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Title:   Author  item
                                            Cole, Johnitem
                                            Null, Daniel
  Submitted to: Journal of Dairy Science
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 12/19/2012
                                    Publication  Date: 4/1/2013
                                    Citation: Cole, J.B., Null, D.J. 2013. Visualization of the transmission of direct genomic values for paternal and maternal chromosomes for 15 traits in US Brown Swiss, Holstein, and Jersey cattle. Journal of Dairy Science. 96(4):2713-2726.Interpretive Summary: In response to the recent availability of reliable haplotypes for most genotyped animals, and the interest in those data, an online query to display that information has been developed. Direct genomic values of paternal and maternal haplotypes are available for 171,420 Brown Swiss, Holstein, and Jersey bulls and cows that received genomic evaluations in April 2012. Query results are available to all users, and several options for controlling output are available. Challenges related to the application of haplotypes to mating decisions, such as independent assortment and crossing-over, are discussed, and some strategies for use are described.
                                Technical Abstract: Reliable haplotypes are available for 171,420 Brown Swiss, Holstein, and Jersey bulls and cows that received genomic evaluations in April 2012. Differences in least-squares means of direct genomic values (DGV) for paternal and maternal haplotypes of Bos taurus autosome (BTA) 1, 6, 14, and 18 for lifetime net merit (NM$) were significant in all but one case. Those chromosomes were chosen to represent cases with and without known QTL, and other chromosomes may differ as well. Paternal haplotypes had higher DGV than maternal haplotypes in most cases, and differences were larger when quantitative trait loci (QTL) were present. Longer chromosomes generally accounted for more variance than shorter chromosomes, and differences among breeds were consistent with known genes of large effect. For example, BTA 18 accounted for 2.5%, 7%, and 2.6% of the variance in NM$ for Brown Swiss (BS), Holsteins (HO), and Jerseys (JE), respectively. Distributions of the number of positive DGV inherited from sires and dams were negatively skewed in all breeds, and modes were slightly higher for paternally than maternally derived haplotypes in HO and BS (22 versus 20 and 22 versus 21, respectively), and slightly lower in BS (17 versus 19). Graphical representations of DGV are available to all users through a query on the Animal Improvement Programs Laboratory (ARS, USDA, Beltsville, MD) website, and strategies for the use of those data in selection programs, are being studied.


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