Your browser doesn't support javascript.
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 71.959
Filtrar
1.
Yi Chuan ; 41(11): 1023-1040, 2019 Nov 20.
Artigo em Chinês | MEDLINE | ID: mdl-31735705

RESUMO

Heritability, one of the central quantitative genetic parameters, is critically important to measure the genetic variation of traits, especially in the studies of the response to selection in evolutionary biology and agriculture, and the prediction of disease risks in medicine. The statistical model and method for estimating heritability have been continually developed and improved, since the genetic variance components was first proposed by Fisher in 1918. Recently, the term "microbiability" (m 2), an analogous concept and estimated method to heritability, was introduced in gut microbiome research for evaluating the effect of entire microbiota on a host phenotype. In this review, we summarize the progress of statistical methods in the heritability estimation, as well as the current state of gut microbiome associations with the host genome, with a particular focus on the concept and estimated methods of microbiability. Our review will provide a reference for the future study of host phenotypic variation that can be inferred by the gut microbiota.


Assuntos
Evolução Biológica , Modelos Genéticos , Característica Quantitativa Herdável , Microbioma Gastrointestinal , Genoma , Fenótipo
2.
Genome Biol ; 20(1): 193, 2019 09 09.
Artigo em Inglês | MEDLINE | ID: mdl-31500668

RESUMO

Technical variation in feature measurements, such as gene expression and locus accessibility, is a key challenge of large-scale single-cell genomic datasets. We show that this technical variation in both scRNA-seq and scATAC-seq datasets can be mitigated by analyzing feature detection patterns alone and ignoring feature quantification measurements. This result holds when datasets have low detection noise relative to quantification noise. We demonstrate state-of-the-art performance of detection pattern models using our new framework, scBFA, for both cell type identification and trajectory inference. Performance gains can also be realized in one line of R code in existing pipelines.


Assuntos
Genômica/métodos , Análise de Célula Única/métodos , Perfilação da Expressão Gênica , Modelos Genéticos , Análise de Sequência de RNA , Software
4.
BMC Bioinformatics ; 20(1): 460, 2019 Sep 06.
Artigo em Inglês | MEDLINE | ID: mdl-31492104

RESUMO

BACKGROUND: Uncovering the evolutionary principles of gene coexpression network is important for our understanding of the network topological property of new genes. However, most existing evolutionary models only considered the evolution of duplication genes and only based on the degree of genes, ignoring the other key topological properties. The evolutionary mechanism by which how are new genes integrated into the ancestral networks are not yet to be comprehensively characterized. Herein, based on the human ribonucleic acid-sequencing (RNA-seq) data, we develop a new evolutionary model of gene coexpression network which considers the evolutionary process of both duplication genes and de novo genes. RESULTS: Based on the human RNA-seq data, we construct a gene coexpression network consisting of 8061 genes and 638624 links. We find that there are 1394 duplication genes and 126 de novo genes in the network. Then based on human gene age data, we reproduce the evolutionary process of this gene coexpression network and develop a new evolutionary model. We find that the generation rates of duplication genes and de novo genes are approximately 3.58/Myr (Myr=Million year) and 0.31/Myr, respectively. Based on the average degree and coreness of parent genes, we find that the gene duplication is a random process. Eventually duplication genes only inherit 12.89% connections from their parent genes and the retained connections have a smaller edge betweenness. Moreover, we find that both duplication genes and de novo genes prefer to develop new interactions with genes which have a large degree and a large coreness. Our proposed model can generate an evolutionary network when the number of newly added genes or the length of evolutionary time is known. CONCLUSIONS: Gene duplication and de novo genes are two dominant evolutionary forces in shaping the coexpression network. Both duplication genes and de novo genes develop new interactions through a "rich-gets-richer" mechanism in terms of degree and coreness. This mechanism leads to the scale-free property and hierarchical architecture of biomolecular network. The proposed model is able to construct a gene coexpression network with comprehensive biological characteristics.


