Improving genomic predictions by correction of genotypes from genotyping by sequencing in livestock populations

Background: Genotyping by sequencing(GBS) is a robust method to genotype markers. Many factors can influence the genotyping quality. One is that heterozygous genotypes could be wrongly genotyped as homozygotes,dependent on the genotyping depths. In this study, a method correcting this type of genotyping error was demonstrated. The efficiency of this correction method and its effect on genomic prediction were assessed using simulated data of livestock populations.Results: Chip array(Chip) and four depths of GBS data was simulated. After quality control(call rate ≥ 0.8 and MAF ≥ 0.01), the remaining number of Chip and GBS SNPs were both approximately 7,000, averaged over 10 replicates. GBS genotypes were corrected with the proposed method. The reliability of genomic prediction was calculated using GBS, corrected GBS(GBSc), true genotypes for the GBS loci(GBSr) and Chip data. The results showed that GBSc had higher rates of correct genotype calls and higher correlations with true genotypes than GBS. For genomic prediction, using Chip data resulted in the highest reliability. As the depth increased to 10, the prediction reliabilities using GBS and GBSc data approached those using true GBS data. The reliabilities of genomic prediction using GBSc data were 0.604, 0.672, 0.684 and 0.704 after genomic correction, with the improved values of 0.013, 0.009, 0.006 and 0.001 at depth = 2, 4, 5 and 10, respectively.Conclusions: The current study showed that a correction method for GBS data increased the genotype accuracies and, consequently, improved genomic predictions. These results suggest that a correction of GBS genotype is necessary, especially for the GBS data with low depths.     

Dynamic headspace gas chromatography/mass spectrometry characterization of volatiles produced in fish oil enriched mayonnaise during storage

Protection against lipid oxidation and formation of unpleasant fishy and rancid off-flavors in oil-in-water food emulsions, such as fish oil enriched mayonnaise, is difficult to achieve. Volatile profiles from stored mayonnaises with different oil phase compositions were collected using a developed dynamic headspace sampling technique, in which interfering acetic acid was removed in situ with potassium hydroxide, and subsequently 148 volatiles were characterized and monitored by gas chromatography/mass spectrometry. Multivariate statistics showed correlation between the concentration of 62 volatiles and the fish oil and storage parameters, indicating the formation of lipid oxidation products, which impose fishy off-flavors. Further verification was obtained by gas chromatography/olfactometry, by which, among 78 odors, cis-4-heptenal and trans,cis-2,4-heptadienal were detected as distinct fishy notes. In total, 27 volatiles, including 1-penten-3-one, cis-2-penten-1-ol, cis-3-hexenal, cis-4-heptenal, 1-octen-3-one, 1,cis-5-octadien-3-one, 1-octen-3-ol, trans,cis-2, 4-heptadienal, and trans,cis-2,6-nonadienal, were suggested to contribute to the developed unpleasant fishy and rancid off-flavors.     

Effect of Embryo Density on In vitro Developmental Characteristics of Bovine Preimplantative Embryos with Respect to Micro and Macroenvironments

To overcome developmental problems as a consequence of single embryo culture, the Well of the Well (WOW) culture system has been developed. In this study, we aimed to examine the effect of embryo densities with respect to both microenvironment and macroenvironment on developmental rates and embryo quality to get a deeper insight into developmentally important mechanisms. WOW diameter and depth significantly affected developmental rates (p < 0.05). WOWs with diameter of 500 μm reached significantly higher blastocyst rates (32.5 vs 21.1% vs 20.3%) compared to embryos cultured in WOWs of 300 μm diameter or plain cultured controls. Embryos cultured in WOWs with 700 μm depth reached significant higher developmental rates compared with embryos cultured in WOWs of 300 μm depth and control embryos (30.6 vs 22.6% vs 20.3%). Correlation of the embryo per WOW volume with developmental rates was higher (r² = 0.92, p = 0.0004) than correlation of WOW diameter or WOW depth with developmental rates. However, the embryo per WOW volume did not affect differential cell counts. An embryo per culture dish volume of 1 : 30 μl was identified to be optimal when the embryo per WOW volume was 1 : 0.27 μl increasing developmental rates up to the level of mass embryo production. Giving the opportunity to track each embryo over the complete culture period while keeping high developmental rates with normal mitotic dynamics, the results of this work will provide benefit for the single culture of embryos in human assisted reproduction, mammalian embryos with high economic interest as well as for scientific purpose.     

