RESUMEN
A long-standing goal of evolutionary biology is to decode how changes in gene regulatory networks contribute to human-specific traits. Human accelerated regions (HARs) are prime candidates for driving gene regulatory modifications in human development. The RBFOX1 locus is densely populated with HARs, providing a set of potential regulatory elements that could have changed its expression in the human lineage. Here, we examined the role of RBFOX1-HARs using transgenic zebrafish reporter assays and identified 15 transcriptional enhancers that are active in the developing nervous system, 9 of which displayed differential activity between the human and chimpanzee sequences. The engineered loss of two selected RBFOX1-HARs in knockout mouse models modified Rbfox1 expression at specific developmental stages and tissues in the brain, influencing the expression and splicing of a high number of Rbfox1 target genes. Our results provided insight into the spatial and temporal changes in gene expression driven by RBFOX1-HARs.
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Elementos de Facilitación Genéticos , Evolución Molecular , Factores de Empalme de ARN , Animales , Humanos , Ratones , Animales Modificados Genéticamente , Regulación del Desarrollo de la Expresión Génica , Redes Reguladoras de Genes , Sitios Genéticos , Ratones Noqueados , Pan troglodytes/genética , Factores de Empalme de ARN/genética , Factores de Empalme de ARN/metabolismo , Pez Cebra/genéticaRESUMEN
Cyphocharax magdalenae, a Colombian freshwater fish species, plays a vital role in nutrients distribution and serves as a significant food source for other fish species and local fishing communities. Considered a short-distance migratory species, C. magdalenae populations face substantial extinction risk due to human activities impacting their habitats. To address the lack of knowledge on genetic diversity and population structure, this study used next-generation sequencing technology to develop species-specific microsatellite loci and conducted a population genetics analysis of C. magdalenae in the middle and lower sections of the Cauca River, Colombia. Out of 30 pairs of microsatellite primers evaluated in 324 individuals, 14 loci were found to be polymorphic, at linkage equilibrium and, in at least one population, their genotypic frequencies were in Hardy-Weinberg equilibrium. Results showed high genetic diversity levels compared to other neotropical Characiformes, with inbreeding coefficients similar to those reported for phylogenetically related species. Moreover, C. magdalenae exhibits seasonal population structure (rainy-dry) consisting of two genetic stocks showing bottleneck signals and high effective population sizes. This information is essential for understanding the current species genetics and developing future management programs for this fishery resource.
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Characiformes , Ríos , Animales , Humanos , Colombia , Characiformes/genética , Genética de Población , Repeticiones de Microsatélite/genética , Sitios Genéticos , Variación GenéticaRESUMEN
INTRODUÇÃO: A hipercolesterolemia familiar (HF) é um distúrbio genético bem reconhecido que se manifesta como níveis significativamente elevados de LDL-c sérico devido a aberrações no metabolismo das lipoproteínas. A maioria dos casos de HF, especificamente 85-90%, está associada a mutações patogênicas no gene do receptor de LDL (LDLR). Além disso, a presença de mutações de perda de função (LOF) no gene PCSK9 tem sido associada a um risco reduzido de doença cardiovascular, um fenômeno observado mesmo quando variantes patogênicas de LDLR coexistem. MÉTODOS: Este estudo incluiu um homem de 46 anos com dislipidemia e uso inconsistente de rosuvastatina. Na história familiar consta uma irmã (caso índice) e um sobrinho diagnosticados com HF portadores de variante patogênica de LDLR (c.313+1G>A, heterozigoto). RESULTADOS: O paciente relatou o aparecimento de dor precordial típica um mês antes da consulta. O exame físico revelou arco corneano. Os resultados laboratoriais iniciais mostraram colesterol total em 254 mg/dL, LDL-c em 191 mg/dL, HDL-c em 49 mg/dL e triglicerídeos em 69 mg/dL. Um escore Dutch MedPed de 11 confirmou HF. A ecocardiografia transtorácica indicou função ventricular esquerda normal. A angiografia coronária revelou calcificação significativa e estenose da artéria coronária direita (RCA) e da artéria circunflexa esquerda proximal (LCx). A intervenção incluiu angioplastia LCx e manejo conservador da RCA. Medicamentos pós-alta incluíram AAS 100mg/dia, Clopidogrel 75mg/dia, Rosuvastatina 40mg/ dia e Ezetimibe 10mg/dia. O nível de LDL-c diminuiu para 76 mg/dL no acompanhamento. A análise genética confirmou a variante familiar de LDLR e identificou uma mutação LOF coexistente de PCSK9 (R46L, heterozigoto). CONCLUSÃO: Este caso destaca a gravidade e complexidade da aterosclerose multivascular associada à HF. Embora a variante LOF de PCSK9 seja potencialmente protetora, sua influência nos resultados clínicos permanece incerta. Essa ambiguidade reforça a progressão multifatorial da aterosclerose e a resposta variável ao tratamento em pacientes com HF. Isso ressalta a importância de identificar fatores genéticos e não genéticos adicionais que contribuem para a doença, além dos loci genéticos conhecidos para entender e gerenciar melhor essa condição clínica.
