RAPD, RFLP and SSLP analyses of phylogenetic relationships between cultivated and wild species of rice.

RAPD, RFLP, nuclear SSLP and chloroplast SSLP analyses were carried out to clarify the phylogenetic relationships among A-genome species of rice. In total, 12 cultivars of Oryza sativa (4 Japonica, 3 Javanica and 5 Indica), one cultivar of O. glaberrima, and 17 wild accessions (12 O. rufipogon, 2 O. glumaepatula, 1 O. longistaminata, 1 O. meridionalis and 1 O. barthii) were used. Their banding patterns were scored and compared to evaluate the similarity between accessions. Genetic differentiation within and between taxa was examined based on the average similarity indices. Except for chloroplast SSLP analysis, the average similarities were higher within O. sativa than within O. rufipogon, and O. sativa Indica had greater intrasubspecific variation than Japonica and Javanica. Comparisons between cultivated and wild species showed that O. sativa was closely related to O. rufipogon, while O. glaberrima was closely related to O. barthii. This indicated that two cultivated species, O. sativa and O. glaberrima, originated from O. rufipogon and O. barthii, respectively. Domestication of O. sativa seemed to be diphyletic, since strong similarity was observed between O. sativa Japonica-Javanica and O. rufipogon from China and between O. sativa Indica and O. rufipogon from tropical Asia. In addition, dendrograms for RAPD, RFLP, and nuclear and chloroplast SSLP analyses were constructed to reveal the overall genetic relationships among A-genome species. In all analyses, O. sativa and O. glaberrima formed groups with O. rufipogon and O. barthii, respectively. However, their manners of clustering with other wild species were not the same. The results of RAPD and RFLP analyses indicate that O. glumaepatula was relatively close to the groups of O. sativa and O. glaberrima whereas O. longistaminata and O. meridionalis were highly differentiated from other A-genome species. On the other hand, clear interspecific relationships were not obtained by nuclear or chloroplast SSLP analyses.     

Evolutionary relationships among rice species with AA genome based on SINE insertion analysis

Previous studies based on morphological and molecular markers indicated that there are two cultivated and five wild rice species within the Oryza genus with the AA genome. In the cultivated rice species, Oryza sativa, a retroposon named p-SINE1 has been identified. Some of the p-SINE1 members characterized previously showed interspecific insertion polymorphisms in the species with the AA genome. In this study, we identified new p-SINE1 members showing interspecific insertion polymorphisms from representative strains of four wild rice species with the AA genome: O. barthii, O. glumaepatula, O. longistaminata, and O. meridionalis. Some of these members were present only in strains of one species, whereas the others were present in strains of two or more species. The p-SINE1 insertion patterns in the strains of the Asian and African cultivated rice species O. sativa and O. glaberrima were very similar to those of the Asian and African wild rice species O. rufipogon and O. barthii, respectively. This is consistent with the previous hypothesis that O. sativa and O. glaberrima are derived from specific wild rice species. Phylogenetic analysis based on the p-SINE1 insertion patterns showed that the strains of each of the five wild rice species formed a cluster. The strains of O. longistaminata appear to be distantly related to those of O. meridionalis. The strains of these two species appear to be distantly related to those of three other species, O. rufipogon, O. barthii and O. glumaepatula. The latter three species are closely related to one another with O. barthii and O. glumaepatula being most closely related. A phylogenetic tree including a hypothetical ancestor with all loci empty for p-SINE1 insertion showed that the strains of O. longistaminata are related most closely to the hypothetical ancestor. This indicates that O. longistaminata and O. meridionalis diverged early on, whereas the other species diverged relatively recently, and suggests that the Oryza genus with AA genome might have originated in Africa, rather than in Asia.     

