| genetic variations of aa genome oryza species measured by mite-aflp. | mites (miniature inverted-repeat transposable elements) are the major transposable elements in oryza species. we have applied the mite-aflp technique to study the genetic variation and species relationship in the aa-genome oryza species. high polymorphism was detected within and between species. the genetic variation in the cultivated species, oryza sativa and oryza glaberrima, was comparatively lower than in their ancestral wild species. in comparison between geographical lineages of the aa gen ... | 2003 | 12845436 |
| a comparative study of genetic relationships among the aa-genome oryza species using rapd and ssr markers. | in order to estimate genetic relationships of the aa-genome oryza species, rapd and ssr analyses were performed with 45 accessions, including 13 cultivated varieties (eight oryza sativa and five oryza glaberrima) and 32 wild accessions (nine oryza rufipogon, seven oryza nivara, three oryza glumaepatula, four oryza longistaminata, six oryza barthii, and three oryza meridionalis). a total of 181 clear and repeatable bands were amplified from 27 selected rapd primers, and 101 alleles were detected ... | 2003 | 14504744 |
| evaluation of pcr primers for universal nifh gene targeting and for assessment of transcribed nifh pools in roots of oryza longistaminata with and without low nitrogen input. | the bias of widely used degenerate nifh-specific primer sets was first tested using denaturing gradient gel electrophoresis (dgge), and their application for profiling of complex communities assessed for roots of oryza longistaminata. when primers (p) with mismatches at nondegenerate positions were used on genomic dna of azotobacter vinelandii, which harbors three single divergent nifh genes, template-to-product ratios were highly skewed. in contrast, we obtained no evidence for a large pcr bias ... | 2008 | 18631250 |
| elucidation of xa21-mediated innate immunity. | in the early 1970s, the xa21 gene from the wild rice species oryza longistaminata drew attention of rice breeders because of its broad-spectrum resistance to diverse strains of a serious bacterial disease of rice in asia and africa, called 'bacterial blight disease', caused by the gram-negative bacterium, xanthomonas oryzae pv. oryzae (xoo). in 1995, we isolated the gene controlling this resistance and in 2009 demonstrated that xa21 recognizes a highly conserved peptide, called 'ax21' (activator ... | 2010 | 20590657 |
| global characterization of the root transcriptome of a wild species of rice, oryza longistaminata, by deep sequencing. | oryza longistaminata, an aa genome type (2 n = 24), originates from africa and is closely related to asian cultivated rice (o. sativa l.). it contains various valuable traits with respect to tolerance to biotic and abiotic stress, qtls with agronomically important traits and high ability to use nitrogen efficiently (nue). however, only limited genomic or transcriptomic data of o. longistaminata are currently available. | 2010 | 21159186 |
| identification of rhizome-specific genes by genome-wide differential expression analysis in oryza longistaminata. | rhizomatousness is a key component of perenniality of many grasses that contribute to competitiveness and invasiveness of many noxious grass weeds, but can potentially be used to develop perennial cereal crops for sustainable farmers in hilly areas of tropical asia. oryza longistaminata, a perennial wild rice with strong rhizomes, has been used as the model species for genetic and molecular dissection of rhizome development and in breeding efforts to transfer rhizome-related traits into annual r ... | 2011 | 21261937 |
| comparative proteomics reveals differential induction of both biotic and abiotic stress response associated proteins in rice during xanthomonas oryzae pv. oryzae infection. | xanthomonas oryzae pv. oryzae (xoo) causes bacterial blight disease in rice and brutally affects the yield up to 50 % of total production. here, we report a comparative proteomics analysis of total foliar protein isolated from infected rice leaves of susceptible pusa basmati 1 (pb1) and resistant oryza longistaminata genotypes. two-dimensional gel electrophoresis (2-de) coupled with matrix-assisted laser desorption/ionization time-of-flight (maldi-tof) approaches identified 29 protein spots enco ... | 2015 | 25648443 |
| markers for selection of the rice xa21 disease resistance gene. | six molecular markers were mapped to a 7.4-cm region of rice chromosome 11 containing the xa21 gene, which confers resistance to the pathogen xanthomonas oryzae pv oryzae. three markers, rg103, 248 and 818, co-segregated with xa21 in a population of 1141 plants. multiple copies of all marker loci were present within the region that was introgressed from oryza longistaminata into o. sativa. the marker loci were cloned and primers were designed that defined sequence-tagged sites. physical mapping ... | 1996 | 24162490 |
| the blast algorithms: practical application in molecular cloning, marker-assisted selection (mas) and introgression of wheat. | blast (basic local alignment search) analyses of hordeum chilense rapd markers have shown dna sequence similarities with several plant genes. biologically significant hits were scored for: plastocianin (hordeum vulgare), alpha-gliadin (triticum aestivum), grandel-6 retrotransposon (zea diploperennis), retrofit (gag/pol) copia-like, transposon-like element (oryza longistaminata), copia-like retrotransposon hopscotch polyprotein (gag/pol) (zea mays) and several retrotransposons/retroelements from ... | 2000 | 11092750 |