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Sitios Genéticos , Proproteína Convertasa 9 , Hiperlipoproteinemia Tipo II , Dolor en el Pecho , Enfermedades Genéticas CongénitasRESUMEN
A fundamental goal in evolutionary biology is to understand the genetic architecture of adaptive traits. Using whole-genome data of 3955 of Darwin's finches on the Galápagos Island of Daphne Major, we identified six loci of large effect that explain 45% of the variation in the highly heritable beak size of Geospiza fortis, a key ecological trait. The major locus is a supergene comprising four genes. Abrupt changes in allele frequencies at the loci accompanied a strong change in beak size caused by natural selection during a drought. A gradual change in Geospiza scandens occurred across 30 years as a result of introgressive hybridization with G. fortis. This study shows how a few loci with large effect on a fitness-related trait contribute to the genetic potential for rapid adaptive radiation.
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Adaptación Biológica , Pico , Pinzones , Introgresión Genética , Especiación Genética , Selección Genética , Animales , Pico/anatomía & histología , Ecuador , Pinzones/anatomía & histología , Pinzones/genética , Frecuencia de los Genes , Metagenómica , Sitios GenéticosRESUMEN
BACKGROUND: The genus Ternstroemia is associated with the vulnerable tropical montane cloud forest in Mexico and with other relevant vegetation types worldwide. It contains threatened and pharmacologically important species and has taxonomic issues regarding its species limits. This study describes 38 microsatellite markers generated using a genomic-based approach. METHODS AND RESULTS: We tested 23 of these markers in a natural population of Ternstroemia lineata. These markers are highly polymorphic (all loci polymorphic with 3-14 alleles per locus and expected heterozygosity between 0.202 and 0.908), most of them (19 out of 23) are in Hardy-Weinberg Equilibrium and free of null alleles (18 out of 23). Also we found no evidence of linkage among them. Finally, we tested the transferability to six other American species of Ternstroemia, two other Pentaphylacaceae species, and four species from different families within the order Ericales. CONCLUSIONS: These molecular resources are promising tools to investigate genetic diversity loss and as barcodes for ethnopharmacological applications and species delimitation in the family Pentaphylacaceae and some Ericales, among other applications.
