| genetic differentiation of wild relatives of rice as assessed by rflp analysis. | to study genetic diversity and relationships of wild relatives of rice, 58 accessions of oryza rufipogon, oryza nivara, oryza sativa f. spontanea and the cultivated oryza sativa, representing a wide range of their distribution, were analyzed using the restriction fragment length polymorphism (rflp) technique. all 30-used rflp probes detected polymorphisms among the oryza accessions, with an average of 3.8 polymorphic fragments per probe. considerable genetic diversity was scored among the oryza ... | 2002 | 12582876 |
| genetic diversity in the northernmost oryza rufipogon populations estimated by ssr markers. | to estimate genetic diversity of the residual northern populations of oryza rufipogon, a total of 232 individuals from six populations were analyzed using microsatellites (ssrs). the o. rufipogon populations with different status included three from dongxiang (jiangxi province) and three from chaling (hunan province) in china. the 23 rice ssr primer pairs selected from the ricegenes database detected a total of 115 alleles, indicating that all the ssr loci were polymorphic in this study. the tot ... | 2003 | 12920513 |
| gene flow from cultivated rice (oryza sativa) to its weedy and wild relatives. | transgene escape through gene flow from genetically modified (gm) crops to their wild relative species may potentially cause environmental biosafety problems. the aim of this study was to assess the extent of gene flow between cultivated rice and two of its close relatives under field conditions. | 2004 | 14602665 |
| fitness estimation through performance comparison of f1 hybrids with their parental species oryza rufipogon and o. sativa. | introgression of crop genes into populations of wild relatives has important implications for germplasm conservation as well as for the persistence of novel transgenes in wild populations. studies of hybrid fitness can be used to evaluate the potential for introgression to occur following episodes of interspecific hybridization. | 2004 | 14724120 |
| [identification of quantitative trait loci controlling plant height and days to heading from yuanjiang common wild rice (oryza rufipogon griff.)]. | an advanced backcross strategy was used to identify quantitative trait loci (qtls) associated with plant height and days to heading in the bc3f2 population derived from an accession of common wild rice (oryza rufipogon griff.) from yuanjiang in yunnan province of china, as the donor, and an elite indica cultivar "teqing", as the recipient. based on analyses of 116 ssr markers distributed throughout the rice genome and by using single-point analysis, four putative qtls derived from o. rufipogon w ... | 2004 | 15552048 |
| phylogenetic relationships among a-genome species of the genus oryza revealed by intron sequences of four nuclear genes. | the a-genome group in oryza consists of eight diploid species and is distributed world-wide. here we reconstructed the phylogeny among the a-genome species based on sequences of nuclear genes and mite (miniature inverted-repeat transposable elements) insertions. thirty-seven accessions representing two cultivated and six wild species from the a-genome group were sampled. introns of four nuclear single-copy genes on different chromosomes were sequenced and analysed by both maximum parsimony (mp) ... | 2005 | 15948847 |
| nucleotide polymorphism in the adh1 locus region of the wild rice oryza rufipogon. | nucleotide variation in the alcohol dehydrogenase (adh1) locus region of the wild rice oryza rufipogon and its related species was analysed to clarify the maintenance mechanism of dna variation in oryza species. the estimated nucleotide diversity in the adh1 locus region of o. rufipogon was 0.002, which was one of the lowest values detected in nuclear loci of plant species investigated so far. tests of neutrality detected significantly negative deviation from the neutral mutation model for the c ... | 2004 | 15480535 |
| distribution of fertility-restorer genes for wild-abortive and honglian cms lines of rice in the aa genome species of genus oryza. | rice (oryza sativa) is one of the most important cereal plants in the world. wild-abortive (wa) and honglian (hl) cytoplasmic male sterility (cms) have been used extensively in the production of hybrid seeds. although a variable number of fertility-restorer genes (rf) for wa and hl-cms have been identified in various cultivars, information on rf in oryza species with the aa-genome is sparse. therefore the distribution and heredity of rf for wa and hl-cms in wild rice species of oryza with the aa ... | 2005 | 15987696 |
| population structure and conservation genetics of wild rice oryza rufipogon (poaceae): a region-wide perspective from microsatellite variation. | oryza rufipogon griff. is the most agriculturally important but seriously endangered wild rice species. to better estimate how genetic structure can be used to obtained a conservation perspective of the species, genetic variability at six polymorphic microsatellite dna loci was examined. high levels of genetic variability were detected at six loci in 1245 individuals of 47 natural populations covering most of the species' range in china (overall rs = 3.0740, ho = 0.2290, hs = 0.6700). partitioni ... | 2004 | 15078440 |
| comparison of population genetic structures of common wild rice (oryza rufipogon griff.), as revealed by analyses of quantitative traits, allozymes, and rflps. | we investigated genetic diversity among and within natural populations of asian common wild rice, oryza rufipogon, from three different classes of data: quantitative traits, allozymes, and restriction fragment length polymorphisms (rflps). the seven populations examined showed polymorphism to varying degrees. the amount of intrapopulation variability appeared to be influenced not only by breeding system but also by the evolutionary history of each population. interpopulation differentiation was ... | 2004 | 14997180 |
| polymorphism at the esterase isozyme locus est10 associated with phylogenetic differentiation in rice. | a new esterase isozyme locus, est10, with 6 alleles including the null form, has been found in rice by using polyacrylamide gel electrophoresis. thirty f(2) populations of all possible combinations between 5 different band morphs were studied. the segregation pattern indicated that bands 1, 2, 3, 4, and the null form (0) were allelic with each other. the alleles of est10 were distributed at different frequencies among different varietal groups of rice and also between cultivated rice and its wil ... | 2003 | 14532707 |
| 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 |
| microsatellite analysis of genetic diversity and population genetic structure of a wild rice (oryza rufipogon griff.) in china. | genetic diversity and population genetic structure of natural oryza rufipogon populations in china were studied based on ten microsatellite loci. for a total of 237 individuals of 12 populations collected from four regions, a moderate to high level of genetic diversity was observed at population levels with the number of alleles per locus ( a) ranging from 2 to 18 (average 10.6), and polymorphic loci ( p) from 40.0% to 100% (average 83.3%). the observed heterozygosity ( h(o)) varied from 0.163 t ... | 2003 | 12845446 |
| mapping qtls influencing rice floral morphology using recombinant inbred lines derived from a cross between oryza sativa l. and oryza rufipogon griff. | to understand the genetic basis of floral traits associated with the mating system in rice, we analyzed pistil, stamen and glume traits using a recombinant inbred line population, derived from a cross between an asian cultivated rice ( oryza sativa l.), pei-kuh, and a wild rice ( oryza rufipogon griff.), w1944. quantitative trait loci (qtls) affecting floral morphology were detected by composite interval mapping using a linkage map constructed using 147 markers, mostly rflps. a total of 7, 4, 14 ... | 2003 | 12845437 |
