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Accuracy of genomic predictions in Bos indicus (Nellore) cattle. Repositório Alice
NEVES, H. H.; CARVALHEIRO, R.; O'BRIEN, A. M.; UTSUNOMIYA, Y. T.; CARMO, A. S. do; SCHENKEL, F. S.; SÖLKNER, J.; MCEWAN, J. C.; VAN TASSELL, C. P.; COLE, J. B.; SILVA, M. V. G. B.; QUEIROZ, S. A.; SONSTEGARD, T. S.; GARCIA, J. F..
2014
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Nellore cattle; Genomic selection.
Ano: 2014 URL: http://www.alice.cnptia.embrapa.br/handle/doc/987574
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Combining Individual Phenotypes of Feed Intake With Genomic Data to Improve Feed Efficiency in Sea Bass ArchiMer
Besson, Mathieu; Allal, Francois; Chatain, Beatrice; Vergnet, Alain; Clota, Frederic; Vandeputte, Marc.
Measuring individual feed intake of fish in farms is complex and precludes selective breeding for feed conversion ratio (FCR). Here, we estimated the individual FCR of 588 sea bass using individual rearing under restricted feeding. These fish were also phenotyped for their weight loss at fasting and muscle fat content that were possibly linked to FCR. The 588 fish were derived from a full factorial mating between parental lines divergently selected for high (F+) or low (F–) weight loss at fasting. The pedigree was known back to the great grand-parents. A subset of 400 offspring and their ancestors were genotyped for 1,110 SNPs which allowed to calculate the genomic heritability of traits. Individual FCR and growth rate in aquarium were both heritable...
Tipo: Text Palavras-chave: Aquaculture; Feed conversion ratio; Fine phenotyping; Genomic selection; Individual feed intake; Restricted feeding; Selective breeding.
Ano: 2019 URL: https://archimer.ifremer.fr/doc/00486/59799/62927.pdf
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Development and validation of a 26K Axiom® SNP array for Coffea canephora. Repositório Alice
CARNEIRO, F. de A.; MARRACCINI, P.; SILVA JUNIOR, O. B. da; GRATTAPAGLIA, D.; ANDRADE, A. C..
World coffee production is higly affected by climate changes due to the occurrence of severe droughts and high temperatures resulting in low flow er viability, fruit development and yield. Faster breeding methods are required to obtain adapted coffee plants to a changed climate cenario, as conventional breeding in perennial crops such as coffee, requires a long time. With the recent advances in coffee genomics, such as the availability of a C. canephora reference genome , the objective of this work was to develop and validate a 26K Axiom SNP array for C. canephora aiming at a reliable high throughput genotyping platform to be used in the breeding programmes of the species. The chip design was based on a whole - genome resequencing panel comprised by DNA...
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Coffe canephora Conilon; Coffee genomics; Climate change; Genomic selection; Genetic diversity; Coffea canephora; Coffee plant.
Ano: 2017 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1084572
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Future directions in breeding for disease resistance in aquaculture species R. Bras. Zootec.
Houston,Ross D..
ABSTRACT Infectious disease is a major constraint for all species produced via aquaculture. The majority of farmed fish and shellfish production is based on stocks with limited or no selective breeding. Since disease resistance is almost universally heritable, there is huge potential to select for improved resistance to key diseases. This short review discusses the current methods of breeding more resistant aquaculture stocks, with success stories and current bottlenecks highlighted. The current implementation of genomic selection in breeding for disease resistance and routes to wider-scale implementation and improvement in aquaculture are discussed. Future directions are highlighted, including the potential of genome editing tools for mapping causative...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Genome editing; Genomic selection; Selective breeding.
