Base de dados : MEDLINE
Pesquisa : E05.820.150.760 [Categoria DeCS]
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  1 / 91 MEDLINE  
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[PMID]:28464791
[Au] Autor:Duggan BM; Rae AM; Clements DN; Hocking PM
[Ad] Endereço:The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK. Brendan.Duggan@roslin.ed.ac.uk.
[Ti] Título:Higher heritabilities for gait components than for overall gait scores may improve mobility in ducks.
[So] Source:Genet Sel Evol;49(1):42, 2017 05 02.
[Is] ISSN:1297-9686
[Cp] País de publicação:France
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Genetic progress in selection for greater body mass and meat yield in poultry has been associated with an increase in gait problems which are detrimental to productivity and welfare. The incidence of suboptimal gait in breeding flocks is controlled through the use of a visual gait score, which is a subjective assessment of walking ability of each bird. The subjective nature of the visual gait score has led to concerns over its effectiveness in reducing the incidence of suboptimal gait in poultry through breeding. The aims of this study were to assess the reliability of the current visual gait scoring system in ducks and to develop a more objective method to select for better gait. RESULTS: Experienced gait scorers assessed short video clips of walking ducks to estimate the reliability of the current visual gait scoring system. Kendall's coefficients of concordance between and within observers were estimated at 0.49 and 0.75, respectively. In order to develop a more objective scoring system, gait components were visually scored on more than 4000 pedigreed Pekin ducks and genetic parameters were estimated for these components. Gait components, which are a more objective measure, had heritabilities that were as good as, or better than, those of the overall visual gait score. CONCLUSIONS: Measurement of gait components is simpler and therefore more objective than the standard visual gait score. The recording of gait components can potentially be automated, which may increase accuracy further and may improve heritability estimates. Genetic correlations were generally low, which suggests that it is possible to use gait components to select for an overall improvement in both economic traits and gait as part of a balanced breeding programme.
[Mh] Termos MeSH primário: Patos/genética
Característica Quantitativa Herdável
Velocidade de Caminhada/genética
[Mh] Termos MeSH secundário: Animais
Fenótipo
Seleção Artificial
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Em] Mês de entrada:1710
[Cu] Atualização por classe:180218
[Lr] Data última revisão:
180218
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170504
[St] Status:MEDLINE
[do] DOI:10.1186/s12711-017-0317-2


  2 / 91 MEDLINE  
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[PMID]:29369555
[Au] Autor:Kashtanov SN; Sulimova GE; Shevyrkov VL; Svishcheva GR
[Ti] Título:[Breeding of the Russian sable: Stages of industrial domestication and genetic variability].
[So] Source:Genetika;52(9):1001-11, 2016 Sep.
[Is] ISSN:0016-6758
[Cp] País de publicação:Russia (Federation)
[La] Idioma:rus
[Ab] Resumo:Creating farms for sable breeding was associated with the commercial destruction of natural populations and, consequently, the overall decline in the species number. The gene pool of the first farm-bred sable population in Russia, established in the vicinity of Moscow ("Pushkinskiy" fur farm), was formed by crossing of animals removed from nine natural populations. In the first eight years of farm operation, approximately one thousand animals were used for sable breeding; some of these animals were able to adapt to the farm management and, subsequently, to the selection for a number of quantitative traits in the period of industrial domestication. It took about ten years for breeders to work out the breeding and selection technologies, which became successfully employed in the established affiliated sable breeding farms. The main achievement in sable breeding over the 85-year historical period of breeding in Russia is the creation of two unique breeds, black sable (1969) and Saltykovskaya 1 (2007). In general, industrial domestication in fur farming and the subsequent breeding works made the fur of many species (mink, fox, Arctic fox) obtained from natural populations uncompetitive, which undoubtedly reduced the hunting interest in the animals living in the wild. Consequently, hunting for fur-bearing animals of most species decreased and has only local importance. Owing to the specific features of sable biology, the fur of farm-bred animals cannot yet completely replace the furs obtained by hunting; however, the farm-bred sable population is constantly growing. This review presents the results of the analysis of the level of genetic variability in natural and farm populations at nuclear and mitochondrial loci. The comparative analysis makes it possible to estimate the loss of genetic diversity upon the species adaptation to the new conditions of existence.
