RESUMO
MAIN CONCLUSION: PROG1 is necessary but insufficient for the main culm inclination while TAC1 partially takes part in it, and both genes promote tiller inclination in Asian wild rice. Asian wild rice (Oryza rufipogon), the ancestor of cultivated rice (O. sativa), has a prostrate architecture, with tillers branching from near the ground. The main culm of each plant grows upward and then tilts during the vegetative stage. Genes controlling tiller angle have been reported; however, their genetic contributions to the culm movement have not been quantified. Here, we quantified their genetic contributions to angular kinematics in the main culm and tillers. For the main culm inclination, one major QTL surrounding the PROG1 region was found. In cultivated rice, tillers firstly inclined and lately rose, while it kept inclining in wild rice. It was suggested that PROG1 affected the tiller elevation angle in the later kinematics, whereas TAC1 was weakly associated with the tiller angle in the whole vegetative stage. Micro-computed tomography (micro-CT) suggested that these angular changes are produced by the bending of culm bases. Because near-isogenic lines (NILs) of wild rice-type Prog1 and Tac1 alleles in the genetic background of cultivated rice did not show the prostrate architecture, the involvement of another gene(s) for inclination of the main culm was suggested. Our findings will not only contribute to the understanding of the morphological transition during domestication but also be used in plant breeding to precisely reproduce the ideal plant architecture by combining the effects of multiple genes.
Assuntos
Oryza , Oryza/genética , Oryza/anatomia & histologia , Microtomografia por Raio-X , Fenômenos Biomecânicos , Melhoramento Vegetal , AlelosRESUMO
Understanding the genetic basis of reproductive barriers between species has been a central issue in evolutionary biology. The S1 locus in rice causes hybrid sterility and is a major reproductive barrier between two rice species, Oryza sativa and Oryza glaberrima The O. glaberrima-derived allele (denoted S1g) on the S1 locus causes preferential abortion of gametes with its allelic alternative (denoted S1s) in S1g/S1s heterozygotes. Here, we used mutagenesis and screening of fertile hybrid plants to isolate a mutant with an allele, S1mut, which does not confer sterility in the S1mut/S1g and S1mut/S1s hybrids. We found that the causal mutation of the S1mut allele was a deletion in the peptidase-coding gene (denoted "SSP") in the S1 locus of O. glaberrima No orthologous genes of SSP were found in the O. sativa genome. Transformation experiments indicated that the introduction of SSP in carriers of the S1s allele did not induce sterility. In S1mut/S1s heterozygotes, the insertion of SSP led to sterility, suggesting that SSP complemented the loss of the functional phenotype of the mutant and that multiple factors are involved in the phenomenon. The polymorphisms caused by the lineage-specific acquisition or loss of the SSP gene were implicated in the generation of hybrid sterility. Our results demonstrated that artificial disruption of a single gene for the reproductive barrier creates a "neutral" allele, which facilitates interspecific hybridization for breeding programs.
Assuntos
Cruzamentos Genéticos , Genes de Plantas , Oryza/genética , Infertilidade das Plantas/genética , Alelos , Mapeamento Cromossômico , Cromossomos/ultraestrutura , Deleção de Genes , Heterozigoto , Hibridização Genética , Mutagênese , Mutação , Fenótipo , Pólen/genética , Polimorfismo Genético , Domínios Proteicos , Reprodução/genéticaRESUMO
Spelt wheat (Triticum aestivum subsp. spelta), a subspecies of common wheat, is a genetic resource for the breeding of bread wheat (T. aestivum subsp. aestivum); however, genetic analyses of agronomic traits in bread wheat × spelt crosses are insufficient. Here, we conducted QTL analysis in the recombinant inbred lines from a bread wheat × spelt cross. In addition to the major Q locus, QSpd.obu-4D was detected with the spelt allele conferring a higher spikelet density than the bread wheat allele. The effect of QSpd.obu-4D was evident in the presence of the Q allele of bread wheat, suggesting that this variation might be cryptic in spelt wheat with the q allele. Two QTLs with stable effects were identified for grain length, one of which (QGl.obu-1A) has never been detected in a bread wheat × spelt cross. The spelt wheat allele at QHt.obu-7B conferring later heading was identified in the Vrn-B3 region and could be a novel gene source for modifying heading time. Furthermore, QGi.obu-2B, responsible for low grain dormancy of spelt wheat, was detected. Further exploration and identification of useful QTLs could accelerate the utilization of spelt wheat as a genetic resource for bread wheat breeding programs.
