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1.
Sex Transm Infect ; 93(4): 238-239, 2017 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-25795661

RESUMO

A range of prevention strategies have been considered in an attempt to reduce HIV transmission. The use of continuous antiretrovirals (ARVs) in high-risk HIV-negative individuals (pre-exposure prophylaxis or PrEP) and the short-term use of ARVs following a high-risk exposure (postexposure prophylaxis or PEP) are among these strategies. We report a case of the contemporaneous use of PEP and PrEP in a sexual liaison between two men.In an attempt to reduce the number of new cases of HIV infection, a range of prevention strategies have been advocated. Prior to the availability of ARV therapy, the key prevention measure was condom promotion and modifying sexual behaviour such as partner number reduction within high-risk groups. This was followed by: the introduction of PEP, treating all HIV cases with ARVs to reduce the probability of transmission (treatment as prevention) and in the past few years the use of PrEP. Case-control, observational and randomised clinical trial data exist to support these strategies. We describe what we believe is the first reported use of PrEP and PEP in a sexual liaison between two men in Sydney.


Assuntos
Fármacos Anti-HIV/uso terapêutico , Infecções por HIV/prevenção & controle , Profilaxia Pós-Exposição , Profilaxia Pré-Exposição , Parceiros Sexuais/psicologia , Sexo sem Proteção/psicologia , Infecções por HIV/psicologia , Homossexualidade Masculina , Humanos , Masculino , Aceitação pelo Paciente de Cuidados de Saúde , Assunção de Riscos , Resultado do Tratamento
2.
Theor Appl Genet ; 127(9): 2051-64, 2014 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-25119868

RESUMO

KEY MESSAGE: A high-resolution genetic linkage map of B. oleracea was developed from a B. napus SNP array. The work will facilitate genetic and evolutionary studies in Brassicaceae. A broccoli population, VI-158 × BNC, consisting of 150 F2:3 families was used to create a saturated Brassica oleracea (diploid: CC) linkage map using a recently developed rapeseed (Brassica napus) (tetraploid: AACC) Illumina Infinium single nucleotide polymorphism (SNP) array. The map consisted of 547 non-redundant SNP markers spanning 948.1 cM across nine chromosomes with an average interval size of 1.7 cM. As the SNPs are anchored to the genomic reference sequence of the rapid cycling B. oleracea TO1000, we were able to estimate that the map provides 96 % coverage of the diploid genome. Carotenoid analysis of 2 years data identified 3 QTLs on two chromosomes that are associated with up to half of the phenotypic variation associated with the accumulation of total or individual compounds. By searching the genome sequences of the two related diploid species (B. oleracea and B. rapa), we further identified putative carotenoid candidate genes in the region of these QTLs. This is the first description of the use of a B. napus SNP array to rapidly construct high-density genetic linkage maps of one of the constituent diploid species. The unambiguous nature of these markers with regard to genomic sequences provides evidence to the nature of genes underlying the QTL, and demonstrates the value and impact this resource will have on Brassica research.


Assuntos
Brassica/genética , Mapeamento Cromossômico , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Carotenoides/genética , DNA de Plantas/genética , Ligação Genética , Genoma de Planta
3.
Theor Appl Genet ; 126(10): 2655-70, 2013 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-23959525

RESUMO

Mycotoxins caused by Fusarium spp. is a major concern on food and feed safety in oats, although Fusarium head blight (FHB) is often less apparent than in other small grain cereals. Breeding resistant cultivars is an economic and environment-friendly way to reduce toxin content, either by the identification of resistance QTL or phenotypic evaluation. Both are little explored in oats. A recombinant-inbred line population, Hurdal × Z595-7 (HZ595, with 184 lines), was used for QTL mapping and was phenotyped for 3 years. Spawn inoculation was applied and deoxynivalenol (DON) content, FHB severity, days to heading and maturity (DH and DM), and plant height (PH) were measured. The population was genotyped with DArTs, AFLPs, SSRs and selected SNPs, and a linkage map of 1,132 cM was constructed, covering all 21 oat chromosomes. A QTL for DON on chromosome 17A/7C, tentatively designated as Qdon.umb-17A/7C, was detected in all experiments using composite interval mapping, with phenotypic effects of 12.2­26.6 %. In addition, QTL for DON were also found on chromosomes 5C, 9D, 13A, 14D and unknown_3, while a QTL for FHB was found on 11A. Several of the DON/FHB QTL coincided with those for DH, DM and/or PH. A half-sib population of HZ595, Hurdal × Z615-4 (HZ615, with 91 lines), was phenotyped in 2011 for validation of QTL found in HZ595, and Qdon.umb-17A/7C was again localized with a phenotypic effect of 12.4 %. Three SNPs closely linked to Qdon.umb-17A/7C were identified in both populations, and one each for QTL on 5C, 11A and 13A were identified in HZ595. These SNPs, together with those yet to be identified, could be useful in marker-assisted selection to pyramiding resistance QTL.


