Model averaging for genome‐enabled prediction with reproducing kernel Hilbert spaces: a case study with pig litter size and wheat yield

Predictive ability of yet‐to‐be observed litter size (pig) grain yield (wheat) records of several reproducing kernel Hilbert spaces (RKHS) regression models combining different number of Gaussian or t kernels was evaluated. Predictive performance was assessed as the average (over 50 replicates) predictive correlation in the testing set. Predictions from these models were combined using three different types of model averaging: (i) mean of predicted phenotypes obtained in each model, (ii) weighted average using mean squared error as weight or (iii) using the marginal likelihood as weight. (ii) and (iii) were obtained in a validation set with 5% of the data. Phenotypes consisted of 2598, 1604 and 1879 average litter size records from three commercial pig lines and wheat grain yield of 599 lines evaluated in four macro‐environments. SNPs from the PorcineSNP60 BeadChip and 1447 DArT markers were used as predictors for the pig and wheat data analyses, respectively. Gaussian and univariate t kernels led to same predictive performance. Multikernel RKHS regression models overcame shortcomings of single kernel models (increasing the predictive correlation of RKHS models by 0.05 where 3 Gaussian or t kernels were fitted in the RKHS models simultaneously). None of the proposed averaging strategies improved the predictive correlations attained with single models using multiple kernel fitting.     

Estimates of genetic correlations between days to calving and reproductive and weight traits in Nelore cattle

Data comprising 53,181 calving records were analyzed to estimate the genetic correlation between days to calving (DC), and days to first calving (DFC), and the following traits: scrotal circumference (SC), age at first calving (AFC), and weight adjusted for 550 d of age (W550) in a Nelore herd. (Co)variance components were estimated using the REML method fitting bivariate animal models. The fixed effects considered for DC were contemporary group, month of last calving, and age at breeding season (linear and quadratic effects). Contemporary groups were composed by herd, year, season, and management group at birth; herd and management group at weaning; herd, season, and management group at mating; and sex of calf and mating type (multiple sires, single sire, or AI). In DFC analysis, the same fixed effects were considered excluding the month of last calving. For DC, a repeatability animal model was applied. Noncalvers were not considered in analyses because an attempt to include them, attributing a penalty, did not improve the identification of genetic differences between animals. Heritability estimates ranged from 0.04 to 0.06 for DC, from 0.06 to 0.13 for DFC, from 0.42 to 0.44 for SC, from 0.06 to 0.08 for AFC, and was 0.30 for W550. The genetic correlation estimated between DC and SC was low and negative (-0.10), between DC and AFC was high and positive (0.76), and between DC and W550 was almost null (0.07). Similar results were found for genetic correlation estimates between DFC and SC (-0.14), AFC (0.94), and W550 (-0.02). The genetic correlation estimates indicate that the use of DC in the selection of beef cattle may promote favorable correlated responses to age at first mating and, consequently, higher gains in sexual precocity can be expected.     

Procalcitonin gene expression after LPS stimulation in the porcine animal model

Procalcitonin (PCT), recognised as a marker of sepsis, was investigated in a porcine model of endotoxic shock. The results showed that continuous IV infusion (1-4 h) of LPS (40 μg/kg) in pigs was able to induce a generalised increase of PCT expression in lung, heart, kidney and liver. The increase in PCT was significant only in kidney and was accompanied by an increase in IL-6 gene expression. In vitro results demonstrated that peripheral blood mononuclear cells (PBMCs), as well as endothelial cells, were potentially capable of contributing to in vivo extrathyroidal PCT production. These findings support previous data from pigs concerning the occurrence of widespread activation of PCT extrathyroidal gene expression during endotoxic shock in pigs. Nevertheless, the levels of PCT detected were very low, suggesting the need for additional studies to validate the pig as a reliable animal model for investigating the role of PCT in sepsis.     

Can Microfiltered Seminal Plasma Preserve the Morphofunctional Characteristics of Porcine Spermatozoa in the Absence of Antibiotics? A Preliminary Study

Artificial insemination is extensively performed in pig farms in Europe, the United States and Canada. Antibiotics are typically added to the inseminating dose to limit bacterial growth during liquid phase storage at 16°C, as bacterial contamination is unavoidable. The World Organization for Animal Health (OIE) and the Food and Agriculture Organization (FAO) take action to control and reduce antibiotic use in animals as more bacteria are becoming resistant to antimicrobials. To avoid the use of antibiotics, we prepared inseminating doses using microfiltered seminal plasma (SP). Microfiltration is a common technology used to reduce bacterial contamination but may retain seminal substances, influencing sperm quality during storage. Therefore, the aim of this study was to evaluate the morphofunctional parameters of spermatozoa during storage at 16°C in doses prepared with or without microfiltered SP, with or without the addition of antibiotics, in a Latin square design. Artificial insemination doses with microfiltered SP and without antibiotic addition preserved spermatozoa viability, mitochondrial membrane potential, acrosome integrity and objective motility, with absolute values equal or even better than those observed in conventional doses. In conclusion, although the results could be considered preliminary due to the small sample size, this study suggests that microfiltration of SP can be a simple method, feasible on farms, to replace antibiotic use in extended doses stored in the liquid phase at 16°C for up to 7 days.     

