Yoshishige Inagaki

Efficient gene targeting by homologous recombination in rice

Modification of genes through homologous recombination, termed gene targeting, is the most direct method to characterize gene function. In higher plants, however, the method is far from a common practice. Here we describe an efficient and reproducible procedure with a strong positive/negative selection for gene targeting in rice, which feeds more than half of the worlds population and is an important model plant. About 1% of selected calli and their regenerated fertile plants were heterozygous at the targeted locus, and only one copy of the selective marker used was found at the targeted site in their genomes. The procedures applicability to other genes will make it feasible to obtain various gene-targeted lines of rice.

Colour-enhancing protein in blue petals

The coloration of blue flowers depends on the production of the appropriate anthocyanin pigments, the presence of metal ions and co-pigments, and the vacuolar pH. An increase in vacuolar pH enhances blue coloration, but little is known about the proteins responsible for raising the vacuolar pH. Here we show that a mutant purple-flowering Japanese morning glory (Ipomoea nil) plant that carries a recessive mutation in the gene encoding a vacuolar Na+/H+-exchanger is unable to increase its vacuolar pH to create the normal bright blue petals.

Isolation of a Suppressor-mutator/Enhancer-like transposable element, Tpn1, from Japanese morning glory bearing variegated flowers.

The Japanese morning glory has an extensive history of genetic studies. Many mutants in the colors and shapes of its flowers and leaves have been isolated since the 17th century, and more than 200 genetic loci have been localized for the 10 linkage groups. They include over 20 mutable loci, several with variegated flower phenotypes. In a line of Japanese morning glory bearing variegated flowers called flecked, a transposable element of 6.4 kb, termed Tpn1, was found within one of the anthocyanin biosynthesis genes encoding dihydroflavonol-4-reductase (DFR). The 6.4-kb element carries 28-bp perfect terminal inverted repeats, the outer 13 bp being identical to those of the maize transposable element Suppressor-mutator/Enhancer. It is flanked by 3-bp direct repeats within the second intron of the DFR gene, 9 bp upstream of the third exon. When somatic and germinal excision occurs, it produces excision sequences characteristic of plant transposable elements. Cosegregation data of the variegated flower phenotype and the DFR gene carrying Tpn1 indicated that the mutable phenotype is due to excision of Tpn1 from the DFR gene. Sequences homologous to Tpn1 are present in multiple copies in the genome of Japanese morning glory.

Genomic organization of the genes encoding dihydroflavonol 4-reductase for flower pigmentation in the Japanese and common morning glories

Genomic DNA segments (approximately 17kb) containing three DFR genes in the Japanese and common morning glories were sequenced. The three DFR genes in both plants were found to be arranged in a tandem array, and all of them comprised six exons with identical intron positions. Their DFR-B genes carrying longer introns than the DFR-A and DFR-C genes were expressed extensively in the young buds of pigmented flowers, and the transcription starting site for the DFR-B mRNA of the Japanese morning glory was determined. The DFR-B gene of the common morning glory was expressed considerably in stems, moderately in sepals and leaves, whereas the DFR-A and DFR-C genes of the same plant were expressed scarcely but significantly in the young flower buds and stems. Several novel mobile element-like sequences of around 200bp were found in the genomic DFR regions. A phylogenetic tree indicated that each DFR gene in the Japanese morning glory is most closely related to the corresponding DFR gene in the common morning glory, and that the DFR-B gene is the most diversified gene among the three DFR genes. These structural and functional features of the DFR genes and their evolutionary implications are discussed.

Trans-activation and stable integration of the maize transposable element Ds cotransfected with the Ac transposase gene in transgenic rice plants

To develop an efficient gene tagging system in rice, a plasmid was constructed carrying a non-autonomous maize Ds element in the untranslated leader sequence of a hygromycin B resistance gene fused with the 35S promoter of cauliflower mosaic virus. This plasmid was cotransfected by electroporation into rice protoplasts together with a plasmid containing the maize Ac transposase gene transcribed from the 35S promoter. Five lines of evidence obtained from the analyses of hygromycin B-resistant calli, regenerated plants and their progeny showed that the introduced Ds was trans-activated by the Ac transposase gene in rice. (1) Cotransfection of the two plasmids is necessary for generation of hygromycin B resistant transformants. (2) Ds excision sites are detected by Southern blot hybridization. (3) Characteristic sequence alterations are found at Ds excision sites. (4) Newly integrated Ds is detected in the rice genome. (5) Generation of 8 by target duplications is observed at the Ds integration sites on the rice chromosomes. Our results also show that Ds can be trans-activated by the transiently expressed Ac transposase at early stages of protoplast culture and integrated stably into the rice genome, while the cotransfected Ac transposase gene is not integrated. Segregation data from such a transgenic rice plant carrying no Ac transposase gene showed that four Ds copies were stably integrated into three different chromosomes, one of which also contained the functional hph gene restored by Ds excision. The results indicate that a dispersed distribution of Ds throughout genomes not bearing the active Ac transposase gene can be achieved by simultaneous transfection with Ds and the Ac transposase gene.

Floricultural Traits and Transposable Elements in the Japanese and Common Morning Gloriesaa

ABSTRACT: The Japanese morning glory has an extensive history of genetic studies and over 200 different spontaneous mutant lines have been described. Of these, we identified that two mutable alleles, flecked and speckled, for flower variegations are caused by integration of transposable elements, belonging to the En/Spm family, into the DFR‐B and CHI genes for flower pigmentation, respectively. The mutable flaked allele of the common morning glory bearing variegated flowers is caused by insertion of a new transposable element, Tip 100, into one of the CHS genes for pigmentation and that Tip 100 belongs to the Ac/Ds family. These results are discussed with regard to spontaneous transposon mutagenesis and generation of floricultural traits of morning glories.