Assuntos
Avena/genética , Mapeamento Cromossômico , Resistência à Doença/genética , Fusarium/fisiologia , Doenças das Plantas/microbiologia , Locos de Características Quantitativas/genética , Tricotecenos/metabolismo , Análise de Variância , Avena/imunologia , Avena/microbiologia , Segregação de Cromossomos/genética , Cromossomos de Plantas/genética , Cruzamentos Genéticos , Marcadores Genéticos , Fenótipo , Doenças das Plantas/genética , Doenças das Plantas/imunologia , Característica Quantitativa Herdável
4.
Chromosome Res ; 20(6): 699-715, 2012 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-22968763

RESUMO

Thirteen common wheat "Chinese Spring" (CS)-Thinopyrum junceum addition lines and three common wheat "Fukuhokomuji"(Fuku)-Elymus rectisetus addition lines were characterized and verified as disomic additions of a Th. junceum or E. rectisetus chromosome in the wheat backgrounds by fluorescent genomic in situ hybridization. Another Fuku-E. rectisetus addition line, A1048, was found to contain multiple segregating E. rectisetus chromosomes. Seven partial CS-Th. junceum amphiploids were identified to combine 12-16 Th. junceum chromosomes with CS wheat chromosomes. The disomic addition lines AJDAj5, 7, 8, 9, and HD3508 were identified to contain a Th. junceum chromosome in homoeologous group 1. Two of them, AJDAj7 and AJDAj9, had the same Th. junceum chromosome. AJDAj2, 3, and 4 contained a Th. junceum chromosome in group 2, HD3505 in group 4, AJDAj6 and AJDAj11 in group 5, and AJDAj1 probably in group 6. The disomic addition lines A1026 and A1057 were identified to carry an E. rectisetus chromosome in group 1 and A1034 in group 5. E. rectisetus chromosomes in groups 1-6 were detected in A1048. The homoeologous group of the Th. junceum chromosome in HD3515 could not be determined in this study. Several Th. junceum and E. rectisetus chromosomes in the addition lines were found to contain genes for resistance to Fusarium head blight, tan spot, Stagonospora nodorum blotch, and stem rust (Ug99 races). Understanding of the homoeology of the Th. junceum and E. rectisetus chromosomes with wheat will facilitate utilization of the favorable genes on these alien chromosomes in wheat improvement.


Assuntos
Cruzamento/métodos , Cromossomos de Plantas/genética , Resistência à Doença/genética , Elymus/genética , Doenças das Plantas/microbiologia , Triticum/genética , Southern Blotting , Eletroforese em Gel de Poliacrilamida , Hibridização in Situ Fluorescente , Polimorfismo de Fragmento de Restrição , Especificidade da Espécie
5.
BMC Genomics ; 12: 77, 2011 Jan 27.
Artigo em Inglês | MEDLINE | ID: mdl-21272354

RESUMO

BACKGROUND: Genetic markers are pivotal to modern genomics research; however, discovery and genotyping of molecular markers in oat has been hindered by the size and complexity of the genome, and by a scarcity of sequence data. The purpose of this study was to generate oat expressed sequence tag (EST) information, develop a bioinformatics pipeline for SNP discovery, and establish a method for rapid, cost-effective, and straightforward genotyping of SNP markers in complex polyploid genomes such as oat. RESULTS: Based on cDNA libraries of four cultivated oat genotypes, approximately 127,000 contigs were assembled from approximately one million Roche 454 sequence reads. Contigs were filtered through a novel bioinformatics pipeline to eliminate ambiguous polymorphism caused by subgenome homology, and 96 in silico SNPs were selected from 9,448 candidate loci for validation using high-resolution melting (HRM) analysis. Of these, 52 (54%) were polymorphic between parents of the Ogle1040 × TAM O-301 (OT) mapping population, with 48 segregating as single Mendelian loci, and 44 being placed on the existing OT linkage map. Ogle and TAM amplicons from 12 primers were sequenced for SNP validation, revealing complex polymorphism in seven amplicons but general sequence conservation within SNP loci. Whole-amplicon interrogation with HRM revealed insertions, deletions, and heterozygotes in secondary oat germplasm pools, generating multiple alleles at some primer targets. To validate marker utility, 36 SNP assays were used to evaluate the genetic diversity of 34 diverse oat genotypes. Dendrogram clusters corresponded generally to known genome composition and genetic ancestry. CONCLUSIONS: The high-throughput SNP discovery pipeline presented here is a rapid and effective method for identification of polymorphic SNP alleles in the oat genome. The current-generation HRM system is a simple and highly-informative platform for SNP genotyping. These techniques provide a model for SNP discovery and genotyping in other species with complex and poorly-characterized genomes.