| convergent evolution of perenniality in rice and sorghum. | annual and perennial habit are two major strategies by which grasses adapt to seasonal environmental change, and these distinguish cultivated cereals from their wild relatives. rhizomatousness, a key trait contributing to perenniality, was investigated by using an f(2) population from a cross between cultivated rice (oryza sativa) and its wild relative, oryza longistaminata. molecular mapping based on a complete simple sequence-repeat map revealed two dominant-complementary genes controlling rhi ... | 0 | 12642667 |
| genetic analysis of a hybrid sterility gene that causes both pollen and embryo sac sterility in hybrids between oryza sativa l. and oryza longistaminata. | oryza longistaminata originates from african wild rice and contains valuable traits conferring tolerance to biotic and abiotic stress. however, interspecific crosses between o. longistaminata and oryza sativa cultivars are hindered by reproductive barriers. to dissect the mechanism of interspecific hybrid sterility, we developed a near-isogenic line (nil) using indica variety rd23 as the recipient parent and o. longistaminata as the donor parent. both pollen and embryo sac semi-sterility were ob ... | 2017 | 28657614 |
| genome and comparative transcriptomics of african wild rice oryza longistaminata provide insights into molecular mechanism of rhizomatousness and self-incompatibility. | | 2015 | 26358679 |
| plant regeneration from leaf and seed-derived calli and suspension cultures of the african perennial wild rice, oryza longistaminata. | plant regeneration from 2-month-old callus cultures derived from immature leaves of 7-day-old aseptic seedlings and mature embryos of the african wild rice oryza longistaminata was achieved at 20% and 100% frequency, respectively. the morphogenic potential of the embryo-derived calluses dropped from 100% at the third subculture to 12.5 % at the 12th subculture. five-month-old morphogenic calluses were used to establish a fast-growing suspension culture which, when plated onto semisolid medium, s ... | 1990 | 24227175 |
| baum: improving genome assembly by adaptive unique mapping and local overlap-layout-consensus approach. | it is highly desirable to assemble genomes of high continuity and consistency at low cost. the current bottleneck of draft genome continuity using the second generation sequencing (sgs) reads is primarily caused by uncertainty among repetitive sequences. even though the single-molecule real-time sequencing technology is very promising to overcome the uncertainty issue, its relatively high cost and error rate add burden on budget or computation. many long-read assemblers take the overlap-layout-c ... | 2018 | 29346504 |
| overcoming the species hybridization barrier by ploidy manipulation in the genus oryza. | in most eudicot and monocot species, interspecific and interploidy crosses generally display abnormalities in the endosperm that are the major cause of a post-zygotic hybridization barrier. in some eudicot species, however, this type of hybridization barrier can be overcome by the manipulation of ploidy levels of one parental species, suggesting that the molecular mechanisms underlying the species hybridization barrier can be circumvented by genome dosage. we previously demonstrated that endospe ... | 2018 | 29271099 |
| differential transcriptome profiling of chilling stress response between shoots and rhizomes of oryza longistaminata using rna sequencing. | rice (oryza sativa) is very sensitive to chilling stress at seedling and reproductive stages, whereas wild rice, o. longistaminata, tolerates non-freezing cold temperatures and has overwintering ability. elucidating the molecular mechanisms of chilling tolerance (ct) in o. longistaminata should thus provide a basis for rice ct improvement through molecular breeding. in this study, high-throughput rna sequencing was performed to profile global transcriptome alterations and crucial genes involved ... | 2017 | 29190752 |
| fine mapping of pi57(t) conferring broad spectrum resistance against magnaporthe oryzae in introgression line il-e1454 derived from oryza longistaminata. | wild species of the genus oryza are excellent gene pools for improvement of agronomic traits of asian cultivated rice. the blast resistance gene pi57(t) in the introgression line il-e1454 derived from oryza longistaminata was previously mapped on rice chromosome 12. inoculation with 322 magnaporthe oryzae isolates collected from 6 countries indicated that pi57(t) conferred broad spectrum resistance against m. oryzae. two mapping populations consisting of 29070 and 10375 f2 plants derived from th ... | 2017 | 29016662 |
| letter to the editor: author response - analysis of rhizome development in oryza longistaminata, a wild rice species. | | 2017 | 28505342 |
| letter to the editor: bud position and carbohydrate play a more significant role than light condition in the developmental transition between rhizome buds and aerial shoot buds of oryza longistaminata. | | 2017 | 28460115 |
