Identification of Genomic Signatures of Selection Associated with Cranial Morphology and Conformation in Arabian Horses

The most identifiable feature of Arabian horses is their finely chiseled head. Moreover, some individuals have 5 lumbar vertebrae instead of 6, and 17 pairs of ribs instead of the usual 18. Because of that, Arabians have a shorter back and a more horizontal pelvis, which increases their capacity to carry weight and contributes to their unique pattern of locomotion.

The objectives of this study were to 1) identify genomic regions undergoing selection in Arabians; 2) investigate haplotype structure and ancestry within the breed; 3) identify candidate genes for cranial and body morphology. For that, 36 Arabians were genotyped at 2 million SNP markers across the genome. Regions harboring signatures of selection were identified using EHH and two F_ST-based statistics (di and hapFLK); local haplotype sharing among individuals was calculated with hapQTL.

A total of 361 genes were retrieved within signatures of selection from 28 autosomes using BioMart. Candidate genes were prioritized using Endeavour-GW and functional and enrichment analyses were performed using DAVID and FunRich3. A statistical overrepresentation of genes present in pathways involved in skull and spinal cord development (such as Wnt and Notch pathways) was detected. Genes associated with cellular migration and development of osseous tissue were also identified. Examples include ATF2, ALX1, and NKD1.

WGS data from 14 Arabians will be used for the annotation of biologically relevant alleles within these candidate genes and to investigate their association with the Arabian’s distinctive cranial morphology and body conformation.