Assuntos
Avena/genética , Genoma de Planta/genética , Polimorfismo de Nucleotídeo Único/genética , Análise de Sequência de DNA/métodos , Biologia Computacional , Etiquetas de Sequências Expressas , Genótipo
6.
PLoS One ; 11(5): e0155376, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27175781

RESUMO

Barley yellow dwarf viruses (BYDVs) are responsible for the disease barley yellow dwarf (BYD) and affect many cereals including oat (Avena sativa L.). Until recently, the molecular marker technology in oat has not allowed for many marker-trait association studies to determine the genetic mechanisms for tolerance. A genome-wide association study (GWAS) was performed on 428 spring oat lines using a recently developed high-density oat single nucleotide polymorphism (SNP) array as well as a SNP-based consensus map. Marker-trait associations were performed using a Q-K mixed model approach to control for population structure and relatedness. Six significant SNP-trait associations representing two QTL were found on chromosomes 3C (Mrg17) and 18D (Mrg04). This is the first report of BYDV tolerance QTL on chromosome 3C (Mrg17) and 18D (Mrg04). Haplotypes using the two QTL were evaluated and distinct classes for tolerance were identified based on the number of favorable alleles. A large number of lines carrying both favorable alleles were observed in the panel.


Assuntos
Avena/genética , Avena/virologia , Resistência à Doença/genética , Estudo de Associação Genômica Ampla , Luteovirus/fisiologia , Doenças das Plantas/genética , Doenças das Plantas/virologia , Alelos , Mapeamento Cromossômico , Genética Populacional , Genoma de Planta , Genótipo , Haplótipos , Fenótipo , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Característica Quantitativa Herdável
7.
Plant Genome ; 9(2)2016 07.
Artigo em Inglês | MEDLINE | ID: mdl-27898818

RESUMO

Hexaploid oat ( L., 2 = 6 = 42) is a member of the Poaceae family and has a large genome (∼12.5 Gb) containing 21 chromosome pairs from three ancestral genomes. Physical rearrangements among parental genomes have hindered the development of linkage maps in this species. The objective of this work was to develop a single high-density consensus linkage map that is representative of the majority of commonly grown oat varieties. Data from a cDNA-derived single-nucleotide polymorphism (SNP) array and genotyping-by-sequencing (GBS) were collected from the progeny of 12 biparental recombinant inbred line populations derived from 19 parents representing oat germplasm cultivated primarily in North America. Linkage groups from all mapping populations were compared to identify 21 clusters of conserved collinearity. Linkage groups within each cluster were then merged into 21 consensus chromosomes, generating a framework consensus map of 7202 markers spanning 2843 cM. An additional 9678 markers were placed on this map with a lower degree of certainty. Assignment to physical chromosomes with high confidence was made for nine chromosomes. Comparison of homeologous regions among oat chromosomes and matches to orthologous regions of rice ( L.) reveal that the hexaploid oat genome has been highly rearranged relative to its ancestral diploid genomes as a result of frequent translocations among chromosomes. Heterogeneous chromosome rearrangements among populations were also evident, probably accounting for the failure of some linkage groups to match the consensus. This work contributes to a further understanding of the organization and evolution of hexaploid grass genomes.


Assuntos
Avena/genética , Genoma de Planta/genética , Sintenia , Mapeamento Cromossômico , Cromossomos de Plantas/genética , Ligação Genética , Genótipo , América do Norte , Polimorfismo de Nucleotídeo Único , Poliploidia
8.
PLoS One ; 9(5): e96276, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-24820172

RESUMO

Tocochromanols are recognized for nutritional content, plant stress response, and seed longevity. Here we present a systems biological approach to characterize and develop predictive assays for genes affecting tocochromanol variation in barley. Major QTL, detected in three regions of a SNP linkage map, affected multiple tocochromanol forms. Candidate genes were identified through barley/rice orthology and sequenced in genotypes with disparate tocochromanol profiles. Gene-specific markers, designed based on observed polymorphism, mapped to the originating QTL, increasing R2 values at the respective loci. Polymorphism within promoter regions corresponded to motifs known to influence gene expression. Quantitative PCR analysis revealed a trend of increased expression in tissues grown at cold temperatures. These results demonstrate utility of a novel method for rapid gene identification and characterization, and provide a resource for efficient development of barley lines with improved tocochromanol profiles.


Assuntos
Alelos , Hordeum/genética , Biologia de Sistemas/métodos , Mapeamento Cromossômico , Polimorfismo de Nucleotídeo Único/genética , Locos de Características Quantitativas/genética
9.
PLoS One ; 8(3): e58068, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-23533580

RESUMO

A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources.


Assuntos
Avena/genética , Mapeamento Cromossômico/métodos , Polimorfismo de Nucleotídeo Único/genética , Sintenia/genética , Genoma de Planta/genética
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