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1.
Nat Commun ; 12(1): 1050, 2021 02 16.
Artigo em Inglês | MEDLINE | ID: mdl-33594080

RESUMO

Attributing the similarity between individuals to genetic and non-genetic factors is central to genetic analyses. In this paper we use the genomic relationship ([Formula: see text]) among 417,060 individuals to investigate the phenotypic covariance between pairs of individuals for 32 traits across the spectrum of relatedness, from unrelated pairs through to identical twins. We find linear relationships between phenotypic covariance and [Formula: see text] that agree with the SNP-based heritability ([Formula: see text]) in unrelated pairs ([Formula: see text]), and with pedigree-estimated heritability in close relatives ([Formula: see text]). The covariance increases faster than [Formula: see text] in distant relatives ([Formula: see text]), and we attribute this to imperfect linkage disequilibrium between causal variants and the common variants used to construct [Formula: see text]. We also examine the effect of assortative mating on heritability estimates from different experimental designs. We find that full-sib identity-by-descent regression estimates for height (0.66 s.e. 0.07) are consistent with estimates from close relatives (0.82 s.e. 0.04) after accounting for the effect of assortative mating.


Assuntos
Genoma Humano , Filogenia , Adulto , Idoso , Bancos de Espécimes Biológicos , Índice de Massa Corporal , Escolaridade , Humanos , Padrões de Herança/genética , Desequilíbrio de Ligação , Pessoa de Meia-Idade , Modelos Genéticos , Fenótipo , Polimorfismo de Nucleotídeo Único/genética , Característica Quantitativa Herdável , Análise de Regressão , Reino Unido
2.
Nat Commun ; 12(1): 627, 2021 01 27.
Artigo em Inglês | MEDLINE | ID: mdl-33504798

RESUMO

Over 130 X-linked genes have been robustly associated with developmental disorders, and X-linked causes have been hypothesised to underlie the higher developmental disorder rates in males. Here, we evaluate the burden of X-linked coding variation in 11,044 developmental disorder patients, and find a similar rate of X-linked causes in males and females (6.0% and 6.9%, respectively), indicating that such variants do not account for the 1.4-fold male bias. We develop an improved strategy to detect X-linked developmental disorders and identify 23 significant genes, all of which were previously known, consistent with our inference that the vast majority of the X-linked burden is in known developmental disorder-associated genes. Importantly, we estimate that, in male probands, only 13% of inherited rare missense variants in known developmental disorder-associated genes are likely to be pathogenic. Our results demonstrate that statistical analysis of large datasets can refine our understanding of modes of inheritance for individual X-linked disorders.


Assuntos
Deficiências do Desenvolvimento/genética , Genes Ligados ao Cromossomo X , Doenças Genéticas Ligadas ao Cromossomo X/genética , Variação Genética , Cromossomos Humanos X/genética , Feminino , Genes Recessivos , Humanos , Padrões de Herança/genética , Masculino , Herança Multifatorial/genética , Mutação/genética , Fenótipo , Caracteres Sexuais
3.
Nat Commun ; 11(1): 5562, 2020 11 03.
Artigo em Inglês | MEDLINE | ID: mdl-33144568

RESUMO

Cigarette smoking is the leading cause of preventable morbidity and mortality. Genetic variation contributes to initiation, regular smoking, nicotine dependence, and cessation. We present a Fagerström Test for Nicotine Dependence (FTND)-based genome-wide association study in 58,000 European or African ancestry smokers. We observe five genome-wide significant loci, including previously unreported loci MAGI2/GNAI1 (rs2714700) and TENM2 (rs1862416), and extend loci reported for other smoking traits to nicotine dependence. Using the heaviness of smoking index from UK Biobank (N = 33,791), rs2714700 is consistently associated; rs1862416 is not associated, likely reflecting nicotine dependence features not captured by the heaviness of smoking index. Both variants influence nearby gene expression (rs2714700/MAGI2-AS3 in hippocampus; rs1862416/TENM2 in lung), and expression of genes spanning nicotine dependence-associated variants is enriched in cerebellum. Nicotine dependence (SNP-based heritability = 8.6%) is genetically correlated with 18 other smoking traits (rg = 0.40-1.09) and co-morbidities. Our results highlight nicotine dependence-specific loci, emphasizing the FTND as a composite phenotype that expands genetic knowledge of smoking.