Ano: 2017 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-35982017000600545
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Genetic diversity and genomic selection in Eucalyptus benthamii. Repositório Alice
AGUIAR, A. V. de; SOUZA, B.; ABREU, L.; PAPPAS, M. de C. R.; AZEVEDO, V. C. R.; SANTOS, P. E. T. dos; SOUSA, V. A. de; SANTOS, R..
bitstream/item/184826/1/2018-RAC-Ananda-IMEC-Genetic.pdf
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Diversidade genética; Seleção genômica; Genetic diversity; Genomic selection; Eucalyptus benthamii.
Ano: 2018 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1097868
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Genetic improvement of beef cattle through opportunities in genomics R. Bras. Zootec.
Miller,Stephen.
Genomics will improve the efficiency of beef cattle genetic improvement programs through the incorporation of genomic predictions into traditional genetic evaluations. The global dairy cattle breeding industry has been changed considerably in the last year through the implementation of genomic selection. Now proven to work in dairy cattle breeding, the challenge remains for the beef industry to successfully implement this technology. The primary challenge in beef cattle is the required resource population that relates genomic profile to phenotypic performance, which is quite large and its establishment will require collaboration or a significant investment by any one enterprise. Another challenge in beef cattle is the requirement for genomic predictions to...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Breeding strategies; DNA; Genomic selection; Phenotype; Recording; Single nucleotide polymorphisms.
Ano: 2010 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-35982010001300027
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Genome selection in fruit breeding: application to table grapes. Repositório Alice
VIANA, A. P.; RESENDE, M. D. V. de; RIAZ, S.; WALKER, M. A..
Genomic selection (GS) has recently been proposed as a new selection strategy which represents an innovative paradigm in crop improvement, now widely adopted in animal breeding. Genomic selection relies on phenotyping and high-density genotyping of a sufficiently large and representative sample of the target breeding population, so that the majority of loci that regulate a quantitative trait are in linkage disequilibrium with one or more molecular markers and can thus be captured by selection. In this study we address genomic selection in a practical fruit breeding context applying it to a breeding population of table grape obtained from a cross between the hybrid genotype D8909-15 (Vitis rupestris × Vitis arizonica/girdiana), which is resistant to dagger...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Uva de mesa; Melhoramento genético; MAS; SSR markers; Linkage disequilibrium; Genomic selection; Fruta; Uva; Melhoramento vegetal; Marcador molecular; Fruits; Table grapes; Plant breeding; Marker assisted selection.
Ano: 2016 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1047486
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Genome selection in fruit breeding: application to table grapes Scientia Agricola
Viana,Alexandre Pio; Resende,Marcos Deon Vilela de; Riaz,Summaira; Walker,Michael Andrew.
ABSTRACT Genomic selection (GS) has recently been proposed as a new selection strategy which represents an innovative paradigm in crop improvement, now widely adopted in animal breeding. Genomic selection relies on phenotyping and high-density genotyping of a sufficiently large and representative sample of the target breeding population, so that the majority of loci that regulate a quantitative trait are in linkage disequilibrium with one or more molecular markers and can thus be captured by selection. In this study we address genomic selection in a practical fruit breeding context applying it to a breeding population of table grape obtained from a cross between the hybrid genotype D8909-15 (Vitis rupestris × Vitis arizonica/girdiana), which is resistant...
Tipo: Info:eu-repo/semantics/article Palavras-chave: MAS; SSR markers; Linkage disequilibrium; Genomic selection.
Ano: 2016 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0103-90162016000200142
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Genome wide association analysis for birth and weaning weight in Canchim beef cattle. Repositório Alice
BUZANSKAS, M. E.; GROSSI, D. A.; SCHENKEL, D. A.; VENTURA, R.; REGITANO, L. C. de A.; ALENCAR, M. M. de; MUNARI, D. P..
2013
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Alleles; Beef cattle; Genes; Genomic selection; SNP.
