Os04g0619300

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Annotated Information

Function

Low temperatures during the booting stage reduce rice yields by causing cold-induced male sterility[1]. Ctb1 is a QTL for cold tolerance, which is located in the introgression on chromosome 4[2]. Researches mapped Ctb1 to a 17-kb region containing two genes that encode an F-box protein and a ser/thr protein kinase. Both genes were cloned from a cold-tolerant variety, Norin-PL8, and introduced into a cold-sensitive variety, Hokkai241, and a cold-sensitive line, BT4-74-8. The cold tolerance of T2 and T3 progenies was assessed by measuring the degree of spikelet fertility in plants treated with cool water irrigation (19◦C, 25 cm) or cool air (12◦C, 4 days). The results indicated that the F-box protein gene confers cold tolerance. Cold tolerance is associated with greater anther length, which is one of major factors in cold tolerance at the booting stage. Ctb-1 expressed cold tolerance by producing a large anther. The transgenic plants had longer anthers than non-transformed controls. The F-box protein encoded by Ctb1 interact with a subunit of the E3 ubiquitin ligase, Skp1, suggesting that an ubiquitin–proteasome pathway is involved in cold tolerance at the booting stage[1].

Table. 1 Cold tolerance, heading date and anther length of the near-isogenic lines(NILs) and parental varieties[2]

Fig. 1. Relation between cold tolerance and anther length shown in Table 1. Circles represent the NILs: open circles represent the NILs without either Ctb-1or Ctb-2, and closed circles represent the NILs with Ctb-1and/or Ctb-2. Open and closed triangles represent Kirara397 and Norin-PL8, respectively[2]

GO assignment(s): GO:0003674 GO:0005634 GO:0008150

Expression

Fig. 2 RT-PCR and structural analysis of the Ctb1 candidate genes. (a) Expression of genes encoding F-box protein (FB) and a ser/thr protein kinase(PK) in mature leaves (L) and young panicles (YP) from a cold sensitive variety Kirara397 (K) and a cold-tolerant variety Norin-PL8 (N). ACTIN gene was used as a reference. (b) Diagrams of DNA fragments containing the FB and PK genes cloned from Norin-PL8 genomic DNA. Black rectangles, black triangles, and open triangles indicate putative exons, initiation codons, and stop codons, respectively[1].

Sequence analyses indicated no polymorphism between Norin-PL8 and Kirara397 in the coding regions but several polymorphisms (mostly single nucleotide polymorphisms) in the 5’ upstream regions of both F-box protein (FB) and a ser/thr protein kinase(PK). Comparing the expression of the genes in Norin-PL8 and Kirara397 by RT-PCR analysis, PK was expressed in mature leaves and young panicles. By contrast, FB was expressed preferentially in young panicles, suggesting that FB was a more likely candidate to be Ctb1. No differences were observed in expression levels between Norin-PL8 and Kirara397[1].

Knowledge Extension

Rice is a staple crop cultivated worldwide. However, since it is a cold-sensitive plant that evolved in tropical and subtropical areas, rice yields are greatly reduced under low temperature conditions. One of the factors reducing rice yields is cold-induced male sterility (CIMS). In CIMS, the growth stage that is sensitive to cold is the booting stage, especially the young microspore stage just after meiosis[3]. Low temperatures at the young microspore stage cause the degeneration of microspores and hypertrophy of tapetal cells[4].

Evolution

K.Saito et al[2] concluded that there are at least two QTLs for cold tolerance in the introgression on chromosome 4 of rice, and tentatively designated as Ctb-1 and Ctb-2.

