Genetic diversity and evolutionary relationships ofOryza species with the B- and C-genomes as revealed by SSR markers

Genetic diversity and evolutionary relationships of 72 accessions representing six species with the B-, C-, and BC-genomes in the genusOryza were investigated by seven microsatellite markers. Of four diploid species,Oryza officinalis maintained the highest diversity (P=71.4%, He=0.565), followed by Oryza eichingeri (P=57.1%, He=0.376), Oryzapunctata (P=57.1%, He=0.272) and Oryza rhizomatis (P=42.9%, He=0.222). In comparison, a higher level of genetic diversity was revealed in the tetraploid (P=71.4%, He=0.461-0.637). UPGMA dendrograms based on genetic distance revealed an obvious genetic differentiation between Asian and African races ofO. eichingeri. Three BBCC species clustered with different accessions of the diploidO. punctata, suggestive of their multiple origins. The results inferred from the dendrogram suggested that diploid species,O. officinalis and AfricanO. eichingeri might be the C-genome donors for tetraploid species,Oryza minuta andO. punctata, respectively, while the C-genome ancestor ofOryza malampuzhaensis seemed to be eitherO. rhizomatis or the Sri LankanO. eichingeri species. The genetic relationship among the CC and BBCC species further indicated that the tetraploid species with the BC-genome have originated independently, at least three times in history. In addition, we have demonstrated successful cross-species amplification of seven rice SSR loci acrossOryza species with B-and C-genomes.     

Differentiation and inter-genomic relationships among C, E and D genomes in the Oryzaofficinalis complex (Poaceae) as revealed by multicolor genomic in situ hybridization

The multicolor genomic in situ hybridization (McGISH) method was used to study differentiation and relationships among the C, D and E genomes in the officinalis complex of the genus Oryza. The chromosomes of Oryza alta (CCDD genomes) were hybridized with labelled probes of the C genome (from diploid Oryza eichingeri and Oryza officinalis) and the E genome (from Oryza australiensis) simultaneously. By adjusting the post-hybri- dization washing stringency in a gradual series, differentiation between the genomes was detected according to the homology between the target genomes and the probes. The McGISH results indicate that the C, D and E genomes share a substantial amount of similar sequences, and differentiation between the D and C genomes of O. alta is less than that between the E genome and each of the C and D genomes. The differentiation within the C genomes of the diploid species (O. officinalis and O. eichingeri) and the C genome of O. alta was clearly discerned by McGISH, suggesting strongly that neither O. officinalis nor O. eichingeri was the direct C-genome donor of O. alta. The evidence of the GISH results also indicates that the E genome was considerably differentiated from the C and D genomes. Therefore, the E genome should not be the direct donor of O. alta; on the contrary, the E genome is closer to the C than to the D genome. McGISH is an efficient method in revealing the relationships among the genomes in question, particularly under the gradual stringent-washing condition. Received: 14 February 2000 / Accepted: 14 November 2000     

Phylogenetic relationships among Oryza species revealed by AFLP markers

 The genus Oryza to which cultivated rice belongs has 22 wild species. Seventy-seven accessions of 23 Oryza species, five related genera, and three outgroup taxa were fingerprinted using amplified fragment length polymorphism (AFLP). A total of 1191 polymorphic markers were obtained using five AFLP primer combinations. AFLP data were analyzed to study species relationships using different clustering algorithms, and the resulting phenograms were tested for stability and robustness. The findings suggest a common ancestry to the genus Oryza. Moreover, the results demonstrate that: (1) evolution in Oryza has followed a polyphyletic path wherein multiple lineages underwent independent divergence after separation early in the evolution from a common ancestor/pool of related taxa; (2) newly assigned genomes, GG for O. meyeriana and HHJJ for O. ridleyi complexes, are among the most diverged in the genus; (3) CCDD tetraploids have a relatively ancient origin among the Officinalis complex; (4) O. malampuzhaensis, O. indandamanica, O. alta, and O. grandiglumis are diverged enough to deserve species status; (5) O. officinalis and O. eichingeri (CC) are putative progenitors of O. minuta ^* O. malampuzhaensis and tetraploid O. punctata, respectively, (6) O. brachyantha is most diverged species in the genus. AFLP is reliable molecular technique and provides one of the most informative approaches to ascertain genetic relationships in Oryza, which may also be true for other related species/organisms. Received: 1 July 1998 / Accepted: 2 November 1998     

Genomic, regulatory and epigenetic mechanisms underlying duplicated gene evolution in the natural allotetraploid Oryza minuta

Background

Polyploid species contribute to Oryza diversity. However, the mechanisms underlying gene and genome evolution in Oryza polyploids remain largely unknown. The allotetraploid Oryza minuta, which is estimated to have formed less than one million years ago, along with its putative diploid progenitors (O. punctata and O. officinalis), are quite suitable for the study of polyploid genome evolution using a comparative genomics approach.

