Differentially expressed genes identified through RNA‐seq with extreme values of principal components for beef fatty acid in Nelore cattle

The aim of this study was to identify differentially expressed genes (DEG) in the Longissimus thoracis muscle of Nelore cattle related to fatty acid (FA) profile through RNA sequencing and principal component analysis (PCA). Two groups of 10 animals each were selected containing PC1 and PC2 extreme DEG values (HIGH × LOW) for each FA group. The intramuscular fat (IMF) was compared between cluster groups by ANOVA, and only the sum of monounsaturated FA (MUFA) and ω3 showed significant differences (p < .05). Interestingly, the highest percentage (95%) of phenotypic variation explained by the sum of the first two PC was observed for ω3, which also displayed the lowest number of DEG (n = 1). The lowest percentage (59%) was observed for MUFA, which also revealed the largest number of DEG (n = 66). Since only MUFA and ω3 exhibited significant differences between cluster groups, we can conclude that the differences observed for the remaining groups are not due to the percentage of IMF. Several genes that have been previously associated with meat quality and FA traits were identified as DEG in this study. The functional analysis revealed one KEGG pathway and eight GO terms as significant (p < .05), in which we highlighted the purine metabolism, glycolytic process, adenosine triphosphate binding and bone development. These results strongly contribute to the knowledge of the biological mechanisms involved in meat FA profile of Nelore cattle.     

Cryopreservation of ram semen: Manual versus programmable freezing and different lengths of equilibration

The aim of our study was to examine effects of the length of semen equilibration as well as two freezing techniques on ram sperm post-thaw quality. The ejaculates of Wallachian sheep rams (n = 12) were collected by an electro-ejaculation, equilibrated in a Triladyl® (0, 2, 4, 6, and 8 h) containing glycerol and egg yolk and frozen by programmable freezing (PF) or manual freezing (MF). After thawing, sperm samples were subjected to the motility (computer-assisted sperm analysis [CASA]), viability (SYBR-14/PI), and fertilizing ability (FA) (in vitro penetration/fertilization test on bovine oocytes) assays. It was found that the equilibration of 6 h (E-6) ensured higher post-thaw sperm motility and progressive movement compared with other lengths tested, irrespective of a freezing technique. The E-6 sperm viability did not differ between PF and MF but was lower (P < 0.05) than control. Sperm FA (E-6) was similar in PF (60.44%) and MF (62%) but slightly lower than in fresh (72.8%). Our data demonstrate that the use of MF was comparable with PF, which can be applied in the field conditions without need in a piece of cost-expensive equipment, which can greatly benefit the gene bank of animal genetic resources.     

Multiplex real-time PCR for the detection and differentiation of equid herpesvirus 1 (EHV-1) and equid herpesvirus 4 (EHV-4)

A multiplex real-time PCR was designed to detect and differentiate equid herpesvirus 1 (EHV-1) and equid herpesvirus 4 (EHV-4). The PCR targets the glycoprotein B gene of EHV-1 and EHV-4. Primers and probes were specific to each equine herpesvirus type and can be used in monoplex or multiplex PCRs, allowing the differentiation of these two closely related members of the Alphaherpesvirinae. The two probes were minor-groove binding probes (MGB) labelled with 6-carboxy-fluorescein (FAM) and VIC for detection of EHV-1 and EHV-4, respectively. Ten EHV-1 isolates, six EHV-1 positive clinical samples, one EHV-1 reference strain (EHV-1.438/77), three EHV-4 positive clinical samples, two EHV-4 isolates and one EHV-4 reference strain (EHV-4 405/76) were included in this study. EHV-1 isolates, clinical samples and the reference strain reacted in the EHV-1 real-time PCR but not in the EHV-4 real-time PCR and similarly EHV-4 clinical samples, isolates and the reference strain were positive in the EHV-4 real-time PCR but not in the EHV-1 real-time PCR. Other herpesviruses, such as EHV-2, EHV-3 and EHV-5 were all negative when tested using the multiplex real-time PCR. When bacterial pathogens and opportunistic pathogens were tested in the multiplex real-time PCR they did not react with either system. The multiplex PCR was shown to be sensitive and specific and is a useful tool for detection and differentiation of EHV-1 and EHV-4 in a single reaction. A comprehensive equine herpesvirus disease investigation procedure used in our laboratory is also outlined. This procedure describes the combination of alphaherpesvirus multiplex real-time PCR along with existing gel-based PCRs described by other authors.     