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Ericales , Humanos , Ericales/genética , Genoma , Genómica , Heterocigoto , Repeticiones de Microsatélite/genética , Alelos , Secuenciación de Nucleótidos de Alto Rendimiento , Sitios Genéticos/genéticaAsunto(s)
Aciltransferasas , Hepatopatías , Enfermedad del Hígado Graso no Alcohólico , Fosfolipasas A2 Calcio-Independiente , Aciltransferasas/genética , Adulto , Sitios Genéticos , Predisposición Genética a la Enfermedad , Genotipo , Humanos , Hígado , Hepatopatías/genética , Enfermedad del Hígado Graso no Alcohólico/genética , Fosfolipasas A2 Calcio-Independiente/genética , Polimorfismo Genético , Polimorfismo de Nucleótido SimpleRESUMEN
BACKGROUND: Eosinophilic esophagitis (EoE) is a chronic inflammatory disorder of the esophagus marked by eosinophilic infiltration. Cumulative evidence indicates that the risk of EoE involves the complex interplay of both genetic and environmental factors. Because only a few genetic loci have been identified in EoE, the genetic underpinning of EoE remains largely elusive. OBJECTIVE: We sought to identify genetic loci associated with EoE. METHODS: Four EoE cohorts were genotyped using the Illumina single nucleotide polymorphism array platform, totaling 1,930 cases and 13,634 controls of European ancestry. Genotype imputation was performed with the Michigan Imputation Server using the Trans-Omics for Precision Medicine reference panel including whole-genome sequencing data from more than 100,000 individuals. Meta-analysis was conducted to identify potential novel genetic loci associated with EoE. RESULTS: Our study identified 11 new genome-wide significant loci, of which 6 are common variant loci, including 5q31.1 (rs2106984, P = 4.16 × 10-8; odds ratio [OR], 1.26, RAD50), 15q22.2 (rs2279293, P = 1.23 × 10-10; OR, 0.69, RORA), and 15q23 (rs56062135, P = 2.91 × 10-11; OR, 1.29, SMAD3), which have been previously associated with allergic conditions. Interestingly, a low-frequency synonymous mutation within the MATN2 gene was identified as the most significant single nucleotide polymorphism at the 8q22.1 locus. We also identified 5 sex-specific loci in the EoE cases, including an inflammatory bowel disease-associated locus at 9p24.1 (rs62541556, P = 4.4 × 10-8; OR, 1.11, JAK2). CONCLUSIONS: Our findings demonstrate shared genetic underpinnings between EoE and other immune-mediated diseases and provide novel candidate genes for therapeutic target identification and prioritization.
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Esofagitis Eosinofílica , Esofagitis Eosinofílica/genética , Femenino , Sitios Genéticos , Predisposición Genética a la Enfermedad , Estudio de Asociación del Genoma Completo , Humanos , Masculino , Polimorfismo de Nucleótido SimpleRESUMEN
BACKGROUND: We used Illumina paired-end sequencing to isolate and characterize microsatellites of Canthon cyanellus, a Neotropical roller dung beetle, encompassing several lineages within its distribution range. METHODS AND RESULTS: We examined C. cyanellus specimens collected at eight different localities in Mexico (two or three specimens per locality). We initially performed amplification tests with 16 loci, but two of which were unsuccessful. The 14 remaining microsatellites were polymorphic, with 2-16 alleles each. The expected and observed heterozygosity ranged from 0.11 to 0.76 and from 0.20 to 0.78, respectively. CONCLUSIONS: These microsatellites will help to assess structure at the population and lineage levels, identify zones of potential hybridization between lineages, and draw a more precise geographic delimitation of C. cyanellus lineages.
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Escarabajos/genética , Repeticiones de Microsatélite , Alelos , Animales , Sitios Genéticos , Heterocigoto , Secuenciación de Nucleótidos de Alto Rendimiento , Análisis de Secuencia de ADNRESUMEN
Transposable Elements (TEs) are ubiquitous genetic elements with the ability to move within a genome. TEs contribute to a large fraction of the repetitive elements of a genome, and because of their nature, they are not routinely analyzed in RNA-Seq gene expression studies. Amyotrophic Lateral Sclerosis (ALS) is a lethal neurodegenerative disease, and a well-accepted model for its study is the mouse harboring the human SOD1G93A mutant. In this model, landmark stages of the disease can be recapitulated at specific time points, making possible to understand changes in gene expression across time. While there are several works reporting TE activity in ALS models, they have not explored their activity through the disease progression. Moreover, they have done it at the expense of losing their locus of expression. Depending on their genomic location, TEs can regulate genes in cis and in trans, making locus-specific analysis of TEs of importance in order to understand their role in modulating gene expression. Particularly, the locus-specific role of TEs in ALS has not been fully elucidated. In this work, we analyzed publicly available RNA-Seq datasets of the SOD1G93A mouse model, to understand the locus-specific role of TEs. We show that TEs become up-regulated at the early stages of the disease, and via statistical associations, we speculate that they can regulate several genes, which in turn might be contributing to the genetic dysfunction observed in ALS.
