Genome-wide interaction study reveals epistatic interactions for beef lipid-related traits in Nellore cattle.

Gene-gene interactions cause hidden genetic variation in natural populations and could be responsible for the lack of replication that is typically observed in complex traits studies. This study aimed to identify gene-gene interactions using the empirical Hilbert-Schmidt Independence Criterion method to test for epistasis in beef fatty acid profile traits of Nellore cattle. The dataset contained records from 963 bulls, genotyped using a 777 962k SNP chip. Meat samples of Longissimus muscle, were taken to measure fatty acid composition, which was quantified by gas chromatography. We chose to work with the sums of saturated (SFA), monounsaturated (MUFA), polyunsaturated (PUFA), omega-3 (OM3), omega-6 (OM6), SFA:PUFA and OM3:OM6 fatty acid ratios. The SNPs in the interactions where P < 10 - 8 were mapped individually and used to search for candidate genes. Totals of 602, 3, 13, 23, 13, 215 and 169 candidate genes for SFAs, MUFAs, PUFAs, OM3s, OM6s and SFA:PUFA and OM3:OM6 ratios were identified respectively. The candidate genes found were associated with cholesterol, lipid regulation, low-density lipoprotein receptors, feed efficiency and inflammatory response. Enrichment analysis revealed 57 significant GO and 18 KEGG terms ( P < 0.05), most of them related to meat quality and complementary terms. Our results showed substantial genetic interactions associated with lipid profile, meat quality, carcass and feed efficiency traits for the first time in Nellore cattle. The knowledge of these SNP-SNP interactions could improve understanding of the genetic and physiological mechanisms that contribute to lipid-related traits and improve human health by the selection of healthier meat products.

Genome-wide scan reveals genomic regions and candidate genes underlying direct and maternal effects of preweaning calf mortality in Nellore cattle.

We conducted analysis to estimate genetic parameters and to identify genomic regions and candidate genes affecting direct and maternal effects of preweaning calf mortality (PWM) in Nellore cattle. Phenotypic records of 67,196 animals, and 8443 genotypes for 410,936 SNPs were used. Analysis were performed through the weighted single-step GBLUP approach and considering a threshold animal model via Bayesian Inference. Direct and maternal heritability estimates were of 0.2143 ± 0.0348 and 0.0137 ± 0.0066, respectively. The top 10 genomic regions accounted for 13.61 and 14.23% of the direct and maternal additive genetic variances and harbored a total of 63 and 91 positional candidate genes, respectively. Two overlapping regions on BTA2 were identified for both direct and maternal effects. Candidate genes are involved in biological mechanisms i.e. embryogenesis, immune response, feto-maternal communication, circadian rhythm, hormone alterations, myometrium adaptation, and milk secretion, which are critical for the successful calf growth and survival during preweaning period.

Genome-wide association study identified genomic regions and putative candidate genes affecting meat color traits in Nellore cattle.

Single and multiple-trait GWAS were conducted to detect genomic regions and candidate genes associated with meat color traits (L*, lightness; a*, redness; b*, yellowness) in Nellore cattle. Phenotypic records of 5000 animals, and 3794 genotypes for 614,274 SNPs were used. The BLUPF90 family programs were used through single step GWAS approach. The top 10 genomic regions from single-trait GWAS explained 13.64%, 15.12% and 13% of genetic variance of L*, a* and b*, which harbored 129, 70, and 84 candidate genes, respectively. Regarding multiple-trait GWAS, the top 10 SNP windows explained 17.46%, 18.98% and 13.74% of genetic variance of L*, a* and b*, and harbored 124, 86, and 82 candidate genes, respectively. Pleiotropic effects were evidenced by the overlapping regions detected on BTA 15 and 26 associated with L* and a* (genetic correlation of -0.53), and on BTA 18 associated with a* and b* (genetic correlation of 0.60). Similar genomic regions located on BTA 2, 5, 6, and 18 were detected through single and multi-trait GWAS. Overlapped regions harbored a total of 30 functional candidate genes involved in mitochondrial activity, structural integrity of muscles, lipid oxidation, anaerobic metabolism, and muscular pH.

Genome-enabled prediction of reproductive traits in Nellore cattle using parametric models and machine learning methods.

