Genes encoding membrane proteins showed stable expression in rice under aerobic condition: novel set of reference genes for expression studies
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A set of reference genes expressing stably under aerobic and anaerobic conditions in rice is essential to execute omics studies relating to aerobic adaptations. Stability of expression of ten rice reference genes, viz. Actin, eEF-1a, eIF-5C, Exp1, Exp2, Memp, SKP1A, TF-SUI1, TPH, and UBQ5 was validated across six experimental sets in shoot and root tissues at seedling, tillering, and panicle initiation stages. Comprehensively, Memp (Membrane protein), TPH (Tumor protein homolog), and Exp1 (Expressed protein) were revealed as the most stable set with acceptable M and V value according to the gold standards of qRT-PCR using various algorithms/tools. The identified set of reference genes was validated using root trait genes, which showed concurrence with the functional expression patterns in the aerobic and anaerobic adapted cultivars. The Memp (Membrane protein), TPH (Tumor protein homolog), and Exp1 (Expressed protein) genes are the most stable reference genes across the root and shoot at various developmental stages under aerobic and anaerobic conditions in rice. This is the first study for accurate and reliable relative gene expression analysis in rice grown in aerobic and anaerobic conditions.
KeywordsAerobic Anaerobic Gene expression qRT-PCR Reference gene Rice
Quantitative real-time polymerase chain reaction
Coefficient of variation
Days after germination
Deeper rooting 1
- PI stage
Panicle initiation stage
Tumor protein homolog
The authors are thankful to Director, ICAR-IIRR (Institute Research Council Project Codes ABR/CI/BT/12 and ABR/CI/BT/15) and Director, Institute of Biotechnology, PJTSAU for providing necessary facilities for research. Amol S. Phule acknowledges the University Grant Commission (UGC), New Delhi, India for providing National Fellowship for furnishing the doctoral programme.
PAK, MSM, and KMB conceived, planned, and designed study. ASP, KMB, PS, and MBB conducted experiments. KMB and ASP analyzed the data and wrote the manuscript. PAK and MSM critically edited manuscript.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
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