Capture of a genomic HMG domain sequence by the En/Spm-related transposable element Tpn1 in the Japanese morning glory.

Abstract The non-autonomous transposable element Tpn1 from the Japanese morning glory is an En/Spm-related DNA element found in the second intron of the DFR-B gene for flower pigmentation in the mutable line flecked, which shows variegation for flower color. It carries a genomic DNA segment containing at least four exon sequences encoding part of a HMG-box sequence. Spliced hybrid transcripts containing the DFR-B exon(s) and the HMG exons in Tpn1 were detected in the flower buds of the flecked line, and they were polyadenylated within Tpn1. Thus, Tpn1 can be regarded as a specialized transducing transposon carrying a part of the genomic sequence for a HMG box. The possible implications of the finding for evolution are discussed.

Somatic mutations caused by excision of the transposable element, Tpn1, from the DFR gene for pigmentation in sub-epidermal layer of periclinally chimeric flowers of Japanese morning glory and their germinal transmission to their progeny.

Pigmentation in flowers of Japanese morning glory is intense in the epidermal layer, lighter in the subepidermis, and much lighter in the internal tissues; by contrast coloration in stems occurs only in the sub-epidermal layer. The a-3f mutant of Japanese morning glory bears white flowers with normal-colored flecks and sectors, and its variegation also occurs in leaves and stems. The mutable line can produce chimeric flowers pigmented uniformly in the sub-epidermal tissue and variegated in the epidermal layer, and stems of these flowers are also pigmented. Since they give selfed progeny that segregate to give a ratio of three germinal revertants bearing fully colored flowers to one flecked mutant, it has been [OR Imai (1934) has] postulated that somatic mutations in the sub-epidermal layer can be transmitted to the next generation and that the germ cells in the reproductive organs must form from the cells of the sub-epidermal layer. Recently, we found that the 6.4-kb En/Spm-related transposable element, Tpn1, resides within the DFR-B gene for anthocyanin biosynthesis in the mutable a-3f line. To test whether somatic mutations caused by Tpn1 excision from the DFR-B gene in the subepidermis of periclinally chimeric flowers are transmissible to their progeny, we have examined the structure of the DFR-B region in the germinal revertants derived from the chimeric flowers and compared the sequences generated by the somatic excision of Tpn1 in periclinally chimeric flowers with those in their germinal revertants. Our results confirm that somatic mutations caused by Tpn1 excision from the DFR-B gene in the sub-epidermal tissue of chimeric flowers can be transmitted to their progeny, which results in the generation of germinal revertants.

Structural analysis of Tpn1, a transposable element isolated from Japanese morning glory bearing variegated flowers

The 6.4 kb transposable element Tpn1 belonging to the En/Spm family was found within one of the DFR (dihydroflavonol-4-reductase) genes for anthocyanin biosynthesis in a line of Japanese morning glory (Pharbitis nil) bearing variegated flowers. Sequencing of the Tpn1 element revealed that it is 6412 by long and carries 28-bp perfect terminal inverted repeats. Its subterminal repetitive regions, believed to be the cis-acting sequences for transposition, show striking structural features. Twenty-two copies of the 10-bp sequence motif GACAACGGTT can be found as direct or inverted repeats within 650 by of the 5′ end of the element, and 33 copies of the sequence motif lie within 800 by of the 3′ terminus. All these 22 copies of the sequence motif near the 5′ terminus and 30 copies in the 3′ terminal region are arranged as inverted repeats and 3–8 by AT-rich sequences are detected between these inverted repeats. In addition, four copies of 122-bp tandem repeats and six copies of 104-bp tandem repeats are present in the 5′ and 3′ subterminal repetitive regions, respectively. No large open reading frame characteristic of autonomous elements of the En/Spm family can be detected within the element. The results are discussed with respect to heritable changes in flower variegation in this line of Japanese morning glory.

DNA rearrangements at the region of the dihydroflavonol 4-reductase gene for flower pigmentation and incomplete dominance in morning glory carrying the mutable flaked mutation

Abstract The a-3flecked[J] variegated line of Japanese morning glory bearing white flowers with normal-colored flecks and sectors has been shown to carry a 6.4-kb transposable element, Tpn1, inserted within the DFR-B gene, one of the anthocyanin biosynthesis genes encoding dihydroflavonol 4-reductase (DFR). The aflaked[M] variegated line of morning glory also bears white flowers with normal-colored flakes and sectors, and it was shown to carry multiple DNA rearrangements, including insertions of mobile element-like sequences, MELSIP1 and MELSIP2, in its DFR gene region. Unlike the a-3flecked[J] mutation, the mutable aflaked[M] allele exhibited incomplete dominance. Interestingly, not only intensely colored flakes but also white spots and sectors were often observed in lightly colored flowers of morning glory in the heterozygous state A[M]/aflaked[M]. The interspecific F1 hybrids between Japanese morning glory and morning glory carrying both a-3flecked[J]/A-3[M] and A[J]/ aflaked[M] in the heterozygous condition bear lightly colored flowers with intensely colored sectors as well as white flakes. The results clearly demonstrated that the DFR gene in the aflaked[M] line of morning glory is active and complements the DFR-B gene carrying Tpn1 in the a-3flecked[J] line of Japanese morning glory. Interspecific allelic interactions between the mutable aflaked[M] gene of morning glory and the corresponding wild-type A[J] gene of Japanese morning glory resulted in incomplete dominance and the formation of white flakes and sectors. The appearance of the white flakes may be due to a somatic mutation of the A[J] gene.