Assuntos
Evolução Molecular , Regulação da Expressão Gênica , Redes Reguladoras de Genes , Modelos Genéticos , Duplicação Gênica , Humanos , Análise de Sequência de RNA
5.
Genome Biol ; 20(1): 162, 2019 08 09.
Artigo em Inglês | MEDLINE | ID: mdl-31399036

RESUMO

BACKGROUND: General translational cis-elements are present in the mRNAs of all genes and affect the recruitment, assembly, and progress of preinitiation complexes and the ribosome under many physiological states. These elements include mRNA folding, upstream open reading frames, specific nucleotides flanking the initiating AUG codon, protein coding sequence length, and codon usage. The quantitative contributions of these sequence features and how and why they coordinate to control translation rates are not well understood. RESULTS: Here, we show that these sequence features specify 42-81% of the variance in translation rates in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Arabidopsis thaliana, Mus musculus, and Homo sapiens. We establish that control by RNA secondary structure is chiefly mediated by highly folded 25-60 nucleotide segments within mRNA 5' regions, that changes in tri-nucleotide frequencies between highly and poorly translated 5' regions are correlated between all species, and that control by distinct biochemical processes is extensively correlated as is regulation by a single process acting in different parts of the same mRNA. CONCLUSIONS: Our work shows that general features control a much larger fraction of the variance in translation rates than previously realized. We provide a more detailed and accurate understanding of the aspects of RNA structure that directs translation in diverse eukaryotes. In addition, we note that the strongly correlated regulation between and within cis-control features will cause more even densities of translational complexes along each mRNA and therefore more efficient use of the translation machinery by the cell.


Assuntos
Regulação da Expressão Gênica , Biossíntese de Proteínas , RNA Mensageiro/química , Animais , Arabidopsis/genética , Humanos , Camundongos , Modelos Genéticos , Conformação de Ácido Nucleico , Motivos de Nucleotídeos , Saccharomyces cerevisiae/genética , Schizosaccharomyces/genética
6.
Genet Sel Evol ; 51(1): 45, 2019 Aug 19.
Artigo em Inglês | MEDLINE | ID: mdl-31426753

RESUMO

BACKGROUND: Crossbreeding is widely used in pig production because of the benefits of heterosis effects and breed complementarity. Commonly, sire lines are bred for traits such as feed efficiency, growth and meat content, whereas maternal lines are also bred for reproduction and longevity traits, and the resulting three-way crossbred pigs are used for production of meat. The most important genetic basis for heterosis is dominance effects, e.g. removal of inbreeding depression. The aims of this study were to (1) present a modification of a previously developed model with additive, dominance and inbreeding depression genetic effects for analysis of data from a purebred sire line and three-way crossbred pigs; (2) based on this model, present equations for additive genetic variances, additive genetic covariance, and estimated breeding values (EBV) with associated accuracies for purebred and crossbred performances; (3) use the model to analyse four production traits, i.e. ultra-sound recorded backfat thickness (BF), conformation score (CONF), average daily gain (ADG), and feed conversion ratio (FCR), recorded on Danbred Duroc and Danbred Duroc-Landrace-Yorkshire crossbred pigs reared in the same environment; and (4) obtain estimates of genetic parameters, additive genetic correlations between purebred and crossbred performances, and EBV with associated accuracies for purebred and crossbred performances for this data set. RESULTS: Additive genetic correlations (with associated standard errors) between purebred and crossbred performances were equal to 0.96 (0.07), 0.83 (0.16), 0.75 (0.17), and 0.87 (0.18) for BF, CONF, ADG, and FCR, respectively. For BF, ADG, and FCR, the additive genetic variance was smaller for purebred performance than for crossbred performance, but for CONF the reverse was observed. EBV on Duroc boars were more accurate for purebred performance than for crossbred performance for BF, CONF and FCR, but not for ADG. CONCLUSIONS: Methodological developments led to equations for genetic (co)variances and EBV with associated accuracies for purebred and crossbred performances in a three-way crossbreeding system. As illustrated by the data analysis, these equations may be useful for implementation of genomic selection in this system.


