Comparison of four direct algorithms for computing inbreeding coefficients

One widely used measure in genetic analyses of livestock species is the inbreeding coefficient. Computation costs of inbreeding coefficients are of importance for large populations. Very recently, a ‘direct’ method for computing inbreeding coefficients was modified using a relatively efficient method to construct lists of ancestors in which the integrity of chronological order within each ancestral path is kept. Using simulated data, the computational efficiency of the recently modified algorithm was investigated by comparing it with three other algorithms – the original direct algorithm, its previously modified algorithm and another direct algorithm. The recently modified algorithm became considerably faster than the original algorithm and its previous modification when the number of generations increased, and it was fast relative to the other direct algorithm when the average number of generations and family size were not large. When only animals born in the most recent year were evaluated with the knowledge of inbreeding coefficients for their ancestors, the recently modified algorithm outperformed the other algorithms, indicating its possible advantage in updating situations.     

Prevalence of avian influenza,Newcastle disease,and infectious bronchitis viruses in broiler flocks infected with multifactorial respiratory diseases in Iran, 2015–2016

In this study, the prevalence and spatial distribution of Newcastle disease, infectious bronchitis, and avian influenza have been evaluated in commercial broiler farms in 31 provinces in Iran. In this survey, a total of 233 affected broiler chicken farms were sampled. The infectious bronchitis virus (alone) was detected with highest frequency in 60 farms, and separately or combined with other agents, in 110 farms; Newcastle disease virus, separately, was detected in 28 farms, and in 63 farms separately or combined with other infectious agents; and avian influenza H9N2 was detected in 22 farms separately and in 51 farms separately or concomitant with other infectious agents. The sample tested negative for all H5 serotypes. The results of the present study show that the most prevalent avian viral infectious disease contributing to respiratory syndromes in broiler farms in Iran was infectious bronchitis due to infectious bronchitis virus serotypes variant 2 and 793/B. On the other hand, combined with the alternation of dominant viruses and circulating strains, flocks are exposed to unremitting anamorphic viral infections. Thus, the permanent monitoring of cases that have occurred and the review of vaccination plans of affected flocks every year are some of the necessary measures needed for strategic control of respiratory syndrome in broilers. It is noteworthy that execution of epidemiologic examinations on the cogent factors of prevalence of this syndrome and defeat of vaccination strategy in the flocks is urgent and has to be fulfilled on the definite causes of time.

     

Impact of including information from bulls and their daughters in the training population of multiple‐step genomic evaluations in dairy cattle: A simulation study

The objective of this study was to investigate the impact of accounting for parent average (PA) and genotyped daughters’ average (GDA) on the estimation of deregressed estimated breeding values (dEBVs) used as pseudo‐phenotypes in multiple‐step genomic evaluations. Genomic estimated breeding values (GEBVs) were predicted, in eight different simulated scenarios, using dEBVs calculated based on four methods. These methods included PA and GDA in the dEBV (VR) or only GDA (VRpa) and excluded both PA and GDA from the dEBV with either all information or only information from PA and GDA (JA and NEW, respectively). In general, VR and NEW showed the lowest and highest GEBV reliabilities across scenarios, respectively. Among all deregression methods, VRpa and NEW provided the most consistent bias estimates across the majority of scenarios, and they significantly yielded the least biased GEBVs. Our results indicate that removing PA and GDA information from dEBVs used in multiple‐step genomic evaluations can increase the reliability of GEBVs, when both bulls and their daughters are included in the training population.     

Developmental competence of in vitro matured ovine oocytes vitrified in solutions with different concentrations of trehalose

This study aimed to determine the optimum concentration of trehalose in solutions used for vitrification of in vitro matured (IVM) ovine oocytes. IVM oocytes were randomly divided into four experimental (vitrified) and one control (fresh) groups. Experimental groups were treated with different concentrations (0.0, 0.25, 0.5 and 1.0 M) of trehalose. After warming, some viable oocytes were exposed to 0.25% pronase to test zona pellucida hardening, whereas the others were fertilized and cultured in vitro for 8 days to evaluate their developmental competence. Blastocysts quality was assessed by differential staining and TUNEL test. Survival and developmental rates of oocytes vitrified in the presence of 0.5 M trehalose were significantly higher than those of the other vitrified groups. Furthermore, there was a significant difference between fresh and vitrified groups in total blastocyst rate. Analysis of blastocysts quality also revealed a significant difference between the group treated with 0.5 M trehalose and other groups in terms of apoptotic index. Furthermore,zona pellucida digestion time period was longer in trehalose‐free (0.0 M) group compared to other groups. In conclusion, we found that IVM ovine oocytes vitrified in solutions containing 0.5 M trehalose are fertilization‐competent and are able to produce good‐quality blastocysts with an apoptotic index comparable to that of the fresh oocytes. Therefore, 0.5 M may be considered the optimum concentration of trehalose to be used in solutions prepared for vitrification of oocytes.     

Vitrification of mouse preantral follicles versus slow freezing: Morphological and apoptosis evaluation

The aim of this study was evaluation of survivability, maturation rate and apoptotic gene expression of preantral follicles after vitrification and slow freezing technique. Normal mouse preantral follicles were randomly divided into three experimental groups. In the control group, follicles were cultured immediately; in the vitrification and slow freezing groups, follicles were cultured after vitrification‐warming and slow freezing‐thawing procedures. Follicular viability was assessed by using 0.4% trypan blue, and molecular evaluation of messenger RNA levels of apoptosis‐related genes was performed by the semi‐quantitative RT‐PCR method after 3 h of culture. Oocyte maturation rates were also evaluated on day 14 of culture. Survival and maturation rate in the slow freezing group were significantly lower than those in control and vitrification groups (P ≤ 0.05). Although there was no difference in Survivin expression among the three experimental groups, Bcl‐2 expression was significantly lower in the slow freezing group compared to the other groups (P ≤ 0.05). The expression of Bax, P53, Fas and Bax/Bcl‐2 ratio in the slow freezing group was significantly higher than control and vitrification groups (P ≤ 0.05). Preantral follicle vitrification seems to be better than slow freezing as seen in the survival, maturation and expression rates of apoptotic gene variants.     