Assuntos
Predisposição Genética para Doença , Característica Quantitativa Herdável , Tabagismo/genética , Loci Gênicos , Estudo de Associação Genômica Ampla , Humanos , Padrões de Herança/genética , Desequilíbrio de Ligação/genética , Metanálise como Assunto , Anotação de Sequência Molecular , Fenótipo , Polimorfismo de Nucleotídeo Único/genética
4.
Nat Commun ; 11(1): 5553, 2020 11 03.
Artigo em Inglês | MEDLINE | ID: mdl-33144570

RESUMO

Cas9/gRNA-mediated gene-drive systems have advanced development of genetic technologies for controlling vector-borne pathogen transmission. These technologies include population suppression approaches, genetic analogs of insecticidal techniques that reduce the number of insect vectors, and population modification (replacement/alteration) approaches, which interfere with competence to transmit pathogens. Here, we develop a recoded gene-drive rescue system for population modification of the malaria vector, Anopheles stephensi, that relieves the load in females caused by integration of the drive into the kynurenine hydroxylase gene by rescuing its function. Non-functional resistant alleles are eliminated via a dominantly-acting maternal effect combined with slower-acting standard negative selection, and rare functional resistant alleles do not prevent drive invasion. Small cage trials show that single releases of gene-drive males robustly result in efficient population modification with ≥95% of mosquitoes carrying the drive within 5-11 generations over a range of initial release ratios.


Assuntos
Anopheles/genética , Malária/parasitologia , Alelos , Animais , Proteína 9 Associada à CRISPR/metabolismo , Feminino , Genética Populacional , Proteínas de Fluorescência Verde/metabolismo , Heterozigoto , Padrões de Herança/genética , Quinurenina 3-Mono-Oxigenase/genética , Masculino , Modelos Genéticos , Mosaicismo , Fenótipo , Filogenia , RNA Guia/metabolismo
5.
Med Sci (Paris) ; 36(10): 945-948, 2020 Oct.
Artigo em Francês | MEDLINE | ID: mdl-33026341

RESUMO

More than 10 million enslaved Africans were transported to the Americas between 1500 and 1900. Recent genetic studies investigate regional African ancestry components in present-day Africa-Americans, and allow comparison with the extensive records documenting these deportations. The genetic evidence generally agrees with the historical records but brings additional insights in this dark episode of human history.


Assuntos
Afro-Americanos/genética , Pessoas Escravizadas , Escravização/história , Genética Populacional , África , Oceano Atlântico , Comércio/história , DNA Mitocondrial/análise , DNA Mitocondrial/genética , Pessoas Escravizadas/história , Fluxo Gênico/fisiologia , Variação Genética , História do Século XVI , História do Século XVII , História do Século XVIII , História do Século XIX , Humanos , Padrões de Herança/genética , Estados Unidos
6.
Mol Cell ; 80(2): 246-262.e4, 2020 10 15.
Artigo em Inglês | MEDLINE | ID: mdl-32949493

RESUMO

CRISPR-Cas9-based gene drive systems possess the inherent capacity to spread progressively throughout target populations. Here we describe two self-copying (or active) guide RNA-only genetic elements, called e-CHACRs and ERACRs. These elements use Cas9 produced in trans by a gene drive either to inactivate the cas9 transgene (e-CHACRs) or to delete and replace the gene drive (ERACRs). e-CHACRs can be inserted at various genomic locations and carry two or more gRNAs, the first copying the e-CHACR and the second mutating and inactivating the cas9 transgene. Alternatively, ERACRs are inserted at the same genomic location as a gene drive, carrying two gRNAs that cut on either side of the gene drive to excise it. e-CHACRs efficiently inactivate Cas9 and can drive to completion in cage experiments. Similarly, ERACRs, particularly those carrying a recoded cDNA-restoring endogenous gene activity, can drive reliably to fully replace a gene drive. We compare the strengths of these two systems.