This study aimed to assess the predictive ability of different machine learning (ML) methods for genomic prediction of reproductive traits in Nellore cattle. The studied traits were age at first calving (AFC), scrotal circumference (SC), early pregnancy (EP) and stayability (STAY). The numbers of genotyped animals and SNP markers available were 2342 and 321 419 (AFC), 4671 and 309 486 (SC), 2681 and 319 619 (STAY) and 3356 and 319 108 (EP). Predictive ability of support vector regression (SVR), Bayesian regularized artificial neural network (BRANN) and random forest (RF) were compared with results obtained using parametric models (genomic best linear unbiased predictor, GBLUP, and Bayesian least absolute shrinkage and selection operator, BLASSO). A 5-fold cross-validation strategy was performed and the average prediction accuracy (ACC) and mean squared errors (MSE) were computed. The ACC was defined as the linear correlation between predicted and observed breeding values for categorical traits (EP and STAY) and as the correlation between predicted and observed adjusted phenotypes divided by the square root of the estimated heritability for continuous traits (AFC and SC). The average ACC varied from low to moderate depending on the trait and model under consideration, ranging between 0.56 and 0.63 (AFC), 0.27 and 0.36 (SC), 0.57 and 0.67 (EP), and 0.52 and 0.62 (STAY). SVR provided slightly better accuracies than the parametric models for all traits, increasing the prediction accuracy for AFC to around 6.3 and 4.8% compared with GBLUP and BLASSO respectively. Likewise, there was an increase of 8.3% for SC, 4.5% for EP and 4.8% for STAY, comparing SVR with both GBLUP and BLASSO. In contrast, the RF and BRANN did not present competitive predictive ability compared with the parametric models. The results indicate that SVR is a suitable method for genome-enabled prediction of reproductive traits in Nellore cattle. Further, the optimal kernel bandwidth parameter in the SVR model was trait-dependent, thus, a fine-tuning for this hyper-parameter in the training phase is crucial.

3D printing of canine hip dysplasia: anatomic models and radiographs / Impressão 3D da displasia coxofemoral canina: modelos anatômicos e radiografias

Canine Hip Dysplasia (CHD) is a highly prevalent articular pathological condition. In this sense, radiography becomes an important diagnostic method to determine the presence and severity of the disease. The objective was to create 3D models and their respective radiographs representing the CHD (3D AMCHD). The research was carried out in the Laboratory of 3D Educational Technologies of UFAC, under no. 23107.007273/2017-49 (CEUA/UFAC). A canine skeleton (hip bone, femurs and patellae) was used without anatomical deformities compatible with DCF (pelvis, femurs and patella), which were scanned in order to obtain the files of the base model. In these files the deformations representing the different degrees of CHD were performed. Subsequently, the 3D AMCHD files were printed, mounted and X-rayed. The 3D AMCHD represented the bone deformations of the different degrees of CHD. In the radiographs of the 3D AMCHD it was possible to observe and determine each of the bones that constituted the hip joints. This allowed to reproduce the correct positioning to represent the CHD diagnosis and establish the precise points to determine the Norberg angle. In this way, it was evidenced that the 3D AMCHD can be a possible tool to be used in the Teaching of Veterinary Medicine.(AU)

A displasia coxofemoral canina (DCF) é uma condição patológica articular de grande prevalência. Nesse sentido, a radiografia torna-se um método de diagnóstico importante para determinar a presença e a gravidade da doença. O objetivo do presente trabalho foi criar modelos 3D e suas respectivas radiografias representando a DCF (MADCF 3D). A pesquisa foi realizada no Laboratório de Tecnologias Educacionais 3D da UFAC, sob o nº. 23107.007273/2017-49 (Ceua/Ufac). Foram utilizados esqueletos caninos (pelve, fêmures e patelas) sem deformidades anatômicas compatíveis com a DCF, os quais foram digitalizados a fim de se obterem os arquivos do modelo base. Nesses arquivos foram realizadas as deformações que representavam os diferentes graus da DCF. Posteriormente, os arquivos dos MADCF 3D foram impressos, montados e radiografados. Os MADCF 3D representaram as deformações ósseas dos diferentes graus da DCF. Nas radiografias dos MADCF 3D, foi possível observar e determinar cada um dos ossos que constituíam as articulações coxofemorais. Isso permitiu reproduzir o posicionamento correto para representação do diagnóstico DCF e estabelecer os pontos precisos para determinar o ângulo de Norberg. Dessa forma, evidenciou-se que os MADCF 3D podem ser uma possível ferramenta a ser empregada no ensino de medicina veterinária.(AU)

Genomic reaction norm models exploiting genotype × environment interaction on sexual precocity indicator traits in Nellore cattle.

