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.     

Genetic and genomic analyses for predicted methane‐related traits in Japanese Black steers

The objectives of this study were to estimate genetic parameters and to perform a genome‐wide association study (GWAS) for predicted methane‐related traits in Japanese Black steers. The methane production and yield traits were predicted using on‐farm measurable traits, such as dry matter intake and average daily gain. A total of 4,578 Japanese Black steers, which were progenies of 362 sires genotyped with imputed 551,995 single nucleotide polymorphisms (SNPs), had phenotypes of predicted methane‐related traits during the total fattening period (52 weeks). For the estimation of genetic parameters, the estimated heritabilities were moderate (ranged from 0.57 to 0.60). In addition, the estimated genetic correlations of methane production traits with most of carcass traits and feed‐efficiency traits were unfavorable, but those of methane yield traits were favorable or low. For the GWAS, no genome‐wide significant SNP was detected, but a total of four quantitative trait locus (QTL) regions that explained more than 5.0% of genetic variance were localized on the genome, and some candidate genes associated with growth and feed‐efficiency traits were located on the regions. Our results suggest that the predicted methane‐related traits are heritable and some QTL regions for the traits are localized on the genome in Japanese Black steers.     

Effect of catechins on mutagenesis of Salmonella typhimurium TA 102 elicited by tert-butyl hydroperoxide (t-BuOOH)

Green tea, one of the most popular beverages consumed in Asian countries, has been reported to possess anticarcinogenic and antimutagenic properties. The aim in this study is to test the radical scavenging effect of catechins and caffeine, which were major components of green tea, and if they really prevent oxygen radical-induced mutagenesis. We used TA102 strain of Salmonella typhimurium which is sensitive to hydroxyl radical in the Ames mutation assay. We found that caffeine did not show any effects on mutagenesis in this system, but catechin significantly reduced mutagenesis or genotoxicity caused by hydroxyl radical. This radical-scavenging action of catechins may indeed contribute to the anticarcinogenic activity of green tea as has been proposed.     

Plasma high density lipoprotein in anemic cattle infected with Theileria sergenti.

Changes in plasma concentration of lipid composition were analysed in cattle with anemia due to Theileria sergenti infection. Plasma levels of phospholipids, cholesterol, free cholesterol, high density lipoprotein cholesterol, and vitamin E decreased to 40-67% of the pre-infection levels, corresponding to the decrease of PCV due to the infection. However, no definite changes were detected in plasma level of triglyceride. By gradient centrifugation, it was confirmed that lipid components, other than triglyceride, occur in high density lipoprotein (HDL) and these decreases lowered the HDL value. There was no correlation between this phenomenon and liver function. As similar changes in lipid composition were also observed in phlebotomized calves, it was considered that this phenomenon might partially depend on the acceleration of erythropoiesis as a reaction to anemia caused by T. sergenti infection.     

Treatment with a High Dose Combination of PMSG/hCG Preparation of Mares Clinically Diagnosed with Ovarian Quiescence during the Breeding Season (Investigation from 1975 to 2000)

A total of 88 thoroughbred mares were diagnosed with clinical ovarian quiescence and subjected to four treatment regimens. Using PMSG, hCG or combinations of both. A high dose combination of 5,000IU PMSG with 5,000IU hCG showed significantly higher rates of marked estrus and ovulation induction (P<0.01) as well as conception rates (P<0.05). In the present study, the administration of a high-dose combination of PMSG with hCG was shown to be an effective treatment of ovarian quiescence in light mares.     

Provision of beta‐glucan prebiotics (cellooligosaccharides and kraft pulp) to calves from pre‐ to post‐weaning period on pasture

We conducted two feeding experiments to evaluate the effects of supplementation with either cellooligosaccharide or kraft pulp on growth performance in grazing beef calves (Japanese Black) from 4 weeks pre‐weaning to 12 to 16 weeks post‐weaning. In Experiment 1 (20‐week duration), nine calves (2.9‐month‐old females) were assigned to either a control group (CON) or an experimental group (CEL) fed cellooligosaccharide at a rate of 10 g/day mixed with concentrate. Average daily weight gain tended to be greater in CEL than in CON, especially after 1 month of weaning. In Experiment 2 (16‐week duration), 10 calves (2.0‐month‐old females) were assigned to either a control group or an experimental group (KRA) fed kraft pulp at a rate of 10% replacement of total digestible nutrients with concentrate. The proportion of fibrolytic bacteria increased and that of methanogenic Archaea decreased in the rumen microbial community composition of KRA calves in Experiment 2, whereas the decrease in Fibrobacter and Archaea was observed in CEL calves at first 4 weeks in Experiment 1. We conclude that beta‐glucan prebiotic supplementation to grazing calves at pre‐weaning would affect rumen microbial composition and modified rumen fermentation characteristics, leading to a better rumen environment via different means.     

