Czechowski et al. reported the first use of microarray data for the identification of superior reference genes.
Among these, we identified one gene (gi45348456) showing homology to Arabidopsis ubiquitin (UBQ9, AT5G37640.1) and another one (Ljwgs_018207.1) showing homology to a regulatory subunit of Protein Phosphatase 2A (PDF1, AT5G37640.7), which has been suggested as a superior reference gene for normalization of gene transcript levels in Arabidopsis [66].
Finally, we added a Polypyrimidine tract-binding protein 1 (PTB1), a SAND family protein, an Elongation factor 1-alpha (EF1α), a DIM1 homolog/YLS8 (DIM1) and a F-box family protein (FBOX) genes, which were considered as superior reference genes for normalizing gene expression in citrus in a previous systematic analysis conducted in our laboratory [ 58] (Additional file 7).
A large-scale study of reference genes in Arabidopsis revealed superior reference genes using Affymetrix microarray data [ 10].
As a result of this evaluation, we recommend 4 non-classical housekeeping genes as superior references for normalization of gene expression measures in different tomato developmental stages, and provide primer sequences whose performance in real-time PCR experiments is demonstrated.
As a result of this evaluation, we recommend the use of GhUBQ14 and GhPP2A1 housekeeping genes as superior references for normalization of gene expression measures in different cotton plant organs; GhACT4 and GhUBQ14 for flower development, GhACT4 and GhFBX6 for the floral organs and GhMZA and GhPTB for fruit development.
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In this way, a superior set of reference genes for rice was identified that are suitable for organ, development and stress based experiments.