Brazilian beef cattle are raised predominantly on pasture in a wide range of environments. In this scenario, genotype by environment (G×E) interaction is an important source of phenotypic variation in the reproductive traits. Hence, the evaluation of G×E interactions for heifer's early pregnancy (HP) and scrotal circumference (SC) traits in Nellore cattle, belonging to three breeding programs, was carried out to determine the animal's sensitivity to the environmental conditions (EC). The dataset consisted of 85 874 records for HP and 151 553 records for SC, from which 1800 heifers and 3343 young bulls were genotyped with the BovineHD BeadChip. Genotypic information for 826 sires was also used in the analyses. EC levels were based on the contemporary group solutions for yearling body weight. Linear reaction norm models (RNM), using pedigree information (RNM_A) or pedigree and genomic information (RNM_H), were used to infer G×E interactions. Two validation schemes were used to assess the predictive ability, with the following training populations: (a) forward scheme-dataset was split based on year of birth from 2008 for HP and from 2011 for SC; and (b) environment-specific scheme-low EC (-3.0 and -1.5) and high EC (1.5 and 3.0). The inclusion of the H matrix in RNM increased the genetic variance of the intercept and slope by 18.55 and 23.00% on average respectively, and provided genetic parameter estimates that were more accurate than those considering pedigree only. The same trend was observed for heritability estimates, which were 0.28-0.56 for SC and 0.26-0.49 for HP, using RNM_H, and 0.26-0.52 for SC and 0.22-0.45 for HP, using RNM_A. The lowest correlation observed between unfavorable (-3.0) and favorable (3.0) EC levels were 0.30 for HP and -0.12 for SC, indicating the presence of G×E interaction. The G×E interaction effect implied differences in animals' genetic merit and re-ranking of animals on different environmental conditions. SNP marker-environment interaction was detected for Nellore sexual precocity indicator traits with changes in effect and variance across EC levels. The RNM_H captured G×E interaction effects better than RNM_A and improved the predictive ability by around 14.04% for SC and 21.31% for HP. Using the forward scheme increased the overall predictive ability for SC (20.55%) and HP (11.06%) compared with the environment-specific scheme. The results suggest that the inclusion of genomic information combined with the pedigree to assess the G×E interaction leads to more accurate variance components and genetic parameter estimates.

Differential expression of immune response genes associated with subclinical mastitis in dairy buffaloes.

Buffalo milk production has become of significant importance on the world scale, however, there are few studies involving biotechnological tools specifically for buffalo. To verify the effects caused by subclinical mastitis on the components of milk and to study the innate immune system in the udder of dairy buffaloes with subclinical mastitis, we evaluated the levels of expression of the lactoferrin (LTF), tumor necrosis factor alpha (TNF-α), interleukin-1 beta (IL-1ß), interleukin-8 (IL-8), and toll-like receptors 2 (TLR-2) and 4 (TLR-4) genes in buffaloes with and without subclinical mastitis. Milk samples were collected for the determination of milk components: somatic cell score (SCS), fat, protein, lactose, total solids and solids-not-fat (SNF), as well as for RNA extraction of milk cells, complementary DNA synthesis, and expression profile quantification by quantitative real-time PCR. For gene expression, the ΔΔCt was estimated using contrasts of the target genes expression adjusted for the expression of the housekeeping genes between both groups. Linear regression analysis was performed to determine the relationship between the genes studied and the milk components. Subclinical mastitis induced changes in the fat, lactose and SNF in milk of buffaloes, and the messenger RNA abundance was upregulated for TLR-2, TLR-4, TNF-α, IL-1ß and IL-8 genes in milk cells of buffaloes with subclinical mastitis, whereas the LTF gene was not differentially expressed. Results of linear regression analysis showed that TLR-2 gene expression most explains the variation in SCS, and the change in a unit of ΔCt of the TNF-α gene would result in a higher increase in SCS. The study of these immune function genes that are active in the mammary gland is important to characterize the action mechanism of the innate immunity that occurs in subclinical mastitis in dairy buffaloes and may aid the development of strategies to preserve the health of the udder.