Assuntos
Deleção de Genes , Tecnologia de Impulso Genético , Animais , Proteína 9 Associada à CRISPR/metabolismo , Cromossomos/genética , Drosophila melanogaster/genética , Feminino , Proteínas de Fluorescência Verde/metabolismo , Padrões de Herança/genética , Mutagênese/genética , RNA Guia/genética , Transgenes
7.
Med Sci (Paris) ; 36(8-9): 813-816, 2020.
Artigo em Francês | MEDLINE | ID: mdl-32821057

RESUMO

The prediction of a person's aspect from analysis of an anonymous DNA sample has made significant progress in the last decade. Pigmentation (eyes, hair and, more recently, skin colour) can now be determined with good accuracy; face shape is still not amenable to prediction (except, in general lines, from ancestry). Age can apparently also be determined from methylation profiles. Police forces are, understandably, very interested in this technology, with a tendency to over-estimate its accuracy. Legislation varies greatly, with some nations opting for complete prohibition (Germany) and others allowing wide application of the approach (United Kingdom).


Assuntos
Genética Forense/tendências , Fenótipo , Adulto , Grupos Étnicos/genética , Genética Forense/métodos , Estudos de Associação Genética , Humanos , Recém-Nascido , Padrões de Herança/genética , Masculino , Polimorfismo de Nucleotídeo Único , Retratos como Assunto , Pigmentação da Pele/genética , Gêmeos/genética
8.
PLoS One ; 15(8): e0237834, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32853269

RESUMO

Water deficit is one of the major limitations to food production worldwide and most climate change scenarios predict an aggravation of the situation. To face the expected increase in drought stress in the coming years, breeders are working to elucidate the genetic control of barley growth and productivity traits under water deficit. Barley is known as a relatively drought tolerant crop and genetic variability was observed for drought tolerance traits. The objectives of the present study were the quantification of morphological and physiological responses in a collection of 209 spring barley genotypes to drought stress, and the genetic analysis by genome-wide association study to find quantitative trait loci (QTL) and the allele contributions for each of the investigated traits. In six pot experiments, 209 spring barley genotypes were grown under a well-watered and water-limited regime. Stress phases were initiated individually for each genotype at the beginning of tillering and spiking for the vegetative- and the generative stage experiments, respectively, and terminated when the transpiration rates of stress treatments reached 10% of the well-watered control. After the stress phase, a total of 42 productivity related traits such as the dry matter of plant organs, tiller number, leaf length, leaf area, amount of water soluble carbohydrates in the stems, proline content in leaves and osmotic adjustment of corresponding well-watered and stressed plants were analysed, and QTL analyses were performed to find marker-trait associations. Significant water deficit effects were observed for almost all traits and significant genotype x treatment interactions (GxT) were observed for 37 phenotypic traits. Genome-wide association studies (GWAS) revealed 77 significant loci associated with 16 phenotypic traits during the vegetative stage experiment and a total of 85 significant loci associated with 13 phenotypic traits during the generative stage experiment for traits such as leaf area, number of green leaves, grain yield, harvest index and stem length. For traits with significant GxT interactions, genotypic differences for relative values were analysed using one way ANOVA. More than 110 loci for GxT interaction were found for 17 phenotypic traits explaining in many cases more than 50% of the genetic variance.


Assuntos
Hordeum/genética , Hordeum/fisiologia , Locos de Características Quantitativas/genética , Estações do Ano , Água , Adaptação Fisiológica , Análise de Variância , Biomassa , Desidratação , Secas , Variação Genética , Genótipo , Hordeum/anatomia & histologia , Padrões de Herança/genética , Fenótipo , Análise de Regressão
9.
PLoS Biol ; 18(7): e3000745, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32667908

RESUMO

Mutations create genetic variation for other evolutionary forces to operate on and cause numerous genetic diseases. Nevertheless, how de novo mutations arise remains poorly understood. Progress in the area is hindered by the fact that error rates of conventional sequencing technologies (1 in 100 or 1,000 base pairs) are several orders of magnitude higher than de novo mutation rates (1 in 10,000,000 or 100,000,000 base pairs per generation). Moreover, previous analyses of germline de novo mutations examined pedigrees (and not germ cells) and thus were likely affected by selection. Here, we applied highly accurate duplex sequencing to detect low-frequency, de novo mutations in mitochondrial DNA (mtDNA) directly from oocytes and from somatic tissues (brain and muscle) of 36 mice from two independent pedigrees. We found mtDNA mutation frequencies 2- to 3-fold higher in 10-month-old than in 1-month-old mice, demonstrating mutation accumulation during the period of only 9 mo. Mutation frequencies and patterns differed between germline and somatic tissues and among mtDNA regions, suggestive of distinct mutagenesis mechanisms. Additionally, we discovered a more pronounced genetic drift of mitochondrial genetic variants in the germline of older versus younger mice, arguing for mtDNA turnover during oocyte meiotic arrest. Our study deciphered for the first time the intricacies of germline de novo mutagenesis using duplex sequencing directly in oocytes, which provided unprecedented resolution and minimized selection effects present in pedigree studies. Moreover, our work provides important information about the origins and accumulation of mutations with aging/maturation and has implications for delayed reproduction in modern human societies. Furthermore, the duplex sequencing method we optimized for single cells opens avenues for investigating low-frequency mutations in other studies.


