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ABSTRACT: Chloroplast is a new hotspot in the field of plant transformation system of plant genetic engineering. Plastid transformation has several advantages: high expression, multiple expressed genes in a single transformation event, absence of gene silencing, et al. A series of elements for construction of dicistronic site-specific integration expression vector of rice chloroplast have been cloned, including trnl-trnA (rice chloroplast homologous recombination fragments), Prrn (16S rRNA operon promotor), PpsbA (the 3' untranslated region of the chloroplastpsbA gene), hptll gene (encoding hygromycin phosphotransferase) and EGFP (encoding enhanced green fluorescence protein). All the elements were constructed into a rice chloroplast dicistronic expression vector pCTE04 (-trnl-Prrn-RBS-hptlI-RBS-EGFP-PpsbA- trnA-). Then pCTE04 was introduced into chloroplasts of Dunaliella salina through particle bombardment. Strong green fluorescence was observed in chloroplasts of some bombarded Dunaliella salina cells under a stereo fluorescence microscope, indicating that pCTE04 could be expressed in Dunaliella salina chloroplasts transiently. It provides a solid foundation for further genetic engineering in rice chloroplast transformation.
Journal of Biomedical Nanotechnology 12/2011; 7(6):801-6. · 4.22 Impact Factor
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Gang Wei,
Yong Tao,
Guozhen Liu,
Chen Chen,
Renyuan Luo,
Hongai Xia,
Qiang Gan,
Haipan Zeng,
Zhike Lu,
Yuning Han, [......],
Honglin Xu,
Xiaoli Wei,
Mengliang Cao,
Huafeng Deng,
Yeyun Xin,
Xiqin Fu, Longping Yuan,
Jun Yu,
Zhen Zhu,
Lihuang Zhu
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ABSTRACT: By using a whole-genome oligonucleotide microarray, designed based on known and predicted indica rice genes, we investigated transcriptome profiles in developing leaves and panicles of superhybrid rice LYP9 and its parental cultivars 93-11 and PA64s. We detected 22,266 expressed genes out of 36,926 total genes set collectively from 7 tissues, including leaves at seedling and tillering stages, flag leaves at booting, heading, flowering, and filling stages, and panicles at filling stage. Clustering results showed that the F1 hybrid's expression profiles resembled those of its parental lines more than that which lies between the 2 parental lines. Out of the total gene set, 7,078 genes are shared by all sampled tissues and 3,926 genes (10.6% of the total gene set) are differentially expressed genes (DG). As we divided DG into those between the parents (DG(PP)) and between the hybrid and its parents (DG(HP)), the comparative results showed that genes in the categories of energy metabolism and transport are enriched in DG(HP) rather than in DG(PP). In addition, we correlated the concurrence of DG and yield-related quantitative trait loci, providing a potential group of heterosis-related genes.
Proceedings of the National Academy of Sciences 05/2009; 106(19):7695-701. · 9.68 Impact Factor
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ABSTRACT: Hybrid rice plays an important role in China's aim to improve rice production as it accounts for some 50% of rice planting
area but produces about 60% of the total rice grain. However, the existing three-line system used in hybrid rice production
has its limitations. The two-line system, which makes use of photoperiod-sensitive genic male-sterile (PGMS) and thermo-sensitive
genic male-sterile (TGMS) lines to generate the male-sterile parental line, was developed to overcome some of these limitations.
The sterility of the male-sterile line of two-line hybrid rice, however, fluctuates when the temperature-sensitive phase of
fertility encounters abnormal low temperatures during hybrid seed production, which induces selfing and decreases the purity
of hybrid. We describe here the strategy of utilizing a herbicide resistance gene in two-line hybrid rice to eliminate this
fluctuation in the sterility of the P/TGMS lines during hybrid seed production and reports the development of the herbicide
resistance restorer line Bar68-1 and its herbicide-resistant early season hybrid rice Xiang125s/Bar68-1. When the restorer
line and its derived hybrid are herbicide resistant, the selfed seeds can be removed easily from the hybrid by herbicide spraying.