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Esclerosis Amiotrófica Lateral/genética , Elementos Transponibles de ADN/genética , Progresión de la Enfermedad , Sitios Genéticos , Superóxido Dismutasa/genética , Animales , Simulación por Computador , Modelos Animales de Enfermedad , Perfilación de la Expresión Génica , Ratones Transgénicos , Mapas de Interacción de Proteínas/genética , RNA-Seq , Reproducibilidad de los Resultados , Programas InformáticosRESUMEN
Smooth-shelled blue mussels, Mytilus spp., have a worldwide antitropical distribution and are ecologically and economically important. Mussels of the Mytilus edulis species complex have been the focus of numerous taxonomic and biogeographical studies, in particular in the Northern hemisphere, but the taxonomic classification of mussels from South America remains unclear. The present study analysed 348 mussels from 20 sites in Argentina, Chile, Uruguay and the Falkland Islands on the Atlantic and Pacific coasts of South America. We sequenced two mitochondrial locus, Cytochrome c Oxidase subunit I (625 bp) and 16S rDNA (443 bp), and one nuclear gene, ribosomal 18S rDNA (1770 bp). Mitochondrial and nuclear loci were analysed separately and in combination using maximum likelihood and Bayesian inference methods to identify the combination of the most informative dataset and model. Species delimitation using five different models (GMYC single, bGMYC, PTP, bPTP and BPP) revealed that the Mytilus edulis complex in South America is represented by three species: native M. chilensis, M. edulis, and introduced Northern Hemisphere M. galloprovincialis. However, all models failed to delimit the putative species Mytilus platensis. In contrast, however, broad spatial scale genetic structure in South America using Geneland software to analyse COI sequence variation revealed a group of native mussels (putatively M. platensis) in central Argentina and the Falkland Islands. We discuss the scope of species delimitation methods and the use of nuclear and mitochondrial genetic data to the recognition of species within the Mytilus edulis complex at regional and global scales.
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Variación Genética , Mytilus edulis/clasificación , Mytilus edulis/genética , Filogenia , Animales , Argentina , Secuencia de Bases , Teorema de Bayes , Chile , ADN Ribosómico/genética , Complejo IV de Transporte de Electrones/genética , Islas Malvinas , Femenino , Genes Mitocondriales , Sitios Genéticos , Haplotipos , Especificidad de la Especie , UruguayRESUMEN
RESUMEN El parkinsonismo constituye un conjunto de signos y síntomas clínicos caracterizados por bradicinesia y temblor en reposo o rigidez, cuya causa más frecuente es la enfermedad de Parkinson (EP). La gran mayoría de los casos de EP son esporádicos, sin embargo, existe una minoría en la cual la etiología se debe a una mutación heredada, ya sea autosómica dominante (AD), autosómica recesiva (AR) o herencia ligada al X. La identificación de estas causas heredables es importante para una adecuada consejería genética y tratamiento. Se presenta el caso de un paciente con EP de inicio temprano en el que se identificó una mutación AD en el gen GIGYF2 o PARK11, asociado a una breve revisión de la literatura
SUMMARY Parkinsonism constitutes a set of clinical signs and symptoms characterized by bradykinesia and tremor at rest and / or rigidity. The main etiology is Parkinson's disease (PD), but there are other causes such as atypical parkinsonism. The vast majority of PD cases are sporadic, however, there is a minority where the etiology is due to an inherited mutation, either autosomal dominant (AD), autosomal recessive (RA), or X-linked inheritance. Identifying these heritable causes is important for proper genetic counseling and treatment. We present the case of a patient with early-onset PD where an AD mutation in the GIGYF2 gene (PARK11) was identified. We subsequently present a brief review of the literature.
