Potencial de linhagens experimentais de milho, oriundas de populações braquíticas, para produção de híbridos

Pós-graduação em Agronomia - FEIS

Capacidade combinatória de linhagens S4 de milho super-doce (Zea mays L.), portadoras do gene shrunken-2

Pós-graduação em Agronomia (Agricultura) - FCA

Capacidade de combinação de linhagens de pepino (Cucumis sativus L.) do grupo japonês

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Capacidade combinatória e heterose em cruzamentos de linhagens de pepino do grupo caipira

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

Estimativas de heterose e capacidades de combinação em cebola para resistência a raiz rosada

Pós-graduação em Agronomia (Proteção de Plantas) - FCA

Divergência genética entre linhagens de milho estimada por microssatélites e correlação com desempenho de híbridos simples

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Capacidade de combinação para seleção de genótipos de milho

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Efeitos gênicos de caracteres associados à eficiência no uso de nitrogênio em milho

Os objetivos deste trabalho foram determinar o controle genético da eficiência no uso do nitrogênio (EUN), identificar a importância das eficiências na absorção (EAN) e na utilização (EUtN) na sua composição,  e quantificar relação entre produção de matéria seca da parte aérea (MPS) e do sistema radicular com a EUN e  com seus componentes. Foram avaliadas 41 combinações híbridas em duas disponibilidades de N: baixa (BN)  e alta (AN). Utilizou-se o delineamento de blocos ao acaso com duas repetições, em arranjo fatorial simples  (combinação híbrida x disponibilidade de N). As análises estatísticas foram realizadas por meio das equações  de modelos mistos. Correlações de elevada magnitude foram detectadas entre EAN e EUN, bem como entre  essas eficiências e a MPS, tanto em BN como em AN. Em ambas as disponibilidades de N, efeitos genéticos  aditivos apresentaram maior importância para os caracteres associados à EUN. Dessa forma, a seleção baseada  no desempenho individual de linhagens quanto à MPS pode possibilitar a obtenção de genótipos com alta  EUN. Independentemente da disponibilidade de N, a EAN é o componente mais importante da EUN.

Diallel cross among fresh market tomato inbreeding lines

The general combining ability (GCA), specific combining ability (SCA), and heterosis were studied in a complete diallel cross among fresh market tomato breeding lines with reciprocal excluded. Fifteen genotypes (five parents and ten hybrids) were tested using a randomized complete block design, with three replications, and the experiments were conducted in Itatiba, São Paulo state, Brazil, in 2005/06. The yield components evaluated were fruit yield per plant (FP), fruit number per plant (FN), average fruit weight (FW); cluster number per plant (CN); fruit number per cluster (FC), fruit wall thickness (FT) and number of locules per fruit (NL). Fruit quality components evaluated were total soluble solids (SS); total titratable acidity (TA); SS/TA ratio, fruit length (FL); fruit width (WI); length to width ratio (FL/WI). The data for each trait was first subjected to analysis of variance. Griffing's method 2, model 1 was employed to estimate the general (GCA) and specific (SCA) combining abilities. Parental and hybrid data for each trait were used to estimate of mid-parent heterosis. For plant fruit yield, IAC-2 was the best parental line with the highest GCA followed by IAC-4 and IAC-1 lines. The hybrids IAC-1 x IAC-2, IAC-1 x IAC-4 and IAC-2 x IAC-4 showed the highest effects of SCA. High heterotic responses were found for fruit yield and plant fruit number with values up to 49.72% and 47.19%, respectively. The best hybrids for fruit yield and plant fruit number were IAC-1 x IAC-2, IAC-1 x IAC-4 and IAC-2 x IAC-5, for fruit yield and plant fruit number, the main yield components.

Genetic analysis of resistance to root-lesion nematode (Pratylenchus thornei) in wheat

The inheritance of resistance to root-lesion nematode was investigated in five synthetic hexaploid wheat lines and two bread wheat lines using a half-diallel design of F-1 and F-2 crosses. The combining ability of resistance genes in the synthetic hexaploid wheat lines was compared with the performance of the bread wheat line 'GS50a', the source of resistance to Pratylenchus thornei used in Australian wheat breeding programmes. Replicated glasshouse trials identified P. thornei resistance as polygenic and additive in gene action. General combining ability (GCA) of the parents was more important than specific combining ability (SCA) effects in the inheritance of P. thornei resistance in both F-1 and F-2 populations. The synthetic hexaploid wheat line 'CPI133872' was identified as the best general combiner, however, all five synthetic hexaploid wheat lines possessed better GCA than 'GS50a'. The synthetic hexaploid wheat lines contain novel sources of P. thornei resistance that will provide alternative and more effective sources of resistance to be utilized in wheat breeding programmes.