8个野生稻种的叶片硅体研究

用强酸溶液分离8个野生稻种叶片中的硅体并用光学显微镜和电子扫描显微镜进行观测研究.结果显示,(1)叶片含有3种类型的硅体,即不规则硅体、哑铃形硅体和扇形硅体,前2种硅体不能作为属内分类的依据,但短药野生稻哑铃形硅体的表面纹饰独特,可作为识别该物种的特征.(2)同一个物种的扇形硅体变异很大,统计学表明它总以其中的某一种类型占有优势,紧穗野生稻和短舌野生稻中小型硅体占优势,药用野生稻和普通野生稻中约有一半为中型硅体,另一半为小型硅体,其余4种野生稻包括斑点野生稻、澳洲野生稻、展颖野生稻和短药野生稻中绝大多数为中型硅体,即野生稻的扇形硅体以中、小型为主.(3)根据扇面长/扇柄长的比值,将扇形硅体划分为长柄型、中间形和短柄型3种形态,依此对8个稻种的硅体分类.结果表明,斑点野生稻、药用野生稻、紧穗野生稻和澳洲野生稻以长柄型为优势;普通野生稻、短舌野生稻、展颖野生稻和短药野生稻则以中间型为主,且扇形硅体的扇面长/扇柄长的比值的大小与野生稻染色体组型或原产地有关.     

The Structural Features of Leaf Epidermis in Oryza and Their Systematic Significance

The rice genus (Oryza L. ) belongs to the grass family(Poaceae) and contains 24 annual or perennial species, including two cultivated rice species, i.e., the Asian rice ( O. sativa L. ) and African rice (O. glaberrima Steud. ), and 22 wild species distributed throughout the tropics of the world. Species in this genus have been extensively studied by scientists with different approaches, including morphological characterization and cytological and molecular investigations. The leaf epidermis is an important morphological character which has been studied for taxonomic identification and studies on systematic relationships of species, particularly in grasses. In this study, morphological features of the leaf epidermis of 23 rice species were observed through light microscopy. The results showed that some characters of the rice leaf epidermis had significant diversity between species and these characters were valuable for the identifying Oryza species, and for assessing systematic relationships in the genus. For example, O.schlechteri, O.ridleyi, O.longiglumis, O.granulata, and O. rneyeriana had elliptic stomatal complexes, whereas the other species had rhombic stomatal complexes. In most cases, papillae on the surface of the epidermis were variable in size and distribution between species. The size of papillae varied from small ( 1.5～4.4µm in diameter), medium-sized (9～18µm), to large (21～30µm) , and the pattern of papillary size and distribution were very useful for identification of rice species. In addition, the number and location of the small papillae in stomatal complexes were particularly different between species. Based on the following combinations of leaf-epidermic characters, i.e., the size and distribution of papillae on the abaxial surface of the epidermis, the number and location of the small papillae in stomatal complexes, and the shape of stomatal complexes, the 23 studied Oryza species could be divided into three major groups. The first group comprises O.longiglumis, O.ridleyi, O.meyeriana, and O.granulata. In these species, neither large nor medium-sized papillae, in some cases extremely rare small papillae, were found on the surfaces of epidermis, and there were no small papillae found in stomatal complexes. All species in the first group had elliptic stomatal complexes. The second group consists of O.brachyantha, diploid and tetraploid O.officinalis, O.minuta, O.eichingeri, O. punctata, O.latifolia, O.alta, O.grandiglumis, O.rhizomatis, and O.australiensis. In these species usually no large papillae were observed, but medium-sized and densely populated small papillae were found to cover the surface of epidermis, and at least four small papillae were found in stomatal complexes (in guard cells) of most species. The third group contains O.sativa, O.nivara, O.rufipogon, O.longistaminata, O. glumaepatula, O.meridionalis, O.barthii, O.glaberrima and O. schlechteri. The abaxial leaf epidermis of these species was usually covered with large papillae, medium-sized, and small papillae. In addition, more than 4 (usually 6～8 ) small papillae were found in guard cells or/and subsidiary cells of the stomatal complexes. Most species in the second and third groups had rhombic stomatal complexes. These results agree mostly with previous re-ports on the biosystematic studies of rice species by applying other methodologies.     