Asunto(s)
Enfermedad de Parkinson , Trastornos Parkinsonianos , Sitios Genéticos , GenéticaRESUMEN
Our study investigated the underlying mechanism for the 14q24 renal cell carcinoma (RCC) susceptibility risk locus identified by a genome-wide association study (GWAS). The sentinel single-nucleotide polymorphism (SNP), rs4903064, at 14q24 confers an allele-specific effect on expression of the double PHD fingers 3 (DPF3) of the BAF SWI/SNF complex as assessed by massively parallel reporter assay, confirmatory luciferase assays, and eQTL analyses. Overexpression of DPF3 in renal cell lines increases growth rates and alters chromatin accessibility and gene expression, leading to inhibition of apoptosis and activation of oncogenic pathways. siRNA interference of multiple DPF3-deregulated genes reduces growth. Our results indicate that germline variation in DPF3, a component of the BAF complex, part of the SWI/SNF complexes, can lead to reduced apoptosis and activation of the STAT3 pathway, both critical in RCC carcinogenesis. In addition, we show that altered DPF3 expression in the 14q24 RCC locus could influence the effectiveness of immunotherapy treatment for RCC by regulating tumor cytokine secretion and immune cell activation.
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Carcinoma de Células Renales/genética , Cromosomas Humanos Par 14 , Proteínas de Unión al ADN/genética , Sitios Genéticos , Neoplasias Renales/genética , Factor de Transcripción STAT3/genética , Factores de Transcripción/genética , Carcinogénesis/genética , Carcinogénesis/inmunología , Carcinogénesis/patología , Carcinoma de Células Renales/inmunología , Carcinoma de Células Renales/patología , Carcinoma de Células Renales/terapia , Línea Celular Tumoral , Cromatina/química , Cromatina/inmunología , Ensamble y Desensamble de Cromatina/inmunología , Citocinas/genética , Citocinas/inmunología , Proteínas de Unión al ADN/inmunología , Regulación de la Expresión Génica , Predisposición Genética a la Enfermedad , Genoma Humano , Estudio de Asociación del Genoma Completo , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Inmunoterapia/métodos , Neoplasias Renales/inmunología , Neoplasias Renales/patología , Neoplasias Renales/terapia , Polimorfismo de Nucleótido Simple , Factor de Transcripción STAT3/inmunología , Linfocitos T Citotóxicos , Factores de Transcripción/inmunologíaRESUMEN
OBJECTIVE: This work was undertaken in order to identify Parkinson's disease (PD) risk variants in a Latino cohort, to describe the overlap in the genetic architecture of PD in Latinos compared to European-ancestry subjects, and to increase the diversity in PD genome-wide association (GWAS) data. METHODS: We genotyped and imputed 1,497 PD cases and controls recruited from nine clinical sites across South America. We performed a GWAS using logistic mixed models; variants with a p-value <1 × 10-5 were tested in a replication cohort of 1,234 self-reported Latino PD cases and 439,522 Latino controls from 23andMe, Inc. We also performed an admixture mapping analysis where local ancestry blocks were tested for association with PD status. RESULTS: One locus, SNCA, achieved genome-wide significance (p-value <5 × 10-8 ); rs356182 achieved genome-wide significance in both the discovery and the replication cohorts (discovery, G allele: 1.58 OR, 95% CI 1.35-1.86, p-value 2.48 × 10-8 ; 23andMe, G allele: 1.26 OR, 95% CI 1.16-1.37, p-value 4.55 × 10-8 ). In our admixture mapping analysis, a locus on chromosome 14, containing the gene STXBP6, achieved significance in a joint test of ancestries and in the Native American single-ancestry test (p-value <5 × 10-5 ). A second locus on chromosome 6, containing the gene RPS6KA2, achieved significance in the African single-ancestry test (p-value <5 × 10-5 ). INTERPRETATION: This study demonstrated the importance of the SNCA locus for the etiology of PD in Latinos. By leveraging the demographic history of our cohort via admixture mapping, we identified two potential PD risk loci that merit further study. ANN NEUROL 2021;90:353-365.
