Functional & Integrative Genomics

, Volume 6, Issue 1, pp 47–59 | Cite as

Structure and expression analysis of early auxin-responsive Aux/IAA gene family in rice (Oryza sativa)

  • Mukesh Jain
  • Navneet Kaur
  • Rohini Garg
  • Jitendra K. Thakur
  • Akhilesh K. Tyagi
  • Jitendra P. KhuranaEmail author
Original Paper


Auxin exerts pleiotropic effects on plant growth and development by regulating the expression of early auxin-responsive genes of auxin/indoleacetic acid (Aux/IAA), small auxin-up RNA, and GH3 classes. These genes have been studied extensively in dicots like soybean and Arabidopsis. We had earlier characterized a cDNA of the first monocot member of Aux/IAA family from rice. The achievement of the large scale rice genome sequencing combined with the availability of full-length cDNA sequences from Knowledge-based Oryza Molecular Biological Encyclopedia provided us the opportunity to draw up the first comprehensive list of Aux/IAA genes in a monocot. By screening the available databases, we have identified 31 Aux/IAA genes having high sequence identity within the conserved domains I, II, III, and IV. The genomic organization as well as chromosomal location of all the Oryza sativa indoleacetic acid (OsIAA) genes is reported. The rice Aux/IAA proteins can be classified in two groups (A and B) on the basis of their phylogenetic relationship with Arabidopsis Aux/IAA proteins. An evolutionary pattern of the rice Aux/IAA genes has been discussed by analyzing their structure (exon/intron organization) and duplications. Interestingly, the duplication of rice Aux/IAA genes was found to be associated with chromosomal block duplication events in rice. The in-silico analysis has been complemented with real-time polymerase chain reaction analysis to quantify transcript levels of all Aux/IAA family members. OsIAA genes showed differential and overlapping organ-specific expression patterns in light- and dark-grown seedlings/plants. Although auxin enhanced the transcript abundance of most of the OsIAA genes, the effect was more pronounced on OsIAA9, 14, 19, 20, 24, and 31. These results provide a foundation for future studies on elucidating the precise role of rice Aux/IAA genes in early steps of auxin signal transduction.


Aux/IAA Auxin Phylogenetic analysis Oryza sativa (rice) Real-time PCR 



MJ acknowledges the award of Senior Research Fellowship from the Council of Scientific and Industrial Research, New Delhi. This research work was financially supported by the Department of Biotechnology, Government of India, and the University Grants Commission, New Delhi. We gratefully acknowledge the KOME, TAIR, TIGR, and the IRGSP database resources for availability of detailed sequence information on rice and Arabidopsis.

Supplementary material

10142_2005_5_MOESM1_ESM.pdf (9 kb)
Table S1 Primer sequences for real-time PCR expression analysis (PDF 9 kb)
10142_2005_5_MOESM2_ESM.pdf (6 kb)
Table S2 Phenotypes of the Tos17 insertion mutants of rice Aux/IAA genes (PDF 6 kb)
10142_2005_5_MOESM3_ESM.pdf (30 kb)
Fig. S1 Multiple alignments of the full_length rice and Arabidopsis Aux/IAA proteins obtained with ClustalX and manual correction. Conserved residues (present in more than 50% of aligned sequences) in the domains I to IV are highlighted in gray boxes. Amino acids considered as conserved are: (K and R; D and E; I, L and V). Gaps (marked with dashes) have been introduced to maximize the alignments. Conserved domains are underlined and indicated by Roman numerals (PDF 30 kb)


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Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  • Mukesh Jain
    • 1
  • Navneet Kaur
    • 1
  • Rohini Garg
    • 1
  • Jitendra K. Thakur
    • 1
  • Akhilesh K. Tyagi
    • 1
  • Jitendra P. Khurana
    • 1
    Email author
  1. 1.Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular BiologyUniversity of Delhi South CampusNew DelhiIndia

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