Is single-step genomic REML with the algorithm for proven and young more computationally efficient when less generations of data are present?

Efficient computing techniques allow the estimation of variance components for virtually any traditional dataset. When genomic information is available, variance components can be estimated using genomic REML (GREML). If only a portion of the animals have genotypes, single-step GREML (ssGREML) is the method of choice. The genomic relationship matrix (G) used in both cases is dense, limiting computations depending on the number of genotyped animals. The algorithm for proven and young (APY) can be used to create a sparse inverse of G (GAPY~-1) with close to linear memory and computing requirements. In ssGREML, the inverse of the realized relationship matrix (H⁻¹) also includes the inverse of the pedigree relationship matrix, which can be dense with a long pedigree, but sparser with short. The main purpose of this study was to investigate whether costs of ssGREML can be reduced using APY with truncated pedigree and phenotypes. We also investigated the impact of truncation on variance components estimation when different numbers of core animals are used in APY. Simulations included 150K animals from 10 generations, with selection. Phenotypes (h² = 0.3) were available for all animals in generations 1–9. A total of 30K animals in generations 8 and 9, and 15K validation animals in generation 10 were genotyped for 52,890 SNP. Average information REML and ssGREML with G⁻¹ and GAPY~-1 using 1K, 5K, 9K, and 14K core animals were compared. Variance components are impacted when the core group in APY represents the number of eigenvalues explaining a small fraction of the total variation in G. The most time-consuming operation was the inversion of G, with more than 50% of the total time. Next, numerical factorization consumed nearly 30% of the total computing time. On average, a 7% decrease in the computing time for ordering was observed by removing each generation of data. APY can be successfully applied to create the inverse of the genomic relationship matrix used in ssGREML for estimating variance components. To ensure reliable variance component estimation, it is important to use a core size that corresponds to the number of largest eigenvalues explaining around 98% of total variation in G. When APY is used, pedigrees can be truncated to increase the sparsity of H and slightly reduce computing time for ordering and symbolic factorization, with no impact on the estimates.     

Combinations of cactus pear with different roughage sources on the production,chemical composition,and milk fatty acid profile of F1 Holstein/Zebu cows

Tropical Animal Health and Production - The qualities of food, mainly of animal origin, have always been of concern to consumers. It is known that the composition of animals’ diets can...     

First report of Lagochilascaris (Nematoda: Ascarididae) eggs in a public park in Southern Brazil

Public parks, especially in developing countries, are places where stray animals run free and may contaminate the environment with different species of parasites. In an evaluation of environmental sanitation of these sites, soil samples were collected monthly from public parks in the Pelotas city, Rio Grande do Sul State, Southern Brazil. Eggs of the nematode Lagochilascaris sp. were found in a public playground. This is the first report of identification of this nematode in Southern Brazil.     

Correlation between carcass condemnations in slaughterhouses and official notifications of cattle testing positive for tuberculosis

Tropical Animal Health and Production - The objective of this study was to analyze the correlation between condemnations in slaughterhouses situated in Minas Gerais State and notifications to the...     

Distribution of cytosolic oestrogen and progesterone receptors in the genital tract of the mare

The distribution of oestrogen and progesterone receptors in the equine genital tract was investigated by means of a modified dextran-coated charcoal method on samples collected from the vagina, the cervix and the uterus of 30 healthy adult Polish mares, divided into two groups on the basis of their serum progesterone levels. The concentrations of oestrogen and progesterone receptors were significantly (P<0·05) lower in the vagina and the cervix than in the uterus, in agreement with data from human beings, cattle and pigs, which showed that the highest concentrations of oestrogen and progesterone receptors were localised respectively in the body and in the horns of the uterus.     

Effect of Brazilian red propolis administration on hematological, biochemical variables and parasitic response of Santa Inês ewes during and after flushing period

Brazilian red propolis was administered orally to Santa Inês ewes, and evaluation was made of general health and hematological, biochemical, and parasitic responses during and after flushing. Thirty mature, nonlactating, nonpregnant Santa Inês ewes (40?±?2 kg and 2.5 years old) were grazing tropical pasture (Brachiaria decumbens and Pennisetum purpureum) and, as flushing after synchronization, were supplemented with a concentrate–roughage mixture at a rate of 4 % body weight (BW). Ewes were divided according to BW and fecal egg count (FEC) into two groups (n?=?15 each): control and propolis that received propolis ethanolic extract at rates of, respectively, 0 and 3 g/ewe/day. The treatments lasted 21 days until the end of flushing period. BW and body condition score (BCS) were recorded, and blood and fecal samples were taken weekly for 8 weeks. Mean values of BW and BCS were not (P?>?0.05) affected by propolis administration. Propolis increased (P?<?0.01) total leukocytes (WBC), but no significant differences were observed for other hematological parameters. Propolis increased (P?<?0.01) total protein and globulin concentrations and decreased (P?<?0.01) triglycerides, glutamate oxaloacetate transaminase, and glutamate pyruvate transaminase. Propolis decreased (P?<?0.05) FEC. Propolis administration had good impact on ewe health and may be a promising feed additive during critical periods such as flushing.     

