3 Biotech

, 8:383 | Cite as

Genes encoding membrane proteins showed stable expression in rice under aerobic condition: novel set of reference genes for expression studies

  • Amol S. Phule
  • Kalyani M. Barbadikar
  • M. S. Madhav
  • P. Senguttuvel
  • M. B. B. Prasad Babu
  • P. Ananda KumarEmail author
Original Article


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.


Aerobic Anaerobic Gene expression qRT-PCR Reference gene Rice 



Quantitative real-time polymerase chain reaction


Cycle threshold


Coefficient of variation


Days after germination


Deeper rooting 1


Expressed protein


Membrane protein

PI stage

Panicle initiation stage


Standard deviation


Stability value


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.

Author contributions

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.

Supplementary material

13205_2018_1406_MOESM1_ESM.docx (658 kb)
Supplementary material 1 (DOCX 657 KB)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Amol S. Phule
    • 1
    • 2
  • Kalyani M. Barbadikar
    • 1
  • M. S. Madhav
    • 1
  • P. Senguttuvel
    • 1
  • M. B. B. Prasad Babu
    • 1
  • P. Ananda Kumar
    • 1
    Email author
  1. 1.Biotechnology DivisionICAR-Indian Institute of Rice ResearchHyderabadIndia
  2. 2.Institute of BiotechnologyProfessor Jayashankar Telangana State Agricultural UniversityHyderabadIndia

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