Bos taurus-indicus hybridization correlates with intralocus sexual-conflicting effects of PRDM9 on male and female fertility in Holstein cattle. Conflicting effects of PRDM9 on male and female fertility in Holstein cattle

Initially, we analyzed the major BTA1 haplotypes present in Israeli Holsteins based on the 10 most telomeric SNPs of BovineSNP50 BeadChip. Sequencing of representative haplotype-carriers indicated that for all frequent haplotypes (> 2%) the PRDM9 variable ZF-array consisted of seven tandem ZnF-repeats. Two rare haplotypes (frequency < 4%) carried an indicine PRDM9, while all others were variants of the taurine type. These two haplotypes included the minor SNP allele, which was perfectly linked with a previously described PRDM9 allele known to induce unique localization of recombination hotspots. One of them had a significant (p = 0.03) negative effect on IL sire fertility. This haplotype combined the rare minor alleles of the only SNPs with significant (p < 0.05) negative substitution effects on US sire fertility (SCR). Analysis of telomeric SNPs indicated general agreement of allele frequencies (R = 0.95) and of the substitution effects on sire fertility (SCR, R = 0.6) between the US and IL samples. Surprisingly, the alleles that had the negative impact on male fertility had the most positive substitution effects on female fertility traits (DPR, CCR and HCR).