Estimation of inbreeding in Japanese Noma horses using genome-wide SNP genotyping

The Noma horse breed is the smallest among the eight native Japanese horse breeds. The population of Noma horses has been decreasing consistently, and they are listed as a critical breed; thus, conservation measures are urgently required. In this study, we estimated the pedigree-based inbreeding (FPED) and genomic inbreeding coefficients (FIS and FROH) of 24 Noma horses bred in Imabari City, Ehime Prefecture. We used 65 K equine SNP chip (GeneSeek/Neogen) data, and identified a total of 31,133 autosomal SNP genotypes after quality control steps. They were used to estimate the genomic inbreeding coefficient. We found that two full siblings had identical FPED (0.303) and different FIS (-0.157 and 0.077). When the mean FIS value was compared between this study (-0.098) and the previous study (Kakoi et al. 2007) (-0.130), this study had higher inbreeding values. A total of 815 ROH segments larger than 1 Mb were identified in 24 horses, and 78.7% of them were longer than 4 Mb, confirming recent inbreeding in this population. FROH (FROH–All, FROH1–2Mb, FROH2–4Mb, FROH4–8Mb, FROH8–16Mb, FROH> 16Mb) was calculated for different ROH lengths (all segments, 1–2, 2–4, 4–8, 8–16, and > 16 Mb, respectively). These estimates increased with increasing ROH length suggesting higher inbreeding in recent generations.