Application of robust procedures for estimation of breeding values in multiple-trait random regression test-day model

Robust procedures for estimation of breeding values were applied to multiple‐trait random regression test‐day (TD) model to reduce the influence of outliers on inferences. Robust estimation methods consisted of correcting selected observations (defined as outliers) in the process of solving mixed‐model equations in such a way that ‘new’ observations gave residuals (actual observation minus predicted) within k residual standard deviations for a given day in milk in 305‐day lactation. Data were 980 503 TD records on 63 346 Canadian Jersey cows. Milk, fat, protein and somatic cell score in the first three lactations were analysed jointly in the model that included fixed herd‐TD effect and regressions within region–age–season of calving, and regressions with random coefficients for animal genetic and permanent environmental effects. All regressions were orthogonal polynomials of order 4. Robust procedures for k = 1.5, 2.0, 2.5, 2.75 and 3.0 were contrasted with the regular best linear unbiased prediction (BLUP) method in terms of numbers and distributions of outliers, and estimated breeding values (EBV) of animals. Distributions of outliers were similar across traits and lactations. Early days in milk (from 5 to 15) were associated with larger frequency of outliers compared with the remaining part of lactation. Several, computationally simple, robust methods (for k > 2.0) reduced the influence of outlier observations in the model and improved the overall model performance. Differences in rankings of animals from robust evaluations were small compared with the regular BLUP method. No clear associations between changes in EBV (rankings) of top animals from different methods and the occurrence of outliers were detected.     

The effect of starvation stress on the protein profiles in Flexibacter chinensis

Background: Analysis of many proteins produced during the transition into the stationary phase and under stress conditions (including starvation stress) demonstrated that a number of novel proteins were induced in common to each stress and could be the reason for cross-protection in bacterial cells. It is necessary to investigate the synthesis of these proteins during different stress conditions. Methods: The changes in protein profile of Flexibacter chinensis at various stages of the starvation process and the other stresses were investigated using two-dimensional gel electrophoresis which has proven to be a powerful tool for investigation of the changes in protein profiles under such conditions. Results: Most starvation proteins were synthesized during the early stationary phase and many of these proteins remained during long-term starvation. Some of these proteins were transiently synthesized. The sequencing result of one of the proteins showed that there was a 62.5% identity in 8 amino acids overlapped with the 5' residue of a 10 kDa chaperon protein which is known to be involved in the starvation stress response in other organisms. Conclusion: There are many proteins synthesized in common with many stresses in Flexibacter chinensis. Some of these proteins must play a major role in the stability of the cell under different stresses.     

Diversity of Starch Pasting Properties in Iranian Hexaploid Wheat Landraces

Wheat landraces possess a wide diversity in starch physical properties that could be useful in breeding for improved quality of specific products, such as various types of Asian noodles. The pasting properties (using a Rapid Visco-Analyser [RVA]) and flour swelling volume (FSV, using silver nitrate to inactivate α-amylase activity) of wholemeal, were measured for 242 hexaploid accessions of Iranian landrace wheat. FSV values and the peak viscosities were positively correlated (r = 0.73***). FSV values in the landraces ranged from 8.3 to 15.9 mL/g and peak viscosities ranged from 139 to 305 RVA units (RVU). In comparison, FSV of cvs. Eradu and Klasic were 18.6 and 15.0 mL/g, and peak viscosities were 355 and 303 RVU, respectively. Of the landraces, Iranian Wheat Accession (IWA) 8602488 had the highest peak viscosity (305 RVU) and exceptionally high hot- and cool-paste viscosities. Two accessions, IWA 8602430 and 8600544, displayed pasting characteristics considered desirable for high-quality Japanese white-salted noodles. Four landraces were identified that had starch with unusually high resistance to shearthinning. Texture profile analysis was done on the wholemeal gels formed in the RVA canister. The variation in parameters such as hardness, chewiness, and adhesiveness in the landraces greatly exceeded that in the cultivars. The hot-paste viscosity, breakdown, setback, and final viscosity values, but not the peak viscosity or FSV, were highly significantly correlated with the hardness, chewiness, and adhesiveness of the gel. The Iranian landraces appear to present useful genetic variation for developing wheats for special uses.     

Carbon storage in biomass,litter, and soil of different native and introduced fast-growing tree plantations in the South Caspian Sea

Replantation of degraded forest using rapidgrowth trees can play a significant role in global carbon budget by storing large quantities of carbon in live biomass,forest floor,and soil organic matter.We assessed the potential of 20-year old stands of three rapid-growth tree species,including Alnus subcordata,Populus deltoides and Taxodium distichum,for carbon(C) storage at ecosystem level.In September 2013,48 replicate plots(16 m × 16 m) in 8 stands of three plantations were established.36 trees were felled down and fresh biomass of different components was weighed in the field.Biomass equations were fitted using data based on the 36 felled trees.The biomass of understory vegetation and litter were measured by harvesting all the components.The C fraction of understory,litter,and soil were measured.The ecosystem C storage was as follows: A.subcordata(626.5 Mg ha~(-1)) [ P.deltoides(542.9Mg ha~(-1)) [ T.distichum(486.8 Mg ha~(-1))(P \ 0.001),of which78.1–87.4% was in the soil.P.deltoides plantation reached the highest tree biomass(206.6 Mg ha~(-1)),followed by A.subcordata(134.5 Mg ha~(-1)) and T.distichum(123.3 Mg ha~(-1)).The highest soil C was stored in theplantation of A.subcordata(555.5 Mg ha~(-1)).The C storage and sequestration of the plantations after 20 years were considerable(25–30 Mg ha~(-1) year~(-1)) and broadleaves species had higher potential.Native species had a higher soil C storage while the potential of introduced species for live biomass production was higher.     

