From RiceWiki
Jump to: navigation, search

The rice Os03g0149100 was reported as crown rootless1 (OsCrl1)[1] and Adventitious rootless1(OsARL1) [2] respectively in 2005 by researchers from Japan and China. (in chronological order)

Annotated Information

Figure 1. Mutant VS. WT(from reference) [1].
Figure 2. Mutant VS. WT(from reference) [2].


OsCrl1 encodes an ASYMMETRIC LEAVES2 (AS2) / LATERAL ORGAN BOUNDARIES (LOB) domain transcription factor which acts as a positive regulator for crown and lateral root formation in rice [1][2]. As an auxin-responsive factor involved in auxin-mediated cell dedifferentiation, OsCrl1 can promote the initial cell division in the pericycle cells adjacent to the peripheral vascular cylinder in the stem[2].Manipulation of the regulation of this gene (and its homologs in other crops) has great potential for increasing the ability of crops to absorb water and nutrients from the soil through improvement in their root architecture, which is required for achieving high yields[2]. OsCrl1 genes is well known as early auxin-response genes,an essential gene for crown root formation in rice.[3]



1. Mutation reported by Yoshiaki Inukai et al. [1]:

  • Two-week-old OsCrl1 mutants had normal seminal root development but did not form any crown roots, whereas wild-type plants formed several crown roots at the same developmental stage(Figures 1A and 1B).
  • In the wild type, crown root primordia (arrow in Figure 1C) formed on the outside, adjacent to the peripheral vascular cylinder (arrowhead in Figure 1C) of the stem. By contrast, OsCrl1 did not produce any crown root primordia(Figure 1D).
  • The number of lateral roots from a seminal root in OsCrl1 also decreased to;70% of that in the wild type (Figures 1A and 1B), indicating that OsCrl1 is involved in both crown root and lateral root formation.
  • At later stages of development, wild type can produce significant crown root, while the OsCrl1 only produce crown root occasionally (Figures 1E and 1F).

2. Mutation reported by Hongjia Liu et al. [2]:

  • In contrast to a normal rice plant, OsArl1 mutant seedlings lack adventitious roots (Figure 2a).
  • Due to its lack of essential root structure, the homozygous OsArl1 mutant cannot grow to maturity (Figure 2b), although at the seedling stage no significant difference was observed in shoot morphology between the wild type and the mutant.
  • Cross sections at the base of the stem of 5-day-old seedlings revealed that the formation of adventitious primordium is impaired in the OsArl1 mutant (Figure 2c,d).
  • Adventitious root primordia were induced at the fourth node of 8-week-old wild-type plants by submergence for 24 h (Figure 1e), but were not induced in the OsArl1 mutant (Figure 2f).

Interestingly,constitutive expression of the OsIAA4 and OsCrl1 genes was observed in the OsWRKY31 overexpressor lines of T2 progenies and their expressions were not increased further by the treatment of the overexpressor plants with IBA (Figure 8C). These results suggest that OsWRKY31 may be involved in auxin signaling. We also found that the induction of OsWRKY31 was even faster than the expression of auxin-inducible OsIAA4 and OsCrl1 genes following treatment of rice seedlings with IBA (Figure 8B).The early auxin response of OsWRKY31 expression suggests that OsWRKY31 is a member of the early auxin response family. However, constitutive expression of auxin-inducible OsIAA4 and OsCrl1 genes in OsWRKY31 overexpressor lines did not exhibit corresponding phenotypes,such as more or longer lateral roots (Figure 8)[3]. An explanation for this dissimilarity may be that the constitutive expression in some of the rice Aux/IAA genes,such as OsIAA4, might lead to the stabilization of these proteins at some specific stage or condition of development.In support of this idea, some SLR1/IAA14 overexpressing Arabidopsis plants exhibit an slr (solitary-root)-1-like phenotype, which was interpreted by Fukaki et al. to be the accumulation of IAA14 proteins in these 35S::IAA14 plants at the CaMV35S promoter, which is constitutively active in most plant tissues. Furthermore, even though rice Crl1 is a positive regulator of crown and lateral root formation, its expression has been found to be insufficient to initiate crown or lateral root development.[3]

Expression Pattern

  • Semi-quantitative RT-PCR analysis by Yoshiaki Inukai et al. shows that OsCrl1 transcripts accumulated in unelongating basal internodes. And the localized expression of OsCrl1 in stems and roots corresponds well to the areas of crown and lateral root initiation, confirming that 'OsCrl1 is involved in the initiation of these root systems[1].
  • The RNA in situ hybridization analysis by Hongjia Liu et al. showed that this gene is expressed at the beginning of primordium formation[2].
  • The expression of OsCrl1 was induced within 1 h and increased dramatically until 3 h after IAA treatment, then it gradually decreased. This suggests that OsCrl1 is a member of the early auxin response family[1].
Figure 3. An unrooted dendogram of the AS2/LOB family proteins in Arabidopsis, maize and rice(from reference) [1].

