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ABSTRACT: Spotted leaf 5 (spl5), a lesion mimic mutant, was first identified in rice (Oryza sativa L.) japonica cv. Norin8 in 1978. This mutant exhibits spontaneous disease-like lesions in the absence of any pathogens and resistance
to rice blast and bacterial blight; however, the target gene has not yet been isolated. In the present study, we employed
a map-based cloning strategy to finely map the spl5 gene. In an initial mapping with 100 F2 individuals (spl5/spl5) derived from a cross between the spl5 mutant and indica cv. 93-11, the spl5 gene was located in a 3.3-cM region on chromosome 7 using six simple sequence repeat (SSR) markers. In a high-resolution
genetic mapping, two F2 populations with 3,149 individuals (spl5/spl5) were derived from two crosses between spl5 mutant and two indica cvs. 93-11 and Zhefu802 and six sequence-tagged site (STS) markers were newly developed. Finally, the spl5 gene was mapped to a region of 0.048cM between two markers SSR7 and RM7121. One BAC/PAC contig map covering these markers’
loci and the spl5 gene was constructed through Pairwise BLAST analysis. Our bioinformatics analysis shows that the spl5 gene is located in the 80-kb region between two markers SSR7 and RM7121 with a high average ratio of physical to genetic
distance (1.67Mb/cM) and eighteen candidate genes. The analysis of these candidate genes indicates that the spl5 gene represents a novel class of regulators controlling cell death and resistance response in plants.
Molecular Breeding 04/2012; 24(4):387-395. · 2.85 Impact Factor
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ABSTRACT: Wild rice species is an important source of useful genes for cultivated rice improvement. Some accessions ofOryza eichingeri (2n = 24, CC) from Africa confer strong resistance to brown planthopper (BPH), whitebacked planthopper (WBPH) and bacterial blight
(BB). In the present study, restriction fragments length polymorphism (RFLP) and simple sequence repeats (SSR) analysis were
performed on disomic backcross plants betweenOryza sativa (2n = 24, AA) andO. eichingeri in order to identify the presence ofO. eichingeri segments and further to localize BPH-resistant gene. In the introgression lines, 1–6O. eichingeri segments were detected on rice chromosomes 1, 2, 6, or/and 10. The dominant BPH resistant gene, tentatively named Bph13(t),
was mapped to chromosome 2, being 6.1 and 5.5 cM away from two microsatellite markers RM240 and RM250, respectively. The transfer
and localization of this gene fromO. eichingeri will contribute to the improvement of BPH resistance in cultivated rice.
Keywordscultivated rice-
Oryza eichingeri
-brown planthopper resistance-gene mapping
Chinese Science Bulletin 04/2012; 46(17):1459-1462. · 1.32 Impact Factor
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ABSTRACT: With 6 figures and 4 tablesAbstractBacterial blight (BB) of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major production constraint in commercial hybrid rice production because most of the parental lines used in hybrid production are susceptible to Xoo. In this study, the cloned BB resistance gene Xa21 was transferred into ‘D62B’, a maintainer line of three-line indica hybrid rice using the double right-border vector pDRBXa21 through an Agrobacterium tumefaciens-mediated system. Molecular and resistance analysis revealed that Xa21 was integrated into the genome of transgenic ‘D62B’, and the homozygous, single-copy and marker-free maintainer line D62B-Xa21 was obtained in the T2 generation. D62B-Xa21 was then backcrossed with ‘D62A’ to produce a homozygous transgenic sterile line D62A-Xa21. The introduction of Xa21 did not cause any obvious alteration to sterility and other agronomic traits of the sterile line through iodine–potassium iodide (I2/KI) staining of pollen grains and field observation. Reverse transcriptase–polymerase chain reaction revealed a normal expression pattern of the Xa21 gene in the transgenic lines. The hybrid combinations derived from D62A-Xa21 could inherit high resistance to BB.
Plant Breeding 02/2011; 130(4):438 - 443. · 1.60 Impact Factor
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ABSTRACT: Polymerase chain reaction (PCR) is a simple, quick and highly sensitive method. However the accuracy of the conventional PCR assay was often affected by false positives and false negatives. In this study, a protocol competitive PCR was used to reduce the false results in screening for selectable marker-free (SMF) Xa2l transgenic rice plants. The competitive template of Xa21 was the endogenous Xa2l homologous sequence located on chromosome 11. The competitive template of the selectable marker gene, hygromycin phosphotransferase (hpt), was an additive DNA extracted from hpt transgenic Nipponbare (Oryza sativa L). Through competitive PCR analysis of transgenic T1 plants produced by double right border binary vector, false positive or false negative samples were effectively diminished, and genuine SMF Xa21 transgenic plants were obviously obtained. Comparing with the conventional non-competitive PCR, competitive PCR increased the accuracy for selecting SMF Xa21 transgenic plants. The results of bacterial blight (BB) resistance tests and hygromycin B resistance assay of SMF Xa21 transgenic plants testified the reliability of this method.
