Studies involving the effects of single genes on quantitative traits may involve closed populations, selection may be practiced, and the quantitative trait of concern may also be influenced by background genes that are inherited in a polygenic manner. It is shown analytically that analysis of such data by ordinary least squares, the usual method of analysis, can lead to finding an excess of spurious significant effects of single genes, when no effect exists, for both randomly and directionally selected populations and can lead to bias in estimates of single-gene effects when selection has been practiced. The bias depends on heritability of the polygenic effects on the trait, selection intensity, mode of inheritance, magnitude of gene effect, gene frequency, and data structure. It is argued that when genotypes of individuals can be identified for all individuals with observations on the trait, use of mixed-model procedures under an animal model treating single-gene effects as fixed effects can provide unbiased estimates of single-gene effects and exact tests of associated hypotheses for pedigreed populations, even when selection is practiced. Results are illustrated through computer simulation.

SUMMARYMale progeny from two commercial sire strains, were fed on a high energy or low energy diet and kept at an environmental temperature of 23 C or 13°C after day 22 to day 57. In the cold 42.4% of strain A and 29.6% of strain B died from right ventricular failure (RVF) and ascites secondary to pulmonary hypertension (PH) prior to day 57. Of the birds surviving to day 57, 9.4% (strain A) and 6.4% (strain B) had RVF and ascites. In the warm, 17.3% (A) and 7.4% (B) died from RVF and ascites before day 57 and 4.6% and 3.2%, respectively had ascites at day 57. Chickens on the high energy diet were significantly heavier at day 56 than those on the low energy diet, particularly those kept in the cold. However, chickens on the latter diet had better weight gain between days 42 and 56, again more marked in cold conditions. The higher metabolic rate elicited by cold would increase oxygen consumption and blood flow in these broilers which, because of their rapid growth, already had a high metabolic rate. The cause of PH was probably insufficient pulmonary vascular capillary capacity for the blood flow necessary to meet their metabolic oxygen requirement.

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Animal geneticists predict higher genetic responses to selection by increasing the accuracy of selection using BLUP with information on relatives. Comparison of different selection methods is usually made with the same total number tested and with the same number of parents and mating structure so as to give some acceptable (low) level of inbreeding. Use of family information by BLUP results in the individuals selected being more closely related, and the levels of inbreeding are increased, thereby breaking the original restriction on inbreeding. An alternative is to compare methods at the same level of inbreeding. This would allow more intense selection (fewer males selected) with the less accurate methods. Stochastic simulation shows that, at the same level of inbreeding, differences between the methods are much smaller than if inbreeding is unrestricted. If low to moderate inbreeding levels are targeted, as in a closed line of limited size, then selection on phenotype can yield higher genetic responses than selection on BLUP. Extra responses by BLUP are at the expense of extra inbreeding. The results derived here show that selection on BLUP of breeding values may not be optimal in all cases. Thus, current theory and teaching on selection methods are queried. Revision of the methodology and a reappraisal of the optimization results of selection theory are required.

The objective of this study was to use previously calculated estimated breeding values for cell- (CMIR) and antibody-mediated immune responses (AMIR) to determine associations between immune response (IR) and economically important diseases of dairy cattle. In total, 699 Holsteins were classified as high, average, or low for CMIR, AMIR, and overall IR (combined CMIR and AMIR), and associations with mastitis, metritis, ketosis, displaced abomasums, and retained fetal membranes were determined. The incidence of mastitis was higher among average cows as compared with cows classified as high AMIR [odds ratio (OR)=2.5], high CMIR (OR=1.8), or high IR (OR=1.8). Low-CMIR cows had a higher incidence of metritis (OR=11.3) and low-IR cows had a higher incidence of displaced abomasum (OR=4.1) and retained fetal membrane (OR=2.8) than did average responders. Results of this study show that cows classified as high immune responders have lower occurrence of disease, suggesting that breeding cattle for enhanced IR may be a feasible approach to decrease the incidence of infectious and metabolic diseases in the dairy industry.

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