The primers used were 5´-agc aac gtg tcc aag ctg ct-3´ and 5´-tgt agc cgc cgt acc cta at-3´ for OsCrl1 (AB200234).[3]

Subcellular localization

  • The subcellular localization analysis by Hongjia Liu et al. suggests that OsCrl1 is a nuclear protein, which is expressed in nuclei[2].


Yoshiaki Inukai et al. made a BLAST search by using the AS2/LOB domain sequence of OsCrl1. They found that some AS2/LOB proteins in Arabidopsis, maize (Zea mays), and rice are more similar to OsCrl1 than to other AS2/LOB proteins (Figure 3)[1].

Knowledge Extension

  • The LATERAL ORGAN BOUNDARIES DOMAIN (LBD) genes define a large, plant-specific family of largely unknown function[4][5][6]. The LOB protein encodes a conserved approximately 100-amino acid domain which contains a motif resembling a zinc finger and another similar to a leucine zipper[4][5]. However, both motifs have atypical spacing and until now, the biochemical function of the LOB domain has not been defined, although proteins containing LOB domains have been assumed to be transcription factors[4].The discovery of OsCrl1 implies that some members of the LOB domain gene family may play an important role in organ development in plants[2].
  • In Arabidopsis, LOB defines a subgroup of LBD genes that also includes LBD10/ASL2, LBD25/ASL3, LBD36/ASL1, and AS2/LBD6[5][6]. Among this subgroup, AS2 (ASYMMETRIC LEAVES2) is the only gene with clearly defined functions. AS2 is required to prevent expression of the class I KNOX homeobox genes BREVIPEDICELLUS (BP), KNAT2, and KNAT6 in the leaf. AS2 is expressed on the adaxial side of lateral organs and misexpression leads to the formation of adaxialized leaves implicating AS2 in adaxial cell fate specification[6].

Labs working on this gene

  • Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
  • Field Production Science Center, University of Tokyo, Nishi-Tokyo, Tokyo 188-0002, Japan
  • State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou 310029,China
  • Department of Biology and Environmental Science, School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
  • Department of Crop Physiology, Tamil Nadu Agricultural University, Coimbatore 641003, Tamil Nadu, India
  • University of Agriculture Faisalabad, Sub-Campus Depalpur, Okara 38040, Pakistan
  • Graduate School of Agricultural and Life Sciences,University of Tokyo, Tokyo 113-8657
  • Faculty of Agriculture, Kagawa University, Miki, Kagawa 761-0795, Japan
  • 1State Key Laboratory of Agrobiotechnology, Department of Plant Pathology, China Agricultural University,Yuanmingyuan West Road 2, Beijing 100094,China


  1. 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 Inukai Y, Sakamoto T, Ueguchi-Tanaka M, et al. Crown rootless1, which is essential for crown root formation in rice, is a target of an AUXIN RESPONSE FACTOR in auxin signaling[J]. The Plant Cell Online, 2005, 17(5): 1387-1396.
  2. 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 Liu H, Wang S, Yu X, et al. ARL1, a LOB‐domain protein required for adventitious root formation in rice[J]. The Plant Journal, 2005, 43(1): 47-56.
  3. 3.0 3.1 3.2 3.3 Juan Zhang, Youliang Peng, Zejian Guo.Constitutive expression of pathogen-inducible OsWRKY31 enhances disease resistance and affects root growth and auxin response in transgenic rice plants,Cell Research ,2008, 18:508-521.
  4. 4.0 4.1 4.2 Husbands A, Bell E M, Shuai B, et al. LATERAL ORGAN BOUNDARIES defines a new family of DNA-binding transcription factors and can interact with specific bHLH proteins[J]. Nucleic Acids Research, 2007, 35(19): 6663-6671.
  5. 5.0 5.1 5.2 Shuai B, Reynaga-Peña C G, Springer P S. The lateral organ boundaries gene defines a novel, plant-specific gene family[J]. Plant physiology, 2002, 129(2): 747-761.
  6. 6.0 6.1 6.2 Mangeon A, Bell E M, Lin W, et al. Misregulation of the LOB domain gene DDA1 suggests possible functions in auxin signalling and photomorphogenesis[J]. Journal of experimental botany, 2011, 62(1): 221-233.