[Mh] Termos MeSH primário: Variação Genética
Mustelidae/fisiologia
Seleção Artificial
[Mh] Termos MeSH secundário: Animais
Feminino
Masculino
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180205
[Lr] Data última revisão:
180205
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180126
[St] Status:MEDLINE


  3 / 91 MEDLINE  
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[PMID]:29273553
[Au] Autor:Raza SHA; Gui L; Khan R; Schreurs NM; Xiaoyu W; Wu S; Mei C; Wang L; Ma X; Wei D; Guo H; Zhang S; Wang X; Kaleri HA; Zan L
[Ad] Endereço:College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China; National Beef Cattle Improvement Center of Northwest A&F University, Yangling 712100, PR China.
[Ti] Título:Association between FASN gene polymorphisms ultrasound carcass traits and intramuscular fat in Qinchuan cattle.
[So] Source:Gene;645:55-59, 2018 Mar 01.
[Is] ISSN:1879-0038
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Fatty acid synthase (FASN) is an enzyme involved with fat deposition and fatty acid composition in cattle. This study was conducted to detect single nucleotide polymorphisms (SNPs) of the FASN gene and explore their relationships with ultrasound carcass traits in order to assess the potential use of the FASN gene for the breeding selection of Qinchuan cattle for desirable carcass traits. The frequencies of SNP g.12740C>T, g.13192T>C and g.13232C>T were identified in 525 individual Qinchuan cattle which were also assessed for backfat depth, eye muscle area and intramuscular fat by ultrasound. According to the PIC values, g.13192T>C possessed an intermediate polymorphism (0.25T, g.12740C>T possessed low polymorphism (PIC<0.25). Chi-square tests showed that g.13192T>C were in Hardy-Weinberg disequilibrium (c2C was associated with a greater eye muscle area and the TT genotype at g.13232C>T was associated with greater intramuscular fat. When these genotypes were combined there was no difference in eye muscle area and intramuscular fat between the diplotypes. The H H diplotype was associated with carcass traits that are likely to provide economic advantage in Qinchuan cattle. Variations in the FASN genes and their corresponding genotypes may be considered as molecular markers for economic traits in cattle breeding.
[Mh] Termos MeSH primário: Ácido Graxo Sintase Tipo I/genética
Estudos de Associação Genética/métodos
Polimorfismo de Nucleotídeo Único
[Mh] Termos MeSH secundário: Tecido Adiposo Branco/metabolismo
Animais
Composição Corporal
Bovinos
Feminino
Carne
Locos de Características Quantitativas
Seleção Artificial
Análise de Sequência de DNA
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
EC 2.3.1.85 (Fatty Acid Synthase, Type I)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180129
[Lr] Data última revisão:
180129
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171224
[St] Status:MEDLINE


  4 / 91 MEDLINE  
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[PMID]:28692120
[Au] Autor:Lopes FB; Ferreira JL; Lobo RB; Rosa GJM
[Ad] Endereço:Department of Animal Sciences, , , USA camult@gmail.com.
[Ti] Título:Bayesian analyses of genetic parameters for growth traits in Nellore cattle raised on pasture.
[So] Source:Genet Mol Res;16(3), 2017 Jul 06.