Assuntos
Cruzamento , Depressão por Endogamia , Modelos Genéticos , Modelos Estatísticos , Suínos/genética , Animais , Cruzamentos Genéticos , Feminino , Variação Genética , Hibridização Genética , Masculino
7.
BMC Bioinformatics ; 20(1): 444, 2019 Aug 28.
Artigo em Inglês | MEDLINE | ID: mdl-31455207

RESUMO

BACKGROUND: Mining epistatic loci which affects specific phenotypic traits is an important research issue in the field of biology. Bayesian network (BN) is a graphical model which can express the relationship between genetic loci and phenotype. Until now, it has been widely used into epistasis mining in many research work. However, this method has two disadvantages: low learning efficiency and easy to fall into local optimum. Genetic algorithm has the excellence of rapid global search and avoiding falling into local optimum. It is scalable and easy to integrate with other algorithms. This work proposes an epistasis mining approach based on genetic tabu algorithm and Bayesian network (Epi-GTBN). It uses genetic algorithm into the heuristic search strategy of Bayesian network. The individual structure can be evolved through the genetic operations of selection, crossover and mutation. It can help to find the optimal network structure, and then further to mine the epistasis loci effectively. In order to enhance the diversity of the population and obtain a more effective global optimal solution, we use the tabu search strategy into the operations of crossover and mutation in genetic algorithm. It can help to accelerate the convergence of the algorithm. RESULTS: We compared Epi-GTBN with other recent algorithms using both simulated and real datasets. The experimental results demonstrate that our method has much better epistasis detection accuracy in the case of not affecting the efficiency for different datasets. CONCLUSIONS: The presented methodology (Epi-GTBN) is an effective method for epistasis detection, and it can be seen as an interesting addition to the arsenal used in complex traits analyses.


Assuntos
Algoritmos , Mineração de Dados , Epistasia Genética , Teorema de Bayes , Redes Reguladoras de Genes , Loci Gênicos , Humanos , Degeneração Macular/genética , Modelos Genéticos , Polimorfismo de Nucleotídeo Único/genética
8.
BMC Evol Biol ; 19(1): 172, 2019 08 23.
Artigo em Inglês | MEDLINE | ID: mdl-31443631

RESUMO

BACKGROUND: The evolution of multi-cellular animals has produced a conspicuous trend toward increased body size. This trend has introduced at least two novel problems: an expected elevated risk of somatic disorders, such as cancer, and declining evolvability due to generally reduced population size, lower reproduction rate and extended generation time. Low population size is widely recognized to explain the high mutation rates in animals by limiting the presumed universally negative selection acting on mutation rates. RESULTS: Here, we present evidence from stochastic modeling that the direction and strength of selection acting on mutation rates is highly dependent on the evolution of somatic maintenance, and thus longevity, which modulates the cost of somatic mutations. CONCLUSIONS: We argue that the impact of the evolution of longevity on mutation rates may have been critical in facilitating animal evolution.


Assuntos
Evolução Biológica , Tamanho Corporal , Modelos Genéticos , Taxa de Mutação , Animais , Simulação por Computador , Longevidade , Método de Monte Carlo , Mutação , Neoplasias/genética , Fenótipo , Densidade Demográfica , Seleção Genética
9.
Genet Epidemiol ; 43(7): 800-814, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31433078

