Eight breeds of horse, namely Hokkaido, Kiso, Noma, Taishu, Misaki, Tokara, Miyako, and Yonaguni horses, have currently been conserved as the Japanese native horse. Since to uncover their genetic properties involved in reproductive traits and hereditary disorders is important for their breeding and conservation programs, we investigated genotype distribution and allele frequencies of the genes associated with reproductive traits and hereditary disorders in the populations of the eight Japanese native horse breeds. We genotyped single nucleotide polymorphisms of FKBP6(g.11040315G>A and g.11040379C>A), CRISP3 (c.622G>A and c.716A>G), and PLCZ1 (g.45586821C>T) genes associated with stallion fertility including semen qualities and impaired acrosome reaction, and found that both desirable and undesirable alleles of FKBP6 and CRISP3 genes are present in the populations, while only undesirable allele of PLCZ1 was observed in these populations. We also genotyped single nucleotide polymorphisms of GYS1 (c.926G>A), RYR1 (c.7360C>G), and SCN4A (c.4248C>G) genes which are associated with polysaccharide storage myopathy, malignant hyperthermia, and hyperkalaemic periodic paralysis, respectively, and found that no mutant alleles responsible for these hereditary disorders are present in the populations of Japanese native horse breeds. These findings will be informative for future breeding and conservation programs for these horse breeds.

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In this study, we focused on the STARD3 gene which is involved in cholesterol distribution and homeostasis in cells, and investigated the effects of the STARD3 gene polymorphism on carcass traits and fatty acid composition. We searched for polymorphisms in the STARD3 gene by whole-genome resequencing and selected a missense S396L from 280 detected polymorphisms. We genotyped S396L polymorphism for Japanese Black cattle population (n = 441) and then analyzed the effects on carcass traits and fatty acid composition. As a result, the polymorphism showed strong association with fatty acid composition (C14:0, C16:0, C18:1, SFA and MUFA) (p<0.0001). Although further research is warranted to clarify whether S396L directly impacts fatty acid composition, it is obvious that there is a novel QTL for fatty acid composition on BTA19 in the Japanese Black cattle. In conclusion, these results contribute to the identification of a novel causative mutation on BTA19 for fatty acid composition and development of a useful DNA marker for improving the beef quality of Japanese Black cattle.

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