RESUMEN
In line with open-source genetics, we report a novel linear regression technique for genome-wide association studies (GWAS), called Open GWAS algoriTHm (OATH). When individual-level data are not available, OATH can not only completely reproduce reported results from an experimental model, but also recover underreported results from other alternative models with a different combination of nuisance parameters using naïve summary statistics (NSS). OATH can also reliably evaluate all reported results in-depth (e.g., p-value variance analysis), as demonstrated for 42 Arabidopsis phenotypes under three magnesium (Mg) conditions. In addition, OATH can be used for consortium-driven genome-wide association meta-analyses (GWAMA), and can greatly improve the flexibility of GWAMA. A prototype of OATH is available in the Genetic Analysis Repository (https://github.com/gc5k/GEAR).
Asunto(s)
Estudio de Asociación del Genoma Completo , Reproducción/genética , Estadística como Asunto , Algoritmos , Arabidopsis/efectos de los fármacos , Arabidopsis/genética , Pueblo Asiatico/genética , Estudios de Cohortes , Simulación por Computador , Sitios Genéticos , Humanos , Magnesio/farmacología , Modelos Genéticos , Polimorfismo de Nucleótido Simple/genética , Carácter Cuantitativo Heredable , Reproducibilidad de los ResultadosRESUMEN
BACKGROUND: Phosphorus (P) is an essential element for plant growth and development but it is often a limiting nutrient in soils. Hence, P acquisition from soil by plant roots is a subject of considerable interest in agriculture, ecology and plant root biology. Root architecture, with its shape and structured development, can be considered as an evolutionary response to scarcity of resources. SCOPE: This review discusses the significance of root architecture development in response to low P availability and its beneficial effects on alleviation of P stress. It also focuses on recent progress in unravelling cellular, physiological and molecular mechanisms in root developmental adaptation to P starvation. The progress in a more detailed understanding of these mechanisms might be used for developing strategies that build upon the observed explorative behaviour of plant roots. CONCLUSIONS: The role of root architecture in alleviation of P stress is well documented. However, this paper describes how plants adjust their root architecture to low-P conditions through inhibition of primary root growth, promotion of lateral root growth, enhancement of root hair development and cluster root formation, which all promote P acquisition by plants. The mechanisms for activating alterations in root architecture in response to P deprivation depend on changes in the localized P concentration, and transport of or sensitivity to growth regulators such as sugars, auxins, ethylene, cytokinins, nitric oxide (NO), reactive oxygen species (ROS) and abscisic acid (ABA). In the process, many genes are activated, which in turn trigger changes in molecular, physiological and cellular processes. As a result, root architecture is modified, allowing plants to adapt effectively to the low-P environment. This review provides a framework for understanding how P deficiency alters root architecture, with a focus on integrated physiological and molecular signalling.
Asunto(s)
Regulación de la Expresión Génica de las Plantas , Fósforo/metabolismo , Desarrollo de la Planta , Raíces de Plantas/crecimiento & desarrollo , Raíces de Plantas/genética , Plantas/genética , Adaptación Fisiológica , Transporte Biológico , Óxido Nítrico , Reguladores del Crecimiento de las Plantas/metabolismo , Raíces de Plantas/anatomía & histología , Raíces de Plantas/metabolismo , Plantas/anatomía & histología , Plantas/metabolismo , Especies Reactivas de Oxígeno/metabolismo , Transducción de SeñalRESUMEN
The increasing concentration of atmospheric CO2 and the nutritional quality of human diets are the two important issues we are facing. At present, the atmospheric CO2 concentration is about 380 micromol mol(-1), and to be reached 550 micromol mol(-1) by 2050. A great deal of researches indicated that the quality of agricultural products is not only determined by inherited genes, but also affected by the crop growth environmental conditions. This paper summarized the common methods adopted at home and abroad for studying the effects of CO2 enrichment on the quality of agricultural products, and reviewed the research advances in evaluating the effects of elevated CO2 on the quality of rice, wheat, soybean, and vegetables. Many experimental results showed that elevated CO2 concentration causes a decrease of protein content in the grains of staple food crops and an overall decreasing trend of trace elements contents in the crops, but improves the quality of vegetable products to some extent. Some issues and future directions regarding the effects of elevated CO2 concentration on the quality of agricultural products were also discussed, based on the present status of related researches.
