[en] Baroque horses represent a distinctive group of breeds that emerged mainly between the 16th and 18th centuries, shaped by the demands of European royalty and their courts. Although recognised as separate breeds, they share common ancestry, breeding goals, and historical gene flow. This study aimed to evaluate their genomic diversity, population structure, and admixture patterns. We analysed 1 160 individuals from eight breeds - Lipizzan, Old Kladruby Horse, Pura Raza Española, Lusitano, Friesian, Criollo, Peruvian Paso, and Puerto Rican Paso Fino - using 34 026 single-nucleotide polymorphisms, with the Croatian Arab horse included as an outgroup. The Lipizzan was further divided into national subpopulations, the two Old Kladruby subpopulations defined by colour (black and grey), and within the Pura Raza Española, the Carthusian strain was treated as a distinct subpopulation. Observed genetic diversity, measured by heterozygosity and haplotype richness, was broadly comparable across breeds, although clear differences were observed between breeds with the lowest values (Friesian) and those with the highest values (Lusitano and Criollo). Genomic inbreeding coefficients, estimated using runs of homozygosity (FROH>2Mb) and homozygosity-by-descent segments (FHBD), ranged from ∼0.06 to ∼0.29 and ∼0.14 to ∼0.27, respectively. These values indicate relatively high levels of inbreeding, which may reflect the closed breeding structure of the populations and their relatively limited effective population sizes. In contrast, most individual inbreeding coefficient (FIS) values were negative, reflecting deliberate avoidance of close-relative matings. Estimates of contemporary effective population size (NeLD) ranged from ∼50 to ∼240 across breeds, depending on the method. Historical NeLD trajectories revealed two distinct demographic decline patterns: one occurring around 12 generations ago and the other around 22 generations ago. Evidence of recent between-breed gene flow was detected among Iberian breeds and between Croatian Arab and Lusitano, whereas shared historical ancestry among Baroque breeds was evident across populations. These results provide new insights into the genomic architecture of Baroque horses and offer valuable guidance for managing their genetic diversity.
Vostra-Vydrova, H; Czech University of Life Science Prague, Kamycka 129, 16500 Prague, Czech Republic
Moravcikova, N; Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovak Republic
Kasarda, R; Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovak Republic
Shihabi, M; University of Zagreb, Faculty of Agriculture, Svetošimunska cesta 25, 10000 Zagreb, Croatia
Druet, Tom ; Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Lège, Belgium
Halvonik, A; Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovak Republic
Hofmanova, B; Czech University of Life Science Prague, Kamycka 129, 16500 Prague, Czech Republic
Dovc, P; Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
Zorc, M; Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
Molina, A; Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
Demyda-Peyrás, S; Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
Valera, M; Departamento de Agronomía, ETSIA, Universidad de Sevilla, Sevilla, Spain
Kovács, M; Doctoral School of Animal Science, University of Debrecen, Böszörményi str 138, 4032 Debrecen, Hungary, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Böszörményi str 138, 4032 Debrecen, Hungary
Posta, J; Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Böszörményi str 138, 4032 Debrecen, Hungary
Rogić, B; Faculty of Agriculture, University of Banja Luka, Bulevar vojvode Petra Bojovica 1A, 78000 Banja Luka, Bosnia and Herzegovina
Cubric-Curik, V; University of Zagreb, Faculty of Agriculture, Svetošimunska cesta 25, 10000 Zagreb, Croatia
Vostry, L; Czech University of Life Science Prague, Kamycka 129, 16500 Prague, Czech Republic. Electronic address: vostry@af.czu.cz
Curik, I; University of Zagreb, Faculty of Agriculture, Svetošimunska cesta 25, 10000 Zagreb, Croatia, Institute of Animal Sciences, Hungarian University of Agriculture and Life Sciences (MATE), Guba S. str. 40, H-7400 Kaposvár, Hungary
SRDA - Slovak Research and Development Agency AEI - Agencia Estatal de Investigación Hungarian University of Agriculture and Life Sciences Czech Science Foundation Ministry of Education, Science, Research and Sport of the Slovak Republic HRZZ - Croatian Science Foundation
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