Ano: 2013 URL: http://www.alice.cnptia.embrapa.br/handle/doc/963172
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Genome-enabled prediction of breeding values for feedlot average daily weight gain in nelore cattle. Repositório Alice
SOMAVILLA, A. L.; REGITANO, L. C. de A.; ROSA, G. J. M.; MOKRY, F. B.; MUDADU, M. de A.; TIZIOTO, P. C.; OLIVEIRA, P. S. N. de; SOUZA, M. M. de; COUTINHO, L. L.; MUNARI, D. P..
Nelore is the most economically important cattle breed in Brazil, and the use of genetically improved animals has contributed to increase beef production efficiency. The Brazilian beef feedlot industry has grown considerably in the last decade, so the selection of animals with higher growth rates on feedlot has become quite important. Genomic selection could be used to reduce generation intervals and improve the rate of genetic gains. The aim of this study was to evaluate the prediction of genomic estimated breeding values for average daily gain in 718 feedlot-finished Nelore steers. Analyses of three Bayesian model specifications (Bayesian GBLUP, BayesA, and BayesCπ) were performed with four genotype panels (Illumina BovineHD BeadChip, TagSNPs,...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Genomic selection; Bos taurus indicus; Growth.
Ano: 2017 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1070097
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Genome-wide association for mapping QTLs linked to protein and oil contents in soybean PAB
Dias,Douglas Antônio; Polo,Leandra Regina Texeira; Lazzari,Fabiane; Silva,Glacy Jaqueline da; Schuster,Ivan.
Abstract: The objective of this work was to identify single-nucleotide polymorphism (SNP) markers linked with quantitative trait loci (QTLs) associated with increased contents of protein and oil in soybean. A total of 169 Brazilian soybean varieties, genotyped with 6,000 SNP markers, were evaluated. Protein and oil contents were obtained with the near-infrared reflectance method. Correlation and multiple linear regression analyses were used to identify linkage disequilibrium between SNP markers and the QTLs associated with the two characteristics. Seven QTLs were found to be associated with protein content, on six chromosomes (2, 6, 11, 12, 13, and 16), explaining 60.9% of the variation in this trait. For oil content, eight QTLs were identified on six...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Glycine max; Association genetics; Genomic selection; Grain quality; Linkage disequilibrium; Marker-assisted selection..
Ano: 2017 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-204X2017001000896
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Genomic analysis for managing small and endangered populations: a case study in Tyrol Grey cattle. Repositório Alice
MÉSZÁROS, G.; BOISON, S. A.; O'BRIEN, A. M. P.; FERENCAKOVIC, M.; CURIK, I.; SILVA, M. V. G. B.; UTSONOMIYA, Y. T.; GARCIA, J. F.; SÖLKNER, J..
Analysis of genomic data is increasingly becoming part of the livestock industry. Therefore, the routine collection of genomic information would be an invaluable resource for effective management of breeding programs in small, endangered populations. The objective of the paper was to demonstrate how genomic data could be used to analyse (1) linkage disequlibrium (LD), LD decay and the effective population size (NeLD); (2) Inbreeding level and effective population size (NeROH) based on runs of homozygosity (ROH); (3) Prediction of genomic breeding values (GEBV) using small within-breed and genomic information from other breeds. The Tyrol Grey population was used as an example, with the goal to highlight the potential of genomic analyses for small breeds. In...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: SNP chip; Breed management; Endangered breeds; Genomic selection; Linkage disequilibrium; Runs of homozygosity.
Ano: 2015 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1037600
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Genomic evaluation for novel stayability traits in Nellore cattle. Repositório Alice
RAMOS, P. V. B.; SILVA, F. F. e; SILVA, L. O. C. da; SANTIAGO, G. G.; MENEZES, G. R. de O.; VIANA, J. M. S.; TORRES JUNIOR, R. A. de A.; GONDO, A.; LUIZ F. BRITO.
