Application of qRT-PCR and RNA-Seq analysis for the identification of housekeeping genes useful for normalization of gene expression values

StrigaQuantitative real-time PCR is a powerful tool for quantifying gene expression, but correct normalization of expression levels requires identification of control genes that have stable expression across tissues and life stages.

Researchers from Institute for Sustainable Agriculture, Spain have evaluated the suitability of six candidate housekeeping genes across key life stages of Striga hermonthica (a root parasitic weed that attacks many of the staple crops in Africa, India and Southeast Asia) from seed conditioning to flower initiation using qRT-PCR and high-throughput cDNA sequencing. Based on gene expression analysis by qRT-PCR and RNA-Seq across heterogeneous Striga life stages, they determined that using the combination of three genes, UBQ1, PP2A and TUB1 provides the best normalization for gene expression throughout the parasitic life cycle. The housekeeping genes characterized here provide robust standards that will facilitate powerful descriptions of parasite gene expression patterns.

  • Fern√°ndez-Aparicio M, Huang K, Wafula EK, Honaas LA, Wickett NJ, Timko MP, Depamphilis CW, Yoder JI, Westwood JH. (2012) Application of qRT-PCR and RNA-Seq analysis for the identification of housekeeping genes useful for normalization of gene expression values during Striga hermonthica development. Mol Biol Rep [Epub ahead of print]. [abstract]