Sheng wu gong cheng xue bao = Chinese journal of biotechnology 05/2009; 25(4):605-10.
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Baisheng Yu,
Zhongwei Lin,
Haixia Li,
Xiaojiao Li,
Jiayang Li,
Yonghong Wang,
Xia Zhang,
Zuofeng Zhu, Wenxue Zhai,
Xiangkun Wang,
Daoxin Xie,
Chuanqing Sun
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ABSTRACT: A critical step during rice (Oryza sativa) cultivation is dense planting: a wider tiller angle will increase leaf shade and decrease photosynthesis efficiency, whereas a narrower tiller angle makes for more efficient plant architecture. The molecular basis of tiller angle remains unknown. This research demonstrates that tiller angle is controlled by a major quantitative trait locus, TAC1 (Tiller Angle Control 1). TAC1 was mapped to a 35-kb region on chromosome 9 using a large F(2) population from crosses between an indica rice, IR24, which displays a relatively spread-out plant architecture, and an introgressed line, IL55, derived from japonica rice Asominori, which displays a compact plant architecture with extremely erect tillers. Genetic complementation further identified the TAC1 gene, which harbors three introns in its coding region and a fourth 1.5-kb intron in the 3'-untranslated region. A mutation in the 3'-splicing site of this 1.5-kb intron from 'AGGA' to 'GGGA' decreases the level of tac1, resulting in a compact plant architecture with a tiller angle close to zero. Further sequence verification of the mutation in the 3'-splicing site of the 1.5-kb intron revealed that the tac1 mutation 'GGGA' was present in 88 compact japonica rice accessions and TAC1 with 'AGGA' was present in 21 wild rice accessions and 43 indica rice accessions, all with the spread-out form, indicating that tac1 had been extensively utilized in densely planted rice grown in high-latitude temperate areas and at high altitudes where japonica rice varieties are widely cultivated.
The Plant Journal 01/2008; 52(5):891-8. · 6.16 Impact Factor
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ABSTRACT: Paracentric inversion is known to inhibit genetic recombination between normal and inverted chromosomal segments in heterozygous arrangements. Insect inversion polymorphisms have been studied to reveal adaptive processes for maintaining genetic variation. We report the first paracentric inversion in rice (Oryza sativa), which was discovered in our effort to clone the floral organ number gene FON3. Recombination at the FON3 locus on the long arm of chromosome 11 was severely suppressed over a distance of more than 36 cM. An extensive screening among 8,242 F(2) progeny failed to detect any recombinants. Cytological analysis revealed a loop-like structure on pachytene chromosomes, whereas FISH analysis showed the migration of a BAC clone from a distal location to a position closer to the centromere. Interestingly, the locations where the genetic recombination suppression began were coincided with the positions of two physical gaps on the chromosome 11, suggesting a correlation between the physical gaps, the inversion breakpoints. Transposons and retrotransposons, and tandemly arranged members of gene families were among the sequences immediately flanking the gaps. Taken together, we propose that the genetic suppression at the FON3 locus was caused by a paracentric inversion. The possible genetic mechanism causing such a spontaneous inversion was proposed.
Molecular and General Genetics 04/2007; 277(3):263-72. · 2.63 Impact Factor
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ABSTRACT: Rice tillering is an important agronomic trait for grain production. The HIGH-TILLERING DWARF1 (HTD1) gene encodes an ortholog of Arabidopsis MAX3. Complementation analyses for HTD1 confirm that the defect in HTD1 is responsible for both high-tillering and dwarf phenotypes in the htd1 mutant. The rescue of the Arabidopsis max3 mutant phenotype by the introduction of Pro(35S):HTD1 indicates HTD1 is a carotenoid cleavage dioxygenase that has the same function as MAX3 in synthesis of a carotenoid-derived signal molecule. The HTD1 gene is expressed in both shoot and root tissues. By evaluating Pro(HTD1):GUS expression, we found that the HTD1 gene is mainly expressed in vascular bundle tissues throughout the plant. Auxin induction of HTD1 expression suggests that auxin may regulate rice tillering partly through upregulation of HTD1 gene transcription. Restoration of dwarf phenotype after the removal of axillary buds indicates that the dwarfism of the htd1 mutant may be a consequence of excessive tiller production. In addition, the expression of HTD1, D3 and OsCCD8a in the htd1 and d3 mutants suggests a feedback mechanism may exist for the synthesis and perception of the carotenoid-derived signal in rice. Characterization of MAX genes in Arabidopsis, and identification of their orthologs in pea, petunia and rice indicates the existence of a conserved mechanism for shoot-branching regulation in both monocots and dicots.
