Transcriptional Dynamics of Two Seed Compartments with Opposing Roles in Arabidopsis Seed Germination    

Abstract

Seed germination is a critical stage in the plant life cycle and the first step toward successful plant establishment. Therefore, understanding germination is of important ecological and agronomical relevance. Previous research revealed that different seed compartments (testa, endosperm, and embryo) control germination, but little is known about the underlying spatial and temporal transcriptome changes that lead to seed germination. We analyzed genome-wide expression in germinating Arabidopsis (Arabidopsis thaliana) seeds with both temporal and spatial detail and provide Web-accessible visualizations of the data reported (vseed.nottingham.ac.uk). We show the potential of this highresolution data set for the construction of meaningful coexpression networks, which provide insight into the genetic control of germination. The data set reveals two transcriptional phases during germination that are separated by testa rupture. The first phase is marked by large transcriptome changes as the seed switches from a dry, quiescent state to a hydrated and active state. At the end of this first transcriptional phase, the number of differentially expressed genes between consecutive time points drops. This increases again at testa rupture, the start of the second transcriptional phase. Transcriptome data indicate a role for mechano-induced signaling at this stage and subsequently highlight the fates of the endosperm and radicle: senescence and growth, respectively. Finally, using a phylotranscriptomic approach, we show that expression levels of evolutionarily young genes drop during the first transcriptional phase and increase during the second phase. Evolutionarily old genes show an opposite pattern, suggesting a more conserved transcriptome prior to the completion of germination.

Single-seed oxygen consumption measurements and population-based threshold models link respiration and germination rates under diverse conditions

“…Thus, seeds appear to have an especially sensitive response to Ψ with respect to both respiration and germination. Earlier analyses of the water relations of germination suggested that effects on cellular turgor and associated expansion might transduce effects of Ψ into metabolic consequences (Bradford, 1986), as also proposed recently on the basis of molecular data (Dekkers et al, 2013;Nonogaki, 2014). However, P. Bello and K.J.…”

Dynamic Proteomics Emphasizes the Importance of Selective mRNA Translation and Protein Turnover during Arabidopsis Seed Germination

“…Notably, a peptidyl-prolyl cis-trans isomerase (cyclophilin family) named ROC1 (At4g38740) was specifically neosynthesized between 0 and 8 HAI, and its protein level subsequently remained abundant in the hydrated seeds up to radicle protrusion (supplemental Tables S1 and S7). Peptidylprolyl cis-trans isomerases catalyze the conversion of pepti- Table S8), transcriptome data could be found for, respectively, 19,22,16,17,12,6,24, and 12 AGIs in a previously published data set (18). The raw Affymetrix CEL data were normalized using the GC-Robust Multiarray Average algorithm (39).…”

“…A high proportion of the genome is already expressed in the mature dry Arabidopsis seed; over 10,000 transcripts have been detected (15)(16)(17)(18)(19). Proteomic studies disclosed that only protein translation is required for radicle protrusion, indicating that germination-specific proteins are translated from stored mRNAs (20,21).…”

DELAY OF GERMINATION 1 mediates a conserved coat-dormancy mechanism for the temperature- and gibberellin-dependent control of seed germination

“…Weakening of the micropylar endosperm (CAP) covering the RAD must occur before ER. Hormonal signaling and interaction between the RAD and CAP as the key seed compartments controls the expression of downstream genes encoding cell-wall-remodeling proteins (CWRPs) (21,22). These proteins alter the biomechanical properties of cell walls, encouraging growth in RAD tissues and weakening in CAP tissues, to control the timing of germination.…”