Genomic predictions across Nordic Holstein and Nordic Red using the genomic best linear unbiased prediction model with different genomic relationship matrices

This study investigated genomic predictions across Nordic Holstein and Nordic Red using various genomic relationship matrices. Different sources of information, such as consistencies of linkage disequilibrium (LD) phase and marker effects, were used to construct the genomic relationship matrices (G‐matrices) across these two breeds. Single‐trait genomic best linear unbiased prediction (GBLUP) model and two‐trait GBLUP model were used for single‐breed and two‐breed genomic predictions. The data included 5215 Nordic Holstein bulls and 4361 Nordic Red bulls, which was composed of three populations: Danish Red, Swedish Red and Finnish Ayrshire. The bulls were genotyped with 50 000 SNP chip. Using the two‐breed predictions with a joint Nordic Holstein and Nordic Red reference population, accuracies increased slightly for all traits in Nordic Red, but only for some traits in Nordic Holstein. Among the three subpopulations of Nordic Red, accuracies increased more for Danish Red than for Swedish Red and Finnish Ayrshire. This is because closer genetic relationships exist between Danish Red and Nordic Holstein. Among Danish Red, individuals with higher genomic relationship coefficients with Nordic Holstein showed more increased accuracies in the two‐breed predictions. Weighting the two‐breed G‐matrices by LD phase consistencies, marker effects or both did not further improve accuracies of the two‐breed predictions.     

The molecular basis for wine grape quality--a volatile subject

Volatile organic compounds are important flavor components of finished wines. In addition to winemaking practices, which shape wine quality, cultivation of the grape berries in the vineyard each season affects the production of volatile organic compounds as well as other chemical components that ultimately contribute to our perception of flavor in finished wines. By studying how berry flavor components are determined by the interplay of vine genotypes, the environment, and cultivation practices at the molecular level, scientists will develop advanced tools and knowledge that will aid viticulturalists in consistently producing balanced, flavorful berries for wine production.     

Bayesian analysis of the linear reaction norm model with unknown covariates

The reaction norm model is becoming a popular approach for the analysis of genotype x environment interactions. In a classical reaction norm model, the expression of a genotype in different environments is described as a linear function (a reaction norm) of an environmental gradient or value. An environmental value is typically defined as the mean performance of all genotypes in the environment, which is usually unknown. One approximation is to estimate the mean phenotypic performance in each environment and then treat these estimates as known covariates in the model. However, a more satisfactory alternative is to infer environmental values simultaneously with the other parameters of the model. This study describes a method and its Bayesian Markov Chain Monte Carlo implementation that makes this possible. Frequentist properties of the proposed method are tested in a simulation study. Estimates of parameters of interest agree well with the true values. Further, inferences about genetic parameters from the proposed method are similar to those derived from a reaction norm model using true environmental values. On the other hand, using phenotypic means as proxies for environmental values results in poor inferences.     

Computer tomographic investigation of subcutaneous adipose tissue as an indicator of body composition

Background

Modern computer tomography (CT) equipment can be used to acquire whole-body data from large animals such as pigs in minutes or less. In some circumstances, computer assisted analysis of the resulting image data can identify and measure anatomical features. The thickness of subcutaneous adipose tissue at a specific site measured by ultrasound, is used in the pig industry to assess adiposity and inform management decisions that have an impact on reproduction, food conversion performance and sow longevity. The measurement site, called "P2", is used throughout the industry. We propose that CT can be used to measure subcutaneous adipose tissue thickness and identify novel measurement sites that can be used as predictors of general adiposity.

