Database mining to identify salinity tolerance genes in rice (Oryza sativa, L.) [electronic resource].

Includes reference.

Data mining is the process of identifying patterns and relationships in data that often are not obvious in large, complex data sets. As such, DNA microarrays generate huge amounts of data of the expression profiles of thousands of genes. A variety of visualization and data mining techniques have been developed in the recent years to help the biologists find interesting relationships in microarray data. The increasing role of public databases of model organisms and bioinformatics in data mining presents a new opportunity as well as a challenge to researchers to develop more focused molecular tools for gene discovery and deployment. Abiotic stress is a major limiting factor in agricultural crop production in many countries. The major abiotic stresses of economic importance include drought, cold, heat, salinity, soil mineral deficiency, and toxicity. Salinity is usually exacerbated by intensive irrigation. World wide, crop production is affected by salinity on nearly 50% of all irrigated land. Approximately 10 million hectares are not being used for agricultural production due to salinity problems. To limit the effect of salt in plant productivity, amelioration and utilization of salt affected soils are needed. Two approaches are used to solve the problem: by using technical approaches (water and soil management) and biological approaches. Among species, rice (Oryza sativa) may play a major role because of its role as the second most consumed cereal not only in the world but also in Egypt. Since the genome of rice became completely sequenced, rice is increasingly becoming the model plant for cereals. As a step towards the characterization of genes that contribute to combating salinity stress, ESTs libraries of rice (Oryza sativa) roots treated with 150 mM NaCl for different time series and data mining techniques have been utilized to discover genes and proteins relationship in salt tolerant public dataset and gene expression microarray datasets. This analysis has identified novel genes specifically effective against salinity; cDNA libraries that have been established for Oryza sativa L. 1,418 ESTs generated with RNA from stressed rice, In addition 1,106 ESTs from unstressed rice. ESTs libraries of Rice (Oryza sativa) roots treated with 150 mM Nacl for different time series that ranged from 1 hour, 3 hours, 6 hours, 24 hours and 1 week after salt shock.

Summary in Arabic.

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