Identification of an active transposon in intact rice plants

Abstract

A transposable element that is active in intact plants has been identified in rice (Oryza sativa L.). The 607-bp element itself, termed nonautonomous DNA-based active rice transposon (nDart), has no coding capacity. It was found inserted in the gene encoding Mg-protoporphyrin IX methyltransferase in a chlorophyll-deficient albino mutant isolated from backcross progeny derived from a cross between wild-type japonica varieties. The nDart has 19-bp terminal inverted repeats (TIRs) and, when mobilized, generates an 8-bp target-site duplication (TSD). At least 13 nDart elements were identified in the genome sequence of the japonica cultivar Nipponbare. Database searches identified larger elements, termed DNA-based active rice transposon (Dart) that contained one ORF for a protein that contains a region with high similarity to the hAT dimerization motif. Dart shares several features with nDart, including identical TIRs, similar subterminal sequences and the generation of an 8-bp TSD. These shared features indicate that the nonautonomous element nDart is an internal deletion derivative of the autonomous element Dart. We conclude that these active transposon systems belong to the hAT superfamily of class II transposons. Because the transposons are active in intact rice plants, they should be useful tools for tagging genes in studies of functional genomics.

Molecular identification of a major quantitative trait locus, qLTG3–1 , controlling low-temperature germinability in rice

“…There are no simple sequence repeat (SSR) markers showing polymorphisms available in the target region because the two parents are genetically closely related. We sequenced the target regions of both Hayamasari and Italica Livorno by direct sequencing of both strands of PCR products using a BigDye Terminator v3.1 cycle sequencing kit (Applied Biosystems) (33). Fourteen polymorphisms including SSR, single nucleotide polymorphisms, and indels were detected and six of these were used for high-resolution mapping.…”

Multiple introgression events surrounding the Hd1 flowering-time gene in cultivated rice, Oryza sativa L.

“…DNA extraction, PCR methods, and sequencing were performed as described previously (Fujino et al 2004(Fujino et al , 2005. The provided seeds were sown without propagation.…”

Transposition and target preferences of an active nonautonomous DNA transposon nDart1 and its relatives belonging to the hAT superfamily in rice

“…The results indicate that transposition tagging of Tos17 activated by tissue culture occupies only a small fraction of various causes of somaclonal variation. While endogenous active DNA transposons, which are free from somaclonal variation because no tissue culture is involved in generating insertion mutants, have been extensively used for gene tagging in maize, snapdragon, petunia, and morning glories (May and Martienssen 2003;Chopra et al 2006), only a few active endogenous DNA transposons, mPing, nDart1, dTok, and nDaiZ, have been identified in rice (Nakazaki et al 2003;Fujino et al 2005;Moon et al 2006;Naito et al 2006;Tsugane et al 2006;Nishimura et al 2008;Shimatani et al 2009;Huang et al 2009). Of these active nonautonomous DNA elements, nDart1 appears to be more suitable than the others for transposon tagging in rice because their transposition can be controlled under natural growth conditions, i.e., the transposition of nDart1 can be induced by crossing with a line containing an active autonomous aDart1 element and stabilized by segregating aDart1 (Tsugane et al 2006;Nishimura et al 2008;Shimatani et al 2009).…”

“…The integration of 0.6-kb nDart1 elements in the nDart1-3 subgroup of the hAT superfamily into the 5 0 -untranslated region (5 0 -UTR) of the OsClpP5 gene, the initiation codon region of the MgPIX MT gene, and the GID1/Thl gene exon 2 confer mutable virescent, albino, and dwarf phenotypes, respectively (Maekawa et al 1999;Fujino et al 2005;Tsugane et al 2006). Among these actively transposed nDart1 elements, nDart1 recovered from the OsClpP5 and GID1/Thl genes in the mutable pylv (pale-yellow-leaf variegated) line displaying pale-yellow leaves with dark-green sectors in the seedlings and its derivative plant, respectively, is named nDart1-0 ( Fig.…”