41 results on '"Silva, F.F."'
Search Results
2. New constraints for paleogeographic reconstructions at ca. 1.88 Ga from geochronology and paleomagnetism of the Carajás dyke swarm (eastern Amazonia)
- Author
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Antonio, P.Y.J., D'Agrella-Filho, M.S., Nédélec, A., Poujol, M., Sanchez, C., Dantas, E.L., Dall'Agnol, R., Teixeira, M.F.B., Proietti, A., Martínez Dopico, C.I., Oliveira, D.C., Silva, F.F., Marangoanha, B., and Trindade, R.I.F.
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- 2021
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3. Effects of nutrient intake level on mammary parenchyma growth and gene expression in crossbred (Holstein × Gyr) prepubertal heifers
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Weller, M.M.D.C.A., Albino, Ronan L., Marcondes, M.I., Silva, W., Daniels, K.M., Campos, M.M., Duarte, M.S., Mescouto, M.L., Silva, F.F., and Guimarães, S.E.F.
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- 2016
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4. Effect of maternal nutrition and days of gestation on pituitary gland and gonadal gene expression in cattle
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Weller, M.M.D.C.A., Fortes, M.R.S., Marcondes, M.I., Rotta, P.P., Gionbeli, T.R.S., Valadares Filho, S.C., Campos, M.M., Silva, F.F., Silva, W., Moore, S., and Guimarães, S.E.F.
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- 2016
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5. A genome-wide association study reveals a novel candidate gene for sperm motility in pigs
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Diniz, D.B., Lopes, M.S., Broekhuijse, M.L.W.J., Lopes, P.S., Harlizius, B., Guimarães, S.E.F., Duijvesteijn, N., Knol, E.F., and Silva, F.F.
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- 2014
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6. Genome‐wide association study and annotating candidate gene networks affecting age at first calving in Nellore cattle
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Mota, R.R., Guimarães, S.E.F., Fortes, M.R.S., Hayes, B., Silva, F.F., Verardo, L.L., Kelly, M.J., de Campos, C.F., Guimarães, J.D., Wenceslau, R.R., Penitente‐Filho, J.M., Garcia, J.F., and Moore, S.
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- 2017
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7. Identification and expression levels of pig miRNAs in skeletal muscle
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Verardo, L.L., Nascimento, C.S., Silva, F.F., Gasparino, E., Toriyama, E., Barbosa, A.R., Périssé, I.V., Costa, K.A., Lopes, P.S., and Guimarães, S.E.F.
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- 2013
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8. Use of molecular markers to improve relationship information in the genetic evaluation of beef cattle tick resistance under pedigree‐based models
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Junqueira, V.S., Cardoso, F.F., Oliveira, M.M., Sollero, B.P., Silva, F.F., and Lopes, P.S.
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- 2017
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9. Effects of equine chorionic gonadotropin and type of ovulatory stimulus in a timed-AI protocol on reproductive responses in dairy cows
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Souza, A.H., Viechnieski, S., Lima, F.A., Silva, F.F., Araújo, R., Bó, G.A., Wiltbank, M.C., and Baruselli, P.S.
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- 2009
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10. Genetic evaluation of age at first calving for Guzerá beef cattle using linear, threshold, and survival Bayesian models
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Brito, L.C., Casellas, J., Varona, L., Lopes, P.S., Ventura, H.T., Peixoto, M.G.C.D., Lázaro, S.F., and Silva, F.F.
- Abstract
Age at first calving (AFC) is characterized as a censored trait due to missing values provided by recording mistakes and nonoccur-rence or delay in calving communication. In this context, we aimed to compare several statistical methods for genetic evaluation of AFC in Guzerá beef cattle under a Bayesian approach. Seven different methods were used for this purpose. The traditional linear mixed model (LM), which considers only uncensored records; the LM with simulated records (SM), which is based on data augmentation framework; the penalty method, in which a constant of 21 d was added to censored records; the bivariate threshold-linear method considering (TLcens) or not (TLmiss) censored information; and the piecewise Weibull proportional hazards model considering (PWPHcens) or not (PWPH) censored records. Heritability estimates ranged from 0.19 (TLcens) to 0.28 (SM) in non-survival approaches; and 0.40 and 0.46 to PWPH and PWPHcens methods, respectively. In general, breeding values correlations between different methods and the percentage of selected bulls in common indicated reranking, with these correlation ranging from -0.28 (between SM and PWPH) to 0.99 (between TLmiss and LM). The traditional LM, which considers only uncensored records, should be preferred due to its robustness and simplicity. Based on cross-validation analyses, we conclude that the TLmiss could be also a suitable alternative for breeding value prediction, and censored methods did not improve the analysis.
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- 2018
11. Genotype by feed interaction for feed efficiency and growth performance traits in pigs
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Godinho, R.M., Bastiaansen, J.W.M., Sevillano, C.A., Silva, F.F., Guimarães, S.E.F., and Bergsma, R.
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Genotype by feed interaction ,Feed efficiency ,Genetic gain ,WIAS ,Fokkerij en Genomica ,Animal Breeding and Genomics ,Correlated response ,Breeding program - Abstract
A major objective of pork producers is to reduce production cost. Feeding may account for over 75% of pork production costs. Thus, selecting pigs for feed efficiency (FE) traits is a priority in pig breeding programs. While in the Americas, pigs are typically fed high-input diets, based on corn and soybean meal (CS); in Western Europe, pigs are commonly fed diets based on wheat and barley with high amounts of added protein-rich coproducts (WB), e.g., from milling and seed-oil industries. These two feeding scenarios provided a realistic setting for investigating a specific type of genotype by environment interaction; thus, we investigated the genotype by feed interaction (GxF). In the presence of a GxF, different feed compositions should be considered when selecting for FE. This study aimed to 1) verify the presence of a GxF for FE and growth performance traits in different growth phases (starter, grower, and finisher) of 3-way crossbred growing-finishing pigs fed either a CS (547 boars and 558 gilts) or WB (567 boars and 558 gilts) diet; and 2) to assess and compare the expected responses to direct selection under the 2 diets and the expected correlated responses for one diet to indirect selection under the other diet. We found that GxF did not interfere in the ranking of genotypes under both diets for growth, protein deposition, feed intake, energy intake, or feed conversion rate. Therefore, for these traits, we recommend changing the diet of growing-finishing pigs from high-input feed (i.e., CS) to feed with less valuable ingredients, as WB, to reduce production costs and the environmental impact, regardless of which diet is used in selection. We found that GxF interfered in the ranking of genotypes and caused heterogeneity of genetic variance under both diets for lipid deposition (LD), residual energy intake (REI), and residual feed intake (RFI). Thus, selecting pigs under a diet different from the diet used for growing-finishing performance could compromise the LD in all growth phases, compromise the REI and RFI during the starter phase, and severely compromise the REI during the grower phase. In particular, when pigs are required to consume a WB diet for growing-finishing performance, pigs should be selected for FE under the same diet. Breeding pigs for FE under lower-input diets should be considered, because FE traits will become more important and lower-input diets will become more widespread in the near future.
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- 2018
12. The effect of rural extension on farm technical efficiency in Brazil
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Freitas, C.O.D., Silva, F.F., and Braga, M.J.
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Farm Management - Abstract
The objective of the present research was to identify the effect of rural extension on the productive performance of Brazilian agricultural establishments, using as a measure of performance the technical efficiency of farms. The data used refers to the microdata of the 2006 Agricultural Census, accessed directly from the IBGE secrecy room. For this, an approach that combines the stochastic production frontier structure, taking into account the selection bias in the adoption of the rural extension (Heckman's approach), with the entropy balancing method was used. The results show that the rural extension contributes, in fact, to increase the efficiency in the use of the productive factors, with the producers adopting, more technically efficient than the non-adopters. When considering the differences according to the size of the establishment, an even greater effect was observed for the group of large producers. In addition, in general, public rural extension generated higher technical efficiency scores than those obtained by establishments attended by the private service. Acknowledgement
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- 2018
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13. Short communication: Molecular characterization and antimicrobial resistance of pathogenic Escherichia coli isolated from raw milk and Minas Frescal cheeses in Brazil.