Potential to increase yield in lucerne (Medicago sativa subsp sativa) through introgression of Medicago sativa subsp falcata into Australian adapted material

The effect of interspecific heterosis in crosses between Medicago sativa subsp. sativa and M. sativa subsp. falcata was assessed. Three sativa and 3 falcata plants were crossed in a diallel design. Progeny dry matter yield and natural plant height were assessed in a replicated field experiment at Gatton, Queensland. Yield data were analysed using the method of residual maximum likelihood (REML) and Griffing's model 1. There were significant differences between the reciprocal, general combining ability (GCA), and specific combining ability (SCA) effects. As expected, S-1 populations were lower yielding than their respective intraspecific cross and falcata x falcata crosses were significantly lower yielding than sativa x sativa crosses. Some of the interspecific crosses indicated substantial SCA effects, yielding at least as well as the best sativa x sativa crosses. We have demonstrated the potential usefulness of unselected M. sativa subsp. falcata as a heterotic group in the improvement of yield in northern Australian adapted lucerne material, and discuss how it could be incorporated into future breeding to overcome the yield stagnation currently being experienced in Australian programs.

Combining food web and species distribution models for improved community projections

The ability to model biodiversity patterns is of prime importance in this era of severe environmental crisis. Species assemblage along environmental gradient is subject to the interplay of biotic interactions in complement to abiotic environmental filtering. Accounting for complex biotic interactions for a wide array of species remains so far challenging. Here, we propose to use food web models that can infer the potential interaction links between species as a constraint in species distribution models. Using a plant-herbivore (butterfly) interaction dataset, we demonstrate that this combined approach is able to improve both species distribution and community forecasts. Most importantly, this combined approach is very useful in rendering models of more generalist species that have multiple potential interaction links, where gap in the literature may be recurrent. Our combined approach points a promising direction forward to model the spatial variation of entire species interaction networks. Our work has implications for studies of range shifting species and invasive species biology where it may be unknown how a given biota might interact with a potential invader or in future climate.

Combining MAR elements and transposable vectors for more reliable transgene integration and expression

Integration without cytotoxic effects and long-term expression of a transgene constitutes a major challenge in gene therapy and biotechnology applications. In this context, transposons represent an attractive system for gene transfer because of their ability to promote efficient integration of a transgene in a variety of cell lines. However, the transgene integration can lead to insertional mutagenesis and/or unstable transgene expression by epigenetic modifications. These unwanted events may be limited by the use of chromatin control elements called MARs (matrix attachment regions). Indeed, the insertion of these DNA elements next to the transgene usually results in higher and more stable expression by maintaining transgene chromatin in an active configuration and preventing gene silencing. In this study, we tested if the inclusion of the MAR 1-68 in the piggyBac transposon system may lead to efficient and safer transgene integration and ensure reliable stable and long-term expression of a transgene. The MAR-containing transposon construct was tested in CHO cells, for biotechnology applications, and in mesoangioblast cells that can differentiate into muscle cells and are important candidates for potential stem cell therapies of myopathies. We showed that the addition of the MAR 1 -68 in the piggyBac transposon did not interfere with transposition, thereby maintaining high frequency of transgene integrations in these cells. Moreover, the MAR allowed higher transgene expression from fewer transposon integration events. We also found that enriched transgene-expressing cell populations could be obtained without the need of selection pressure. Since antibiotic-enforced selection protocols often result in a higher integrated copy number and mosaic expression patterns, this strategy could benefit many applications in which a low copy number of integrated transgenes and antibiotic-free conditions are desired. In addition, the intramuscular transplantation of mouse tibialis anterior muscles with mesoangioblasts containing the transposon led to widespread and sustained myofiber transgene expression after differentiation of these cells in vivo. These findings indicated that piggyBac vectors may provide a viable approach to achieve stable gene transfer in the context of Duchenne muscular dystrophy therapy. - L'intégration sans effets cytotoxiques et l'expression à long terme d'un transgène constituent un défi majeur en thérapie génique et en biotechnologie. Dans ce contexte, les transposons représentent un système attrayant pour le transfert de gènes en raison de leur capacité à promouvoir l'intégration efficace d'un transgène dans une variété de lignées cellulaires. Toutefois, l'intégration d'un transgène peut conduire à une mutagénèse insertionnelle et/ou à une expression instable due au silençage du transgène suite à des modifications épigénétiques. Ces événements indésirables de silençage génique peuvent être diminués par l'utilisation d'éléments de contrôle de la chromatine appelés MAR (matrix attachment region). En effet, l'insertion de ces éléments d'ADN à proximité du transgène se traduit généralement par une expression plus élevée et plus stable de celui-ci, en permettant le maintien d'une chromatine dans une configuration active autour du transgène et en empêchant l'inactivation du gène. Dans cette étude, nous avons testé si l'inclusion du MAR 1-68 dans le système transposon piggyBac peut améliorer l'efficacité d'intégration de façon sécuritaire et l'expression à long terme d'un transgène. Le transposon contenant l'élément MAR a été testé dans les cellules CHO, couramment utilisées en biotechnologie, et dans des cellules progénitrices appelées mésoangioblastes, qui peuvent se différencier en cellules musculaires, et qui constituent ainsi des candidats prometteurs pour la thérapie à partir de cellules souches de patients souffrant de myopathie. Nous avons montré que l'addition du MAR 1-68 dans le transposon piggyBac n'interfère pas avec la transposition et permet de maintenir une fréquence élevée d'intégration du transgène dans ces deux types cellulaires. De plus, il semble que cette association mène à une meilleure expression du transgène à partir de peu d'événements d'intégration du transposon. En outre, ces populations enrichies en cellules exprimant de façon stable le transgène ont pu être obtenues sans avoir recours à une pression de sélection. Etant donné que les protocoles de sélection basée sur l'utilisation d'antibiotiques conduisent souvent à un nombre plus élevé de copies intégrées et à la variégation de l'expression du transgène et qu'ils impliquent une longue culture in vitro, cette stratégie pourrait profiter à des applications pour lesquelles on souhaite un faible nombre de copies intégrées et/ou l'utilisation d'antibiotiques n'est pas souhaitable. De plus, la transplantation intramusculaire de mésoangioblastes contenant le transposon dans le muscle tibial antérieur de souris a conduit, après la différentiation de ces cellules in vivo, à une expression constante et étendue du transgène dans les myofibres. Ces résultats indiquent que les vecteurs piggyBac pourraient fournir une approche viable pour assurer un transfert de gènes stables dans le contexte d'un traitement de la dystrophic musculaire de Duchenne.