Assuntos
Envelhecimento/genética , Mamíferos/genética , Mitocôndrias/genética , Mutação/genética , Oócitos/metabolismo , Especificidade de Órgãos/genética , Animais , Análise Mutacional de DNA , DNA Mitocondrial/genética , Feminino , Frequência do Gene/genética , Deriva Genética , Células Germinativas/metabolismo , Padrões de Herança/genética , Modelos Logísticos , Masculino , Camundongos , Modelos Genéticos , Taxa de Mutação , Nucleotídeos/genética , Linhagem
10.
Ann Hematol ; 99(7): 1475-1483, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32524201

RESUMO

Large deletions in the ß-globin gene cluster lead to increased HbF levels by delaying the γ- to ß-globin switch process. However, these deletions when inherited as a homozygous condition or when co-inherited with ß-thalassemia result in variable clinical phenotypes. Individuals or families with a clinically presenting child, where the parents had HbF levels ≥ 10%, were further screened for the presence of large ß-globin cluster deletions. Six deletions in the ß-globin gene cluster were screened by GAP-PCR, and the uncharacterized deletions were further analyzed by gene dosage or by multiplex ligation-dependent probe amplification (MLPA). Among 192 individuals suspected for the inheritance of large deletions, 138 were heterozygous for large deletions, 45 were compound heterozygous of a large ß-globin cluster deletion and ß-thalassemia, and 9 were found to be homozygous for deletions. Among the heterozygotes, the Asian Indian inversion-deletion was found to be the most common deletion (39.9%), followed by the HPFH-3 deletion (30.0%). Other deletions 49.3 kb, δß-thalassemia (21.2%), and 32.6 kb deletion (4.4%) were also found to be prevalent in our population. Patients compound heterozygous or homozygous for HPFH-3 and 32.6 kb deletions showed a milder clinical presentation, as compared with the patients compound heterozygous or homozygous for the Asian Indian inversion-deletion and 49.3 kb δß-thalassemia. This comprehensive study highlights the mutation spectrum of large ß-globin cluster deletions and the clinical heterogeneity in the patients homozygous or compound heterozygous with ß-thalassemia, thus asserting the need for molecular characterization of these deletions.


Assuntos
Hemoglobina Fetal/genética , Estudos de Associação Genética , Heterogeneidade Genética , Talassemia beta/epidemiologia , Talassemia beta/genética , Talassemia delta/epidemiologia , Talassemia delta/genética , Idade de Início , Criança , Mortalidade da Criança , Pré-Escolar , Feminino , Hemoglobina Fetal/análise , Estudos de Associação Genética/estatística & dados numéricos , Humanos , Índia/epidemiologia , Lactente , Padrões de Herança/genética , Masculino , Talassemia beta/sangue , Talassemia beta/mortalidade , Talassemia delta/sangue , Talassemia delta/mortalidade
11.
Rev. cuba. hematol. inmunol. hemoter ; 36(2): e1102, abr.-jun. 2020. tab, graf
Artigo em Espanhol | LILACS, CUMED | ID: biblio-1149897

