Resampling-based inferences for compositional regression with application to beef cattle microbiomes.

Gut microbiomes are increasingly found to be associated with many health-related characteristics of humans as well as animals. Regression with compositional microbiomes covariates is commonly used to identify important bacterial taxa that are related to various phenotype responses. Often the dimension of microbiome taxa easily exceeds the number of available samples, which creates a serious challenge in the estimation and inference of the model. The sparse log-contrast regression method is useful for such cases as it can yield a model estimate that depends on only a small number of taxa. However, a formal statistical inference procedure for individual regression coefficients has not been properly established yet. We propose a new estimation and inference procedure for linear regression models with extremely low-sample-sized compositional predictors. Under the compositional log-contrast regression framework, the proposed approach consists of two steps. The first step is to screen relevant predictors by fitting a log-contrast model with a sparse penalty. The screened-in variables are used as predictors in the non-sparse log-contrast model in the second step, where each of the regression coefficients is tested using nonparametric, resampling-based methods such as permutation and bootstrap. The performances of the proposed methods are evaluated by a simulation study, which shows they outperform traditional approaches based on normal assumptions or large sample asymptotics. Application to steer microbiome data successfully identifies key bacterial taxa that are related to important cattle quality measures.

Thrombin as a Potential Proxy to Select for Horn Fly Abundance in Beef Cattle.

Horn flies are a major nuisance to cattle and induce significant economic losses. Fly abundance varies within and across breeds and genetic analyses have shown sufficient genetic variation to permit selection. A major bottleneck for selecting against horn fly abundance is the complexity of measuring fly attraction phenotypes. Easy-to-measure proxy phenotypes could be an attractive option to indirectly estimate fly abundance. In the current study, thrombin was investigated as a potential proxy to assess fly abundance. Fly counts and blood samples were collected on 355 cows. Pearson correlation between subjective fly count and thrombin was -0.13, indicating a decrease in fly abundance with the increase in thrombin concentration. When thrombin was discretized into three classes, there was a 22% difference in fly count between the top and bottom classes. Heritability estimates of thrombin were 0.38 and 0.39 using linear and threshold models, respectively. The correlation between estimated thrombin breeding values and fly count was around -0.18. There was a noticeably lower density of high fly counts among animals with high breeding values for thrombin. These results indicate that thrombin could be used in combination with other biological factors to estimate fly abundance and as a proxy for selection against fly abundance.

Influence of growth rate on occurrences of pale muscle in broilers.

BACKGROUND: Pale broiler breast meat is a defect in commercial production operations. The incidence of pale broiler breast meat was examined in two commercial processing plants which had average growth rates of 59 g day(-1) and 46 g day(-1) and final average weights of 3.36 kg and 1.93 kg. Color measurements of dorsal and ventral surfaces and pH were completed to evaluate the impact of selection for growth on meat water-holding capacity. RESULTS: L* greater than 60 were observed in 57% of broilers selected for greater yield and 26% of slower growing broilers. Average L* between 10 growers was significantly different (P = 0.001). Pearson's correlation coefficients for pH and L* were - 0.51 and - 0.27 for the faster growing broilers and slower growing broilers, respectively. The Pearson correlation coefficients between water-holding capacity and L* and pH was - 0.35 and 0.42, respectively. There was a higher correlation between production factors (age, weight and grower) and a* and b* than L* for ventral surface measurements. CONCLUSION: Breasts from broilers selected for faster growth tend to have lighter color. Weak correlation with water-holding capacity suggests that quality remains the same and light color is probably related to other factors.