Results

Here, we performed a comparative study of a large genomic region surrounding the Shattering4 locus in O. minuta, as well as in O. punctata and O. officinalis. Duplicated genomes in O. minuta have maintained the diploid genome organization, except for several structural variations mediated by transposon movement. Tandem duplicated gene clusters are prevalent in the Sh4 region, and segmental duplication followed by random deletion is illustrated to explain the gene gain-and-loss process. Both copies of most duplicated genes still persist in O. minuta. Molecular evolution analysis suggested that these duplicated genes are equally evolved and mostly manipulated by purifying selection. However, cDNA-SSCP analysis revealed that the expression patterns were dramatically altered between duplicated genes: nine of 29 duplicated genes exhibited expression divergence in O. minuta. We further detected one gene silencing event that was attributed to gene structural variation, but most gene silencing could not be related to sequence changes. We identified one case in which DNA methylation differences within promoter regions that were associated with the insertion of one hAT element were probably responsible for gene silencing, suggesting a potential epigenetic gene silencing pathway triggered by TE movement.

Conclusions

Our study revealed both genetic and epigenetic mechanisms involved in duplicated gene silencing in the allotetraploid O. minuta.     

Genetic variation and population structure inOryza malampuzhaensis Krish.et Chand. endemic to Western Ghats, South India

Oryza malampuzhaensis Krish.et Chand. (2n = 4x = 48; Poaceae,Oryza) is endemic to Western Ghats, South India, and shows a highly localized distribution over a small geographical area in this region. This is the most poorly understood taxon in genusOryza and is often misidentified asO. officinalis owing to their close morphology. We assessed the nature and distribution of genetic variation among 11 populations ofO. malampuzhaensis using random amplified polymorphic DNA markers. The analysis revealed low genetic variation inO. malampuzhaensis. Cluster analysis of pairwise genetic distances of populations revealed three distinct clusters and the grouping of populations largely corresponded to their geographical proximity. Restricted gene flow and a geography-dependent differentiation were evident among populations. The altitude-influenced differences in ecological factors among the natural habitats of the populations seem to be the cause of the geography-dependent differentiation. Genetically isolated smaller populations and a narrow genetic base inO. malampuzhaensis point to its vulnerability to genetic drift and genetic depauperation. ThusO. malampuzhaensis appears to be under the threat of extinction and needs to be conserved by use of suitable methods. The present study also identified molecular markers diagnostic forO. malampuzhaensis.     

Phylogeny and species delimitation of the C‐genome diploid species in Oryza

Abstract The diploid Oryza species with C‐genome type possesses abundant genes useful for rice improvement and provides parental donors of many tetraploid species with the C‐genome (BBCC, CCDD). Despite extensive studies, the phylogenetic relationship among the C‐genome species and the taxonomic status of some taxa remain controversial. In this study, we reconstructed the phylogeny of three diploid species with C‐genome (Oryza officinalis, O. rhizomatis, and O. eichingeri) based on sequences of 68 nuclear single‐copy genes. We obtained a fully resolved phylogenetic tree, clearly indicating the sister relationship of O. officinalis and O. rhizomatis, with O. eichingeri being the more divergent lineage. Incongruent phylogenies of the C‐genome species found in previous studies might result from lineage sorting, introgression/hybridization and limited number of genetic markers used. We further applied a recently developed Bayesian species delimitation method to investigate the species status of the Sri Lankan and African O. eichingeri. Analyses of two datasets (68 genes with a single sample, and 10 genes with multiple samples) support the distinct species status of the Sri Lankan and African O. eichingeri. In addition, we evaluated the impact of the number of sampled individuals and loci on species delimitation. Our simulation suggests that sampling multiple individuals is critically important for species delimitation, particularly for closely related species.     

