Horse breeds: selection, diversity, and differences among five Italian breeds

Selection changes populations; it does not create a single formula

Today’s horse breeds reflect a combination of natural selection and directed breeding. From the second half of the 19th century, studbooks and the modernization of breeding methods increased pressure to fix desired traits. Later, some programs directed selection toward ease of riding and athletic performance; in other populations, some of the former agricultural draught work gave way to meat production. These changes describe breeding trends, not a universal aptitude of every horse simply because it belongs to a particular breed.

Local populations may retain characteristics shaped by their environment and by limited human intervention. But when their uses and population sizes decline, genetic diversity and the number of breeding animals may also decrease.

Five local breeds under analysis

The study examined Bardigiano, Haflinger, Maremmano, Murgese, and Cavallo Agricolo Italiano da Tiro Pesante Rapido, known in English as the Italian Heavy Draught Horse. Initially, 1,620 animals were genotyped; after quality control, the analysis included 1,498 horses and 54,825 genetic markers distributed across the genome.

The researchers looked for runs of homozygosity—stretches in which the copies inherited from both parents are identical—and calculated a genomic inbreeding coefficient based on the proportion of autosomal markers covered by these runs. They also identified “islands” of homozygosity shared by at least 70% of the animals as possible signals of selection.

What they found and what it means

The coefficient based on runs of homozygosity ranged from 0.15 to 0.23. Bardigiano and Haflinger showed the highest values; Maremmano, Murgese, and Cavallo Agricolo Italiano da Tiro Pesante Rapido showed the lowest. The authors consider selective breeding a likely explanation for the higher values, but these results describe the populations and data analyzed: they do not allow the inbreeding level of an individual horse to be inferred from its breed.

The team detected 23 islands of homozygosity across the breeds, on 12 chromosomes. Most appeared in the three breeds classified by the study as cold-blooded, with a particular concentration on equine chromosome 3. The regions overlapped with 83 quantitative trait loci and 76 genes associated with morphology and health. This overlap identifies regions that warrant further study; by itself, it does not prove that a specific gene causes a trait or that all visible differences between breeds have an identified genetic explanation.

A limited finding

The figures apply to five local Italian breeds and the horses sampled for this study. They are neither a ranking of all the world’s breeds nor a direct comparison of temperament, appearance, or individual performance. The work offers indications about diversity and selection in these populations; it does not make breed labels guarantees of each animal’s characteristics.