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Ribeiro Júnior, J.C., Silva, F.F., Lima, J.B.A., Ossugui, E.H., Teider Junior, P.I., Campos, A.C.L.P., Navarro, A., Tamanini, R., Ribeiro, J., Alfieri, A.A., and Beloti, V.
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RAW milk , *DRUG resistance in microorganisms , *ESCHERICHIA coli , *CHEESE , *MILK industry , *HUMAN origins - Abstract
The aim of this study was to quantify, identify, evaluate antimicrobial resistance, and characterize the virulence factors of enteropathogenic (EPEC), Shiga-toxigenic (STEC), and enterohemorrhagic (EHEC) Escherichia coli in raw milk (RM) and legal (LMFC) and illegal (IMFC) Minas Frescal cheeses in southern and northeast Brazil. Illegal cheeses are those made without official inspection service or sanitary surveillance. We evaluated samples of RM produced in Paraná (southern) and Maranhão (northeast) States, LMFC produced using pasteurized milk in inspected industries, and IMFC potentially produced with raw milk. Mean total coliform counts were 8.4 × 104 cfu/mL for RM, 1.4 × 107 cfu/mL for LMFC, and 2.9 × 107 cfu/mL for IMFC. Mean E. coli counts were 2.4 × 103 cfu/mL for RM, 1.9 × 102 cfu/mL for LMFC, and 1.1 × 105 cfu/mL for IMFC. Among the 205 E. coli isolates from RM, 9.75% were identified as EPEC, mainly (90%) in samples from Paraná. Of the total isolates from the cheese samples, 97.4% (n = 111) came from IMFC, of which 1.8 and 2.7% were identified as EPEC and STEC, respectively; no EHEC was detected. The phylogenetic group A (60%) and typical EPEC (68%) predominated, which confirms the possible human origin of pathogenic isolates in RM and IMFC. Of these, 50% were resistant to at least one antibiotic, and streptomycin was the antimicrobial with the highest number (8) of EPEC and STEC resistant isolates. This study reports the first isolation of serogroup O28ac in Brazilian milk. We found no predominance of a specific serogroup of EPEC or STEC in milk or cheese or clonal isolates in the same sample, indicating different origins of the contamination in these products, presumably mostly related to poor hygienic handling. [ABSTRACT FROM AUTHOR]
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- 2019
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14. Hydraulic properties of sphagnum peat moss and tuff (scoria) and their potential effects on water availability
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da SILVA, F.F., WALLACH, R., and CHEN, Y.
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- 1993
15. After genome-wide association studies : Gene networks elucidating candidate genes divergences for number of teats across two pig populations
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Verardo, L.L., Lopes, M.S., Wijga, S., Madsen, O., Silva, F.F., Groenen, M.A.M., Knol, E.F., Lopes, P.S., and Guimarães, S.E.F.
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Complex trait ,WIAS ,Fokkerij en Genomica ,Animal Breeding and Genomics ,Genetic diversity ,Genomewide association study - Abstract
Number of teats (NT) is an important trait affecting both piglet’s welfare and the production level of pig farms. Biologically, embryonic mammary gland development requires the coordination of many signaling pathways necessary for the proper development of teats. Several QTL for NT have been identified; however, further analysis is still lacking. Therefore, gene networks derived from genomewide association study (GWAS) results can be used to examine shared pathways and functions of putative candidate genes. Besides, such analyses may also be helpful to understand the genetic diversity between populations for the same trait or traits. In this study, we identified significant SNP for Landrace-based (line C) and Large White–based (line D) dam lines. Besides, gene– transcription factor (TF) networks were constructed aiming to obtain the most likely candidate genes for NT in each line followed by a comparative analysis between both lines to access similarities or dissimilarities at the marker and gene level. We identified 24 and 19 significant SNP (Bayes factor ≥ 100) for lines C and D, respectively. Only 1 significant SNP overlapped both lines. Network analysis illustrated gene interactions consistent with known mammal’s breast biology and captured known TF. We observed different sets of putative candidate genes for NT in each line evaluated that may have common effects on the phenotype. Based on these results, we demonstrated the importance of post-GWAS analyses increasing the biological understanding of relevant genes for a complex trait. Moreover, we believe that this genomic diversity across lines should be taken into account, considering breed-specific reference populations for genomic selection.
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- 2016
16. Fatty acids intake and deposition in the Longissimus of Nellore steers supplemented at pasture
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Oliveira, A.P., Silva, R.R., Souza, S.O., Carvalho, G.G.P., Silva, F.F., Lisboa, M.M., Pereira, M.M.S., Carvalho, V.M., Mendes, F.B.L., and Oliveira, A.C.
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Ácidos graxos monoinsaturados ,Monounsaturated fatty acids ,Ácidos graxos saturados ,Polyunsaturated fatty acids ,Ruminantes ,Saturated fatty acids ,Ruminants ,Ácidos graxos poliinsaturados - Abstract
The aim of this work was to study the correlation between intake and deposition of fatty acids in the Longissimus muscle of Nellore steers supplemented at pasture. The fieldwork was implanted in an area of 52 ha, formed of Brachiaria brizantha. Forty Nellore steers with initial average weight of 373.7 ± 14.9 kg and 26 months of age were used. The animals were distributed into four treatments: Control= T00 (supply only mineral salt), T03= Supply of concentrate in the amount of 0.3 % of Body Weight; T06= Supply of concentrate in the amount of 0.6 % of Live Weight , T09= Supply of concentrate in the amount of 0.9 % of live weight. Samples of concentrates and forages were collected for fatty acids analysis. The experiment lasted for 98 days. After this period the animals were slaughtered. Longissimus samples were vacuum packed and frozen for analysis of fatty acid composition. The results were statistically analyzed by estimating Pearson linear correlation coefficients. The results showed that there are correlations between the fatty acids consumed and fatty acids deposited in the muscle. Objetivou-se estudar a correlação entre consumo e deposição de ácidos graxos no músculo Longissimus de novilhos nelore suplementados em pastagens. O trabalho de campo foi implantado numa área de 52 ha, formada de Brachiaria brizantha. Foram utilizados 40 novilhos da raça Nelore com peso inicial médio de 373,7 ± 14,9 kg e 26 meses de idade, distribuídos em quatro tratamentos: Controle= T00 (fornecimento apenas de sal mineral), T03= fornecimento de 0,3% concentrado em função do peso vivo; T06= fornecimento de 0,6 % concentrado em função do peso vivo; T09= fornecimento de 0,9 % concentrado em função do peso vivo. Amostras dos concentrados e da forragem foram coletadas para análise da composição de ácidos graxos. O período experimental foi de 98 dias. Após este período, os animais foram abatidos. Os resultados foram analisados por correlação linear de Pearson e teste t. Constatou-se que existem correlações entre os ácidos graxos consumidos e depositados no músculo.
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- 2014
17. Sire evaluation for total number born in pigs using a genomic reaction norms approach
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Silva, F.F., Mulder, H.A., Knol, E.F., Lopes, M.S., Guimaraes, S.E.F., Lopes, P.S., Mathur, P.K., Viana, J.M.S., and Bastiaansen, J.W.M.