Meta-analysis of fungicide efficacy on soybean target spot and cost–benefit assessment

Target spot of soybean has spread in Brazil, the southeastern United States and Argentina in the last decade. A collaborative network of field Uniform Fungicide Trials (UFT) in Brazil was created in 2011 to study the target spot control efficacy of fungicides, including azoxystrobin + benzovindiflupyr (AZ_BF), carbendazim (CZM), fluxapyroxad + pyraclostrobin (FLUX_PYRA), epoxiconazole + FLUX_PYRA (EPO_FLUX_PYRA), mancozeb (MZB) and prothioconazole + trifloxystrobin (PROT_TRIF). Network meta-analysis was used to conduct a quantitative synthesis of UFT data collected from 2012 to 2016 and to evaluate the effects of disease pressure (DP, low ≤ 35% target spot severity in the nontreated control < high) and year of experiment on the overall mean efficacy and yield response to each of the tested fungicides. Based on mean percentage control of target spot severity, the tested fungicides fall into three efficacy groups (EG): high EG, FLUX_PYRA (76.2% control relative to the nontreated control) and EPO_FLUX_PYRA (75.7% control); intermediate EG, PROT_TRIF (66.5% control) and low EG, MZB (49.6% control), AZ_BF (46.7% control) and CZM (32.4% control). DP had a significant effect on yield response. At DP_Low, the highest response was due to PROT_TRIF (+342 kg ha⁻¹, +12.8%) and EPO_FLUX_PYRA (+295.5 kg ha⁻¹, +11.2%), whereas at DP_High, EPO_FLUX_PYRA and FLUX_PYRA outperformed the other treatments, with yield responses of 503 kg ha⁻¹ (+20.2%) and 469 kg ha⁻¹ (+19.1%), respectively. The probability of a positive return on fungicide investment ranged from 0.26 to 0.56 at DP_Low and from 0.34 to 0.66 at DP_High.     

Fate of diuron and terbuthylazine in soils amended with two-phase olive oil mill waste

The addition of organic amendments to soil increases soil organic matter content and stimulates soil microbial activity. Thus, processes affecting herbicide fate in the soil should be affected. The objective of this work was to investigate the effect of olive oil production industry organic waste (alperujo) on soil sorption-desorption, degradation, and leaching of diuron [3-(3,4-dichlorophenyl)-1,1-dimethylurea] and terbuthylazine [N2-tert-butyl-6-chloro-N4-ethyl-1,3,5-triazine-2,4-diamine], two herbicides widely used in olive crops. The soils used in this study were a sandy soil and a silty clay soil from two different olive groves. The sandy soil was amended in the laboratory with fresh (uncomposted) alperujo at the rate of 10% w/w, and the silty clay soil was amended in the field with fresh alperujo at the rate of 256 kg per tree during 4 years and in the laboratory with fresh or composted alperujo. Sorption of both herbicides increased in laboratory-amended soils as compared to unamended or field-amended soils, and this process was less reversible in laboratory-amended soils, except for diuron in amended sandy soil. Addition of alperujo to soils increased half-lives of the herbicides in most of the soils. Diuron and terbuthylazine leached through unamended sandy soil, but no herbicide was detected in laboratory-amended soil. Diuron did not leach through amended or unamended silty clay soil, whereas small amounts of terbuthylazine were detected in leachates from unamended soil. Despite their higher sorption capacity, greater amounts of terbuthylazine were found in the leachates from amended silty clay soils. The amounts of dissolved organic matter from alperujo and the degree of humification can affect sorption, degradation, and leaching of these two classes of herbicides in soils. It appears that adding alperujo to soil would not have adverse impacts on the behavior of herbicides in olive production.     

