Micron, a microsatellite-targeting transposable element in the rice genome.

We have isolated a new family of mobile elements, Micron, which occur within microsatellites dispersed throughout the rice (Oryza sativa) genome. The first of these segments, Micron 001, was found in a microsatellite consisting of a (TA)n sequence upstream of the rice phytochrome A (phyA) gene. PCR analysis of related rice species suggests that Micron 001 integrated into this microsatellite locus prior to the divergence of the two wild species O. rufipogon and O. barthii from a common ancestor. Micron elements are short (393-bp), possess subterminal inverted repeats and the single strands have the potential to form stable secondary structures via several internal repeats. Aside from the absence of terminal inverted repeats, these characteristics resemble those of MITEs (Miniature Inverted-Repeat Transposable Elements). We estimate that 100-200 copies of Micron-related sequences are present in the rice nuclear genome, while the chloroplast and mitochondrial genomes lack this sequence. Nineteen homologs of Micron 001 exhibited extremely high nucleotide sequence conservation (greater than 90%), suggesting a recent spread of Micron elements within the genus Oryza. Surprisingly, nucleotide sequence alignments showed that all of the Micron elements are flanked on both sides by microsatellite sequence consisting mainly of (TA)n. Twenty-three elements were mapped to seven separate chromosomes. Therefore Micron elements form a family of dispersed, highly conserved repeats. This is the first report of a transposable element that targets microsatellite loci.

Human serum immunoglobulin G3 subclass bound preferentially to asialo-, agalactoimmunoglobulin A1/Sepharose.

As we reported before, exoglycosidase treatment of human serum IgA1 changed it to a sticky molecule. In order to examine the presence of the specific binding protein to the sticky IgA1 in human serum, IgA1, asialo-IgA1 (IgA1-S) and asialo-, agalacto-IgA1 (IgA1-SG)/Sepharose column chromatography of normal human serum was carried out. Purified hinge glycopeptide (HGP33) prepared from IgA1 was used for the preparation of HGP/Sepharose. A portion of the serum protein was bound to those columns and eluted with the buffer containing 1.0 M NaCl. About four times the amount of protein was eluted from the IgA1-SG/Sepharose column than that from IgA1/Sepharose. Most of the eluted protein was IgG, and the IgG1 and IgG3 subclasses but neither IgG2 nor IgG4 was dominant. Under the lower salt concentration, a portion of IgG was also bound to the HGP-SG/Sepharose column. The obtained results coincide well with the previous report of the co-present of IgG1 and IgG3 with deposited IgA1 in IgA nephropathy patients (Aucouturier, P., et al. (1989) Clin. Immunol. Immunopathol. 51, 338-347). Thus, the results solved the question of why the IgG3 was co-present with deposited IgA1 in IgA nephropathy patients.

Chemical induction of disease resistance in rice is correlated with the expression of a gene encoding a nucleotide binding site and leucine-rich repeats.

Probenazole (3-allyloxy-1,2-benzisothiazole-1,1-dioxide) is an agricultural chemical primarily used to prevent rice blast disease. Probenazole-treated rice acquires resistance to blast fungus irrespective of the rice variety. The chemical is applied prophylactically, and is thought to induce or bolster endogenous plant defenses. However, the mechanisms underlying this effect have not been established. To understand the mode of the chemical's action, we screened for novel probenazole-responsive genes in rice by means of differential display and identified a candidate gene, RPR1. RPR1 contains a nucleotide binding site and leucine-rich repeats, thus sharing structural similarity with known disease resistance genes. The expression of RPR1 in rice can be up-regulated by treatment with chemical inducers of systemic acquired resistance (SAR) and by inoculation with pathogens. RPR1-related sequences in rice varieties seem to be varied in sequence and/or expression, indicating that RPR1 itself is not a crucial factor for induced resistance in rice. However, Southern blot analysis revealed the existence of homologous sequences in all varieties examined. While the role of RPR1 has yet to be clarified, this is the first report of the identification of a member of this gene class and its induction during the systemic expression of induced disease resistance.

