PSXII-1 - Genetic regions associated with cryptorchidism in related wagyu cattle

Abstract: Wagyu cattle have gained popularity in recent years due to their high levels of intramuscular marbling and their calving ease in crossbred cattle. The small effective population size of Wagyu cattle outside of Japan has led to inbreeding and an increased presentation of autosomal recessive traits. Cryptorchidism, the absence of at least one testicle from the scrotum, is the most common genital defect in males and is seen more commonly in inbred populations suggesting an autosomal recessive inheritance. The objective of this study was to identify genetic regions associated with unilateral cryptorchidism in related Wagyu cattle. All individuals in the study shared a common cow ancestor in their pedigree. Fourteen individuals, three cases and eleven controls, were genotyped using the Illumina BovineHD BeadChip (San Diego, CA). There were 450,083 SNPs that remained for the haplotype analysis after SNPs were removed for quality control parameters of genotyping call rate ( < 90%), minor allele frequency ( < 1%) and failure to meet Hardy Weinberg equilibrium testing (p < 1 x 10^-5). No animals were removed due to low call rate ( < 90%). Haplotypes were detected within the SNP and Variation Suite v8.2 (Golden Helix, Bozeman, MT) for an association with cryptorchidism using a chi-square test (p < 0.05) and false discovery rate (FDR < 0.05). There were 107,439 different SNP haplotype combinations among 49,627 haplotypes identified in the Wagyu cattle. The average haplotype size was 21.7 kb in Wagyu cattle. Prior to multiple testing correction, 1,233 haplotypes were associated (p < 0.05), with 6 haplotypes on BTA7 (p = 0.001 to p = 0.002) being of particular interest as the SNPs for those haplotypes were identical and homozygous, whereas none of the controls were homozygous for the SNPs. The SNP haplotype pattern observed on BTA7 was consistent with an autosomal recessive trait. When applying multiple testing corrections (FDR < 0.05), none of the haplotypes were significant. Additional unilateral cryptorchid bulls that share the same common cow ancestor have been identified and will be tested to see if the haplotypes on BTA7 are segregating with the phenotype. Identifying genetic regions associated with cryptorchidism will allow the identification of carriers for this trait that can then be used for choosing mates that are not carrying this trait. Reducing the number of cryptorchid males in a breed with a small effective population size would allow breeders to utilize the genetics of carriers without increasing the frequency of cryptorchidism.