Prognostic value of energy expenditure and respiratory quotient measuring in patients with liver cirrhosis.

BACKGROUND & AIMS: Resting energy expenditure (REE) and respiratory quotient (RQ) as measured by indirect calorimetry (IC) may correlate with muscle mass and represent prognostic indicators in treating patients with liver cirrhosis. We aimed to assess the correlation of IC-measured REE and RQ with skeletal muscle mass (SM), mortality, and REE values as estimated by Harris-Benedict, European guidelines (EG), and Brazilian guidelines-DITEN (BG) equations in patients with liver cirrhosis. METHODS: In this prospectively designed study, REE was measured in 126 male patients with liver cirrhosis by IC and predicted by Harris-Benedict, EG (35 kcal/kg current weight), and BG (30 kcal/kg current weight) guidelines. Measurements were obtained at the time of admission to the study. Body composition was determined by whole-body dual-energy X-ray absorptiometry. The association between REE and 3-year survival was investigated. RESULTS: Cirrhosis etiology was classified as alcohol related (59.0%), viral (20.1%), cryptogenic (11.8%), or other (9.0%). Mean Child-Pugh and MELD indexes were 8.30 ± 2.0 and 14.38 ± 6.12, respectively. RQ showed a moderate correlation with SM (r = 0.64), while IC-measured REE was inversely associated with mortality (multivariate Cox Regression, HR = 0.88, 95% CI: 0.78; 1, p = 0.04). Among the predictive equations for REE, only Harris-Benedict yielded values close to the IC, with a positive Pearson correlation (r = 0.77), excellent accuracy (Cb = 0.98), and positive Lin's concordance correlation (CCC = 0.75). However, a large standard deviation was observed; HB-measured REE did not correlate with mortality. CONCLUSIONS: RQ and REE, as measured by IC, may be valuable tools for evaluating the severity of cirrhosis, by reflecting SM and predicting mortality, respectively. The predictive equations for REE included in this study cannot replace IC for this purpose. REGISTERED AT: www.clinicalTrials.gov (NCT02421848).

Evolution of Biomarkers of Atherogenic Risk in Liver Transplantation Recipients.

BACKGROUND: Cardiovascular disease is a major contributing factor to long-term mortality after liver transplantation (LT). METHODS: This study evaluated the evolution of atherogenic risk in liver transplant recipients (LTRs). Thirty-six subjects were prospectively enrolled at 12 months and followed for 48 months after liver transplantation. Serum biomarkers of endothelial dysfunction (sICAM-1 and sVCAM-1), chronic inflammation (serum amyloid A), and oxidative stress (myeloperoxidase) were measured at 12 and 48 months after LT. Additionally, at 12 months all patients underwent a cardiac computed tomography (CT) scan and a coronary artery calcium score (CACS). RESULTS: The prevalence of risk factors of metabolic syndrome (MS) increased over the course of the study. The patients' sVCAM-1 and sICAM-1 increased from 1.82 ± 0.44 ng/mL to 9.10 ± 5.82 ng/mL (P < .001) and 0.23 ± 0.09 ng/mL to 2.7 ± 3.3 ng/mL, respectively from month 12 to 48. Serum myeloperoxidase increased from 0.09 ± 0.07 ng/mL to 3.46 ± 3.92 ng/mL (P < .001) over the course of the study. Serum amyloid A also increased from 21.4 ± 40.7 ng/mL at entry to 91.5 ± 143.6 ng/mL at end of study (P < .001). CONCLUSION: No association between these biomarkers and MS was noted. The cardiac CT revealed mild and moderate disease in 19% and 25% of the cohort, respectively. No association between serum biomarkers and CACS was noted. Serum biomarkers of atherogenic risk increase rapidly in LTRs and precede coronary plaques.

Access to Liver Transplantation in Different ABO-Blood Groups and "Exceptions Points" in a Model for End-Stage Liver Disease Allocation System: A Brazilian Single-Center Study.

