Sex-independent transmission ratio distortion system responsible for reproductive barriers between Asian and African rice species

* A sex-independent transmission ratio distortion (siTRD) system detected in the interspecific cross in rice was analyzed in order to understand its significance in reproductive barriers. The S(1) gene, derived from African rice Oryza glaberrima, induced preferential abortion of both male and female gametes possessing its allelic alternative (), from Asian rice O. sativa, only in the heterozygote. * The siTRD was characterized by resolving it into mTRD and fTRD occurring through male and female gametes, respectively, cytological analysis of gametophyte development, and mapping of the S(1) locus using near-isogenic lines. The allelic distribution of the S(1) locus in Asian and African rice species complexes was also analyzed. * The siTRD system involved at least two components affecting male and female gametogeneses, respectively, including a modifier(s) that enhances fTRD. The chromosomal location of the major component causing the mTRD was delimited within an approx. 40 kb region. The S(1) locus induced hybrid sterility in any pairwise combination between Asian and African rice species complexes. * The allelic state of the S(1) locus has diverged between Asian and African rice species complexes, suggesting that the TRD system has a significant role in the reproductive barriers in rice.     

Assessing hybrid sterility in <Emphasis Type="Italic">Oryza glaberrima</Emphasis> × <Emphasis Type="Italic">O. sativa</Emphasis> hybrid progenies by PCR marker analysis and crossing with wide compatibility varieties

Interspecific crossing of the African indigenous rice Oryza glaberrima with Oryza sativa cultivars is hindered by crossing barriers causing 100% spikelet sterility in F₁ hybrids. Since hybrids are partially female fertile, fertility can be restored by back crossing (BC) to a recurrent male parent. Distinct genetic models on spikelet sterility have been developed predicting, e.g., the existence of a gamete eliminator and/or a pollen killer. Linkage of sterility to the waxy starch synthase gene and the chromogen gene C, both located on chromosome 6, have been demonstrated. We selected a segregating BC₂F₃ population of semi-sterile O. glaberrima × O. sativa indica hybrid progenies for analyses with PCR markers located at the respective chromosome-6 region. These analyses revealed that semi-sterile plants were heterozygous for a marker (OSR25) located in the waxy promoter, whereas fertile progenies were homozygous for the O. glaberrima allele. Adjacent markers showed no linkage to spikelet sterility. Semi-sterility of hybrid progenies was maintained at least until the F₄ progeny generation, suggesting the existence of a pollen killer in this plant material. Monitoring of reproductive plant development showed that spikelet sterility was at least partially due to an arrest of pollen development at the microspore stage. In order to address the question whether genes responsible for F₁ sterility in intraspecific hybrids (O. sativa indica × japonica) also cause spikelet sterility in interspecific hybrids, crossings with wide compatibility varieties (WCV) were performed. WCV accessions possess "neutral" S-loci (Sⁿ) improving fertility in intraspecific hybrids. This experiment showed that the tested Sⁿ-loci had no fertility restoring effect in F₁ interspecific hybrids. Pollen development was completely arrested at the microspore stage and grains were never obtained after selfing. This suggests that distinct or additional S-loci are responsible for sterility of O. glaberrima × O. sativa hybrids.Communicated by H.C. Becker     

Patterns of sequence divergence and evolution of the S orthologous regions between Asian and African cultivated rice species