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dairy-cattle ,merit ,milk ,genotype ,pedigree ,production traits ,Animal Breeding and Genomics ,genetic-parameters ,models ,matrices ,WIAS ,environment interaction ,Fokkerij en Genomica - Abstract
In the era of genome-wide selection (GWS), genotype-by-environment (G×E) interactions can be studied using genomic information, thus enabling the estimation of SNP marker effects and the prediction of genomic estimated breeding values (GEBVs) for young candidates for selection in different environments. Although G×E studies in pigs are scarce, the use of artificial insemination has enabled the distribution of genetic material from sires across multiple environments. Given the relevance of reproductive traits such as the total number born (TNB) and the variation in environmental conditions encountered by commercial dams, understanding G×E interactions can be essential to choose the best sires for different environments. The present work proposes a two-step reaction norm approach for G×E analysis using genomic information. The first step provided estimates of environmental effects (herd-year-season - HYS), and the second step provided estimates of the intercept and slope for the TNB across different HYS levels, obtained from the first step, using a random regression model. In both steps, pedigree (A) and genomic (G) relationship matrices were considered. The genetic parameters (variance components, h2 and genetic correlations) were very similar when estimated using the A and G relationship matrices. The reaction norm graphs showed considerable differences in environmental sensitivity between sires, indicating a reranking of sires in terms of genetic merit across the HYS levels. Based on the G matrix analysis, SNP by environment interactions were observed. For some SNPs, the effects increased at increasing HYS levels, while for others, the effects decreased at increasing HYS levels or showed no changes between HYS levels. Cross-validation analysis demonstrated better performance of the genomic approach with respect to traditional pedigrees for both the G×E and standard models. The genomic reaction norm model resulted in an accuracy of GEBVs for “juvenile” boars varying from 0.14 to 0.44 across different HYS levels, while the accuracy of the standard genomic prediction model, without reaction norms, varied from 0.09 to 0.28. These results show that it is important and feasible to consider G×E interactions in evaluations of sires using genomic prediction models and that genomic information can increase the accuracy of selection across environments.
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- 2014
18. 229P - Evaluation of human epidermal growth factor receptor 2 overexpression (HER2+) after administration of neoadjuvant treatment (NAT) and prognostic impact in breast cancer (BC)
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Machado, D.H.R., Branco, F., Silva, F.F., André, S., Brito, M., Casanova, M., Nave, M., Moreira, A., and Passos-Coelho, J.L.C.
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- 2018
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19. Genome wide association study reveals new candidate genes for resistance to nematodes in Creole goat.
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Silva, F.F., Bambou, J.C., Oliveira, J.A., Barbier, C., Fleury, J., Machado, T., and Mandonnet, N.
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GOAT diseases , *NEMATODES , *GENOMES , *GENOMICS , *GOAT behavior - Abstract
An alternative control for gastrointestinal nematode (GIN) infection in goats can be achieved by genetic improvement of the host resistance through identification of genes controlling the resistance mechanisms and their use in breeding programs under a marker-assisted selection or gene introgression frameworks. In this context, we aimed to develop genome wide association studies (GWAS) for resistance to H. contortus in Creole goats from Guadeloupe to identify possible candidate genes associated with GIN resistance in this population. Resistance was characterized by the fecal egg counting (FEC). A total of 182 Creole goats were phenotyped for FEC and genotyped through Illumina Goat SNP50 BeadChip. After SNP quality control analysis, 46,643 SNP markers were used for GWAS. The significant associations were identified by fitting a linear mixed model. A total of seven QTL (on the chromosomes 4, 6, 11, and 17) associated to FEC were reported and candidate genes recording was performed at these positions. The identified genes were related to the intestine damage ( PROM1 ), inflammation process ( FGFBP1 ), immune response ( LIMCH1 ), hemorrhage control ( ADAMTS3 ), and muscle weakness ( SUCLG1 ). Network analysis provided annotation results linking all identified candidate genes, which are biologically related to resistance mechanisms approaching H. contortus infections. [ABSTRACT FROM AUTHOR]
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- 2018
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20. Accounting for genetic architecture in single- and multipopulation genomic prediction using weights from genomewide association studies in pigs.
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Veroneze, R., Lopes, P.S., Lopes, M.S., Hidalgo, A.M., Guimarães, S.E.F., Harlizius, B., Knol, E.F., Arendonk, J.A.M., Silva, F.F., and Bastiaansen, J.W.M.
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GENETIC research ,BIOLOGY ,GENOMICS ,MOLECULAR genetics ,SWINE genetics - Abstract
We studied the effect of including GWAS results on the accuracy of single- and multipopulation genomic predictions. Phenotypes (backfat thickness) and genotypes of animals from two sire lines ( SL1, n = 1146 and SL3, n = 1264) were used in the analyses. First, GWAS were conducted for each line and for a combined data set (both lines together) to estimate the genetic variance explained by each SNP. These estimates were used to build matrices of weights (D), which was incorporated into a GBLUP method. Single population evaluated with traditional GBLUP had accuracies of 0.30 for SL1 and 0.31 for SL3. When weights were employed in GBLUP, the accuracies for both lines increased (0.32 for SL1 and 0.34 for SL3). When a multipopulation reference set was used in GBLUP, the accuracies were higher (0.36 for SL1 and 0.32 for SL3) than in single-population prediction. In addition, putting together the multipopulation reference set and the weights from the combined GWAS provided even higher accuracies (0.37 for SL1, and 0.34 for SL3). The use of multipopulation predictions and weights estimated from a combined GWAS increased the accuracy of genomic predictions. [ABSTRACT FROM AUTHOR]
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- 2016
- Full Text
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21. Supervised independent component analysis as an alternative method for genomic selection in pigs.
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Azevedo, C.F., Silva, F.F., Resende, M.D.V., Lopes, M.S., Duijvesteijn, N., Guimarães, S.E.F., Lopes, P.S., Kelly, M.J., Viana, J.M.S., and Knol, E.F.
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SWINE genetics , *SINGLE nucleotide polymorphisms , *INDEPENDENT component analysis , *PHENOTYPES , *SWINE carcasses - Abstract
The objective of this work was to evaluate the efficiency of the supervised independent component regression ( SICR) method for the estimation of genomic values and the SNP marker effects for boar taint and carcass traits in pigs. The methods were evaluated via the agreement between the predicted genetic values and the corrected phenotypes observed by cross-validation. These values were also compared with other methods generally used for the same purposes, such as RR- BLUP, SPCR, SPLS, ICR, PCR and PLS. The SICR method was found to have the most accurate prediction values. [ABSTRACT FROM AUTHOR]
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- 2014
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22. Back-to-back energization of a 60kV cable network - inrush currents phenomenon.
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da Silva, F.F., Bak, C.L., and Hansen, M.L.
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- 2010
- Full Text
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23. Linear and Poisson models for genetic evaluation of tick resistance in cross-bred Hereford x Nellore cattle.
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Ayres, D.R., Pereira, R.J., Boligon, A.A., Silva, F.F., Schenkel, F.S., Roso, V.M., and Albuquerque, L.G.
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CATTLE breeding ,TREATMENT of cattle diseases ,HEREFORD cattle ,RHIPICEPHALUS ,CATTLE parasites ,LINEAR statistical models ,POISSON processes ,GENETICS - Abstract
Cattle resistance to ticks is measured by the number of ticks infesting the animal. The model used for the genetic analysis of cattle resistance to ticks frequently requires logarithmic transformation of the observations. The objective of this study was to evaluate the predictive ability and goodness of fit of different models for the analysis of this trait in cross-bred Hereford x Nellore cattle. Three models were tested: a linear model using logarithmic transformation of the observations ( MLOG); a linear model without transformation of the observations ( MLIN); and a generalized linear Poisson model with residual term ( MPOI). All models included the classificatory effects of contemporary group and genetic group and the covariates age of animal at the time of recording and individual heterozygosis, as well as additive genetic effects as random effects. Heritability estimates were 0.08 ± 0.02, 0.10 ± 0.02 and 0.14 ± 0.04 for MLIN, MLOG and MPOI models, respectively. The model fit quality, verified by deviance information criterion ( DIC) and residual mean square, indicated fit superiority of MPOI model. The predictive ability of the models was compared by validation test in independent sample. The MPOI model was slightly superior in terms of goodness of fit and predictive ability, whereas the correlations between observed and predicted tick counts were practically the same for all models. A higher rank correlation between breeding values was observed between models MLOG and MPOI. Poisson model can be used for the selection of tick-resistant animals. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
24. Identification and validation of differentially expressed genes from pig skeletal muscle.
- Author
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Verardo, L.L., Nascimento, C.S., Silva, F.F., Gasparino, E., Martins, M.F., Toriyama, E., Faria, V.R., Botelho, M.E., Costa, K.A., Lopes, P.S., and Guimarães, S.E.F.
