No abstract

The horse is central to many Indigenous cultures across the American Southwest and the Great Plains. However, when and how horses were first integrated into Indigenous lifeways remain contentious, with extant models derived largely from colonial records. We conducted an interdisciplinary study of an assemblage of historic archaeological horse remains, integrating genomic, isotopic, radiocarbon, and paleopathological evidence. Archaeological and modern North American horses show strong Iberian genetic affinities, with later influx from British sources, but no Viking proximity. Horses rapidly spread from the south into the northern Rockies and central plains by the first half of the 17th century CE, likely through Indigenous exchange networks. They were deeply integrated into Indigenous societies before the arrival of 18th-century European observers, as reflected in herd management, ceremonial practices, and culture.

Summary The American Paint Horse Association (APHA) records pedigree and performance information for their breed, a stock‐type horse valued as a working farm or ranch horse and as a pleasure horse. As the name implies, the breed is also valued for its attractive white‐spotting patterns on the coat. The APHA utilizes visual inspections of photographs to determine if coat spotting exceeds threshold anatomical landmarks considered characteristic of desirable patterns. Horses with sufficient white patterning enter the ‘Regular’ registry, rather than the ‘Solid Paint‐Bred’ division, providing a threshold modeled phenotype. Genetic studies previously defined sequence variants corresponding to 35 alleles for white spotting in the horse. Here, we calculate the allele frequencies for nine common white‐spotting alleles in the American Paint Horse using a sample of 1054 registered animals. The APHA spotting phenotype is altered by additive interactions among spotting loci, and epistatically by the MC1R and ASIP genes controlling pigment production. The W20 allele within the KIT gene, independent of other known spotting alleles, was strongly associated with the APHA‐defined white‐spotting phenotype (P = 1.86 × 10−18), refuting reports that W20 acts only as a modifier of other underlying white‐spotting patterns. The parentage of an individual horse, either American Paint or American Quarter Horse, did not alter the likelihood of its entering the APHA Regular Registry. An empirical definition of the action of these genetic loci on the APHA‐defined white‐spotting phenotype will allow more accurate application of genome‐assisted selection for improving color production and the marketability of APHA horses.

Equine recurrent laryngeal neuropathy (RLN) is a bilateral mononeuropathy with an unknown etiology. In Thoroughbreds (TB), we previously demonstrated that the haplotype association for height (LCORL/NCAPG locus on ECA3, which affects body size) and RLN was coincident. In the present study, we performed a genome-wide association scan (GWAS) for RLN in 458 American Belgian Draft Horses, a breed fixed for the LCORL/NCAPG risk alelle. In this breed, RLN risk is associated with sexually dimorphic differences in height, and we identified a novel locus contributing to height in a sex-specific manner: MYPN (ECA1). Yet this specific locus contributes little to RLN risk, suggesting that other growth traits correlated to height may underlie the correlation to this disease. Controlling for height, we identified a locus on ECA15 contributing to RLN risk specifically in males. These results suggest that loci with sex-specific gene expression play an important role in altering growth traits impacting RLN etiology, but not necessarily adult height. These newly identified genes are promising targets for novel preventative and treatment strategies.

The American Paint Horse Association (APHA) officially records pedigree and performance information for their breed; these registered stock-type horses are valued for utility in work on the farm and ranch and as pleasure horses. As the name of the breed implies, the breed is also valued for attractive white spotting patterns on the coat. Current APHA procedures utilize visual inspections of photographs to determine if white spotting phenotypes exceed threshold anatomical landmarks considered by the association as characteristic of desirable patterns. Horses with sufficient white patterning enter the "Regular" registry, rather than the "Solid Paint-Bred" division. Genetic studies have now defined causative sequence variants for 35 alleles likely contributing to white spotting phenotypes in the horse. Here, the allele frequency was calculated for nine white spotting alleles commonly found in the American Paint horse breed using a sample of 1,065 APHA registered animals. Epistatic interactions were documented among five spotting loci, and with the MC1R and ASIP genes controlling black and red pigment production. The W20 allele within the KIT gene, in the absence of other spotting loci, was strongly associated with the APHA-defined white spotting phenotype (p = 1.86 x10 -18 ), refuting advertisements reporting that W20 acts only as a modifier of other white spotting patterns. An empirical definition of the action of these loci on the desired APHAdefined white spotting phenotype will allow for a more accurate application of genome-assisted selection in this breed, providing breeders with a powerful tool to increase the marketability of their horses.