Genome Wide Association Analysis and Fine Mapping for Cystic Ovaries, Metritis and Retained Placenta in Canadian Holsteins

Genomic technologies could help in gaining insights into the genetics basis of cystic ovaries (CO), metritis (ME), and retained placenta (RP) which cause reduction in milk production and pregnancy rate, and are a substantial risk factor for culling in dairy cattle. The objectives of this study were to identify target QTL regions for CO, ME and RP, carry out fine mapping of these regions, and run an in-silico search for positional and functional candidate genes in Holstein cattle. The association analyses were performed using a generalized quasi-likelihood score test, using the autosomal SNPs from Illumina Bovine HD BeadChip, and 2219, 2260 and 2788 animals with breeding values for CO, ME and RP, respectively. A false discovery rate of 5% at chromosome-wise level identified 469, 1001, and 945 SNPs associated with CO, ME, and RP, respectively. Most of the significant SNPs were on chromosome 17, 20 and 21 for CO (62%), 8, 12 and 20 for ME (81%), and 23, 29 and 8 for RP (61%). A total of 712 genes either hold or were nearby (10kbp) the significant SNPs. The in-silico functional analysis suggested 172 biological processes and 75 pathways, which included oocyte meiosis and GnRH signaling pathway. The identified significant SNPs will be validated and their ability to predict the genetic merit for CO, ME, and RP in Holstein cattle will be assessed.