Asunto(s)
Sitios Genéticos/genética , Variación Genética/genética , Estudio de Asociación del Genoma Completo/métodos , Hispánicos o Latinos/genética , Enfermedad de Parkinson/etnología , Enfermedad de Parkinson/genética , Adulto , Anciano , Estudios de Cohortes , Femenino , Humanos , Masculino , Persona de Mediana Edad , Enfermedad de Parkinson/diagnóstico , Polimorfismo de Nucleótido Simple/genética , América del Sur/etnologíaRESUMEN
Fcγ receptors (FcγR), cell-surface glycoproteins that bind antigen-IgG complexes, control both humoral and cellular immune responses. The FCGR locus on chromosome 1q23.3 comprises five homologous genes encoding low-affinity FcγRII and FcγRIII, and displays functionally relevant polymorphism that impacts on human health. Recurrent events of non-allelic homologous recombination across the FCGR locus result in copy-number variation of ~82.5 kbp-long fragments known as copy-number regions (CNR). Here, we characterize a recently described deletion that we name CNR5, which results in loss of FCGR3A, FCGR3B, and FCGR2C, and generation of a recombinant FCGR3B/A gene. We show that the CNR5 recombination spot lies at the beginning of the third FCGR3 intron. Although the FCGR3B/A-encoded hybrid protein CD16B/A reaches the plasma membrane in transfected cells, its possible natural expression, predictably restricted to neutrophils, could not be demonstrated in resting or interferon γ-stimulated cells. As the CNR5-deletion was originally described in an Ecuadorian family from Llano Grande (an indigenous community in North-Eastern Quito), we characterized the FCGR genetic variation in two populations from the highlands of Ecuador. Our results reveal that CNR5-deletion is relatively frequent in Llano Grande (5 carriers out of 36 donors). Furthermore, we found a high frequency of two strong-phagocytosis variants: the FCGR3B-NA1 haplotype and the CNR1 duplication, which translates into an increased FCGR3B and FCGR2C copy-number. CNR1 duplication was particularly increased in Llano Grande, 77.8% of the studied sample carrying at least one such duplication. In contrast, an extended haplotype CD16A-176V - CD32C-ORF+2B.2 - CD32B-2B.4 including strong activating and inhibitory FcγR variants was absent in Llano Grande and found at a low frequency (8.6%) in Ecuador highlands. This particular distribution of FCGR polymorphism, possibly a result of selective pressures, further confirms the importance of a comprehensive, joint analysis of all genetic variations in the locus and warrants additional studies on their putative clinical impact. In conclusion, our study confirms important ethnic variation at the FCGR locus; it shows a distinctive FCGR polymorphism distribution in Ecuador highlands; provides a molecular characterization of a novel CNR5-deletion associated with CD16A and CD16B deficiency; and confirms its presence in that population.