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SWINE breeding ,MEAT ,MEAT industry ,MYOGENESIS ,PHENOTYPES ,SWINE breeds - Abstract
Pig is an important animal for meat production; this is generally associated with characteristics determined prenatally during myogenesis. Expressed sequence tags ( EST) can provide direct information on the transcriptome and indirect information on the relation between the genome and phenotype, giving information about differentially expressed genes ( DEG). In this work, the identification and annotation of DEG from EST libraries of three pig breeds ( Duroc, Large White and Local Breed Piau) were performed followed by real-time PCR analyses during pre- and postnatal stages (21, 40, 70 and 90 days of pregnancy and 107, 121 and 171 days postnatal) from commercial breed animals for analysis of genes expression levels. Therefore, 34 genes differentially expressed were identified, of which 21 grouped in a network related with muscle development. From this, the expression profile of 13 genes was measured, to confirm their relationship with myogenesis like ANKRD2, MYBPC1, NEB and MYL2. These genes showed a prenatal high expression in this study. Besides, novels candidates for muscle development ( TP53 and DCTN1) were listed. These findings can contribute to better explaining gene function mechanism and are helpful in uncovering the pathways that mediate pre- and postnatal skeletal muscle development in vertebrates. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
25. Genotype by environment interaction for Holstein cattle populations using autoregressive and within- and across-country multi-trait reaction norms test-day models.
- Author
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Silva, D.A., Lopes, P.S., Costa, C.N., Silva, A.A., Silva, H.T., Silva, F.F., Veroneze, R., Thompson, G., and Carvalheira, J.
- Abstract
The progenies of international bulls in diverse climatic conditions and management levels may lead to different expressions of their genetic potential resulting in a re-ranking of these bulls. Therefore, evaluate the presence of genotype by environment interaction (G × E) within and across countries is important to guide the decision-making on alternative selection strategies. Thus, a two-step reaction norm (RN) approach was used to investigate the presence of G × E in Portuguese and Brazilian Holstein cattle. In step 1, we performed a within-country genetic evaluation using an autoregressive model to obtain precorrected phenotypes and environmental gradients (herd test-day solutions, HTD levels). In step 2, the precorrected phenotypes were considered as two distinct traits in a bi-trait RN model to estimate variance components across HTD levels, genetic correlation between HTD levels in Portugal and Brazil, and RN of the estimated breeding values. Additionally, the genetic correlation between countries using a bi-trait random regression (RR) sire model was obtained. In step 1, genetic additive variance for milk yield (MY) in Portugal was 14.1% higher than in Brazil. For somatic cell score (SCS), the genetic additive variance in Portugal was 12.7% lower than in Brazil. Although similar heritability estimates for SCS were observed in both countries, MY heritabilities were 0.31 for Portugal and 0.23 for Brazil. Genetic correlations (SD) between both countries obtained using RR sire model were 0.78 (0.051) for MY and 0.75 (0.062) for SCS. In step 2, MY genetic correlations among HTD levels within countries were higher than 0.94 for Portugal and 0.98 for Brazil. Somatic cell score genetic correlations among HTD levels ranged from 0.70 to 0.99 for Portugal and from 0.84 to 0.99 for Brazil. The average (SD) of genetic correlation estimates between Portuguese and Brazilian HTD levels were 0.74 (0.009) for MY and 0.57 (0.060) for SCS. These results suggest the presence of G × E for MY and SCS of Holstein cattle between both countries. Although there was no indication of G × E between Brazilian herd environments, the low genetic correlation for SCS indicates potential re-ranking of bulls between extreme environmental gradient in Portugal. Overall, the results of this study evidence the importance of national and international genetic evaluation systems to assist dairy farmers in the selection of the best genotypes to obtain the expected returns from investments in imported semen and to realize genetic progress in dairy populations under local environmental conditions. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
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26. Genomic analyses for predicted milk fatty acid composition throughout lactation in North American Holstein cattle.
- Author
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Freitas, P.H.F., Oliveira, H.R., Silva, F.F., Fleming, A., Miglior, F., Schenkel, F.S., and Brito, L.F.
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ANIMAL herds , *HOLSTEIN-Friesian cattle , *DAIRY cattle , *FATTY acids , *SHORT-chain fatty acids , *MILKFAT , *MILKING - Abstract
Milk fat composition has important implications in the nutritional and processing properties of milk. Additionally, milk fat composition is associated with cow physiological and health status. The main objectives of this study were (1) to estimate genetic parameters for 5 milk fatty acid (FA) groups (i.e., short-chain, medium-chain, long-chain, saturated, and unsaturated) predicted from milk infrared spectra using a large data set; (2) to predict genomic breeding values using a longitudinal single-step genomic BLUP approach; and (3) to conduct a single-step GWAS aiming to identify genomic regions, candidate genes, and metabolic pathways associated with milk FA, and consequently, to understand the underlying biology of these traits. We used 629,769 test-day records of 201,465 first-parity Holstein cows from 6,105 herds. A total of 8,865 genotyped (Illumina BovineSNP50K BeadChip, Illumina, San Diego, CA) animals were considered for the genomic analyses. The average daily heritability ranged from 0.24 (unsaturated FA) to 0.47 (medium-chain and saturated FA). The reliability of the genomic breeding values ranged from 0.56 (long-chain fatty acid) to 0.74 (medium-chain fatty acid) when using the default τ and ω scaling parameters, whereas it ranged from 0.58 (long-chain fatty acid) to 0.73 (short-chain fatty acid) when using the optimal τ and ω values (i.e., τ = 1.5 and ω = 0.6), as defined in a previous study in the same population. Relevant chromosomal regions were identified in Bos taurus autosomes 5 and 14. The proportion of the variance explained by 20 adjacent single nucleotide polymorphisms ranged from 0.71% (saturated FA) to 15.12% (long-chain FA). Important candidate genes and pathways were also identified. In summary, our results contribute to a better understanding of the genetic architecture of predicted milk FA in dairy cattle and reinforce the relevance of using genomic information for genetic analyses of these traits. [ABSTRACT FROM AUTHOR]
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- 2020
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27. Short communication: Genetic parameter estimates for caprine arthritis encephalitis in dairy goats.
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Schultz, E.B., Santana, T.E.Z., Silva, F.F., Garcia, A.O., Oliveira, H.R., Rodrigues, M.T., and Brito, L.F.
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GOATS , *ENCEPHALITIS , *ARTHRITIS , *RETROVIRUS diseases , *MILK quality , *ESTIMATES - Abstract
Caprine arthritis encephalitis (CAE) is a chronic disease caused by a retrovirus from the Lentivirus genus. No effective vaccines or treatments exist, and therefore genetic selection for CAE resistance might be a feasible alternative. To our best knowledge, no other studies have investigated the genetic architecture of CAE resistance in dairy goats. In this context, this study was designed to estimate genetic parameters for CAE infection in Alpine and Saanen goats using a Bayesian threshold model. A total of 542 adult goats (and >3-generation pedigree), which were group-housed in a population with high CAE prevalence, were tested based on a serological infection assessment test (negative = 1 or positive = 2) and used for this study. Genetic parameters were estimated using the BLUPF90 family programs. There was considerable genetic variability for CAE resistance, and pedigree-based heritability was significantly different from zero (0.026 < heritability < 0.128). Our findings indicate that the prevalence of CAE in goat herds can be reduced or eliminated through direct genetic selection for CAE resistance in addition to proper management strategies. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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28. Short communication: Time-dependent genetic parameters and single-step genome-wide association analyses for predicted milk fatty acid composition in Ayrshire and Jersey dairy cattle.