RESUMO

The power of genetic association analyses can be increased by jointly meta-analyzing multiple correlated phenotypes. Here, we develop a meta-analysis framework, Meta-MultiSKAT, that uses summary statistics to test for association between multiple continuous phenotypes and variants in a region of interest. Our approach models the heterogeneity of effects between studies through a kernel matrix and performs a variance component test for association. Using a genotype kernel, our approach can test for rare-variants and the combined effects of both common and rare-variants. To achieve robust power, within Meta-MultiSKAT, we developed fast and accurate omnibus tests combining different models of genetic effects, functional genomic annotations, multiple correlated phenotypes, and heterogeneity across studies. In addition, Meta-MultiSKAT accommodates situations where studies do not share exactly the same set of phenotypes or have differing correlation patterns among the phenotypes. Simulation studies confirm that Meta-MultiSKAT can maintain the type-I error rate at the exome-wide level of 2.5 × 10-6 . Further simulations under different models of association show that Meta-MultiSKAT can improve the power of detection from 23% to 38% on average over single phenotype-based meta-analysis approaches. We demonstrate the utility and improved power of Meta-MultiSKAT in the meta-analyses of four white blood cell subtype traits from the Michigan Genomics Initiative (MGI) and SardiNIA studies.


Assuntos
Estudos de Associação Genética , Metanálise como Assunto , Frequência do Gene/genética , Genótipo , Humanos , Itália , Leucócitos/metabolismo , Modelos Genéticos , Mutação/genética , Fenótipo
10.
BMC Evol Biol ; 19(1): 167, 2019 08 07.
Artigo em Inglês | MEDLINE | ID: mdl-31390981

RESUMO

BACKGROUND: Little is known about the long-term patterns of body size evolution in Crocodylomorpha, the > 200-million-year-old group that includes living crocodylians and their extinct relatives. Extant crocodylians are mostly large-bodied (3-7 m) predators. However, extinct crocodylomorphs exhibit a wider range of phenotypes, and many of the earliest taxa were much smaller (< 1.2 m). This suggests a pattern of size increase through time that could be caused by multi-lineage evolutionary trends of size increase or by selective extinction of small-bodied species. Here, we characterise patterns of crocodylomorph body size evolution using a model fitting-approach (with cranial measurements serving as proxies). We also estimate body size disparity through time and quantitatively test hypotheses of biotic and abiotic factors as potential drivers of crocodylomorph body size evolution. RESULTS: Crocodylomorphs reached an early peak in body size disparity during the Late Jurassic, and underwent an essentially continual decline since then. A multi-peak Ornstein-Uhlenbeck model outperforms all other evolutionary models fitted to our data (including both uniform and non-uniform), indicating that the macroevolutionary dynamics of crocodylomorph body size are better described within the concept of an adaptive landscape, with most body size variation emerging after shifts to new macroevolutionary regimes (analogous to adaptive zones). We did not find support for a consistent evolutionary trend towards larger sizes among lineages (i.e., Cope's rule), or strong correlations of body size with climate. Instead, the intermediate to large body sizes of some crocodylomorphs are better explained by group-specific adaptations. In particular, the evolution of a more aquatic lifestyle (especially marine) correlates with increases in average body size, though not without exceptions. CONCLUSIONS: Shifts between macroevolutionary regimes provide a better explanation of crocodylomorph body size evolution on large phylogenetic and temporal scales, suggesting a central role for lineage-specific adaptations rather than climatic forcing. Shifts leading to larger body sizes occurred in most aquatic and semi-aquatic groups. This, combined with extinctions of groups occupying smaller body size regimes (particularly during the Late Cretaceous and Cenozoic), gave rise to the upward-shifted body size distribution of extant crocodylomorphs compared to their smaller-bodied terrestrial ancestors.


Assuntos
Tamanho Corporal , Fósseis , Répteis/genética , Animais , Evolução Biológica , Modelos Genéticos , Filogenia , Répteis/classificação , Répteis/fisiologia , Crânio/anatomia & histologia
11.
Genet Sel Evol ; 51(1): 43, 2019 Aug 13.
Artigo em Inglês | MEDLINE | ID: mdl-31409294

