The Use of RNA-seq Approaches to Identify Genes Involved in Response and Tolerance to Abiotic Stresses in Rice -CFDA 10.310
Plant, Soil and Nutrition Research
Project Number: 8062-21000-036-15
General Cooperative Agreement
Start Date: May 01, 2013
End Date: Jan 14, 2014
The goal of this research is to use RNA seq technologies to study the expression of genes associated with aluminum tolerance in rice. Our preliminary work demonstrates that as a species, rice is capable of growing at Al concentrations that are between 5-15 times higher than that for maize, sorghum, and wheat, leading us to hypothesize that rice may be a source of novel Al tolerance genes. We will use RNA seq on roots of selected genetic variants of rice (Al tolerant and sensitive and from the different rice subpopulations) to search for candidate rice aluminum tolerance genes.
1) Grow different rice genotypes on hydroponic media with or without Al – harvest roots for mRNA isolation.
2) Generate cDNA libraries from mRNA-seq and employ Illumina sequencing.
3) The filtered reads will be aligned to the rice genome using computational programs developed by Dr. Fei (TopHat program).
3) Differentially expressed genes will be identified with DESeq program developed by Dr. Fei.