A herbicide resistance gene bar was transferred into a restorer line by particle bombardment. The resulting transgenic restorer line Bar68-1 and its hybrid
Xiang125s/Bar68-1 inherited stable herbicide resistance. The purity of Xiang125s/Bar68-1 was increased by spraying the seed
bed with herbicide, which resulted in a significant increase in yield, grain quality, and disease resistance in comparison
to the controls in a regional trial.
Molecular Breeding 09/2007; 20(3):287-292. · 2.85 Impact Factor
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ABSTRACT: A plant expression vector harboring four antifungal genes was delivered into the embryogenic calli of '9311', an indica restorer line of Super Hybrid Rice, via modified biolistic particle bombardment. Southern blot analysis indicated that in the regenerated hygromycin-resistant plants, all the four antifungal genes, including RCH10, RAC22, beta-Glu and B-RIP, were integrated into the genome of '9311', co-transmitted altogether with the marker gene hpt in a Mendelian pattern. Some transgenic R1 and R2 progenies, with all transgenes displaying a normal expression level in the Northern blot analysis, showed high resistance to Magnaporthe grisea when tested in the typical blast nurseries located in Yanxi and Sanya respectively. Furthermore, transgenic F1 plants, resulting from a cross of R2 homozygous lines with high resistance to rice blast with the non-transgenic male sterile line Peiai 64S, showed not only high resistance to M. grisea but also enhanced resistance to rice false smut (a disease caused by Ustilaginoidea virens) and rice kernel smut (another disease caused by Tilletia barclayana).
Science in China Series C Life Sciences 03/2007; 50(1):31-9. · 1.61 Impact Factor
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Ligeng Ma,
Chen Chen,
Xigang Liu,
Yuling Jiao,
Ning Su,
Lin Li,
Xiangfeng Wang,
Mengliang Cao,
Ning Sun,
Xiuqing Zhang,
Jingyue Bao,
Jian Li,
Soren Pedersen,
Lars Bolund,
Hongyu Zhao, Longping Yuan,
Gane Ka-Shu Wong,
Jun Wang,
Xing Wang Deng,
Jian Wang
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ABSTRACT: Arabidopsis and rice are the only two model plants whose finished phase genome sequence has been completed. Here we report the construction of an oligomer microarray based on the presently known and predicted gene models in the rice genome. This microarray was used to analyze the transcriptional activity of the gene models in representative rice organ types. Expression of 86% of the 41,754 known and predicted gene models was detected. A significant fraction of these expressed gene models are organized into chromosomal regions, about 100 kb in length, that exhibit a coexpression pattern. Compared with similar genome-wide surveys of the Arabidopsis transcriptome, our results indicate that similar proportions of the two genomes are expressed in their corresponding organ types. A large percentage of the rice gene models that lack significant Arabidopsis homologs are expressed. Furthermore, the expression patterns of rice and Arabidopsis best-matched homologous genes in distinct functional groups indicate dramatic differences in their degree of conservation between the two species. Thus, this initial comparative analysis reveals some basic similarities and differences between the Arabidopsis and rice transcriptomes.
Genome Research 10/2005; 15(9):1274-83. · 13.61 Impact Factor
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Jun Yu,
Jun Wang,
Wei Lin,
Songgang Li,
Heng Li,
Jun Zhou,
Peixiang Ni,
Wei Dong,
Songnian Hu,
Changqing Zeng, [......],
Bailin Hao,
Siqi Liu,
Wen Wang, Longping Yuan,
Mengliang Cao,
Jason McDermott,
Ram Samudrala,
Jian Wang,
Gane Ka-Shu Wong,
Huanming Yang
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ABSTRACT: We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000-40,000. Only 2%-3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.
PLoS Biology 03/2005; 3(2):e38. · 11.45 Impact Factor
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ABSTRACT: 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.
Genome 09/2004; 47(4):697-704. · 1.65 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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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
