Genomic prediction for meat and carcass traits in Nellore cattle using a Markov blanket algorithm

This study was carried out to evaluate the advantage of preselecting SNP markers using Markov blanket algorithm regarding the accuracy of genomic prediction for carcass and meat quality traits in Nellore cattle. This study considered 3675, 3680, 3660 and 524 records of rib eye area (REA), back fat thickness (BF), rump fat (RF), and Warner–Bratzler shear force (WBSF), respectively, from the Nellore Brazil Breeding Program. The animals have been genotyped using low-density SNP panel (30 k), and subsequently imputed for arrays with 777 k SNPs. Four Bayesian specifications of genomic regression models, namely Bayes A, Bayes B, Bayes Cπ and Bayesian Ridge Regression methods were compared in terms of prediction accuracy using a five folds cross-validation. Prediction accuracy for REA, BF and RF was all similar using the Bayesian Alphabet models, ranging from 0.75 to 0.95. For WBSF, the predictive ability was higher using Bayes B (0.47) than other methods (0.39 to 0.42). Although the prediction accuracies using Markov blanket of SNP markers were lower than those using all SNPs, for WBSF the relative gain was lower than 13%. With a subset of informative SNPs markers, identified using Markov blanket, probably, is possible to capture a large proportion of the genetic variance for WBSF. The development of low-density and customized arrays using Markov blanket might be cost-effective to perform a genomic selection for this trait, increasing the number of evaluated animals, improving the management decisions based on genomic information and applying genomic selection on a large scale.     

The effect of salinity on corn yield using the CERES-maize model

In most cases, when calculating soil water availability, only thewater content is considered. The effect of salinity on the wiltingpoint is neglected. The objective of this work is to use asimulation model (CERES-maize) in order to predict cornyields as a function of water salinity under severalenvironmental, agrotechnical, and plant characteristics. A modelis presented in which the wilting point is a function of the soilsalt content. At high salinity, the water content at wilting pointis higher than at low salinity, resulting in an insufficient amountof available water and, therefore, a reduced yield. The modelwas used to simulate several theoretical and experimentalsituations for forage corn and grain corn. Simulation resultsshowed that nitrogen fertilization increases the salinity thresholdvalue and the yield sensitivity (rate of yield reduction per unitof salinity). The also showed that forage corn is more sensitiveto salinity than grain corn. If the soil is not leached, a heaviersoil texture has a higher salinity threshold value. On the otherhand, if the soil is leached, the soil texture has no influence onthe salinity threshold value and the yield is less sensitive tosalinity in sandy soils. The determination coefficient (r²= 0.75) indicated that the results of the simulations were in goodagreement with the field data.     

Outbreak of shoot blight and dieback of Eucalyptus spp., caused by Pseudoplagiostoma eucalypti in Brazil

An outbreak of a new and severe disease was observed in Eucalyptus plantations of Bahia state, Brazil. An Ascomycota fungus has been frequently associated with the main symptoms of the disease namely leaf spot, branch cankers, shoot blight, defoliation, and dieback. Based on morphological characteristics, phylogenetic analysis (ITS and TEF-1α genes), and pathogenicity test on Eucalyptus plants, Pseudoplagiostoma eucalypti was identified as the causal agent of the disease. Although P. eucalytpi has been known from in Brazil since 1998, this is the first report of it causing severe disease and die-back on Eucalyptus spp. and we also record new symptoms associated with the pathogen.     

Delineating site-specific management zones on pasture soil using a probabilistic and objective model and geostatistical techniques

Precision Agriculture - In recent years, different algorithms have been utilised to delineate management zones, areas with similar properties, within agricultural fields. However, there are few...     

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.     

Genetic diversity and aggressiveness of Calonectria pteridis in Eucalyptus spp.