Microbial and sensory characteristics of camel meat during refrigerated storage as affected by gamma irradiation

The present study was undertaken to assess the microbiological profile of fresh camel meat and the possibility of improving microbial quality and extending the refrigerated storage life of meat by using low-dose gamma irradiation. Camel meat samples were subjected to 0 (control), 1.5 and 3 kGy doses and stored at 3 +/- 1 degrees C. the microbial and sensory attributes were evaluated. Exposure to 1.5 kGy dose significantly reduced the initial counts of Aerobic Plate Counts (APCs), psychrophilic bacteria, Lactic Acid Bacteria (LAB), molds and yeasts, Staphylococcus aureus, Listeria monocytogenes and Enterococci. Moreover, Pseudomonas, coliforms and Escherichia coli were below the detection levels. Irradiation at 3 kGy significantly reduced the initial counts of APCs LAB and Enterococci by 99.5, 93.5 and 93.9%, respectively. Pseudomonas, coliforms, S. aureus, L. monocytogenes and E. coli were not found at dose of 3 kGy during entire storage period, also psychrophilic bacteria and molds and yeasts were below the detection levels during 6 days of storage. This study shows that irradiation had no significant effects on the sensory attributes of camel meat. Refrigerated shelf-life of the meat irradiated at 1.5 and 3 kGy were 15 and 21 days, respectively, compared to 7 days for non-irradiated controls.     

Evaluation of different media and methods of cultivation on the production and viability of entomopathogenic fungi, Verticillium lecanii (Zimm.) Viegas

For mass production of V. lecanii, three types of cultivation methods including liquid, solid and diphasic production systems were investigated. In the liquid state of production, six media were tested in stationary culture conditions. Among the six media tested, Molasses Yeast Broth (MYB) supported maximum sporulation (8.33 x 10(8) spores mL(-1)) and biomass production (746 mg/100 mL). In the MYB, 4% molasses concentration was found to produce highest spore count (8.56 x 10(8) spores mL(-1)) and biomass (776 mg/100 mL) followed by 5 and 6% molasses. Among the six solid substrates tested, rice grains supported highest spore production (1.14 g/100 g). In diphasic state of production, combination of MYB and rice grains produced the greatest amount of spores, (1.70 g/100 g). Results of this study indicated that diphasic method using MYB as liquid medium and rice as solid substrate are the best method and media for mass production of V1-7 isolate of V. lecanii.     

Association of Lecithin Cholesterol Acyltransferase rs5923 Polymorphism in Iranian Individuals with Extremely Low High-Density Lipoprotein Cholesterol: Tehran Lipid and Glucose Study

Background:

The serum concentration of high-density lipoprotein cholesterol (HDL-C) is one of the important heritable risk factors for cardiovascular disease and is a target for therapeutic intervention. In this study, we aimed to evaluate the effects of lecithin cholesterol acyltransferase (LCAT) gene polymorphism rs5923 on LCAT enzyme activity and serum HDL-C concentration.

Methods:

The study population was selected from consecutive individuals with HDL-C ≤ 5^th percentile (n = 73) and extremely high HDL-C ≥ 95^th percentile (n = 57) who had participated in the Tehran Lipid and Glucose Study. The rs5923 polymorphism was genotyped using direct sequencing. LCAT activity was measured by fluorometric assay kit, and lipid concentrations were measured using the enzymatic colorimetric method.

Results:

The genotype frequencies were significantly different between the high HDL-C group (CC 94.7%, CT 5.3%) and the low HDL-C group (CC 83.6%, CT 16.4%) (P = 0.048). The T-allele frequencies in subjects with low and high HDL-C were 0.082 and 0.026, respectively (P = 0.16). The association of the single-nucleotide polymorphism rs5923 with low HDL-C was not statistically significant after adjustment for age, sex, and BMI (odd ratio = 2.65, 95% confidence interval = 0.32-21.5, P = 0.36, regression logistic analysis). Also, the effects of LCAT enzyme activity did not depend on the HDL-C level (P = 0.24).

Conclusion:

rs5923 polymorphism is not associated with low HDL-C levels in Iranian population. Key Words: Polymorphism, Single nucleotide, Lipoproteins     

Bioresource Efficacy of Phosphate Rock,Sulfur, and Thiobacillus Inoculum in Improving Soil Phosphorus Availability

In order to improve the effectiveness of phosphate rock as phosphorus fertilizer, elemental sulfur and Thiobacillus have been evaluated as amendments. First, Thiobacillus was isolated from different soil samples. Then, a greenhouse pot experiment was conducted using a completely randomized factorial design with three factors included: elemental sulfur at four levels of 0, 1000, 2000, and 5000 mg kg^?1; phosphate rock at three levels of 0, 1000 and 2000 mg kg^?1; four Thiobacillus inoculums (T₁, T₂, T₃, T₄) and without inoculation (T₀) in three replications. Results showed that all the four Thiobacillus inoculums increased significantly extractable soil-P. Combined application of phosphate rock and sulfur in equal proportion (1:1) along with inoculum Thiobacillus had a significant effect in improving phosphorus availability in soil. Combined application of sulfur (at rates of 1000 and 2000 mg kg^–1) and Thiobacillus significantly increased phosphorus uptake by plants as compared to the control.