A strong postzygotic reproductive barrier separates the recently diverged Asian and African cultivated rice species, Oryza sativa and O. glaberrima. Recently a model of genetic incompatibilities between three adjacent loci: S(1)A, S(1) and S(1)B (called together the S(1) regions) interacting epistatically, was postulated to cause the allelic elimination of female gametes in interspecific hybrids. Two candidate factors for the S(1) locus (including a putative F-box gene) were proposed, but candidates for S(1)A and S(1)B remained undetermined. Here, to better understand the basis of the evolution of regions involved in reproductive isolation, we studied the genic and structural changes accumulated in the S(1) regions between orthologous sequences. First, we established an 813 kb genomic sequence in O. glaberrima, covering completely the S(1)A, S(1) and the majority of the S(1)B regions, and compared it with the orthologous regions of O. sativa. An overall strong structural conservation was observed, with the exception of three isolated regions of disturbed collinearity: (1) a local invasion of transposable elements around a putative F-box gene within S(1), (2) the multiple duplication and subsequent divergence of the same F-box gene within S(1)A, (3) an interspecific chromosomal inversion in S(1)B, which restricts recombination in our O. sativa×O. glaberrima crosses. Beside these few structural variations, a uniform conservative pattern of coding sequence divergence was found all along the S(1) regions. Hence, the S(1) regions have undergone no drastic variation in their recent divergence and evolution between O. sativa and O. glaberrima, suggesting that a small accumulation of genic changes, following a Bateson-Dobzhansky-Muller (BDM) model, might be involved in the establishment of the sterility barrier. In this context, genetic incompatibilities involving the duplicated F-box genes as putative candidates, and a possible strengthening step involving the chromosomal inversion might participate to the reproductive barrier between Asian and African rice species.     

Diversification of the rice Waxy gene by insertion of mobile DNA elements into introns.

The waxy (wx) gene of Oryza glaberrima was cloned, and its nucleotide sequence was determined. A waxy mutant of O. glaberrima showing a glutinous phenotype was found to contain a substitution mutation generating a termination codon in the coding region of the wx gene. The Wx sequence of O. glaberrima was different from that of Oryza sativa by substitutions and insertions/deletions, among which only a few substitutions occurred in several exons not to severely alter the amino acid sequence of the Wx protein. The most striking difference observed in introns was a 139-bp deletion (or insertion) in intron 10 of O. glaberrima (or O. sativa). In O. sativa, 125 bp of the 139-bp sequence was flanked by direct repeats of a 14-bp sequence. A sequence homologous to the 125-bp sequence was found in the region preceding exon 2; this sequence was also flanked by direct repeats of another 14-bp sequence. This result and the observation that the 125-bp sequence was interspersed in rice genomes indicate that they are SINEs (short interspersed elements) in the plant system. We also identified a DNA sequence with long terminal inverted repeats in intron 13 of both O. glaberrima and O. sativa. This sequence was present in multiple copies in rice genomes, suggesting that it is a transposable element. These results obtained suggest that mobile DNA elements have diversified the rice Waxy gene by inserting into introns, each of which may originally have a length of about 100 bp.     

Genetics of Hybrid Sterility and Hybrid Breakdown in an Intersubspecific Rice (Oryza Sativa L.) Population

F(1) hybrid sterility and ``hybrid breakdown' of F(2) and later generations in rice (Oryza sativa L.) are common and genetically complicated. We used a restriction fragment length polymorphism linkage map and F(4) progeny testing to investigate hybrid sterility and hybrid breakdown in a cross between ``widely compatible' O. sativa ssp. japonica cultivar Lemont from the Southern U.S. and ssp. indica cultivar Teqing from China. Our results implicate different genetic mechanisms in hybrid sterility and hybrid breakdown, respectively. Hybrid sterility appeared to be due to recombination within a number of putative differentiated ``supergenes' in the rice genome, which may reflect cryptic structural rearrangements. The cytoplasmic genome had a large effect on fertility of both male and female gametes in the F(1) hybrids. There appeared to be a pair of complementary genes that behaved like ``wide compatibility' genes. This pair of genes and the ``gamete eliminator' (S(1)) or ``egg killer' (S-5) may influence the phenotypic effects of presumed supergenes in hybrids. Hybrid breakdown appeared to be largely due to incompatibilities between indica and japonica alleles at many unlinked epistatic loci in the genome. These proposed mechanisms may partly account for the complicated nature of postreproductive barriers in rice.     

QTL detection for rice grain quality traits using an interspecific backcross population derived from cultivated Asian (O. sativa L.) and African (O. glaberrima S.) rice.

