Submitted to: Journal of Dairy Science
Publication Type: Peer reviewed journal
Publication Acceptance Date: 8/1/2013
Publication Date: 8/1/2013
Citation: Weller, J.I., Van Raden, P.M., Wiggans, G.R. 2013. Application of a posteriori granddaughter and modified granddaughter designs to determine Holstein haplotype effects. Journal of Dairy Science. 96(8)5376-5387. Interpretive Summary: A posteriori and modified granddaughter designs were applied to determine haplotype effects of genotyped Holstein bulls and cows. Of 33 traits analyzed with the a posteriori granddaughter design, the within-family haplotype effect was important for all but 2 traits. Of 21 traits analyzed with the modified granddaughter design, the within-family haplotype effect was important for 8 traits. These results and further DNA sequencing of the sires may allow breeders to select directly on causative mutations instead of indirectly using genetic markers.
Technical Abstract: A posteriori and modified granddaughter designs were applied to determine haplotype effects for Holstein bulls and cows with BovineSNP50 genotypes. The a posteriori granddaughter design was applied to 52 sire families, each with '100 genotyped sons with genetic evaluations based on progeny tests. For 33 traits (milk, fat, and protein yields; fat and protein percentages; somatic cell score; productive life; daughter pregnancy rate; heifer and cow conception rates; service-sire and daughter calving ease; service-sire and daughter stillbirth; 18 conformation traits; and net merit), the analysis was applied to the autosomal segment with the single nucleotide polymorphism (SNP) with the greatest effect in the genomic evaluation of each trait. All traits except 2 had a within-family haplotype effect. The same design was applied with the genetic evaluations of sons corrected for SNP effects associated with chromosomes besides the one under analysis. Number of within-family contrasts was 166 without adjustment and 211 with adjustment. Of the 52 bulls analyzed, 36 had BovineHD genotypes that were used to test for concordance between sire quantitative trait loci and SNP genotypes; complete concordance was not obtained for any effects. Of the 31 traits with effects from the a posteriori granddaughter design, 21 were analyzed with the modified granddaughter design. Only sires with a contrast for the a posteriori granddaughter design and >=200 granddaughters with a record usable for genetic evaluation were included. Calving traits could not be analyzed because individual cow evaluations were not computed. Eight traits had within-family haplotype effects. With respect to milk and fat yields and fat percentage, the results on BTA 14 corresponded to the hypothesis that a missense mutation in DGAT1 is the main causative mutation, although other polymorphisms in that gene also modify fat yield and percentage. The positive allele for protein concentration was less frequent, which indicated that selection on that locus could be effective. Although the results can be used to determine causative mutations for most of the analyzed traits, complete DNA sequencing probably will be needed for of most of the analyzed sires.