Polymorphism and phylogenetic relationships among species in the genus Oryza as determined by analysis of nuclear RFLPs

Summary Ninety-three accessions representing 21 species from the genus Oryza were examined for restriction fragment length polymorphism. The majority (78%) of the accessions, for which five individuals were tested, were found to be monomorphic. Most of the polymorphic accessions segregated for only one or two probes and appeared to be mixed pure lines. For most of the Oryza species tested, the majority of the genetic variation (83%) was found between accessions from different species with only 17% between accessions within species. Tetraploid species were found to have, on average, nearly 50% more alleles (unique fragments) per individual than diploid species reflecting the allopolyploid nature of their genomes.Classification of Oryza species based on RFLPs matches remarkably well previous classifications based on morphology, hybridization and isozymes. In the current study, four species complexes could be identified corresponding to those proposed by Vaughan (1989): the O. ridleyi complex, the O. meyeriana complex, the O. officinalis complex and the O. sativa complex. Within the O. sativa complex, accessions of O. rufipogon from Asia (including O. nivara) and perennial forms of O. rufipogon from Australia clustered together with accessions of cultivated rice O. sativa. Surprisingly, indica and japonica (the two major subspecies of cultivated rice) showed closer affinity with different accessions of wild O. Rufipogon than to each other, supporting a hypothesis of independent domestication events for these two types of rice. Australian annual wild rice O. meridionalis (previously classified as O. rufipogon) was clearly distinct from all other O. rufipogon accessions supporting its recent reclassification as O. meridionalis (Ng et al. 1981). Using genetic relatedness as a criterion, it was possible to identify the closest living diploid relatives of the currently known tetraploid rice species. Results from these analyses suggest that BBCC tetraploids (O. malampuzhaensis, O. punctata and O. minuta) are either of independent origins or have experienced introgression from sympatric C-genome diploid rice species. CCDD tetraploid species from America (O. latifolia, O. alta and O. grandiglumis) may be of ancient origin since they show a closer affinity to each other than to any known diploid species. Their closest living diploid relatives belong to C genome (O. eichingeri) and E genome (O. Australiensis) species. Comparisons among African, Australian and Asian rice species suggest that Oryza species in Africa and Australia are of polyphyletic origin and probably migrated to these regions at different times in the past.Finally, on a practical note, the majority of probes used in this study detected polymorphism between cultivated rice and its wild relatives. Hence, RFLP markers and maps based on such markers are likely to be very useful in monitoring and aiding introgression of genes from wild rice into modern cultivars.     

A genome-specific repetitive DNA sequence from Oryza eichingeri: characterization,localization, and introgression to O. sativa

In the course of transferring the brown planthopper resistance from a diploid, CC-genome wild rice species, Oryza eichingeri (IRGC acc. 105159 and 105163), to the cultivated rice variety 02428, we have isolated many alien addition and introgression lines. The O. eichingeri chromatin in some of these lines has previously been identified using genomic in situ hybridization and molecular-marker analysis. Here we cloned a tandemly repetitive DNA sequence from O. eichingeri IRGC acc105163, and detected it in 25 introgression lines. This repetitive DNA sequence showed high specificity to the rice CC genome, but was absent from all the four tetraploid species with BBCC or CCDD genomes. The monomer in this repetitive DNA sequence is 325–366-bp long, with a copy number of about 5,000 per 1 C of the O. eichingeri genome, showing 88% homology to a repetitive DNA sequence isolated from Oryza officinalis (2n=2x=24, CC). Fluorescent in situ hybridization revealed 11 signals distributed over eight O. eichingeri chromosomes, mostly in terminal or subterminal regions. Received: 28 November 2000 / Accepted: 3 April 2001     

Comparative studies of isozymes in Oryza sativa,O. minuta,and their interspecific derivatives: evidence for homoeology and recombination

Enzyme electrophoresis was used to compare the isozyme phenotypes of Oryza sativa, IR31917 (AA genome), and two O. minuta accessions (Om 101089 and Om101141; BBCC genome) for ten enzyme systems. Between the two species, two systems were monomorphic (isocitrate dehydrogenase and alcohol dehydrogenase) and eight were polymorphic (shikimate dehydrogenase, phosphogluconate dehydrogenase, phosphoglucose isomerase, malate dehydrogenase, glutamate oxaloacetate transaminase, esterase, aminopeptidase, and endopeptidase). Polymorphism between O. minuta accessions was detected for shikimate dehydrogenase and glutamate oxaloacetate. As expected, the quaternary structure of the O. minuta isozymes was comparable to that of O. sativa. Possible allelic relationships with known O. sativa alleles and their genomic designation are discussed. Combined with chromosome data, the interspecific variation was exploited to monitor the relative genetic contribution of the two parents in the IR31917/Om101141 F₁ hybrids and recurrent (IR31917) backcross progenies. The isozyme content of F₁ hybrid reflected its triploid nature (ABC genome composition), while that of the backcross progenies paralleled the duplication of the A genome and the gradual loss of O. minuta chromosomes during the backcrossing process. Evidence is provided for a degree of homoeology between the A, B, and C genomes, and for introgression from O. minuta into O. sativa.     

