Identification of SNP associated with fertility trait using pool-based genome-wide association study in Japanese Black cattle

Female fertility, a fundamental trait required for animal reproduction, has gradually declined in Japanese Black cattle. The objective of this study was to identify genomic regions associated with female fertility traits in Japanese Black cattle. We performed a DNA pool-based genome-wide association study (GWAS) to estimate the associations between genotypes and 3 fertility traits (age at first calving, calving interval, number of calves produced at 4 yr of age), using Illumina BovineSNP50 Beadchip v2. In the GWAS analyses, 100 animals with the highest and 100 animals with the lowest values in each trait were selected from 3,973 animals, based on pedigree and phenotypic information, and then pooled as the high and low groups, respectively. The GWAS revealed that 1 SNP on BTA 5 was associated with age at first calving and 2 SNPs on BTA 12 and 20 were associated with calving interval at 5% significance level. To confirm the significant differences of allele frequencies between high and low groups in each SNP, we individually genotyped the SNPs for high and low groups. The statistical analysis revealed that there were significant differences (P < 0.05) in each SNP. In the present study, we performed further analysis, using 1 of 3 SNPs (Hapmap53957-rs29016480 on BTA12). To evaluate the effect of the SNP, we genotyped the SNP using 516 animals randomly selected from 3,596 animals and investigated the association with calving interval by analysis of variance. As a result, this SNP showed significant effects on calving interval (P = 0.0118). In addition, Tukey-Kramer HSD test revealed significant differences between AA (n = 212) and GG (n = 52) genotypes (p < 0.05), and the animals with GG type had 24.07 d shorter calving interval than the animals with AA type. Thus, the result suggests that this SNP could be used as a marker to select Japanese Black cattle with superior calving interval.