[Is] ISSN:1676-5680
[Cp] País de publicação:Brazil
[La] Idioma:eng
[Ab] Resumo:This study was carried out to investigate (co)variance components and genetic parameters for growth traits in beef cattle using a multi-trait model by Bayesian methods. Genetic and residual (co)variances and parameters were estimated for weights at standard ages of 120 (W120), 210 (W210), 365 (W365), and 450 days (W450), and for pre- and post-weaning daily weight gain (preWWG and postWWG) in Nellore cattle. Data were collected over 16 years (1993-2009), and all animals were raised on pasture in eight farms in the North of Brazil that participate in the National Association of Breeders and Researchers. Analyses were run by the Bayesian approach using Gibbs sampler. Additive direct heritabilities for W120, W210, W365, and W450 and for preWWG and postWWG were 0.28 ± 0.013, 0.32 ± 0.002, 0.31 ± 0.002, 0.50 ± 0.026, 0.61 ± 0.047, and 0.79 ± 0.055, respectively. The estimates of maternal heritability were 0.32 ± 0.012, 0.29 ± 0.004, 0.30 ± 0.005, 0.25 ± 0.015, 0.23 ± 0.017, and 0.22 ± 0.016, respectively, for W120, W210, W365, and W450 and for preWWG and postWWG. The estimates of genetic direct additive correlation among all traits were positive and ranged from 0.25 ± 0.03 (preWWG and postWWG) to 0.99 ± 0.00 (W210 and preWWG). The moderate to high estimates of heritability and genetic correlation for weights and daily weight gains at different ages is suggestive of genetic improvement in these traits by selection at an appropriate age. Maternal genetic effects seemed to be significant across the traits. When the focus is on direct and maternal effects, W210 seems to be a good criterium for the selection of Nellore cattle considering the importance of this breed as a major breed of beef cattle not only in Northern Brazil but all regions covered by tropical pastures. As in this study the genetic correlations among all traits were high, the selection based on weaning weight might be a good choice because at this age there are two important effects (maternal and direct genetic effects). In contrast, W120 should be preferred when the objective is improving the maternal ability of the dams. Furthermore, selection for postWWG can be used if the animals show both heavier weaning weights and high growth rate after weaning because it is possible to shorten the time between weaning and slaughter based on weaning weight, postWWG, and desired weight at the time of slaughter.
[Mh] Termos MeSH primário: Peso Corporal/genética
Bovinos/genética
Característica Quantitativa Herdável
Seleção Artificial
[Mh] Termos MeSH secundário: Animais
Teorema de Bayes
Bovinos/crescimento & desenvolvimento
Feminino
Masculino
Herança Materna
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171019
[Lr] Data última revisão:
171019
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170711
[St] Status:MEDLINE
[do] DOI:10.4238/gmr16039606


  5 / 91 MEDLINE  
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[PMID]:28671246
[Au] Autor:Saowaphak P; Duangjinda M; Plaengkaeo S; Suwannasing R; Boonkum W
[Ad] Endereço:Department of Animal Science, Faculty of Agriculture, , Thailand.
[Ti] Título:Genetic correlation and genome-wide association study (GWAS) of the length of productive life, days open, and 305-days milk yield in crossbred Holstein dairy cattle.
[So] Source:Genet Mol Res;16(2), 2017 Jun 29.
[Is] ISSN:1676-5680
[Cp] País de publicação:Brazil
[La] Idioma:eng
[Ab] Resumo:In this study, we estimated the genetic parameters and identified the putative quantitative trait loci (QTL) associated with the length of productive life (LPL), days open (DO), and 305-day milk yield for the first lactation (FM305) of crossbred Holstein dairy cattle. Data comprising 4,739 records collected between 1986 and 2004 were used to estimate the variance-covariance components using the multiple-trait animal linear mixed models based on the average information restricted maximum likelihood (AI-REML) algorithm. Thirty-six animals were genotyped using the Illumina BovineSNP50 Bead Chip [>50,000 single nucleotide polymorphisms (SNPs)] to identify the putative QTL in a genome-wide association study. The heritability of the production trait FM305 was 0.25 and that of the functional traits, LPL and DO, was low (0.10 and 0.06, respectively). The genetic correlation estimates demonstrated favorable negative correlations between LPL and DO (-0.02). However, we observed a favorable positive correlation between FM305 and LPL (0.43) and an unfavorable positive correlation between FM305 and DO (0.1). The GWAS results indicated that 23 QTLs on bovine chromosomes 1, 4, 5, 8, 15, 26, and X were associated with the traits of interest, and the putative QTL regions were identified within seven genes (SYT1, DOCK11, KLHL13, IL13RA1, PRKG1, GNA14, and LRRC4C). In conclusion, the heritability estimates of the LPL and DO were low. Therefore, the approach of multiple-trait selection indexes should be applied, and the QTL identified here should be considered for use in marker-assisted selection in the future.