| 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 |
| assessment of population genetic structure in common wild rice oryza rufipogon griff. using microsatellite and allozyme markers. | the genetic structure of five natural populations of common wild rice oryza rufipogon griff. from china, was investigated with 21 microsatellite loci and compared to estimates of genetic diversity and genetic differentiation detected by 22 allozyme loci. microsatellite loci, as expected, have much higher levels of genetic diversity (mean values of a = 3.1, p = 73.3%, ho = 0.358 and he = 0.345) than allozyme loci (mean values of a = 1.2, p = 12.7%, ho = 0.020 and he = 0.030). genetic differentiat ... | 2002 | 12582886 |
| genetic differentiation for nuclear, mitochondrial and chloroplast genomes in common wild rice ( oryza rufipogon griff.) and cultivated rice ( oryza sativa l.). | the genetic differentiation of nuclear, mitochondrial (mt) and chloroplast (cp) genomes was investigated by southern and pcr analysis using 75 varieties of cultivated rice ( oryza sativa l.) and 118 strains of common wild rice (cwr, oryza rufipogon griff.) from ten countries of asia. the distinguishing differences between the indica and japonica cultivars were detected both in the nuclear genome and the cytoplasmic genome, confirming that the indica-japonica differentiation is of major importanc ... | 2002 | 12582589 |
| polyphyletic origin of cultivated rice: based on the interspersion pattern of sines. | the wild rice species oryza rufipogon with wide intraspecific variation is thought to be the progenitor of the cultivated rice species oryza sativa with two ecotypes, japonica and indica. to determine the origin of cultivated rice, subfamily members of the rice retroposon p-sine1, which show insertion polymorphism in the o. sativa -o. rufipogon population, were identified and used to "bar code" each of 101 cultivated and wild rice strains based on the presence or absence of the p-sine1 members a ... | 2003 | 12519908 |
| phylogeography of asian wild rice, oryza rufipogon, reveals multiple independent domestications of cultivated rice, oryza sativa. | cultivated rice, oryza sativa l., represents the world's most important staple food crop, feeding more than half of the human population. despite this essential role in world agriculture, the history of cultivated rice's domestication from its wild ancestor, oryza rufipogon, remains unclear. in this study, dna sequence variation in three gene regions is examined in a phylogeographic approach to investigate the domestication of cultivated rice. results indicate that india and indochina may repres ... | 2006 | 16766658 |
| search for and analysis of single nucleotide polymorphisms (snps) in rice (oryza sativa, oryza rufipogon) and establishment of snp markers. | we searched for snps in 417 regions distributed throughout the genome of three oryza sativa ssp. japonica cultivars, two indica cultivars, and a wild rice (o. rufipogon). we found 2800 snps in approximately 250,000 aligned bases for an average of one snp every 89 bp, or one snp every 232 bp between two randomly selected strains. graphic representation of the frequency of snps along each chromosome showed uneven distribution of polymorphism-rich and -poor regions, but little obvious association w ... | 2002 | 12465716 |
| identification of quantitative trait loci controlling drought tolerance at seedling stage in chinese dongxiang common wild rice (oryza rufipogon griff.). | common wild rice (oryza rufipogon griff.) is the ancestor of cultivated rice (o. sativa l.), which has a greater genetic diversity and important traits that remain to be employed in cultivated rice. in this study, a set of introgression lines (bc4f5 and/or bc4f6) carrying various introgressed segments from common wild rice, collected from dongxiang county, jiangxi province, china, in the background of an indica (o. sativa l. ssp. indica) cultivar, guichao 2, was used. a total of 12 drought-relat ... | 2006 | 16800386 |
| molecular mapping of a novel gene, grh5, conferring resistance to green rice leafhopper (nephotettix cincticeps uhler) in rice, oryza sativa l. | the green rice leafhopper (grh), nephotettix cincticeps uhler, is one of the most serious insect pests affecting cultivated rice (oryza sativa l.) in temperate regions of east asia. an accession of the wild rice species, oryza rufipogon griff. (w1962), was found to be highly resistant to grh by an antibiosis test. to understand the genetic basis of the grh resistance, a bc1f1 population derived from a cross between a susceptible japonica variety, taichung 65 (t65), and a highly resistant accessi ... | 2006 | 16835766 |
| [qtl analysis of anther length and ratio of stigma exsertion, two key traits of classification for cultivated rice (oryza sativa l.) and common wild rice (o. rufipogon griff.)]. | a genetic map including 120 rflp markers covering 1418.2 cm has been constructed using a bc1 population derived from a cross between common wild rice (oryza rufipogon griff.) from dongxiang, jiangxi province, china, and an elite indica variety guichao 2. the linkage orders and genetic distances of markers in this map are consistent with the map constructed by rice genome program of japan except the markers of short arm of chromosome 1. the qtls analysis of anther length and ratio of stigma exser ... | 2001 | 11554349 |
| clonality in wild rice (oryza rufipogon, poaceae) and its implications for conservation management. | correlations were examined between habitat characters and clonal structures determined by the rapd (random amplified polymorphic dna) assay in five populations of oryza rufipogon in china. nine of 175 decameric primers were used in the study because they reproducibly amplified polymorphisms. the extent of clonality together with the clonal and sexual reproductive strategies varied greatly among the five populations and correlated with the habitats where they occur. the populations under serious ... | 2001 | 11410470 |
| multilocus analysis of nucleotide variation of oryza sativa and its wild relatives: severe bottleneck during domestication of rice. | varying degrees of reduction of genetic diversity in crops relative to their wild progenitors occurred during the process of domestication. such information, however, has not been available for the asian cultivated rice (oryza sativa) despite its importance as a staple food and a model organism. to reveal levels and patterns of nucleotide diversity and to elucidate the genetic relationship and demographic history of o. sativa and its close relatives (oryza rufipogon and oryza nivara), we investi ... | 2007 | 17218640 |
| genetic erosion in northern marginal population of the common wild rice oryza rufipogon griff. and its conservation, revealed by the change of population genetic structure. | in order to monitor genetic erosion within the northern marginal population of common wild rice oryza rufipogon griff. from dongxiang, jiangxi province, china, allozyme diversity encoded by 22 loci was analyzed electrophoretically from all the existing subpopulations in 1980, 1985 and 1994. the sample collected from the nine large subpopulations in 1980 showed the highest levels of genetic diversity (a = 1.27, p = 18.20%, ho = 0.042 and he = 0.049) and a slight deviation from hardy-weinberg expe ... | 2000 | 11206853 |