Effect of exogenous application of salicylic acid on salt-stressed sorghum growth and nutrient contents

This study was conducted to investigate the effect of salinity and foliar application of salicylic acid (SA) on sorghum biomass and nutrient contents. Treatments were comprised of salinity levels (0 and 100?mM NaCl) and SA concentrations (0.3, 0.7, 1.1 and 1.5?mM). Salinity increased sodium (Na), chlorine (Cl) and copper (Cu) but decreased nitrogen (N), phosphorus (P), potassium (K), magnesium (Mg), sulfur (S), iron (Fe), zinc (Zn) and manganese (Mn) contents and the root and shoot dry matter. Fe and Zn were the most affected nutrients by salinity. However, SA reduced Na and Cl but increased plant dry matter and nutrient content. SA had greater positive effects on root than on shoot dry matter. Maximum increases through SA were achieved in N, K, Fe, Mn, Cu, and shoot weight under salt stress but in Zn and root weight under non-saline condition. In most cases 1.1?mM was the most effective SA concentration in reducing the negative effects of salinity.     

Molecular survey of <Emphasis Type="Italic">Toxoplasma</Emphasis> infection in sheep and goat from Fars province,Southern Iran

Toxoplasmosis is a widespread zoonotic disease that causes significant morbidity and mortality in human fetus and in immunocompromised patients. Moreover, it becomes a major cause of abortion in sheep and goats. Since consumption of meat of infected lamb and goat is considered as the main sources of human infection in Iran, this study was undertaken to determine the prevalence of Toxoplasma infection in edible tissues of sheep and goats in Shiraz in 2008. Samples of brain, tongue, liver, and muscles of neck, intercostals, and femoral were taken from 56 sheep and 22 goats and tested by PCR. The total prevalence of Toxoplasma infection among animals was found to be 33.3%. Five out of 22 goats (22.7%) and 21 out of 56 sheep (37.5%) were infected by Toxoplasma. Differences between the prevalence rate of infection among females (nine out of 14 = 46%) and males animals (12 out of 45 = 29.5%) was significant (P = 0.013). Furthermore, a positive correlation was found between the age of animals and the rate of infection; animals greater than 2 years old showed a higher rate of infection (47%) in comparison with those less than 2 years old (25%, P = 0.04). The highest infected tissue was tongue (21.8%) followed by brain (19.2%) and femoral and intercostal muscles (17.9%). This study demonstrated a high level of Toxoplasma infection in slaughtered animals in Shiraz and these should be considered as the main sources of infection for human population in the region.     

Gnomonia fragariae, a Cause of Strawberry Root Rot and Petiole Blight

Gnomonia fragariae has been occasionally listed among the fungi associated with diseased strawberry plants. However its pathogenicity has not been established. During the investigation on strawberry decline in Latvia and Sweden, a fungus was repeatedly recovered from discoloured root and crown tissues of severely stunted plants. Attempts to induce sporulation of the isolates grown on several agar media resulted in the formation of mature ascomata only on potato carrot agar and oatmeal agar. On morphological grounds and comparisons with reference herbarium specimens these isolates were identified as Gnomonia fragariae. The pathogenicity of the fungus was evaluated initially in the detached leaf assay and subsequently in three bioassays on strawberry plants. All the bioassays showed that G. fragariae was pathogenic on strawberry and capable of causing severe root rot and petiole blight. The symptoms that developed in the greenhouse experiments closely resembled those observed in the fields. The fungus did not cause rapid plant death but growth and development of inoculated strawberry plants was severely affected. To our knowledge this is the first time when pathogenicity of G. fragariae as a root rot pathogen has been clearly established. Our study shows that G. fragariae is one of the serious pathogens involved in the root rot complex of strawberry in Latvia and Sweden.     

Comparison of models for genetic evaluation of survival traits in dairy cattle: a simulation study.

Three models for the analysis of functional survival data in dairy cattle were compared using stochastic simulation. The simulated phenotype for survival was defined as a month after the first calving (from 1 to 100) in which a cow was involuntarily removed from the herd. Parameters for simulation were based on survival data of the Canadian Jersey population. Three different levels of heritability of survival (0.100, 0.050 and 0.025) and two levels of numbers of females per generation (2000 or 4000) were considered in the simulation. Twenty generations of random mating and selection (on a second trait, uncorrelated with survival) with 20 replicates were simulated for each scenario. Sires were evaluated for survival of their daughters by three models: proportional hazard (PH), linear multiple-trait (MT), and random regression (RR) animal models. Different models gave different ranking of sires with respect to survival of their daughters. Correlations between true and estimated breeding values for survival to five different points in a cow's lifetime after the first calving (120 and 240 days in milk after first, second, third and fourth calving) favoured the PH model, followed by the RR model evaluations. Rankings of models were independent of the heritability level, female population size and sire progeny group size (20 or 100). The RR model, however, showed a slight superiority over MT and PH models in predicting the proportion of sire's daughters that survived to the five different end-points after the first calving.