RESUMO

Introducción: La enfermedad granulomatosa crónica es una inmunodeficiencia primaria causada por mutaciones en la enzima NADPH oxidasa. Esta compromete la producción de especies reactivas del oxígeno, que son importantes contra patógenos. La prueba de la oxidación de la dihidrorodamina es un método eficaz para diagnosticar la enfermedad. Objetivo: Demostrar la utilidad de la prueba de la oxidación de la dihidrorodamina y del patrón de herencia en la confirmación del diagnóstico de la enfermedad granulomatosa crónica de un paciente. Métodos: Estudio de caso de una familia con diagnóstico de enfermedad granulomatosa crónica. Se tomó muestra de sangre periférica para citometría de flujo a tres individuos. Se realizó la prueba de la oxidación de la dihidrorodamina bajo estímulo con acetato de forbolmiristato y se evaluaron las subpoblaciones linfocitarias. Las muestras se leyeron en un citómetro GALLIOS, Beckman Coulter. Los datos obtenidos se analizaron en el programa informático Kaluza. Resultados: El paciente masculino tuvo un valor de oxidación de la dihidrorodamina positiva de 0,87 por ciento, que confirmó un patrón de herencia ligado al cromosoma X; mientras que la madre y hermana gemela portadoras tuvieron valores de 46,76 por ciento y 37,32 por ciento, respectivamente. Se encontraron alteraciones en las subpoblaciones linfocitarias. Conclusiones: La prueba de la oxidación de la dihidrorodamina es un método muy efectivo, rápido y sencillo que confirma el diagnóstico de la enfermedad granulomatosa crónica y determina el patrón de herencia y fenotipo de la enfermedad. Además, permite identificar a las mujeres portadoras según la distribución de los neutrófilos normales y los que tienen el gen CYBB mutado(AU)


Introduction: Chronic granulomatous disease is a primary immunodeficiency caused by mutations in the NADPH oxidase enzymes. This compromises the production of oxygen reactive species, which are important against pathogens. The dihydrorhodamine oxidation test is an effective method for diagnosing the disease. Objective: To demonstrate the usefulness of the dihydrorhodamine oxidation test and the inheritance pattern in confirming the diagnosis of chronic granulomatous disease in a patient. Methods: A case study of a family with a diagnosis of chronic granulomatous disease. A peripheral blood sample was taken from three individuals and by flow cytometry. The dihydrorhodamine oxidation test was performed under stimulation with phorbolmyristate acetate, and lymphocyte subpopulations were evaluated. The samples were read on a GALLIOS, Beckman Coulter cytometer. The data obtained were analyzed using the computer program Kaluza. Results: The male patient had a positive dihydrorhodamine oxidation value of 0.87 percent, which confirmed an inheritance pattern linked to the X chromosome; while the carrier mother and twin sister had values 8203;8203;of 46.76 percent and 37.32 percent, respectively. Alterations were found in the lymphocyte subpopulations. Conclusions: The dihydrorhodamine oxidation test is a very effective, fast and simple method that confirms the diagnosis of chronic granulomatous disease and determines the inheritance pattern and phenotype of the disease. In addition, it allows the identification of female carriers according to the distribution of normal neutrophils and those with the CYBB mutation(AU)


Assuntos
Humanos , Portador Sadio/congênito , NADPH Oxidases/análise , Padrões de Herança/genética , Doença Granulomatosa Crônica/diagnóstico , Relatos de Casos , Cuba , Triagem de Portadores Genéticos/métodos , Anamnese/métodos
12.
Nat Commun ; 11(1): 2085, 2020 04 29.
Artigo em Inglês | MEDLINE | ID: mdl-32350251

RESUMO

Allopolyploidy generates diversity by increasing the number of copies and sources of chromosomes. Many of the best-known evolutionary radiations, crops, and industrial organisms are ancient or recent allopolyploids. Allopolyploidy promotes differentiation and facilitates adaptation to new environments, but the tools to test its limits are lacking. Here we develop an iterative method of Hybrid Production (iHyPr) to combine the genomes of multiple budding yeast species, generating Saccharomyces allopolyploids of at least six species. When making synthetic hybrids, chromosomal instability and cell size increase dramatically as additional copies of the genome are added. The six-species hybrids initially grow slowly, but they rapidly regain fitness and adapt, even as they retain traits from multiple species. These new synthetic yeast hybrids and the iHyPr method have potential applications for the study of polyploidy, genome stability, chromosome segregation, and bioenergy.


