Genetic diversity and signatures of selection in Icelandic horses and Exmoor ponies

Abstract Background The Icelandic horse and Exmoor pony are ancient, native breeds, adapted to harsh environmental conditions and they have both undergone severe historic bottlenecks. However, in modern days, the selection pressures on these breeds differ substantially. The aim of this study was to assess genetic diversity in both breeds through expected (H E ) and observed heterozygosity (H O ) and effective population size (Ne). Furthermore, we aimed to identify runs of homozygosity (ROH) to estimate and compare genomic inbreeding and signatures of selection in the breeds. Results H O was estimated at 0.34 and 0.33 in the Icelandic horse and Exmoor pony, respectively, aligning closely with H E of 0.34 for both breeds. Based on genomic data, the Ne for the last generation was calculated to be 125 individuals for Icelandic horses and 42 for Exmoor ponies. Genomic inbreeding coefficient (F ROH ) ranged from 0.08 to 0.20 for the Icelandic horse and 0.12 to 0.27 for the Exmoor pony, with the majority of inbreeding attributed to short ROHs in both breeds. Several ROH islands associated with performance were identified in the Icelandic horse, featuring target genes such as DMRT3 , DOCK8 , EDNRB , SLAIN1 , and NEURL1 . Shared ROH islands between both breeds were linked to metabolic processes ( FOXO1 ), body size, and the immune system ( CYRIB ), while private ROH islands in Exmoor ponies were associated with coat colours ( ASIP , TBX3 , OCA2 ), immune system ( LYG1 , LYG2 ), and fertility ( TEX14 , SPO11 , ADAM20 ). Conclusions Evaluations of genetic diversity and inbreeding reveal insights into the evolutionary trajectories of both breeds, highlighting the consequences of population bottlenecks. While the genetic diversity in the Icelandic horse is acceptable, a critically low genetic diversity was estimated for the Exmoor pony, which requires further validation. Identified signatures of selection highlight the differences in the use of the two breeds as well as their adaptive trait similarities. The results provide insight into genomic regions under selection pressure in a gaited performance horse breed and various adaptive traits in small-sized native horse breeds. This understanding contributes to preserving genetic diversity and population health in these equine populations.