Two new genomes in the Oryza complex identified on the basis of molecular divergence analysis using total genomic DNA hybridization

The genus Oryza to which cultivated rice belongs has 24 species (2n = 24 or 48), representing seven genomes (AA, BB, CC, EE, FF, BBCC and CCDD). The genomic constitution of five of these species is unknown. These five species have been grouped into two species complexes, the tetraploid ridleyi complex (O. ridleyi, O.␣longiglumis) and the diploid meyeriana complex (O.␣granulata, O. meyeriana, O. indandamanica). To evaluate the genomic structure of these species in terms of divergence at the molecular level vis-à-vis other known genomes of Oryza, we used the total genomic DNA hybridization approach. Total genomic DNA (after restriction digestion) of 79 accessions of 23 Oryza species, 6 related genera, 5 outgroup taxa (2 monocots, 3 dicots) and 6 F₁s and BC₁s derived from crosses of O.␣sativa with wild species were hybridized individually with ³²P-labeled total genomic DNA from 12 Oryza species: O. ridleyi, O. longiglumis, O. granulata, O.␣meyeriana, O. brachyantha, O. punctata, O. officinalis, O. eichingeri, O. alta, O. latifolia, O. australiensis, and O.␣sativa. The labeled genomic DNAs representing the ridleyi and meyeriana complexes cross-hybridized best to all the accessions of their respective species, less to those representing other genomes of Oryza and related genera, and least to outgroup taxa. In general, the hybridization differential measured in terms of signal intensities was >50-fold under conditions that permit detection of 70–75% homologous sequences, both in the presence and in the absence of O. sativa DNA as competitor. In contrast, when total DNAs representing other Oryza genomes were used as probes, species of the O.␣ridleyi and O.␣meyeriana complexes did not show any significant cross-hybridization (<5%). These results demonstrate that the genome(s) of both of these complexes are highly diverged and distinct from all other known genomes of Oryza. We, therefore, propose new genomic designations for these two species complexes: GG for the diploid O. meyeriana complex and HHJJ for the allotetraploid O. ridleyi complex. The results also suggest that the uniqueness of these genomes is not restricted to species-specific highly repetitive DNA sequences, but also applies to dispersed sequences present in single or low to moderate copy numbers. Furthermore these appear to share relatively more genome-specific repeat sequences between themselves than with other genomes of rice. The study also demonstrates the potential of total genomic DNA hybridization as a simple but powerful tool, complementary to existing approaches, for ascertaining the genomic makeup of an organism. Received: 26 July 1996 / Accepted: 17 September 1996     

Diversity of centromeric repeats in two closely related wild rice species, Oryza officinalis and Oryza rhizomatis

Oryza officinalis (CC, 2n=24) and Oryza rhizomatis (CC, 2n=24) belong to the Oryza genus, which contains more than 20 identified wild rice species. Although much has been known about the molecular composition and organization of centromeres in Oryza sativa, relatively little is known of its wild relatives. In the present study, we isolated and characterized a 126-bp centromeric satellite (CentO-C) from three bacterial artificial chromosomes of O. officinalis. In addition to CentO-C, low abundance of CentO satellites is also present in O. officinalis. In order to determine the chromosomal locations and distributions of CentO-C (126-bp), CentO (155 bp) and TrsC (366 bp) satellite within O. officinalis, fluorescence in situ hybridization examination was done on pachytene or metaphase I chromosomes. We found that only ten centromeres (excluding centromere 7 and 2) contain CentO-C arrays in O. officinalis, while centromere 7 comprises CentO satellites, and centromere 2 is devoid of any detectable satellites. For TrsC satellites, it was detected at multiple subtelomeric regions in O. officinalis, however, in O. rhizomatis, TrsC sequences were detected both in the four centromeric regions (CEN 3, 4, 10, 11) and the multiple subtelomeric regions. Therefore, these data reveal the evolutionary diversification pattern of centromere DNA within/or between close related species, and could provide an insight into the dynamic evolutionary processes of rice centromere.     