Matrix Metalloproteinases -2 and -9 in Swine Luteal Tissue Angiogenesis and Angioregression

Veterinary Research Communications - Ribeiro, L.A., Turba, M.E., Bernardini, C., Zannoni, A., Bacci, M.L. and Forni, M., 2007. Matrix metalloproteinases -2 and -9 in swine luteal tissue...     

Comparison of different nonlinear functions to describe Nelore cattle growth

This work aims to compare different nonlinear functions for describing the growth curves of Nelore females. The growth curve parameters, their (co)variance components, and environmental and genetic effects were estimated jointly through a Bayesian hierarchical model. In the first stage of the hierarchy, 4 nonlinear functions were compared: Brody, Von Bertalanffy, Gompertz, and logistic. The analyses were carried out using 3 different data sets to check goodness of fit while having animals with few records. Three different assumptions about SD of fitting errors were considered: constancy throughout the trajectory, linear increasing until 3 yr of age and constancy thereafter, and variation following the nonlinear function applied in the first stage of the hierarchy. Comparisons of the overall goodness of fit were based on Akaike information criterion, the Bayesian information criterion, and the deviance information criterion. Goodness of fit at different points of the growth curve was compared applying the Gelfand's check function. The posterior means of adult BW ranged from 531.78 to 586.89 kg. Greater estimates of adult BW were observed when the fitting error variance was considered constant along the trajectory. The models were not suitable to describe the SD of fitting errors at the beginning of the growth curve. All functions provided less accurate predictions at the beginning of growth, and predictions were more accurate after 48 mo of age. The prediction of adult BW using nonlinear functions can be accurate when growth curve parameters and their (co)variance components are estimated jointly. The hierarchical model used in the present study can be applied to the prediction of mature BW in herds in which a portion of the animals are culled before adult age. Gompertz, Von Bertalanffy, and Brody functions were adequate to establish mean growth patterns and to predict the adult BW of Nelore females. The Brody model was more accurate in predicting the birth weight of these animals and presented the best overall goodness of fit.     

Analysis of beef cattle longitudinal data applying a nonlinear model

The objective of this work was to evaluate the Nelore beef cattle, growth curve parameters using the Von Bertalanffy function in a nested Bayesian procedure that allowed estimation of the joint posterior distribution of growth curve parameters, their (co)variance components, and the environmental and additive genetic components affecting them. A hierarchical model was applied; each individual had a growth trajectory described by the nonlinear function, and each parameter of this function was considered to be affected by genetic and environmental effects that were described by an animal model. Random samples of the posterior distributions were drawn using Gibbs sampling and Metropolis-Hastings algorithms. The data set consisted of a total of 145,961 BW recorded from 15,386 animals. Even though the curve parameters were estimated for animals with few records, given that the information from related animals and the structure of systematic effects were considered in the curve fitting, all mature BW predicted were suitable. A large additive genetic variance for mature BW was observed. The parameter a of growth curves, which represents asymptotic adult BW, could be used as a selection criterion to control increases in adult BW when selecting for growth rate. The effect of maternal environment on growth was carried through to maturity and should be considered when evaluating adult BW. Other growth curve parameters showed small additive genetic and maternal effects. Mature BW and parameter k, related to the slope of the curve, presented a large, positive genetic correlation. The results indicated that selection for growth rate would increase adult BW without substantially changing the shape of the growth curve. Selection to change the slope of the growth curve without modifying adult BW would be inefficient because their genetic correlation is large. However, adult BW could be considered in a selection index with its corresponding economic weight to improve the overall efficiency of beef cattle production.     

Novel biodegradable plastics in sheep nutrition - Effects of NaOH pretreatment of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) on in vivo digestibility and on in vitro disappearance (Rusitec)

The use of biodegradable polymers in animal nutrition can be considered not only as a possible way of waste recycling but could also be beneficial in the derivation of animal products from the conversion of these energy-rich substances within the nutritional chain. However, earlier studies with swine and sheep as well as in vitro studies have shown a poor digestibility of untreated biodegradable plastics (Kunkel and Seo 1994; Forni et al. 1999a,b). The low accessibility of the polymeric chains, particularly if only coarsely milled, to the gastric juices, enzymes and gastrointestinal micro-organisms of farm animals, and the relatively short incubation time during the passage through the digestive tract obviously limit the degradation of these biodegradable polymers. Therefore, the present study focused on the effects of pretreatment and of increasing the dietary proportion of the biodegradable plastic poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV). PHBV is an aliphatic biodegradable polymer produced by bacteria (de Koning et al. 1996). Pretreatment with NaOH was chosen to reduce the chain length and to form absorbable monomers such as β-hydroxybutyrate, a natural metabolite in the digestive turnover and metabolism of ruminants. NaOH is an inexpensive and effective substance for breaking down PHBV, which was found to increase the apparent PHBV digestibility by 37 % in swine (Forni et al. 1999a). In addition, NaOH pretreatment is commonly used in ruminant nutrition to enhance the digestibility and intake of straw and poor quality hay which are both rich in biological polymers such as cellulose and lignin (Flachowsky 1987).