Assuntos
Hibridização Genética , Saccharomyces/genética , Evolução Molecular Direcionada , Tamanho do Genoma , Genoma Fúngico , Instabilidade Genômica , Genótipo , Padrões de Herança/genética , Mitocôndrias/genética , Fenótipo , Característica Quantitativa Herdável
13.
Exp Mol Pathol ; 115: 104471, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32446860

RESUMO

Megalencephaly-polymicrogyria-polydactyly-hydrocephalus (MPPH) syndrome is a developmental brain disorder characterized by an enlarged brain size with bilateral perisylvian polymicrogyria and a variable degree of ventriculomegaly. MPPH syndrome is associated with oromotor dysfunction, epilepsy, intellectual disability and postaxial hexadactyly. The molecular diagnosis of this disorder is established by the identification of a pathogenic variant in either AKT3, CCND2 or PIK3R2. Previously reported AKT3 variants are associated with various brain abnormalities and may lead to megalencephaly. MPPH syndrome is usually due to germline pathogenic AKT3 variants. Somatic mosaic pathogenic variants associated with hemimegalencephaly, which is similar to MPPH, have also been observed. A Hungarian Roma family with two half-siblings, which present with intellectual disability, dysmorphic features, epilepsy, brain malformations, and megalencephaly was studied. Whole exome sequencing (WES) analysis was performed. WES analysis revealed a heterozygous c.1393C > T p.(Arg465Trp) pathogenic missense AKT3 variant in both affected half-siblings. The variant was verified via Sanger sequencing and was not present in the DNA sample from the healthy mother, which was derived from peripheral blood, suggesting maternal germline mosaicism. In conclusion, this is the first report in which maternal germline mosaicism of a rare pathogenic AKT3 variant leads to autosomal dominantly inherited MPPH syndrome.


Assuntos
Dedos/anormalidades , Células Germinativas/metabolismo , Hidrocefalia/congênito , Padrões de Herança/genética , Megalencefalia/genética , Mosaicismo , Polidactilia/genética , Polimicrogiria/genética , Proteínas Proto-Oncogênicas c-akt/genética , Dedos do Pé/anormalidades , Adolescente , Criança , Feminino , Dedos/diagnóstico por imagem , Humanos , Hidrocefalia/diagnóstico por imagem , Hidrocefalia/genética , Imagem por Ressonância Magnética , Masculino , Megalencefalia/diagnóstico por imagem , Linhagem , Fenótipo , Polidactilia/diagnóstico por imagem , Polimicrogiria/diagnóstico por imagem , Irmãos , Síndrome , Dedos do Pé/diagnóstico por imagem
14.
Nat Commun ; 11(1): 2214, 2020 05 05.
Artigo em Inglês | MEDLINE | ID: mdl-32371941

RESUMO

MSH1 is a plant-specific protein. RNAi suppression of MSH1 results in phenotype variability for developmental and stress response pathways. Segregation of the RNAi transgene produces non-genetic msh1 'memory' with multi-generational inheritance. First-generation memory versus non-memory comparison, and six-generation inheritance studies, identifies gene-associated, heritable methylation repatterning. Genome-wide methylome analysis integrated with RNAseq and network-based enrichment studies identifies altered circadian clock networks, and phytohormone and stress response pathways that intersect with circadian control. A total of 373 differentially methylated loci comprising these networks are sufficient to discriminate memory from nonmemory full sibs. Methylation inhibitor 5-azacytidine diminishes the differences between memory and wild type for growth, gene expression and methylation patterning. The msh1 reprogramming is dependent on functional HISTONE DEACETYLASE 6 and methyltransferase MET1, and transition to memory requires the RNA-directed DNA methylation pathway. This system of phenotypic plasticity may serve as a potent model for defining accelerated plant adaptation during environmental change.


Assuntos
Proteínas de Arabidopsis/genética , Arabidopsis/genética , Metilação de DNA , Proteína MutS de Ligação de DNA com Erro de Pareamento/genética , Característica Quantitativa Herdável , Interferência de RNA , Transgenes/genética , Adaptação Fisiológica/genética , DNA (Citosina-5-)-Metiltransferases/genética , Epigênese Genética , Perfilação da Expressão Gênica/métodos , Ontologia Genética , Redes Reguladoras de Genes , Estudo de Associação Genômica Ampla/métodos , Desacetilase 6 de Histona/genética , Padrões de Herança/genética , Plantas Geneticamente Modificadas , Transdução de Sinais/genética
15.
PLoS One ; 15(4): e0231144, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32271818

