Researchers have identified several good candidate genes for hoof health in a Mongolian horse breed named in recognition of its tough feet.
The candidates for the Baicha Iron Hoof horse include the CSPG4, PEAK1, EXPH5, WWP2 and HAS3 genes.
Haige Han, Imtiaz Randhawa and their fellow researchers said thousands of years of natural and artificial selection since the domestication of the horse has shaped the distinctive genomes of Chinese Mongolian horse populations.
Consequently, genomic signatures of selection can provide insights into the human-driven selection history of specific traits and evolutionary adaptations to diverse environments.
In their study, the researchers sought to identify genomic regions under selection for the population-specific traits of gait, black coat color, and hoof quality. Other global breeds were used to identify regional-specific signatures of selection.
In Wushen horses, the researchers identified the region on chromosome ECA23 harboring DMRT3, the major gene for gait.
The ability to pace has been selected in Wushen horses by local herdsmen since pacing improves the comfort of riding, particularly over long distances. In addition, Wushen horses are bred to race with a paced gait since this is a popular type of racing in Inner Mongolia.
Turning to the dark coat color of the Abaga Black horse, the study team said the genomic region containing the ASIP gene, presumed responsible for the coat color, on chromosome ECA22 was not immediately evident as a selection signature for coat color in the breed, when compared to other Mongolian horses.
However, by relaxing the threshold to include the top 1% of single nucleotide polymorphisms (SNPs), there was evidence for variation at the ECA22 location containing ASIP.
“The weaker-than-expected signal may be explained by the breeding history of this population. Although it is recorded that local herdsmen have favored black horses since the 13th century and it is common to see black horses in this geographic area, the Abaga Black has only been officially recognized as a distinct breed since 2006.
“Therefore the selection history may not be long enough to be captured by the initial stringent threshold criteria.”
It is also possible, they said, that there is a novel gene in this population contributing to the coat color seen in this population that may be different from the common black coat color observed in modern horse breeds.
The Baicha Iron Hoof horse is a mountain-type Chinese Mongolian horse, commonly known simply as the “Iron Hoof” for its strong, tough hooves.
To test the hypothesis that the “iron hoof” trait is underpinned by genes on which positive selection acts, the researchers looked for candidate genes for hoof health in this breed versus other Chinese Mongolian horses.
A total of 193 genes were identified. The highest-ranked candidate genes were on chromosome ECA1 and contained CSPG4, PEAK1, SEMA7A, CSK and PSTPIP1 (also known as CD2BP1).
The second-ranked region, on chromosome ECA7, flanked the EXPH5 gene. Furthermore, six candidate genes were identified on ECA3: WWP2, PSMD7, NQO1, NOB1, NFAT5 and HAS3. Additionally, they identified several genes associated with rheumatoid arthritis.
“The Baicha Iron Hoof is a critically endangered breed. The identification of genetic variants under selection in this population that distinguish them from other local populations emphasizes the need for efforts to protect and conserve ancient, heritage and landrace livestock with distinct microevolutionary histories,” the authors said.
In further work, an analysis of regional subgroups (Asian compared to European) identified a single location on chromosome ECA3 containing the ZFPM1 gene that is a marker of selection for the major domestication event leading to the globally widespread DOM2 horse clade.
“The signal of selection detected in Asian populations highlights the importance of inclusion of modern breeds in the interpretation of paleogenomic data for inference of population history.
“The coincidence of a selection peak among modern horse breeds at an evolutionarily critical locus, raises the question of whether DOM2 horses replaced all locally domesticated horses, or whether some other archaic lineages still survive, with their ancestors not yet identified.”
The study team comprised Haige Han and Manglai Dugarjaviin, with the Inner Mongolia Agricultural University; Imtiaz Randhawa, with the University of Queensland; David MacHugh, Lisa Katz and Emmeline Hill, with University College Dublin; and Beatrice A. McGivney, with Plusvital Ltd, also in Dublin.
Han, H., Randhawa, IAS, MacHugh, DE et al. Selection signatures for local and regional adaptation in Chinese Mongolian horse breeds reveal candidate genes for hoof health. BMC Genomics 24, 35 (2023). https://doi.org/10.1186/s12864-023-09116-8
The study, published under a Creative Commons Licensecan be read here.