Origin and evolution of twin microsatellites in the genus Oryza.

An ancestral sequence of twin microsatellites of rice was found in a wild species. Twin microsatellite loci, RM20A and RM20B, were located on separate regions of chromosomes 11 and 12, which had been duplicated during rice evolution. These twin microsatellites showed different allele diversities in A genome species of the genus Oryza. This difference was caused by repetition of a simple sequence consisting of (TAA)n. Oryza longistaminata contains a short poly(A) sequence in this region instead of the poly(TAA) found in other species. A sequence comparison of RM20-related amplicons suggested that the poly(A)-containing sequence is the ancestral sequence of the RM20A and RM20B microsatellites. A simple base substitution in the poly(A) sequence may have produced the longer microsatellite motif (TAA). This mutation may have occurred on one of the chromosomes of a hypothetical ancestor of the A genome species before duplication of the chromosome segments.

Highly polymorphic microsatellites of rice consist of AT repeats, and a classification of closely related cultivars with these microsatellite loci.

Microsatellites consisting of AT repeats are highly polymorphic in rice genomes and can be used to distinguish between even closely related japonica cultivars in Japan. Polymorphisms of 20 microsatellite loci were determined using 59 japonica cultivars, including both domestic and modern Japanese cultivars. Although the polymorphisms of these 20 microsatellite loci indicated that the Japanese cultivars were genetically quite similar, microsatellites consisting of AT repeats showed high gene diversity even among such closely related cultivars. Combinations of these hypervariable microsatellites can be employed to classify individual cultivars, since the microsatellites were stable within each cultivar. An identification system based on these highly polymorphic microsatellites could be used to maintain the purity of rice seeds by eliminating contamination. A parentage diagnosis using 17 polymorphic microsatellite loci clearly demonstrated that plants which carried desired chromosome regions had been selected in breeding programs. Thus, these hypervariable microsatellites consisting of AT repeats should promote the selection of plants which carry desired chromosomes from genetically similar parents. Backcrossing could also help to eliminate unnecessary chromosome regions with microsatellite polymorphisms at an early stage in breeding programs.

A codominant DNA marker closely linked to the rice nuclear restorer gene, RF-1, identified with inter-SSR fingerprinting.

A new molecular marker (OSRRf) closely linked to the nuclear restorer gene (Rf-1) for fertility in rice has been found. The Rf-1 gene is essential for hybrid rice seed production. A PCR-fingerprinting technique using simple sequence repeats (SSRs) was applied to compare two near-isogenic lines with (MTC-10R) or without (MTC-10A) the Rf-1 gene. Of 76 inter-SSR primers tested, only one primer, (AG)8YC, generated polymorphisms. The tetranucleotide repeats generating polymorphisms were found within each amplicon. the genetic distance between OSRRf and Rf-1 was 3.7 +/- 1.1 cM. As in the case of a codominant marker, this marker will be applied not only to breeding both restorer lines and maintainer lines, but also to the purity management of hybrid rice seeds.

Microsatellite DNA markers for rice chromosomes.

We found 369 complete microsatellites, of which (CGG/GCC)n was the most frequent, in 11 798 rice sequences in the database. Of these microsatellites, 35 out of 45 could be successfully converted into microsatellite DNA markers using sequence information in their flanking regions. Thus, the time and labor used to develop new microsatellite DNA markers could be saved by using these published sequences. Twenty eight polymorphic markers between Asominori (japonica) and IR24 (indica) have been correctly mapped on the rice genome and microsatellites appear to be randomly distributed in the rice chromosomes. Integration of these markers with the published microsatellite DNA markers showed that about 35% of the rice chromosomes were covered by the 56 microsatellite DNA markers. These microsatellites were hypervariable and were easily to assay by PCR; they were distributed to all chromosomes and therefore, one can easily select plants carrying desired chromosome regions using these microsatellite DNA markers. Thus, microsatellite maps should aid the development of new breeds of rice saving time, labor, and money.