The Plant Journal 01/2007; 48(5):687-98. · 6.16 Impact Factor
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ABSTRACT: Anther culture offers a rapid method of generating homozygous lines for breeding program and genetic analysis. To produce homozygous transgenic lines of rice (Oryza sativa L.) in one step, we developed an efficient protocol of anther-callus-based transformation mediated by Agrobacterium after optimizing several factors influencing efficient transformation, including callus induction and Agrobacterium density for co-cultivation. Using this protocol, we obtained 145 independent green transformants from five cultivars of japonica rice by transformation with a binary vector pCXK1301 bearing the rice gene, Xa21 for resistance to bacterial blight, of which 140 were further confirmed by PCR and Southern hybridization analysis, including haploids (32.1%), diploids (62.1%) and mixoploids (7.5%). Fifteen diploids were found to be doubled haploids, which accounted for 10.7% of the total positive lines. Finally, by including 28 from colchicine induced or spontaneous diploidization of haploids later after transformation, a total of 43 doubled haploids (30.7%) of Xa21 transgenic lines were obtained. We also generated two RNAi transgenic haploids of the rice OsMADS2 gene, a putative redundant gene of OsMADS4 based on their sequence similarity, to investigate its possible roles in rice flower development by this method. Flowers from the two OsMADS2 RNAi transgenic haploids displayed obvious homeotic alternations, in which lodicules were transformed into palea/lemma-like tissues, whereas identities of other floral organs were maintained. The phenotypic alternations were proved to result from specific transcriptional suppression of OsMADS2 gene by the introduced RNAi transgene. The results confirmed that OsMADS2 is involved in lodicule development of rice flower and functionally redundant with OsMADS4 gene. Our results demonstrated that rice anther culture could be adapted to gene transformation and RNAi analysis in rice.
Science in China Series C Life Sciences 11/2006; 49(5):414-28. · 1.61 Impact Factor
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Xuewei Chen,
Junjun Shang,
Dexi Chen,
Cailin Lei,
Yan Zou, Wenxue Zhai,
Guozhen Liu,
Jichen Xu,
Zhongzhuan Ling,
Gang Cao,
Bingtian Ma,
Yuping Wang,
Xianfeng Zhao,
Shigui Li,
Lihuang Zhu
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ABSTRACT: Rice blast, caused by the fungal pathogen Magnaporthe grisea, is one of the most devastating diseases in rice worldwide. The dominant resistance gene, Pi-d2 [previously named Pi-d(t)2], present in the rice variety Digu, confers gene-for-gene resistance to the Chinese blast strain, ZB15. Pi-d2 was previously mapped close to the centromere of chromosome 6. In this study, the Pi-d2 gene was isolated by a map-based cloning strategy. Pi-d2 encodes a receptor-like kinase protein with a predicted extracellular domain of a bulb-type mannose specific binding lectin (B-lectin) and an intracellular serine-threonine kinase domain. Pi-d2 is a single-copy gene that is constitutively expressed in the rice variety Digu. Transgenic plants carrying the Pi-d2 transgene confer race-specific resistance to the M. grisea strain, ZB15. The Pi-d2 protein is plasma membrane localized. A single amino acid difference at position 441 of Pi-d2 distinguishes resistant and susceptible alleles of rice blast resistance gene Pi-d2. Because of its novel extracellular domain, Pi-d2 represents a new class of plant resistance genes.