An interspecific advanced backcross population derived from a cross between Oryza sativa "V20A" (a popular male-sterile line used in Chinese rice hybrids) and Oryza glaberrima (accession IRGC No. 103544 from Mali) was used to identify quantitative trait loci (QTL) associated with grain quality and grain morphology. A total of 308 BC3F1 hybrid families were evaluated for 16 grain-related traits under field conditions in Changsha, China, and the same families were evaluated for RFLP and SSR marker segregation at Cornell University (Ithaca, N.Y.). Eleven QTL associated with seven traits were detected in six chromosomal regions, with the favorable allele coming from O. glaberrima at eight loci. Favorable O. glaberrima alleles were associated with improvements in grain shape and appearance, resulting in an increase in kernel length, transgressive variation for thinner grains, and increased length to width ratio. Oryza glaberrima alleles at other loci were associated with potential improvements in crude protein content and brown rice yield. These results suggested that genes from O. glaberrima may be useful in improving specific grain quality characteristics in high-yielding O. sativa hybrid cultivars.     

Hybrid male sterility in rice is due to epistatic interactions with a pollen killer locus

In intraspecific crosses between cultivated rice (Oryza sativa) subspecies indica and japonica, the hybrid male sterility gene S24 causes the selective abortion of male gametes carrying the japonica allele (S24-j) via an allelic interaction in the heterozygous hybrids. In this study, we first examined whether male sterility is due solely to the single locus S24. An analysis of near-isogenic lines (NIL-F(1)) showed different phenotypes for S24 in different genetic backgrounds. The S24 heterozygote with the japonica genetic background showed male semisterility, but no sterility was found in heterozygotes with the indica background. This result indicates that S24 is regulated epistatically. A QTL analysis of a BC(2)F(1) population revealed a novel sterility locus that interacts with S24 and is found on rice chromosome 2. The locus was named Epistatic Factor for S24 (EFS). Further genetic analyses revealed that S24 causes male sterility when in combination with the homozygous japonica EFS allele (efs-j). The results suggest that efs-j is a recessive sporophytic allele, while the indica allele (EFS-i) can dominantly counteract the pollen sterility caused by S24 heterozygosity. In summary, our results demonstrate that an additional epistatic locus is an essential element in the hybrid sterility caused by allelic interaction at a single locus in rice. This finding provides a significant contribution to our understanding of the complex molecular mechanisms underlying hybrid sterility and microsporogenesis.     

A gene block causing cross-incompatibility hidden in wild and cultivated rice

Unidirectional cross-incompatibility was detected in advanced generations of backcrossing between wild (Oryza rufipogon) and cultivated (O. sativa) rice strains. The near-isogenic line (NIL) of T65wx (Japonica type) carrying an alien segment of chromosome 6 from a wild strain gave a reduced seed setting only when crossed with T65wx as the male. Cytological observations showed that abortion of hybrid seeds occurred as a consequence of a failure of early endosperm development followed by abnormalities in embryo development. The genetic basis of cross-incompatibility reactions in the female and male was investigated by testcrosses using recombinant inbred lines (RILs) that were established through dissecting the introgressed segments of wild and cultivated (Indica type) strains. The results revealed that the cross-incompatibility reaction was controlled by Cif in the female and by cim in the male. When the female plant with Cif was crossed with the male plant with cim, a failure of early endosperm development was observed in the hybrid zygotes. Among cultivars of O. sativa, cim was distributed predominantly in the Japonica type but not in the Indica type. In addition, a dominant suppressor, Su-Cif, which changes the reaction in the female from incompatible to compatible was proposed to present near the centromere of chromosome 6 of the Indica type. Further, the death of young F(1) zygotes was controlled by the parental genotypes rather than by the genotype of the hybrid zygote itself since all three genes acted sporophytically, which strongly suggests an involvement of parent-of-origin effects. We discuss the results in relation to the origin of a crossing barrier as well as their maintenance within the primary gene pool.     

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.     

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 detected in only a few plant species. We previously reported an S(6) locus-mediated siTRD, in which the S(6) allele from an Asian wild rice strain (Oryza rufipogon) was transmitted more frequently than the S(6)(a) allele from an Asian cultivated rice strain (O. sativa) through both male and female gametes in heterozygous plants. Here, we report on the effect of a difference in genetic background on S(6) locus-mediated siTRD, based on the analysis using near-isogenic lines and the original wild strain as a parental strain for crossing. We found that the degree of TRD through the male gametes varied depending on the genetic background of the female (pistil) plants. Despite the occurrence of TRD through both male and female gametes, abnormality was detected in ovules, but not in pollen grains, in the heterozygote. These results suggest the involvement of unlinked modifiers and developmentally distinct, sex-specific genetic mechanisms in S(6) locus-mediated siTRD, raising the possibility that siTRD driven by a single locus may be affected by multiple genetic factors harbored in natural populations.     