| [a study of the genetic diversity of common wild rice (o. rufipogon griff.) and cultivated rice (o. sativa l.) by rflp analysis]. | the genetic diversity of cultivated rice and common wild rice from 10 countries in asia were evaluated by rflp analysis using 44 probes of single copy. we used the parameters such as proportion of polymorphic loci (p), average number of alleles per locus (a), average number genotype per locus (ng), degree of heterozygate per locus (ho) and average gene diversity (hs) showing genetic diversity. it is indicated that the common wild rice from china has the largest genetic diversity in the 10 countr ... | 2000 | 10887694 |
| rapd variation within and between natural populations of the wild rice oryza rufipogon from china and brazil | genetic variation within and between eight natural populations of oryza rufipogon from china and brazil was investigated at the dna level by analysis of rapd fragments. out of 60 random primers, which were initially screened against dna from four individuals, 20 generated highly reproducible rapd fragments which were then used for further population analysis. with these primers, 95 discernible dna fragments were produced and 78 (82.1%) were polymorphic, which indicated that high levels of geneti ... | 1999 | 10383685 |
| unusual inheritance of evolutionarily-related double-stranded rnas in interspecific hybrid between rice plants oryza sativa and oryza rufipogon. | endogenous, 14 kb double-stranded rnas (dsrnas) have been found in two ecospecies of cultivated rice (temperate japonica rice and tropical japonica rice, oryza sativa l.) and in wild rice (o. rufipogon, an ancestor of o. sativa). a comparison of the nucleotide and deduced amino acid sequences of the core regions of the rna-dependent rna polymerase domains found in these three dsrnas suggested that these dsrnas probably evolved independently within each host plant from a common ancestor. these ds ... | 1999 | 10380800 |
| construction of a bacterial artificial chromosome (bac) library of common wild rice (oryza rufipogon griff.) for map-based cloning of genes selected during the domestication of rice. | as a prerequisite for the map-based cloning of genes from common wild rice (oryza rufipogon griff.), which plays an important role in the domestication of cultivated rice (o. sativa l.), we constructed a median-insert size bacterial artificial chromosome (bac) library of the common wild rice isolate, yjcwr, collected from yuanjiang, yunnan province, china. the library consists of 52,992 clones, with an average insert size of 50 kb, and all clones were pooled into 46 three-dimensional super-pools ... | 2008 | 17999149 |
| diverse endophytic nitrogen-fixing bacteria isolated from wild rice oryza rufipogon and description of phytobacter diazotrophicus gen. nov. sp. nov. | twenty-three nitrogen-fixing bacteria were isolated from surface-sterilized stems and roots of wild rice oryza rufipogon. four clusters were defined among these bacteria by sds-page protein patterns and further confirmed by is-pcr finger-printing analysis. phylogenetic analysis of 16s rrna gene sequences showed that the representative strains ls 8 and ls 18 of cluster ii formed a monophyletic group sharing 94.0-97.3% similarities with defined enterobacterial species within the genera salmonella, ... | 2008 | 18060384 |
| [cloning and analyzing of rice blast resistance gene pi-ta+ allele from jinghong erect type of common wild rice (oryza rufipogon griff) in yunnan]. | a 4,672 bp dna sequence including the whole coding region and partial non-coding region of rice blast resistance gene pi-ta+ has been cloned from jinghong erect type of common wild rice (oryza rufipogon griff) in yunnan by polymerase chain reaction method. the coding region shares 99.86% and 98.78% identity with the corresponding regions of the reported cultivated rice yashiro-mochi and yuanjiang type of common wild rice respectively. there are 4 nucleotides difference in the coding region and 6 ... | 2008 | 18244911 |
| identification of trait-improving quantitative trait loci alleles from a wild rice relative, oryza rufipogon. | wild species are valued as a unique source of genetic variation, but they have rarely been used for the genetic improvement of quantitative traits. to identify trait-improving quantitative trait loci (qtl) alleles from exotic species, an accession of oryza rufipogon, a relative of cultivated rice, was chosen on the basis of a genetic diversity study. an interspecific bc2 testcross population (v20a/o. rufipogon//v20b///v20b////ce64) consisting of 300 families was evaluated for 12 agronomically im ... | 1998 | 9755218 |
| copia-like retrotransposons in rice: sequence heterogeneity, species distribution and chromosomal locations. | degenerated oligonucleotide primers were used to amplify, clone, and analyze sequence heterogeneity and chromosomal distribution of 23 pcr fragments corresponding to the reverse transcriptase domain of copia-like retrotransposons in rice. of the 23 fragments 22 could be aligned by their deduced amino acid sequences and were divided into 6 groups according to the phylogenetic and southern blot analyses. amino acid sequence differences among the 22 aligned fragments ranged from 1 to 64%. southern ... | 1997 | 9154986 |
| molecular evolution of the pi-ta gene resistant to rice blast in wild rice (oryza rufipogon). | rice blast disease resistance to the fungal pathogen magnaporthe grisea is triggered by a physical interaction between the protein products of the host r (resistance) gene, pi-ta, and the pathogen avr (avirulence) gene, avr-pita. the genotype variation and resistant/susceptible phenotype at the pi-ta locus of wild rice (oryza rufipogon), the ancestor of cultivated rice (o. sativa), was surveyed in 36 locations worldwide to study the molecular evolution and functional adaptation of the pi-ta gene ... | 2008 | 18622033 |
| variation in the nucleotide sequence of a prolamin gene family in wild rice. | variation in the dna sequence of the 10 kda prolamin gene family within the wild rice species oryza rufipogon was probed using the direct sequencing of pcr-amplified genes. a comparison of the nucleotide and deduced amino-acid sequences of eight asian strains of o. rufipogon and one strain of the related african species o. longistaminata is presented. | 1990 | 2103437 |
| identification and mapping of yield and yield related qtls from an indian accession of oryza rufipogon. | cultivated rice (oryza sativa l.) is endowed with a rich genetic variability. in spite of such a great diversity, the modern rice cultivars have narrow genetic base for most of the agronomically important traits. to sustain the demand of an ever increasing population, new avenues have to be explored to increase the yield of rice. wild progenitor species present potential donor sources for complex traits such as yield and would help to realize the dream of sustained food security. | 2005 | 15949048 |
| molecular mapping of the fertility restorer gene for ms-cw-type cytoplasmic male sterility of rice. | cytoplasmic male sterility (cms) of rice (oryza sativa l.) was first reported using the cytoplasm of a chinese wild rice, oryza rufipogon griff. strain w1. however, it was not possible to characterize this ms-cw-type cms in more detail until a restorer line had been developed due to the lack of restorer genes among cultivars thus far tested. the breeding of a restorer line (w1-r) was eventually achieved by transferring the restorer gene(s) of w1 to a cultivar. we report here the characterization ... | 2005 | 15947907 |
| [mapping qtls controlling vascular bundle and panicle-related traits from yuanjiang common wild rice (oryza rufipogon griff.)]. | an advanced backcross population (bc3f2), derived from the cross between yuanjiang common wild rice as the donor parent and teqing as recurrent parent, was used to map qtls controlling the number of vascular bundle and panicle-related traits from yuanjiang common wild rice. seven qtls controlling the number of large vascular bundles in peduncle were detected on chromosome 1, 2, 3, 4, 7 and 10. five qtls for the number of small vascular bundles in peduncle were mapped on chromosome 1, 2, 3, 4 and ... | 2005 | 15759865 |
