Mapping QTLs for aluminum tolerance in maize

Aluminum toxicity is one of the major constraints for plant development in acid soils, limiting food production in many countries. Cultivars genetically adapted to acid soils may offer an environmental compatible solution, providing a sustainable agriculture system. The aim of this work was to identify genomic regions associated with Al tolerance in maize, and to quantify the genetic effects on the phenotypic variation. A population of 168 F-3:4 families derived from a cross between two contrasting maize inbred lines for Al tolerance was evaluated using the NSRL and RSRL parameters in nutrient solution containing toxic level of aluminum. Variance analyses indicated that the NSRL was the most reliable phenotypic index to measure Al tolerance in the population, being used for further QTL mapping analysis. RFLP and SSR markers were selected for bulked segregant analysis, and additional SSR markers, flanking the polymorphisms of interest, were chosen in order to saturate the putative target regions. Seven linkage groups were constructed using 17 RFLP and 34 SSR markers. Five QTLs were mapped on chromosomes 2, 6 and 8, explaining 60% of the phenotypic variation. QTL(4) and marker umc043 were located on chromosomes 8 and 5, close to genes encoding for enzymes involved in the organic acids synthesis pathways, a widely proposed mechanism for Al tolerance in plants. QTL(2) was mapped in the same region as Alm2, also associated with Al tolerance in maize. In addition, dominant and additive effects were important in the control of this trait in maize.

Determinação precoce do sexo fetal pela análise do DNA no plasma materno

Purpose: to verify the viability of early diagnosis of fetal gender in maternal plasma by the real-time polymerase chain reaction (real-time PCR) starting at the 5th week of pregnancy. Methods: peripheral blood was collected from pregnant women with single fetus starting at the 5th week of gestation. After centrifugation, 0.4 mL plasma was separated for fetal DNA extraction. The DNA was analyzed in duplicate by real-time PCR for two genomic regions, one of the Y chromosome and the other common to both sexes, through the TaqMan® method, which uses a pair of primers and a fluorescent probe. Patients who aborted were excluded. Results: a total of 79 determinations of fetal DNA in maternal plasma were performed in 52 pregnant women. The results of the determinations were compared to fetal gender after delivery. Accuracy according to gestational age was 92.6% (25 of 27 cases) at 5 weeks with 87% sensitivity, and 95.6% (22 of 23 cases) at 6 weeks with 92% sensitivity. Starting at the 7th week of pregnancy, accuracy was 100% (29 of 29 cases). Specificity was 100% regardless of gestational age. Conclusion: real-time PCR for the detection of fetal gender in maternal plasma starting at the 5th week of gestation has good sensitivity and excellent specificity. There was agreement of the results in 100% of the cases in which male gender was diagnosed, regardless of gestational age, and from the 7th week of gestation for female gender diagnosis.

Development and validation of a Xanthomonas axonopodis pv. citri DNA microarray platform (XACarray) generated from the shotgun libraries previously used in the sequencing of this bacterial genome

Background. From shotgun libraries used for the genomic sequencing of the phytopathogenic bacterium Xanthomonas axonopodis pv. citri (XAC), clones that were representative of the largest possible number of coding sequences (CDSs) were selected to create a DNA microarray platform on glass slides (XACarray). The creation of the XACarray allowed for the establishment of a tool that is capable of providing data for the analysis of global genome expression in this organism. Findings. The inserts from the selected clones were amplified by PCR with the universal oligonucleotide primers M13R and M13F. The obtained products were purified and fixed in duplicate on glass slides specific for use in DNA microarrays. The number of spots on the microarray totaled 6,144 and included 768 positive controls and 624 negative controls per slide. Validation of the platform was performed through hybridization of total DNA probes from XAC labeled with different fluorophores, Cy3 and Cy5. In this validation assay, 86% of all PCR products fixed on the glass slides were confirmed to present a hybridization signal greater than twice the standard deviation of the deviation of the global median signal-to-noise ration. Conclusions. Our validation of the XACArray platform using DNA-DNA hybridization revealed that it can be used to evaluate the expression of 2,365 individual CDSs from all major functional categories, which corresponds to 52.7% of the annotated CDSs of the XAC genome. As a proof of concept, we used this platform in a previously work to verify the absence of genomic regions that could not be detected by sequencing in related strains of Xanthomonas. © 2010 Moreira et al; licensee BioMed Central Ltd.

Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds

Intense selective pressures applied over short evolutionary time have resulted in homogeneity within, but substantial variation among, horse breeds. Utilizing this population structure, 744 individuals from 33 breeds, and a 54,000 SNP genotyping array, breed-specific targets of selection were identified using an FST-based statistic calculated in 500-kb windows across the genome. A 5.5-Mb region of ECA18, in which the myostatin (MSTN) gene was centered, contained the highest signature of selection in both the Paint and Quarter Horse. Gene sequencing and histological analysis of gluteal muscle biopsies showed a promoter variant and intronic SNP of MSTN were each significantly associated with higher Type 2B and lower Type 1 muscle fiber proportions in the Quarter Horse, demonstrating a functional consequence of selection at this locus. Signatures of selection on ECA23 in all gaited breeds in the sample led to the identification of a shared, 186-kb haplotype including two doublesex related mab transcription factor genes (DMRT2 and 3). The recent identification of a DMRT3 mutation within this haplotype, which appears necessary for the ability to perform alternative gaits, provides further evidence for selection at this locus. Finally, putative loci for the determination of size were identified in the draft breeds and the Miniature horse on ECA11, as well as when signatures of selection surrounding candidate genes at other loci were examined. This work provides further evidence of the importance of MSTN in racing breeds, provides strong evidence for selection upon gait and size, and illustrates the potential for population-based techniques to find genomic regions driving important phenotypes in the modern horse. © 2013 Petersen et al.

Análise comparativa das metodologias de hibridização reversa e sequenciamento direto para a genotipagem do vírus da hepatite C

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Alterações genômicas em tumores de glândulas salivares

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Identificação de marcadores moleculares de resposta à quimioterapia neoadjuvante e associação de radioterapia e quimioterapia em pacientes com carcinoma epidermóide de orofaringe

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Perfil de alterações genômicas em angiofibromas nasofaringeos juvenis

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Identificação de assinaturas de seleção e anotação do genoma em bovinos da raça Nelore

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Isolamento e identificação de bactérias solubilizadoras de fósforo e produtoras de auxinas em solo com cana-de-açúcar

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Aplicação da técnica de RT-PCR in situ na detecção da co-infecção pelo Coronavírus grupo 3 (TCoV) e Astrovírus (TAstV-2) em perus com quadro agudo de enterite

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Genome-wide scans to uncover loci underlying bovine reproductive biology

Pós-graduação em Medicina Veterinária - FCAV

Caracterização morfológica, morfométrica e molecular de Hepatozoon spp. (Apicomplexa, Hepatozoidae) de serpentes brasileiras naturalmente infectadas

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

O controle epigenético da expressão gênica na carcinogênese mamária: investigação de genes candidatos a supressores tumorais mapeados em 3p21.3

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Dinâmica evolutiva de DNAs repetitivos com ênfase em espécies da tribo Phanaeini

Pós-graduação em Ciências Biológicas (Genética) - IBB