RESUMO

BACKGROUND: Random regression models (RRM) are widely used to analyze longitudinal data in genetic evaluation systems because they can better account for time-course changes in environmental effects and additive genetic values of animals by fitting the test-day (TD) specific effects. Our objective was to implement a random regression model for the evaluation of dairy production traits in French goats. RESULTS: The data consisted of milk TD records from 30,186 and 32,256 first lactations of Saanen and Alpine goats. Milk yield, fat yield, protein yield, fat content and protein content were considered. Splines were used to model the environmental factors. The genetic and permanent environmental effects were modeled by the same Legendre polynomials. The goodness-of-fit and the genetic parameters derived from functions of the polynomials of orders 0 to 4 were tested. Results were also compared to those from a lactation model with total milk yield calculated over 250 days and to those of a multiple-trait model that considers performance in six periods throughout lactation as different traits. Genetic parameters were consistent between models. Models with fourth-order Legendre polynomials led to the best fit of the data. In order to reduce complexity, computing time, and interpretation, a rank reduction of the variance covariance matrix was performed using eigenvalue decomposition. With a reduction to rank 2, the first two principal components correctly summarized the genetic variability of milk yield level and persistency, with a correlation close to 0 between them. CONCLUSIONS: A random regression model was implemented in France to evaluate and select goats for yield traits and persistency, which are independent i.e. no genetic correlation between them, in first lactation.


Assuntos
Cabras/genética , Lactação/genética , Modelos Genéticos , Modelos Estatísticos , Animais , Indústria de Laticínios , Feminino , Cabras/fisiologia , Masculino , Leite , Análise de Regressão
12.
Stud Hist Philos Biol Biomed Sci ; 76: 101174, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31405540

RESUMO

The theme of this paper is that Fisher's "Fundamental Theorem of Natural Selection" has various deficiencies as a quantification of the effect of natural selection in a Mendelian population which are not shared by a new different theorem described in this paper. The deficiencies in Fisher's theorem are listed in this paper. The new theorem focuses on the implications of changes in gene frequencies under natural selection and not, as does the Fundamental Theorem of Natural Selection, on changes in mean population fitness. Whereas the algebra in the new theorem corresponds in places to that in the Fundamental Theorem of Natural Selection, the approach, perspective and conclusion of the new theorem are different from those of the Fundamental Theorem of Natural Selection.


Assuntos
Evolução Biológica , Frequência do Gene , Seleção Genética , Modelos Genéticos
13.
J Anim Sci ; 97(9): 3658-3668, 2019 Sep 03.
Artigo em Inglês | MEDLINE | ID: mdl-31373628

RESUMO

Mixing of pigs into new social groups commonly induces aggressive interactions that result in skin lesions on the body of the animals. The relationship between skin lesions and aggressive behavioral interactions in group-housed pigs can be analyzed within the framework of social genetic effects (SGE). This study incorporates the quantification of aggressive interactions between pairs of animals in the modeling of SGE for skin lesions in different regions of the body in growing pigs. The dataset included 792 pigs housed in 59 pens. Skin lesions in the anterior, central, and caudal regions of the body were counted 24 h after pig mixing. Animals were video-recorded for 9 h postmixing and trained observers recorded the type and duration of aggressive interactions between pairs of animals. The number of seconds that pairs of pigs spent engaged in reciprocal fights and unilateral attack behaviors were used to parametrize the intensity of social interactions (ISI). Three types of models were fitted: direct genetic additive model (DGE), traditional social genetic effect model (TSGE) assuming uniform interactions between dyads, and an intensity-based social genetic effect model (ISGE) that used ISI to parameterize SGE. All models included fixed effects of sex, replicate, lesion scorer, weight at mixing, premixing lesion count, and the total time that the animal spent engaged in aggressive interactions (reciprocal fights and unilateral attack behaviors) as a covariate; a random effect of pen; and a random direct genetic effect. The ISGE models recovered more direct genetic variance than DGE and TSGE, and the estimated heritabilities (h^D2) were highest for all traits (P < 0.01) for the ISGE with ISI parametrized with unilateral attack behavior. The TSGE produced estimates that did not differ significantly from DGE (P > 0.5). Incorporating the ISI into ISGE, even in a small dataset, allowed separate estimation of the genetic parameters for direct and SGE, as well as the genetic correlation between direct and SGE (rs), which was positive for all lesion traits. The estimates from ISGE suggest that if behavioral observations are available, selection incorporating SGE may reduce the consequences of aggressive behaviors after mixing pigs.