RESUMO

Walnut shell suture strength directly impacts the ability to maintain shell integrity during harvest and processing, susceptibility to insect damage and other contamination, and the proportion of kernel halves recovered during cracking. Suture strength is therefore an important breeding objective. Here, two methods of phenotyping this trait were investigated: 1) traditional, qualitative and rather subjective scoring on an interval scale by human observers, and; 2) quantitative and continuous measurements captured by a texturometer. The aim of this work was to increase the accuracy of suture strength phenotyping and to then apply two mapping approaches, quantitative trait loci (QTL) mapping and genome wide association (GWAS) models, in order to dissect the genetic basis of the walnut suture trait. Using data collected on trees within the UC Davis Walnut Improvement Program (n = 464), the genetic correlation between the texturometer method and qualitatively scored method was high (0.826). Narrow sense heritability calculated using quantitative measurements was 0.82. A major QTL for suture strength was detected on LG05, explaining 34% of the phenotypic variation; additionally, two minor QTLs were identified on LG01 and LG11. All three QTLs were confirmed with GWAS on corresponding chromosomes. The findings reported in this study are relevant for application towards a molecular breeding program in walnut.


Assuntos
Estudo de Associação Genômica Ampla , Juglans/anatomia & histologia , Juglans/genética , Locos de Características Quantitativas/genética , Análise de Variância , Estudos de Associação Genética , Genótipo , Padrões de Herança/genética , Desequilíbrio de Ligação/genética , Fenótipo , Polimorfismo de Nucleotídeo Único/genética , Análise de Componente Principal , Característica Quantitativa Herdável , Software
16.
Nat Commun ; 11(1): 1741, 2020 04 08.
Artigo em Inglês | MEDLINE | ID: mdl-32269224

RESUMO

Parental exposure to pathogens can prime offspring immunity in diverse organisms. The mechanisms by which this heritable priming occurs are largely unknown. Here we report that the soil bacteria Pseudomonas vranovensis is a natural pathogen of the nematode Caenorhabditis elegans and that parental exposure of animals to P. vranovensis promotes offspring resistance to infection. Furthermore, we demonstrate a multigenerational enhancement of progeny survival when three consecutive generations of animals are exposed to P. vranovensis. By investigating the mechanisms by which animals heritably adapt to P. vranovensis infection, we found that parental infection by P. vranovensis results in increased expression of the cysteine synthases cysl-1 and cysl-2 and the regulator of hypoxia inducible factor rhy-1 in progeny, and that these three genes are required for adaptation to P. vranovensis. These observations establish a CYSL-1, CYSL-2, and RHY-1 dependent mechanism by which animals heritably adapt to infection.


Assuntos
Adaptação Fisiológica , Proteínas de Caenorhabditis elegans/metabolismo , Caenorhabditis elegans/enzimologia , Caenorhabditis elegans/microbiologia , Cisteína Sintase/metabolismo , Padrões de Herança/genética , Pseudomonas/fisiologia , Adaptação Fisiológica/genética , Animais , Caenorhabditis elegans/embriologia , Caenorhabditis elegans/genética , Proteínas de Caenorhabditis elegans/genética , Cisteína Sintase/genética , Embrião não Mamífero/metabolismo , Regulação da Expressão Gênica no Desenvolvimento , Modelos Biológicos
17.
Nat Med ; 26(3): 398-407, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32161412

RESUMO

Development of tau-based therapies for Alzheimer's disease requires an understanding of the timing of disease-related changes in tau. We quantified the phosphorylation state at multiple sites of the tau protein in cerebrospinal fluid markers across four decades of disease progression in dominantly inherited Alzheimer's disease. We identified a pattern of tau staging where site-specific phosphorylation changes occur at different periods of disease progression and follow distinct trajectories over time. These tau phosphorylation state changes are uniquely associated with structural, metabolic, neurodegenerative and clinical markers of disease, and some (p-tau217 and p-tau181) begin with the initial increases in aggregate amyloid-ß as early as two decades before the development of aggregated tau pathology. Others (p-tau205 and t-tau) increase with atrophy and hypometabolism closer to symptom onset. These findings provide insights into the pathways linking tau, amyloid-ß and neurodegeneration, and may facilitate clinical trials of tau-based treatments.