水稻CMS相关基因在稻属AA基因组中的分布及其单核苷酸多态性

水稻线粒体基因组嵌合基因orf79 和 orfH79分别被认为与BT-型和HL-型水稻CMS有关, 两者具有98%的同源性, 并且其DNA序列只存在4核苷酸的差异。对于这两个嵌合基因, 前者来源于栽培稻(Oryza. sativa L.), 而后者则来源于普通野生稻(O. rufipogon Griff.)。这意味着orf79/ orfH79可能在广泛分布于稻属AA基因组中。为了调查orf79/ orfH79在稻属物种中的分布和变异, 190份栽培稻品系[包括156份亚洲栽培稻(O. sativa var. landrace)和34份非洲栽培稻(O. glaberrima)]以及104份稻属AA基因组野生稻品系(包括O. rufipogon、O.nivara、O. glumaepatula、O. barthii、O. longistaminata和O. meridionalis 6个种), 被用于PCR扩增检测。31份具有控制粤泰A和笹锦A的特异片段的稻属AA基因组水稻品系被检测出。所有特异片段均被回收并测序, 基于DNA 序列的聚类结果显示31份水稻材料被分成了两组, 分别代表为BT-型和HL-型水稻不育细胞质组群。结果也进一步表明: HL-型水稻CMS胞质主要分布于一年生的O. nivara中; BT-型水稻CMS胞质可能来源于栽培稻变种或多年生野生稻O. rufipogon。     

Nuclear- and chloroplast-microsatellite variation in A-genome species of rice.

Simple sequence length polymorphism analysis was carried out to reveal microsatellite variation and to clarify the phylogenetic relationships among A-genome species of rice. Total DNA from 29 cultivars (23 Oryza sativa and 6 O. glaberrima) and 30 accessions of wild A-genome species (12 O. rufipogon, 5 O. glumaepatula, 2 O. longistaminata, 6 O. meridionalis, and 5 O. barthii) was used as a template for PCR to detect 24 nuclear and 10 chloroplast microsatellite loci. Microsatellite allelic diversity was examined based on amplified banding patterns. Microsatellites amplified clearly in all 59 accessions, with an average of 18.4 alleles per locus. The polymorphism information content (PIC) value ranged from 0.85 to 0.94, with an average of 0.89. At the species level, high average PIC values were observed in O. sativa (0.79) and O. rufipogon (0.80). For chloroplast microsatellites, the average number of alleles per locus and the average PIC value were 2.9 and 0.38, respectively. While the magnitude of diversity was much greater for nuclear microsatellites than for chloroplast microsatellites, they showed parallel patterns of differentiation for each taxonomic group. Using the ratio of common alleles (estimated as size of amplified fragments) as a similarity index, the average percentages of common microsatellite alleles were calculated between taxa. For both nuclear and chloroplast microsatellites, O. sativa showed the highest similarity values to O. rufipogon, and O. glaberrima was most similar to O. barthii. These data support previous evidence that these cultivars originated from the corresponding wild ancestral species.     

Genetic diversity and phylogenetic relationship in AA Oryza species as revealed by Rim2/Hipa CACTA transposon display

CACTA is a class 2 transposon, that is very abundantly present in plant genomes. Using Rim2/Hipa CACTA transposon display (hereafter Rim2/Hipa-TD), we analyzed several A-genome diploid Oryza species that have a high distribution of the CACTA motifs. High levels of polymorphism were detected within and between the Oryza species. The African taxa, O. glaberrima and O. barthii, both showed lower levels of polymorphism than the Asian taxa, O. sativa, O. rufipogon, and O. nivara. However, O. longistaminata, another African taxon, showed levels of polymorphism that were similar to the Asian taxa. The Latin American taxon, O. glumaepatula, and the Australian taxon, O. meridionalis, exhibited intermediate levels of polymorphism between those of the Asian and African taxa. The lowest level of polymorphism was observed in O. glaberrima (32.1%) and the highest level of polymorphism was observed in O. rufipogon (95.7%). The phylogenetic tree revealed three major groups at the genetic similarity level of 0.409. The first group consisted of three Asian taxa, O. sativa, O. rufipogon and O. nivara. The second group consisted of three African taxa, O. glaberrima, O. barthii, O. longistaminata, and an American taxon, O. glumaepatula. The third group contained an Australian taxon, O. meridionalis. The clustering patterns of these species matched well with their geographical origins. Rim2/Hipa-TD appears to be a useful marker system for studying the genetic diversity and species relationships among the AA diploid Oryza species.     