Labs working on this gene

Natl Agr Res Ctr Hokkaido Reg, Hitsujigaoka 1, Sapporo, Hokkaido 0628555, Japan

Univ Florida, IFAS, Ctr Citrus Res & Educ, Lake Alfred, FL 33850 USA

N Carolina State Univ, Dept Bot, Raleigh, NC 27695 USA

Structured Information

Gene Name	Os04g0619300
Description	Cyclin-like F-box domain containing protein
Version	NM_001060432.1 GI:115460593 GeneID:4337020
Length	3063 bp
Definition	Oryza sativa Japonica Group Os04g0619300, complete gene.
Source	Oryza sativa Japonica Group ORGANISM Oryza sativa Japonica Group Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Ehrhartoideae; Oryzeae; Oryza.
Chromosome	Chromosome 4
Location	Chromosome 4:31857495..31860557
Sequence Coding Region	31858937..31860304
Expression	GEO Profiles:Os04g0619300
Genome Context	<gbrowseImage1> name=NC_008397:31857495..31860557 source=RiceChromosome04 preset=GeneLocation </gbrowseImage1>
Gene Structure	<gbrowseImage2> name=NC_008397:31857495..31860557 source=RiceChromosome04 preset=GeneLocation </gbrowseImage2>
Coding Sequence	<cdnaseq>atggaagatttacaagattgtgactgcaaaagccttgttgctgttcctggttctgtggttctgcacctctttaggctgtttaatcagcaggataattcctggcagaagtacacattagcctactttcttttggtcaggaatgagtacttctctagggattcaaggaagcattcagatgggaagaaccaacttcttgactgctgtgatgattcagaattagatttggatgtgctgtatgctgatttggatagtaaagaactggagcttaagttgcagaaacctgttgtcaagactcaatcaaaaggtgactcaagtgccagtggatcaaatgattgcttctttcctggccttcacgacgacctggctcaggactgccttgcttgggcgagcagatcagactacccatcgctttcttgtttgaataagaagttcaatttgttaatcaacagcgggtatctgtacagactgagaagaaaatatggcattgttgaacactgggtgtatctagcgtgtagcttgatgccctgggaagcatttgatccttcacgcaagcgatggatgaggctcccaagaatgccatgcgacgagtgcttctcttgtgcagacaaggaatcgcttgccgtcgggacacaactgcttgtgtttggccgtgaatatacaggtcttgctatttggatgtacaatttactggcccgtggttggtcccgatgcactccaatgaacctgcctcgctgcctctttgcctcaggaagctttggtgagattgctattgttgctggtgggtgtgataagaatggacaggtgctgaaatctgccgagctgtacaattcagagactggtcattgggagactttgccagacatgaacttgccgaggaggctctcatctggtttcttcatggatggaaagttttatgtcattgggggtgtgtcaagtcagagggattctttgacttgtggagaggaatacaatcttgaaacaaggacatggagaagaatacatgatatgtaccctggagggactagtgcctctcaatctcctcccctagttgctgttgtgaataatcagctttatgcagctgatcaggcaacaaatgtggtaaagaagtacgacaaaggaaataacacctggaacatagtgaagccattgccagtcagagctgactcttccaatggttggggcctagctttcaaggcatgtggtgatagattgcttgttattggtggccatagagtaccccgtggtgaagtaatattgctgcattcttggtgccctgaagatgggaatggtggtgctgactgggaagtgctctcggtgaaggagcgtgctggtgtattcgtttataactgcgcaataatggggtgctga</cdnaseq>
Protein Sequence	<aaseq>MEDLQDCDCKSLVAVPGSVVLHLFRLFNQQDNSWQKYTLAYFLL VRNEYFSRDSRKHSDGKNQLLDCCDDSELDLDVLYADLDSKELELKLQKPVVKTQSKG DSSASGSNDCFFPGLHDDLAQDCLAWASRSDYPSLSCLNKKFNLLINSGYLYRLRRKY GIVEHWVYLACSLMPWEAFDPSRKRWMRLPRMPCDECFSCADKESLAVGTQLLVFGRE YTGLAIWMYNLLARGWSRCTPMNLPRCLFASGSFGEIAIVAGGCDKNGQVLKSAELYN SETGHWETLPDMNLPRRLSSGFFMDGKFYVIGGVSSQRDSLTCGEEYNLETRTWRRIH DMYPGGTSASQSPPLVAVVNNQLYAADQATNVVKKYDKGNNTWNIVKPLPVRADSSNG WGLAFKACGDRLLVIGGHRVPRGEVILLHSWCPEDGNGGADWEVLSVKERAGVFVYNC AIMGC</aaseq>