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Freitas, P.H.F., Oliveira, H.R., Silva, F.F., Fleming, A., Schenkel, F.S., Miglior, F., and Brito, L.F.
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JERSEY cattle , *DAIRY cattle , *ANIMAL herds , *CATTLE genetics , *FATTY acids , *CATTLE , *MILKFAT , *MILK - Abstract
Milk fat content and fatty acid (FA) composition have great economic value to the dairy industry as they are directly associated with taste and chemical-physical characteristics of milk and dairy products. In addition, consumers' choices are not only based on the nutritional aspects of food, but also on products known to promote better health. Milk FA composition is also related to the metabolic status and physiological stages of cows and thus can also be used as indicator for other novel traits of interest (e.g., metabolic diseases and methane yield). Genetic selection is a promising alternative to manipulate milk FA composition. In this study, we aimed to (1) estimate time-dependent genetic parameters for 5 milk FA groups (i.e., short-chain, medium-chain, long-chain, saturated, and unsaturated) predicted based on milk mid-infrared spectroscopy, for Canadian Ayrshire and Jersey breeds, and (2) conduct a time-dependent, single-step genome-wide association study to identify genomic regions, candidate genes, and metabolic pathways associated with milk FA. We analyzed 31,709 test-day records of 9,648 Ayrshire cows from 268 herds, and 34,341 records of 11,479 Jersey cows from 883 herds. The genomic database contained a total of 2,330 Ayrshire and 1,019 Jersey animals. The average daily heritability ranged from 0.18 (long-chain FA) to 0.34 (medium-chain FA) in Ayrshire, and from 0.25 (long-chain and unsaturated FA) to 0.52 (medium-chain and saturated FA) in Jersey. Important genomic regions were identified in Bos taurus autosomes BTA3, BTA5, BTA12, BTA13, BTA14, BTA16, BTA18, BTA20, and BTA21. The proportion of the variance explained by 20 adjacent SNP ranged from 0.71% (saturated FA) to 1.11% (long-chain FA) in Ayrshire, and from 0.70% (unsaturated FA) to 3.09% (medium-chain FA) in Jersey cattle. Important candidate genes and pathways were also identified, such as the PTK2 and TRAPPC9 genes, associated with milk fat percentage, and HMGCS , FGF10 , and C6 genes, associated with fertility traits and immune response. Our findings on the genetic parameters and candidate genes contribute to a better understanding of the genetic architecture of milk FA composition in Ayrshire and Jersey dairy cattle. [ABSTRACT FROM AUTHOR]
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- 2020
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29. Autoregressive single-step test-day model for genomic evaluations of Portuguese Holstein cattle.
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Silva, A.A., Silva, D.A., Silva, F.F., Costa, C.N., Lopes, P.S., Caetano, A.R., Thompson, G., and Carvalheira, J.
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DAIRY cattle , *HOLSTEIN-Friesian cattle , *AUTOREGRESSIVE models , *MILK yield , *GENETIC models , *LACTATION - Abstract
The multiple-lactation autoregressive test-day (AR) model is the adopted model for the national genetic evaluation of dairy cattle in Portugal. Under this model, animals' permanent environment effects are assumed to follow a first-order autoregressive process over the long (auto-correlations between parities) and short (auto-correlations between test-days within lactation) terms. Given the relevance of genomic prediction in dairy cattle, it is essential to include marker information in national genetic evaluations. In this context, we aimed to evaluate the feasibility of applying the single-step genomic (G)BLUP to analyze milk yield using the AR model in Portuguese Holstein cattle. In total, 11,434,294 test-day records from the first 3 lactations collected between 1994 and 2017 and 1,071 genotyped bulls were used in this study. Rank correlations and differences in reliability among bulls were used to compare the performance of the traditional (A-AR) and single-step (H-AR) models. These 2 modeling approaches were also applied to reduced data sets with records truncated after 2012 (deleting daughters of tested bulls) to evaluate the predictive ability of the H-AR. Validation scenarios were proposed, taking into account young and proven bulls. Average EBV reliabilities, empirical reliabilities, and genetic trends predicted from the complete and reduced data sets were used to validate the genomic evaluation. Average EBV reliabilities for H-AR (A-AR) using the complete data set were 0.52 (0.16) and 0.72 (0.62) for genotyped bulls with no daughters and bulls with 1 to 9 daughters, respectively. These results showed an increase in EBV reliabilities of 0.10 to 0.36 when genomic information was included, corresponding to a reduction of up to 43% in prediction error variance. Considering the 3 validation scenarios, the inclusion of genomic information improved the average EBV reliability in the reduced data set, which ranged, on average, from 0.16 to 0.26, indicating an increase in the predictive ability. Similarly, empirical reliability increased by up to 0.08 between validation tests. The H-AR outperformed A-AR in terms of genetic trends when unproven genotyped bulls were included. The results suggest that the single-step GBLUP AR model is feasible and may be applied to national Portuguese genetic evaluations for milk yield. [ABSTRACT FROM AUTHOR]
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- 2019
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30. Genomic prediction of lactation curves for milk, fat, protein, and somatic cell score in Holstein cattle.
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Oliveira, H.R., Brito, L.F., Silva, F.F., Lourenco, D.A.L., Jamrozik, J., and Schenkel, F.S.
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GENOMICS , *LACTATION , *MILK yield , *HOLSTEIN-Friesian cattle , *DAIRY cattle breeds - Abstract
Application of random regression models (RRM) in a 2-step genomic prediction might be a feasible way to select young animals based on the complete pattern of the lactation curve. In this context, the prediction reliability and bias of genomic estimated breeding value (GEBV) for milk, fat, and protein yields and somatic cell score over days in milk (DIM) using a 2-step genomic approach were investigated. In addition, the effect of including cows in the training and validation populations was investigated. Estimated breeding values for each DIM (from 5 to 305 d) from the first 3 lactations of Holstein animals were deregressed and used as pseudophenotypes in the second step. Individual additive genomic random regression coefficients for each trait were predicted using RRM and genomic best linear unbiased prediction and further used to derive GEBV for each DIM. Theoretical reliabilities of GEBV obtained by the RRM were slightly higher than theoretical reliabilities obtained by the accumulated yield up to 305 d (P305). However, validation reliabilities estimated for GEBV using P305 were higher than for GEBV using RRM. For all traits, higher theoretical and validation reliabilities were estimated when incorporating genomic information. Less biased GEBV estimates were found when using RRM compared with P305, and different validation reliability and bias patterns for GEBV over time were observed across traits and lactations. Including cows in the training population increased the theoretical reliabilities and bias of GEBV; nonetheless, the inclusion of cows in the validation population does not seem to affect the regression coefficients and the theoretical reliabilities. In summary, the use of RRM in 2-step genomic prediction produced fairly accurate GEBV over the entire lactation curve for all analyzed traits. Thus, selecting young animals based on the pattern of lactation curves seems to be a feasible alternative in genomic selection of Holstein cattle for milk production traits. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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31. Military Concepts and Emergency Medical Services (EMS) in Portugal.
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Rocha Da Silva, F.F.
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- 1985
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32. Effects of including physically effective fiber from sugarcane in whole corn grain diets on the ingestive, digestive, and ruminal parameters of growing beef bulls.
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Alhadas, H.M., Valadares Filho, S.C., Silva, F.F., Silva, F.A.S., Pucetti, P., Pacheco, M.V.C., Silva, B.C., and Tedeschi, L.O.