RESUMO
BACKGROUND: Pre-harvest sprouting frequently occurs in Triticum aestivum (wheat) and Hordeum vulgare (barley) at the end of the maturity period due to high rainfall, particularly in Asian monsoon areas. Seed dormancy is a major mechanism preventing pre-harvest sprouting in these crops. RESULTS: We identified orthologous sequences of the major Hordeum vulgare (barley) seed dormancy gene Qsd1 in hexaploid wheat cv. Chinese Spring by performing genomic clone sequencing, followed by transcript sequencing. We detected 13 non-synonymous amino acid substitutions among the three sub-genomes of wheat and found that the Qsd1 sequence in the B sub-genome is most similar to that in barley. The Qsd1 sequence in A genome diploid wheat is highly similar to that in the hexaploid A sub-genome. Wheat orthologs of Qsd1 showed closer similarities to barley Qsd1 than did those of other accessions in the DNA database. Like barley Qsd1, all three wheat Qsd1s showed embryo-specific gene expression patterns, indicating that barley and wheat Qsd1 share an orthologous origin. The alignment of four hexaploid wheat cultivars indicated that the amino acid sequences of three spring cultivars, Chinese Spring, Haruyo Koi, and Fielder, are exactly the same in each sub-genome. Only Kitahonami has three amino acid substitutions at the B sub-genome. CONCLUSIONS: Kitahonami has a longer seed dormancy period than does Chinese Spring. Sequence polymorphisms between Chiniese Spring and Kitahonami in the B sub-genome may underlie the phenotypic differences in seed dormancy between these hexaploid wheat cultivars.
Assuntos
Genoma de Planta/genética , Dormência de Plantas/genética , Proteínas de Plantas/química , Proteínas de Plantas/genética , Alinhamento de Sequência , Triticum/crescimento & desenvolvimento , Triticum/genética , Sequência de Aminoácidos , Regulação da Expressão Gênica de Plantas , Haplótipos/genética , Proteínas de Plantas/metabolismo , Homologia de Sequência de Aminoácidos , Especificidade da EspécieRESUMO
Pre-harvest sprouting (PHS) is one of the serious problems for wheat production, especially in rainy regions. Although seed dormancy is the most critical trait for PHS resistance, the control of heading time should also be considered to prevent seed maturation during unfavorable conditions. In addition, awning is known to enhance water absorption by the spike, causing PHS. In this study, we conducted QTL analysis for three PHS resistant related traits, seed dormancy, heading time and awn length, by using recombinant inbred lines from 'Zenkouji-komugi' (high PHS resistance) × 'Chinese Spring' (weak PHS resistance). QTLs for seed dormancy were detected on chromosomes 1B (QDor-1B) and 4A (QDor-4A), in addition to a QTL on chromosome 3A, which was recently cloned as TaMFT-3A. In addition, the accumulation of the QTLs and their epistatic interactions contributed significantly to a higher level of dormancy. QDor-4A is co-located with the Hooded locus for awn development. Furthermore, an effective QTL, which confers early heading by the Zenkouji-komugi allele, was detected on the short arm of chromosome 7B, where the Vrn-B3 locus is located. Understanding the genetic architecture of traits associated with PHS resistance will facilitate the marker assisted selection to breed new varieties with higher PHS resistance.
RESUMO
[This corrects the article on p. 260 in vol. 66, PMID: 27162497.].
RESUMO
The genetic mechanisms of reproductive isolation have been widely investigated within Asian cultivated rice (Oryza sativa); however, relevant genes between diverged species have been in sighted rather less. Herein, a gene showing selfish behavior was discovered in hybrids between the distantly related rice species Oryza longistaminata and O. sativa. The selfish allele S13l in the S13 locus impaired male fertility, discriminately eliminating pollens containing the allele S13s from O. sativa in heterozygotes (S13s/S13l). Genetic analysis revealed that a gene encoding a chromatin-remodeling factor (CHR) is involved in this phenomenon and a variety of O. sativa owns the truncated gene OsCHR745, whereas its homologue OlCHR has a complete structure in O. longistaminata. CRISPR-Cas9-mediated loss of function mutants restored fertility in hybrids. African cultivated rice, which naturally lacks the OlCHR homologue, is compatible with both S13s and S13l carriers. These results suggest that OlCHR is a Killer gene, which leads to reproductive isolation.