Ultrastructure of Oryza glumaepatula, a wild rice species endemic of tropical America

Orv'za gluniaepatula is a perennial wild rice species, endemic to tropical America, previously known as the Latin American race of Orrza rufipogon. In Costa Rica, it is found in the northern region of the country, mainly in the wetland of the Medio Queso River, Los Chiles, Alajuela. It is diploid, of AA type genome and because of its genetic relatedness to cultivated rice it is included in the O. saliva complex. We describe the ultrastructure of leaf blade, spikelet, ligule and auricles. Special emphasis is given to those traits of major taxonomic value for O. glumaepatula and to those characters that distinguish this species from O. rufipogon and O. sativa. O. glumaepatula has a leaf blade covered with tombstone-shaped, oblong and spheroid epicuticular wax papillae. It has diamond-shaped stomata surrounded by spherical papillae, rows of zipper-like silica cells, bulky prickle trichomes of ca. 40 microm in length and small hirsute trichomes of ca. 32 tpm in length. The central vein is covered with large, globular papillae of ca. 146 microm in length, a characteristic that distinguishes this species from O. rufipogon and O. sativa. The border of the leaf blade exhibits a row of even-sized bulky prickle trichomes of ca. 42.5 microm in length. Auricles have attenuated trichomes of ca. 5.5 mm in length on the edges and small bicellular trichomes of 120 microm in length on the surface. The ligule has a large number of short attenuated trichomes on its surface of 100 microm in length. These latter two traits have important taxonomic value since they were found in O. glumaepatula but not found in O. sativa or in O. rufipogon. The spikelet has the typical morphology of the Oryza genus. Fertile lemmas have abundant spines, a trait shared with O. rufipogon but not with O. sativa. The sterile lemmas are wing-shaped with serrated borders, a characteristic that distinguishes this species from O. rufipogon and O. sativa. All the ultrastructure characters observed in O. glumaepatula from Costa Rica are also common to the specimens from Brazil.     

Chloroplast genome sequence confirms distinctness of Australian and Asian wild rice

Cultivated rice (Oryza sativa) is an AA genome Oryza species that was most likely domesticated from wild populations of O. rufipogon in Asia. O. rufipogon and O. meridionalis are the only AA genome species found within Australia and occur as widespread populations across northern Australia. The chloroplast genome sequence of O. rufipogon from Asia and Australia and O. meridionalis and O. australiensis (an Australian member of the genus very distant from O. sativa) was obtained by massively parallel sequencing and compared with the chloroplast genome sequence of domesticated O. sativa. Oryza australiensis differed in more than 850 sites single nucleotide polymorphism or indel from each of the other samples. The other wild rice species had only around 100 differences relative to cultivated rice. The chloroplast genomes of Australian O. rufipogon and O. meridionalis were closely related with only 32 differences. The Asian O. rufipogon chloroplast genome (with only 68 differences) was closer to O. sativa than the Australian taxa (both with more than 100 differences). The chloroplast sequences emphasize the genetic distinctness of the Australian populations and their potential as a source of novel rice germplasm. The Australian O. rufipogon may be a perennial form of O. meridionalis.     

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 at the respective loci. A phylogenetic tree constructed based on the bar codes given to the rice strains showed that O. sativa strains were classified into two groups corresponding to japonica and indica, whereas O. rufipogon strains were in four groups, in which annual O. rufipogon strains formed a single group, differing from the perennial O. rufipogon strains of the other three groups. Japonica strains were closely related to the O. rufipogon perennial strains of one group, and the indica strains were closely related to the O. rufipogon annual strains, indicating that O. sativa has been derived polyphyletically from O. rufipogon. The subfamily members of p-SINE1 constitute a powerful tool for studying the classification and relationship of rice strains, even when one has limited knowledge of morphology, taxonomy, physiology, and biochemistry of rice strains.     