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SUGARCANE , *WHOLE grain foods , *CORN , *MICROBIOLOGICAL synthesis , *ANIMAL nutrition , *MAGIC squares , *BULLS - Abstract
The objective of this study was to evaluate the inclusion of physically effective fiber (peNDF) from sugarcane in feedlot diets containing whole corn grain on ingestive, digestive, and ruminal parameters. Five rumen-cannulated Nellore bulls (BW = 393 ± 9 kg) distributed in an incomplete 5 × 5 Latin square received diets containing 5% (D5), 15% (D15), 25% (D25), or 35% (D35) sugarcane. All diets included a mineral-protein supplement. Omasal digesta collection and fecal spot collection were carried out to estimate ruminal and total digestibility. The ruminal contents were emptied to calculate ingestion (ki), passage (kp), and digestion (kd) rates. The linear, quadratic, and cubic effects of including sugarcane (i.e., different peNDF contents) were evaluated using orthogonal contrasts. The intake of total digestible nutrients (TDN , P = 0.06), dry matter (DM , P = 0.03), and organic matter (OM , P = 0.03) showed a quadratic pattern, with the highest estimated values occurring between 6.14 and 10.2% of peNDF. Ruminal digestibility [%, (P = 0.01) and kg/d, (P = < 0.01)] and total digestibility (kg/d, P = 0.03) of OM, ki (P = < 0.01), kp (P = 0.01) and kd (P = < 0.01) rates of OM, ki (P = 0.07), kp (P = 0.01), and kd (P = 0.05) rates of neutral detergent fiber (NDF) and microbial crude protein synthesis (MPS) (P = < 0.01) were also maximized, with inclusion levels between 6.14 and 10.2% of peNDF, although the efficiency of MPS tended to increase linearly (P = 0.08). The total concentration of volatile fatty acids (VFA) decreased linearly (P = 0.03), while the rumen ammonia pool [concentration (mmol/L) x volume of rumen liquid (L)] increased linearly (P = < 0.01). Ruminal pH responded linearly with the addition of sugarcane to the diet. We conclude that feedlot animals might benefit from diets containing between 6.14 and 10.2% of peNDF when whole corn grain diets are used. • Levels of 6.14 to 10.2% peNDF in finishing diets improve TDN intake. • Inclusion of peNDF in whole corn diets improves ruminal pH and fibre digestion. • Improvement in intake and ruminal pH allow greater microbial synthesis. • Fibre content in the diet is directly related to microbial efficiency. [ABSTRACT FROM AUTHOR]
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- 2021
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33. Single-step genome-wide association for longitudinal traits of Canadian Ayrshire, Holstein, and Jersey dairy cattle.
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Oliveira, H.R., Lourenco, D.A.L., Masuda, Y., Misztal, I., Tsuruta, S., Jamrozik, J., Brito, L.F., Silva, F.F., Cant, J.P., and Schenkel, F.S.
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JERSEY cattle , *DAIRY cattle , *CATTLE genetics , *SINGLE nucleotide polymorphisms , *MILK yield , *GENE expression , *SOMATIC cells - Abstract
Estimating single nucleotide polymorphism (SNP) effects over time is essential to identify and validate candidate genes (or quantitative trait loci) associated with time-dependent variation of economically important traits and to better understand the underlying mechanisms of lactation biology. Therefore, in this study, we aimed to estimate time-dependent effects of SNP and identifying candidate genes associated with milk (MY), fat (FY), and protein (PY) yields, and somatic cell score (SCS) in the first 3 lactations of Canadian Ayrshire, Holstein, and Jersey breeds, as well as suggest their potential pattern of phenotypic effect over time. Random regression coefficients for the additive direct genetic effect were estimated for each animal using single-step genomic BLUP, based on 2 random regression models: one considering MY, FY, and PY in the first 3 lactations and the other considering SCS in the first 3 lactations. Thereafter, SNP solutions were obtained for random regression coefficients, which were used to estimate the SNP effects over time (from 5 to 305 d in lactation). The top 1% of SNP that showed a high magnitude of SNP effect in at least 1 d in lactation were selected as relevant SNP for further analyses of candidate genes, and clustered according to the trajectory of their SNP effects over time. The majority of SNP selected for MY, FY, and PY increased the magnitude of their effects over time, for all breeds. In contrast, for SCS, most selected SNP decreased the magnitude of their effects over time, especially for the Holstein and Jersey breeds. In general, we identified a different set of candidate genes for each breed, and similar genes were found across different lactations for the same trait in the same breed. For some of the candidate genes, the suggested pattern of phenotypic effect changed among lactations. Among the lactations, candidate genes (and their suggested phenotypic effect over time) identified for the second and third lactations were more similar to each other than for the first lactation. Well-known candidate genes with major effects on milk production traits presented different suggested patterns of phenotypic effect across breeds, traits, and lactations in which they were identified. The candidate genes identified in this study can be used as target genes in studies of gene expression. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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34. Genome-wide association for milk production traits and somatic cell score in different lactation stages of Ayrshire, Holstein, and Jersey dairy cattle.
- Author
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Oliveira, H.R., Cant, J.P., Brito, L.F., Feitosa, F.L.B., Chud, T.C.S., Fonseca, P.A.S., Jamrozik, J., Silva, F.F., Lourenco, D.A.L., and Schenkel, F.S.
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LACTATION , *LACTATION in cattle , *SOMATIC cells , *MILK yield , *DAIRY cattle , *JERSEY cattle - Abstract
We performed genome-wide association analyses for milk, fat, and protein yields and somatic cell score based on lactation stages in the first 3 parities of Canadian Ayrshire, Holstein, and Jersey cattle. The genome-wide association analyses were performed considering 3 different lactation stages for each trait and parity: from 5 to 95, from 96 to 215, and from 216 to 305 d in milk. Effects of single nucleotide polymorphisms (SNP) for each lactation stage, trait, parity, and breed were estimated by back-solving the direct breeding values estimated using the genomic best linear unbiased predictor and single-trait random regression test-day models containing only the fixed population average curve and the random genomic curves. To identify important genomic regions related to the analyzed lactation stages, traits, parities and breeds, moving windows (SNP-by-SNP) of 20 adjacent SNP explaining more than 0.30% of total genetic variance were selected for further analyses of candidate genes. A lower number of genomic windows with a relatively higher proportion of the explained genetic variance was found in the Holstein breed compared with the Ayrshire and Jersey breeds. Genomic regions associated with the analyzed traits were located on 12, 8, and 15 chromosomes for the Ayrshire, Holstein, and Jersey breeds, respectively. Especially for the Holstein breed, many of the identified candidate genes supported previous reports in the literature. However, well-known genes with major effects on milk production traits (e.g., diacylglycerol O-acyltransferase 1) showed contrasting results among lactation stages, traits, and parities of different breeds. Therefore, our results suggest evidence of differential sets of candidate genes underlying the phenotypic expression of the analyzed traits across breeds, parities, and lactation stages. Further functional studies are needed to validate our findings in independent populations. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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35. Invited review: Advances and applications of random regression models: From quantitative genetics to genomics.
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Oliveira, H.R., Brito, L.F., Lourenco, D.A.L., Silva, F.F., Jamrozik, J., Schaeffer, L.R., and Schenkel, F.S.
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REGRESSION analysis , *QUANTITATIVE genetics - Abstract
An important goal in animal breeding is to improve longitudinal traits; that is, traits recorded multiple times during an individual's lifetime or physiological cycle. Longitudinal traits were first genetically evaluated based on accumulated phenotypic expression, phenotypic expression at specific time points, or repeatability models. Until now, the genetic evaluation of longitudinal traits has mainly focused on using random regression models (RRM). Random regression models enable fitting random genetic and environmental effects over time, which results in higher accuracy of estimated breeding values compared with other statistical approaches. In addition, RRM provide insights about temporal variation of biological processes and the physiological implications underlying the studied traits. Despite the fact that genomic information has substantially contributed to increase the rates of genetic progress for a variety of economically important traits in several livestock species, less attention has been given to longitudinal traits in recent years. However, including genomic information to evaluate longitudinal traits using RRM is a feasible alternative to yield more accurate selection and culling decisions, because selection of young animals may be based on the complete pattern of the production curve with higher accuracy compared with the use of traditional parent average (i.e., without genomic information). Moreover, RRM can be used to estimate SNP effects over time in genome-wide association studies. Thus, by analyzing marker associations over time, regions with higher effects at specific points in time are more likely to be identified. Despite the advances in applications of RRM in genetic evaluations, more research is needed to successfully combine RRM and genomic information. Future research should provide a better understanding of the temporal variation of biological processes and their physiological implications underlying the longitudinal traits. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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36. Application of single-step genomic evaluation using multiple-trait random regression test-day models in dairy cattle.