The population structure of African cultivated rice oryza glaberrima (Steud.): evidence for elevated levels of linkage disequilibrium caused by admixture with O. sativa and ecological adaptation

Genome-wide linkage disequilibrium (LD) was investigated for 198 accessions of Oryza glaberrima using 93 nuclear microsatellite markers. Significantly elevated levels of LD were detected, even among distantly located markers. Free recombination among loci at the population genetic level was shown (1) by a lack of decay in LD among markers on the same chromosome and (2) by a strictly increasing composite likelihood function for the recombination parameter. This suggested that the elevation in LD was due not to physical linkage but to other factors, such as population structure. A Bayesian clustering analysis confirmed this hypothesis, indicating that the sample of O. glaberrima in this study was subdivided into at least five cryptic subpopulations. Two of these subpopulations clustered with control samples of O. sativa, subspecies indica and japonica, indicating that some O. glaberrima accessions represent admixtures. The remaining three O. glaberrima subpopulations were significantly associated with specific combinations of phenotypic traits-possibly reflecting ecological adaptation to different growing environments.     

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.     

水稻籼粳杂种生殖障碍的基因定位分析

籼稻(Oryza sativa L.ssp.indica)与粳稻(O.sativa ssp.japonica)杂交优势明显但存在生殖隔离。生殖障碍主要表现为胚囊败育、花粉败育、开花时花药不开裂和雌雄异熟。应用具有137个标记位点的籼、粳杂交(“窄叶青8号”/“京系17”)F_1花药培养获得的127个双单倍体(DH)群体构建的RFLP图谱,对控制籼、粳杂种小穗败育的基因座位进行了定位研究。结果在第1、3、4、5、6、7、8、12染色体上检测到10个基因座位,其中第3、12染色体上的2个不育基因位点stj-3和stj-12与同一杂交组合F_2分离群体中发现的异常分离热点处于相同的染色体区段。Ssj-6的基因加性效应为负值,有增加籼、粳亲和性的作用;其余的不育基因座位皆有增加籼、粳杂种不育性的作用。     

Characterization of a plant SINE, p-SINE1, in rice genomes.

We have previously found that a short interspersed element (SINE), named p-SINE1, is present in the Waxy gene of Oryza sativa in two copies. Here, we cloned five members of p-SINE1 located at other loci in O. sativa and determined their nucleotide sequences. These sequences had a T-rich pyrimidine tract at their defined 3' end and were flanked by direct repeats of a sequence of mostly 14-15 bp long like p-SINE1s in the Waxy gene. The consensus sequence derived from total seven members of p-SINE1 was 123 bp in length and had an internal promoter region for RNA polymerase III. The 5'-half region of the sequence was partially homologous to the tRNA-related block of rabbit C family, one of SINEs in the animal system. Two of the seven p-SINE1 members were not present in the corresponding loci in African rice, Oryza glaberrima, and may thus be available for classification of some rice strains. Comparison of the nucleotide sequences of the Waxy gene between O. sativa and O. glaberrima showed that base substitutions have frequently occurred in a p-SINE1 member (p-SINE1-r1) and a transposable element Tnr1 also present in the Waxy gene, suggesting that these elements, which appear as repetitive sequences in the rice chromosome, tend to acquire base substitutions at a higher frequency than do unique sequences.     

Female control of male gamete delivery during fertilization in Arabidopsis thaliana

Fertilization in both animals and plants relies on the correct targeting of the male gametes to the female gametes. In flowering plants, the pollen tube carries two male gametes through the maternal reproductive tissues to the embryo sac, which contains two female gametes. The pollen tube then releases its two male gametes into a specialized receptor cell of the embryo sac, the synergid cell. The mechanisms controlling this critical step of gamete delivery are unknown. Here, data based on the new sirène (srn) mutant of Arabidopsis thaliana provide the first evidence for female control over male gamete delivery. Live imaging of fertilization shows that wild-type pollen tubes do not stop their growth and do not deliver their contents in srn embryo sacs.     