Cow stayability plays a major role on the overall profitability of the beef cattle industry, as it is directly related to reproductive efficiency and cow's longevity. Stayability (STAY63) is usually defined as the ability of the cow to calve at least three times until 76 months of age. This is a late-measured and lowly heritable trait, which consequently constrains genetic progress per time unit. Thus, the use of genomic information associated with novel stayability traits measured earlier in life will likely result in higher prediction accuracy and faster genetic progress for cow longevity. In this study, we aimed to compare pedigree-based and single-step GBLUP (ssGBLUP) methods as well as to estimate genetic correlations between the proposed stayability...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Cow fertility; Genomic selection; Threshold model; Longevity; Reproductive traits.
Ano: 2020 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1120235
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Genomic prediction in contrast to a genome-wide association study in explaining heritable variation of complex growth traits in breeding populations of Eucalyptus. Repositório Alice
MÜLLER, B. S. F.; NEVES, L. G.; ALMEIDA FILHO, J. E. de; RESENDE JUNIOR, M. F. R.; MUÑOZ, P. R.; SANTOS, P. E. T. dos; PALUDZYSZYN FILHO, E.; KIRST, M.; GRATTAPAGLIA, D..
Background: The advent of high-throughput genotyping technologies coupled to genomic prediction methods established a new paradigm to integrate genomics and breeding. We carried out whole-genome prediction and contrasted it to a genome-wide association study (GWAS) for growth traits in breeding populations of Eucalyptus benthamii (n =505) and Eucalyptus pellita (n =732). Both species are of increasing commercial interest for the development of germplasm adapted to environmental stresses. Results: Predictive ability reached 0.16 in E. benthamii and 0.44 in E. pellita for diameter growth. Predictive abilities using either Genomic BLUP or different Bayesian methods were similar, suggesting that growth adequately fits the infinitesimal model. Genomic...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Genomic selection; GWAS; Seleção genômica; SNP genotyping; Espécie exótica; Eucalipto; Melhoramento genético vegetal; Eucalyptus benthamii; Eucalyptus pellita; Genetic relationships; Marker-assisted selection; Plant breeding.
Ano: 2017 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1080149
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Genomic prediction in contrast to a genome-wide association study in explaining heritable variation of complex growth traits in breeding populations of Eucalyptus. Repositório Alice
MÜLLER, B. S. F.; NEVES, L. G.; ALMEIDA FILHO, J. E. de; RESENDE JUNIOR, M. F. R.; MUÑOZ, P. R.; SANTOS, P. E. T. dos; PALUDZYSZYN FILHO, E.; KIRST, M.; GRATTAPAGLIA, D..
Background: The advent of high-throughput genotyping technologies coupled to genomic prediction methods established a new paradigm to integrate genomics and breeding. We carried out whole-genome prediction and contrasted it to a genome-wide association study (GWAS) for growth traits in breeding populations of Eucalyptus benthamii (n =505) and Eucalyptus pellita (n =732). Both species are of increasing commercial interest for the development of germplasm adapted to environmental stresses. Results: Predictive ability reached 0.16 in E. benthamii and 0.44 in E. pellita for diameter growth. Predictive abilities using either Genomic BLUP or different Bayesian methods were similar, suggesting that growth adequately fits the infinitesimal model. Genomic...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Genomic selection; GWAS; SNP genotyping; Genetic relationships; Seleção genômica; Eucalipto; Espécie exótica; Melhoramento genético vegetal; Eucalyptus benthamii; Eucalyptus pellita; Marker-assisted selection; Genetic relationships; Plant breeding.
Ano: 2017 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1080081
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Genomic selection in Coffea canephora. Repositório Alice
CARNEIRO, F. de A.; MARRACCINI, P.; BALESTRE, M.; GRATTAPAGLIA, D.; ANDRADE, A. C..
Coffee is one of the most heavily globally traded commodities and its production is based on Coffea arabica and Coffea canephora and Brazil being the world's largest coffee producer. It is believed that all this production will be affected due to climatic changes, with low flower viability, fruit development, yield and beverage quality. An alternative to assist in obtaining coffee plants more adapted to future climatic conditions would be genomic selection (GS). The implementation of these programs requires a lot of genetic markers, which are more readily discovered now after the reference genome of C. canephora became available. Another important factor is the high genetic variability of C. canephora, due to its level of allogamy, being of great...