Body development, carcass, and meat quality of confined lambs fed increasing levels of whole rice meal

The objective of this trial was to evaluate the effect of whole rice meal (WRM) inclusion in the concentrate upon body development, carcass traits, and meat quality of lambs. Twenty-four castrated lambs with an average initial body weight of 17.90?±?2.72 kg were randomly blocked according to two genetic groups (Corriedale and Texel by Corriedale crossbreds). Three isocaloric (11.3 MJ/kg of metabolizable energy) and isonitrogenous (17 % crude protein) diets were offered to the animals for 74 days. Diets consisted of 40 % forage and 60 % concentrate diet, on a dry matter basis, with 0, 15, or 30 % of WRM inclusion into the concentrate. Body growth (after slaughter), carcass, and meat traits were evaluated on each animal. Results obtained indicated that genotype did not affect body growth, carcass, and meat traits except for yellowness. No significant interaction between diet and genotype were detected. Inclusion of up to 30 % WRM did not significantly (P?>?0.05) affect body growth, carcass, and meat traits, except for meat color. Meat luminosity progressively increased (36.32?+?0.055X) while redness (15.13???0.03X) decreased with the inclusion of WRM in the diet, but still remained within acceptable values. The study indicates that WRM may be included up to 30 % in the concentrate replacing corn without adverse effects upon body development, carcass traits, and meat quality of lambs.     

Mapping genomic regions for reproductive traits in beef cattle: Inclusion of the X chromosome

Although the second largest chromosome of the genome, the X chromosome is usually excluded from genome-wide association studies (GWAS). Considering the presence and importance of genes on this chromosome that are involved in reproduction, the aim of this study was to evaluate the effect of its inclusion in GWAS on reproductive traits (scrotal circumference [SC], early pregnancy [P16] and age at first calving [AFC]) in a Nelore herd. Genotype data from 3,263 animals with the above-mentioned phenotypes were used. The results showed an increase in the variances explained by the autosomal markers for all traits when the X chromosome was not included. For SC, there was an increase of more than 10% for the windows on chromosomes 2 and 6. For P16, the effect was increased by almost 20% for windows on chromosome 5. The same pattern was found for AFC, with an increase of more than 10% for the most important windows. The results indicate that the noninclusion of the X chromosome can overestimate the effects of autosomes on SC, P16 and AFC not only because of the additive effect of the X chromosome itself but also because of its epistatic effect on autosomal genes.     

Risk factors for stillbirths in two swine farms in the south of Brazil

We evaluated stillbirth risk factors in two commercial swine farms of the Rio Grande do Sul State (south of Brazil). The study was conducted during 1 month in Farm A and during 2 months in Farm B, both during 1999. Data for all farrowings that occurred during the study period were recorded (101 for Farm A and 373 for Farm B), without interference in the farm management. In Farm A, 39% of all litters born during the period of interest had stillborn piglets and the stillborn risk for piglets was 12%. In Farm B, 25% of all litters had stillborn piglets whereas the stillborn risk was 2%. Variables considered as potential risk factors for stillbirths were: parity (1, 2–3, 4+); breed (purebred or crossbred); sow body-condition (normal or fat); use of oxytocin during parturition (yes or no); obstetric intervention through vaginal palpation (yes or no); farrowing duration (<4 or ≥4 h); mummified fetuses (yes or no); total litter size (<12 or ≥12 piglets); and litter birth weight (<11 or ≥11 kg). All stillborn piglets had their classification validated by necropsy. In multivariable logistic-regressions, the cases were the litters having at least one stillborn piglet. In Farm A, litters having at least 12 pigs and in which oxytocin was used during the parturition had 20.8-times-higher odds of stillborn occurrence. In Farm B, litters from sows having parity ≥4 had 2.2-times-higher odds of stillborn occurrence than litters from parity 2 to 3 females, litters having ≥12 pigs had 2.0-times-higher odds of a stillborn piglet than smaller litters and farrowings in which vaginal palpation was performed had 8.0-times-higher odds. Farrowing room management to minimize stillborn risk should target higher-parity females, large litters and optimization of practices of obstetric interventions.     