RESUMO
Low-temperature adaptation in rice is mediated by the ability of a genotype to tolerate chilling temperatures. A genetic locus on chromosome 11 was analysed for chilling tolerance at the plumule stage in rice. The tolerant allele of A58, a japonica landrace in Japan, was inherited as a recessive gene (ctp-1A58), whereas the susceptible alleles from wild rice (Ctp-1W107) and modern variety (Ctp-1HY) were the dominant genes. Another recessive tolerant allele (ctp-1Silewah) was found in a tropical japonica variety (Silewah). Fine-mapping revealed that a candidate gene for the ctp-1 locus encoded a protein similar to the nucleotide-binding domain and leucine-rich repeat (NLR) protein, in which frameshift mutation by a 73 bp-deletion might confer chilling tolerance in ctp-1A58. Analysis of near-isogenic lines demonstrated that ctp-1A58 imparted tolerance effects only at severe chilling temperatures of 0.5 °C and 2 °C, both at plumule and seedling stages. Chilling acclimation treatments at a wide range of temperatures (8 °C-16 °C) for 72 h concealed the susceptible phenotype of Ctp-1W107 and Ctp-1HY. Furthermore, short-term acclimation treatment of 12 h at 8 °C was enough to be fully acclimated. These results suggest that the NLR gene induces a susceptible response upon exposure to severe chilling stress, however, another interacting gene(s) for acclimation response could suppress the maladaptive phenotype caused by the Ctp-1 allele. This study provides new insights for the adaptation and breeding of rice in a low-temperature environment.
RESUMO
Low or excessive soil fertility is a major constraint to potato production. The influence of each individual nutrient element on potato plants under field studies remains ambiguous due to the influence of environmental variations. Creating an in vitro model plant with deficient or excessive nutrient content will provide a more controlled study and allow for a better understanding of how the concentration of one element can affect the uptake of other elements. Here we designed a tissue culture-based nutrition control system to systematically analyze the effects of essential nutrients on potato plants. Insufficient or excessive nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), and magnesium (Mg) contents were created by modifying the Murashige and Skoog (MS) medium. Deficient to toxic plant nutrient statuses were successfully defined by the evaluation of dry biomass and morphological symptoms. The results showed that plant shoot growth, nutrient uptake and content, and nutrient interactions were all significantly impacted by the changes in the MS media nutrient concentrations. These tissue culture systems can be successfully used for further investigations of nutrient effects on potato production in response to biotic and abiotic stresses in vitro.
RESUMO
We characterized a spontaneous dwarf mutant showing extremely short internodes and dark green leaves originating from azuki bean (Vigna angularis (Willd.) Ohwi & Ohashi) cultivar "Erimo-shouzu." F(1) plants of 3 cross combinations between the dwarf mutant and several representative wild-type plants, Erimo-shouzu, V. angularis accession Acc2265 and wild relative V. riukiuensis accession Acc2482, supported the dwarf genotype being recessive. In a total of 3328 F(2) progeny of these 3 crosses, 65 dwarfs (2.0%) and 5 chimeric dwarfs (0.2%) segregated and the remainder were wild-type plants (97.8%). In F(3) progeny derived from self-pollinated dwarf F(2) plants, we observed wild type (54.3%), dwarf (39.1%), and chimeric dwarf (6.5%) plants. Two types of chimeric plants were observed: dwarf branches on the axils of wild-type plant stems and wild-type branches on the axils of dwarf stems. In 21 dwarf F(2) plants, the dwarf trait cosegregated with simple sequence repeat marker CEDG154 on chromosome 4. Conversely, homozygote F(2) plants at this chromosomal segment from the dwarf mutant frequently (>90%) expressed the wild-type phenotype. We concluded that the dwarf phenotype is mitotically and meiotically inheritable and controlled by a single genetically unstable locus, designated Azuki Dwarf1 (AD1), which converts between 2 phenotypic states bidirectionally.