Assuntos
Bem-Estar do Animal , Comportamento Animal , Suínos/fisiologia , Agressão , Animais , Feminino , Masculino , Modelos Genéticos , Fenótipo , Pele/lesões , Suínos/genética
14.
Stud Hist Philos Biol Biomed Sci ; 76: 101188, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31326324

RESUMO

This paper elaborates a general framework to make sense of teleological explanations in Darwinian evolutionary biology. It relies on an attempt to tie natural selection to a sense of optimization. First, after assessing the objections made by any attempt to view selection as a maximising process within population genetics, it understands Grafen's Formal Darwinism (FD) as a conceptual link established between population genetics and behavioral ecology's adaptationist framework (without any empirical commitments). Thus I suggest that this provides a way to make sense of teleological explanations in biology under their various modes. Then the paper criticizes two major ways of accounting for teleology: a Darwinian one, the etiological view of biological functions, and a non-Darwinian one, here labeled "intrinsic teleology" view, which covers several subtypes of accounts, including plasticity-oriented conceptions of evolution or organizational views of function. The former is centered on traits while the latter is centered on organisms; this is shown to imply that both accounts are unable to provide a systematic understanding of biological teleology. Finally the paper argues that viewing teleology as maximization of inclusive fitness along the FD lines as understood here allows one to make sense of both the design of organisms and the individual traits as adaptions. Such notion is thereby claimed to be the proper meaning of teleology in evolutionary biology, since it avoids the opposed pitfalls of etiological views and intrinsic-teleology view, while accounting for the same features as they do.


Assuntos
Evolução Biológica , Biologia/métodos , Aptidão Genética , Modelos Genéticos , Filosofia
15.
Stud Hist Philos Biol Biomed Sci ; 76: 101186, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31326325

RESUMO

I distinguish two roles for a fitness concept in the context of explaining cumulative adaptive evolution: fitness as a predictor of gene frequency change, and fitness as a criterion for phenotypic improvement. Critics of inclusive fitness argue, correctly, that it is not an ideal fitness concept for the purpose of predicting gene-frequency change, since it relies on assumptions about the causal structure of social interaction that are unlikely to be exactly true in real populations, and that hold as approximations only given a specific type of weak selection. However, Hamilton took this type of weak selection, on independent grounds, to be responsible for cumulative assembly of complex adaptations. In this special context, I argue that inclusive fitness is distinctively valuable as a criterion for improvement and a standard for optimality. Yet to call inclusive fitness a criterion for improvement and a standard for optimality is not to make any claim about the frequency with which inclusive fitness optimization actually occurs in nature. This is an empirical question that cannot be settled by theory alone. I close with some reflections on the place of inclusive fitness in the long running clash between 'causalist' and 'statisticalist' conceptions of fitness.


Assuntos
Evolução Biológica , Biologia/métodos , Frequência do Gene , Aptidão Genética , Modelos Genéticos , Filosofia
16.
BMC Bioinformatics ; 20(1): 404, 2019 Jul 25.
Artigo em Inglês | MEDLINE | ID: mdl-31345171