Is Oryza malampuzhaensis Krish. et Chand. (Poaceae) a valid species? Evidence from morphological and molecular analyses

Phylogenetic relationship between O. malampuzhaensis Krish. et Chand. (2n = 4x = 48; Poaceae, Oryzeae), a South Indian endemic wild rice with a disputed taxonomic identity, and eight other species belonging to the O. officinalis complex of the genus Oryza was examined using 62 morphological characters and 445 random amplified polymorphic DNA (RAPD) markers. Multivariate and cluster analyses using both the data sets clearly separated all accessions of O. malampuzhaensis into a distinct group. Genetic distances between O. malampuzhaensis and other species in O. officinalis complex were comparable with the distance between any other two taxa with species rank in this complex. Case-by-case taxonomic treatment of O. malampuzhaensis in relation to other species examined is presented. A taxonomic key for the discrimination of O. malampuzhaensis from other species in the O. officinalis complex has been constructed. Based on the present results, we strongly argue to restore the species rank to O. malampuzhaensis, as originally proposed by Krishnaswamy and Chandrasekharan (1958).     

A tourist element in the 5'-flanking region of the catalase gene CatA reveals evolutionary relationships among Oryza species with various genome types

Tourist-OsaCatA, a transposable element, was found in the 5′-flanking region of the rice gene CatA. The characteristics of this element are similar to those of the other Tourist elements so far found in Oryza sativa. PCR and sequence analyses of 37 accessions of 18 species revealed that all the Oryza species examined, except for one accession, have either a full-length or a partial Tourist element at this locus. Unlike the Tourist elements previously reported, this Tourist element is found in all four Oryza species complexes in the Oryzeae tribe. All AA genome Oryza species, except O. longistaminata, contain the full-length Tourist element. O. longistaminata and the species of the O. officinalis, O. meyeriana and O. ridleyi complexes contain the partial element. A phylogenetic tree of Oryza species based on the nucleotide sequences of these Tourist elements was constructed. The O. longistaminata accessions were placed near the neighboring cluster of the officinalis complex. We propose that the ancestor of O. longistaminata and that of other species with the AA genome diverged, and the ancestor(s) of the O. officinalis, O. ridleyi and O. meyeriana complexes then diverged from the ancestor of O. longistaminata in the course of the evolution of the Oryza species. The Tourist elements associated with CatA and its orthologs thus provide useful tools for examining evolutionary relationships among Oryza species. Received: 12 March 1999 / Accepted: 7 July 1999     

Phylogenetic analysis of Oryza species, based on simple sequence repeats and their flanking nucleotide sequences from the mitochondrial and chloroplast genomes

Simple sequence repeats (SSR) and their flanking regions in the mitochondrial and chloroplast genomes were sequenced in order to reveal DNA sequence variation. This information was used to gain new insights into phylogenetic relationships among species in the genus Oryza. Seven mitochondrial and five chloroplast SSR loci equal to or longer than ten mononucleotide repeats were chosen from known rice mitochondrial and chloroplast genome sequences. A total of 50 accessions of Oryza that represented six different diploid genomes and three different allopolyploid genomes of Oryza species were analyzed. Many base substitutions and deletions/insertions were identified in the SSR loci as well as their flanking regions. Of mononucleotide SSR, G (or C) repeats were more variable than A (or T) repeats. Results obtained by chloroplast and mitochondrial SSR analyses showed similar phylogenetic relationships among species, although chloroplast SSR were more informative because of their higher sequence diversity. The CC genome is suggested to be the maternal parent for the two BBCC genome species (O. punctata and O. minuta) and the CCDD species O. latifolia, based on the high level of sequence conservation between the diploid CC genome species and these allotetraploid species. This is the first report of phylogenetic analysis among plant species, based on mitochondrial and chloroplast SSR and their flanking sequences.     