Assuntos
Fabaceae/genética , Loci Gênicos , Instabilidade Genômica/genética , Proteínas de Plantas/genética , Quimerismo , Mapeamento Cromossômico , Cromossomos de Plantas/genética , Estudos de Associação Genética , Ligação Genética , Genótipo , Repetições de Microssatélites/genética , Mutação/genética , FenótipoRESUMO
A dwarfing gene (allele) sd1-d has been intensively utilized to develop short-culm indica varieties in southeast Asia up to now. Before the first sd1-d-carrying variety IR8 was released, rice researchers had recognized the general tendency that culm length is higher in indica varieties than in temperate-japonica ones. Inter-subspecific difference of the tall (wild-type) allele SD1 at the sd1 locus was examined on the common genetic background, using five isogenic lines developed by substituting sd1-d of the recurrent parent IR36 by SD1s of two indica varieties, two temperate-japonica varieties and one tropical-japonica variety. The two indica -donor isogenic lines had longer culms than the three japonica-donor isogenic lines consistently in two different environmental conditions. Moreover, nonsynonymous single-nucleotide polymorphism between the two subspecies was detected at two sites in Exon 1 and Exon 3 of the sd1 locus. It is demonstrated that the inter-subspecific differentiation of SD1 contributes height difference between indica and japonica. The indica-originating and japonica-originating alleles at the sd1 locus were designated as SD1-in(t) and SD1-ja(t), respectively.
Assuntos
Alelos , Genes de Plantas/genética , Oryza/genética , Oxirredutases/genética , Substituição de Aminoácidos/genética , Ordem dos Genes , Variação Genética , Genótipo , Oryza/classificação , Oryza/enzimologia , Polimorfismo de Nucleotídeo Único , Especificidade da EspécieRESUMO
Limitations for the application of genome editing technologies on elite wheat (Triticum aestivum L.) varieties are mainly due to the dependency on in vitro culture and regeneration capabilities. Recently, we developed an in planta particle bombardment (iPB) method which has increased process efficiency since no culture steps are required to create stably genome-edited wheat plants. Here, we report the application of the iPB method to commercially relevant Japanese elite wheat varieties. The biolistic delivery of gold particles coated with plasmids expressing CRISPR/Cas9 components designed to target TaQsd1 were bombarded into the embryos of imbibed seeds with their shoot apical meristem (SAM) exposed. Mutations in the target gene were subsequently analyzed within flag leaf tissue by using cleaved amplified polymorphic sequence (CAPS) analysis. A total of 9/358 (2.51%) of the bombarded plants (cv. "Haruyokoi," spring type) carried mutant alleles in the tissue. Due to the chimeric nature of the T0 plants, only six of them were inherited to the next (T1) generation. Genotypic analysis of the T2 plants revealed a single triple-recessive homozygous mutant of the TaQsd1 gene. Compared to wild type, the homozygous mutant exhibited a 7 days delay in the time required for 50% seed germination. The iPB method was also applied to two elite winter cultivars, "Yumechikara" and "Kitanokaori," which resulted in successful genome editing at slightly lower efficiencies as compared to "Haruyokoi." Taken together, this report demonstrates that the in planta genome editing method through SAM bombardment can be applicable to elite wheat varieties that are otherwise reluctant to callus culture.
RESUMO
Phenotypic plasticity is an adaptive mechanism adopted by plants in response to environmental heterogeneity. Cultivated and wild species adapt in contrasting environments; however, it is not well understood how genetic changes responsible for phenotypic plasticity were involved in crop evolution. We investigated the genetic control of phenotypic plasticity in Asian cultivated (Oryza sativa) and wild rice (O. rufipogon) under 5 environmental conditions (2 nutrient and 3 density levels). Quantitative trait locus (QTL) analysis was conducted for traits affecting plant architecture and biomass production. By analysing the phenotypic means, QTLs of large effects were detected as a cluster on chromosome 7 under all the environmental conditions investigated; this might have contributed to transitions of plant architecture during domestication, as reported previously. Multiple QTLs of plasticity were also found within this QTL cluster, demonstrating that allele-specific environmental sensitivity might control plasticity. Furthermore, QTLs controlling plasticity without affecting phenotypic means were also identified. The mode of action and direction of allele effects of plasticity QTLs varied depending on the traits and environmental signals. These findings confirmed that cultivated and wild rice show distinctive genetic differentiation for phenotypic plasticity, which might have contributed to adaptation under contrasting environmental heterogeneity during the domestication of rice.