| identification of qtls for yield-related traits in rils derived from the cross between plia-1 carrying oryza longistaminata chromosome segments and norin 18 in rice. | to improve rice yield, a wide genetic pool is necessary. it is therefore important to explore wild rice relatives. oryza longistaminata is a distantly related wild rice relative that carries the aa genome. its potential for improving agronomic traits is not well studied. introgression line (plia-1) that carries oryza longistaminata's chromosome segments, showed high performance in yield-related traits under non-fertilized conditions. therefore, to illustrate oryza longistaminata's potential for ... | 2016 | 28163588 |
| analysis of rhizome development in oryza longistaminata, a wild rice species. | vegetative reproduction is a form of asexual propagation in plants. a wide range of plants develop rhizomes, modified stems that grow underground horizontally, as a means of vegetative reproduction. in rhizomatous species, despite their distinct developmental patterns, both rhizomes and aerial shoots derive from axillary buds. therefore, it is of interest to understand the basis of rhizome initiation and development. oryza longistaminata, a wild rice species, develops rhizomes. we analyzed bud i ... | 2016 | 27516415 |
| competitive and allelopathic effects of wild rice accessions (oryza longistaminata) at different growth stages. | the competitive and allelopathic effects of wild rice (oryza longistaminata) accessions on barnyard grass at different growth stages determined by days after sowing (0, 30, 60 and 90 days) were studied in greenhouse pot experiments. wild rice accession rl159 exhibited the greatest height and tillering. the weed suppression rates of wild rice accessions ol and f1 on barnyard grass were significantly higher than for other rice accessions, with the lowest being o. sativa cultivar rd23. the highest ... | 2016 | 29023044 |
| anther development of maize (zea mays) and longstamen rice (oryza longistaminata) revealed by cryo-sem, with foci on locular dehydration and pollen arrangement. | key message: pollen maturation in poaceae. another development has been extensively examined by various imaging tools, including transmission electron microscopy, scanning electron microscopy, and light microscopy, but none is capable of identifying liquid water. cryo-scanning electron microscopy with high-pressure rapid freeze fixation is excellent in preserving structures at cellular level and differentiating gas- versus liquid-filled space, but rarely used in anther study. we applied this tec ... | 2015 | 25666915 |
| a systems-wide comparison of red rice (oryza longistaminata) tissues identifies rhizome specific genes and proteins that are targets for cultivated rice improvement. | the rhizome, the original stem of land plants, enables species to invade new territory and is a critical component of perenniality, especially in grasses. red rice (oryza longistaminata) is a perennial wild rice species with many valuable traits that could be used to improve cultivated rice cultivars, including rhizomatousness, disease resistance and drought tolerance. despite these features, little is known about the molecular mechanisms that contribute to rhizome growth, development and functi ... | 2014 | 24521476 |
| genetic mapping of sterile genes with epistasis in backcross designs. | the mapping of sterile genes is an essential issue, which should be solved for the investigation of sterility mechanism in wide hybridization of plants. however, the methods formerly developed cannot address the problem of mapping sterile loci with epistasis. in this study, we developed a new method to map sterile genes with epistasis in wide hybridizations of plants using a backcross design. the maximum likelihood method was used to estimate the parameters of recombination fractions and effects ... | 2014 | 24105436 |
| tissue-specific transcriptomic profiling of sorghum propinquum using a rice genome array. | sorghum (sorghum bicolor) is one of the world's most important cereal crops. s. propinquum is a perennial wild relative of s. bicolor with well-developed rhizomes. functional genomics analysis of s. propinquum, especially with respect to molecular mechanisms related to rhizome growth and development, can contribute to the development of more sustainable grain, forage, and bioenergy cropping systems. in this study, we used a whole rice genome oligonucleotide microarray to obtain tissue-specific g ... | 2013 | 23536906 |
| 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 o ... | 1998 | 9750262 |
| saturated molecular map of the rice genome based on an interspecific backcross population. | a molecular map has been constructed for the rice genome comprised of 726 markers (mainly restriction fragment length polymorphisms; rflps). the mapping population was derived from a backcross between cultivated rice, oryza sativa, and its wild african relative, oryza longistaminata. the very high level of polymorphism between these species, combined with the use of polymerase chain reaction-amplified cdna libraries, contributed to mapping efficiency. a subset of the probes used in this study wa ... | 1994 | 7896104 |
| phylogenetic relationships of annual and perennial wild rice: probing by direct dna sequencing. | the phylogenetic relationships between asian wild rice strains were analyzed by direct sequencing of pcr-amplified dna fragments. the sequence of three introns located in the phytochrome gene was determined for eight strains of the asian wild rice, oryza rufipogon, and one strain of the related african species, oryza longistaminata. the number of nucleotide substitutions per site between various strains within a single species, o. rufipogon, ranged between 0.0017 and 0.0050, while those between ... | 1991 | 24221388 |