Calonectria leaf blight, caused by Calonectria pteridis, is currently one of the main foliar diseases in eucalypt plantations in Brazil. In warm and high rainfall regions, the disease can be a limiting factor for eucalypt production when planting susceptible genotypes. The most effective method for controlling this disease in the field is the use of resistant genotypes, which requires knowledge of the genetic variability and aggressiveness of the pathogen population for effective deployment of plant resistance. This work evaluated the genetic diversity and aggressiveness of C. pteridis populations obtained from infected eucalypt plants in Monte Dourado (Pará state) and Imperatriz (Maranhão state), Brazil. To study the genetic diversity, 16 ISSR primers were tested, five of which amplified polymorphic, reproducible and informative bands. Thirty-one closely related genotypes were identified from 84 isolates studied, indicating that the population has a low genetic diversity. The aggressiveness of seven isolates, selected according to geographic origin and their clustering in the ISSR-based dendogram, was determined by inoculation of a hybrid Eucalyptus grandis × E. urophylla clone under controlled conditions. Disease severity was assessed by both measuring the percentage of plant defoliation and assigning a score according to a diagrammatic scale of symptoms. A high correlation between the two evaluation methods was observed, which revealed significant differences in aggressiveness among the isolates. The diagrammatic scale is recommended for disease evaluation because results are obtained much faster, before the occurrence of severe defoliation. No correlation between clustering in the ISSR-based phylogenetic analysis and aggressiveness was observed.     

Genetic parameters for spawning and growth traits in the Pacific white shrimp (Penaeus (Litopenaeus) vannamei)

The aim of this study was to estimate genetic parameters for spawning traits and growth traits in a breeding line of Pacific white shrimp, Penaeus (Litopenaeus) vannamei, selected for growth and survival. Traits studied were number of eggs (NE) and number of nauplii (NN) and female body weight at insemination (FWI) and body weight at 130 days of age (BW130). Genetic parameters were estimated using a multivariate animal model. Heritability for NE and NN were estimated as 0.13 ± 0.04 and 0.03 ± 0.04 respectively. The contribution to NN total variation due to ‘factors associated with male’ effect was estimated as 0.47 ± 0.07. In the cases of FWI and BW130, heritability was estimated as 0.44 ± 0.08 and 0.19 ± 0.03 respectively. Genetic correlation between FWI and NE was estimated as 0.49 ± 0.15, between FWI and NN as 0.54 ± 0.39 and between NE and NN as 0.27 ± 0.41, whereas the genetic correlations of FWI, NE and NN with BW130 were 0.30 ± 0.13, ?0.21 ± 0.19 and ?0.25 ± 0.38 respectively. Although it is important to perform more studies on this issue, our results found no evidence of a genetic antagonistic effect between female reproductive traits and body weight at harvesting (130 days of age) in P. vannamei.     

Depletion study and estimation of withdrawal periods for florfenicol and florfenicol amine in pacu (Piaractus mesopotamicus)

The intensive production of farmed fish is at a global all‐time high, and the control of bacteria proliferation in fish farms requires the frequent use of antimicrobials. This practice raises important environmental concerns related to the emergence of antimicrobial‐resistant bacteria strains. Only a few antimicrobial drugs have been approved for use in aquaculture, one of which is florfenicol. This work studies the depletion and withdrawal period of florfenicol and its main metabolite, florfenicol amine, in pacu (Piaractus mesopotamicus), a neotropical characin widely farmed in the southern hemisphere. Juvenile pacu (average weight of 724 g) were stocked in a closed‐loop laboratory system with controlled water temperature (25.8°C), and were fed for 10 consecutive days with a diet containing an intended dose of 10 mg/florfenicol per kg bw. Muscle and skin tissues were collected at 1, 3, 6, 8, 10, 12 and 16 days post‐treatment, and florfenicol and florfenicol amine were quantified using a validated ultra‐high performance liquid chromatography‐tandem mass spectrometry (UPLC‐MS/MS) method. The limits of quantitation for florfenicol and florfenicol amine were 10 ng/g in muscle and 50 ng/g in skin. Considering a maximum residue limit of 1000 ng/g for the sum of florfenicol and florfenicol amine in muscle with skin in natural proportions a withdrawal period of 5 days (water temperature 25.8°C) or 129 degree days was calculated on the basis of the upper limit of the one‐sided 95% confidence interval for the 99^th percentile derived from the residue depletion study.