| 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 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 |
| the complete nucleotide sequence of wild rice (oryza nivara) chloroplast genome: first genome wide comparative sequence analysis of wild and cultivated rice. | we determined the complete nucleotide sequence of the chloroplast genome of wild rice, oryza nivara and compared it with the corresponding published sequence of relative cultivated rice, oryza sativa. the genome was 134,494 bp long with a large single-copy region of 80,544 bp, a small single-copy region of 12,346 bp and two inverted repeats of 20,802 bp each. the overall a+t content was 61.0%. the o. nivara chloroplast genome encoded identical functional genes to o. sativa in the same order alon ... | 2004 | 15556301 |
| 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 |
| 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 |
| sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. | rice (oryza sativa l.) chromosome 3 is evolutionarily conserved across the cultivated cereals and shares large blocks of synteny with maize and sorghum, which diverged from rice more than 50 million years ago. to begin to completely understand this chromosome, we sequenced, finished, and annotated 36.1 mb ( approximately 97%) from o. sativa subsp. japonica cv nipponbare. annotation features of the chromosome include 5915 genes, of which 913 are related to transposable elements. a putative functi ... | 2005 | 16109971 |
| 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 analysis of rice domestication syndrome with the wild annual species, oryza nivara. | with a small and sequenced genome, rice provides an excellent system for studying the genetics of cereal domestication. we conducted a quantitative trait locus (qtl) analysis of key domestication traits using an f2 population derived from a cross between the cultivated rice, oryza sativa, and the annual wild species, o. nivara. we found that the qtl of large phenotypic effects were targeted by domestication selection for effective harvest and planting, including a reduction in seed shattering an ... | 2006 | 16539615 |
| characterization and mapping of a shattering mutant in rice that corresponds to a block of domestication genes. | easy shattering reduces yield due to grain loss during harvest in cereals. shattering is also a hindrance in breeding programs that use wild accessions because the shattering habit is often linked to desirable traits. we characterized a shattering mutant line of rice, hsh, which was derived from a nonshattering japonica variety, hwacheong, by n-methyl-n-nitrosourea (mnu) treatment. the breaking tensile strength (bts) of the grain pedicel was measured using a digital force gauge to evaluate the d ... | 2006 | 16582442 |
| genetic diversity and origin of weedy rice (oryza sativa f. spontanea) populations found in north-eastern china revealed by simple sequence repeat (ssr) markers. | weedy rice (oryza sativa f. spontanea) is one of the most notorious weeds occurring in rice-planting areas worldwide. the objectives of this study are to determine the genetic diversity and differentiation of weedy rice populations from liaoning province in north-eastern china and to explore the possible origin of these weedy populations by comparing their genetic relationships with rice varieties (o. sativa) and wild rice (o. rufipogon) from different sources. | 2006 | 17056615 |
| 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 |
| interspecific rice hybrid of oryza sativa x oryza nivara reveals a significant increase in seed protein content. | wild species offer a potential reservoir of genetic variation for crop improvement. besides the valuable genes for disease resistance that the wild species have provided for rice improvement, recent studies have shown that these wild species could also provide favorable alleles for the improvement of yield and yield-related traits. the present study reports yet another potential of wild relatives of rice, which involves the improvement of seed protein content. a significant increase in seed prot ... | 2008 | 18163552 |
| 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 |
| a novel bacterial blight resistance gene from oryza nivara mapped to 38 kb region on chromosome 4l and transferred to oryza sativa l. | bacterial blight (bb) of rice caused by xanthomonas oryzae pv oryzae (xoo) is one of the major constraints to productivity in south-east asia. the strategy of using major genes, singly or in combination, continues to be the most effective approach for bb management. currently, more than two dozen genes have been designated but not all the known genes are effective against all the prevalent pathotypes. the challenge, therefore, is to continue to expand the gene pool of effective and potentially d ... | 2008 | 19061530 |
| 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 |
| potential gene flow from transgenic rice (oryza sativa l.) to different weedy rice (oryza sativa f. spontanea) accessions based on reproductive compatibility. | the possibility of gene flow from transgenic crops to wild relatives may be affected by reproductive capacity between them. the potential gene flow from two transgenic rice lines containing the bar gene to five accessions of weedy rice (wr1-wr5) was determined through examination of reproductive compatibility under controlled pollination. | 2009 | 19418443 |