BACKGROUND: In the Model for End-Stage Liver Disease (MELD) system, patients with "MELD exceptions" points may have unfair privilege in the competition for liver grafts. Furthermore, organ distribution following identical ABO blood types may also result in unjust organ allocation. The aim of this study was to investigate access to liver transplantation in a tertiary Brazilian center, regarding "MELD exceptions" situations and among ABO-blood groups. METHODS: A total of 465 adult patients on the liver waitlist from August 2015 to August 2016 were followed up until August 2017. Patients were divided into groups according to ABO-blood type and presence of "exceptions points." RESULTS: No differences in outcomes were observed among ABO-blood groups. However, patients from B and AB blood types spent less time on the list than patients from A and O groups (median, 46, 176, 415, and 401 days, respectively; P = .03). "Exceptions points" were granted for 141 patients (30.1%), hepatocellular carcinoma being the most common reason (52.4%). Patients with "exceptions points" showed higher transplantation rate, lower mortality on the list, and lower delta-MELD than non-exceptions patients (56.7% vs 19.1% [P < .01]; 18.4% vs 38.5% [P < .01], and 2.0 ± 2.6 vs 6.9 ± 7.0 [P < .01], respectively). Patients with refractory ascites had a higher mortality rate than those with other "exceptions" or without (48%). CONCLUSIONS: The MELD system provides equal access to liver transplantation among ABO-blood types, despite shorter time on the waitlist for AB and B groups. The current MELD exception system provides advantages for candidates with "exception points," resulting in superior outcomes compared with those without exceptions.

Stratifying Mortality in a Model for End-Stage Liver Disease Waiting List: A Brazilian Single-Center Study.

BACKGROUND: The Model for End-Stage Liver Disease (MELD) system reliably predicts mortality in cirrhotic patients. However, the etiology of liver disease and presence of portal vein thrombosis are not directly taken into account in MELD score. Its impact on the outcomes of patients on the waiting list is still unclear. The aim of this study was to investigate mortality and access to transplantation regarding etiology of liver disease and portal vein thrombosis (PVT). METHODS: A total of 465 adult patients on the liver waiting list from August 2015 to August 2016 were followed up until August 2017. Patients were divided into groups according to the etiology of liver disease and presence of PVT. RESULTS: The most frequent etiologies were hepatitis C (26.88%), alcoholic cirrhosis (26.02%) and cryptogenic cirrhosis (10.75%). Death while on the waiting list occurred in 168 patients (36.1%) and was more frequent in nonalcoholic steatohepatitis (NASH, 65.4%) and alcoholic cirrhosis (41.3%). A total of 142 (30.5%) patients underwent transplantation and viral, autoimmune, and biliary diseases showed higher proportion of transplantation (36.3%, 53.8%, and 34%, respectively; P < .01). Mean delta-MELD at the study endpoint was higher in patients with autoimmune hepatitis, biliary diseases, and NASH (8.3 ± 7.2, 8.3 ± 9.1, and 7.5 ± 9.1, respectively; P < .01). A total 77 patients (16.7%) presented PVT. There was no significant difference in outcomes between patients with and without PVT. CONCLUSIONS: Patients with NASH and alcoholic liver disease had higher mortality while on the waiting list, whereas patients with viral and autoimmune hepatitis had higher transplantation rate. Outcomes were not influenced by PVT.

Transient Elastography in Acute Cellular Rejection Following Liver Transplantation: Systematic Review.

BACKGROUND: Transient elastography (TE) is a noninvasive technique that measures liver stiffness. When an inflammatory process is present, this is shown by elevated levels of stiffness. Acute cellular rejection (ACR) is a consequence of an inflammatory response directed at endothelial and bile epithelial cells, and it is diagnosed through liver biopsy. This is a systematic review of the viability of TE in ACR following liver transplantation. METHODS: The Cochrane Library, Embase, and Medline PubMed databases were searched and updated to November 2016. The MESH terms used were "Liver Transplantation," "Graft Rejection," "Elasticity Imaging Techniques" (PubMed), and "Elastography" (Cochrane and Embase). RESULTS: Seventy studies were retrieved and selected using the PICO (patient, intervention, comparison or control, outcome) criteria. Three prospective studies were selected to meta-analysis and evaluation. A total of 33 patients with ACR were assessed with TE. One study showed a cutoff point of >7.9 kPa to define graft damage and <5.3 kPa to exclude graft damage (receiver operating characteristic 0.93; P < .001). Another study showed elevated levels of liver stiffness in ACR patients. However, in this study, no cutoff point for ACR was suggested. The final prospective study included 27 patients with ACR at liver biopsy. Cutoff points were defined as TE > 8.5 kPa, moderate to severe ACR, with a specificity of 100% and receiver operating characteristic curve of 0.924. The measurement of TE < 4.2 kPa excludes the possibility of any ACR (P = .02). CONCLUSIONS: TE may be an important tool for the severity of ACR in patients following liver transplantation. Further studies should be performed to better define the cutoff points and applicability of the exam.