| [genetic diversity of common wild rice (oryza rufipogon griff) by using ssr markers and phenotypic traits in guangxi province]. | in this paper, allelic variation and genetic diversity among geographies and growth habit types were studied by using 223 accessions of common wild rice primary core collection in guangxi province, with 34 ssr primers locating on 12 chromosomes of rice and 19 phenotypic traits. in the results, 24.91 alleles were detected per locus on average with a range from 7 to 48. compared to the cultivated rice, the wild rice showed more allelic variations. the ratio of heterozygote of ssr locus was 32.01% ... | 2004 | 15493143 |
| nucleotide polymorphism in the adh2 region of the wild rice oryza rufipogon. | dna variation in the alcohol dehydrogenase (adh2) region of the wild rice oryza rufipogon and its related species was analyzed to clarify maintenance mechanisms of the dna variation in these species. a dimorphic pattern was detected in the adh2 region of o. rufipogon. the silent nucleotide diversity (pi) in the adh2 region in o. rufipogon was 0.011, which was higher than that of the adh1 region in o. rufipogon. especially, a high nucleotide diversity was detected at synonymous sites of the catal ... | 2005 | 16133310 |
| identification and characterization of australian wild rice strains of oryza meridionalis and oryza rufipogon by sine insertion polymorphism. | of the rice species with an aa genome, oryza meridionalis has been identified in northern australia as a species of the annual type, among those previously classified as oryza perennis, oryza rufipogon or oryza nivara. this notion has, however, led to some confusion to determine which strains belong to o. meridionalis and how different these strains are from the o. rufipogon strains of the annual type. in this paper, we examined australian wild rice strains for the presence or absence of p-sine1 ... | 2005 | 16172525 |
| genetic structure of oryza rufipogon griff. in china. | oryza rufipogon griff. (common wild rice; cwr) is the ancestor of asian cultivated rice (oryza sativa l.). investigation of the genetic structure and diversity of cwr in china will provide information about the origin of cultivated rice and the grain quality and yield. in this study, we used 36 simple sequence repeat (ssr) markers to assay 889 accessions, which were highly representative of whole germplasm in china. the analysis revealed a hierarchical genetic structure within cwr. first, cwr ha ... | 2008 | 18827837 |
| genetic identification of quantitative trait loci for contents of mineral nutrients in rice grain. | in present study, fe, zn, mn, cu, ca, mg, p and k contents of 85 introgression lines (ils) derived from a cross between an elite indica cultivar teqing and the wild rice (oryza rufipogon) were measured by inductively coupled argon plasma (icap) spectrometry. substantial variation was observed for all traits and most of the mineral elements were significantly positive correlated or independent except for fe with cu. a total of 31 putative quantitative trait loci (qtls) were detected for these eig ... | 2009 | 19166498 |
| dna polymorphism in the superwoman1 (spw1) locus of the wild rice oryza rufipogon and its related species. | the level and pattern of nucleotide variation in the superwoman1(spw1) locus of the wild rice oriza rufipogon and its related species were analyzed. spw1 is orthologous to apetela3(ap3) in arabidopsis thaliana. the estimated level of nucleotide variation for the entire region (pi = 0.0046) was intermediate among those for other genes of o. rufipogon, although the estimates varied considerably among the spw1 domains. complicated haplotype structure was detected, resulting in a high proportion of ... | 2008 | 19168991 |
| dna variation in the metallothionein genes in wild rice oryza rufipogon: relationship between dna sequence polymorphism, codon bias and gene expression. | this study examines the relationship between dna sequence variation and level of gene expression in four metallothionein genes from wild rice oryza rufipogon. the nucleotide diversity was 0.0028 to 0.0117 over the entire coding and non-coding region, and it was negatively correlated with gene expression for three type 2 metallothionein genes. in contrast, codon bias and percent of preferred codons correlated positively with gene expression. these results indicate that the intensity of natural se ... | 2005 | 16172530 |
| cross-species bacterial artificial chromosome (bac) library screening via overgo-based hybridization and bac-contig mapping of a yield enhancement quantitative trait locus (qtl) yld1.1 in the malaysian wild rice oryza rufipogon. | the construction of bac-contig physical maps is an important step towards a partial or ultimate genome sequence analysis. here, we describe our initial efforts to apply an overgo approach to screen a bac library of the malaysian wild rice species, oryza rufipogon. overgo design is based on repetitive element masking and sequence uniqueness, and uses short probes (approximately 40 bp), making this method highly efficient and specific. pairs of 24-bp oligos that contain an 8-bp overlap were develo ... | 2005 | 16217554 |
| construction of introgression lines carrying wild rice (oryza rufipogon griff.) segments in cultivated rice (oryza sativa l.) background and characterization of introgressed segments associated with yield-related traits. | introgression lines (ils) are useful tools for precise mapping of quantitative trait loci (qtls) and the evaluation of gene action or interaction in theoretical studies. a set of 159 ils carrying variant introgressed segments from chinese common wild rice (oryza rufipogon griff.), collected from dongxiang county, jiangxi province, in the background of indica cultivar (oryza sativa l.), guichao 2, was developed using 126 polymorphic simple sequence repeats (ssr) loci. the 159 ils represented 67.5 ... | 2006 | 16331476 |
| genetic evaluation of in situ conserved and reintroduced populations of wild rice (oryza rufipogon: poaceae) in china. | we evaluated the genetic consequences and efficiency of conservation practices in oryza rufipogon using microsatellite dna markers. spatial autocorrelation analysis from 12 microsatellite loci revealed that microsatellite alleles were exclusively distributed in patches within the population, indicating that large populations were unlikely to be homogeneous. an in situ conserved stand of o. rufipogon, which has been protected by a concrete wall from a large population, captured only 67.9% of the ... | 2005 | 16382362 |
| substitution mapping of dth1.1, a flowering-time quantitative trait locus (qtl) associated with transgressive variation in rice, reveals multiple sub-qtl. | a quantitative trait locus (qtl), dth1.1, was associated with transgressive variation for days to heading in an advanced backcross population derived from the oryza sativa variety jefferson and an accession of the wild rice relative oryza rufipogon. a series of near-isogenic lines (nils) containing different o. rufipogon introgressions across the target region were constructed to dissect dth1.1 using substitution mapping. in contrast to the late-flowering o. rufipogon parent, o. rufipogon allele ... | 2006 | 16452146 |
| molecular analysis of utility of a retrotransposon, p-sine1-r2 in the asian wild rice and weedy rice populations. | the distribution of a retrotransposon, p-sine1-r2 located at the waxy locus was analyzed by the pcr assay in the perennial wild rice (oryza rufipogon) which inhabited in four isolated and six disturbed populations and in the weedy rice population. the level of clonality of the wild rice species was determined in populations subject to level of water supply and another disturbance. the results showed that all four isolated populations carried the genotype (-/-) and (-/+), while three genotypes (- ... | 2009 | 19579957 |