Two new genomes in the Oryza complex identified on the basis of molecular divergence analysis using total genomic DNA hybridization

The genus Oryza to which cultivated rice belongs has 24 species (2n?=?24 or 48), representing seven genomes (AA, BB, CC, EE, FF, BBCC and CCDD). The genomic constitution of five of these species is unknown. These five species have been grouped into two species complexes, the tetraploid ridleyi complex (O. ridleyi, O.?longiglumis) and the diploid meyeriana complex (O.?granulata, O. meyeriana, O. indandamanica). To evaluate the genomic structure of these species in terms of divergence at the molecular level vis-à-vis other known genomes of Oryza, we used the total genomic DNA hybridization approach. Total genomic DNA (after restriction digestion) of 79 accessions of 23 Oryza species, 6 related genera, 5 outgroup taxa (2 monocots, 3 dicots) and 6 F₁s and BC₁s derived from crosses of O.?sativa with wild species were hybridized individually with ³²P-labeled total genomic DNA from 12 Oryza species: O. ridleyi, O.?longiglumis, O. granulata, O.?meyeriana, O. brachyantha, O. punctata, O. officinalis, O. eichingeri, O. alta, O. latifolia, O. australiensis, and O.?sativa. The labeled genomic DNAs representing the ridleyi and meyeriana complexes cross-hybridized best to all the accessions of their respective species, less to those representing other genomes of Oryza and related genera, and least to outgroup taxa. In general, the hybridization differential measured in terms of signal intensities was >50-fold under conditions that permit detection of 70–75% homologous sequences, both in the presence and in the absence of O. sativa DNA as competitor. In contrast, when total DNAs representing other Oryza genomes were used as probes, species of the O.?ridleyi and O.?meyeriana complexes did not show any significant cross-hybridization (<5%). These results demonstrate that the genome(s) of both of these complexes are highly diverged and distinct from all other known genomes of Oryza. We, therefore, propose new genomic designations for these two species complexes: GG for the diploid O. meyeriana complex and HHJJ for the allotetraploid O. ridleyi complex. The results also suggest that the uniqueness of these genomes is not restricted to species-specific highly repetitive DNA sequences, but also applies to dispersed sequences present in single or low to moderate copy numbers. Furthermore these appear to share relatively more genome-specific repeat sequences between themselves than with other genomes of rice. The study also demonstrates the potential of total genomic DNA hybridization as a simple but powerful tool, complementary to existing approaches, for ascertaining the genomic makeup of an organism.     

GISH-based comparative genomic analysis in Urochloa P. Beauv.

The genus Urochloa P. Beauv. [syn. Brachiaria (Trin.) Griseb.] comprises species of great economic relevance as forages. The genomic constitution for the allotetraploid species Urochloa brizantha (cv. Marandu) and Urochloa decumbens (cv. Basilisk) and the diploid Urochloa ruziziensis was previously proposed as BBB¹B¹, B¹B¹B²B² and B²B², respectively. Evidence indicates U. ruziziensis as the ancestral donor of genome B² in U. decumbens allotetraploidy, but the origin of the genomes B and B¹ is still unknown. There are diploid genotypes of U. brizantha and U. decumbens that may be potential ancestors of the tetraploids. The aim of this study was to determine the genomic constitution and relationships between genotypes of U. brizantha (2x and 4x), U. decumbens (2x and 4x) and U. ruziziensis (2x) via genomic in situ hybridization (GISH). Additionally, chromosome number and genome size were verified for the diploid genotypes. The diploids U. brizantha and U. decumbens presented 2n?=?2x?=?18 chromosomes and DNA content of 1.79 and 1.44 pg, respectively. The GISH analysis revealed high homology between the diploids U. brizantha and U. decumbens, which suggests relatively short divergence time. The GISH using genomic probes from the diploid accessions on the tetraploid accessions’ chromosomes presented similar patterns, highlighting the genome B¹ present in both of the tetraploids. Based on GISH results, the genomic constitution was proposed for the diploid genotypes of U. brizantha (B¹B¹) and U. decumbens (B¹′B¹′) and both were pointed as donors of genome B¹ (or B¹′), present in the allotetraploid genotypes.