RESUMO

BACKGROUND: It has been shown that the deregulation of miRNAs is associated with the development and progression of many human diseases. To reduce time and cost of biological experiments, a number of algorithms have been proposed for predicting miRNA-disease associations. However, the existing methods rarely investigated the cause-and-effect mechanism behind these associations, which hindered further biomedical follow-ups. RESULTS: In this study, we presented a CCA-based model in which the possible molecular causes of miRNA-disease associations were comprehensively revealed by extracting correlated sets of genes and diseases based on the co-occurrence of miRNAs in target gene profiles and disease profiles. Our method directly suggested the underlying genes involved, which could be used for experimental tests and confirmation. The inference of associated diseases of a new miRNA was made by taking into account the weight vectors of the extracted sets. We extracted 60 pairs of correlated sets from 404 miRNAs with two profiles for 2796 target genes and 362 diseases. The extracted diseases could be considered as possible outcomes of miRNAs regulating the target genes which appeared in the same set, some of which were supported by independent source of information. Furthermore, we tested our method on the 404 miRNAs under the condition of 5-fold cross validations and received an AUC value of 0.84606. Finally, we extensively inferred miRNA-disease associations for 100 new miRNAs and some interesting prediction results were validated by established databases. CONCLUSIONS: The encouraging results demonstrated that our method could provide a biologically relevant prediction and interpretation of associations between miRNAs and diseases, which were of great usefulness when guiding biological experiments for scientific research.


Assuntos
Algoritmos , Biologia Computacional/métodos , Doença/genética , Estudos de Associação Genética , MicroRNAs/genética , Bases de Dados Genéticas , Humanos , MicroRNAs/metabolismo , Modelos Genéticos
17.
Genet Sel Evol ; 51(1): 40, 2019 Jul 16.
Artigo em Inglês | MEDLINE | ID: mdl-31311493

RESUMO

BACKGROUND: In modern dairy breeding programmes, high contributions from foreign sires are nearly always present. Genotyping, and therefore genomic selection (GS), concern only a subpopulation of the breeding programme's wider dairy population. These features of a breeding programme contribute in different ways to the rate of genetic gain for the wider industry. METHODS: A deterministic recursive gene flow model across subpopulations of animals in a dairy industry was created to predict the commercial performance of replacement heifers and future artificial insemination bulls. Various breeding strategies were assessed by varying the reliability of breeding values, the genetic contributions from subpopulations, and the genetic trend and merit of the foreign subpopulation. RESULTS: A higher response in the true breeding goal measured in standard deviations (SD) of true merit (G) after 20 years of selection can be achieved when genetic contributions shift towards higher merit alternatives compared to keeping them fixed. A foreign annual genetic trend of 0.08 SD of the breeding goal, while the domestic genetic trend is 0.10 SD, results in the overall net present value of genetic gain increasing by 1.2, 2.3, and 3.4% after 20 years as the reliability of GS in the domestic population increased from 0.3 to 0.45, 0.60 and 0.75. With a foreign genetic trend of 0.10 SD, these increases are more modest; 0.9, 1.7, and 2.4%. Increasing the foreign genetic trend so that it is higher than the domestic trend erodes the benefits of increasing the reliability of domestic GS further. CONCLUSIONS: Having a foreign source of genetic material with a high rate of genetic progress contributes substantially to the benefits of domestic genetic progress while at the same time reducing the expected returns from investments to improve the accuracy of genomic prediction in the home country.


Assuntos
Bovinos/genética , Indústria de Laticínios , Modelos Genéticos , Seleção Genética , Seleção Artificial , Animais , Feminino , Fluxo Gênico , Masculino
18.
Medicine (Baltimore) ; 98(26): e16170, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31261547