- Author
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Oliveira, H.R., Lourenco, D.A.L., Masuda, Y., Misztal, I., Tsuruta, S., Jamrozik, J., Brito, L.F., Silva, F.F., and Schenkel, F.S.
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DAIRY cattle , *GENOMICS , *GENOTYPES , *ANIMAL genetics , *LACTATION - Abstract
Test-day traits are important for genetic evaluation in dairy cattle and are better modeled by multiple-trait random regression models (RRM). The reliability and bias of genomic estimated breeding values (GEBV) predicted using multiple-trait RRM via single-step genomic best linear unbiased prediction (ssGBLUP) were investigated in the 3 major dairy cattle breeds in Canada (i.e., Ayrshire, Holstein, and Jersey). Individual additive genomic random regression coefficients for the test-day traits were predicted using 2 multiple-trait RRM: (1) one for milk, fat, and protein yields in the first, second, and third lactations, and (2) one for somatic cell score in the first, second, and third lactations. The predicted coefficients were used to derive GEBV for each lactation day and, subsequently, the daily GEBV were compared with traditional daily parent averages obtained by BLUP. To ensure compatibility between pedigree and genomic information for genotyped animals, different scaling factors for combining the inverse of genomic (G-1) and pedigree A22 ( -1 ) relationship matrices were tested. In addition, the inclusion of only genotypes from animals with accurate breeding values (defined in preliminary analysis) was compared with the inclusion of all available genotypes in the analyzes. The ssGBLUP model led to considerably larger validation reliabilities than the BLUP model without genomic information. In general, scaling factors used to combine the G-1 and A22 -1 matrices had small influence on the validation reliabilities. However, a greater effect was observed in the inflation of GEBV. Less inflated GEBV were obtained by the ssGBLUP compared with the parent average from traditional BLUP when using optimal scaling factors to combine the G-1 and A22 -1 matrices. Similar results were observed when including either all available genotypes or only genotypes from animals with accurate breeding values. These findings indicate that ssGBLUP using multiple-trait RRM increases reliability and reduces bias of breeding values of young animals when compared with parent average from traditional BLUP in the Canadian Ayrshire, Holstein, and Jersey breeds. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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37. RNA sequencing differential gene expression analysis of isolated perfused bovine udders experimentally inoculated with Streptococcus agalactiae.
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Sbardella, A.P., Weller, M.M.D.C.A., Fonseca, I., Stafuzza, N.B., Bernardes, P.A., e Silva, F.F., da Silva, M.V.G.B., Martins, M.F., and Munari, D.P.
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UDDER , *RNA sequencing , *GENE expression , *STREPTOCOCCUS agalactiae , *DAIRY cattle - Abstract
The aim of this study was to elucidate the differential gene expression in the RNA sequencing transcriptome of isolated perfused udders collected from 4 slaughtered Holstein x Zebu crossbred dairy cows experimentally inoculated with Streptococcus agalactiae. We studied 3 different statistical tools (edgeR, baySeq, and Cuffdiff 2). In summary, 2 quarters of each udder were experimentally inoculated with Strep. agalactiae and the other 2 were used as a control. Mammary tissue biopsies were collected at times 0 and 3 h after infection. The total RNA was extracted and sequenced on an Illumina HiSeq 2000 (Illumina Inc., San Diego, CA). Transcripts were assembled from the reads aligned to the bovine UMD 3.1 reference genome, and the statistical analyses were performed using the previously mentioned tools (edgeR, baySeq, and Cuffdiff 2). Finally, the identified genes were submitted to pathway enrichment analysis. A total of 1,756, 1,161, and 3,389 genes with differential gene expression were identified when using edgeR, baySeq, and Cuffdiff 2, respectively. A total of 122 genes were identified by the overlapping of the 3 methods; however, only the platelet activation presented a significantly enriched pathway. From the results, we suggest the FCER1G, GNAI2, ORAI1, and VASP genes shared among the 3 methods in this pathway for posterior biological validation. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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38. Association between chitosan and unsaturated fatty acids supplementation on ruminal fermentation, digestive metabolism, and ruminal kinetics in beef heifers.
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Gordiano, L.A., Ferreira, F.G., Ribeiro, C.V.D.M., de Carvalho, G.G.P., Silva, F.F., de Araújo, M.L.G.M.L., Alba, H.D.R., e Silva, R.D.G., Azevedo, J.A.G., and Freitas Jr, J.E. de
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UNSATURATED fatty acids , *RUMEN fermentation , *HEIFERS , *FEED analysis , *CHITOSAN , *CATTLE nutrition , *LACTIC acid - Abstract
• Unsaturated fatty acids (UFA) supplementation with or without chitosan decreased methane. • Chitosan (CHI) associated with UFA did not influence the ruminal digestibility of nutrients. • Ruminal fermentation was altered with UFA supplementation associated with CHI. • UFA sources associated with CHI alter reticular flows of nutrients. • Chitosan associated UFA change the ruminal kinetics of beef heifers. This study evaluated the effects of supplementation of chitosan and unsaturated fatty acid (UFAs) sources on intake, digestibility, ruminal and nitrogen metabolism, blood metabolites, and feeding behavior of beef heifers. Five crossbred Simental x Zebu heifers (335 ± 53.2 kg of initial BW), ruminally cannulated, were randomly assigned according to a 5 × 5 Latin square design containing the following treatments: 1) CON, the control diet without supplementation; 2) SO, control diet supplemented with 25.3 g/kg of soybean oil; 3) WRS, control diet supplemented with 160 g/kg of whole raw soybean (WRS); 4) SOCHI, SO diet plus 14 g/kg of CHI; 5) WRSCHI, WRS diet plus 14 g/kg of CHI. No interaction effects between CHI and WRS were observed on nutrient intakes and digestibilities. Heifers fed SO, or WRS diets with or without CHI had lower enteric methane (CH 4) emissions (P < 0.01) than those fed CON. Moreover, animals fed SO and WRS had higher CH 4 emissions than those fed SOCHI and WRSCHI. No interaction between CHI and WRS was observed on nitrogen balance. However, heifers fed SO or WRS diets with or without CHI had lower nitrogen (N) intake (P = 0.001) and fecal N (P = 0.015) than those fed CON. Besides, animals fed SO and WRS diets showed lower retained N (P = 0.010) and efficiency (P = 0.005) than those fed SOCHI and WRSCHI. Heifers fed SO, or WRS diets with or without CHI showed lower rumination efficiencies of dry matter (DM; P < 0.01) and neutral detergent fiber (NDF; P = 0.013) than those fed CON. Heifers fed SO or WRS with or without CHI, showed lower reticular flows of DM (P = 0.049), NDF (P = 0.002), and potentially digestible NDF (P = 0.002) than those fed CON. In addition, animals fed SO or WRS diets with or without CHI showed a lower rumen digestion rate of DM, turnover rates of DM and NDF, and passage rates of DM and pdNDF than those fed CON. The supply of CHI to beef heifers fed diets with SO and WRS alters ruminal fermentation, methane production, nitrogen balance, feeding behavior, and ruminal dynamics. Nevertheless, the results strengthen the evidence that the provision of CHI in beef cattle diets can positively influence the effect of fatty acid sources. Besides, fatty acids sources provided alone have a negative influence on most metabolism parameters in beef heifers. [ABSTRACT FROM AUTHOR]
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- 2023
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39. Effects of increasing palm kernel cake inclusion in supplements fed to grazing lambs on growth performance, carcass characteristics, and fatty acid profile.
