title: Transcriptome atlas of the Arabidopsis funiculus--a study of maternal seed subregions.
abstract: The funiculus anchors the structurally complex seed to the maternal plant, and is the only direct route of transport for nutrients and maternal signals to the seed. While our understanding of seed development is becoming clearer, current understanding of the genetics and cellular mechanisms that contribute to funiculus development is limited. Using laser microdissection combined with global RNA-profiling experiments we compared the genetic profiles of all maternal and zygotic regions and subregions during seed development. We found that the funiculus is a dynamic region of the seed that is enriched for mRNAs associated with hormone metabolism, molecular transport, and metabolic activities corresponding to biological processes that have yet to be described in this maternal seed structure. We complemented our genetic data with a complete histological analysis of the funiculus from the earliest stages of development through to seed maturation at the light and electron microscopy levels. The anatomy revealed signs of photosynthesis, the endomembrane system, cellular respiration, and transport within the funiculus, all of which supported data from the transcriptional analysis. Finally, we studied the transcriptional programming of the funiculus compared to other seed subregions throughout seed development. Using newly designed in silico algorithms, we identified a number of transcriptional networks hypothesized to be responsible for biological processes like auxin response and glucosinolate biosynthesis found specifically within the funiculus. Taken together, patterns of gene activity and histological observations reveal putative functions of the understudied funiculus region and identify predictive transcriptional circuits underlying these biological processes in space and time.
authors: Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.
authors: Deirdre
authors: D
authors: Khan
authors: Jenna L
authors: JL
authors: Millar
authors: Ian J
authors: IJ
authors: Girard
authors: Ainsley
authors: A
authors: Chan
authors: Ryan C
authors: RC
authors: Kirkbride
authors: Julie M
authors: JM
authors: Pelletier
authors: Sara
authors: S
authors: Kost
authors: Michael G
authors: MG
authors: Becker
authors: Edward C
authors: EC
authors: Yeung
authors: Claudio
authors: C
authors: Stasolla
authors: Robert B
authors: RB
authors: Goldberg
authors: John J
authors: JJ
authors: Harada
authors: Mark F
authors: MF
authors: Belmonte
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000254:growth & development; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D016000:Cluster Analysis; D035264:Flowers / Q000235:genetics / Q000254:growth & development; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D005961:Glucosinolates / Q000378:metabolism; D007210:Indoleacetic Acids / Q000378:metabolism; D061346:Laser Capture Microdissection; D020411:Oligonucleotide Array Sequence Analysis; D010937:Plant Growth Regulators / Q000378:metabolism; D012639:Seeds / Q000235:genetics* / Q000254:growth & development; D059467:Transcriptome
chemical_list: D029681:Arabidopsis Proteins; D005961:Glucosinolates; D007210:Indoleacetic Acids; D010937:Plant Growth Regulators
keywords: Arabidopsis thaliana; chalazal seed coat; funiculus; laser microdissection; seed; seed coat; transcriptome