SNP array-based genomic inbreeding and relatedness analyses in an endangered Japanese equine breed, the Taishu horse

Taishu horses are an endangered Japanese breed facing challenges due to limited genetic diversity and insufficient profiling. In this study, we aimed to elucidate population genetics for this breed with a particular view to measures of inbreeding and relatedness that will support enhancement of the breed’s genetic diversity. We applied SNP-array techniques to assess inbreeding (runs of homozygosity [ROH], and F IS and F ROH indices) and relatedness (kinship, multi-dimensional scaling [MDS], and genetic relationship matrix [GRM]) in nearly all extant Taishu horses as of 2021 (n=48; age range: 1-27 years). Short ROH accounted for the majority of detected segments (22.75% of total ROH), while medium to very long ROH were present in all horses, indicating persistent, multi-generational inbreeding. Mean F IS and F ROH were -0.053 ± 0.098 and 0.194 ± 0.076, respectively. F IS and F ROH were broadly constant, irrespective of year of birth, which indicates a degree of success for the breeding program. Kinship, MDS, and GRM analyses identified close genetic relationships involving one horse of unknown pedigree and confirmed that all 48 individuals formed a single genetic cluster. This study establishes the inbreeding status of Taishu horses and demonstrates the utility of relatedness analyses, which could be used to evaluate suitable candidates for re-introduction into this population, and is of general interest to those involved in conservation efforts for other endangered equine breeds.