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Gonadotropin-releasing hormone receptor ( GnRHR ) plays a critical physiological role in animal reproduction and is a potential marker for improving sperm quality. In the present study, eight SNPs (g.539T > C, g.640A > G, g.655T > C, g.707T > C, g.812A > G, g.18951A > T g.16867T > C and g.18953Indel GGCAAAGTAA) were detected in the GnRHR gene from one-hundred-sixty-five water buffalo by direct sequencing and identification of overlapping peaks. All SNPs were associated significantly with the ejaculate volume and two genes (g.655T > C and g.707T > C) were correlated with sperm abnormalities. Furthermore, three haplotypes (H1:TAI, H2:CT-, and H3:TT-) were identified by linkage disequilibrium analysis and were composed of four combined genotypes. Notably, buffalo with the combined genotypes H1H2 and H1H3 had the higher ejaculate volume compared to the other combined genotypes. Among the eight SNPs and four combined genotypes, the deletion of GGCAAAGTAA at position 18953 bp in GnRHR was associated significantly with a higher ejaculate volume. Moreover, the GGCAAAGTAA deletion may lead to the miR8661 binding failure and subsequent changes in GnRHR gene expression. In the present study, we demonstrate that there is a significant association between SNPs in the GnRHR gene and the sperm ejaculate volume of Chinese water buffalo. To the best of our knowledge, this study is the first to address the association between the SNPs in the GnRHR gene and the sperm quality of Chinese buffalo. [ABSTRACT FROM AUTHOR]