Gene Identification and Expression Analysis of 86,136 Expressed Sequence Tags (EST) from the Rice Genome

Zhou, Yan; Tang, Jiabin; Walker, Michael G.; Zhang, Xiuqing; Hu, Songnian; Xu, Huayong; Deng, Yajun; Dong, Jianhai; Ye, Lin; Lin, Li; Li, Jun; Wang, Xuegang; Xu, Hao; Pan, Y. B.; Lin, Wei; Liu, Jing; Wei, Liping; Liu, Siqi; Yang, Huanming; Yu, Jun; Wang, Jian

doi:10.1016/s1672-0229(03)01005-2

Cited by 18 publications

(10 citation statements)

References 18 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Yamamoto and Sasaki 1997;Kawasaki et al 2001;Reddy et al 2002;Wu et al 2002;Yu et al 2002;Kikuchi et al 2003;Zhou et al 2003;Jantasuriyat et al 2005) were searched for HD-Zip sequences in order to verify the accuracy of the genomic predictions. ESTs and cDNAs of all HD-Zip genes (Table 1) except Oshox18 and -26 and the two predicted pseudogenes (Oshox30 and -31) were present in the databases.…”

Section: Resultsmentioning

confidence: 99%

A genome-wide survey of HD-Zip genes in rice and analysis of drought-responsive family members

et al. 2007

View full text Add to dashboard Cite

The homeodomain leucine zipper (HD-Zip) genes encode transcription factors that have diverse functions in plant development and have often been implicated in stress adaptation. The HD-Zip genes are the most abundant group of homeobox (HB) genes in plants and do not occur in other eukaryotes. This paper describes the complete annotation of the HD-Zip families I, II and III from rice and compares these gene families with Arabidopsis in a phylogeny reconstruction. Orthologous pairs of rice and Arabidopsis HD-Zip genes were predicted based on neighbour joining and maximum parsimony (MP) trees with support of conserved intron-exon organization. Additionally, a number of HD-Zip genes appeared to be unique to rice. Searching of EST and cDNA databases and expression analysis using RT-PCR showed that 30 out of 31 predicted rice HD-Zip genes are expressed. Most HD-Zip genes were broadly expressed in mature plants and seedlings, but others showed more organ specific patterns. Like in Arabidopsis and other dicots, a subset of the rice HD-Zip I and II genes was found to be regulated by drought stress. We identified both drought-induced and drought-repressed HD-Zip genes and demonstrate that these genes are differentially regulated in drought-sensitive versus drought-tolerant rice cultivars. The drought-repressed HD-Zip family I gene, Oshox4, was selected for promoter-GUS analysis, showing that drought-responsiveness of Oshox4 is controlled by the promoter and that Oshox4 expression is predominantly vascular-specific. Loss-of-function analysis of Oshox4 revealed no specific phenotype, but overexpression analysis suggested a role for Oshox4 in elongation and maturation processes.

show abstract

Section: Resultsmentioning

confidence: 99%

A genome-wide survey of HD-Zip genes in rice and analysis of drought-responsive family members

et al. 2007

View full text Add to dashboard Cite

show abstract

“…We further compared genes that were identified in LYP9 with a set of EST data published recently (Zhou et al, 2003). In Zhou's study, three shoot (young leaves) cDNA libraries were constructed from LYP9 and PA64s at the trefoil stage, but mRNAs from 93-11 were extracted from root tissues at the tillering stage.…”

Section: Comparisons Of Our Sage Results With Other Gene Expression Datamentioning

confidence: 99%

“…EST sequences (BGI ESTs) used for our analysis were published previously (Zhou et al, 2003). Although there were data from three cDNA libraries (Ls, Ps, and Ns) generated from rice leaves, Ls and Ps were constructed from leaf materials at the trefoil stage from LYP9 and PA64s, respectively, and Ns was made from cDNAs isolated from leaves of 93-11 at the first tillering stage.…”

Section: Other Rice Datamentioning

confidence: 99%

Serial Analysis of Gene Expression Study of a Hybrid Rice Strain (LYP9) and Its Parental Cultivars

et al. 2005

Self Cite

View full text Add to dashboard Cite

Using the serial analysis of gene expression technique, we surveyed transcriptomes of three major tissues (panicles, leaves, and roots) of a super-hybrid rice (Oryza sativa) strain, LYP9, in comparison to its parental cultivars, 93-11 (indica) and PA64s (japonica). We acquired 465,679 tags from the serial analysis of gene expression libraries, which were consolidated into 68,483 unique tags. Focusing our initial functional analyses on a subset of the data that are supported by full-length cDNAs and the tags (genes) differentially expressed in the hybrid at a significant level (P , 0.01), we identified 595 up-regulated (22 tags in panicles, 228 in leaves, and 345 in roots) and 25 down-regulated (seven tags in panicles, 15 in leaves, and three in roots) in LYP9. Most of the tag-identified and up-regulated genes were found related to enhancing carbon-and nitrogen-assimilation, including photosynthesis in leaves, nitrogen uptake in roots, and rapid growth in both roots and panicles. Among the downregulated genes in LYP9, there is an essential enzyme in photorespiration, alanine:glyoxylate aminotransferase 1. Our study adds a new set of data crucial for the understanding of molecular mechanisms of heterosis and gene regulation networks of the cultivated rice.

show abstract

“…Among these embryos, most of the storage proteins exhibit overdominance and stress-induced proteins display additivity (14). We also carried out transcriptome profiling for the hybrid and its parents using both sequencingbased (15)(16)(17) and hybridization-based methods (18). We now report a rather large-scale comparative transcriptome analysis of the triad, concerning 7 tissues sampled across developmental times and different tissues.…”

mentioning

confidence: 99%

A transcriptomic analysis of superhybrid rice LYP9 and its parents

Wei

Tao²,

Liu³

et al. 2009

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

Self Cite

183

218

View full text Add to dashboard Cite

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 (DGHP), the comparative results showed that genes in the categories of energy metabolism and transport are enriched in DGHP rather than in DGPP. In addition, we correlated the concurrence of DG and yield-related quantitative trait loci, providing a potential group of heterosisrelated genes.heterosis ͉ hybrid rice ͉ transcriptome ͉ quantitative trait loci ͉ differentially expressed genes

show abstract

Gene Identification and Expression Analysis of 86,136 Expressed Sequence Tags (EST) from the Rice Genome

Cited by 18 publications

References 18 publications

A genome-wide survey of HD-Zip genes in rice and analysis of drought-responsive family members

A genome-wide survey of HD-Zip genes in rice and analysis of drought-responsive family members

Serial Analysis of Gene Expression Study of a Hybrid Rice Strain (LYP9) and Its Parental Cultivars

A transcriptomic analysis of superhybrid rice LYP9 and its parents

Contact Info

Product

Resources

About