Wagyu cattle have seen an upsurge in popularity within the United States in recent years, as consumers seek improved meat quality and intramuscular fat, also known as marbling. The small effective population size of Wagyu cattle, paired with the growing interest in the breed, has led to increased inbreeding. As inbreeding has increased, the emergence of deleterious traits (i.e. progressive bovine myeloenecphaly, factor XI deficiency, and spherocytosis) has increased. Cryptorchidism, when one or both testes fail to descend into the scrotum, can lead to reduced fertility and is observed more frequently in certain cattle lines suggesting a genetic component to the disorder. This study hypothesized that cryptorchidism is recessively inherited. To test this hypothesis, a population of 18 Wagyu cattle from an extended family were genotyped, and a haplotype and genome-wide association analysis were completed to identify genomic regions associated with cryptorchidism. There were 218 haplotypes that trended towards an association (P < 0.05) though none were significant after multiple testing corrections were applied (False Discovery Rate (FDR) < 0.05). Two loci were associated (P < 1 x 10-5) with cryptorchidism on BTA4 and BTA13 in a dominant inheritance model and one locus on BTA4 was associated in an additive model. While this study identified loci associated with cryptorchidism in cattle, due to the small sample size, additional animals need to be evaluated to identify and validate the genomic regions associated with cryptorchidism.
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