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qLTG3–1 is a key regulator of low-temperature germinability in rice.

Annotated Information


qLTG3–1 ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.[1]

Based on the results of Genome-wide analysis, a hypothetical model of the role of qLTG3-1 in seed germination is proposed. qLTG3-1 has a role in the up-regulation of genes involved in phytoalexin biosynthesis and PBZ1, which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, PBZ1, and PBZ1-inducible genes of a putative phenylalanine ammonia-lyase (PAL) and COMT, might induce PCD. Therefore, qLTG3-1 may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)[2]

Figure.1 Proposed hypothetical model of the role of qLTG3-1 in seed germination.[2]

Gene and Protein structure

qLTG3–1 consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A)

Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)

Figure.2 the strucrure of qLTG3–1 and qLTG3–1.[1]


The expression of qLTG3–1 is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the qLTG3–1 expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of qLTG3–1 were strongly associated with the promotion of seed germination.(Figure .3)

The analysis of qLTG3–1 promoter activity in transgenic rice plants carrying an qLTG3–1::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)

The coding region of qLTG3–1 fused to modified green fluorescent protein determines the subcellular localization of the qLTG3–1 protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)

Figure.3 Expression of qLTG3–1. (A) Tissue specificity. (B) Germination.[1]
Figure.4 (A-B)GUS expression and subcellular localization. (C–E)Subcellular localization of GFP in onion epidermal cells expressing a qLTG3–1-GFP fusion as shown by confocal microscopy.[1]

Labs working on this gene

Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan

QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan


  1. 1.0 1.1 1.2 1.3 Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano. Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.
  2. 2.0 2.1 Cite error: Invalid <ref> tag; no text was provided for refs named ref2

3.Kenji Fujino;Yasuyuki Matsuda.Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice Cryobiology, 2009, 59(3): 387-388.

4.Kenji Fujino;Hiroshi Sekiguchi Origins of functional nucleotide polymorphisms in a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice Plant Molecular Biology, 2011, 75(1-2): 1-10.

Structured Information