Genome-wide atlas of transcription through maize development.
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Reference Summary: Sekhon, RS et al. 2011. Plant J 66:553-562
Abstract: Maize is an important model species and a major constituent of human and animal diets. It has also emerged as a potential feedstock and a model system for bioenergy research due to recent worldwide interest in developing plant biomass-based, carbon-neutral liquid fuels. To understand how the underlying genome sequence results in specific plant phenotypes, information on the temporal and spatial transcription patterns of genes is crucial. We present here a comprehensive atlas of global transcription profiles across developmental stages and plant organs. We used a NimbleGen microarray containing 80,301 probe sets to profile transcription patterns in 60 distinct tissues representing 11 major organ systems of the inbred line B73. Of the 30,892 probe sets representing the filtered B73 gene models, 91.4% were expressed in at least one tissue. Interestingly, 44.5% of the probe sets were expressed in all the tissues indicating a substantial overlap of gene expression among distinct plant organs. Clustering of maize tissues based on global gene expression profiles lead to formation of groups of biologically related tissues. We utilized this data set to examine expression of genes that encode enzymes in the lignin biosynthetic pathway and found that expansion of distinct gene families was accompanied by the appearance of divergent, tissue-specific transcription patterns of the paralogs. This comprehensive expression atlas represents a valuable resource for gene discovery and functional characterization in maize.
Reference Type: Article
de Leon, N
(Natalia de Leon)
Bibliography: Sekhon RS, Lin Haining, Childs KL, Hirsch CN, Buell CR, de Leon N, Kaeppler SM (2011) Genome-wide atlas of transcription through maize development.. Plant J 66(0):553-562
Editorial Board Member Comment: Who could resist browsing through an atlas of transcription through maize development? Certainly not I. These authors undertook the yeoman's task of obtaining transcript profiles from 60 different tissue/developmental stage combinations. A data set like this could be approached from many different directions and I was eager to see what direction these authors would choose. The mandatory "overview" information was all there - most of the predicted genes are expressed in at least one tissue and a bunch of them are tissue specific. The large number of tissues and developmental stages sampled allow observation of relationships in expression patterns among tissues and organs as well as gene expression changes that occur in the course of development. The authors focus on expression patterns in leaves and seeds and present detailed results for genes in the lignin biosynthetic pathway. Tissue- and organ- expression patterns of different paralogs of lignin biosynthetic gene yielded some surprising results. This paper reveals the tip of the iceberg in terms of information that can be extracted from this data set, which will soon be released to the community. The data will be a great resource, so get on your favorite database and start mining! Paul Scott
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chi3 chalcone flavanone isomerase3
tps23 terpene synthase23
Cannon, E; MaizeGDB Staff; PLEXdb Staff 2011. Renormalization of maize atlas Nimblegen microarray data to B73 RefGen_v2
anthers R1 B73 ?
cob immature V18 B73 ?
cob pre-pollination R1 B73 ?
coleoptile 6 day, B73 ?
embryo, 16 days after pollination B73 ?
embryo, 18 days after pollination B73 ?
embryo, 20 days after pollination B73 ?
embryo, 22 days after pollination B73 ?
embryo, 24 days after pollination B73 ?
endosperm, 12 days after pollination B73 ?
endosperm, 14 days after pollination B73 ?
endosperm, 16 days after pollination B73 ?
endosperm, 18 days after pollination B73 ?
endosperm, 20 days after pollination B73 ?
endosperm, 22 days after pollination B73 ?
endosperm, 24 days after pollination B73 ?
germinating seed 24h B73 ?
husk, innermost R1 B73 ?
husk, innermost R2 B73 ?
husk, outer R2 B73 ?
internode, 1st above ground V5 B73 ?
internode, 1st above ground, V7 B73 ?
internode, 4th V9 B73 ?
kernel, 10 days afer pollination B73 ?
kernel, 12 days after pollination B73 ?
kernel, 14 days after pollination B73 ?
kernel, 16 days after pollination B73 ?
kernel, 18 days after pollination B73 ?
kernel, 20 days after pollination B73 ?
kernel, 22 days after pollination B73 ?
kernel, 24 days after pollination B73 ?
kernel 2 days after pollination B73 ?
kernel 4 days after pollination B73 ?
kernel 6 days after pollination B73 ?
kernel 8 days after pollination B73 ?
leaf, 11th V9 B73 ?
leaf, 13th R2 B73 ?
leaf, 13th V9 B73 ?
leaf, 13th VT B73 ?
leaf, 17th and above immature V9 B73 ?
leaf 1st with sheath V3 B73 ?
leaf 8th V9 B73 ?
leaf base of expanding leaf V5 B73 ?
leaf base of expanding leaf V7 B73 ?
leaf expanding V3 B73 ?
leaf tip expanding leaf V5 B73 ?
leaf tip expanding V7 B73 ?
leaves V1 B73 ?
NimbleGen RMA LOG2 ?
pericarp, 18 days after pollination B73 ?
root primary 6 days after sowing B73 ?
root primary V1 B73 ?
root primary vegetative emergence VE B73 ?
shoot apical meristem and stem V1 B73 ?
shoot apical meristem and stem V3 B73 ?
shoot apical meristem and stem V4 B73 ?
shoot seedling VE B73 ?
shoot tip V5 B73 ?
silks R1 B73 ?
tassel immature V13 B73 ?
tassel meiotic V18 B73 ?