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Variaciones en el Número de Copia de ADN , Genética de Población , Polimorfismo de Nucleótido Simple , Receptores de IgG/genética , Alelos , Línea Celular , Ecuador , Proteínas Ligadas a GPI/genética , Expresión Génica , Sitios Genéticos , Variación Genética , Genotipo , Granulocitos/metabolismo , HumanosRESUMEN
In a rapidly changing climate, flowering time (FL) adaptation is important to maximize seed yield in flax (Linum usitatissimum L.). However, our understanding of the genetic mechanism underlying FL in this multipurpose crop remains limited. With the aim of dissecting the genetic architecture of FL in flax, a genome-wide association study (GWAS) was performed on 200 accessions of the flax core collection evaluated in four environments. Two single-locus and six multi-locus models were applied using 70,935 curated single nucleotide polymorphism (SNP) markers. A total of 40 quantitative trait nucleotides (QTNs) associated with 27 quantitative trait loci (QTL) were identified in at least two environments. The number of QTL with positive-effect alleles in accessions was significantly correlated with FL (r = 0.77 to 0.82), indicating principally additive gene actions. Nine QTL were significant in at least three of the four environments accounting for 3.06-14.71% of FL variation. These stable QTL spanned regions that harbored 27 Arabidopsis thaliana and Oryza sativa FL-related orthologous genes including FLOWERING LOCUS T (Lus10013532), FLOWERING LOCUS D (Lus10028817), transcriptional regulator SUPERMAN (Lus10021215), and gibberellin 2-beta-dioxygenase 2 (Lus10037816). In silico gene expression analysis of the 27 FL candidate gene orthologous suggested that they might play roles in the transition from vegetative to reproductive phase, flower development and fertilization. Our results provide new insights into the QTL architecture of flowering time in flax, identify potential candidate genes for further studies, and demonstrate the effectiveness of combining different GWAS models for the genetic dissection of complex traits.
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Lino , Copas de Floración/crecimiento & desarrollo , Copas de Floración/genética , Lino/genética , Lino/crecimiento & desarrollo , Regulación del Desarrollo de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , Genes de Plantas , Sitios Genéticos/genética , Estudio de Asociación del Genoma Completo/métodos , Desequilibrio de Ligamiento , Sitios de Carácter Cuantitativo , Semillas/genética , Análisis de Secuencia de ADN , Factores de TiempoRESUMEN
BACKGROUND: The genetic diversity of the RHCE gene locus has been explored in diverse populations of different racial backgrounds. Data referring to the diversity of RHCE encoding weakened expression of C, c, E, and e in multiethnic populations is still incomplete. METHODS: Samples from Brazilian blood donors presenting reduced expression of C, c, E, or e on gel method were selected for the study. All exons and flanking introns of RHCE were genotyped though direct Sanger sequencing for the included donors. RESULTS: Sixty-six donors were included: 23 with weak C, 22 with weak c, 6 with weak E, 14 with weak e, and 1 with weak c and E. Among the samples with weak C, the following altered RH*C were encountered: RHCE*CeMA (n = 3), RHCE*Ce941C (n = 1), and RHCE*CeVA (n = 1). RHD*D-CE(4-7)-D was detected in six cases, RHCE*CE was presumably present in five cases, and seven cases were unexplained. Two altered alleles underlay the weak c phenotype: RHCE*ceJAL (n = 20) and RHCE*ce340T (n = 2), and two altered RHCE justified weak e: RHCE*ceMO (n = 6) and RHCE*ceJAL (n = 8). Three variant RHCE were associated with weak E: RHCE*cEJU (n = 4), RHCE*cE382C (n = 1), and RHCE*cEIV (n = 1). The RHCE*cE905A justified one case of weak c and E. CONCLUSION: We describe the distribution of RHCE variants found in association with weak expression of C, c, E, and e in blood donors of multiethnic origin, which differs in comparison to that previously reported for people of African or Caucasian descent.
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Donantes de Sangre , Sistema del Grupo Sanguíneo Rh-Hr/genética , Alelos , Brasil , Exones , Frecuencia de los Genes , Sitios Genéticos , Variación Genética , Genotipo , Humanos , IntronesRESUMEN
The franciscana (Pontoporia blainvillei) is the most threatened small cetacean in the South Atlantic. In this study we report the development of 13 microsatellite markers for franciscanas through next-generation sequencing, and the characterization of those loci in 38 samples from the species' northernmost population (Espírito Santo, Brazil). Besides providing diversity indices for the new, specific loci, we also report on the transferability of heterologous loci which had not been screened in franciscanas before, and review all loci used in previous studies. Expected heterozygosity in the new loci ranged between 0.107 and 0.595, and all but one were in Hardy Weinberg Equilibrium. These are the first microsatellite loci isolated from franciscanas, and they are an important addition to heterologous markers that were available previously.
