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.
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