Methods

Growing pigs (N = 12), were each CT scanned on three occasions. From these data the total volume of adipose tissue was determined and expressed as a proportion of total volume (fat-index). A computer algorithm was used to determined 10,201 subcutaneous adipose thickness measurements in each pig for each scan. From these data, sites were selected where correlation with fat-index was optimal.

Results

Image analysis correctly identified the limits of the relevant tissues and automated measurements were successfully generated. Two sites on the animal were identified where there was optimal correlation with fat-index. The first of these was located 4 intercostal spaces cranial to the caudal extremity of the last rib, the other, a further 5 intercostal spaces cranially.

Conclusion

The approach to image analysis reported permits the creation of various maps showing adipose thickness or correlation of thickness with other variables by location on the surface of the pig. The method identified novel adipose thickness measurement positions that are superior (as predictors of adiposity) to the site which is in current use. A similar approach could be used in other situations to quantify potential links between subcutaneous adiposity and disease or production traits.     

Effectiveness of Rose Bengal test and fluorescence polarization assay in the diagnosis of <Emphasis Type="Italic">Brucella</Emphasis> spp. infections in free range cattle reared in endemic areas in Zambia

The effectiveness of Rose Bengal test (RBT) and fluorescence polarization assay (FPA) in diagnosing cattle brucellosis in endemic areas was assessed and RBT and FPA test agreement was compared (n = 319). The sensitivity of RBT and FPA in detecting low Brucella titres were evaluated in paired sera (n = 34). A logistic regression model was constructed to predict cattle test result in FPA using RBT as the main predictor and incorporating bio-data and animal history. There was 79.3% agreement between the RBT and FPA (Kappa = 0.59; Std error = 0.05; p = 0.000) and a high correspondence between high RBT scores and positive FPA results suggesting that sera with high RBT score may not require confirmation with tests such as competitive-ELISA or CFT. High FPA cut-off points were more likely to miss animals with low antibody titres. The RBT had a reduced ability in detecting low antibody titres compared to the FPA. FPA test interpretation was improved if a priori information, such as sex and age was used. Under the challenging disease surveillance conditions prevailing in rural Africa, field-testing methods that are sensitive and specific; allow single animal contact, low technical skills in data interpretation are suitable.     

Yucca schidigera extract: a potential biofungicide against seedborne pathogens of sorghum

Treatment of seeds with an aqueous extract of yucca (YE), Yucca schidigera, was evaluated for antifungal activity against seedborne pathogens as well as its effect on seed germination and seedling growth of sorghum (Sorghum bicolor). The antifungal effect of YE was observed against Leptosphaeria sacchari (syn. Phoma sorghina) when the extract was applied at 2·5 and 10% concentrations. At 10% concentration, YE significantly reduced not only the incidence of L. sacchari, but also that of Fusarium spp., Cochliobolus lunatus (syn. Curvularia lunata) and Cladosporium spp. The effect of 10% YE on seedborne fungi was broader than the fungicide fludioxonil, particularly with regard to Fusarium. Furthermore, the number of normal, healthy‐looking seedlings increased in a dose‐responsive manner with YE treatment. Seedling vigour was also stimulated by YE but no correlation was observed with the concentrations tested. Under glasshouse conditions, the treatment of seeds with 10% YE increased the emergence of seedlings and plant height and reduced the number of seedlings with crown rot compared to negative controls and saponin. The positive effect was similar to the effect obtained with fungicide‐treated seeds. Treatment of seeds with synthetic saponin inhibited seedborne fungi less effectively and also negatively affected germination and vigour of the seedlings, compared to the treatment with YE. The results demonstrate an agronomic potential for the use of YE as a biofungicide for seed treatment of sorghum. The difference between the antifungal and the vigour‐stimulating effects of YE warrants further investigation.