Antioxidant systems and lymphocyte proliferation in the horse,sheep and dog

To better define the species-specific antioxidant systems and to ascertain the influence of the intracellular redox status on the immune system of different animal species, we determined lymphocyte glutathione peroxidase (GSHPx) activity, plasmatic glutathione levels (GSH) and the effect of H2O2 on the responsiveness of lymphocytes to proliferative stimuli. Among the three species considered, sheep presented the lowest plasmatic GSH and the highest lymphocyte GSHPx activity. On the contrary, dogs showed an inverted pattern (high GSH - low GSHPx). Horses displayed intermediate values for both parameters analysed. The effect of H2O2 on the proliferative capacity of lymphocytes was the same for all three species; the 200 microM dose in particular was strongly inhibiting. Each species, however, showed different rates of inhibition: sheep exhibited the highest sensitivity to the antiproliferative effect of H2O2. Our results confirmed that high H2O2 concentrations (200 microM) are noxious for the cellular functions of all animals; however this effect is mediated by a rigorously species-specific relationship between the intracellular reactive oxygen species (ROS) and the molecular systems involved in cell proliferation.     

Characterization of colletotrichum isolates from tamarillo, passiflora, and mango in Colombia and identification of a unique species from the genus

ABSTRACT This study was conducted to identify the species of Colletotrichum infecting tamarillo, mango, and passiflora in Colombia and to assess whether cross-infection between host species is occurring. Isolates of Colletotrichum spp. from tamarillo (n = 54), passiflora (n = 26), and mango (n = 15) were characterized by various molecular methods and by morphological criteria. Morphological characterization grouped the tamarillo isolates as C. acutatum and the passiflora and mango isolates as C. gloeosporioides. Species-specific primer analysis was reliable and confirmed grouping of the tamarillo isolates (besides Tom-6) as C. acutatum and the mango isolates (besides Man-76) as C. gloeosporioides. However, DNA of the passiflora isolates was not amplified by either C. acutatum- or C. gloeosporioides-specific primers, but reacted with a new primer, Col1, designed according to the internal transcribed spacer (ITS) 1 region of these isolates. Isolates Tom-6 and Man-76 also reacted positively with the Col1 primer. All the isolates reacting with the C. acutatum- and C. gloeosporioides-specific primers failed to react with primer Col1. Isolate Pass-35 from passiflora did not react with any of the taxon-specific primers. Arbitrarily primed polymerase chain reaction (ap-PCR), random amplified polymerase DNA (RAPD)-PCR, and A+T-rich DNA analyses delineated representative isolates into subgroups within the designated species. Molecular analyses indicated that the C. acutatum tamarillo isolates were uniform or clonal, whereas the C. gloeosporioides mango isolates and Colletotrichum passiflora isolates were heterogeneous. Likewise, sequence analysis of the complete ITS (ITS1-5.8S-ITS2) region identified certain isolates to their respective species: tamarillo isolates as C. acutatum; mango isolates as C. gloeosporioides; passiflora, Tom-6, and Man-76 isolates as a Colletotrichum sp. as yet undefined; and the Pass-35 isolate as an additional undefined Colletot-richum sp. Molecular analyses of the population of Colletotrichum isolates from passiflora, Tom-6 from tamarillo, and Man-76 from mango indicate that this population may not be host specific.