| selection on grain shattering genes and rates of rice domestication. | molecular cloning of major quantitative trait loci (qtls) responsible for the reduction of rice grain shattering, a hallmark of cereal domestication, provided opportunities for in-depth investigation of domestication processes. here, we studied nucleotide variation at the shattering loci, sh4 and qsh1, for cultivated rice, oryza sativa ssp. indica and oryza sativa ssp. japonica, and the wild progenitors, oryza nivara andoryza rufipogon. the nonshattering sh4 allele was fixed in all rice cultivar ... | 2009 | 19674325 |
| pericarp color and haplotype diversity in weedy rice (o. sativa f. spontanea) from thailand. | weedy rice (oryza sativa f. spontanea) is an important resource for breeding and evolutionary studies. the present study was carried out to identify the genotype of weedy rice strains responsible for variation of pericarp color by sequencing exon 6 of the rc gene. haplotype analysis revealed that rice strains with light red- and red-pericarp lacked the 14 bp deletion in the rc gene, while rice strains with white-, brown and light green-pericarp contained the 14 bp deletion. a single nucleotide p ... | 2009 | 19943464 |
| 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 |
| independent evolution of a new allele of f1 pollen sterility gene s27 encoding mitochondrial ribosomal protein l27 in oryza nivara. | loss of function of duplicated genes plays an important role in the evolution of postzygotic reproductive isolation. the widespread occurrence of gene duplication followed by rapid loss of function of some of the duplicate gene copies suggests the independent evolution of loss-of-function alleles of duplicate genes in divergent lineages of speciation. here, we found a novel loss-of-function allele of s27 in the asian annual wild species oryza nivara, designated s27-niv (s), that leads to f(1) po ... | 2010 | 20878142 |
| conspecific crop-weed introgression influences evolution of weedy rice (oryza sativa f. spontanea) across a geographical range. | introgression plays an important role in evolution of plant species via its influences on genetic diversity and differentiation. outcrossing determines the level of introgression but little is known about the relationships of outcrossing rates, genetic diversity, and differentiation particularly in a weedy taxon that coexists with its conspecific crop. | 2011 | 21249201 |
| 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 |
| rapid evolutionary divergence and ecotypic diversification of germination behavior in weedy rice populations. | • feral plants have evolved from well-studied crops, providing good systems for elucidation of how weediness evolves. as yet, they have been largely neglected for this purpose. the evolution of weediness can occur by simple back mutations in domestication genes (domestication in reverse). whether the evolutionary steps to weediness always occur in reverse remains largely unknown. • we examined seed germination behavior in recently evolved weedy rice (oryza sativa f. spontanea) populations and th ... | 2011 | 21569036 |
| identification and fine-mapping of xa33, a novel gene for resistance to xanthomonas oryzae pv. oryzae. | abstract broadening of the genetic base for identification and transfer of genes for resistance to insect pests and diseases from wild relatives of rice is an important strategy in resistance breeding programs across the world. an accession of oryza nivara, international rice germplasm collection (irgc) accession number 105710, was identified to exhibit high level and broad-spectrum resistance to xanthomonas oryzae pv. oryzae. in order to study the genetics of resistance and to tag and map the ... | 2011 | 21970567 |
| characterization of chloroplast dna microsatellites from saccharum spp and related species. | microsatellites, or simple sequence repeats (ssrs), and their flanking regions in chloroplast genomes (plastomes) of some species of the family poaceae were analyzed in silico to look for dna sequence variations. comparison of the complete chloroplast dna sequences (cpdnas) of sugarcane (saccharum hybrid cv. sp-80-3280 and s. officinarum cv. nco310) and related species, agrostis stolonifera, brachypodium distachyon, hordeum vulgare subsp vulgare, lolium perenne, oryza nivara, o. sativa sub ... | 2011 | 21948764 |
| introgression from cultivated rice influences genetic differentiation of weedy rice populations at a local spatial scale. | hybridization and introgression can play an important role in genetic differentiation and adaptive evolution of plant species. for example, a conspecific feral species may frequently acquire new alleles from its coexisting crops via introgression. however, little is known about this process. we analyzed 24 weedy rice (oryza sativa f. spontanea) populations and their coexisting rice cultivars from northern italy to study their genetic differentiation, outcrossing, and introgression based on micro ... | 2011 | 21947325 |
| 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 |