Use of single nucleotide polymorphisms in candidate genes associated with daughter pregnancy rate for prediction of genetic merit for reproduction in Holstein cows

Summary We evaluated 69 SNP s in genes previously related to fertility and production traits for their relationship to daughter pregnancy rate ( DPR ), cow conception rate ( CCR ) and heifer conception rate ( HCR ) in a separate population of Holstein cows grouped according to their predicted transmitting ability (PTA) [≤−1 ( n  =   1287) and ≥1.5 ( n  =   1036)] for DPR . Genotyping was performed using Sequenom Mass ARRAY ® . There were a total of 39 SNP s associated with the three fertility traits. The SNP s that explained the greater proportion of the genetic variation for DPR were COQ 9 (3.2%), EPAS 1 (1.0%), CAST (1.0%), C7H19orf60 (1.0%) and MRPL 48 (1.0%); for CCR were GOLGA 4 (2.4%), COQ 9 (1.8%), EPAS 1 (1.1%) and MRPL 48 (0.8%); and for HCR were HSD 17B7 (1.0%), AP 3B1 (0.8%), HSD 17B12 (0.7%) and CACNA 1D (0.6%). Inclusion of 39 SNP s previously associated with DPR in the genetic evaluation system increased the reliability of PTA for DPR by 0.20%. Many of the genes represented by SNP s associated with fertility are involved in steroidogenesis or are regulated by steroids. A large proportion of SNP s previously associated with genetic merit for fertility in Holstein bulls maintained their association in a separate population of cows. The inclusion of these genes in genetic evaluation can improve reliabilities of genomic estimates for fertility.