Population genetic structure of wild rice Oryza glumaepatula distributed in the Amazon flood area influenced by its life-history traits

Wild plant species develop their own way of living to adapt to the specific environment of their habitats. Their life-history traits strongly affect the genetic structure of the population. The wild species Oryza glumaepatula Steud. growing in the Amazon basin seems to have characteristic life-history traits suited for the flood condition. At the vegetative growth stage, the culms frequently break at internodes. With no roots anchoring on the ground, plant bodies floating in the water move downriver by water current and wind. To examine the association between the life-history traits and genetic population structure of Amazonian O. glumaepatula , we analysed allozyme variability at 29 loci of 16 enzymes using 37 populations from five regions. Allozymes were not so variable (total gene diversity H _E = 0.044) compared with Asian wild rice, O. rufipogon Griff. The bottleneck effect and rare opportunity of interspecies gene flow may prevent the development of allozyme variability. Population genotypes tended to be differentiated among geographically isolated regions. Observed heterozygosities were much lower than expected heterozygosities, or gene diversity ( H _O = 0.003 for whole population) and F _IS over polymorphic loci was 0.931, indicating that O. glumaepatula has developed an inbreeding system. But, the intrapopulation gene diversity ( H _S) was higher than interpopulation gene diversity ( D _ST), as generally observed in outbreeding populations. The migration ability of O. glumaepatula makes long-distance seed dispersal possible. This might have led to frequent gene flow among populations.     

Fitness estimation through performance comparison of F1 hybrids with their parental species Oryza rufipogon and O. sativa

BACKGROUND AND AIMS: 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. METHODS: This study estimated relative fitness of interspecific hybrids through performance comparison of F(1) hybrids with their parental species, a cultivated rice (Oryza sativa) Minghui-63 and perennial common wild rice (O. rufipogon) under the cultivation conditions. KEY RESULTS: Compared with their parents, the hybrids had the lowest values of seedling survival ability, pollen viability and seed production; intermediate values of seed germination, spikelet production and flag leaf areas; and the highest values of plant height, number of tillers and panicles. The hybrids performed poorly at the stage of sexual reproduction, although they had a slightly higher hybrid vigour at the vegetative growth stage and better tillering ability than their wild parent. There were no significant differences in composite fitness across the whole life-history between the hybrids and their wild parental species. CONCLUSIONS: Rice genes, including transgenes, might persist in wild rice populations through vegetative and sexual reproduction. Further studies are needed to examine whether the extent of gene flow from rice is sufficiently significant to influence genetic diversity in wild populations of O. rufipogon, a species that has become endangered in some regions of south-east Asia.     

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 genome species, African taxa, O. glaberrima and Oryza barthii, showed lower variation than the Asian taxa, O. sativa, Oryza rufipogon, and Oryza nivara, and Australian taxon Oryza meridionalis. However, another African taxon, Oryza longistaminata, showed high genetic variation. Species relationships were analyzed by the pattern of presence or absence of homologous fragments, because nucleotide sequences of the detected MITE-AFLP fragments revealed that the same fragments in different species shared very high sequence homology. The clustering pattern of the AA-genome species matched well with the geographical origins (Asian, African and Australian), and with the Australian taxon being distant to the others. Therefore, this study demonstrated that the MITE-AFLP technique is amenable for studying the genetic variation and species relationship in rice.     

Characterization of Interspecific Hybrids Between Oryza sativa L. and Three Wild Rice Species of China by Genomic In Situ Hybridization

