A collection of 10,096 indica rice full-length cDNAs reveals highly expressed sequence divergence between Oryza sativa indica and japonica subspecies

Liu, Xiaohui; Lu, Tingting; Yu, Shuliang; Li, Ying; Huang, Yu‐Chen; Huang, Tao; Zhang, Lei; Zhu, Jingjie; Zhao, Qiang; Fan, Danlin; Mu, Jie; Shangguan, Yingying; Feng, Qi; Guan, Jianping; Ying, Kai; Zhang, Yu; Lin, Zhixin; Sun, Zongxiu; Qian, Qian; Lu, Yuping; Han, Bin

doi:10.1007/s11103-007-9174-7

Cited by 53 publications

(38 citation statements)

References 66 publications

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“…Wholegenome microarray technique has been developed and applied to profiling expression of all of the genes in the entire life cycle of rice growth and development. Full-length cDNAs for both indica and japonica rice have been constructed, with a total of Ͼ40,000 full-length cDNA clones available (11,12).…”

Section: The Strategies For Developing Gsrmentioning

confidence: 99%

Strategies for developing Green Super Rice

Zhang

2007

Proc. Natl. Acad. Sci. U.S.A.

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This contribution is part of the special series of Inaugural Articles by members of the National Academy of Sciences elected on May 1, 2007.From a global viewpoint, a number of challenges need to be met for sustainable rice production: (i) increasingly severe occurrence of insects and diseases and indiscriminate pesticide applications; (ii) high pressure for yield increase and overuse of fertilizers; (iii) water shortage and increasingly frequent occurrence of drought; and (iv) extensive cultivation in marginal lands. A combination of approaches based on the recent advances in genomic research has been formulated to address these challenges, with the long-term goal to develop rice cultivars referred to as Green Super Rice. On the premise of continued yield increase and quality improvement, Green Super Rice should possess resistances to multiple insects and diseases, high nutrient efficiency, and drought resistance, promising to greatly reduce the consumption of pesticides, chemical fertilizers, and water. Large efforts have been focused on identifying germplasms and discovering genes for resistance to diseases and insects, N-and P-use efficiency, drought resistance, grain quality, and yield. The approaches adopted include screening of germplasm collections and mutant libraries, gene discovery and identification, microarray analysis of differentially regulated genes under stressed conditions, and functional test of candidate genes by transgenic analysis. Genes for almost all of the traits have now been isolated in a global perspective and are gradually incorporated into genetic backgrounds of elite cultivars by molecular marker-assisted selection or transformation. It is anticipated that such strategies and efforts would eventually lead to the development of Green Super Rice.genomics ͉ rice genetic improvement ͉ sustainable agriculture

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Section: The Strategies For Developing Gsrmentioning

confidence: 99%

Strategies for developing Green Super Rice

Zhang

2007

Proc. Natl. Acad. Sci. U.S.A.

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“…Full-length cDNAs of both KOME (http://red.dna.affrc. go.jp/cDNA/; japonica Nipponbare; Rice Full-Length cDNA Consortium, 2003) and National Center for Gene Research (http://www.ncgr.ac.cn/cDNA/; indica Guangluai 4; Liu et al, 2007) were also included. Transposon insertions and their flanking regions were used to search against the EST/Fl-cDNA database using BLASTN with a threshold e-value of 10 220 .…”

Section: Est Analysis and Gene Predictionmentioning

confidence: 99%

“…First-strand cDNA was synthesized by SuperScript II reverse transcriptase (Invitrogen) at 42°C for 1 h. Genomic DNA of the 10 indica (Guangluai 4, 93-11, Teqing, Kasalath, TN1, Liantangzao, Zhefu 802, Nanjing 6, IR36, and Zhaiyeqing 8) and 11 japonica (Nipponbare, Yangguang, Qiuguang, Shiokari, Lansheng, Juangguang, Jinnanfeng, Suyunuo, Nongken 58, Yueguang, and Xueheaizao) varieties was prepared from 2-week-old rice seedling shoots as described (Liu et al, 2007). The genomic DNA of Oryza rufipogon, Oryza barthii, and Oryza longistaminata was provided by Wang Zixuan (Plant Genome Center).…”

Section: Confirmation Of the Insertion In The Xip-i Gene By Pcr Assaysmentioning

confidence: 99%

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Genome-Wide Analysis of Transposon Insertion Polymorphisms Reveals Intraspecific Variation in Cultivated Rice

et al. 2008

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Insertions and precise eliminations of transposable elements generated numerous transposon insertion polymorphisms (TIPs) in rice (Oryza sativa). We observed that TIPs represent more than 50% of large insertions and deletions (.100 bp) in the rice genome. Using a comparative genomic approach, we identified 2,041 TIPs between the genomes of two cultivars, japonica Nipponbare and indica 93-11. We also identified 691 TIPs between Nipponbare and indica Guangluai 4 in the 23-Mb collinear regions of chromosome 4. Among them, retrotransposon-based insertion polymorphisms were used to reveal the evolutionary relationships of these three cultivars. Our conservative estimates suggest that the TIPs generated approximately 14% of the genomic DNA sequence differences between subspecies indica and japonica. It was also found that more than 10% of TIPs were located in expressed gene regions, representing an important source of genetic variation. Transcript evidence implies that these TIPs induced a series of genetic differences between two subspecies, including interrupting host genes, creating different expression forms, drastically changing intron length, and affecting expression levels of adjacent genes. These analyses provide genome-wide insights into evolutionary history and genetic variation of rice.

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“…The global transcriptomes of its different varieties have been surveyed in depth by the genome-wide analysis of full-length cDNAs (FL-cDNAs) and expressed sequence tags (ESTs) (The Rice Full-Length cDNA Consortium 2003; Zhang et al 2005;Liu et al 2007). However, the approach of massive-scale cloning and sequencing cDNA or EST libraries is relatively low throughput, high cost, shows inherent cloning bias, and is generally not quantitative.…”

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Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq

Lu¹,

Gui²,

Fan³

et al. 2010

Genome Res.

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The functional complexity of the rice transcriptome is not yet fully elucidated, despite many studies having reported the use of DNA microarrays. Next-generation DNA sequencing technologies provide a powerful approach for mapping and quantifying the transcriptome, termed RNA sequencing (RNA-seq). In this study, we applied RNA-seq to globally sample transcripts of the cultivated rice Oryza sativa indica and japonica subspecies for resolving the whole-genome transcription profiles. We identified 15,708 novel transcriptional active regions (nTARs), of which 51.7% have no homolog to public protein data and >63% are putative single-exon transcripts, which are highly different from protein-coding genes (<20%). We found that~48% of rice genes show alternative splicing patterns, a percentage considerably higher than previous estimations. On the basis of the available rice gene models, 83.1% (46,472 genes) of the current rice gene models were validated by RNA-seq, and 6228 genes were identified to be extended at the 59 and/or 39 ends by at least 50 bp. Comparative transcriptome analysis demonstrated that 3464 genes exhibited differential expression patterns. The ratio of SNPs with nonsynonymous/synonymous mutations was nearly 1:1.06. In total, we interrogated and compared transcriptomes of the two rice subspecies to reveal the overall transcriptional landscape at maximal resolution.

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A collection of 10,096 indica rice full-length cDNAs reveals highly expressed sequence divergence between Oryza sativa indica and japonica subspecies

Cited by 53 publications

References 66 publications

Strategies for developing Green Super Rice

Strategies for developing Green Super Rice

Genome-Wide Analysis of Transposon Insertion Polymorphisms Reveals Intraspecific Variation in Cultivated Rice

Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq

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