Genome-wide association study to identify chromosomal regions associated with antibody response to Mycobacterium avium subspecies paratuberculosis in milk of Dutch Holstein-Friesians
Hulzen, K.J.E. van; Schopen, G.C.B. ; Arendonk, J.A.M. van; Nielen, M. ; Koets, A.P. ; Schrooten, C. ; Heuven, H.C.M. - \ 2012
Journal of Dairy Science 95 (2012)5. - ISSN 0022-0302 - p. 2740 - 2748.
single nucleotide polymorphisms - estimated breeding values - quantitative trait loci - genetic-variation - johnes-disease - linkage disequilibrium - short-communication - us holsteins - infection - cattle
Heritability of susceptibility to Johne's disease in cattle has been shown to vary from 0.041 to 0.159. Although the presence of genetic variation involved in susceptibility to Johne's disease has been demonstrated, the understanding of genes contributing to the genetic variance is far from complete. The objective of this study was to contribute to further understanding of genetic variation involved in susceptibility to Johne's disease by identifying associated chromosomal regions using a genome-wide association approach. Log-transformed ELISA test results of 265,290 individual Holstein-Friesian cows from 3,927 herds from the Netherlands were analyzed to obtain sire estimated breeding values for Mycobacterium avium subspecies paratuberculosis (MAP)-specific antibody response in milk using a sire-maternal grandsire model with fixed effects for parity, year of birth, lactation stage, and herd; a covariate for milk yield on test day; and random effects for sire, maternal grandsire, and error. For 192 sires with estimated breeding values with a minimum reliability of 70%, single nucleotide polymorphism (SNP) typing was conducted by a multiple SNP analysis with a random polygenic effect fitting 37,869 SNP simultaneously. Five SNP associated with MAP-specific antibody response in milk were identified distributed over 4 chromosomal regions (chromosome 4, 15, 18, and 28). Thirteen putative SNP associated with MAP-specific antibody response in milk were identified distributed over 10 chromosomes (chromosome 4, 14, 16, 18, 19, 20, 21, 26, 27, and 29). This knowledge contributes to the current understanding of genetic variation involved in Johne's disease susceptibility and facilitates control of Johne's disease and improvement of health status by breeding.
Trends for monthly changes in days open in Holsteins
Pszczola, M.J. ; Aguilar, I. ; Misztal, I. - \ 2009
Journal of Dairy Science 92 (2009)9. - ISSN 0022-0302 - p. 4689 - 4696.
heat-stress - reproductive-performance - dairy-cattle - genetic-parameters - us holsteins - milk-yield - new-york - cows - herds - fertility
A reaction norm approach was used to estimate trends for days open (DO) with a model that indirectly accounted for heat stress. Data included 3.4 million first-parity records of DO of US Holsteins. A fixed effect model included herd-year, month of calving within region (MOC), age class, and regression on 305-d milk yield. An index calculated from the standardized solutions to MOC derived from the fixed effect model was treated as a proxy for an index on heat stress (SI). The lowest index for any region was set to zero. The highest index was 1.00 for the Southeast, 0.56 for the Northeast, 0.54 for the Midwest, 0.33 for the Northwest, and 0.42 for the Southwest. In all regions except the Northwest, the highest DO and the corresponding highest indices were in March-April. Compared with the fixed model, the reaction norm model also included the effect of an animal and a random regression on the SI; the 2 animal solutions are subsequently referred to as an intercept and a slope. Genetic trends were calculated for cows and sires separately. For cows, the trend for the intercept was - 0.1 d/yr, whereas the trend for the slope was 1 d/yr. For sires, the same trends were - 0.3 and 1.5, respectively. Official proofs were used to characterize the 100 top and 100 bottom bulls with at least 50 daughters for the intercept and the slope. Compared with the top bulls, the bottom bulls for the intercept gave 56 kg more milk and their type performance index was higher by 212 points. For the slope, the same numbers were - 435 kg and - 242 points, respectively. Trends for seasonal changes of days open are unfavorable.