In the genus Oryza, interspecific hybrids are useful bridges for transferring the desired genes from wild species to cultivated rice （Oryza sativa L.）. In the present study, hybrids between O. sativa （AA genome） and three Chinese wild rices, namely O. rufipogon （AA genome）, O. officinalis （CC genome）, and O. meyeriana （GG genome）, were produced. Agricultural traits of the F1 hybrids surveyed were intermediate between their parents and appreciably resembled wild rice parents. Except for the O. sativa × O. rufipogon hybrid, the other F1 hybrids were completely sterile. Genomic in situ hybridization （GISH） was used for hybrid verification. Wild rice genomic DNAs were used as probes and cultivated rice DNA was used as a block. With the exception of O. rufipogon chromosomes, this method distinguished the other two wild rice and cultivated rice chromosomes at the stage of mitotic metaphase with different blocking ratios. The results suggest that a more distant phylogenetic relationship exists between O. meyeriana and O. sativa and that O. rufipogon and O. sativa share a high degree of sequence homology. The average mitotic chromosome length of O. officinalis and O. meyeriana was 1.25- and 1.51-fold that of O. sativa, respectively. 4＇,6＇-Diamidino- 2-phenylindole staining showed that the chromosomes of O. officinalis and O. meyeriana harbored more heterochromatin, suggesting that the C and G genomes were amplified with repetitive sequences compared with the A genome. Although chromocenters formed by chromatin compaction were detected with wild rice-specific signals corresponding to the C and G genomes in discrete domains of the F1 hybrid interphase nuclei, the size and number of O. meyeriana chromocenters were bigger and greater than those of O. officinalis. The present results provide an important understanding of the genomic relationships and a tool for the transfer of useful genes from three native wild rice species in China to cultivars.     

Genetic diversity and origin of weedy rice (Oryza sativa f. spontanea) populations found in North-eastern China revealed by simple sequence repeat (SSR) markers

BACKGROUND AND AIMS: 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. METHODS: Simple sequence repeat (SSR) markers were used to estimate the genetic diversity of 30 weedy rice populations from Liaoning, each containing about 30 individuals, selected rice varieties and wild O. rufipogon. Genetic differentiation and the relationships of weedy rice populations were analysed using cluster analysis (UPGMA) and principle component analysis (PCA). KEY RESULTS: The overall genetic diversity of weedy rice populations from Liaoning was relatively high (H(e) = 0.313, I = 0.572), with about 35 % of the genetic variation found among regions. The Liaoning weedy rice populations were closely related to rice varieties from Liaoning and japonica varieties from other regions but distantly related to indica rice varieties and wild O. rufipogon. CONCLUSIONS: Weedy rice populations from Liaoning are considerably variable genetically and most probably originated from Liaoning rice varieties by mutation and intervarietal hybrids. Recent changes in farming practices and cultivation methods along with less weed management may have promoted the re-emergence and divergence of weedy rice in North-eastern China.     

Morphological studies of Asian rice and its related wild species and the recognition of a new Australian taxon

In order to clarify the taxonomy and the interrelationships among Asiatic cultivated rice, Oryza sativa , and its related wild species ( O. rufipogon, O. nivara and O . barthii ), 41 morphological characters were examined. Numerical taxonomic methods were used to analyse the data and to illustrate species relationships.
Distinctive differences among the materials studied suggest the retention of O. rufipogoon, O. nivara and O . sativa as three distinct species. The origin of O. sativa from O. nivara through domestication is discussed. An annual wild taxon from Australia, which had been classified as a form of O. nivara , is shown to be distinct from typical O. nivnra and is raised to specific rank. This species has been named O. meridionalis Ng.     

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 and a standard japonica rice based on these SSILP markers. Using these SSILP markers to genotype 73 O. rufipogon accessions, we found that the indica alleles and japonica alleles of the SSILP markers were predominant in the O. rufipogon accessions, suggesting that SSILPs were highly conserved during the evolution of O. sativa. Cluster analysis based on these markers yielded a dendrogram consisting of two distinct groups： one group （Group I） comprises all the O. rufipogon accesions from tropical （South and Southeast） Asia as well as the standard indica rice; the other group （Group II） comprises all the O. rufipogon accessions from Southern China as well as the standard japonica rice. Further analysis showed that the two groups have significantly higher frequencies of indica alleles and japonica alleles, respectively. These results support the hypothesis that indica rice and japonica rice were domesticated from the O. rufipogon of tropical Asia and from that of Southern China, respectively, and suggest that the indica-japonica differentiation should have formed in O. rufipogon long before the beginning of domestication. Furthermore, with an O. glaberrima accession as an outgroup, it is suggested that the indica-japonica differentiation in O. ruffpogon might occur after its speciation from other AA-genome species.     