The Plant Journal 07/2006; 46(5):794-804. · 6.16 Impact Factor
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ABSTRACT: A rice htd-1 mutant, related to tillering and dwarfing, was characterized. We show that the htd-1 mutant increases its tiller number by releasing axillary buds from dormant stage rather than by initiating more axillary buds. The dwarf is caused by averagely reducing each internode and panicle. Based on this dwarfing pattern, the htd-1 mutant could be grouped into dn-type dwarf defined by Takeda (Gamma Field Symp 16:1, 1977). In addition, the dwarfing of the htd-1 mutant was found independent of GA based on the analyses of two GA-mediated processes. Based on the quantitative determination of IAA and ABA and application of the two hormones exogenously to the seedlings, we inferred that the high tillering capacity of the htd-1 mutant should not be attributed to a defect in the synthesis of IAA or ABA. The genetic analysis of the htd-1 mutant indicated that the phenotypes of high tillering and dwarf were controlled by a recessive gene, termed htd1. By map-based cloning, the htd1 gene was fine mapped in a 30-kb DNA region on chromosome 4. Sequencing the target DNA region and comparing the counterpart DNA sequences between the htd-1 mutant and other rice varieties revealed a nucleotide substitution corresponding to an amino acid substitution from prolin to leucine in a predicted rice gene, OsCCD7, the rice orthologous gene of AtMAX3/CCD7. With the evidence of the association between the presence of one amino acid change in OsCCD7 and the abnormal phenotypes of the htd-1 mutant, OsCCD7 was identified as the candidate of the HTD1 gene.
Planta 12/2005; 222(4):604-12. · 3.00 Impact Factor
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ABSTRACT: In grass, the evolutionary relationship between lemma and palea, and their relationship to the flower organs in dicots have been variously interpreted and wildely debated. In the present study, we carried out morphological and genetic analysis of a palealess mutant (pal) from rice (Oryza sativa L.), and fine mapping the gene responsible for the mutated trait. Together, our findings indicate that the palea is replaced by two leaf-like structures in the pal flowers, and this trait is controlled by one recessive gene, termed palealess1 (pal1). With a large F2 segregating population, the pal1 gene was finally mapped into a physical region of 35 kb. Our results also suggest that the lemma and palea of rice are not homologous organs, palea is likely evolutionarily equivalent to the eudicot sepal, and the pal1 should be an A function gene for rice floral organ identity.
Planta 06/2005; 221(2):222-30. · 3.00 Impact Factor
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ABSTRACT: The genetic loci and phenotypic effects of the transgene Xa21, a bacterial blight (BB) resistance gene cloned from rice, were investigated in transgenic rice produced through an Agrobacterium-mediated transformation system. The flanking sequences of integrated T-DNAs were isolated from Xa21 transgenic rice lines using thermal asymmetric interlaced PCR. Based on the analysis of 24 T-DNA- Xa21 flanking sequences, T-DNA loci in rice could be classified into three types: the typical T-DNA integration with the definite left and right borders, the T-DNA integration linked with the adjacent vector backbone sequences and the T-DNA integration involved in a complicated recombination in the flanking sequences. The T-DNA integration in rice was similar to that in dicotyledonous genomes but was significantly different from the integration produced through direct DNA transformation approaches. All three types of integrated transgene Xa21 could be stably inherited and expressed the BB resistance through derived generations in their respective transgenic lines. The flanking sequences of the typical T-DNA integration consisted of actual rice genomic DNA and could be used as probes to locate the transgene on the rice genetic map. A total of 15 different rice T-DNA flanking sequences were identified. They displayed restriction fragment length polymorphisms (RFLPs) between two rice varieties, ZYQ8 and JX17, and were mapped on rice chromosomes 1, 3, 4, 5, 7, 9, 10, 11 and 12, respectively, by using a double haploid population derived from a cross between ZYQ8 and JX17. The blast search and homology comparison of the rice T-DNA flanking sequences with the rice chromosome-anchored sequence database confirmed the RFLP mapping results. On the basis of genetic mapping of the T-DNA- Xa21 loci, the BB resistance effects of the transgene Xa21 at different chromosome locations were investigated using homozygous transgenic lines with only one copy of the transgene. Among the transgenic lines, no obvious position effects of the transgene Xa21 were observed. In addition, the BB resistance levels of the Xa21 transgenic plants with different transgene copy numbers and on different genetic backgrounds were also investigated. It was observed that genetic background (or genome) effects were more obvious than dosage effects and position effects on the BB resistance level of the transgenic plants.