| haplotype variation in structure and expression of a gene cluster associated with a quantitative trait locus for improved yield in rice. | by constructing nearly isogenic lines (nils) that differ only at a single quantitative trait locus (qtl), we fine-mapped the yield-improving qtl qgy2-1 to a 102.9-kb region on rice chromosome 2. comparison analysis of the genomic sequences in the mapped qtl region between the donor (dongxiang wild rice, oryza rufipogon griff.) and recurrent (guichao2, oryza sativa ssp. indica) parents used for the development of nils identified the haplotypes of a leucine-rich repeat receptor kinase gene cluster ... | 2006 | 16606701 |
| inferring population history from fine-scale spatial genetic analysis in oryza rufipogon (poaceae). | determining the genetic structure of an in situ conserved population can provide insight into the dynamics of population genetic processes associated with successful plant conservation. we used 21 microsatellite loci to analyse the genetic relationships among individuals (n = 813) collected from a small oryza rufipogon population conserved since 1993 in hunan province of china. the analysis revealed four distinct genetic subpopulations (f(st) = 0.145) without geographic isolation. one subpopulat ... | 2006 | 16629809 |
| genome-wide searching of single-nucleotide polymorphisms among eight distantly and closely related rice cultivars (oryza sativa l.) and a wild accession (oryza rufipogon griff.). | we searched the genomes of eight rice cultivars (oryza sativa l. ssp. japonica and ssp. indica) and a wild rice accession (oryza rufipogon griffith) for nucleotide polymorphisms, and identified 7805 polymorphic loci, including single-nucleotide polymorphisms (snps) and insertions/deletions (indels), in predicted intergenic regions. polymorphisms are useful as dna markers for genetic analysis or positional cloning with segregating populations of crosses. pairwise comparison between cultivars and ... | 2006 | 16766512 |
| fine mapping of a quantitative trait locus for grain number per panicle from wild rice (oryza rufipogon griff.). | sil040, an introgression line (il) developed by introgressing chromosomal segments from an accession of oryza rufipogon into an indica cultivar guichao 2, showed significantly less grains per panicle than the recurrent parent guichao 2. quantitative trait locus (qtl) analysis in f2 and f3 generations derived from the cross between sil040 and guichao 2 revealed that gpa7, a qtl located on the short arm of chromosome 7, was responsible of this variation. alleles from o. rufipogon decreased grains ... | 2006 | 16770601 |
| analysis of qtls for yield-related traits in yuanjiang common wild rice (oryza rufipogon griff.). | using an accession of common wild rice (oryza rufipogon griff.) collected from yuanjiang county, yunnan province, china, as the donor and an elite cultivar 93-11, widely used in two-line indica hybrid rice production in china, as the recurrent parent, an advanced backcross populations were developed. through genotyping of 187 ssr markers and investigation of six yield-related traits of two generations (bc(4)f(2) and bc(4)f(4)), a total of 26 qtls were detected by employing single point analysis ... | 2010 | 20227048 |
| identification and fine mapping of a major quantitative trait locus originating from wild rice, controlling cold tolerance at the seedling stage. | cold tolerance at the seedling stage (ctss) is an important trait affecting stable rice production in temperate climates and areas of high elevation. in this study, 331 single nucleotide polymorphism (snp) markers were developed and used along with phenotypic evaluation to identify quantitative trait loci (qtls) associated with ctss from a mapping population of 184 f(2) plants derived from a cold tolerant wild rice, w1943 (oryza rufipogon), and a sensitive indica cultivar, guang-lu-ai 4 (gla4). ... | 2010 | 20526617 |
| identification of a drought tolerant introgression line derived from dongxiang common wild rice (o. rufipogon griff.). | construction of introgression lines using cultivated rice as recipient and wild rice is a novel approach to explore primitive and broad genetic resources in rice breeding. we recently generated a set of 159 introgression lines via a backcrossing program using an elite indica cultivar rice guichao 2 (o. sativa l. ssp. indica) as recipient and a common wild rice dongxiang accession (o. rufipogon griff.) as donor. in this study, we have evaluated the previously constructed 159 introgression lines f ... | 2006 | 16845479 |
| origin of seed shattering in rice (oryza sativa l.). | a critical evolutionary step during rice domestication was the elimination of seed shattering. wild rice disperses seeds freely at maturity to guarantee the propagation, while cultivated rice retains seeds on the straws to make easy harvest and decrease the loss of production. the molecular basis for this key event during rice domestication remains to be elucidated. here we show that the seed shattering is controlled by a single dominant gene, shattering1 (sha1), encoding a member of the triheli ... | 2007 | 17216230 |
| a large-scale field study of transgene flow from cultivated rice (oryza sativa) to common wild rice (o. rufipogon) and barnyard grass (echinochloa crusgalli). | the introgression of transgenes into wild relatives or weeds through pollen-mediated gene flow is a major concern in environmental risk assessment of transgenic crops. a large-scale (1.3-1.8 ha) rice gene flow study was conducted using transgenic rice containing the bar gene as a pollen donor and oryza rufipogon as a recipient. there was a high frequency of transgene flow (11%-18%) at 0-1 m, with a steep decline with increasing distance to a detection limit of 0.01% by 250 m. to our knowledge, t ... | 2006 | 17309736 |
| modern elite rice varieties of the 'green revolution' have retained a large introgression from wild rice around the pi33 rice blast resistance locus. | during the breeding process of cultivated crops, resistance genes to pests and diseases are commonly introgressed from wild species. the size of these introgressions is predicted by theoretical models but has rarely been measured in cultivated varieties. by combining resistance tests with isogenic strains, genotyping and sequencing of different rice accessions, it was shown that, in the elite rice variety ir64, the resistance conferring allele of the rice blast resistance gene pi33 was introgres ... | 2007 | 17587382 |
| adaptation of flowering-time by natural and artificial selection in arabidopsis and rice. | the adaptation of plants to natural environments depends on the adaptation of flowering-time control at the appropriate season to set seeds. possible molecular mechanisms underlying this adaptation have recently been revealed. in arabidopsis thaliana, a model long-day plant, control of floral transition by vernalization and long-day floral promotion pathways is a key regulator in adaptation to different regions. a floral repressor termed flc and a floral promoter termed constans (co), which cont ... | 2007 | 17693414 |
| origins and population genetics of weedy red rice in the usa. | weedy red rice (oryza sativa spontonea) is a persistent and problematic weed of rice culture worldwide. a major hypothesis for the mechanism of production of this weed in south and southeast asia is hybridization between cultivated rice (oryza sativa) and wild rice (oryza rufipogon). however, weedy red rice can often be found outside the range of o. rufipogon leaving questions on the origin and process behind weedy rice infestations. in the usa, weedy red rice was first documented as early as 18 ... | 2007 | 17887969 |