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Coffe; Embrapa Cerrados; Consórcio Pesquisa Café; Coffea arabica; Coffea canephora; Genomic selection; Climatic change.
Ano: 2017 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1084559
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Multi-trait multi-environment models in the genetic selection of segregating soybean progeny. Repositório Alice
VOLPATO, L.; ALVES, R. S.; TEODORO, P. E.; RESENDE, M. D. V. de; NASCIMENTO, M.; NASCIMENTO, A. C. C.; LUDKE, W. H.; SILVA, F. L. da; BORÉM, A..
At present, single-trait best linear unbiased prediction (BLUP) is the standard method for genetic selection in soybean. However, when genetic selection is performed based on two or more genetically correlated traits and these are analyzed individually, selection bias may arise. Under these conditions, considering the correlation structure between the evaluated traits may provide more-accurate genetic estimates for the evaluated parameters, even under environmental influences. The present study was thus developed to examine the efficiency and applicability of multi-trait multi-environment (MTME) models by the residual maximum likelihood (REML/BLUP) and Bayesian approaches in the genetic selection of segregating soybean progeny. The study involved data...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Bayesian-inference; Genomic selection; Breeding values; Seed protein; Mixed models; Inferência Bayesian; Modelo misto; Seleção genômica; Soja; Soybeans; Agronomic traits; Prediction.
Ano: 2019 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1110400
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Regularized quantile regression applied to genome-enabled prediction of quantitative traits. Repositório Alice
NASCIMENTO, M.; SILVA, F. F. e; RESENDE, M. D. V. de; CRUZ, C. D.; NASCIMENTO, A. C. C.; VIANA, J. M. S.; AZEVEDO, C. F.; BARROSO, L. M. A..
Genomic selection (GS) is a variant of marker-assisted selection, in which genetic markers covering the whole genome predict individual genetic merits for breeding. GS increases the accuracy of breeding values (BV) prediction. Although a variety of statistical models have been proposed to estimate BV in GS, few methodologies have examined statistical challenges based on non-normal phenotypic distributions, e.g., skewed distributions. Traditional GS models estimate changes in the phenotype distribution mean, i.e., the function is defined for the expected value of trait-conditional on markers, E(Y|X). We proposed an approach based on regularized quantile regression (RQR) for GS to improve the estimation of marker effects and the consequent genomic estimated...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Seleção genômica; Genomic selection; Regularized regression; SNP effects; Estatística; Marker-assisted selection; Simulation models; Statistics.
Ano: 2017 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1084109
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Use of direct and iterative solvers for estimation of SNP effects in genome-wide selection Genet. Mol. Biol.
Pimentel,Eduardo da Cruz Gouveia; Sargolzaei,Mehdi; Simianer,Henner; Schenkel,Flávio Schramm; Liu,Zengting; Fries,Luiz Alberto; Queiroz,Sandra Aidar de.
The aim of this study was to compare iterative and direct solvers for estimation of marker effects in genomic selection. One iterative and two direct methods were used: Gauss-Seidel with Residual Update, Cholesky Decomposition and Gentleman-Givens rotations. For resembling different scenarios with respect to number of markers and of genotyped animals, a simulated data set divided into 25 subsets was used. Number of markers ranged from 1,200 to 5,925 and number of animals ranged from 1,200 to 5,865. Methods were also applied to real data comprising 3081 individuals genotyped for 45181 SNPs. Results from simulated data showed that the iterative solver was substantially faster than direct methods for larger numbers of markers. Use of a direct solver may allow...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Breeding value; Genomic selection; Mixed model equations; Numerical method.
Ano: 2010 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572010000100033
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