Theoretical and Applied Genetics 09/2004; 109(3):534-42. · 3.30 Impact Factor
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ABSTRACT: We combined cDNA amplified fragment length polymorphism (cDNA-AFLP) with bulked segregant analysis (BSA) to detect genes that control rice blast ( Magnaporthe grisea ) resistance in a double-haploid (DH) population derived from a cross between a blast-resistant variety, Zhai Ye Qing8 (ZYQ8), and a blast-susceptible variety, Jin Xi17 (JX17). In cDNA-AFLP analysis between a blast resistance (R) pool and a blast susceptibility (S) pool from the DH population, 12 transcript-derived fragments (TDFs) that were present in only one of the two pools were detected, 8 of which were from the R pool and 4 from the S pool. Mapping analysis of these TDFs by using the DH mapping population showed that five of them, R1, R8, S9, S16 and S17, were located on chromosome 1. Sequence comparison and allelic analysis showed that R1/S16 and R8/S9 were two pairs of allelic genes. The full-length cDNA sequences of R1/S16, S17 and R8/S were obtained through cDNA library screening, in which only the expression level of R8 cDNA was up-regulated by inoculation with the blast isolate zh10814 and not affected by mock treatment, suggesting that R8 was implicated in the signaling pathways of the rice blast resistance reaction. Protein function prediction showed that R8 cDNA encodes a protein with high identity to a putative calmodulin-binding protein in Arabidopsis thaliana which belongs to the P-loop-containing nucleotide triphosphate hydrolases superfamily that contains a number of various kinases.
Plant Molecular Biology 02/2004; 54(1):99-109. · 4.15 Impact Factor
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ABSTRACT: Ricexa5 gene provides recessive, race-specific resistance to bacterial blight disease caused by the pathogenXanthomonas oryzae pv.oryzae and has great value for research and breeding. In an effort to clonexa5, an F2 population of 4892 individuals was developed from thexa5 near isogenic lines, IR24 and IRBB5. A fine mapping procedure was conducted and tightly linked RFLP markers were used to
screen a BAC library of IRBB56, a resistant rice line containing thexa5 gene. A 213 kb contig covering thexa5 locus was constructed. According to the sequences from the International Rice Genome Sequening Project (IRGSP), the Chinese
Superhybrid Rice Genome Project (SRGP) and some sub-clones of the contig, twelve SSLP and CAPS markers were developed for
fine mapping. Thexa5 gene was mapped to a 0.3 cM interval between markers K5 and T4, which spanned an interval of approximately 24 kb, co-segregating
with marker T2. Sequence analysis of the 24 kb region revealed that an ABC transporter and a basal transcription factor (TFIIa)
were potential candidates for thexa5 resistance gene product. The molecular mechanism by which thexa5 gene provides recessive, race-specific resistance to bacterial blight will be elucidated by the functional tests of the 24
kb DNA and the candidate genes.
Chinese Science Bulletin 11/2003; 48(24):2725-2729. · 1.32 Impact Factor
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ABSTRACT: The rice OsMADS16 gene is phylogenetically related to the angiosperm B-function MADS-box genes. To investigate if OsMADS16 functions as an AP3/DEF orthologue to regulate the development of lodicules and stamens in rice, we isolated its genomic sequences and characterized its functions in planta by RNA interference. The genomic sequence of the OsMADS16 gene shows that it shares high similarity in genomic structure and the deduced amino acid sequence with the maize B-class gene, Si1. Transgenic lines from the introduced gene expressing double-stranded RNA with the OsMADS16 cDNA fragment were male-sterile and displayed alternations of lodicules and stamens, occasionally depressed palea and overgrown glume. The two lodicules were converted into four palea/lemma-like organs and some stamens into carpels. Further investigations of the transcription of OsMADS16 gene in these transgenic lines by RT-PCR revealed that its transcript was significantly reduced. Transcription of a rice PI homologous gene, OsMADS4, was also reduced remarkably in the transgenic plants. Our results demonstrate that OsMADS16 is an AP3/DEF orthologue to specify the identities of lodicules and stamens in rice flower and also support that OsMADS4 is a PI orthologue. In addition, these results suggest that RNA interference is a useful tool for functional genomics in rice.
Plant Molecular Biology 08/2003; 52(5):957-66. · 4.15 Impact Factor
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ABSTRACT: Application and functional study of dwarf and semi-dwarf genes are of great importance to both crop breeding and molecular biology. A new semi-dwarf gene, sd-t(t), non-allelic to sd-1, had been identified in an indica rice variety, Aitaiyin 2. In this study the gene was genetically mapped by using an F(2) population, which consisted of 474 individuals developed from a cross between Aitaiyin 2 and B30. The sd-t(t) gene was located between the RFLP markers R514 and R1408B with a distance of 1.1 cM to R514, and 4.5 cM to R1408B on chromosome 4. A physical contig covering the sd-t(t) mapping region was further constructed by screening a BAC library with R514 and R1408B as probes, and the physical distance between R514 and R1408B was estimated at approximately 147 kb. This result will facilitate map-based cloning of the sd-t(t) gene.
