Summary Overlapping runs of homozygosity (ROH islands) shared by the majority of a population are hypothesized to be the result of selection around a target locus. In this study we investigated the impact of selection for coat color within the Noriker horse on autozygosity and ROH patterns. We analyzed overlapping homozygous regions (ROH islands) for gene content in fragments shared by more than 50% of horses. Long‐term assortative mating of chestnut horses and the small effective population size of leopard spotted and tobiano horses resulted in higher mean genome‐wide ROH coverage ( S ROH ) within the range of 237.4–284.2 Mb, whereas for bay, black and roan horses, where rotation mating is commonly applied, lower autozygosity ( S ROH from 176.4–180.0 Mb) was determined. We identified seven common ROH islands considering all Noriker horses from our dataset. Specific islands were documented for chestnut, leopard spotted, roan and bay horses. The ROH islands contained, among others, genes associated with body size ( ZFAT , LASP1 and LCORL/NCAPG ), coat color ( MC1R in chestnut and the factor PATN1 in leopard spotted horses) and morphogenesis ( HOXB cluster in all color strains except leopard spotted horses). This study demonstrates that within a closed population sharing the same founders and ancestors, selection on a single phenotypic trait, in this case coat color, can result in genetic fragmentation affecting levels of autozygosity and distribution of ROH islands and enclosed gene content.

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Polycystic kidney disease (PKD) is an inherited autosomal kidney disease which is most commonly identified in Persian and Persian related cats. Positive cats have multiple cysts of various sizes that occur in the renal cortex and medulla and occasionally in other abdominal organs. PKD often leads to renal failure which occurs from mid to late in life. Renal cysts can be diagnosed ultrasonographically after 7 weeks of age by an experienced ultrasonographer and a high resolution machine. However, ultrasonography is now being replaced by genetic screening. A total of 340 cats of variable breeds aged from 5 months to 18 years were ultrasonographically examined in the past 7 years at the University Veterinary Small Animal Clinic. Of these, 13.8% were PKD positive with very high prevalence in Persian cats (36%). There was no sex predilection identified. The C>A transversion at position 3284 on exon 29 of PKD1 gene, resulting in a stop mutation has been identified in the heterozygous state in eight affected cats examined (Persian breed). All heterozygous cats were also ultrasonographically positive.

Intensive artificial and natural selection have shaped substantial variation among European horse breeds. Whereas most equine selection signature studies employ divergent genetic population structures in order to derive specific inter-breed targets of selection, we screened a total of 1476 horses originating from 12 breeds for the loss of genetic diversity by runs of homozygosity (ROH) utilizing a 670,000 single nucleotide polymorphism (SNP) genotyping array. Overlapping homozygous regions (ROH islands) indicating signatures of selection were identified by breed and similarities/dissimilarities between populations were evaluated. In the entire dataset, 180 ROH islands were identified, whilst 100 islands were breed specific, all other overlapped in 36 genomic regions with at least one ROH island of another breed. Furthermore, two ROH hot spots were determined at horse chromosome 3 (ECA3) and ECA11. Besides the confirmation of previously documented target genes involved in selection for coat color (MC1R, STX17, ASIP), body size (LCORL/NCAPG, ZFAT, LASP1, HMGA2), racing ability (PPARGC1A), behavioral traits (GRIN2B, NTM/OPCML) and gait patterns (DMRT3), several putative target genes related to embryonic morphogenesis (HOXB), energy metabolism (IGFBP-1, IGFBP-3), hair follicle morphogenesis (KRT25, KRT27, INTU) and autophagy (RALB) were highlighted. Furthermore, genes were pinpointed which might be involved in environmental adaptation of specific habitats (UVSSA, STXBP4, COX11, HLF, MMD).

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