Analysis of random and specific sequences of nuclear and cytoplasmic DNA in diploid and tetraploid american wild rice species (Oryza spp.).

A sample of American wild rice and other accessions of the genus Oryza were studied at polymorphic regions of nuclear, mitochondrial, and chloroplastic genomes. First, flow cytometry, genome-specific RAPD markers, and chromosome counting were utilized to verify the original ploidy and classification of 230 accessions studied. Based on these methods, 8% of the accessions were considered to be misclassified either taxonomically or as a result of contamination. Second, a fine resolution analysis was conducted at genomic regions sampled at random by RAPD markers and at specific sites of the chloroplast and mitochondrial DNA by cleaved amplified polymorphic sequence (CAPS) analysis. Phylogenetic trees resulting from phenetic and cladistic analyses of RAPD, cpDNA, and mtDNA polymorphisms were obtained. The results indicated that the American diploid species O. glumaepatula should be considered an individual species, distinct from O. rufipogon, and confirmed that the American tetraploid species (O. alta, O. grandiglumis, and O. latifolia) belong to the O. officinalis complex. The data indicate that these species should still be treated as a group rather than as three distinct species and that their closest relative is a CC-genome species. It was estimated that the diploid and tetraploid American species diverged from O. sativa - O. nivara (AA genome) and CC- and BBCC-genome species, respectively, 20 million years ago.     

菰核基因组SSR引物的开发及其在稻族植物中的通用性检测

利用数据库中已有的部分菰(Zizania latifolia Turcz.)核基因组序列,采用in silico方法开发其SSR引物,并选取我国不同纬度的5个菰野生种群,对合成的64对引物进行筛选。结果显示:64对引物中有15对至少在一个种群中表现出多态性;共发现84个等位基因,每个位点平均有5.6个等位基因。在5个种群中,观察杂合度为0.000~0.941,预期杂合度为0.072~0.625。种群间的基因流(Nm=0.576)水平较低导致了种群间表现出较高的遗传分化(FST=0.432)。进一步对稻族其他物种的通用性检测发现,15个多态位点中,有8个位点在亚洲栽培稻(Oryza sativa L.)中得到扩增,有9个位点在普通野生稻(O.rufipogon Griff.)中得到扩增。     

Phylogenetic analysis of Oryza rufipogon strains and their relations to Oryza sativa strains by insertion polymorphism of rice SINEs

Oryza rufipogon, the progenitor of the cultivated rice species Oryza sativa, is known by its wide intraspecific variation. In this study, we performed phylogenetic analyses of O. rufipogon strains and their relationships to O. sativa strains by using 26 newly identified p-SINE1 members from O. rufipogon strains, in addition to 23 members previously identified from O. sativa strains. A total of 103 strains of O. rufipogon and O. sativa were examined for the presence and absence of each of the p-SINE1 members at respective loci by PCR with a pair of primers that hybridize to the regions flanking each p-SINE1 member. A phylogenetic tree constructed on the basis of the insertion polymorphism of p-SINE1 members showed that O. rufipogon and O. sativa strains are classified into three groups. The first group consisted of O. rufipogon perennial strains mostly from China and O. sativa ssp. japonica strains, which included javanica strains forming a distinct subgroup. The second group consisted of almost all the O. rufipogon annual strains, a few O. rufipogon perennial strains and O. sativa ssp. indica strains. These groupings, in addition to other results, support the previous notion that annual O. rufipogon originated in the O. rufipogon perennial population, and that O. sativa originated polyphyletically in the O. rufipogon populations. The third group consisted of the other perennial strains and intermediate-type strains of O. rufipogon, in which the intermediate-type strains are most closely related to a hypothetical ancestor with no p-SINE1 members at the respective loci and to those belonging to the other rice species with the AA genome. This suggests that O. rufipogon perennial strains are likely to have originated from the O. rufipogon intermediate-ecotype population.