[Mh] Termos MeSH primário: Bovinos/genética
Lactação/genética
Locos de Características Quantitativas
[Mh] Termos MeSH secundário: Animais
Feminino
Estudo de Associação Genômica Ampla
Genótipo
Longevidade/genética
Leite
Característica Quantitativa Herdável
Reprodução/genética
Seleção Artificial
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171019
[Lr] Data última revisão:
171019
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170704
[St] Status:MEDLINE
[do] DOI:10.4238/gmr16029091


  6 / 91 MEDLINE  
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[PMID]:28619083
[Au] Autor:Boerner V
[Ad] Endereço:Animal Genetics and Breeding Unit, University of New England, Armidale, 2351, Australia. vboerner@une.edu.au.
[Ti] Título:On marker-based parentage verification via non-linear optimization.
[So] Source:Genet Sel Evol;49(1):50, 2017 Jun 15.
[Is] ISSN:1297-9686
[Cp] País de publicação:France
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Parentage verification by molecular markers is mainly based on short tandem repeat markers. Single nucleotide polymorphisms (SNPs) as bi-allelic markers have become the markers of choice for genotyping projects. Thus, the subsequent step is to use SNP genotypes for parentage verification as well. Recent developments of algorithms such as evaluating opposing homozygous SNP genotypes have drawbacks, for example the inability of rejecting all animals of a sample of potential parents. This paper describes an algorithm for parentage verification by constrained regression which overcomes the latter limitation and proves to be very fast and accurate even when the number of SNPs is as low as 50. The algorithm was tested on a sample of 14,816 animals with 50, 100 and 500 SNP genotypes randomly selected from 40k genotypes. The samples of putative parents of these animals contained either five random animals, or four random animals and the true sire. Parentage assignment was performed by ranking of regression coefficients, or by setting a minimum threshold for regression coefficients. The assignment quality was evaluated by the power of assignment (P[Formula: see text]) and the power of exclusion (P[Formula: see text]). RESULTS: If the sample of putative parents contained the true sire and parentage was assigned by coefficient ranking, P[Formula: see text] and P[Formula: see text] were both higher than 0.99 for the 500 and 100 SNP genotypes, and higher than 0.98 for the 50 SNP genotypes. When parentage was assigned by a coefficient threshold, P[Formula: see text] was higher than 0.99 regardless of the number of SNPs, but P[Formula: see text] decreased from 0.99 (500 SNPs) to 0.97 (100 SNPs) and 0.92 (50 SNPs). If the sample of putative parents did not contain the true sire and parentage was rejected using a coefficient threshold, the algorithm achieved a P[Formula: see text] of 1 (500 SNPs), 0.99 (100 SNPs) and 0.97 (50 SNPs). CONCLUSION: The algorithm described here is easy to implement, fast and accurate, and is able to assign parentage using genomic marker data with a size as low as 50 SNPs.
[Mh] Termos MeSH primário: Algoritmos
Técnicas de Genotipagem/métodos
Linhagem
Polimorfismo de Nucleotídeo Único
[Mh] Termos MeSH secundário: Animais
Feminino
Marcadores Genéticos
Técnicas de Genotipagem/veterinária
Masculino
Seleção Artificial
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Genetic Markers)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171006
[Lr] Data última revisão:
171006
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170617
[St] Status:MEDLINE
[do] DOI:10.1186/s12711-017-0324-3


  7 / 91 MEDLINE  
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[PMID]:28536080
[Au] Autor:Zhang D; Li G; Wang Y
[Ad] Endereço:Shanghai Huaxin High Biotechnology Company Limited, 1150 Guiqiao Road, Shanghai 201206, PR China. Electronic address: ff_1113a@126.com.
[Ti] Título:A genome-wide identification and analysis of basic helix-loop-helix transcription factors in cattle.
[So] Source:Gene;626:241-250, 2017 Aug 30.