Assuntos
Doença de Alzheimer/genética , Doença de Alzheimer/metabolismo , Amiloide/metabolismo , Padrões de Herança/genética , Proteínas tau/metabolismo , Adulto , Idoso , Doença de Alzheimer/líquido cefalorraquidiano , Doença de Alzheimer/diagnóstico por imagem , Atrofia , Encéfalo/patologia , Cognição , Progressão da Doença , Feminino , Fluordesoxiglucose F18/química , Humanos , Imagem por Ressonância Magnética , Masculino , Pessoa de Meia-Idade , Neuroimagem , Fosforilação , Placa Amiloide/patologia , Solubilidade , Proteínas tau/líquido cefalorraquidiano
18.
Med Sci (Paris) ; 36(2): 181-184, 2020 Feb.
Artigo em Francês | MEDLINE | ID: mdl-32129759

RESUMO

Evidence for a "homosexuality gene" was claimed in the early 1990's on the basis of linkage studies that, by current criteria, were woefully underpowered. Indeed, follow up studies gave contradictory results. Genome-wide association studies, and very large databases with detailed genetic and phenotypic data, have made possible a re-examination of this issue. While modest heritability (ca. 0.3) for homosexuality is confirmed, no major locus is found and the genetic influence appears extremely polygenic. Thus, there is no single gene, or even small set of genes, that have a strong influence on homosexuality.


Assuntos
Marcadores Genéticos , Homossexualidade/fisiologia , Padrões de Herança/genética , Feminino , Ligação Genética , Estudo de Associação Genômica Ampla/história , Estudo de Associação Genômica Ampla/estatística & dados numéricos , Estudo de Associação Genômica Ampla/tendências , História do Século XX , História do Século XXI , Homossexualidade/estatística & dados numéricos , Humanos , Masculino , Herança Multifatorial/genética , Polimorfismo de Nucleotídeo Único , Prevalência
19.
Nat Commun ; 11(1): 1467, 2020 03 19.
Artigo em Inglês | MEDLINE | ID: mdl-32193382

RESUMO

Unhealthful dietary habits are leading risk factors for life-altering diseases and mortality. Large-scale biobanks now enable genetic analysis of traits with modest heritability, such as diet. We perform a genomewide association on 85 single food intake and 85 principal component-derived dietary patterns from food frequency questionnaires in UK Biobank. We identify 814 associated loci, including olfactory receptor associations with fruit and tea intake; 136 associations are only identified using dietary patterns. Mendelian randomization suggests our top healthful dietary pattern driven by wholemeal vs. white bread consumption is causally influenced by factors correlated with education but is not strongly causal for coronary artery disease or type 2 diabetes. Overall, we demonstrate the value in complementary phenotyping approaches to complex dietary datasets, and the utility of genomic analysis to understand the relationships between diet and human health.


Assuntos
Bancos de Espécimes Biológicos , Comportamento Alimentar , Estudos de Associação Genética , Genômica , Ingestão de Alimentos , Loci Gênicos , Estudo de Associação Genômica Ampla , Humanos , Padrões de Herança/genética , Análise da Randomização Mendeliana , Polimorfismo de Nucleotídeo Único/genética , Análise de Componente Principal , Receptores Odorantes/metabolismo , Fatores de Risco , Reino Unido
20.
Nat Genet ; 52(4): 458-462, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-32203469

RESUMO

There is currently much debate regarding the best model for how heritability varies across the genome. The authors of GCTA recommend the GCTA-LDMS-I model, the authors of LD Score Regression recommend the Baseline LD model, and we have recommended the LDAK model. Here we provide a statistical framework for assessing heritability models using summary statistics from genome-wide association studies. Based on 31 studies of complex human traits (average sample size 136,000), we show that the Baseline LD model is more realistic than other existing heritability models, but that it can be improved by incorporating features from the LDAK model. Our framework also provides a method for estimating the selection-related parameter α from summary statistics. We find strong evidence (P < 1 × 10-6) of negative genome-wide selection for traits, including height, systolic blood pressure and college education, and that the impact of selection is stronger inside functional categories, such as coding SNPs and promoter regions.


Assuntos
Padrões de Herança/genética , Estudo de Associação Genômica Ampla/métodos , Genótipo , Humanos , Desequilíbrio de Ligação/genética , Modelos Genéticos , Herança Multifatorial/genética , Fenótipo , Polimorfismo de Nucleotídeo Único/genética , Característica Quantitativa Herdável , Tamanho da Amostra , Software
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