Gene Sequence	<dnaseqindica>1443..2810#gctctccatgccctccccgtctcactgacggtggtcccaccgccccacgctccccccccgtgggccccgttcgtcggcgaccgaccgctagctccggcgaccccctccccgccgacgagatccggccgtctccggtgagctccccccccccactctctctcctccccggcgcgcggcgcgttgtcccacgagaaacccgcgtaaccgctctcctctcttgcttccttgtggcccgtgcgccaacgcgcaggttttcttggagccgctcgtcgtggctggggtggcgccggggggaatggaggcggccggcgctcgcgcgggcggtggcggccgggatctcgccggcggcgcgcctcggtgaggtcaggatgtggctcaattctctcgtttggttgcgaaggtctttctgttctttttttctctctttttgtttggtgagtgcttgagctgaagtcgtggctcgtagatttagaggaaagttaattctgttttgttgtgagttagtggttggtgaattagttggggaaaacgtctgcattttttttctgtttggttcagagcgagaaaaattcgagatttttggagagctttgtgtcatggagagcagcaaccagatgtggccgtttcttttgcttgcggatgtttctttttttttgggtgagaatagagaggtttttttgcttgcattctgcaaatcttggggttattttctgttttgctggattttcctttttgttaggatagataattagttgtcgtcttccgtgtgaattggtcaggtcagatagccaccttagaggttatttttttcttgtgttgaatccaaatctagaactagcagatgatagtagtaatgtactagccggtgctttggtacaaagtctaattattcctctgttttagatgaaacttgatggtagaaatgttttggatataatttgtttcttgaggcaaatgcttttttggatcaagttggctaagaagcagaaaccagtttggatgcccaggctagcagaatcagccatgtaggcaaatatttttttgttggtatcaacaataaaaaatgattgcatatgattactaacggaagatttggaatcgttggtcttagtggtacaaaattttagttgtttacttgattctgaatacgccaaagctgggggaaatatatatttttccatcaaatcaactctgaagatttttttagtgaaataaatgtacctattaagacgaacatgcctagatgagtccattgtttaactctgtagtggtatctgagctaaaattatgtatattgtttgctctgttcttgatccagaaatttagtgcatttcaaatacgctgtgctcattttgctatttatctcaaaatattttccagatgtgatctgtgatctgtccaacctttgtgtactcgggctcattccacagttaacaaaaaagatggaagatttacaagattgtgactgcaaaagccttgttgctgttcctggttctgtggttctgcacctctttaggctgtttaatcagcaggataattcctggcagaagtacacattagcctactttcttttggtcaggaatgagtacttctctagggattcaaggaagcattcagatgggaagaaccaacttcttgactgctgtgatgattcagaattagatttggatgtgctgtatgctgatttggatagtaaagaactggagcttaagttgcagaaacctgttgtcaagactcaatcaaaaggtgactcaagtgccagtggatcaaatgattgcttctttcctggccttcacgacgacctggctcaggactgccttgcttgggcgagcagatcagactacccatcgctttcttgtttgaataagaagttcaatttgttaatcaacagcgggtatctgtacagactgagaagaaaatatggcattgttgaacactgggtgtatctagcgtgtagcttgatgccctgggaagcatttgatccttcacgcaagcgatggatgaggctcccaagaatgccatgcgacgagtgcttctcttgtgcagacaaggaatcgcttgccgtcgggacacaactgcttgtgtttggccgtgaatatacaggtcttgctatttggatgtacaatttactggcccgtggttggtcccgatgcactccaatgaacctgcctcgctgcctctttgcctcaggaagctttggtgagattgctattgttgctggtgggtgtgataagaatggacaggtgctgaaatctgccgagctgtacaattcagagactggtcattgggagactttgccagacatgaacttgccgaggaggctctcatctggtttcttcatggatggaaagttttatgtcattgggggtgtgtcaagtcagagggattctttgacttgtggagaggaatacaatcttgaaacaaggacatggagaagaatacatgatatgtaccctggagggactagtgcctctcaatctcctcccctagttgctgttgtgaataatcagctttatgcagctgatcaggcaacaaatgtggtaaagaagtacgacaaaggaaataacacctggaacatagtgaagccattgccagtcagagctgactcttccaatggttggggcctagctttcaaggcatgtggtgatagattgcttgttattggtggccatagagtaccccgtggtgaagtaatattgctgcattcttggtgccctgaagatgggaatggtggtgctgactgggaagtgctctcggtgaaggagcgtgctggtgtattcgtttataactgcgcaataatggggtgctgaattacatttctttcggtataatccgtatatgcctcttgtttagcaacccacccatttcttgctgctgcttagctaccccctataatgacctgtaattcagaaaaatgacaccccccttttcgtggagctctcaatgaaatgtttgggagagagcatagagcattcagttcagtttacctggaacttcttttaactcgttcaaaatttgttcttcttgtccagtatgaaatttatgcagtattctttattcatc</dnaseqindica>
External Link(s)	NCBI Gene:Os04g0619300, RefSeq:Os04g0619300