Combining chromosomal arm status and significantly aberrant genomic locations reveals new cancer subtypes.

Many types of tumors exhibit characteristic chromosomal losses or gains, as well as local amplifications and deletions. Within any given tumor type, sample specific amplifications and deletions are also observed. Typically, a region that is aberrant in more tumors, or whose copy number change is stronger, would be considered as a more promising candidate to be biologically relevant to cancer. We sought for an intuitive method to define such aberrations and prioritize them. We define V, the "volume" associated with an aberration, as the product of three factors: (a) fraction of patients with the aberration, (b) the aberration's length and (c) its amplitude. Our algorithm compares the values of V derived from the real data to a null distribution obtained by permutations, and yields the statistical significance (p-value) of the measured value of V. We detected genetic locations that were significantly aberrant, and combine them with chromosomal arm status (gain/loss) to create a succinct fingerprint of the tumor genome. This genomic fingerprint is used to visualize the tumors, highlighting events that are co-occurring or mutually exclusive. We apply the method on three different public array CGH datasets of Medulloblastoma and Neuroblastoma, and demonstrate its ability to detect chromosomal regions that were known to be altered in the tested cancer types, as well as to suggest new genomic locations to be tested. We identified a potential new subtype of Medulloblastoma, which is analogous to Neuroblastoma type 1.

A genetic risk score combining 32 SNPs is associated with body mass index and improves obesity prediction in people with major depressive disorder.

BACKGROUND: Obesity is strongly associated with major depressive disorder (MDD) and various other diseases. Genome-wide association studies have identified multiple risk loci robustly associated with body mass index (BMI). In this study, we aimed to investigate whether a genetic risk score (GRS) combining multiple BMI risk loci might have utility in prediction of obesity in patients with MDD. METHODS: Linear and logistic regression models were conducted to predict BMI and obesity, respectively, in three independent large case-control studies of major depression (Radiant, GSK-Munich, PsyCoLaus). The analyses were first performed in the whole sample and then separately in depressed cases and controls. An unweighted GRS was calculated by summation of the number of risk alleles. A weighted GRS was calculated as the sum of risk alleles at each locus multiplied by their effect sizes. Receiver operating characteristic (ROC) analysis was used to compare the discriminatory ability of predictors of obesity. RESULTS: In the discovery phase, a total of 2,521 participants (1,895 depressed patients and 626 controls) were included from the Radiant study. Both unweighted and weighted GRS were highly associated with BMI (P <0.001) but explained only a modest amount of variance. Adding 'traditional' risk factors to GRS significantly improved the predictive ability with the area under the curve (AUC) in the ROC analysis, increasing from 0.58 to 0.66 (95% CI, 0.62-0.68; χ(2) = 27.68; P <0.0001). Although there was no formal evidence of interaction between depression status and GRS, there was further improvement in AUC in the ROC analysis when depression status was added to the model (AUC = 0.71; 95% CI, 0.68-0.73; χ(2) = 28.64; P <0.0001). We further found that the GRS accounted for more variance of BMI in depressed patients than in healthy controls. Again, GRS discriminated obesity better in depressed patients compared to healthy controls. We later replicated these analyses in two independent samples (GSK-Munich and PsyCoLaus) and found similar results. CONCLUSIONS: A GRS proved to be a highly significant predictor of obesity in people with MDD but accounted for only modest amount of variance. Nevertheless, as more risk loci are identified, combining a GRS approach with information on non-genetic risk factors could become a useful strategy in identifying MDD patients at higher risk of developing obesity.