Better Selection Criteria With Prognostic Factors for Liver Transplantation.

BACKGROUND: Liver transplantation has evolved significantly in recent years, with each advancement part of the effort toward increasing patient and graft survival as well as quality of life. The objective of this study was to evaluate the prognostic factors and selection criteria for liver transplantation. METHODS: Our study was a statistical analysis, logistic regression, and survival evaluation of a total of 80 liver transplants that were performed between June 1, 2016 and September 24, 2016. Recipient factors evaluated included age, retransplantation, hemodialysis, cardiac risk, portal vein thrombosis, hospitalization, fulminant hepatitis, previous surgery, renal failure, and Model for End-stage Liver Disease (MELD) score. Donor factors included age, cardiac arrest, acidosis, days in the intensive care unit, steatosis, and vasoactive drug use. RESULTS: Of the 80 patients transplanted, 65 deceased donor liver transplants (DDLTs) and 15 living donor liver transplants (LDLTs) were performed. LDLT overall 1-year patient survival was 77.5% and graft survival 75%, and DDLT overall patient survival was 89.23% and graft survival was 86.15%. On evaluated score criteria analyzed we observed a significant score on recipient (P = .01) and not significant on donor (P =.45). Isolated factors evaluated included recipient age (relative risk [RR] 3.15, 95% confidence interval [CI] 0.89 to 11.09; P = .074), retransplant (RR 4.22, 95% CI 1.36 to 13.1; P = .013), and hemodialysis (RR 4.23, 95% CI 1.45 to 12.31, P = .008). On donor evaluation, we observed moderate and severe steatosis (RR 3.8, 95% CI 0.86 to 16.62; P = .06). CONCLUSION: In conclusion, we demonstrate a relevant model of criteria selection of liver transplant patients that is able to make a better match between the donor and recipient allocation for a better graft and patient survival.

Effect of Hepatic Preconditioning with the Use of Methylene Blue on the Liver of Wistar Rats Submitted to Ischemia and Reperfusion.

BACKGROUND: The liver may be injured in situations where it is submitted to ischemia, such as partial hepatectomy and liver transplantation. In all cases, ischemia is followed by reperfusion and, although it is essential for the reestablishment of tissue function, reperfusion may cause greater damage than ischemia, an injury characterized as ischemia-reperfusion (I/R) damage. The aim of this work was to analyze the effect of ischemic preconditioning with the use of methylene blue (MB; 15 mg/kg) 5 or 15 minutes before I/R (IRMB5' and IRMB15', respectively) on the hepatic injury occurring after I/R. METHODS: Twenty-eight male Wistar rats were used, and liver samples submitted to partial ischemia (IR) or not (NI) were obtained from the same animal. The samples were divided into 7 groups. Data were analyzed statistically by means of the nonparametric Mann-Whitney test and Wilcoxon Matched test, with the level of significance set at 5% (P < .05). RESULTS: The rate of oxygen consumption by state 3 mitochondria was inhibited in all ischemic groups compared with the sham group (SH vs IR: P = .0052; SH vs IRMB5': P = .0006; SH vs IRMB15': P = .0048), which did not occur in the nonischemic contralateral portion of the same liver (SH vs NI: P = .7652; SH vs NIMB5': P = .059; SH vs NIMB15': P = .3153). The inhibition of the rate of oxygen consumption by state 3 mitochondria was maintained in the presence of MB (IR vs IRMB5': P = .4563; IR vs IRMB15': P = .9021). The respiratory control ratio was reduced in all ischemic groups compared with the sham group, owing to the inhibition of oxygen consumption in state 3 (SH vs IR: P = .0151; SH vs IRMB5': P = .005; SH vs IRMB15': P = .0007). CONCLUSIONS: Methylene blue had no effect on the mitochondrial respiratory parameters studied, but was able to reduce lipid peroxidation, preventing the production of reactive oxygen species (SH vs IRMB15': P = .0210).

Method for the estimation of genetic merit of animals with uncertain paternity under Bayesian inference.