Assuntos
Oryza/genética , Fenótipo , Cromossomos de Plantas , Produtos Agrícolas/genética , DNA de Plantas/metabolismo , Genes de Plantas , Genoma de Planta , Locos de Características QuantitativasRESUMO
Transmission ratio distortion (TRD) is frequently observed in inter- and intraspecific hybrids of plants, leading to a violation of Mendelian inheritance. Sex-independent TRD (siTRD) was detected in a hybrid between Asian cultivated rice and its wild ancestor. Here we examined how siTRD caused by an allelic interaction at a specific locus arose in Asian rice species. The siTRD is controlled by the S6 locus via a mechanism in which the S6 allele acts as a gamete eliminator, and both the male and female gametes possessing the opposite allele (S6a) are aborted only in heterozygotes (S6/S6a). Fine mapping revealed that the S6 locus is located near the centromere of chromosome 6. Testcross experiments using near-isogenic lines (NILs) carrying either the S6 or S6a alleles revealed that Asian rice strains frequently harbor an additional allele (S6n) the presence of which, in heterozygotic states (S6/S6n and S6a/S6n), does not result in siTRD. A prominent reduction in the nucleotide diversity of S6 or S6a carriers relative to that of S6n carriers was detected in the chromosomal region. These results suggest that the two incompatible alleles (S6 and S6a) arose independently from S6n and established genetically discontinuous relationships between limited constituents of the Asian rice population.
Assuntos
Alelos , Regulação da Expressão Gênica de Plantas , Oryza/genética , Mapeamento Cromossômico , Cruzamentos Genéticos , Genes de Plantas , Variação Genética , Genoma de Planta , Heterozigoto , Modelos Biológicos , Modelos Genéticos , Dados de Sequência Molecular , Nucleotídeos/genética , Mapeamento Físico do CromossomoRESUMO
The complex structure of a single Mendelian factor widespread in the Asian cultivated rice (Oryza sativa) and its wild progenitor (Oryza rufipogon) that caused diverse phenotypes in the timing of flowering under natural field conditions was investigated in near isogenic lines. These near isogenic lines showed differences in flowering time despite all eight accessions collected from tropical regions possessing a recessive gene allelic to the se-pat gene. Fine mapping in two of these near-isogenic lines revealed that cultivated (Patpaku) and wild (W593) accessions had three and two linked quantitative trait loci (QTL) in the candidate regions, respectively, showing that Patpaku and W593 possessed linked QTLs with different effects in addition to the commonly-observed recessive gene (se-pat). Molecular dissection suggested that the tandemly duplicated FT-like genes (Hd3a and RFT1) could be the candidate genes for these QTLs. Interestingly, the linked QTLs differed in their epistases, degree of dominance, and genotype x environment interactions. The nucleotide sequences showed that RFT1 has diverged more rapidly than Hd3a during rice evolution, suggesting phenotypic diversification of the two genes. Phylogenetic analysis implied that the se-pat(+) alleles might have emerged in different lineages within O. sativa. The present results strongly suggest that nucleotide divergence and shuffling of the linked QTLs by recombination might have created novel Mendelian factors that probably contribute to responding to local environments.
Assuntos
Flores/genética , Duplicação Gênica , Oryza/genética , Locos de Características Quantitativas , Alelos , Mapeamento Cromossômico , DNA de Plantas/genética , Epistasia Genética , Evolução Molecular , Genes Dominantes , Genética Populacional , Glicoproteínas de Membrana/genética , Fenótipo , Filogenia , Proteínas de Plantas/genética , Especificidade da EspécieRESUMO
Common wheat has three sets of sub-genomes, making mutations difficult to observe, especially for traits controlled by recessive genes. Here, we produced hexaploid wheat lines with loss of function of homeoalleles of Qsd1, which controls seed dormancy in barley, by Agrobacterium-mediated CRISPR/Cas9. Of the eight transformed wheat events produced, three independent events carrying multiple mutations in wheat Qsd1 homeoalleles were obtained. Notably, one line had mutations in every homeoallele. We crossed this plant with wild-type cultivar Fielder to generate a transgene-free triple-recessive mutant, as revealed by Mendelian segregation. The mutant showed a significantly longer seed dormancy period than wild-type, which may result in reduced pre-harvest sprouting of grains on spikes. PCR, southern blotting, and whole-genome shotgun sequencing revealed that this segregant lacked transgenes in its genomic sequence. This technique serves as a model for trait improvement in wheat, particularly for genetically recessive traits, based on locus information from diploid barley.
