overall genomewide ROH coverage at level 305.1 Mb. But, the study of Grilz-Seger et al (2019a) revealed by use of 700k genotyping array that the genome ROH coverage in Noriker horse depending on the colour variety resulting from different mating strategies.…”

Level of Inbreeding in Norik of Muran Horse: Pedigree vs. Genomic Data

“…Obtained proportion of ROHs across the genome of Norik of Muran horse is comparable to other local horse breeds, e.g. Austrian Noriker (Grilz-Seger et al, 2019), Bosnian mountain and Haflinger horses (Druml et al, 2018;Grilz-Seger et al, 2018) or Polish Konik horse (Kamiński et al, 2017). Compared to pedigree analysis, the genomic inbreeding showed the same trend (Fig.…”

Analysis of ROH patterns in the Noriker horse breed reveals signatures of selection for coat color and body size

“…Previous studies based upon pedigree and genome‐wide SNP data also illustrated genetic fragmentation of the Noriker population into different coat color strains (Druml et al . , ).…”

“…To visualize the population structure of Noriker horses with respect to the different coat color strains, we performed a high‐resolution network analysis based upon an identical‐by‐state‐derived relationship matrix (G), following the description by Druml et al . (). Briefly, we computed genetic distances by subtracting pairwise relationships from 1 and applied the NetView approach in its default setting (number of k nearest neighbors k ‐NN = 10) (Neuditschko et al .…”

“…These pedigree‐based results were additionally confirmed by a genome‐wide population structure analysis (Druml et al . ). A morphological study of 497 Noriker horses using 31 different body measurements also revealed anatomical differences between the coat color strains (Druml et al .…”