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Delfines/genética , Especies en Peligro de Extinción , Repeticiones de Microsatélite/genética , Animales , Sitios Genéticos , Genética de Población , Polimorfismo GenéticoRESUMEN
The endemic tree species Calyptranthes clusiifolia (Myrtaceae) plays a relevant ecological role in the forest fragments where it has a common occurrence. In this study, we reported the development of microsatellite markers for C. clusiifolia what will allow a better understanding of the relationship between the forest fragmentation process and the genetic structure and diversity of tree populations. Seven microsatellite markers were developed using an enriched genomic library and characterized in 30 individuals (from three populations). These seven loci were polymorphic and resulted in a total of 23 alleles. The expected heterozygosity (HE) varied from 0.14 (Caly 06) to 0.73 (Caly 22). Linkage disequilibrium between the loci (p > 0.0007) pairs was not detected. The parentage exclusion power of the first (Pe-1) and the second (Pe-2) parents were 0.6099 and 0.8548, respectively. The microsatellite markers developed are indicated for future studies of the genetic diversity in natural populations of C. clusiifolia.
Asunto(s)
Repeticiones de Microsatélite/genética , Myrtaceae/genética , Alelos , Sitios Genéticos , Polimorfismo GenéticoRESUMEN
The advance of Next Generation Sequencing (NGS) technologies allows high-throughput genotyping at a reasonable cost, although, in the case of peach, this technology has been scarcely developed. To date, only a standard Genotyping by Sequencing approach (GBS), based on a single restriction with ApeKI to reduce genome complexity, has been applied in peach. In this work, we assessed the performance of the double-digest RADseq approach (ddRADseq), by testing 6 double restrictions with the restriction profile generated with ApeKI. The enzyme pair PstI/MboI retained the highest number of loci in concordance with the in silico analysis. Under this condition, the analysis of a diverse germplasm collection (191 peach genotypes) yielded 200,759,000 paired-end (2 × 250 bp) reads that allowed the identification of 113,411 SNP, 13,661 InDel and 2133 SSR. We take advantage of a wide sample set to describe technical scope of the platform. The novel platform presented here represents a useful tool for genomic-based breeding for peach.
Asunto(s)
Genoma de Planta , Genotipo , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Prunus persica/enzimología , Prunus persica/genética , Análisis de Secuencia de ADN/métodos , Biología Computacional/métodos , ADN de Plantas/genética , ADN de Plantas/aislamiento & purificación , Desoxirribonucleasas de Localización Especificada Tipo II/genética , Sitios Genéticos , Técnicas de Genotipaje/métodos , Fitomejoramiento , Polimorfismo de Nucleótido SimpleRESUMEN
Genetics can provide invaluable tools for management and conservation of bee populations, which are declining worldwide. Among these tools, microsatellite are very useful molecular markers for population analyses. The aim of this study was to isolate and characterize microsatellites for Epicharis (Anepicharis) dejeanii and Epicharis (Epicharis) nigrita, two Neotropical species of solitary bees, both exhibiting the habit of nesting in aggregations. Microsatellite loci were identified from two enriched genomic libraries. The characterization and analysis of loci were carried out using 35 females of E. dejeanii and 34 of E. nigrita. In total, we report the development of 12 microsatellite loci for E. dejeanii and 13 for E. nigrita. For E. dejeanii, all loci were polymorphic, the number of alleles per locus ranged from 2 to 12, averaging 8.7 and, observed and expected heterozygosity were 0.485 (range 0.229-0.857) and 0.633 (range 0.288-0.843), respectively. For E. nigrita, only nine out of 13 loci amplified were polymorphic, the number of alleles per locus ranged from 2 to 12, averaging 5.5. For this species, the observed and expected heterozygosity were 0.440 (range 0.118-0.676) and 0.545 (range 0.167-0.814), respectively. Cross-amplification of primers was successful in other Centridini species. The two sets of loci described for E. dejeanii and E. nigrita species are polymorphic and informative and show promising applicability for both population genetic approaches and relatedness on these and other Centridini species.