RESUMO

OBJECTIVE: Non-syndromic cleft of the lip and/or palate (NSCL/P) is one of the most common polygenic diseases. In this study, both case-control and family-based association study were used to confirm whether the Single Nucleotide Polymorphisms (SNPs) were associated with NSCL/P. METHODS: A total of 37 nuclear families and 189 controls were recruited, whose blood DNA was extracted and subjected to genotyping of SNPs of 27 candidate genes by polymerase chain reaction-improved multiple ligase detection reaction technology (PCR-iMLDR). Case-control statistical analysis was performed using the SPSS 19.0. Haplotype Relative Risk (HRR), transmission disequilibrium test (TDT), and Family-Based Association Test (FBAT) were used to test for over-transmission of the target alleles in case-parent trios. The gene-gene interactions on NSCL/P were analyzed by Unphased-3.1.4. RESULTS: In case-control statistical analysis, only C14orf49 chr14_95932477 had statistically significant on genotype model (P = .03) and allele model (P = .03). Seven SNPs had statistically significant on TDT. None of 26 alleles has association with NSCL/P on FBAT. Some SNPs had haplotype-haplotype interactions and genotype-genotype interactions. CONCLUSION: C14orf49 chr14_95932477 was significantly different between cases and controls on genotype model and allele model by case-control design. Seven SNPs were significantly different on HRR. Four SNPs were significantly different on TDT.


Assuntos
Fenda Labial/genética , Fissura Palatina/genética , Predisposição Genética para Doença , Polimorfismo de Nucleotídeo Único , Estudos de Casos e Controles , Fenda Labial/complicações , Fissura Palatina/complicações , Família , Feminino , Estudos de Associação Genética , Humanos , Masculino , Modelos Genéticos , Fosfatases de Fosfoinositídeos/genética , Proteínas de Transporte Vesicular/genética
19.
Yi Chuan ; 41(6): 469-485, 2019 Jun 20.
Artigo em Chinês | MEDLINE | ID: mdl-31257196

RESUMO

The field of circular non-coding RNAs have been gradually attracted wide attention with the developments of high-throughput sequencing. In this review, we systematically summarize three driving models for circRNAs biogenesis: intron-pairing-driven, RNA binding protein-driven and lariat-driven. In addition, we also briefly introduce the current research methods of circRNAs, which include high-throughput library construction methods, identification through bioinformatics and common experimental verification. Here, we also systematically summarize the functions of circRNAs, including microRNA (miRNA) or protein sponges, regulating the alternative splicing (AS) and expression of host genes, and extensive translation. Finally, we provide a systematic characterization and the latest research progress of circRNAs, which provide a new perspective for further studies of circRNAs in plants.


Assuntos
Processamento Alternativo , RNA/genética , Íntrons , MicroRNAs , Modelos Genéticos , Plantas/genética , Proteínas de Ligação a RNA
20.
Microbes Environ ; 34(3): 260-267, 2019 Sep 25.
Artigo em Inglês | MEDLINE | ID: mdl-31257307

RESUMO

The soybean symbiont Bradyrhizobium diazoefficiens grows anaerobically in the presence of nitrate using the denitrification pathway, which involves the nap, nir, nor, and nos genes. We previously showed that NasT acts as a transcription antitermination regulator for nap and nos gene expression. In the present study, we investigated the targets of NasT in B. diazoefficiens during denitrifying growth by performing transcription profiling with RNA-seq and quantitative reverse-transcription PCR. Most of the genes with altered expression in the absence of NasT were related to nitrogen metabolism, specifically several systems for branched-chain amino acid transport. The present results suggest that the reduced expression of genes involved in nitrogen acquisition leads to the induction of alternative sets of genes with similar functions. The ΔnasT mutant of B. diazoefficiens grew better than the wild type under denitrifying conditions. However, this enhanced growth was completely abolished by an additional loss of the narK or bjgb genes, which encode cytoplasmic systems for nitrite and nitric oxide detoxification, respectively. Since the expression of narK and bjgb was increased in the ΔnasT mutant, the growth of the ΔnasT mutant may be promoted by increased detoxification activity.


Assuntos
Bradyrhizobium/genética , Bradyrhizobium/metabolismo , Desnitrificação/genética , Regulação Bacteriana da Expressão Gênica/genética , Genes Bacterianos/genética , Fatores de Transcrição/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Bradyrhizobium/crescimento & desenvolvimento , Perfilação da Expressão Gênica , Modelos Genéticos , Mutação , Nitrito Redutases/genética , Nitrogênio/metabolismo , Fatores de Transcrição/genética , Ativação Transcricional/genética
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA