Improving power and accuracy of genome-wide association studies via a multi-locus mixed linear model methodology

Genome-wide association studies (GWAS) have been widely used in genetic dissection of complex traits. However, common methods are all based on a fixed-SNP-effect mixed linear model (MLM) and single marker analysis, such as efficient mixed model analysis (EMMA). These methods require Bonferroni correction for multiple tests, which often is too conservative when the number of markers is extremely large. To address this concern, we proposed a random-SNP-effect MLM (RMLM) and a multi-locus RMLM (MRMLM) for GWAS. The RMLM simply treats the SNP-effect as random, but it allows a modified Bonferroni correction to be used to calculate the threshold p value for significance tests. The MRMLM is a multi-locus model including markers selected from the RMLM method with a less stringent selection criterion. Due to the multi-locus nature, no multiple test correction is needed. Simulation studies show that the MRMLM is more powerful in QTN detection and more accurate in QTN effect estimation than the RMLM, which in turn is more powerful and accurate than the EMMA. To demonstrate the new methods, we analyzed six flowering time related traits in Arabidopsis thaliana and detected more genes than previous reported using the EMMA. Therefore, the MRMLM provides an alternative for multi-locus GWAS.

Identification and validation of candidate genes associated with domesticated and improved traits in soybean

Soybean, an important source of vegetable oils and proteins for humans, has undergone significant phenotypic changes during domestication and improvement. However, there is limited knowledge about genes related to these domesticated and improved traits, such as flowering time, seed development, alkaline-salt tolerance, and seed oil content (SOC). In this study, more than 106,000 single nucleotide polymorphisms (SNPs) were identified by restriction site associated DNA sequencing of 14 wild, 153 landrace, and 119 bred soybean accessions, and 198 candidate domestication regions (CDRs) were identified via multiple genetic diversity analyses. Of the 1489 candidate domestication genes (CDGs) within these CDRs, a total of 330 CDGs were related to the above four traits in the domestication, gene ontology (GO) enrichment, gene expression, and pathway analyses. Eighteen, 60, 66, and 10 of the 330 CDGs were significantly associated with the above four traits, respectively. Of 134 traitassociated CDGs, 29 overlapped with previous CDGs, 11 were consistent with candidate genes in previous trait association studies, and 66 were covered by the domesticated and improved quantitative trait loci or their adjacent regions, having six common CDGs, such as one functionally characterized gene Glyma15 g17480 (GmZTL3). Of the 68 seed size (SS) and SOC CDGs, 37 were further confirmed by gene expression analysis. In addition, eight genes were found to be related to artificial selection during modern breeding. Therefore, this study provides an integrated method for efficiently identifying CDGs and valuable information for domestication and genetic research.

Impacts of climate changes on crop physiology and food quality

Carbon emissions related to human activities have been significantly contributing to the elevation of atmospheric [CO(2)] and temperature. More recently, carbon emissions have greatly accelerated, thus much stronger effects on crops are expected. Here, we revise literature data concerning the physiological effects of CO(2) enrichment and temperature rise on crop species. We discuss the main advantages and limitations of the most used CO(2)-enrichment technologies, the Open-Top Chambers (OTCs) and the Free-Air Carbon Enrichment (FACE). Within the conditions expected for the next few years, the physiological responses of crops suggest that they will grow faster, with slight changes in development, such as flowering and fruiting, depending on the species. There is growing evidence suggesting that C(3) crops are likely to produce more harvestable products and that both C(3) and C(4) crops are likely to use less water with rising atmospheric [CO(2)] in the absence of stressful conditions. However, the beneficial direct impact of elevated [CO(2)] on crop yield can be offset by other effects of climate change, such as elevated temperatures and altered patterns of precipitation. Changes in food quality in a warmer, high-CO(2) world are to be expected, e.g., decreased protein and mineral nutrient concentrations, as well as altered lipid composition. We point out that studies related to changes in crop yield and food quality as a consequence of global climatic changes should be priority areas for further studies, particularly because they will be increasingly associated with food security. (c) 2009 Elsevier Ltd. All rights reserved.

Inheritance beyond plain heritability : variance-controlling genes in Arabidopsis thaliana

The phenotypic effect of a gene is normally described by the mean-difference between alternative genotypes. A gene may, however, also influence the phenotype by causing a difference in variance between genotypes. Here, we reanalyze a publicly available Arabidopsis thaliana dataset [1] and show that genetic variance heterogeneity appears to be as common as normal additive effects on a genomewide scale. The study also develops theory to estimate the contributions of variance differences between genotypes to the phenotypic variance, and this is used to show that individual loci can explain more than 20% of the phenotypic variance. Two well-studied systems, cellular control of molybdenum level by the ion-transporter MOT1 and flowering-time regulation by the FRI-FLC expression network, and a novel association for Leaf serration are used to illustrate the contribution of major individual loci, expression pathways, and gene-by-environment interactions to the genetic variance heterogeneity.

Efeito de diferentes períodos de irrigação no desenvolvimento, produção e qualidade de sementes na cultura do milho (Zea mays L.)

O presente trabalho foi realizado em área demonstrativa de irrigação do Departamento de Engenharia Rural da Faculdade de Ciências Agrárias e Veterinárias, da Universidade Estadual Paulista (FCAV/UNESP), Jaboticabal - SP, tendo como objetivo avaliar os efeitos da deficiência hídrica no desenvolvimento da planta, na produção e na qualidade fisiológica de sementes da cultura do milho (Zea mays L.). O delineamento experimental foi o inteiramente casualizado, com os tratamentos em esquema fatorial 2 x 3, com quatro repetições. Os tratamentos consistiram da utilização de sementes de milho híbrido BR201 e DINA-70, com três períodos de irrigação: 1) durante todo o ciclo; 2) após o período vegetativo (após a emissão da 12ª folha), e 3) até 20 dias após o florescimento (antes do período de enchimento dos grãos). Concluiu-se que a deficiência hídrica durante o período vegetativo (irrigação após a emissão da 12ª folha) foi a mais prejudicial à cultura e à produção; essa deficiência hídrica não afetou a qualidade fisiológica das sementes produzidas, e o híbrido DINA-70 apresentou melhores resultados para os parâmetros fisiológicos e de produção que o híbrido BR201.

Adubação nitrogenada de cobertura no feijoeiro de invernoprimavera em três sistemas de cultivo

The aim of this study was to evaluate the nitrogen topdressing influence in common bean irrigated (winter-spring), in the first year of no tillage implementation. The experimental design was split-plot with three replications in randomized blocks. The plots were formed by three types of ground cover, corn-grain, corn-grain intercropped with Brachiaria ruziziensis and only B. ruziziensis. The subplots were formed by five doses of nitrogen topdressing (0, 40, 80, 120 and 160 kg ha(-1)), using urea as nitrogen source. It was determined the dry mass of residue present as ground cover, the full flowering time, the leaf nitrogen content, the 100 grains mass, the grain yield, the processing income, the chemical soil properties and economic analysis of common bean grain yield. It was found the common bean grain productivity in succession to corn-grain was positively influenced by nitrogen fertilization, showing it is economically viable only when given 160 kg ha(-1) of nitrogen and the intercropping corn-grain and B. ruziziensis use is the best option when the common bean is sown in succession.

Liming and quality of guava fruit cultivated in Brazil

An experiment was conducted on guava trees Psidium guajava L. (cv. Paluma) grown in the Experimental Citrus Culture Station of Bebedouro, SP, on dystrophic, acid Typical Hapludox in order to assess the effects of application of increasing lime doses to the soil on the quality of guava fruits on the basis of the physicochemical changes observed in the fruits after harvesting. The treatments consisted of increasing lime doses applied before planting, considering 0, 1.85, 3.79, 5.56 and 7.41 t ha(-1), applied in August 1999. Leaf calcium content was assessed at flowering time. After fruit harvesting, calcium content in the pulp, total weight, transverse diameter, length, pulp weight, % pulp, Brix degrees (degrees Brix), titratable acidity, and fruit ratio were determined. Loss of fruit fresh mass, firmness and color were determined daily during a period of 8 days of storage. Lime application to an acid Red Latosol before guava tree planting did not affect the physical characteristics of the fruits but provided a lower loss of fresh matter and greater fruit firmness when the fruits presented Ca levels close to 0.99 g kg(-1). It is important to conduct new studies of the effects of liming on guava fruit quality under different edaphic-climatic conditions and on different guava tree genotypes. (c) 2005 Elsevier B.V. All rights reserved.

Crescimento, produção e qualidade de frutos da bananeira 'Figo cinza', em Botucatu-SP

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

Crescimento e produção de genótipos de bananeiras em clima subtropical

O presente trabalho teve como objetivo avaliar as características de crescimento e o potencial produtivo de genótipos de bananeira em Botucatu/SP. Foram avaliadas características de crescimento, tais como altura de planta, circunferência do pseudocaule, número de folhas e número de dias entre o florescimento e a colheita. Estas medidas foram realizadas na emissão da inflorescência. Foram mensuradas também as características de produção, como peso do cacho, número de frutos, peso médio dos frutos, produtividade, número de pencas; peso, número, comprimento e diâmetro dos frutos da 2a penca. O delineamento adotado foi o inteiramente casualisado, com 11 tratamentos (genótipos), cinco repetições e duas plantas úteis por parcela experimental. Os genótipos que apresentaram melhor desempenho agronômico, dentro de cada grupo genômico, foram 'Grand Naine'(AAA), 'Thap Maeo' (AAB) e 'Fhia 01' (AAAB).

Correlaçôes fenotípicas entre características de produção e crescimento em genótipos de bananeira

The correlations between the characters seen in experimental trials are generated by genetic and environmental factors and are estimated for the purpose of measuring the change in a character when the selection is practised in another. The objective was to correlate bunch weight with characteristics of growth and production of 4 genomic groups of banana: 'Nanicao-IAC-2001', 'Grand Naine', 'Caipira' and 'Nam' ( AAA); 'Ma a', 'Thap Maeo', 'Prata Ana' and 'Prata Zulu' (AAB), 'Fhia 01', 'Fhia 18', 'Prata Grauda' and 'Maca Tropical' (AAAB) and 'Figo Cinza' (ABB), Botucatu, Brazil. Some growth characteristics were evaluated such as: plant heights, the pseudostem circumference, number of leaves, number of days between planting and flowering, number of days between flowering and harvest and number of days from planting to harvest. These characteristics were measured at the flowering time. The production characteristics such as the bunch weigth, number of fruits, average weigth of the fruits, productivity, number of hands and weight, number, length and diameter of the fruits of the 2(nd) hand. The correlations between the characteristics studied varied for each genotype, but they all showed significant correlation between the bunch weight and the characteristics fruit weigth and productivity. The correlations involving all genotypes were predominantly positive and significant.

Desempenho agronômico de bananeiras micropropagadas em Botucatu-SP

O trabalho teve como objetivo avaliar o desempenho agronômico de cultivares de bananeira 'Prata-anã', 'Maçã' e 'Nanicão', no município de Botucatu-SP. As mudas provenientes de micropropagação foram aclimatadas em estufa durante noventa dias e, posteriormente, plantadas no campo, conforme as recomendações técnicas para a cultura. Foram avaliadas características de crescimento, como número de dias do plantio à colheita, número de folhas ativas, altura de plantas e diâmetro do pseudocaule, medidas na época de emissão da inflorescência. Também foram mensuradas características de produção, entre as quais o número de frutos, diâmetro, comprimento e peso da segunda penca, peso total das pencas e número de frutos por cacho, na época da colheita. Os resultados obtidos evidenciaram que o ciclo cultural médio variou com as cultivares, sendo de 416 dias, contados do plantio à colheita para a cv 'Nanicão', que foi a mais precoce, seguido da 'Prata-anã' (434 dias) e da 'Maçã' (437 dias). As três cultivares apresentaram produtividade estimada no primeiro ciclo (planta-mãe) de 30,56 t.ha-1; 19,50 t.ha-1 e 14,37 t.ha-1, respectivamente, para 'Nanicão', 'Prata-anã' e 'Maçã'. Houve correlação positiva entre algumas características de crescimento e produção.

Produção do arroz em função da adubação com silício e nitrogênio no sistema de sequeiro e irrigado por aspersão

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Influência da borda e do isolamento na fenologia e no sucesso reprodutivo de Anadenanthera Falcata (Benth.) Speg. (Fabaceae) em uma região de cerrado Stricto Sensu, Itirapina, São Paulo

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Caracterização morfológica e atributos de qualidade dos frutos de acessos de bananeira em clima subtropical

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Avaliação de genótipos de bananeira (Musa sp.) em Botucatu -SP

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