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Freitas, T.B., Felix, T.L., Pedreira, M.S., Silva, R.R., Silva, F.F., Silva, H.G.O., and Moreira, B.S.
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COMPOSITION of feeds , *SHEEP feeding , *LAMBS , *LAMB carcasses , *ANIMAL nutrition , *FATTY acids , *CONCENTRATE feeds - Abstract
The aim of this study was to evaluate the effects of the inclusion of palm kernel cake (PKC) in the supplement composition for grazing lambs on intake, digestibility, growth performance, carcass characteristics and fatty acid profile of the meat. Thirty-one non-castrated Santa Inês-crossed male lambs (age = 120 ± 15 d; initial body weight = 20 ± 3.9 kg) were divided into 4 groups, following a completely randomized design. Treatments were 0%, 10%, 20%, and 30% PKC substitution for ground corn and wheat bran in the supplement. Animals were stratified to equalize body weight: 8 animals in treatment 0%; 8 in treatment 10%; 6 in treatment 20%; and 9 in treatment 30%. Lambs were fed for 84 d and grazed a predominantly braquiarão grass ( Urochloa brizantha cv. Marandu) and Tifton 85 ( Cynodon dactylon ) grass pasture. The remainder of the supplement contained soybean meal, wheat bran, ground corn, urea, and mineral salt. The level of supplementation was 1.6% BW per animal/d. There was a linear decrease ( P < 0.01) for total DM intake and pasture intake as the inclusion of PKC in the supplement was increased. Feeding increasing PKC in the supplement did not affect ( P ≥ 0.35) lamb growth performance nor did it affect most carcass characteristics ( P ≥ 0.16). However, it did lower conformation ( P = 0.02) and carcass shrink ( P = 0.03). Palmitic fatty acid decreased (linear; P = 0.04) as PKC fed to lambs increased in the supplement. No other fatty acids were affected ( P ≥ 0.10). Feeding up to 30% PKC in a supplement for grazing lambs reduced DMI without altering average daily gain or economic traits of carcass characteristic. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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40. Effect of the dietary inclusion of dried oregano (Origanum vulgare L.) on the characteristics of milk from Holstein×Zebu cows.
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Lacerda, E.C.Q., Bauer, L.C., Oliveira, J.S., Silva, F.F., Carvalho, S.A., Macedo, M.S., de Souza, N.E., and Simionato, J.I.
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RAW milk , *MILK quality , *PASTEURIZATION of milk , *CATTLE feeding & feeds , *OREGANO , *HOLSTEIN-Friesian cattle , *PHYSICAL & theoretical chemistry - Abstract
Abstract: The objective of this study was to evaluate the effects of the inclusion of oregano in the diet of dairy cows on the physicochemical quality of raw milk and the sensory attributes of pasteurized milk. Twelve crossbred Holstein×Zebu cows were divided into three 4×4 Latin squares, and increasing amounts of oregano were added to their diet. Physicochemical analysis of density, cryoscopic index, protein, fat, lactose, total solids extract (TSE), and dry nonfat extracts (DNE) was performed for the raw milk samples. The microbiological quality of pasteurized milk samples was evaluated by performing total and fecal coliform tests. Adding oregano to the diet showed no influence (P>0.05) on the fat, TSE, protein, and cryoscopic index, with mean values of 3.78g/100g, 12.60g/100g, 3.24g/100g, and g −0535 °H, respectively. However, the levels of lactose, DNE, and density were influenced by the amount of oregano (OV) and ranged from 4.82g/100g to 4.64g/100g, 9.22g/100g to 8.88g/100g, and 1.033g/mL to 1.032g/mL, respectively. Based on microbiological analysis, all samples were considered suitable for consumption (<3.0×105 CFU/mL). The sensory attributes of aroma and flavor did not alter the preference (P>0.05). Only a small difference between treatments was observed in the flavor profile for the warmed-over flavor attribute. For the attributes of a sweet aroma, characteristic milk aroma, characteristic milk flavor, and sweet flavor, the intensity ranges were similar. The results showed no changes (P>0.05) in the main components of milk and, therefore, no effect on its sensory attributes. Thus, it is possible to incorporate dry oregano into cattle feed for the purpose of studying its influence on other parameters of milk composition. [Copyright &y& Elsevier]
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- 2014
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41. Effects of plant extract supplementations or monensin on nutrient intake, digestibility, ruminal fermentation and metabolism in dairy cows.
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Silva, S.N.S. e, Chabrillat, T., Kerros, S., Guillaume, S., Gandra, J.R., de Carvalho, G.G.P., Silva, F.F. da, Mesquita, L.G., Gordiano, L.A., Camargo, G.M.F., Ribeiro, C.V. Di M., de Araújo, M.L.G.M.L., Alba, H.D.R., e Silva, R.D.G., and Freitas Jr., J.E. de
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RUMEN fermentation , *INGESTION , *MONENSIN , *PLANT extracts , *DAIRY cattle , *FAT content of milk - Abstract
• Supplementation with monensin and saponins was evaluated in diets for cows. • The combination of saponins with essential oils increased the energy efficiency. • Nutrients digestibility and nitrogen utilization were not affected by the diets. • Monensin decreased ruminal pH and increased rumen ammonia nitrogen concentration. • The long-chain fatty acids profile in cows' milk was not influenced by the diets. This study aimed to evaluate the effects of diet supplementation with monensin and saponins alone or combined with essential oils (EOs) on the nutrient intake and apparent digestibility, rumen fermentation parameters, microbial population, nitrogen balance, ruminal microbial protein synthesis, blood metabolites, and milk composition, yield and fatty acid profile of mid- to late-lactating Jersey cows. Eight ruminally cannulated lactating Jersey cows (average 17.6 ± 5.5 kg/day of milk yield and 100.5 ± 26.6 days of milk (mean ± SD)) were distributed in a replicated 4 × 4 Latin square design with 21-day periods (last seven days for sampling). Treatment sequences were randomly designated to cows and consisted of: (1) CON - Control, no feed additive; (2) SAP - 16 g/cow/day of a supplement based on whole-seed fenugreek powder (variety Fenucold) standardized to diosgenin, one of the major steroidal sapogenins of fenugreek (2000 mg/kg); (3) SAPEO - SAP supplement combined with a blend of natural EOs with major components of carvacrol (2500 mg/kg), cinnamaldehyde (5600 mg/kg) and limonene (3000 mg/kg); and (4) MON - Monensin, inclusion of monensin sodium in the diet at 24 mg/kg DM. Cows fed CON showed higher dry matter, organic matter, crude protein and ether extract intakes than animals fed MON, whereas higher neutral detergent fibre intake was observed in animals fed SAPEO than those fed MON (P < 0.05). Diet and time effects were observed for ruminal pH and concentration of ruminal ammonia nitrogen (P < 0.05). Cows fed SAP showed a higher relative proportion of Fibrobacter succinogenes (P = 0.04) than animals fed MON. Cows fed CON had higher net and digestible energy intakes than animals fed MON (P < 0.05). Cows fed SAPEO showed higher albumin concentrations (P = 0.04) than those fed CON, SAP, and MON. Besides, cows fed CON showed higher urea concentrations (P = 0.04) than those fed SAP and SAPEO. Higher protein and fat levels in the milk were observed in cows fed SAPEO than animals fed MON (P < 0.05). Monensin decreased the concentrations of C4:0, C6:0, C8:0, and C18:1 cis-11 milk fatty acids (P < 0.05). Monensin decreased nutrient intake to a more energetically efficient pathway but did not alter milk production, digestibility, or rumen fermentation. Saponin supplementation associated with essential oils increases milk fat and protein contents in lactating Jersey cows compared to animals fed a monensin-supplemented diet. [ABSTRACT FROM AUTHOR]
- Published
- 2021
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