Genomic characterization and population structure of Croatian Arabian horse

Abstract

The long history of Arabian horse breeding in Croatia spans several centuries and was strongly influenced by the breeding of Arabian horses in Bosnia and Herzegovina. Thus, the modern breeding of the Croatian Arabian horse is closely connected with the horse breeding of the Borike Stud, founded in 1895 in the mountainous region of Bosnia. Our main goal was to study the specifics of the Croatian Arabian horse (ARABCRO), the influence of the “Borike” breeding and the possible influence of other horse breeds. Therefore, we analyzed the population structure and admixture of the ARABCRO population (62 horses) together with 538 horses of Arabian and other origin (530 publicly available genotypes and 8 newly genotyped Shagya horses from Croatia) using high-throughput genomic data (GeneSeek® Genomic Profiler™ Equine SNP BeadChip 70 K). Our analyses (PCA, Neighbour Network, FST and STRUCTURE) revealed that ARABCRO is genetically closely related to the other Arabian horse breeds (populations) with an average FST of 0.09 whereas (the FST between ARABCRO and the Kladrub, Lipizzaner or Thoroughbred breeds, for example, is over 0.14) and thus can be considered a member of a large “Arabian horse metapopulation” (ARABMETA). At the same time, we have shown that ARABCRO is a distinct population with a specific position within ARABMETA, which can be quantified by genomic analyses. We also estimated the conservation status of ARABCRO, i.e., genomic inbreeding level (FROH) and effective population size (Ne) given the small census size of the breed (428 horses in 2021). Estimated genomic inbreeding levels were high (FROH>2Mb = 0.136, FROH>4Mb = 0.100), especially those estimated for recent inbreeding (FROH>8Mb = 0.071 and FROH>16Mb = 0.039), indicating intentional mating practices of very close relatives. The estimated effective population size was small, ranging from Ne = 47 to Ne = 67 (95% CI) and was significantly reduced from Ne = 500 (approximately) from 9 to 12 generations back (generation interval about 10 years). The obtained results will be used in further breeding of ARABCRO, especially with regard to the current conservation status, e.g. by controlled mating and “blood refreshment” with other Arabian horses.