Science in China Series C Life Sciences 09/2002; 45(4):388-96. · 1.61 Impact Factor
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Jun Yu,
Songnian Hu,
Jun Wang,
Gane Ka-Shu Wong,
Songgang Li,
Bin Liu,
Yajun Deng,
Li Dai,
Yan Zhou,
Xiuqing Zhang, [......],
Weimou Zheng,
Shouyi Chen,
Wei Guo,
Guojie Li,
Siqi Liu,
Ming Tao,
Jian Wang,
Lihuang Zhu,
Longping Yuan,
Huanming Yang
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ABSTRACT: We have produced a draft sequence of the rice genome for the most widely cultivated subspecies in China, Oryza sativa L. ssp. indica, by whole-genome shotgun sequencing. The genome was 466 megabases in size, with an estimated 46,022 to 55,615 genes. Functional coverage in the assembled sequences was 92.0%. About 42.2% of the genome was in exact 20-nucleotide oligomer repeats, and most of the transposons were in the intergenic regions between genes. Although 80.6% of predicted Arabidopsis thaliana genes had a homolog in rice, only 49.4% of predicted rice genes had a homolog in A. thaliana. The large proportion of rice genes with no recognizable homologs is due to a gradient in the GC content of rice coding sequences.
Science 05/2002; 296(5565):79-92. · 31.20 Impact Factor
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ABSTRACT: The cloned bacterial blight (BB) resistance gene Xa21 was transferred into Minghui63, a widely used restorer line of indica hybrid rice in China, through an Agrobacterium-mediated system. Molecular and resistance analyses revealed that the Xa21 gene was integrated in the genomes of transgenic plants and their progeny inherited resistance stably. For the purpose of hybrid breeding, Xa21 transgenic homozygous restorer lines were selected through `within-lane'' dosage comparison of hybridization signal in combination with PCR and resistance analyses. The selected transgenic restorer lines were then crossed with a commonly used sterile line, Zhenshan97A, to produce Xa21 transgenic hybrid rice, Shanyou63-Xa21. The hybrid rice plants with Xa21 displayed high broad-spectrum resistance to Xanthomonas oryzae pv. oryzae (Xoo) races and maintained elite agronomic characters of Shanyou63. The propagation of this BB-resistant hybrid variety with Xa21 will benefit rice production.
Molecular Breeding 01/2002; 8(4):285-293. · 2.85 Impact Factor
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Jun Yu,
Songnian Hu,
Jun Wang,
Songgang Li,
Gane Ka-Shu Wong,
Bin Liu,
Yajun Deng,
Li Dai,
Yan Zhou,
Xiuqing Zhang, [......],
Shouyi Chen,
Wei Guo,
Guojie Li,
Siqi Liu,
Guyang Huang,
Ming Tao,
Jian Wang,
Lihuang Zhu,
Longping Yuan,
Huanming Yang
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ABSTRACT: The sequence of the rice genome holds fundamental information for its biology, including physiology, genetics, development, and evolution, as well as information on many beneficial phenotypes of economic significance. Using a “ whole genome shotgun ” approach, we have produced a draft rice genome sequence ofOryza sativa ssp.indica, the major crop rice subspecies in China and many other regions of Asia. The draft genome sequence is constructed from over 4.3 million successful sequencing traces with an accumulative total length of 2214.9 Mb. The initial assembly of the non-redundant sequences reached 409.76 Mb in length, based on 3.30 million successful sequencing traces with a total length of 1797.4 Mb from anindica variant cultivar93-11, giving an estimated coverage of 95.29% of the rice genome with an average base accuracy of higher than 99%. The coverage of the draft sequence, the randomness of the sequence distribution, and the consistency of BIG-ASSEMBLER, a custom-designed software package used for the initial assembly, were verified rigorously by comparisons against finished BAC clone sequences from bothindica andjapanica strains, available from the public databases. Over all, 96.3% of full-length cDNAs, 96.4% of STS, STR, RFLP markers, 94.0% of ESTs and 94.9% unigene clusters were identified from the draft sequence. Our preliminary analysis on the data set shows that our rice draft sequence is consistent with the comman standard accepted by the genome sequencing community. The unconditional release of the draft to the public also undoubtedly provides a fundamental resource to the international scientific communities to facilitate genomic and genetic studies on rice biology.
Chinese Science Bulletin 01/2001; 46(23):1937-1942. · 1.32 Impact Factor