[Is] ISSN:1879-0038
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Basic helix-loop-helix (BHLH) transcription factors comprise a large family of regulatory proteins and play critical roles in the developmental processes of higher organisms. Complete lists of BHLH family members have been identified in about 50 organisms, including fruit fly, zebrafish, mouse, giant panda, worm, yeast, rice and apple. Cattle, Bos taurus, is important for agriculture and animal nutrition, and is also a good model organism for health research. In the present study, 116 putative BHLHs were identified in the cattle genome. Phylogenetic analyses revealed that 111 Bos taurus BHLH (BtBHLH: Bos taurus BHLH) members belong to 44 families, with 48, 26, 16, 4, 13 and 4 members in group A, B, C, D, E and F respectively, and the remaining 5 BtBHLHs are orphan members. All of them were named and assigned into the corresponding BHLH families based on acceptable bootstrap values from in-group phylogenetic analyses with orthologous BHLHs from mouse and other mammalian species. A comparison between annotations deposited in the GenBank and KEGG databases with our analyses indicated that the annotations of 2 of the 116 BtBHLH members were inconsistent with our analytical results. Microarray evidence and expressed sequence tags of only 14 BtBHLH genes was now not available. Chromosomal locations of the BtBHLHs showed that the distribution of the BtBHLHs was uneven and some genes, e.g., BtOligo, BtHes and BtMyf6, may arise from gene duplication. The test of positive selection showed episodic positive selection occurs only in 5 families among the studied mammalian BHLHs. These results provide a solid basis for further studies on BHLH protein regulation of key growth and developmental processes.
[Mh] Termos MeSH primário: Fatores de Transcrição Hélice-Alça-Hélice Básicos/genética
Bovinos/genética
[Mh] Termos MeSH secundário: Animais
Cromossomos/genética
Sequência Conservada
Estudo de Associação Genômica Ampla
Anotação de Sequência Molecular
Seleção Artificial
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Basic Helix-Loop-Helix Transcription Factors)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170801
[Lr] Data última revisão:
170801
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170525
[St] Status:MEDLINE


  8 / 91 MEDLINE  
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[PMID]:28532460
[Au] Autor:Blasco A; Martínez-Álvaro M; García ML; Ibáñez-Escriche N; Argente MJ
[Ad] Endereço:Institute for Animal Science and Technology, Universitat Politècnica de València, Valencia, Spain. ablasco@dca.upv.es.
[Ti] Título:Selection for environmental variance of litter size in rabbits.
[So] Source:Genet Sel Evol;49(1):48, 2017 May 22.
[Is] ISSN:1297-9686
[Cp] País de publicação:France
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: In recent years, there has been an increasing interest in the genetic determination of environmental variance. In the case of litter size, environmental variance can be related to the capacity of animals to adapt to new environmental conditions, which can improve animal welfare. RESULTS: We developed a ten-generation divergent selection experiment on environmental variance. We selected one line of rabbits for litter size homogeneity and one line for litter size heterogeneity by measuring intra-doe phenotypic variance. We proved that environmental variance of litter size is genetically determined and can be modified by selection. Response to selection was 4.5% of the original environmental variance per generation. Litter size was consistently higher in the Low line than in the High line during the entire experiment. CONCLUSIONS: We conclude that environmental variance of litter size is genetically determined based on the results of our divergent selection experiment. This has implications for animal welfare, since animals that cope better with their environment have better welfare than more sensitive animals. We also conclude that selection for reduced environmental variance of litter size does not depress litter size.
[Mh] Termos MeSH primário: Interação Gene-Ambiente
Tamanho da Ninhada de Vivíparos/genética
Coelhos/genética
Seleção Artificial
[Mh] Termos MeSH secundário: Animais
Ecossistema
Feminino
Variação Genética
Masculino
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171006
[Lr] Data última revisão:
171006
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170524
[St] Status:MEDLINE
[do] DOI:10.1186/s12711-017-0323-4


  9 / 91 MEDLINE  
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[PMID]:28526698
[Au] Autor:Goiffon M; Kusmec A; Wang L; Hu G; Schnable PS
[Ad] Endereço:Department of Industrial and Manufacturing Systems Engineering, Iowa State University, Ames, Iowa 50011.
[Ti] Título:Improving Response in Genomic Selection with a Population-Based Selection Strategy: Optimal Population Value Selection.
[So] Source:Genetics;206(3):1675-1682, 2017 Jul.
