Global analysis of gene activity duringArabidopsisseed development and identification of seed-specific transcription factors

Abstract

Most of the transcription factors (TFs) responsible for controlling seed development are not yet known. To identify TF genes expressed at specific stages of seed development, including those unique to seeds, we used Affymetrix GeneChips to profile Arabidopsis genes active in seeds from fertilization through maturation and at other times of the plant life cycle. Seed gene sets were compared with those expressed in prefertilization ovules, germinating seedlings, and leaves, roots, stems, and floral buds of the mature plant. Most genes active in seeds are shared by all stages of seed development, although significant quantitative changes in gene activity occur. Each stage of seed development has a small gene set that is either specific at the level of the GeneChip or up-regulated with respect to genes active at other stages, including those that encode TFs. We identified 289 seed-specific genes, including 48 that encode TFs. Seven of the seed-specific TF genes are known regulators of seed development and include the LEAFY COTYLEDON ( LEC ) genes LEC1, LEC1-LIKE, LEC2 , and FUS3 . The rest represent different classes of TFs with unknown roles in seed development. Promoter-β -glucuronidase ( GUS ) fusion experiments and seed mRNA localization GeneChip datasets showed that the seed-specific TF genes are active in different compartments and tissues of the seed at unique times of development. Collectively, these seed-specific TF genes should facilitate the identification of regulatory networks that are important for programming seed development.

GALACTURONOSYLTRANSFERASE-LIKE5 Is Involved in the Production of Arabidopsis Seed Coat Mucilage

“…Our work also further demonstrates the utility of the Arabidopsis seed coat as a good model system for the identification of GTs involved in pectin, and particularly RG-I, biosynthesis. The usefulness of this model system has been enhanced recently by the establishment of global expression data sets covering seed coat development in Arabidopsis (Le et al, 2010;Dean et al, 2011). Although the exact role of AtGATL5 in the synthesis of RG-I remains to be determined, the work reported here provides impetus for future research using both polysaccharide structural approaches and biochemical studies of possible biosynthetic complexes to further elucidate the functions of AtGATL5 in RG-I synthesis.…”

“…S2A). In addition, data available from transcriptome analyses using RNA extracted from laser-capture-dissected seed coat tissue (Le et al, 2010; http://seedgenenetwork.net/arabidopsis) indicate that AtGATL5 transcript levels are low in the seed coat during early embryogenesis and that the levels rise from the linear cotyledon stage onward (Supplemental Fig. S2B).…”

The Differential Transcription Network between Embryo and Endosperm in the Early Developing Maize Seed

“…S17), implicating a differential transcriptional regulation between embryo and endosperm. It was previously reported that TFs of MADS function in seed and endosperm development (Kang et al, 2008;Sreenivasulu et al, 2008;Bemer et al, 2010;Le et al, 2010;Agarwal et al, 2011;Hehenberger et al, 2012). AGL62, a MADS protein of Arabidopsis, is the direct target of FIS Polycomb group repressive complex2 (PRC2), establishing the molecular basis for FIS PRC2-mediated endosperm cellularization (Hehenberger et al, 2012).…”

“…Several TF family members are likely to play a role in cell fate determination, including C2C2-YABBY (GRMZM2G167824 and GRMZM2G529859) and GeBP (GRMZM2G036966) homologs, as well as in cell growth regulation and germination, including WRKY (Zhang et al, 2011a;GRMZM5G816457) and bHLH (GRMZM2G042920) homologs. On the other hand, the majority of TFs enriched in endosperm were families such as MADS, SBP, NAC, bZIP, Myb, and C2C2-GATA, most of which have been implicated in seed development (Sreenivasulu et al, 2008;Bemer et al, 2010;Le et al, 2010;Agarwal et al, 2011). A total of 33 TF genes were selected for confirmation of the differential expression between embryo and endosperm with real-time RT-PCR analysis.…”

Endosperm and Nucellus Develop Antagonistically in Arabidopsis Seeds

“…To test whether the nucellus undergoes HR-PCD, we analyzed seeds of the metacaspase1 (mc1) and lesions simulating disease1 (lsd1) mutants, which are affected in two major components of the HR-PCD machinery that positively and negatively regulate HR-PCD, respectively (Coll et al, 2010). Based on laser microdissection transcriptomics data, both MC1 and LSD1 are expressed in the chalazal area that includes chalaza and nucellus (Le et al, 2010). Nevertheless, mc1 and lsd1 mutant seeds displayed a wild-type nucellus phenotype (Supplemental Figure 3).…”