| collection and comparative analysis of 1888 full-length cdnas from wild rice oryza rufipogon griff. w1943. | a huge amount of cdna and est resources have been developed for cultivated rice species oryza sativa; however, only few cdna resources are available for wild rice species. in this study, we isolated and completely sequenced 1888 putative full-length cdna (flcdna) clones from wild rice oryza rufipogon griff. w1943 for comparative analysis between wild and cultivated rice species. two cdna libraries were constructed from 3-week-old leaf samples under either normal or cold-treated conditions. homol ... | 2008 | 18687674 |
| contrasting population genetic structure and gene flow between oryza rufipogon and oryza nivara. | the cross compatible wild relatives of crops have furnished valuable genes for crop improvement. understanding the genetics of these wild species may enhance their further use in breeding. in this study, sequence variation of the nuclear lhs1 gene was used to investigate the population genetic structure and gene flow of oryza rufipogon and o. nivara, two wild species most closely related to o. sativa. the two species diverge markedly in life history and mating system, with o. rufipogon being per ... | 2008 | 18712516 |
| diversity and selective sweep in the osamt1;1 genomic region of rice. | ammonium is one of the major forms in which nitrogen is available for plant growth. osamt1;1 is a high-affinity ammonium transporter in rice (oryza sativa l.), responsible for ammonium uptake at low nitrogen concentration. the expression pattern of the gene has been reported. however, variations in its nucleotides and the evolutionary pathway of its descent from wild progenitors are yet to be elucidated. in this study, nucleotide diversity of the gene osamt1;1 and the diversity pattern of seven ... | 2011 | 21385389 |
| quantitative trait loci underlying domestication- and yield-related traits in an oryza sativa x oryza rufipogon advanced backcross population. | to understand the genetic characteristics of the traits related to differentiation between cultivated rice and its wild progenitor, genetic factors controlling domestication- and yield-related traits were identified using a bc3f2 population derived from an accession of common wild rice (donor, oryza rufipogon griff.) collected from yuanjiang, yunnan province, china, and an indica cultivar, teqing (recipient, oryza sativa l.). a genetic linkage map consisting of 125 simple sequence repeat (ssr) m ... | 2008 | 18772947 |
| genetic variation of wild rice populations from thailand and the lao pdr based on molecular markers. | the two wild rice species, oryza rufipogon and o. nivara, which inhabit thailand and the lao pdr, are threatened with the loss of their natural habitats. the losses are primarily attributable to human intervention. before this process advances, it is crucial to obtain basic information on the genetic variations of these species, so important knowledge about the current status of genetic variability. in this study, genetic variation within and between fourteen natural populations of the two popul ... | 2008 | 18819589 |
| genetic control of rice plant architecture under domestication. | the closely related wild rice species oryza rufipogon is considered the progenitor of cultivated rice (oryza sativa). the transition from the characteristic plant architecture of wild rice to that of cultivated rice was one of the most important events in rice domestication; however, the molecular basis of this key domestication transition has not been elucidated. here we show that the prog1 gene controls aspects of wild-rice plant architecture, including tiller angle and number of tillers. the ... | 2008 | 18820696 |
| genetic architecture for the adaptive origin of annual wild rice, oryza nivara. | the wild progenitors of cultivated rice, oryza nivara and oryza rufipogon, provide an experimental system for characterizing the genetic basis of adaptation. the evolution of annual o. nivara from a perennial ancestor resembling its sister species, o. rufipogon, was associated with an ecological shift from persistently wet to seasonally dry habitats. here we report a quantitative trait locus (qtl) analysis of phenotypic differentiation in life history, mating system, and flowering time between o ... | 2009 | 19236476 |
| genetic signature of rice domestication shown by a variety of genes. | cultivated rice was domesticated from common wild rice. however, little is known about genetic adaptation under domestication. we investigated the nucleotide variation of both cultivated rice and its wild progenitors at 22 r-gene and 10 non-r-gene loci. a significant regression was observed between wild rice and rice cultivars in their polymorphic levels, particularly in their nonsynonymous substitutions (theta ( a )). our data also showed that a similar proportion (approximately 60%) of nucleot ... | 2009 | 19290563 |
| identification of quantitative trait loci affecting hemicellulose characteristics based on cell wall composition in a wild and cultivated rice species. | cell wall hemicellulosic polysaccharides are structurally complex and diverse. knowledge about the synthesis of cell wall hemicelluloses and their biological roles is limited. quantitative trait loci (qtl) mapping is a helpful tool for the dissection of complex phenotypes for gene identification. in this study, we exploited the natural variation in cell wall monosaccharide levels between a common wild rice, yuanj, and an elite indica cultivar, teqing, and performed qtl mapping with their introgr ... | 2011 | 21914650 |
| basic helix-loop-helix transcription factor from wild rice (orbhlh2) improves tolerance to salt- and osmotic stress in arabidopsis. | salt stress adversely affects plant growth and development. some plants reduce the damage of high-salt stress by expressing a series of salt-responsive genes. studies of the molecular mechanism of the salt-stress response have focused on the characterization of components involved in signal perception and transduction. in the present work, we cloned and characterized a basic helix-loop-helix (bhlh) encoding gene, orbhlh2, from wild rice (oryza rufipogon), which encodes a homologue protein of ice ... | 2009 | 19324458 |
| normal expression of insect-resistant transgene in progeny of common wild rice crossed with genetically modified rice: its implication in ecological biosafety assessment. | transgene outflow from genetically modified (gm) rice to its wild relatives may cause undesirable ecological consequences. understanding the level of transgene expression in wild rice following gene flow is important for assessing such consequences, providing that transgene escape from gm rice cannot be prevented. to determine the expression of a transgene in common wild rice (oryza rufipogon), we analyzed the content of cry1ac protein in three gm rice lines containing a bt transgene, their f(1) ... | 2009 | 19504082 |
| dna polymorphism in the blast disease resistance gene pita of the wild rice oryza rufipogon and its related species. | intra-and interspecific dna variations in the blast resistance gene pita in wild rice (oryza rufipogon), cultivated rice (o. sativa), and two other related wild rice species (o. meridionalis and o. officinalis) were analyzed to elucidate the nucleotide polymorphism maintenance mechanisms and evolution of pita in these species. nucleotide diversity at silent sites of o. rufipogon pita was 0.0101, an intermediate value relative to other o. rufipogon nuclear genes. a dimorphic pattern of nucleotide ... | 2009 | 19556706 |