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.     

Pollen irradiation in tomato: minor effects on enzymic gene transfer

Summary Pollen irradiation was tested as a possible means of expediting gene transfer in tomato breeding. The experiment was also designed to examine the possibility that irradiation effects which have been previously reported for Nicotiana were due to gametophytic selection against mutated male and female gametes.Pollen from the wild tomato species Solanum pennellii was irradiated with -rays and used in crosses with Lycopersicon esculentum. Pollen from five M1 hybrid plants and five control hybrids was used in backcrosses to an esculentum variety and the same plant also functioned as female parents in crosses with normal S. pennellii pollen. Seven enzymic gene markers which differ between the species were assayed in the backcross populations in the two directions. Allele frequencies did not differ between the populations that were derived from the M1 or F1 hybrids except for one marker, Pgm-2. Elimination of male and female gametes containing the irradiated parent allele of Pgm-2 was observed in a single population. This gene is located on chromosome 4 close to the gamete eliminator (Ge) locus. A review of some of the main characteristics of Ge raises the possibility of the existence of a controlling element activity.     

GENERATIVE CELL SPECIFIC 1 is essential for angiosperm fertilization

The double fertilization process in angiosperms is based on the delivery of a pair of sperm cells by the pollen tube (the male gametophyte), which elongates towards an embryo sac (the female gametophyte) enclosing an egg and a central cell. Several studies have described the mechanisms of gametophyte interaction, and also the fertilization process - from pollination to pollen tube acceptance. However, the mechanisms of gamete interaction are not fully understood. Cytological studies have shown that male gametes possess distinct cell-surface structures and genes specific to male gametes have been detected in cDNA libraries. Thus, studies of isolated gametes may offer clues to understanding the sperm-egg interaction. In this study, we identified a novel protein, designated GCS1 (GENERATIVE CELL SPECIFIC 1), using generative cells isolated from Lilium longiflorum pollen. GCS1 possesses a carboxy-terminal transmembrane domain, and homologues are present in various species, including non-angiosperms. Immunological assays indicate that GCS1 is accumulated during late gametogenesis and is localized on the plasma membrane of generative cells. In addition, Arabidopsis thaliana GCS1 mutant gametes fail to fuse, resulting in male sterility and suggesting that GCS1 is a critical fertilization factor in angiosperms.     

Fine mapping of a gene responsible for pollen semi-sterility in hybrids between Oryza sativa L. and O. glaberrima Steud

Asian cultivated rice (Oryza sativa L.) and African cultivated rice (Oryza glaberrima Steud.) are the two main cultivated rice species in the world, with strong heterosis in their F1 hybrids. However, hybrid sterility is a major barrier, although significant heterosis has been observed. In this study, an F1 pollen semi-sterility locus, S19, was identified on rice chromosome 3 by using near-isogenic lines derived from repeated backcross and marker-assisted selection. The typical pollen semi-sterility was observed in F1 hybrids between S19-NIL and Dianjingyou 1. Cytological study of pollen developmental stages indicated that pollen abortion occurred at the late binucleate stage because of a starch accumulation obstacle in some pollen grains. Molecular analysis revealed that the semi-sterility was caused by the abortion of most male gametophytes carrying the S19 allele from the japonica variety Dianjingyou 1. In a population of 12,780 F2 plants derived from S19-NIL/Dianjingyou 1, the S19 locus was fine-mapped to a chromosomal region of 54 kb based on BAC clones of cv. Nipponbare. Interestingly, an addition of a DNA fragment of about 89 kb to the 54-kb region was found in S19-NIL based on BAC clones of O. glaberrima. Gene prediction analysis identified 12 open reading frames (ORF) based on the region of Dianjingyou 1, while 32 ORFs were predicted in S19-NIL. Map-based cloning of this gene will help us to understand the underlying mechanism of hybrid sterility between the two cultivated rice species.     

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.