Assuntos
Edição de Genes , Genes Recessivos , Mutação , Dormência de Plantas/genética , Sementes , Triticum , Proteínas de Ciclo Celular/genética , Proteínas de Ciclo Celular/metabolismo , Técnicas de Inativação de Genes , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Sementes/genética , Sementes/metabolismo , Triticum/genética , Triticum/metabolismoRESUMO
* 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.
Assuntos
Oryza/genética , Alelos , Mapeamento Cromossômico , Cruzamentos Genéticos , Heterozigoto , Hibridização Genética , Oryza/crescimento & desenvolvimento , Oryza/fisiologia , Pólen/genética , Pólen/crescimento & desenvolvimento , Pólen/fisiologia , Reprodução/fisiologia , Especificidade da EspécieRESUMO
Divergent phenotypes are often detected in domesticated plants despite the existence of invariant phenotypes in their wild forms. One such example in rice is the occurrence of varying degrees of apiculus coloration due to anthocyanin pigmentation, which was previously reported to be caused by a series of alleles at the C locus. The present study reveals, on the basis of comparison of its maps, that the C gene appears to be the rice homolog (OsC1) of maize C1, which belongs to the group of R2R3-Myb factors. Two different types of deletions causing a frameshift were detected in the third exon, and both of the deleted nucleotides corresponded to the positions of putative base-contacting residues, suggesting that the Indica and Japonica types carry loss-of-function mutations with independent origins. In addition, replacement substitutions were frequently detected in OsC1 of strains carrying the previously defined C alleles. Molecular population analysis revealed that 17 haplotypes were found in 39 wild and cultivated rices, and the haplotypes of most cultivated forms could be classified into one of three distinct groups, with few shared haplotypes among taxa, including Indica and Japonica types. The genealogy of the OsC1 gene suggests that allelic diversification causing phenotypic change might have resulted from mutations in the coding region rather than from recombination between preexisting alleles. The McDonald and Kreitman test revealed that the changes in amino acids might be associated with selective forces acting on the lineage of group A whose haplotypes were carried by most Asian cultivated forms. The results regarding a significant implication for genetic diversity in landraces of rice are also discussed.
Assuntos
Alelos , Proteínas de Ligação a DNA/genética , Variação Genética , Oryza/genética , Proteínas de Plantas , Proteínas Proto-Oncogênicas c-myb , Substituição de Aminoácidos , Sequência de Bases , Deleção de Genes , Haplótipos/genética , Dados de Sequência Molecular , Fenótipo , Proteínas de Plantas/genética , Homologia de Sequência do Ácido Nucleico , Zea mays/genéticaRESUMO
During the "Green Revolution" of rice, high-yielding varieties (HYVs) were developed using a semi-dwarf gene (sd1 or OsGA20ox2). The presence or absence of the two mutant alleles (DGWG type in Dee-geo-woo-gen and JKK type in Jikkoku) were surveyed by PCR using 256 accessions of eight wild and two cultivate rice species. The DGWG allele was detected in a landrace (Oryza sativa) and two accessions of wild rice (O. rufipogon), all of which are from China, showing their limited distribution. Genealogical studies of the OsGA20ox2 gene showed that the 62 sequences of O. sativa and O. rufipogon included 20 distinct haplotypes, indicating that the species complex contained OsGA20ox2 genes from two different lineages. The silent site nucleotide diversities (pi and theta(w)) were extremely low in Japonica rice, suggesting a genetic bottleneck. The haplotype network showed that the DGWG and JKK alleles were derived in different lineages. The DGWG carrier (W1944) had unique polymorphisms in the surrounding region of the locus, suggesting that the DGWG allele has been preserved in the wild progenitor, rather than that the DGWG allele has been introgressed from HYVs to W1944. Although a semi-dwarfing plant is a weak competitor under saturated fields, the crossing experiment revealed that the DGWG variant might have been preserved as a hidden variation in the genetic background of wild rice, without expressing a short-stature.