| molecular evolution of the rice blast resistance gene pi-ta in invasive weedy rice in the usa. | the pi-ta gene in rice has been effectively used to control rice blast disease caused by magnaporthe oryzae worldwide. despite a number of studies that reported the pi-ta gene in domesticated rice and wild species, little is known about how the pi-ta gene has evolved in us weedy rice, a major weed of rice. to investigate the genome organization of the pi-ta gene in weedy rice and its relationship to gene flow between cultivated and weedy rice in the us, we analyzed nucleotide sequence variation ... | 2011 | 22043312 |
| fine mapping and candidate gene analysis of spd6, responsible for small panicle and dwarfness in wild rice (oryza rufipogon griff.). | identification of genes in rice that affect production and quality is necessary for improving the critical global food source. cssl58, a chromosome segment substitution line (cssl) containing a chromosome segment of oryza rufipogon in the genetic background of the indica cultivar teqing showed significantly smaller panicles, fewer grains per panicle, smaller grains and dwarfness compared with the recurrent parent teqing. genetic analysis of the bc(4)f(1) and bc(4)f(2) generations, derived from a ... | 2009 | 19588119 |
| over-expression of the rice lrk1 gene improves quantitative yield components. | in rice (oryza sativa l.), the number of panicles, spikelets per panicle and grain weight are important components of grain yield. these characteristics are controlled by quantitative trait loci (qtls) and are derived from variation inherent in crops. as a result of the complex genetic basis of these traits, only a few genes involved in their control have been cloned and characterized. we have previously map-cloned a gene cluster including eight leucine-rich repeat receptor-like kinase (lrk) gen ... | 2009 | 19619185 |
| subspecies-specific intron length polymorphism markers reveal clear genetic differentiation in common wild rice (oryza rufipogon l.) in relation to the domestication of cultivated rice (o. sativa l.). | it is generally accepted that oryza rufipogon is the progenitor of asian cultivated rice (o. sativa). however, how the two subspecies of o. sativa (indica and japonica) were domesticated has long been debated. to investigate the genetic differentiation in o. rufipogon in relation to the domestication of o. sativa, we developed 57 subspecies-specific intron length polymorphism (ssilp) markers by comparison between 10 indica cultivars and 10 japonica cultivars and defined a standard indica rice an ... | 2009 | 19631918 |
| modelling pollen-mediated gene flow in rice: risk assessment and management of transgene escape. | fast development and commercialization of genetically modified plants have aroused concerns of transgene escape and its environmental consequences. a model that can effectively predict pollen-mediated gene flow (pmgf) is essential for assessing and managing risks from transgene escape. a pollen-trap method was used to measure the wind-borne pollen dispersal in cultivated rice and common wild rice, and effects of relative humidity, temperature and wind speed on pollen dispersal were estimated. a ... | 2010 | 20132516 |
| overexpression of a homopeptide repeat-containing bhlh protein gene (orbhlh001) from dongxiang wild rice confers freezing and salt tolerance in transgenic arabidopsis. | dongxiang wild rice (oryza rufipogon) is the northernmost wild rice in the world known to date and has extremely high cold tolerance and many other adversity-resistant properties. to identify the genes responsible for the high stress tolerance, we isolated and characterized a basic helix-loop-helix (bhlh) protein gene orbhlh001 from dongxiang wild rice. the gene encodes an ice1-like protein containing multiple homopeptide repeats. expression of orbhlh001 is induced by salt stress and is predomin ... | 2010 | 20559833 |
| rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus oryza. | rapid progress in comparative genomics among the grasses has revealed similar gene content and order despite exceptional differences in chromosome size and number. large- and small-scale genomic variations are of particular interest, especially among cultivated and wild species, as they encode rapidly evolving features that may be important in adaptation to particular environments. we present a genome-wide study of intermediate-sized structural variation (sv) among rice (oryza sativa) and three ... | 2010 | 20626650 |
| ecological divergence in the presence of gene flow in two closely related oryza species (oryza rufipogon and o. nivara). | ecological divergence plays a prominent role in the process of speciation, but how divergence occurs in the face of gene flow is still less clear, and remains controversial among evolutionists. here we investigated the nucleotide diversity, divergence and gene flow between oryza nivara and o. rufipogon using sequences of seven chloroplast and nuclear loci. by analysing samples from 26 wild populations across the geographic ranges of the two species, we showed that both species were highly struct ... | 2010 | 20653085 |
| association between nonsynonymous mutations of starch synthase iia and starch quality in rice (oryza sativa). | starch quality is one of the most important agronomic traits in asian rice, oryza sativa. starch synthase iia (ssiia) is a major candidate gene for starch quality variation. within ssiia, three nonsynonymous mutations in exon 8 have been shown to affect enzyme activity when expressed in escherichia coli. to search for the variation in ssiia that is responsible for starch quality variation in rice, we sequenced the ssiia exon 8 region and measured starch quality as starch disintegration in alkali ... | 2010 | 20946420 |
| construction of the physical map of the gpa7 locus reveals that a large segment was deleted during rice domestication. | to facilitate cloning gene(s) underlying gpa7, a deep-coverage bac library was constructed for an isolate of common wild rice (oryza rufipogon griff.) collected from dongxiang, jiangxi province, china (dxcwr). gpa7, a quantitative trait locus corresponding to grain number per panicle, is positioned in the short arm of chromosome 7. the bac library containing 96,768 clones represents approximate 18 haploid genome equivalents. the contig spanning dxcwr gpa7 was constructed with a series of ordered ... | 2008 | 18317774 |
| extraordinarily polymorphic ribosomal dna in wild and cultivated rice. | a collection of 481 rice accessions was surveyed for ribosomal dna (rdna) intergenic spacer length polymorphism to assess the extent of genetic diversity in chinese and asian rice germplasm. the materials included 83 accessions of common wild rice, oryza rufipogon, 75 of which were from china; 348 entries of cultivated rice (oryza sativa), representing almost all the rice growing areas in china; and 50 cultivars from south and east asia. a total of 42 spacer length variants (slvs) were detected. ... | 1996 | 18469959 |
| identification and characterization of osebs, a gene involved in enhanced plant biomass and spikelet number in rice. | common wild rice (oryza rufipogon griff.) is an important genetic reservoir for rice improvement. we investigated a quantitative trait locus (qtl), qgp5-1, which is related to plant height, leaf size and panicle architecture, using a set of introgression lines of o. rufipogon in the background of the indica cultivar guichao2 (oryza sativa l.). we cloned and characterized qgp5-1 and confirmed that the newly identified gene osebs (enhancing biomass and spikelet number) increased plant height, leaf ... | 2013 | 23924074 |
| the 172-kb genomic dna region of the o. rufipogon yld1.1 locus: comparative sequence analysis with o. sativa ssp. japonica and o. sativa ssp. indica. | common wild rice (oryza rufipogon) plays an important role by contributing to modern rice breeding. in this paper, we report the sequence and analysis of a 172-kb genomic dna region of wild rice around the rm5 locus, which is associated with the yield qtl yld1.1. comparative sequence analysis between orthologous rm5 regions from oryza sativa ssp. japonica, o. sativa ssp. indica and o. rufipogon revealed a high level of conserved synteny in the content, homology, structure, orientation, and physi ... | 2009 | 18633654 |