Quantitative structure-activity study of insecticidal 2-methoxy-5-(substituted-phenyl)-1, 3, 2-oxazaphospholidine 2-sulfides against Musca domestica L. by topical application

The quantitative relationship between the structure of 2-methoxy-5-(substituted-phenyl)-1, 3, 2-oxazaphospholidine 2-sulfides (5-PMOS) and their insecticidal activity against the house fly. Musca domestica L., was analyzed using reported physicochemical parameters and regression analysis. The electronic nature of the substituent on the phenyl group of 5-PMOS has the most significant effect on the activity, followed by hydrophobic and steric effects; the optimum value of Σρ is zero and the more hydrophobic the substituents on the phenyl group, the higher the insecticidal activity. The plots of observed pLD₅₀, values against calculated pLD₅₀ values for compounds having substituents in the ortho-position deviated downwards from those of compounds having substituents at the meta and/or para positions. This ortho-effect, which reduces the insecticidal activity of compounds having substituents at the ortho-position, was expressed by a dummy parameter D, which has the value 2 for di-ortho-substituted derivatives, 1 for mono-ortho-substituted derivatives and zero for others. Thus, the highest activity was obtained for 2-methoxy-5-phenyl-1, 3, 2-oxazaphospholidine 2-sulfide, and the activity was decreased by the introduction of any substituents on the phenyl group.     

Genetic relationships of fertility traits with test‐day milk yield and fat‐to‐protein ratio in tropical smallholder dairy farms

The test‐day milk fat‐to‐protein ratio (TD‐FPR) could serve as a measure of energy balance status and might be used as a criterion to improve metabolic stability and fertility through genetic selection. Therefore, genetic parameters for fertility traits, test‐day milk yield (TD‐MY) and TD‐FPR, as well as, their relationships during different stages of lactation, were estimated on data collected from 25 968 primiparous Thai dairy crossbred cows. Gibbs sampling algorithms were implemented to obtain (co)variance components using both univariate linear and threshold animal models and bivariate linear‐linear and linear‐threshold animal models with random regression. Average TD‐MY and TD‐FPR were 12.60 and 1.15. Heritability estimates for TD‐MY, TD‐FPR and selected fertility traits ranged from 0.31 to 0.58, 0.17 to 0.19 and 0.02 to 0.05, respectively. Genetic correlations among TD‐FPR and TD‐MY, TD‐FPR and fertility traits, and TD‐MY and fertility traits ranged from 0.05 to ‐0.44, from ‐0.98 to 0.98 and ‐0.22 to 0.79, respectively. Selection for lower TD‐FPR would decrease numbers of inseminations per conception and increase conception at first service and pregnancy within 90 days. In addition, cow selection based only on high milk production has strong effects to prolong days to first service, days open and calving interval.     

Partial characterization of phylogeny,ecology and function of the fibrolytic bacterium Ruminococcus flavefaciens OS14, newly isolated from the rumen of swamp buffalo

The fibrolytic rumen bacterium Ruminococcus flavefaciensOS14 was isolated from swamp buffalo and its phylogenetic, ecological and digestive properties were partially characterized. Isolates from rumen contents of four swamp buffalo were screened for fibrolytic bacteria; one of the 40 isolates showed a distinctive feature of solubilizing cellulose powder in liquid culture and was identified as R. flavefaciens based on its 16S ribosomal DNA sequence. This isolate, OS14, was employed for detection and digestion studies, for which a quantitative PCR assay was developed and defined cultures were tested with representative forages in Thailand. OS14 was phylogenetically distant from other isolated and uncultured R. flavefaciens and showed limited distribution among Thai ruminants but was absent in Japanese cattle. OS14 digested rice straw and other tropical forage to a greater extent than the type strain C94 of R. flavefaciens. OS14 produced more lactate than C94, and digested para grass to produce propionate more extensively in co‐culture with lactate‐utilizing Selenomonas ruminantium S137 than a co‐culture of C94 with S137. These results indicate that phylogenetically distinct OS14 could digest Thai local forage more efficiently than the type strain, possibly forming a symbiotic cross‐feeding relationship with lactate‐utilizing bacteria. This strain might be useful for future animal and other industrial applications.