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The gene Os03g0742900 which encodes Oryza sativa indoleacetic acid 13(OsIAA13) is involved in auxin signaling and controls the expression of genes that are required for lateral root initiation in rice[1].

Annotated Information


A rice gain-of-function mutant, Osiaa13, contains a single amino acid substitution (G to A, which resulted in a single amino acid substitution, glycine (G) to serine (S), in the core sequence in domain II of OsIAA13 required for the degradation of the OsIAA13 protein). The Osiaa13 mutant displayed typical auxin-related phenotypes: the number of lateral roots was significantly reduced and the root gravitropic response was defective. Osiaa13 mutants also exhibited altered GUS staining controlled by the DR5 promoter in lateral root initiation sites. Furthermore, expression levels of several genes that might be associated with lateral root initiation were altered in Osiaa13[1].

Figure 1.JPG

Figure 1 (A, B) Two-week-old wild-type Taichung 65 (A) and mutant (B) seedlings. Scale bars = 5 cm. (C, D) Lateral roots in 2-week-old wild-type (C) and mutant (D). Scale bars = 1 mm. (E, F) Root hairs in 2-week-old wild-type (E) and mutant (F). Scale bars = 1 mm. (G) Root tip angles of wild-type and mutant. Seedlings were grown vertically and then rotated 90◦ for 24 h. (H, I) Root tip of ProDR5:GUS-introduced wild-type (H) and mutant (I). Scale bars = 200 μm. (J, K) Lateral root initiation sites of ProDR5:GUS-introduced wild-type (J) and mutant (K). Scale bars = 200 μm. (L, M) Cross sections through the nodes of ProDR5:GUS-introduced wild-type (L) and mutant (M) at crown root initiation sites. Scale bars = 200 μm.

Figure 2.JPG

Figure 2 Gene isolation and complementation test. (A) High-resolution linkage and physiological map of the OsIAA13 locus. The vertical bars represent molecular markers, and the numbers of recombinant plants are indicated below the linkage map. (B) Structure of the OsIAA13 gene. Black boxes and horizontal lines indicate exons and each domain of the IAA protein, respectively.wild-type containing the ProOsIAA13:Osiaa13 construct (C), Osiaa13 containing the empty vector (D), and wild-type containing the empty vector (E) are shown on the left. Magnifications of crown roots in each transgenic plant are shown in the right. Scale bars = 5 mm.


Comparison of the expression levels of candidate genes between wild-type and Osiaa13 plants revealed that 7 genes are downregulated and 2 genes are upregulated in Osiaa13. The expression levels of 7 genes (Os03g0659700, Os07g0669500,Os09g0531600, Os06g0697000, Os07g0539400, Os12g0577700,and Os03g0399800) were downregulated, and those of 2 genes (Os04g0445100 and Os08g0280200) were upregulated in Osiaa13.

Figure 3.JPG

Figure 3 Gene expressions related to lateral root initiation. Changes in the expression levels of 21 genes in Osiaa13. Vertical bars indicate the expression levels of Osiaa13 relative to that of the wild-type, considering the expression level of the wild-type to be 100%. The genes that are downregulated (<0.7-fold) and upregulated (>1.4-fold) in Osiaa13 are indicated by bars colored dark gray and light gray, respectively.


OsIAA13 shares high sequence similarity with OsIAA11 and OsIAA30 in rice, and with AXR2/IAA7, SLR/IAA14, IAA16, and AXR3/IAA17 in Arabidopsis[2]. It has been reported that lateral root initiation is inhibited in a SLR/IAA14 gain-of-function mutant, and in ARF7 and ARF19 loss-of-function mutants; the latter proteins interact with IAA14/SLR[3,4,5]. The gain-of-function mutant Osiaa11 showed a similar phenotype to Osiaa13: the lateral root number of Osiaa11 was reduced because of a defect in LRP initiation but the crown root number was not reduced [6]. Examination of the RiceXPro database revealed that OsIAA13, OsIAA11, and OsIAA30 show similar gene expression patterns indicating that the function of OsIAA30 might be redundant with OsIAA13 and OsIAA11 in lateral root initiation. Taken together, OsIAA13, OsIAA11, and OsIAA30 may play an important role in lateral root formation but not in crown root formation.

Labs working on this gene

Yoshiaki Inukaia, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan


1. Yuka Kitomi;Hiroki Inahashi;Hinako Takehisa;Yutaka Sato;Yoshiaki Inukai, OsIAA13-mediated auxin signaling is involved in lateral root initiation in rice, Plant Science, 2012, 190: 116-122

2. M. Jain, N. Kaur, R. Garg, J.K. Thakur, A.K. Tyagi, J.P. Khurana, Structure expression analysis of early auxin-responsive Aux/IAA gene family in rice (Oryza sativa), Functional and Integrative Genomics 6 (2006) 47–59.

3. H. Fukaki, S. Tameda, H. Masuda, M. Tasaka, Lateral root formation is blocked by a gain-of-function mutation in the SOLITARY-ROOT/IAA14 gene of Arabidopsis, Plant Journal 29 (2002) 153–168.

4. B. Hughes, A. Lui, D. Nguyen, C. Onodera, H. Quach, A. Smith, G. Yu, A. Theologis, Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: Unique and overlapping functions of ARF7 and ARF19, Plant Cell 17 (2005) 444–463.

5. J.C. Wilmoth, S. Wang, S.B. Tiwari, A.D. Joshi, G. Hagen, T.J. Guilfoyle, J.M. Alonso, J.R. Ecker, J.W. Reed, NPH4/ARF7 and ARF19 promote leaf expansion and auxininduced lateral root formation, Plant Journal 43 (2005) 118–130

6. Z.X. Zhu, Y. Liu, S.J. Liu, C.Z. Mao, Y.R. Wu, P. Wu, A gain-of-function mutation in OsIAA11 affects lateral root development in rice, Molecular Plant 5 (2012) 154–161.

Structured Information