     

Chromosomal polymorphism of ribosomal genes in the genus Oryza

The genes encoding for 18S–5.8S–28S ribosomal RNA (rDNA) are both conserved and diversified. We used rDNA as probe in the fluorescent in situ hybridization (rDNA-FISH) to localized rDNAs on chromosomes of 15 accessions representing ten Oryza species. These included cultivated and wild species of rice, and four of them are tetraploids. Our results reveal polymorphism in the number of rDNA loci, in the number of rDNA repeats, and in their chromosomal positions among Oryza species. The numbers of rDNA loci varies from one to eight among Oryza species. The rDNA locus located at the end of the short arm of chromosome 9 is conserved among the genus Oryza. The rDNA locus at the end of the short arm of chromosome 10 was lost in some of the accessions. In this study, we report two genome specific rDNA loci in the genus Oryza. One is specific to the BB genome, which was localized at the end of the short arm of chromosome 4. Another may be specific to the CC genome, which was localized in the proximal region of the short arm of chromosome 5. A particular rDNA locus was detected as stretched chromatin with bright signals at the proximal region of the short arm of chromosome 4 in O. grandiglumis by rDNA-FISH. We suggest that chromosomal inversion and the amplification and transposition of rDNA might occur during Oryza species evolution. The possible mechanisms of cyto-evolution in tetraploid Oryza species are discussed.     

Molecular diversity in the primary and secondary gene pools of genus Oryza

The objective of the present investigation was to assess the genetic relationships among the species of Oryza that belong to the primary gene pool (sativa complex) and the secondary gene pool (officinalis complex) using three marker systems such as RAPDs, ISSRs and SSRs. A total of 432 clear and reproducible bands were amplified from 18 RAPD primers; 113 bands were detected from 8 ISSR primers and 78 alleles were found to be amplified across the Oryza species from 13 SSR primer pairs. All the three dendrograms constructed, using UPGMA from the genetic similarity matrices based on the three marker data sets, were similar in their groupings. In all the three trees, two accessions of Oryza sativa formed an exclusive group indicating its genomic differentiation from its wild ancestors through the process of domestication. Distinctness between the wild species of the sativa and officinalis complexes was evident in all the trees derived from different markers. The groupings obtained among the species of the sativa complex were in perfect concordance with the species relationships established through classical crossability and cytogenetic analysis. This study has brought out some information on the species relationship between the diploid and tetraploid genomes of the officinalis complex possessing BB, CC and DD genomes. The higher level of similarity observed between the species possessing C and D genomes supports the view of many earlier authors that these two genomes might have originated from a single hybridization event. The results of this study also show that the diploid species possessing C genomes such as Oryza officinalis, Oryza rhizomatis and Oryza eichingeri are distinct from their allotetraploid counterparts possessing BBCC and CCDD genomes indicating a wider genomic differentiation in their evolutionary process.     

Photosynthetic characteristics in <Emphasis Type="Italic">Oryza</Emphasis> species

Photosynthetic rate (P _N), SPAD value, specific leaf area (SLA), flag leaf area (FLA), and nitrogen content (LN) of genus Oryza were investigated and their correlation was analyzed to assess some of the main photosynthetic traits among different species in the genus Oryza. The results revealed wide variation in these traits. The species O. rufipogon and O. australiensis exhibited maximum photosynthetic rate. Comparison of different types of genomes (diploid: 2n=2x=24; tetraploid: 2n=4x=48) and growth habit (shade- or sun-grown) showed the species of diploid (with genome symbol EE; 2n=2x=24) genomes, with perennial and sun-grown species, had high apparent photosynthesis compared to others. The species with BB/BBCC, shade-grown and the tetraploids showed high SPAD value, and the flag leaf in sun-grown species and diploids were thicker (low SLA) compared with others. However, no significant difference could be noticed among the different types of genomes. Higher leaf area was noticed among the species of CC/CCDD genome, perennial shade-grown species and tetraploids than in others. The variety IR 36 exhibited highest leaf nitrogen concentration. Correlation analysis showed a strong relationship between P _N and leaf nitrogen concentration while no marked relationships were observed among other characteristics. It implies that the species with thick and small leaves with high nitrogen concentration and high photosynthesis evolved better than others. O. rufipogon, with the same genome as O. sativa, could be one of the wild rice resources for elite crop improvement.     

Detection of specific chromosome reduction in rice somatic hybrids with the A, B, and C genomes by multi-color genomic in situ hybridization

 A multi-color genomic in situ hybridization (McGISH) method has been developed. Three different rice genomes, A, B and C, involved in rice somatic hybrids were distinguished using three different fluorescent signals. All the rice chromosomes from the different genomes could be identified by different fluorescent colors, and the distribution of each genome in the nucleus was clearly visualized under a fluorescence microscope. The relationship between chromosomal constitution and morphological variations observed in the somatic hybrids, and the utility of McGISH, are discussed based on the results currently obtained. Received: 21 November 1997 / Accepted: 9 December 1997