The use of controlled mating or artificial insemination is impracticable in the case of large herds, mainly because of labour costs and the need to delimit areas during the breeding period. However, the exclusion of information from animals with uncertain paternity reduces genetic progress. The objectives of this study were as follows: (i) propose an iterative empirical Bayesian procedure to implement the hierarchical animal model (ITER); (ii) calculate the posterior probabilities of paternity by the maximum likelihood method following the concepts; (iii) compare an average numerator relationship matrix (ANRM), Bayesian hierarchical (HIER) models and ITER. Records of Nellore animals born between 1984 and 2006 from the zootechnical archive of Agropecuária Jacarezinho Ltda were used. For data consistency, records of contemporary groups (CGs) with fewer than three animals and animals whose records were 3.5 standard deviations above or below the mean of their CG were eliminated. After editing the data, 62,212 animals in the file and 12,876 animals in pedigree file were maintained, respectively. Spearman and Pearson correlations between the posterior mean of the genetic effects of animals were calculated to compare the ranking of animals for selection. Simulated data were used to confirm the veracity of the model. The correlations between ITER and HIER and between ITER and ANRM were similar evaluating different files, which decreased at the same proportion when only high-ranked animals were evaluated. In conclusion, the model proposed herein is a suitable computational alternative to improve the prediction of breeding values of animals in genetic evaluations using large databases, including animals with uncertain paternity.

Reaction norm for yearling weight in beef cattle using single-step genomic evaluation.

When the environment on which the animals are raised is very diverse, selecting the best sires for different environments may require the use of models that account for genotype by environment interaction (G × E). The main objective of this study was to evaluate the existence of G × E for yearling weight (YW) in Nellore cattle using reaction norm models with only pedigree and pedigree combined with genomic relationships. Additionally, genomic regions associated with each environment gradient were identified. A total of 67,996 YW records were used in reaction norm models to calculate EBV and genomic EBV. The method of choice for genomic evaluations was single-step genomic BLUP (ssGBLUP). Traditional and genomic models were tested on the ability to predict future animal performance. Genetic parameters for YW were obtained with the average information restricted maximum likelihood method, with and without adding genomic information for 5,091 animals. Additive genetic variances explained by windows of 200 adjacent SNP were used to identify genomic regions associated with the environmental gradient. Estimated variance components for the intercept and the slope in traditional and genomic models were similar. In both models, the observed changes in heritabilities and genetic correlations for YW across environments indicate the occurrence of genotype by environment interactions. Both traditional and genomic models were capable of identifying the genotype by environment interaction; however, the inclusion of genomic information in reaction norm models improved the ability to predict animals' future performance by 7.9% on average. The proportion of genetic variance explained by the top SNP window was 0.77% for the regression intercept (BTA5) and 0.82% for the slope (BTA14). Single-step GBLUP seems to be a suitable model to predict genetic values for YW in different production environments.

Characterization of tomato leaf curl purple vein virus, a new monopartite New World begomovirus infecting tomato in Northeast Brazil.

A new begomovirus species was identified from tomato plants with upward leaf curling and purple vein symptoms, which was first identified in the Piaui state of Northeast (NE) Brazil in 2014. Tomato leaf samples were collected in 2014 and 2016, and PCR with degenerate primers revealed begomovirus infection. Rolling circle amplification and restriction enzyme digestion indicated a single genomic DNA of ~ 2.6 kb. Cloning and sequencing revealed a genome organization similar to DNA-A components of New World (NW) bipartite begomoviruses, with no DNA-B. The complete nucleotide sequence had the highest identity (80%) with the DNA-A of Macroptilium yellow spot virus (MacYSV), and phylogenetic analyses showed it is a NW begomovirus that clusters with MacYSV and Blainvillea yellow spot virus, also from NE Brazil. Tomato plants agroinoculated with a dimeric clone of this genomic DNA developed upward leaf curling and purple vein symptoms, indistinguishable from those observed in the field. Based on agroinoculation, this virus has a narrow host range, mainly within the family Solanaceae. Co-inoculation experiments with tomato severe rugose virus and tomato mottle leaf curl virus, the two predominant begomoviruses infecting tomato in Brazil, revealed a synergistic interaction among these begomoviruses. The name Tomato leaf curl purple vein virus (ToLCPVV) is proposed for this new begomovirus.