| establishment of a rice transgene flow model for predicting maximum distances of gene flow in southern china. | we aimed to establish a rice gene flow model based on (i) the gaussian plume model, (ii) data from a three-location x 3-yr field experiment on transgene flow to common rice cultivars (oryza sativa), male sterile (ms) lines (o. sativa) and common wild rice (oryza rufipogon), and (iii) 32-yr historical meteorological data collected from 38 meteorological stations in southern china during the rice flowering period. the concept of the gene flow coefficient (gfc) is proposed; that is, the ratio of th ... | 2008 | 18643943 |
| genetic control of a transition from black to straw-white seed hull in rice domestication. | the genetic mechanism involved in a transition from the black-colored seed hull of the ancestral wild rice (oryza rufipogon and oryza nivara) to the straw-white seed hull of cultivated rice (oryza sativa) during grain ripening remains unknown. we report that the black hull of o. rufipogon was controlled by the black hull4 (bh4) gene, which was fine-mapped to an 8.8-kb region on rice chromosome 4 using a cross between o. rufipogon w1943 (black hull) and o. sativa indica cv guangluai 4 (straw-whit ... | 2011 | 21263038 |
| identification of heterotic loci associated with yield-related traits in chinese common wild rice (oryza rufipogon griff.). | many rice breeding programs have currently reached yield plateaus as a result of limited genetic variability in parental strains. dongxiang common wild rice (oryza rufipogon griff.) is the progenitor of cultivated rice (oryza sativa l.) and serves as an important gene pool for the genetic improvement of rice cultivars. in this study, heterotic loci (hls) associated with six yield-related traits were identified in wild and cultivated rice and investigated using a set of 265 introgression lines (i ... | 2011 | 21600393 |
| levels and patterns of nucleotide variation in domestication qtl regions on rice chromosome 3 suggest lineage-specific selection. | oryza sativa or asian cultivated rice is one of the major cereal grass species domesticated for human food use during the neolithic. domestication of this species from the wild grass oryza rufipogon was accompanied by changes in several traits, including seed shattering, percent seed set, tillering, grain weight, and flowering time. quantitative trait locus (qtl) mapping has identified three genomic regions in chromosome 3 that appear to be associated with these traits. we would like to study wh ... | 2011 | 21674010 |
| complex genetic nature of sex-independent transmission ratio distortion in asian rice species: the involvement of unlinked modifiers and sex-specific mechanisms. | transmission ratio distortion (trd), in which one allele is transmitted more frequently than the opposite allele, is presumed to act as a driving force in the emergence of a reproductive barrier. trd acting in a sex-specific manner has been frequently observed in interspecific and intraspecific hybrids across a broad range of organisms. in contrast, sex-independent trd (sitrd), which results from preferential transmission of one of the two alleles in the heterozygote through both sexes, has been ... | 2011 | 21792227 |
| Mapping of quantitative trait loci for fiber and lignin contents from an interspecific cross Oryza sativa+ùOryza rufipogon. | Rice straw is always regarded as a by-product of rice production, but it could be a significant energy source for ruminant animals. Knowledge of the genetic variation and genetic architecture of cell wall traits will facilitate rice breeders by improving relevant traits through selective breeding and genetic engineering. The common wild rice, Oryza rufipogon Griff., which is considered to be the progenitor of Oryza sativa, has been widely utilized for the identification of genes of agronomic imp ... | 2011 | 21726058 |
| heading date 1 (hd1), an ortholog of arabidopsis constans, is a possible target of human selection during domestication to diversify flowering times of cultivated rice. | during the domestication of rice (oryza sativa l.), diversification of flowering time was important in expanding the areas of cultivation. rice is a facultative short day (sd) plant and requires certain periods of dark to induce flowering. heading date 1 (hd1), a regulator of the florigen gene hd3a, is one of the main factors used to generate diversity in flowering. loss-of-function alleles of hd1 are common in cultivated rice and cause the diversity of flowering time. however, it is unclear how ... | 2011 | 21952207 |
| identification of quantitative trait loci associated with salt tolerance at seedling stage from oryza rufipogon. | soil salinity is one of the major abiotic stresses affecting plant growth and crop production. in the present study, salt tolerance at rice seedling stage was evaluated using 87 introgression lines (ils), which were derived from a cross between an elite indica cultivar teqing and an accession of common wild rice (oryza rufipogon griff.). substantial variation was observed for four traits including salt tolerance score (sts), relative root dry weight (rrw), relative shoot dry weight (rsw) and rel ... | 2011 | 22196402 |
| Characterization of a novel high-tillering dwarf 3 mutant in rice. | Tiller number and culm length are important components of plant architecture and determinate grain production in rice. A line SIL046, derived from an introgression lines population developed by an accession of common wild rice (Oryza rufipogon Griff.) and a high-yielding indica cultivar Guichao 2 (Oryza sativa L.), exhibits a higher tiller number and shorter culm length phenotype than the recipient parent Guichao 2 (GC2). Genetic analysis showed that the high-tillering dwarf phenotype was contro ... | 2011 | 21930100 |
| resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. | rice is a staple crop that has undergone substantial phenotypic and physiological changes during domestication. here we resequenced the genomes of 40 cultivated accessions selected from the major groups of rice and 10 accessions of their wild progenitors (oryza rufipogon and oryza nivara) to >15 × raw data coverage. we investigated genome-wide variation patterns in rice and obtained 6.5 million high-quality single nucleotide polymorphisms (snps) after excluding sites with missing data in any acc ... | 2011 | 22158310 |
| identification of heat-sensitive qtl derived from common wild rice (oryza rufipogon griff.). | understanding the responses of rice plants to heat-stress is a challenging, yet crucial, endeavor. a set of introgression lines was previously developed using an advanced backcrossing strategy that involved the elite indica cultivar teqing as the recipient and an accession of common wild rice (oryza rufipongon griff.) as the donor. in this study, we evaluated the responses of 90 of these previously developed introgression lines to heat stress. five quantitative trait loci (qtls) related to heat ... | 2012 | 23352410 |
| molecular characterization and comparative sequence analysis of defense-related gene, oryza rufipogon receptor-like protein kinase 1. | many of the plant leucine rich repeat receptor-like kinases (lrr-rlks) have been found to regulate signaling during plant defense processes. in this study, we selected and sequenced an lrr-rlk gene, designated as oryza rufipogon receptor-like protein kinase 1 (orufrpk1), located within yield qtl yld1.1 from the wild rice oryza rufipogon (accession irgc105491). a 2055 bp coding region and two exons were identified. southern blotting determined orufrpk1 to be a single copy gene. sequence compariso ... | 2012 | 22942769 |