[Is] ISSN:1943-2631
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Genomic selection (GS) identifies individuals for inclusion in breeding programs based on the sum of their estimated marker effects or genomic estimated breeding values (GEBVs). Due to significant correlation between GEBVs and true breeding values, this has resulted in enhanced rates of genetic gain as compared to traditional methods of selection. Three extensions to GS, weighted genomic selection (WGS), optimal haploid value (OHV) selection, and genotype building (GB) selection have been proposed to improve long-term response, and to facilitate the efficient development of doubled haploids. In separate simulation studies, these methods were shown to outperform GS under various assumptions. However, further potential for improvement exists. In this paper, optimal population value (OPV) selection is introduced as selection based on the maximum possible haploid value in a subset of the population. Instead of evaluating the breeding merit of individuals as in GS, WGS, and OHV selection, the proposed method evaluates the breeding merit of a set of individuals as in GB. After testing these selection methods extensively, OPV and GB selection were found to achieve greater responses than GS, WGS, and OHV, with OPV outperforming GB across most percentiles. These results suggest a new paradigm for selection methods in which an individual's value is dependent upon its complementarity with others.
[Mh] Termos MeSH primário: Genoma
Modelos Genéticos
Seleção Artificial
[Mh] Termos MeSH secundário: Animais
Genótipo
Haploidia
Hibridização Genética
Seleção Genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171019
[Lr] Data última revisão:
171019
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170521
[St] Status:MEDLINE
[do] DOI:10.1534/genetics.116.197103


  10 / 91 MEDLINE  
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[PMID]:28521728
[Au] Autor:Gonen S; Ros-Freixedes R; Battagin M; Gorjanc G; Hickey JM
[Ad] Endereço:The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK.
[Ti] Título:A method for the allocation of sequencing resources in genotyped livestock populations.
[So] Source:Genet Sel Evol;49(1):47, 2017 May 18.
[Is] ISSN:1297-9686
[Cp] País de publicação:France
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: This paper describes a method, called AlphaSeqOpt, for the allocation of sequencing resources in livestock populations with existing phased genomic data to maximise the ability to phase and impute sequenced haplotypes into the whole population. METHODS: We present two algorithms. The first selects focal individuals that collectively represent the maximum possible portion of the haplotype diversity in the population. The second allocates a fixed sequencing budget among the families of focal individuals to enable phasing of their haplotypes at the sequence level. We tested the performance of the two algorithms in simulated pedigrees. For each pedigree, we evaluated the proportion of population haplotypes that are carried by the focal individuals and compared our results to a variant of the widely-used key ancestors approach and to two haplotype-based approaches. We calculated the expected phasing accuracy of the haplotypes of a focal individual at the sequence level given the proportion of the fixed sequencing budget allocated to its family. RESULTS: AlphaSeqOpt maximises the ability to capture and phase the most frequent haplotypes in a population in three ways. First, it selects focal individuals that collectively represent a larger portion of the population haplotype diversity than existing methods. Second, it selects focal individuals from across the pedigree whose haplotypes can be easily phased using family-based phasing and imputation algorithms, thus maximises the ability to impute sequence into the rest of the population. Third, it allocates more of the fixed sequencing budget to focal individuals whose haplotypes are more frequent in the population than to focal individuals whose haplotypes are less frequent. Unlike existing methods, we additionally present an algorithm to allocate part of the sequencing budget to the families (i.e. immediate ancestors) of focal individuals to ensure that their haplotypes can be phased at the sequence level, which is essential for enabling and maximising subsequent sequence imputation. CONCLUSIONS: We present a new method for the allocation of a fixed sequencing budget to focal individuals and their families such that the final sequenced haplotypes, when phased at the sequence level, represent the maximum possible portion of the haplotype diversity in the population that can be sequenced and phased at that budget.
[Mh] Termos MeSH primário: Algoritmos
Técnicas de Genotipagem/veterinária
Haplótipos
Gado/genética
Seleção Artificial
Análise de Sequência de DNA/métodos
[Mh] Termos MeSH secundário: Animais
Técnicas de Genotipagem/métodos
Técnicas de Genotipagem/normas
Modelos Genéticos
Linhagem
Polimorfismo Genético
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171006
[Lr] Data última revisão:
171006
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170520
[St] Status:MEDLINE
[do] DOI:10.1186/s12711-017-0322-5



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