Submitted to: Animal Genetics International Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: June 20, 2008
Publication Date: N/A
Selection in Holstein cattle has achieved tremendous phenotypic changes over the past 40 years. However, it is unknown how selection has changed the Holstein genome and how those genome signatures of selection are associated with the phenotypic changes. To categorize genome regions either affected or unaffected by selection, we contrasted genome structure data between 148 contemporary Holsteins and 151 cows from an unselected line of Holsteins bred and maintained at the University of Minnesota since 1964. Marker genotypes from 46,231 SNP were analyzed for allele frequency differences and trait associations using Wright’s Fst test and EPISNPmpi, respectively. Comparison of the most significant marker effects with Fst results revealed strong signatures of selection for production traits on chromosomes 1, 2, 3, 7, 8, 11, and 26. Chr 26 also had significant associations (16 markers; p<1.0E-12) with udder traits that co-localize with strong signatures of selection. Of the 31 SNPs with the most significant effects on both milk and daughter pregnancy rate, 29 had opposite effects on these traits providing strong evidence for the antagonistic effect of selection for production on fertility. These findings identify where selection has affected the genome and assist in searching for genes of large effect.