Feed restriction followed by realimentation in prepubescent Zebu females

In the present study, the effect of restricting the feed intake for 77 days and subsequent compensatory growth for 50 days of Sindi females were evaluated. Eighteen animals with an initial age of 21 months and a mean weight of 211.7 kg were placed into three groups according to the following alimentary regimens: feed ad libitum, feed restricted to 20 % dry matter, and feed restricted to 40 % dry matter. In the feed-restriction phase, the nutrient intake decreased (P?<?0.001) with an increase in the restriction level. As a consequence, the observed decrease in ingestion and serum concentrations of total protein, albumin and globulin, urea, glucose, calcium, and phosphorus were inversely proportional (P?<?0.001) to the restriction level. Significant differences in the nutrient intake and serum concentration were not observed in the realimentation phase (P?<?0.05). When animals in the control group reached the end of the feed-restriction phase, their weights (P?<?0.05) were similar to those in the 20 % restricted group, and both obtained a final weight that was greater than that of animals in the 40 % restricted group. In the feed-restriction phase, the control group had a similar mean daily weight gain (P?>?0.05) to animals in the 20 % restricted group and (P?<?0.05) 40 % restricted group. However, in the realimentation phase, the 40 % restricted group obtained greater weight gain rates (P?<?0.05), better food conversions, and partial compensatory gains. In particular, none of the restricted groups reached the final weight of the control group. In the feed-restriction phase, ingested nitrogen, nitrogen excreted in urine and feces, nitrogen balance and retained nitrogen decreased (P?<?0.05) with an increase in the restriction level. In the realimentation phase, none of the nitrogen balance variables were influenced by the restriction level (P?<?0.05). Females in the 40 % restricted group presented better food conversion rates and greater weight gains in the realimentation phase. Based on the animals’ compensatory weight gain, a feed-restriction rate of 20 and 40 % can be adopted as a nutritional management practice for prepubescent Sindi females.     

Breeding objectives of Brangus cattle in Brazil

Our goal was to define a breeding objective for Brangus beef cattle in Brazil. Bioeconomic models were produced and used to estimate economic values (EVs). The scenarios simulated were typical full-cycle beef production systems that are used in tropical and subtropical regions. The breeding objective contained pregnancy rate (PR), warm carcass weight (WCW), mature cow weight (MCW), number of nematode eggs per gram of faeces (EPG) and tick count (TICK). Two models were used in series to estimate the EV. A deterministic model was used to simulate effects of PR, WCW and MCW on profitability with a constant parasite load. Subsequently, stochastic models were used to estimate economic values for TICK and EPG as consequences of their environmental effects on weight gains, mortality and health costs. The EV of PR, WCW, MCW, EPG and TICK, was US$1.59, US$2.11, −US$0.24, −US$5.35 and −US$20.88, respectively. Results indicate positive emphasis should be placed on PR (12.49%) and WCW (65.07%) with negative emphasis on MCW (13.92%), EPG (2.77%) and TICK (5.75%). In comparison with the indexes usually used, these results suggest a reformulation in the selection indexes of the beef production system in tropical and subtropical regions in order to obtain greater profitability.     

Milk production,intake, digestion,blood parameters,and ingestive behavior of cows supplemented with by-products from the biodiesel industry

This study aimed to evaluate the intake, digestion, blood parameters, and feeding behavior of crossbred dairy cows (Holstein?×?Gir) managed on Panicum maximum Jacq. cv. Tanzania-1 and provided supplementation with groundnut cake, sunflower cake, or palm kernel cake (to replace soybean meal). Sixteen cows were randomly assigned in a Latin square design with four treatments and four experimental periods. The consumption of nutrients from the pasture did not vary between experimental treatments. Cows receiving the palm kernel cake supplement had a reduced crude protein, non-fibrous carbohydrate, and total digestible nutrient intake and an increase in the average consumption of ether extract. There was also a reduction in the digestibility of dry matter. The inclusion of supplements in the diet did not influence the average time spent eating, ruminating, or resting. The mean values of respiratory and heart rates showed thermal comfort during the trial period. There was a reduction in blood urea nitrogen with palm kernel cake supplementation, and the values of total protein, albumin, and glucose were also significantly different with this supplement. It is recommended that cakes of groundnut cake and sunflower cake seed be used for a total replacement of soybean meal supplements for lactating cows, but the use of palm kernel cake is not recommended.

     

Evaluation of iohexol clearance used to estimate glomerular filtration rate in clinically normal foals

OBJECTIVE: To determine whether pharmacokinetic analysis of data derived from a single i.v. dose of iohexol could be used to predict creatinine clearance and evaluate simplified methods for predicting serum clearance of iohexol with data derived from 2 or 3 blood samples in clinically normal foals. ANIMALS: 10 healthy foals. PROCEDURE: Serum disposition of iohexol and exogenous creatinine clearance was determined simultaneously in each foal (5 males and 5 females). A 3-compartment model of iohexol serum disposition was selected via standard methods. Iohexol clearance calculated from the model was compared with creatinine clearance. Separate limited-sample models were created with various combinations of sample times from the terminal slope of the plasma versus time profile for iohexol. Correction factors were determined for the limited-sample models, and iohexol clearance calculated via each method was compared with exogenous creatinine clearance by use of method comparison techniques. RESULTS: Mean exogenous creatinine clearance was 2.17 mL/min/kg. The disposition of iohexol was best described by a 3-compartment open model. Mean clearance value for iohexol was 2.15 mL/min/kg and was not significantly different from mean creatinine clearance. A method for predicting serum iohexol clearance based on a 2-sample protocol (3- and 4-hour samples) was developed. CONCLUSIONS AND CLINICAL RELEVANCE: Iohexol clearance can be used to predict exogenous creatinine clearance and can be determined from 2 blood samples taken after i.v. injection of iohexol. Appropriate correction factors for adult horses and horses with abnormal glomerular filtration rate need to be determined.